diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 53adf4901..bc06ff5b5 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -1,3 +1,21 @@ +@article{__2023, + abstract = {Ecological disasters, wars in regions with microbiological weapons depots, deforestation, domestication of wild animals, consumption of infected animals, contamination of water and food products and their components, experiments with viruses, deficiencies and other defects of the immune system in modern humans and other mammals became the impetus for the evolution of new dangerous and extremely dangerous viruses. Due to the emergence of new dangerous viruses, the importance and demand for knowledge and skills of computational biology, epidemiology and virology in modern society have increased. Modern sequencers are capable of producing large amounts of bioinformatic data that is represented in the form of genomic texts. Comparative сomputational analysis of this information is necessary to clarify the issues of phylogenesis, mutational profiling, molecular evolution, identification of insertions of other genomes, annotation of genome regions, search for targets for vaccine development and pharmacotherapy. In this сontext, authors conducted a computational experiment of comparative analysis of the genomic texts of Belarusian coronavirus samples against a number of selected complete genomes of dangerous and extremely dangerous viruses and coronaviruses of various origins. Data analysis was performed using the YASS, genomic texts were downloaded from the GISAID, the custom genomic data processing pipeline based on the Galaxy bioinformatics platform was also applied. The article presents the results of an analysis of the available scientific literature and the computational experiment comparing the genomic texts of Belarusian coronavirus samples with a number of selected complete genomes of dangerous and especially dangerous viruses and coronaviruses of various origin. A significant similarity of the new coronavirus with the recombinant coronavirus, as well as partial similarity with synthetic coronavirus, Rubella, Ebola 1976, HIV-2 (human immunodeficiency virus), Middle East respiratory syndrome, simian immunodeficiency and Marburg fever viruses have been found.}, + author = {В, Спринджук М. and И, Берник В. and С, Владыко А. and Л, Чжочжуан and П, Титов Л.}, + issn = {1729-7648}, + journal = {Доклады Белорусского государственного университета информатики и радиоэлектроники}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Number: 2 +Place: Республика Беларусь, Минск +Publisher: Учреждение образования «Белорусский государственный университет информатики и радиоэлектроники»}, + number = {2}, + pages = {104--113}, + title = {{ВЫЧИСЛИТЕЛЬНЫЙ} АНАЛИЗ СТРУКТУРНОГО {CОСТАВА} ГЕНОМОВ КОРОНАВИРУСОВ}, + url = {https://cyberleninka.ru/article/n/vychislitelnyy-analiz-strukturnogo-costava-genomov-koronavirusov}, + urldate = {2023-07-31}, + volume = {21}, + year = {2023} +} + @phdthesis{___2019, author = {{Евгений Игоревич}}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, @@ -7,6 +25,41 @@ @phdthesis{___2019 year = {2019} } +@article{achom_plant_2022, + abstract = {Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.}, + author = {Achom, Mingkee and Roy, Proyash and Lagunas, Beatriz and Picot, Emma and Richards, Luke and Bonyadi-Pour, Roxanna and Pardal, Alonso J and Baxter, Laura and Richmond, Bethany L and Aschauer, Nadine and Fletcher, Eleanor M and Rowson, Monique and Blackwell, Joseph and Rich-Griffin, Charlotte and Mysore, Kirankumar S and Wen, Jiangqi and Ott, Sascha and Carré, Isabelle A and Gifford, Miriam L}, + doi = {10.1093/jxb/erab526}, + issn = {0022-0957}, + journal = {Journal of Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + number = {7}, + pages = {2142--2156}, + title = {Plant circadian clock control of {Medicago} truncatula nodulation via regulation of nodule cysteine-rich peptides}, + url = {https://doi.org/10.1093/jxb/erab526}, + urldate = {2022-09-24}, + volume = {73}, + year = {2022} +} + +@article{aciole_barbosa_transcriptomic_2022, + abstract = {Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3\%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.}, + author = {Aciole Barbosa, David and Araújo, Bruno C. and Branco, Giovana Souza and Simeone, Alexandre S. and Hilsdorf, Alexandre W. S. and Jabes, Daniela L. and Nunes, Luiz R. and Moreira, Renata G. and Menegidio, Fabiano B.}, + doi = {10.1007/s10126-021-10081-0}, + issn = {1436-2236}, + journal = {Marine Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Aquaculture, Cobia, LncRNA, Microsatellites, Rachycentron canadum, Transcriptome}, + language = {en}, + month = {February}, + number = {1}, + pages = {255--262}, + title = {Transcriptomic {Profiling} and {Microsatellite} {Identification} in {Cobia} ({Rachycentron} canadum), {Using} {High}-{Throughput} {RNA} {Sequencing}}, + url = {https://doi.org/10.1007/s10126-021-10081-0}, + urldate = {2022-09-24}, + volume = {24}, + year = {2022} +} + @article{afouda_culturing_2020, abstract = {Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23\% to 55.59\%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.}, author = {Afouda, Pamela and Dubourg, Grégory and Levasseur, Anthony and Fournier, Pierre-Edouard and Delerce, Jeremy and Mediannikov, Oleg and Diene, Seydina M. and Nahon, Daniel and Bourlès, Didier and Rolain, Jean-Marc and Raoult, Didier}, @@ -27,6 +80,23 @@ @article{afouda_culturing_2020 year = {2020} } +@article{agboli_interaction_2023, + abstract = {Mosquito-specific viruses (MSVs) comprise a variety of different virus families, some of which are known to interfere with infections of medically important arboviruses. Viruses belonging to the family Mesoniviridae or taxon Negevirus harbor several insect-specific viruses, including MSVs, which are known for their wide geographical distribution and extensive host ranges. Although these viruses are regularly identified in mosquitoes all over the world, their presence in mosquitoes in Germany had not yet been reported.}, + author = {Agboli, Eric and Schulze, Jonny and Jansen, Stephanie and Cadar, Daniel and Sreenu, Vattipally B. and Leggewie, Mayke and Altinli, Mine and Badusche, Marlis and Jöst, Hanna and Börstler, Jessica and Schmidt-Chanasit, Jonas and Schnettler, Esther}, + doi = {10.1186/s13071-023-05985-w}, + issn = {1756-3305}, + journal = {Parasites \& Vectors}, + keywords = {{\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, Aedes, Arbovirus, Culex, Interference, Mesonivirus, Mosquito-specific viruses, Negevirus, RNAi}, + month = {October}, + number = {1}, + pages = {361}, + title = {Interaction of {Mesonivirus} and {Negevirus} with arboviruses and the {RNAi} response in {Culex} tarsalis-derived cells}, + url = {https://doi.org/10.1186/s13071-023-05985-w}, + urldate = {2023-10-17}, + volume = {16}, + year = {2023} +} + @article{aggarwal_role_2021, author = {Aggarwal, Dinesh and Myers, Richard and Hamilton, William L. and Bharucha, Tehmina and Tumelty, Niamh M. and Brown, Colin S. and Meader, Emma J. and Connor, Tom and Smith, Darren L. and Bradley, Declan T. and Robson, Samuel and Bashton, Matthew and Shallcross, Laura and Zambon, Maria and Goodfellow, Ian and Chand, Meera and O'Grady, Justin and Török, M. Estée and Peacock, Sharon J. and Page, Andrew J.}, doi = {10.1016/s2666-5247(21)00208-1}, @@ -39,6 +109,43 @@ @article{aggarwal_role_2021 year = {2021} } +@misc{aguirre_pranzoni_biofoams_2024, + abstract = {White rot fungi are promising organisms for the production of mycelial-based biofoams, providing a sustainable means to of valorizing lignocellulosic wastes. This study focuses on the use of Trametes sanguinea LSR01 and Trametes villosa LSR02, two indigenous fungal species isolated from Argentina, for the production of biofoams from brewery waste. These biofoams were obtained with an average density of 0.30 g cm-3, Young's modulus around 1 MPa and a compressive stress around 19 MPa.  This study also evaluated the variation of laccase activity during each stage of the biofoam production process. Unexpectedly, residual laccase activity was detected in the biofoams after oven drying (60, 80 and 100 °C). This residual laccase ability to oxidize benzyl alcohol to benzaldehyde indicated that biofoams are not enzymatically inert.  This unexpected finding highlights the enzymatic potential of these mycelium-based materials and positions them as promising green catalysts for biotechnological endeavors.}, + address = {Rochester, NY}, + author = {Aguirre Pranzoni, Celeste and Bonilla, José and Carrillo, Ángeles and López-Vidal, Martín and Aguilera, Leonardo J. and Ochoa, Nelio Ariel and Kurina-Sanz, Marcela}, + doi = {10.2139/ssrn.4792539}, + keywords = {{\textgreater}UseGalaxy.eu, Beer Bagasse, Laccase activity, Trametes, White rot fungi, biooxidation}, + language = {en}, + month = {April}, + title = {Biofoams with {Untapped} {Enzymatic} {Potential} {Produced} from {Beer} {Bagasse} by {Indigenous} {Fungal} {Strains}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=4792539}, + urldate = {2024-04-28}, + year = {2024} +} + +@article{ahmad_biosynthetic_2023, + abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73–114 clusters, other lichen associated ascomycetes 8–40, green algae of the genus Trebouxia 14–19, and lichen-associated bacteria 101–105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, + author = {Ahmad, Nadim and Ritz, Manfred and Calchera, Anjuli and Otte, Jürgen and Schmitt, Imke and Brueck, Thomas and Mehlmer, Norbert}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/jof9050546}, + issn = {2309-608X}, + journal = {Journal of Fungi}, + keywords = {\textit{Hypogymnia physodes}, \textit{Hypogymnia tubulosa}, {\textgreater}UseGalaxy.eu, biosynthetic gene cluster, lichen, long read sequencing, polyketide synthesis, reference genome}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {546}, + shorttitle = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}}, + title = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}: {Insights} into {Secondary} {Metabolite} {Pathways}}, + url = {https://www.mdpi.com/2309-608X/9/5/546}, + urldate = {2023-07-31}, + volume = {9}, + year = {2023} +} + @article{ahmad_development_2019, abstract = {Premise Alkanna tinctoria (Boraginaceae) is an important medicinal herb with its main distribution across the Mediterranean region. To reveal its genetic variation and population structure, microsatellite markers were developed and validated in four Greek populations. Methods and Results RNA-Seq data of the related species Arnebia euchroma and Echium plantagineum were assembled and mined to identify conserved ortholog sets containing simple sequence repeat motifs. Fifty potential loci were identified and then tested on A. tinctoria, of which 17 loci were polymorphic. The number of alleles ranged from one to nine, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.820, respectively. Most of these loci could be successfully amplified in eight other species of Boraginaceae (Alkanna graeca, A. hellenica, A. sfikasiana, Echium vulgare, E. plantagineum, Lithospermum officinale, Borago officinalis, and Anchusa officinalis). Conclusions This study provides the first set of microsatellite loci for studying the genetic variation and population structure of A. tinctoria and shows their potential usefulness in other Boraginaceae species.}, author = {Ahmad, Muhammad and Lazic, Desanka and Hansel‐Hohl, Karin and Lexer, Christian and Sehr, Eva Maria}, @@ -77,6 +184,77 @@ @article{ahmed_high_2020 year = {2020} } +@article{ahmed_safety_2023, + abstract = {The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis.}, + author = {Ahmed, Noha A. and Khattab, Rania Abdelmonem and Ragab, Yasser M. and Hassan, Mariam}, + doi = {10.1186/s12864-023-09749-9}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-cas, Enterococcus faecium, Gut microbiota; Human stool, Probiotics, Whole genome sequencing}, + language = {en}, + month = {November}, + number = {1}, + pages = {667}, + title = {Safety assessment of {Enterococcus} lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species}, + url = {https://doi.org/10.1186/s12864-023-09749-9}, + urldate = {2023-12-03}, + volume = {24}, + year = {2023} +} + +@article{akol_multimodal_2023, + abstract = {Forkhead box G1 (FOXG1) has important functions in neuronal differentiation and balances excitatory/inhibitory network activity. Thus far, molecular processes underlying FOXG1 function are largely unexplored. Here, we present a multiomics data set exploring how FOXG1 impacts neuronal maturation at the chromatin level in the mouse hippocampus. At a genome-wide level, FOXG1 i) both represses and activates transcription, ii) binds mainly to enhancer regions, iii) reconfigures the epigenetic landscape through bidirectional alteration of H3K27ac, H3K4me3, and chromatin accessibility, and iv) operates synergistically with NEUROD1. Interestingly, we could not detect a clear hierarchy of FOXG1 and NEUROD1, but instead, provide the evidence that they act in a highly cooperative manner to control neuronal maturation. Genes affected by the chromatin alterations impact synaptogenesis and axonogenesis. Inhibition of histone deacetylases partially rescues transcriptional alterations upon FOXG1 reduction. This integrated multiomics view of changes upon FOXG1 reduction reveals an unprecedented multimodality of FOXG1 functions converging on neuronal maturation. It fuels therapeutic options based on epigenetic drugs to alleviate, at least in part, neuronal dysfunction.}, + author = {Akol, Ipek and Izzo, Annalisa and Gather, Fabian and Strack, Stefanie and Heidrich, Stefanie and Ó hAilín, Darren and Villarreal, Alejandro and Hacker, Christine and Rauleac, Tudor and Bella, Chiara and Fischer, Andre and Manke, Thomas and Vogel, Tanja}, + doi = {10.1073/pnas.2122467120}, + journal = {Proceedings of the National Academy of Sciences}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: Proceedings of the National Academy of Sciences}, + number = {2}, + pages = {e2122467120}, + title = {Multimodal epigenetic changes and altered {NEUROD1} chromatin binding in the mouse hippocampus underlie {FOXG1} syndrome}, + url = {https://www.pnas.org/doi/full/10.1073/pnas.2122467120}, + urldate = {2023-03-15}, + volume = {120}, + year = {2023} +} + +@article{akpinar_characterization_2024, + abstract = {Xylanases are the main enzymes to hydrolyze xylan, the major hemicellulose found in lignocellulose. Xylanases also have a wide range of industrial applications. Therefore, the discovery of new xylanases has the potential to enhance efficiency and sustainability in many industries. Here, we report a xylanase with thermophilic character and superior biochemical properties for industrial use. The new xylanase is discovered in Anoxybacillus ayderensis as an intracellular xylanase (AAyXYN329) and recombinantly produced. While AAyXYN329 shows significant activity over a wide pH and temperature range, optimum activity conditions were determined as pH 6.5 and 65 °C. The half-life of the enzyme was calculated as 72 h at 65 °C. The enzyme did not lose activity between pH 6.0–9.0 at +4 °C for 75 days. Km, kcat and kcat/Km values of AAyXYN329 were calculated as 4.09824 ± 0.2245 μg/μL, 96.75 1/sec, and 23.61/L/g.s −1, respectively. In conclusion, the xylanase of A. ayderensis has an excellent potential to be utilized in many industrial processes.}, + author = {Akpinar, Zuleyha and Karaoglu, Hakan}, + doi = {10.1016/j.pep.2024.106478}, + issn = {1046-5928}, + journal = {Protein Expression and Purification}, + keywords = {{\textgreater}UseGalaxy.eu, Intracellular, Thermophilic, Xylan, xylanase}, + month = {July}, + pages = {106478}, + title = {Characterization of a highly thermostable recombinant xylanase from \textit{{Anoxybacillu}}s \textit{ayderensis}}, + url = {https://www.sciencedirect.com/science/article/pii/S1046592824000500}, + urldate = {2024-05-17}, + volume = {219}, + year = {2024} +} + +@article{alawi_private_2024, + abstract = {Water quality testing does not recognise antimicrobial resistance (AMR) and is often limited to indicators of faecal contamination Escherichia coli and Enterococcus species. In Europe, data on AMR in drinking water is scarce. In Ireland, as in many countries, household drinking water is supplied via mains or via private wells or water schemes. Using citizen science, we identified Irish private drinking water supplies as reservoirs of antimicrobial resistant bacteria (ARB). Gram-negative (n = 464) and Gram-positive (n = 72) bacteria were isolated. We identified instances of potentially opportunistic ARB such as Enterobacter cloacae, Acinetobacter baumannii and Enterococcus species. We report reservoirs of multidrug resistance in Enterococcus casseliflavus, E. cloacae, E. coli, Stenotrophomonas maltophilia, and Serratia rubidaea. We also identified linezolid-resistant Enterococcus in Irish drinking water. Linezolid is a last-resort antibiotic used to treat vancomycin-resistant Enterococcus sp. Additionally, we identified mobile AMR in three water samples, two of which were carried on IncF group, one on IncQ and five on Col-like plasmids. Our work suggests that private drinking water is a potential sink and source of AMR pathogens. This highlights a value of drinking water surveillance in a One Health framework as the surveillance would provide information regarding the movement and persistence of ARB and ARGs that are able to survive in drinking water and subsequently have the opportunity to be mobilised through humans; linking the environment to the human and potentially threatening human health.}, + author = {Alawi, Marwa and Smyth, Cian and Drissner, David and Zimmerer, Anna and Leupold, Denise and Müller, Daria and Do, Thi Thuy and Velasco-Torrijos, Trinidad and Walsh, Fiona}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s44259-024-00024-9}, + issn = {2731-8745}, + journal = {npj Antimicrobials and Resistance}, + keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Water microbiology}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--16}, + title = {Private and well drinking water are reservoirs for antimicrobial resistant bacteria}, + url = {https://www.nature.com/articles/s44259-024-00024-9}, + urldate = {2024-05-17}, + volume = {2}, + year = {2024} +} + @article{alcaraz_development_2021, abstract = {There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01\% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.}, author = {Alcaraz, Alper James G. and Potěšil, David and Mikulášek, Kamil and Green, Derek and Park, Bradley and Burbridge, Connor and Bluhm, Kerstin and Soufan, Othman and Lane, Taylor and Pipal, Marek and Brinkmann, Markus and Xia, Jianguo and Zdráhal, Zbyněk and Schneider, David and Crump, Doug and Basu, Niladri and Hogan, Natacha and Hecker, Markus}, @@ -106,6 +284,76 @@ @article{ali_characterization_2021 year = {2021} } +@article{ali_transcriptome-wide_2022, + abstract = {Seaweed extracts are becoming integrated into crop production systems due to their multiple beneficial effects including growth promotion and induction of defence mechanisms. However, the comprehensive molecular mechanisms of these effects are yet to be elucidated. The current study investigated the transcriptomic changes induced by seaweed extracts derived from Sargassum vulgare and Acanthophora spicifera on tomato and sweet pepper plants. Tomato and sweet pepper plants were subjected to foliar treatment with alkaline extracts prepared from the above seaweeds. Transcriptome changes in the plants were assessed 72h after treatments using RNA-sequencing. The treated plants were also analysed for defense enzyme activities, nutrient composition and phytohormonal profiles. The results showed the significant enrichment of genes associated with several growth and defense processes including photosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, plant-pathogen interaction, secondary metabolite metabolism, MAPK signaling, and amino acid biosynthesis. Activities of defense enzymes were also significantly increased in SWE-treated plants. Plant nutrient profiling showed significant increases in calcium, potassium, nitrogen, sulphur, boron, copper, iron, manganese, zinc, and phosphorous levels in seaweed-extract treated plants. Furthermore, the levels of auxins, cytokinins, and gibberellins were also significantly increased in the treated plants. In addition to these observed effects, were also significant disease reductions of bacterial leaf spot and early blight in SWE-treated plants coupled with an increase in chlorophyll content, plant growth, and fruit yield. The results demonstrated the complex effect of S. vulgare and A. spicifera extracts on the plants’ transcriptome and provide evidence of a strong role of these extracts in increasing plant growth responses while priming the plants against pathogenic attack simultaneously. The current study contributes to the understanding of the molecular mechanisms of seaweed extracts in plants and helps their usage as a viable organic input for sustainable crop production.}, + author = {Ali, Omar and Ramsubhag, Adesh and Jayaraman, Jayaraj}, + doi = {10.1093/aobpla/plac046}, + issn = {2041-2851}, + journal = {AoB PLANTS}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + pages = {plac046}, + title = {Transcriptome-wide modulation by {Sargassum} vulgare and {Acanthophora} spicifera extracts results in a prime-triggered plant signaling cascade in tomato and sweet pepper}, + url = {https://doi.org/10.1093/aobpla/plac046}, + urldate = {2022-11-06}, + year = {2022} +} + +@article{ali_transcriptomic_2022, + abstract = {Extracts of Ascophyllum nodosum are commonly used as commercial biostimulants in crop production. To further understand the seaweed extract-induced phenomena in plants, a transcriptomic study was conducted. RNA-seq differential gene expression analysis of tomato plants treated with a commercial A. nodosum extract formulation (Stimplex) revealed the up-regulation of 635 and down-regulation of 456 genes. Ontology enrichment analysis showed three\ gene categories were augmented, including biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed that the extract had a strong influence on the expression of genes involved in carbon fixation, secondary metabolism, MAPK-signalling, plant hormone signal transduction, glutathione metabolism, phenylpropanoid and stilbenoid metabolism, and plant-pathogen interactions. qRT-PCR validation analysis using 15 genes established a strong correlation with the RNA sequencing results. The activities of defence enzymes were also significantly enhanced by seaweed extract treatment. Furthermore, AN-SWE treated tomato plants had significantly higher chlorophyll and growth hormone content and showed improved plant growth parameters and nutrient profiles than the control. It is postulated that seaweed extract-induced gene regulation was responsible for favourable plant responses that enabled better growth and tolerance to stress conditions. This study provides evidence at the transcriptomic level for the positive effects of foliar application of the Ascophyllum nodosum extract (Stimplex) observed in treated tomato plants.}, + author = {Ali, Omar and Ramsubhag, Adesh and Daniram Benn Jr. Ramnarine, Stephen and Jayaraman, Jayaraj}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41598-022-11263-z}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + language = {en}, + month = {May}, + number = {1}, + pages = {1--13}, + title = {Transcriptomic changes induced by applications of a commercial extract of {Ascophyllum} nodosum on tomato plants}, + url = {https://www.nature.com/articles/s41598-022-11263-z}, + urldate = {2022-09-24}, + volume = {12}, + year = {2022} +} + +@article{aljindan_phenomics_2024, + abstract = {Background +Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. +Methods +The bacterial strain IRMC1622a was identified by 16S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. +Results +The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490µm), in pairs (L 1.7333 ± 0.1054µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. +Conclusions +The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.}, + author = {AlJindan, Reem and Mahmoud, Nehal and AlEraky, Doaa M. and Almandil, Noor B. and AbdulAzeez, Sayed and Borgio, J. Francis}, + doi = {10.1016/j.jiph.2024.05.051}, + issn = {1876-0341}, + journal = {Journal of Infection and Public Health}, + keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Saudi Arabia, bacterial genome, gastrointestinal fistula, long-read sequencing, multidrug-resistant}, + month = {May}, + title = {Phenomics and genomic features of \textit{{Enterococcus} avium} {IRMC1622a} isolated from a clinical sample of hospitalized patient}, + url = {https://www.sciencedirect.com/science/article/pii/S1876034124001977}, + urldate = {2024-06-02}, + year = {2024} +} + +@article{alvandi_pathovar-specific_2023, + abstract = {Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. So far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa as the expected 229 bp DNA fragment was not amplified in the closely-related pathovars nor in other xanthomonads, wheat pathogenic bacteria, and other plant pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/µl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 cfu/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 cfu/g while culture plate method was able to detect the pathogen at a concentration of 50 × 105 cfu/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.}, + author = {Alvandi, Hosna and Taghavi, Seied Mohsen and Khojasteh, Moein and Rahimi, Touraj and Dutrieux, Cecile and Taghouti, Geraldine and Jacques, Marie-Agnès and Portier, Perrine and Osdaghi, Ebrahim}, + doi = {10.1094/PDIS-11-22-2677-SR}, + issn = {0191-2917}, + journal = {Plant Disease}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: Scientific Societies}, + title = {Pathovar-{Specific} {PCR} {Method} for {Detection} and {Identification} of {Xanthomonas} translucens pv. undulosa}, + url = {https://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-11-22-2677-SR}, + urldate = {2023-03-15}, + year = {2023} +} + @article{amaral_tcti_2022, author = {Amaral, Milena do and Freitas, Ana Camila Oliveira and Santos, Ariana Silva and Santos, Everton Cruz dos and Ferreira, Monaliza Macêdo and Gesteira, Abelmon da Silva and Gramacho, Karina Peres and Marinho-Prado, Jeanne Scardini and Pirovani, Carlos Priminho}, doi = {10.1038/s41598-021-04700-y}, @@ -120,6 +368,113 @@ @article{amaral_tcti_2022 year = {2022} } +@article{ambros_distribution_2023, + abstract = {Aim: Temperate phages are known to heavily impact the growth of their host, be it in a positive way, e.g., when beneficial genes are provided by the phage, or negatively when lysis occurs after prophage induction. This study provides an in-depth look into the distribution and variety of prophages in Latilactobacillus curvatus (L. curvatus). This species is found in a wide variety of ecological niches and is routinely used as a meat starter culture., +Methods: Fourty five L. curvatus genomes were screened for prophages. The intact predicted prophages and their chromosomal integration loci were described. Six L. curvatus lysogens were analysed for phage-mediated lysis post induction via UV light and/or mitomycin C. Their lysates were analysed for phage particles via viral DNA sequencing and transmission electron microscopy., +Results: Two hundred and six prophage sequences of any completeness were detected within L. curvatus genomes. The 50 as intact predicted prophages show high levels of genetic diversity on an intraspecies level with conserved regions mostly in the replication and head/tail gene clusters. Twelve chromosomal loci, mostly tRNA genes, were identified, where intact L. curvatus phages were integrated. The six analysed L. curvatus lysogens showed strain-dependent lysis in various degrees after induction, yet only four of their lysates appeared to contain fully assembled virions with the siphovirus morphotype., +Conclusion: Our data demonstrate that L. curvatus is a (pro)phage-susceptible species, harbouring multiple intact prophages and remnant sequences thereof. This knowledge provides a basis to study phage-host interaction influencing microbial communities in food fermentations.}, + author = {Ambros, Conrad L. and Ehrmann, Matthias A.}, + doi = {10.20517/mrr.2023.18}, + issn = {2771-5965}, + journal = {Microbiome Research Reports}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {4}, + pages = {34}, + pmcid = {PMC10688831}, + pmid = {38045928}, + title = {Distribution, inducibility, and characteristics of {Latilactobacillus} curvatus temperate phages}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688831/}, + urldate = {2023-12-28}, + volume = {2}, + year = {2023} +} + +@article{anbazhagan_comparative_2023, + abstract = {Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.}, + author = {Anbazhagan, S. and Himani, K.M. and Karthikeyan, R. and Prakasan, Lakshmi and Dinesh, M. and Nair, Sonu S. and Lalsiamthara, Jonathan and {Abhishek} and Ramachandra, S.G. and Chaturvedi, V.K. and Chaudhuri, Pallab and Thomas, Prasad}, + doi = {10.1007/s10123-023-00374-w}, + issn = {1618-1905}, + journal = {International Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, B. abortus, B. melitensis, Comparative genomics, Pangenome, Virulence genes}, + language = {en}, + month = {May}, + title = {Comparative genomics of {Brucella} abortus and {Brucella} melitensis unravels the gene sharing, virulence factors and {SNP} diversity among the standard, vaccine and field strains}, + url = {https://doi.org/10.1007/s10123-023-00374-w}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{andrade_assessing_2023, + author = {Andrade, Luisa and Ryan, Michael P. and Burke, Liam P. and Hynds, Paul and Weatherill, John and O'Dwyer, Jean}, + doi = {10.2139/ssrn.4350080}, + journal = {SSRN Electronic Journal}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Publisher: Elsevier BV}, + title = {Assessing {Antimicrobial} and {Metal} {Resistance} {Genes} in {Escherichia} {Coli} from {Domestic} {Groundwater} {Supplies} in {Rural} {Ireland}}, + url = {https://doi.org/10.2139/ssrn.4350080}, + year = {2023} +} + +@article{andriyanov_genomic_2024, + abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Delftia tsuruhatensis{\textless}/italic{\textgreater} is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged as an opportunistic human pathogen. To date, the source of {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater} infection is not clear. The majority of studies of {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater} have focused on environmental or clinical strains, while investigations of {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater} strains isolated from food sources are limited. In the present study, we report the case of {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater} isolation from raw bovine milk. Classical bacteriology approaches, as well as next-generation sequencing and comparative genomics, were used to characterize the features of the {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater} MR-6/3H strain. The MR-6/3H strain was resistant to 19 antimicrobials among 23 tested, including all aminoglycosides, phenicol, trimethoprim-sulfamethoxazole, and almost all β-lactams. Phylogenetically, the MR-6/3H was close to clinical origin strains, including those previously isolated in Russia. Comparative genomics revealed the presence of putative antimicrobial resistance genes in the MR-6/3H isolate, mostly associated with efflux systems. Notably, genus-specific OXA-926-like β-lactamase was also detected. In all, 27 putative virulence factors were predicted, the majority of which were associated with motility, adherence, stress survival, siderophore synthesis, and immunomodulation. In the MR-6/3H genome, the five prophage regions were identified, including two with intact levels. Integrons and CRISPR-Cas systems were not detected in the MR-6/3H isolate. Thus, our findings suggest that raw milk can be the potential source of and transmission route for the dissemination of multidrug-resistant {\textless}italic{\textgreater}D. tsuruhatensis{\textless}/italic{\textgreater}.{\textless}/p{\textgreater}}, + author = {Andriyanov, Pavel A. and Kashina, Daria D. and Menshikova, Alena N.}, + doi = {10.3389/fmicb.2023.1321122}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance (AMR), Delftia tsuruhatensis, Genomics, phylogenomic analysis, raw milk}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {Genomic analysis of multidrug-resistant {Delftia} tsuruhatensis isolated from raw bovine milk}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1321122/full}, + urldate = {2024-05-17}, + volume = {14}, + year = {2024} +} + +@article{annor_melibiosex-galmacconkey_2023, + abstract = {The bacterial foodborne enteropathogen Escherichia albertii, despite enjoying increased attention paid to its pathogenesis, global dissemination, and antimicrobial resistance capacity, remains difficult to identify from human foods. The primary objective of this study was to develop and test a selective and differential plating medium for the isolation of E. albertii from enteric pathogens commonly transmitted via fresh poultry meat, namely E. coli and Salmonella enterica. MacConkey agar supplemented with α-D-+-melibiose and the lactose analogue X-gal was prepared and used to differentially enumerate E. albertii, Salmonella, and E. coli from inoculated ground chicken meat. The medium, MXgMac agar, differentiated the inoculated pathogens with a greater degree of efficiency than did the previously developed E. albertii-selective medium xylose–rhamnose–melibiose (XRM) MacConkey agar, based on differential usage of the lactose analogue and melibiose. Chicken-derived feces and litter samples were subsequently tested using the medium and found not to contain E. albertii by 16S rRNA gene amplification. MXgMac agar facilitates improved differential recovery of E. albertii and other enteric pathogens from poultry meat versus other E. albertii selective/differential media.}, + author = {Annor, Samuel D. and Salazar, Karla S. and Pillai, Suresh D. and Kerth, Chris R. and Gill, Jason J. and Taylor, Thomas M.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/applmicrobiol3010010}, + issn = {2673-8007}, + journal = {Applied Microbiology}, + keywords = {\textit{E. coli}, \textit{Escherichia albertii}, \textit{Salmonella}, {\textgreater}UseGalaxy.eu, MacConkey Agar, culture media, food safety, poultry safety}, + language = {en}, + month = {March}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {119--130}, + title = {Melibiose–{X}-{Gal}–{MacConkey} {Agar} for {Presumptive} {Differentiation} of {Escherichia} albertii from {E}. coli and {Salmonella} from {Poultry} {Meat}}, + url = {https://www.mdpi.com/2673-8007/3/1/10}, + urldate = {2023-03-15}, + volume = {3}, + year = {2023} +} + +@article{apostolakos_genomic_2023, + abstract = {Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep’s milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof.}, + author = {Apostolakos, Ilias and Skarlatoudi, Theodora and Vatavali, Kornilia and Giannouli, Agathi and Bosnea, Loulouda and Mataragas, Marios}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms241813883}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, dairy products, lactic acid bacteria, mastitis, probiotics, sheep’s milk, staphylococci, whole-genome sequencing}, + language = {en}, + month = {January}, + note = {Number: 18 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {18}, + pages = {13883}, + title = {Genomic and {Phenotypic} {Characterization} of {Mastitis}-{Causing} {Staphylococci} and {Probiotic} {Lactic} {Acid} {Bacteria} {Isolated} from {Raw} {Sheep}’s {Milk}}, + url = {https://www.mdpi.com/1422-0067/24/18/13883}, + urldate = {2023-10-28}, + volume = {24}, + year = {2023} +} + @article{apostolakos_occurrence_2021, author = {Apostolakos, Ilias and Laconi, Andrea and Mughini-Gras, Lapo and Yapicier, Özlem Şahan and Piccirillo, Alessandra}, doi = {10.3389/fvets.2021.737720}, @@ -132,6 +487,60 @@ @article{apostolakos_occurrence_2021 year = {2021} } +@article{arai_two_2024, + abstract = {Insects harbour diverse maternally inherited bacteria and viruses, some of which have evolved to kill the male progeny of their hosts (male killing: MK). The fly species Drosophila biauraria carries a maternally transmitted MK-inducing partiti-like virus, but it was unknown if it carries other MK-inducing endosymbionts. Here, we identified two male-killing Wolbachia strains (wBiau1 and wBiau2) from D. biauraria and compared their genomes to elucidate their evolutionary processes. The two strains were genetically closely related but had exceptionally different genome structures with considerable rearrangements compared with combinations of other Wolbachia strains. Despite substantial changes in the genome structure, the two Wolbachia strains did not experience gene losses that would disrupt the male-killing expression or persistence in the host population. The two Wolbachia-infected matrilines carried distinct mitochondrial haplotypes, suggesting that wBiau1 and wBiau2 have invaded D. biauraria independently and undergone considerable genome changes owing to unknown selective pressures in evolutionary history. This study demonstrated the presence of three male-killers from two distinct origins in one fly species and highlighted the diverse and rapid genome evolution of MK Wolbachia in the host.}, + author = {Arai, Hiroshi and Watada, Masayoshi and Kageyama, Daisuke}, + doi = {10.1098/rsos.231502}, + journal = {Royal Society Open Science}, + keywords = {{\textgreater}UseGalaxy.eu, Wolbachia, evolution, genome rearrangement, male killing}, + month = {January}, + note = {Publisher: Royal Society}, + number = {1}, + pages = {231502}, + title = {Two male-killing {Wolbachia} from {Drosophila} birauraia that are closely related but distinct in genome structure}, + url = {https://royalsocietypublishing.org/doi/full/10.1098/rsos.231502}, + urldate = {2024-04-28}, + volume = {11}, + year = {2024} +} + +@article{arcari_ceftazidimeavibactam_2023, + abstract = {The first reports of carbapenem-resistant Enterobacterales in our hospital date back to 2006. In that period, few ertapenem-resistant but meropenem-susceptible Klebsiella pneumoniae isolates belonging to sequence type (ST) 37 were retrieved from clinical samples. These strains produced the CTX-M-15 extended spectrum β-lactamase, OmpK35 was depleted due to a nonsense mutation, and a novel OmpK36 variant was identified. Yet, starting from 2010, Klebsiella pneumoniae carbapenemase (KPC)-producing ST512 isolates started prevailing and ST37 vanished from sight. Since 2018 the clinical use of the combination of ceftazidime–avibactam (CZA) has been introduced in clinical practice for the treatment of bacteria producing serine-β-lactamases, but KPC-producing, CZA-resistant K. pneumoniae are emerging. In 2021, four CZA-resistant ST37 isolates producing KPC variants were isolated from the same number of patients. blaKPC gene cloning in Escherichia coli was used to define the role of those KPC variants on CZA resistance, and whole genome sequencing was performed on these isolates and on three ST37 historical isolates from 2011. CZA resistance was due to mutations in the blaKPC genes carried on related pKpQIL-type plasmids, and three variants of the KPC enzyme have been identified in the four ST37 strains. The four ST37 isolates were closely related to each other and to the historical isolates, suggesting that ST37 survived without notice in our hospital for 10 years, waiting to re-emerge as a CZA-resistant K. pneumoniae clone. The ancestor of these contemporary isolates derives from ST37 wild-type porin strains, with no other mutations in chromosomal genes involved in conferring antibiotic resistance (parC, gyrA, ramR, mgrB, pmrB).}, + author = {Arcari, Gabriele and Polani, Riccardo and Bruno, Francesco and Capitani, Valerio and Sacco, Federica and Menichincheri, Gaia and Raponi, Giammarco and Carattoli, Alessandra}, + doi = {10.1099/mgen.0.000931}, + issn = {2057-5858}, + journal = {Microbial Genomics}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Publisher: Microbiology Society,}, + number = {2}, + pages = {000931}, + shorttitle = {Ceftazidime–avibactam resistance in {Klebsiella} pneumoniae sequence type 37}, + title = {Ceftazidime–avibactam resistance in {Klebsiella} pneumoniae sequence type 37: a decade of persistence and concealed evolution}, + url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000931}, + urldate = {2023-03-15}, + volume = {9}, + year = {2023} +} + +@article{arcari_genotypic_2023, + abstract = {In February 2022, a critically ill patient colonized with a carbapenem-resistant K. pneumoniae producing KPC-3 and VIM-1 carbapenemases was hospitalized for SARS-CoV-2 in the intensive care unit of Policlinico Umberto I hospital in Rome, Italy. During ...}, + author = {Arcari, Gabriele and Cecilia, Federico and Oliva, Alessandra and Polani, Riccardo and Raponi, Giammarco and Sacco, Federica and Francesco, Alice De and Pugliese, Francesco and Carattoli, Alessandra}, + doi = {10.3201/eid2911.230921}, + journal = {Emerging Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + note = {Publisher: Centers for Disease Control and Prevention}, + number = {11}, + pages = {2266}, + pmid = {37877547}, + title = {Genotypic {Evolution} of {Klebsiella} pneumoniae {Sequence} {Type} 512 during {Ceftazidime}/{Avibactam}, {Meropenem}/{Vaborbactam}, and {Cefiderocol} {Treatment}, {Italy}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10617348/}, + urldate = {2023-12-28}, + volume = {29}, + year = {2023} +} + @article{arcari_interplay_2022, author = {Arcari, Gabriele and Oliva, Alessandra and Sacco, Federica and Lella, Federica Maria Di and Raponi, Giammarco and Tomolillo, Dario and Curtolo, Ambrogio and Venditti, Mario and Carattoli, Alessandra}, doi = {10.1007/s10096-021-04388-y}, @@ -147,6 +556,145 @@ @article{arcari_interplay_2022 year = {2022} } +@article{arcari_multiplicity_2023, + abstract = {In 2021, Klebsiella pneumoniae sequence type 307 (ST307) strains causing pulmonary and bloodstream infections identified in a hospital in Rome, Italy, reached high levels of resistance to ceftazidime-avibactam (CZA). One of these strains reached high levels of resistance to both CZA and carbapenems and carried two copies of blaKPC-3 and one copy of blaKPC-31 located on plasmid pKpQIL. The genomes and plasmids of CZA-resistant ST307 strains were analyzed to identify the molecular mechanisms leading to the evolution of resistance and compared with ST307 genomes at local and global levels. A complex pattern of multiple plasmids in rearranged configurations, coresident within the CZA-carbapenem–resistant K. pneumoniae strain, was observed. Characterization of these plasmids revealed recombination and segregation events explaining why K. pneumoniae isolates from the same patient had different antibiotic resistance profiles. This study illustrates the intense genetic plasticity occurring in ST307, one of the most worldwide-diffused K. pneumoniae high-risk clones.}, + author = {Arcari, Gabriele and Polani, Riccardo and Santilli, Stefania and Capitani, Valerio and Sacco, Federica and Bruno, Francesco and Garcia-Fernandez, Aurora and Raponi, Giammarco and Villa, Laura and Gentile, Giuseppe and Carattoli, Alessandra}, + doi = {10.1128/aac.00368-23}, + journal = {Antimicrobial Agents and Chemotherapy}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00368--23}, + title = {Multiplicity of {blaKPC} {Genes} and {pKpQIL} {Plasmid} {Plasticity} in the {Development} of {Ceftazidime}-{Avibactam} and {Meropenem} {Coresistance} in {Klebsiella} pneumoniae {Sequence} {Type} 307}, + url = {https://journals.asm.org/doi/full/10.1128/aac.00368-23}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + +@article{ardisasmita_comprehensive_2022, + abstract = {The myriad of available hepatocyte in vitro models provides researchers the possibility to select hepatocyte-like cells (HLCs) for specific research goals. However, direct comparison of hepatocyte models is currently challenging. We systematically searched the literature and compared different HLCs, but reported functions were limited to a small subset of hepatic functions. To enable a more comprehensive comparison, we developed an algorithm to compare transcriptomic data across studies that tested HLCs derived from hepatocytes, biliary cells, fibroblasts, and pluripotent stem cells, alongside primary human hepatocytes (PHHs). This revealed that no HLC covered the complete hepatic transcriptome, highlighting the importance of HLC selection. HLCs derived from hepatocytes had the highest transcriptional resemblance to PHHs regardless of the protocol, whereas the quality of fibroblasts and PSC derived HLCs varied depending on the protocol used. Finally, we developed and validated a web application (HLCompR) enabling comparison for specific pathways and addition of new HLCs. In conclusion, our comprehensive transcriptomic comparison of HLCs allows selection of HLCs for specific research questions and can guide improvements in culturing conditions.}, + author = {Ardisasmita, Arif Ibrahim and Schene, Imre F. and Joore, Indi P. and Kok, Gautam and Hendriks, Delilah and Artegiani, Benedetta and Mokry, Michal and Nieuwenhuis, Edward E. S. and Fuchs, Sabine A.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s42003-022-04046-9}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Data integration, Hepatocytes, RNA sequencing, Stem-cell differentiation}, + language = {en}, + month = {October}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--15}, + title = {A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use}, + url = {https://www.nature.com/articles/s42003-022-04046-9}, + urldate = {2022-12-03}, + volume = {5}, + year = {2022} +} + +@article{aribisala_cheminformatics_2023, + abstract = {Data implicating the mutation in penicillin-binding protein (PBP) 3 and occasionally PBP5 in the resistance of Escherichia coli to beta−lactams is intriguing. Thus, the identification of an improved class of inhibitors of PBP3 and PBP5 is imperative, and in this study, phenolics due to their promising antibacterial activities were screened using structure−based pharmacophore and molecular docking approaches against PBP3, and the ability of the lead phenolics to modulate PBP3 and PBP5 was studied using molecular dynamics simulation. The results demonstrated various inhibitory capacities of the lead phenolics, with lysidicichin (−41.66 kcal/mol) and silicristin (−31.11 kcal/mol) being the most potent against PBP3, while epicatechin 3-O-(3-O-methylgallate) (−38.97 kcal/mol) and epigallocatechin-4-benzyl thioether (−37.01 kcal/mol) had higher affinities towards PBP5. Overall, epicatechin gallate had the best broad-spectrum of activity, as the compound was able to bind favourably to both targets. Additionally, the thermodynamic information confirmed the stability of the lead phenolics with both targets. Conclusively, while these observations are suggestive of the modulatory role of the lead phenolics on the growth of E. coli, further in vitro and in vivo validation of the activity elicited by the phenolics in this study is imperative, and efforts are underway in this direction.}, + author = {Aribisala, Jamiu Olaseni and Idowu, Kehinde and Makhanya, Talent Raymond and Sabiu, Saheed}, + doi = {10.1080/08927022.2023.2228423}, + issn = {0892-7022}, + journal = {Molecular Simulation}, + keywords = {{\textgreater}UseGalaxy.eu, Resistance, molecular docking, molecular dynamics simulation, penicillin−binding proteins, phenolics}, + month = {June}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/08927022.2023.2228423}, + number = {0}, + pages = {1--17}, + title = {Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of {Escherichia} coli towards interventive antibacterial therapy}, + url = {https://doi.org/10.1080/08927022.2023.2228423}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + +@article{aribisala_silico_2024, + abstract = {Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children {\textless} 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (− 19.23 kcal/mol), allosteric site (− 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (− 38.41 kcal/mol) and allosteric (− 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of {\textless} 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.}, + author = {Aribisala, Jamiu Olaseni and S’thebe, Nosipho Wendy and Sabiu, Saheed}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-59489-3}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Drug discovery}, + language = {en}, + month = {April}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {8788}, + title = {In silico exploration of phenolics as modulators of penicillin binding protein ({PBP}) 2× of {Streptococcus} pneumoniae}, + url = {https://www.nature.com/articles/s41598-024-59489-3}, + urldate = {2024-04-28}, + volume = {14}, + year = {2024} +} + +@article{arnold_isolation_2023, + abstract = {Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so‐called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long‐read sequencing‐based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin‐amended soil samples. Through metabolic characterization, whole‐genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO‐TAS4‐2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N‐acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent., In this study, a novel chitinolytic Jeongeupia species “wiesaeckerbachi” was isolated from soil samples, characterized biochemically, and sequenced with the long‐read platform PacBio Sequel IIe. In silico analysis unraveled genomic differences to the closest related type strain Jeongeupia naejangsanensis TAS4‐2 in addition to an usually extensive chitinolytic machinery.}, + author = {Arnold, Nathanael D. and Garbe, Daniel and Brück, Thomas B.}, + doi = {10.1002/mbo3.1372}, + issn = {2045-8827}, + journal = {MicrobiologyOpen}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + number = {4}, + pages = {e1372}, + pmcid = {PMC10404844}, + pmid = {null}, + title = {Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic {Jeongeupia} species}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10404844/}, + urldate = {2023-08-13}, + volume = {12}, + year = {2023} +} + +@phdthesis{arnold_unlocking_2024, + abstract = {This thesis was part of the ChitoMat project, aiming to explore novel enzymes for chitin conversion into tailored chitooligosaccharides. It led to the discovery of a novel chitinolytic bacterium, named Jeongeupia wiesaeckerbachi in a first publication. In the second publication, a comprehensive systems biology approach was used to study J. wiesaeckerbachi's chitinolytic response system, identifying potential enzymes for biotechnological chitin valorization.}, + author = {Arnold, Nathanael David}, + keywords = {{\textgreater}UseGalaxy.eu}, + school = {Technische Universität München}, + title = {Unlocking a {Potent} {Chitin} {Saccharification} {System} in a {Novel} {Bacterium} {Through} {Omics} and {Bioinformatics}}, + url = {https://mediatum.ub.tum.de/1724798}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{ashrafi_two_2022, + author = {Ashrafi, Samad and Kuzmanović, Nemanja and Patz, Sascha and Lohwasser, Ulrike and Bunk, Boyke and Spröer, Cathrin and Lorenz, Maria and Elhady, Ahmed and Frühling, Anja and Neumann-Schaal, Meina and Verbarg, Susanne and Becker, Matthias and Thünen, Torsten}, + doi = {10.1128/spectrum.01099-22}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01099--22}, + title = {Two {New} {Rhizobiales} {Species} {Isolated} from {Root} {Nodules} of {Common} {Sainfoin} ({Onobrychis} viciifolia) {Show} {Different} {Plant} {Colonization} {Strategies}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.01099-22}, + urldate = {2022-09-24}, + volume = {0}, + year = {2022} +} + +@article{bafna_dynamic_2023, + abstract = {The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer–gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35\% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.}, + author = {Bafna, Akanksha and Banks, Gareth and Hastings, Michael H. and Nolan, Patrick M.}, + doi = {10.1101/gr.277581.122}, + issn = {1088-9051, 1549-5469}, + journal = {Genome Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {May}, + pages = {genome;gr.277581.122v2}, + title = {Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock}, + url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.277581.122}, + urldate = {2023-06-10}, + year = {2023} +} + @incollection{bagnacani_tools_2019, abstract = {MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. The use of RNA data in gene expression analysis has become increasingly important to gain insights into the regulatory mechanisms behind miRNA–mRNA interactions. As a result, we are confronted with a growing landscape of tools, while standards for reproducibility and benchmarking lag behind. This work identifies the challenges for reproducible RNA analysis, and highlights best practices on the processing and dissemination of scientific results. We found that the success of a tool does not solely depend on its performances: equally important is how a tool is received, and then supported within a community. This leads us to a detailed presentation of the RNA workbench, a community effort for sharing workflows and processing tools, built on top of the Galaxy framework. Here, we follow the community guidelines to extend its portfolio of RNA tools with the integration of the TriplexRNA (https://triplexrna.org). Our findings provide the basis for the development of a recommendation system, to guide users in the choice of tools and workflows.}, address = {New York, NY}, @@ -166,6 +714,43 @@ @incollection{bagnacani_tools_2019 year = {2019} } +@article{bahrami_integrated_2024, + abstract = {Background: Enhancer RNAs (eRNAs) are involved in gene expression regulation. Although functional roles of eRNAs in the pathophysiology of neoplasms have been reported, their involvement in gastric cancer (GC) is less known. Materials \& methods: A network-based integrative approach was utilized for analyzing transcriptome and epigenome alterations in GC, and an eRNA was selected for experimental validation. Survival analysis and clinicopathological associations were also performed. Results: A hub eRNA, ENSR00000272060, showed significantly increased expression in tumor versus nontumor tissues, as well as an association with clinicopathological features. A seven-gene prognostic model was also constructed. Conclusion: The constructed network provides a comprehensive understanding of the underlying processes implicated in the progression of GC, along with a starting point from which to derive potential diagnostic/prognostic biomarkers.}, + author = {Bahrami, Basireh and Wolfien, Markus and Nikpour, Parvaneh}, + doi = {10.2217/epi-2023-0213}, + issn = {1750-1911}, + journal = {Epigenomics}, + keywords = {{\textgreater}UseGalaxy.eu, biomarkers, enhancer RNA, epigenomics, stomach neoplasms, systems biology}, + month = {February}, + note = {Publisher: Future Medicine}, + number = {3}, + pages = {159--173}, + title = {Integrated analysis of transcriptome and epigenome reveals {ENSR00000272060} as a potential biomarker in gastric cancer}, + url = {https://www.futuremedicine.com/doi/full/10.2217/epi-2023-0213}, + urldate = {2024-02-03}, + volume = {16}, + year = {2024} +} + +@article{baig_genome-wide_2023, + abstract = {β-galactosidase (Lactase), an enzyme belonging to the glycoside hydrolase family causing the hydrolysis and trans-glycosylation of β-D-galactosides, has a vital role in dairy industries. The current investigation emphasizes on in-silico identification and comparative analysis of different fungal lactases present in Aspergillus fumigatus, Aspergillus oryzae, Botrytis cinerea, and Fusarium fujikuroi. Prediction of motifs and domains, chromosomal positioning, gene structure, gene ontology, sub-cellular localization and protein modeling were performed using different bioinformatics tools to have an insight into the structural and functional characteristics of β-galactosidases. Evolutionary and homology relationships were established by phylogenetic and synteny analyses. A total of 14 β-gal genes (GH-35) were identified in these species. Identified lactases, having 5 domains, were predicted to be stable, acidic, non-polar and extracellularly localized with roles in polysaccharide catabolic process. Results showed variable exonic/intronic ratios of the gene structures which were randomly positioned on chromosomes. Moreover, synteny blocks and close evolutionary relationships were observed between Aspergillus fumigatus and Aspergillus oryzae. Structural insights allowed the prediction of best protein models based on the higher ERRAT and Q-MEAN values. And RNA-sequencing analysis, performed on A. fumigatus, elucidated the role of β-gal in germ tube development. This study would pave the way for efficient fungal lactase production as it identified β-gal genes and predicted their various features and also it would provide a road-way to further the understanding of A. fumigatus pathogenicity via the expression insights of β-gal in germ tube development.}, + author = {Baig, Danish Ilyas and Zafar, Zeeshan and Khan, Haris Ahmed and Younus, Amna and Bhatti, Muhammad Faraz}, + doi = {10.1371/journal.pone.0286428}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Aspergillus, Aspergillus fumigatus, Fungal genetics, Fungal structure, Fusarium, Genome analysis, Protein structure, Protein structure prediction}, + language = {en}, + month = {June}, + note = {Publisher: Public Library of Science}, + number = {6}, + pages = {e0286428}, + title = {Genome-wide identification and comparative in-silico characterization of β-galactosidase ({GH}-35) in ascomycetes and its role in germ tube development of {Aspergillus} fumigatus via {RNA}-seq analysis}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286428}, + urldate = {2023-07-31}, + volume = {18}, + year = {2023} +} + @article{baker_no_2020, abstract = {The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.}, author = {Baker, Dannon and Beek, Marius van den and Blankenberg, Daniel and Bouvier, Dave and Chilton, John and Coraor, Nate and Coppens, Frederik and Eguinoa, Ignacio and Gladman, Simon and Grüning, Björn and Keener, Nicholas and Larivière, Delphine and Lonie, Andrew and Pond, Sergei Kosakovsky and Maier, Wolfgang and Nekrutenko, Anton and Taylor, James and Weaver, Steven}, @@ -293,19 +878,43 @@ @article{bartas_changes_2021 year = {2021} } -@article{batut_asaim_2018, - author = {Batut, Bérénice and Gravouil, Kevin and Defois, Clemence and Hiltemann, Saskia and Brugère, Jean-François and Peyretaillade, Eric and Peyret, Pierre}, - journal = {GigaScience}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Oxford University Press}, - number = {6}, - pages = {giy057}, - title = {{ASaiM}: a {Galaxy}-based framework to analyze microbiota data}, - volume = {7}, - year = {2018} +@article{bastide_genome_2024, + abstract = {Social insects’ nests harbor intruders known as inquilines,1 which are usually related to their hosts.2,3 However, distant non-social inquilines may also show convergences with their hosts,4,5 although the underlying genomic changes remain unclear. We analyzed the genome of the wingless and blind bee louse fly Braula coeca, an inquiline kleptoparasite of the western honey bee, Apis mellifera.6,7 Using large phylogenomic data, we confirmed recent accounts that the bee louse fly is a drosophilid8,9 and showed that it had likely evolved from a sap-breeder ancestor associated with honeydew and scale insects’ wax. Unlike many parasites, the bee louse fly genome did not show significant erosion or strict reliance on an endosymbiont, likely due to a relatively recent age of inquilinism. However, we observed a horizontal transfer of a transposon and a striking parallel evolution in a set of gene families between the honey bee and the bee louse fly. Convergences included genes potentially involved in metabolism and immunity and the loss of nearly all bitter-tasting gustatory receptors, in agreement with life in a protective nest and a diet of honey, pollen, and beeswax. Vision and odorant receptor genes also exhibited rapid losses. Only genes whose orthologs in the closely related Drosophila melanogaster respond to honey bee pheromone components or floral aroma were retained, whereas the losses included orthologous receptors responsive to the anti-ovarian honey bee queen pheromones. Hence, deep genomic convergences can underlie major phenotypic transitions during the evolution of inquilinism between non-social parasites and their social hosts.}, + author = {Bastide, Héloïse and Legout, Hélène and Dogbo, Noé and Ogereau, David and Prediger, Carolina and Carcaud, Julie and Filée, Jonathan and Garnery, Lionel and Gilbert, Clément and Marion-Poll, Frédéric and Requier, Fabrice and Sandoz, Jean-Christophe and Yassin, Amir}, + doi = {10.1016/j.cub.2024.01.034}, + issn = {0960-9822}, + journal = {Current Biology}, + keywords = {{\textgreater}UseGalaxy.eu, adaptation, gene family evolution, horizontal transposon transfer, inquilinism, parasitism, phylogenomics}, + month = {February}, + title = {The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates {Drosophila} origins}, + url = {https://www.sciencedirect.com/science/article/pii/S0960982224000356}, + urldate = {2024-02-06}, + year = {2024} +} + +@article{batista_da_silva_discovery_2023, + abstract = {Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo’s eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.}, + author = {Batista da Silva, Iuri and Aciole Barbosa, David and Kavalco, Karine Frehner and Nunes, Luiz R. and Pasa, Rubens and Menegidio, Fabiano B.}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-34198-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Long non-coding RNAs, Transcriptomics}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {12051}, + shorttitle = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}}, + title = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}: {Characidae})}, + url = {https://www.nature.com/articles/s41598-023-34198-5}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} } -@article{batut_asaim_2018-1, +@article{batut_asaim_2018, abstract = {Background. New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics a}, author = {Batut, Bérénice and Gravouil, Kévin and Defois, Clémence and Hiltemann, Saskia and Brugère, Jean-François and Peyretaillade, Eric and Peyret, Pierre}, doi = {10.1093/gigascience/giy057}, @@ -374,6 +983,23 @@ @article{bauer_functional_2021 year = {2021} } +@article{bawin_cuscuta_2024, + abstract = {The Cuscuta genus comprises obligate parasitic plants that have an unusually wide host range. Whether Cuscuta uses different infection strategies for different hosts or whether the infection strategy is mechanistically and enzymatically conserved remains unknown. To address this, we investigated molecular events during the interaction between field dodder (Cuscuta campestris) and two host species of the Solanum genus that are known to react differently to parasitic infection. We found that host gene induction, particularly of cell wall fortifying genes, coincided with a differential induction of genes for cell wall degradation in the parasite in the cultivated tomato (Solanum lycopersicum) but not in a wild relative (Solanum pennellii). This indicates that the parasite can adjust its gene expression in response to its host. This idea was supported by the increased expression of C. campestris genes encoding an endo-β-1,4-mannanase in response to exposure of the parasite to purified mono- and polysaccharides in a host-independent infection system. Our results suggest multiple key roles of the host cell wall in determining the outcome of an infection attempt.}, + author = {Bawin, Thomas and Didriksen, Alena and Faehn, Corine and Olsen, Stian and Sørensen, Iben and Rose, Jocelyn K C and Krause, Kirsten}, + doi = {10.1093/plphys/kiad505}, + issn = {0032-0889}, + journal = {Plant Physiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {258--273}, + title = {Cuscuta campestris fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts}, + url = {https://doi.org/10.1093/plphys/kiad505}, + urldate = {2024-05-17}, + volume = {194}, + year = {2024} +} + @article{bayona-feliu_swisnf_2021, author = {Bayona-Feliu, Aleix and Barroso, Sonia and Muñoz, Sergio and Aguilera, Andrés}, doi = {10.1038/s41588-021-00867-2}, @@ -388,6 +1014,27 @@ @article{bayona-feliu_swisnf_2021 year = {2021} } +@article{bazukyan_silico_2023, + abstract = {A Lactobacillus delbrueckii ssp. lactis strain named A4, isolated from the gut of an Armenian honeybee, was subjected to a probiogenomic characterization because of its unusual origin. A whole-genome sequencing was performed, and the bioinformatic analysis of its genome revealed a reduction in the genome size and the number of the genes—a process typical for the adaptation to endosymbiotic conditions. Further analysis of the genome revealed that Lactobacillus delbrueckii ssp. lactis strain named A4 could play the role of a probiotic endosymbiont because of the presence of intact genetic sequences determining antioxidant properties, exopolysaccharides synthesis, adhesion properties, and biofilm formation, as well as an antagonistic activity against some pathogens which is not due to pH or bacteriocins production. Additionally, the genomic analysis revealed significant potential for stress tolerance, such as extreme pH, osmotic stress, and high temperature. To our knowledge, this is the first report of a potentially endosymbiotic Lactobacillus delbrueckii ssp. lactis strain adapted to and playing beneficial roles for its host.}, + author = {Bazukyan, Inga and Georgieva-Miteva, Dimitrina and Velikova, Tsvetelina and Dimov, Svetoslav G.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects14060540}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{L. delbrueckii} ssp. \textit{lactis}, {\textgreater}UseGalaxy.eu, endosymbionts, honeybees, probiogenomic analysis, probiotics, whole-genome sequencing}, + language = {en}, + month = {June}, + note = {Number: 6 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {6}, + pages = {540}, + title = {In {Silico} {Probiogenomic} {Characterization} of {Lactobacillus} delbrueckii subsp. lactis {A4} {Strain} {Isolated} from an {Armenian} {Honeybee} {Gut}}, + url = {https://www.mdpi.com/2075-4450/14/6/540}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + @article{bazzucchi_near-complete_2020, abstract = {To gain further insight into the genomic features of border disease virus (BDV), we determined the nearly complete genome sequence of isolate TO/121/04 from an aborted ovine fetus. Its genome contains a single open reading frame (ORF), which comprises 11,681 nucleotides encoding a polyprotein of 3893 amino acids. Phylogenetic analysis of the near full-length genome sequence showed that the BDV isolate differed significantly from all ovine pestiviruses identified so far, thus re-affirming the presence in Italy of this novel genetic group, termed BDV-7.}, author = {Bazzucchi, Moira and Pierini, Ilaria and Giammarioli, Monica and De Mia, Gian Mario}, @@ -406,26 +1053,166 @@ @article{bazzucchi_near-complete_2020 year = {2020} } -@article{blacklock_examination_2022, - author = {Blacklock, Emily}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - title = {Examination of crustacean immune responses through {dsRNA}-nanoparticle injection and phylogenetic analysis}, - year = {2022} +@article{beck_trimannose-coupled_2023, + abstract = {Recent studies of severe acute inflammatory lung disease including COVID-19 identify macrophages to drive pulmonary hyperinflammation and long-term damage such as fibrosis. Here, we report on the development of a first-in-class, carbohydrate-coupled inhibitor of microRNA-21 (RCS-21), as a therapeutic means against pulmonary hyperinflammation and fibrosis. MicroRNA-21 is among the strongest upregulated microRNAs in human COVID-19 and in mice with acute inflammatory lung damage, and it is the strongest expressed microRNA in pulmonary macrophages. Chemical linkage of a microRNA-21 inhibitor to trimannose achieves rapid and specific delivery to macrophages upon inhalation in mice. RCS-21 reverses pathological activation of macrophages and prevents pulmonary dysfunction and fibrosis after acute lung damage in mice. In human lung tissue infected with SARS-CoV-2 ex vivo, RCS-21 effectively prevents the exaggerated inflammatory response. Our data imply trimannose-coupling for effective and selective delivery of inhaled oligonucleotides to pulmonary macrophages and report on a first mannose-coupled candidate therapeutic for COVID-19.}, + author = {Beck, Christina and Ramanujam, Deepak and Vaccarello, Paula and Widenmeyer, Florenc and Feuerherd, Martin and Cheng, Cho-Chin and Bomhard, Anton and Abikeeva, Tatiana and Schädler, Julia and Sperhake, Jan-Peter and Graw, Matthias and Safi, Seyer and Hoffmann, Hans and Staab-Weijnitz, Claudia A. and Rad, Roland and Protzer, Ulrike and Frischmuth, Thomas and Engelhardt, Stefan}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-40185-1}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, RNAi, Respiratory distress syndrome, Translational research, Viral infection, miRNAs}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {4564}, + title = {Trimannose-coupled {antimiR}-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage}, + url = {https://www.nature.com/articles/s41467-023-40185-1}, + urldate = {2023-08-01}, + volume = {14}, + year = {2023} } -@article{blagitko-dorfs_combination_2018, - abstract = {DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2′-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi. Transcriptome analyses revealed that a combined treatment with DAC and the HDACi panobinostat or valproic acid affected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative methylome and transcriptome analyses showed that a massive downregulation of genes, including oncogenes (e.g., MYC) and epigenetic modifiers (e.g., KDM2B, SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatments, and for a better understanding of responses in trials where this approach is clinically tested.}, - author = {Blagitko-Dorfs, Nadja and Schlosser, Pascal and Greve, Gabriele and Pfeifer, Dietmar and Meier, Ruth and Baude, Annika and Brocks, David and Plass, Christoph and Lübbert, Michael}, - copyright = {2018 Springer Nature Limited}, - doi = {10.1038/s41375-018-0293-8}, - issn = {1476-5551}, - journal = {Leukemia}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, - language = {En}, - month = {November}, - pages = {1}, - shorttitle = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors}, - title = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors: predominant synergistic gene downregulation associated with gene body demethylation}, +@inproceedings{beerling_enhanced_2023, + abstract = {Enhanced weathering (EW) with crushed basalt on farmlands is a promising scalable atmospheric carbon dioxide removal strategy that urgently requires performance assessment with commercial farming practices. Our large-scale replicated EW field trial in the heart of the U.S. Corn Belt shows cumulative time-integrated carbon sequestration of 15.4 +/- 4.1 t CO2 ha-1 over four years, with additional emissions mitigation of {\textasciitilde}0.1 - 0.4 t CO2,e ha-1 yr-1 for soil nitrous oxide, a potent long-lived greenhouse gas. Maize and soybean yields increased 12-16\% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals and global food and soil security.}, + author = {Beerling, D. and Epihov, D. and Kantola, I. and Masters, M. and Reershemius, Tom and Planavsky, N. and Reinhard, Chris and Jordan, J. and Thorne, Sarah J. and Weber, James and Martin, Maria Val and Freckleton, R. and Hartley, S. and James, R. and Pearce, C. and DeLucia, E. and Banwart, S.}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + title = {Enhanced weathering in the {U}.{S}. {Corn} {Belt} delivers carbon removal with agronomic benefits}, + url = {https://www.semanticscholar.org/paper/Enhanced-weathering-in-the-U.S.-Corn-Belt-delivers-Beerling-Epihov/f3467cbb0f578a9bb789a88d6140e1180a57890d}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{beerling_enhanced_2024, + abstract = {Terrestrial enhanced weathering (EW) of silicate rocks, such as crushed basalt, on farmlands is a promising scalable atmospheric carbon dioxide removal (CDR) strategy that urgently requires performance assessment with commercial farming practices. We report findings from a large-scale replicated EW field trial across a typical maize-soybean rotation on an experimental farm in the heart of the United Sates Corn Belt over 4 y (2016 to 2020). We show an average combined loss of major cations (Ca2+ and Mg2+) from crushed basalt applied each fall over 4 y (50 t ha−1 y−1) gave a conservative time-integrated cumulative CDR potential of 10.5 ± 3.8 t CO2 ha−1. Maize and soybean yields increased significantly (P {\textless} 0.05) by 12 to 16\% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Yield enhancements with EW were achieved with significantly (P {\textless} 0.05) increased key micro- and macronutrient concentrations (including potassium, magnesium, manganese, phosphorus, and zinc), thus improving or maintaining crop nutritional status. We observed no significant increase in the content of trace metals in grains of maize or soybean or soil exchangeable pools relative to controls. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals while simultaneously improving food and soil security.}, + author = {Beerling, David J. and Epihov, Dimitar Z. and Kantola, Ilsa B. and Masters, Michael D. and Reershemius, Tom and Planavsky, Noah J. and Reinhard, Christopher T. and Jordan, Jacob S. and Thorne, Sarah J. and Weber, James and Val Martin, Maria and Freckleton, Robert P. and Hartley, Sue E. and James, Rachael H. and Pearce, Christopher R. and DeLucia, Evan H. and Banwart, Steven A.}, + doi = {10.1073/pnas.2319436121}, + journal = {Proceedings of the National Academy of Sciences}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: Proceedings of the National Academy of Sciences}, + number = {9}, + pages = {e2319436121}, + title = {Enhanced weathering in the {US} {Corn} {Belt} delivers carbon removal with agronomic benefits}, + url = {https://www.pnas.org/doi/full/10.1073/pnas.2319436121}, + urldate = {2024-05-17}, + volume = {121}, + year = {2024} +} + +@article{belair_botryosphaeriaceae_2023, + abstract = {The Botryosphaeriaceae family comprises numerous fungal pathogens capable of causing economically meaningful diseases in a wide range of crops. Many of its members can live as endophytes and turn into aggressive pathogens following the onset of environmental stress events. Their ability to cause disease may rely on the production of a broad set of effectors, such as cell wall-degrading enzymes, secondary metabolites, and peptidases. Here, we conducted comparative analyses of 41 genomes representing six Botryosphaeriaceae genera to provide insights into the genetic features linked to pathogenicity and virulence. We show that these Botryosphaeriaceae genomes possess a large diversity of carbohydrate-active enzymes (CAZymes; 128 families) and peptidases (45 families). Botryosphaeria, Neofusicoccum, and Lasiodiplodia presented the highest number of genes encoding CAZymes involved in the degradation of the plant cell wall components. The genus Botryosphaeria also exhibited the highest abundance of secreted CAZymes and peptidases. Generally, the secondary metabolites gene cluster profile was consistent in the Botryosphaeriaceae family, except for Diplodia and Neoscytalidium. At the strain level, Neofusicoccum parvum NpBt67 stood out among all the Botryosphaeriaceae genomes, presenting a higher number of secretome constituents. In contrast, the Diplodia strains showed the lowest richness of the pathogenicity- and virulence-related genes, which may correlate with their low virulence reported in previous studies. Overall, these results contribute to a better understanding of the mechanisms underlying pathogenicity and virulence in remarkable Botryosphaeriaceae species. Our results also support that Botryosphaeriaceae species could be used as an interesting biotechnological tool for lignocellulose fractionation and bioeconomy.}, + author = {Belair, Marie and Restrepo-Leal, Julián D. and Praz, Coraline and Fontaine, Florence and Rémond, Caroline and Fernandez, Olivier and Besaury, Ludovic}, + doi = {10.1016/j.funbio.2023.03.004}, + issn = {1878-6146}, + journal = {Fungal Biology}, + keywords = {{\textgreater}UseGalaxy.eu, CAZymes, Comparative genomics, Peptidases, Secondary metabolism, Trunk diseases}, + month = {May}, + number = {5}, + pages = {1010--1031}, + shorttitle = {Botryosphaeriaceae gene machinery}, + title = {Botryosphaeriaceae gene machinery: {Correlation} between diversity and virulence}, + url = {https://www.sciencedirect.com/science/article/pii/S1878614623000375}, + urldate = {2023-10-28}, + volume = {127}, + year = {2023} +} + +@article{ben-oz_dual_2023, + abstract = {p53-mediated cell cycle arrest during DNA damage is dependent on the induction of p21 protein, encoded by the CDKN1A gene. p21 inhibits cyclin-dependent kinases required for cell cycle progression to guarantee accurate repair of DNA lesions. Hence, fine-tuning of p21 levels is crucial to preserve genomic stability. Currently, the multilayered regulation of p21 levels during DNA damage is not fully understood. Herein, we identify the human RNA binding motif protein 42 (RBM42) as a regulator of p21 levels during DNA damage. Genome-wide transcriptome and interactome analysis reveals that RBM42 alters the expression of p53-regulated genes during DNA damage. Specifically, we demonstrate that RBM42 facilitates CDKN1A splicing by counteracting the splicing inhibitory effect of RBM4 protein. Unexpectedly, we also show that RBM42, underpins translation of various splicing targets, including CDKN1A. Concordantly, transcriptome-wide mapping of RBM42-RNA interactions using eCLIP further substantiates the dual function of RBM42 in regulating splicing and translation of its target genes, including CDKN1A. Collectively, our data show that RBM42 couples splicing and translation machineries to fine-tune gene expression during DNA damage response.}, + author = {Ben-Oz, Bella M. and Machour, Feras E. and Nicola, Marian and Argoetti, Amir and Polyak, Galia and Hanna, Rawad and Kleifeld, Oded and Mandel-Gutfreund, Yael and Ayoub, Nabieh}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-43495-6}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, DNA damage and repair, DNA damage response}, + language = {en}, + month = {November}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {7628}, + title = {A dual role of {RBM42} in modulating splicing and translation of {CDKN1A}/p21 during {DNA} damage response}, + url = {https://www.nature.com/articles/s41467-023-43495-6}, + urldate = {2023-12-28}, + volume = {14}, + year = {2023} +} + +@article{bennett-keki_sex-biased_2023, + abstract = {Differences in lifespan between males and females are found across many taxa and may be determined, at least in part, by differential responses to diet. Here we tested the hypothesis that the higher dietary sensitivity of female lifespan is mediated by higher and more dynamic expression in nutrient-sensing pathways in females. We first reanalysed existing RNA-seq data, focusing on 17 nutrient-sensing genes with reported lifespan effects. This revealed, consistent with the hypothesis, a dominant pattern of female-biased gene expression, and among sex-biased genes there tended to be a loss of female-bias after mating. We then tested directly the expression of these 17 nutrient-sensing genes in wild-type third instar larvae, once-mated 5- and 16-day-old adults. This confirmed sex-biased gene expression and showed that it was generally absent in larvae, but frequent and stable in adults. Overall, the findings suggest a proximate explanation for the sensitivity of female lifespan to dietary manipulations. We suggest that the contrasting selective pressures to which males and females are subject create differing nutritional demands and requirements, resulting in sex differences in lifespan. This underscores the potential importance of the health impacts of sex-specific dietary responses.}, + author = {Bennett-Keki, Suzanne and Fowler, Emily K. and Folkes, Leighton and Moxon, Simon and Chapman, Tracey}, + doi = {10.1098/rspb.2022.2086}, + journal = {Proceedings of the Royal Society B: Biological Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, diet, fruitfly, lifespan, nutrient-sensing}, + month = {March}, + note = {Publisher: Royal Society}, + number = {1994}, + pages = {20222086}, + title = {Sex-biased gene expression in nutrient-sensing pathways}, + url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2022.2086}, + urldate = {2023-12-03}, + volume = {290}, + year = {2023} +} + +@article{bennett-keki_sex-biased_2023, + abstract = {Differences in lifespan between males and females are found across many taxa and may be determined, at least in part, by differential responses to diet. Here we tested the hypothesis that the higher dietary sensitivity of female lifespan is mediated by higher and more dynamic expression in nutrient-sensing pathways in females. We first reanalysed existing RNA-seq data, focusing on 17 nutrient-sensing genes with reported lifespan effects. This revealed, consistent with the hypothesis, a dominant pattern of female-biased gene expression, and among sex-biased genes there tended to be a loss of female-bias after mating. We then tested directly the expression of these 17 nutrient-sensing genes in wild-type third instar larvae, once-mated 5- and 16-day-old adults. This confirmed sex-biased gene expression and showed that it was generally absent in larvae, but frequent and stable in adults. Overall, the findings suggest a proximate explanation for the sensitivity of female lifespan to dietary manipulations. We suggest that the contrasting selective pressures to which males and females are subject create differing nutritional demands and requirements, resulting in sex differences in lifespan. This underscores the potential importance of the health impacts of sex-specific dietary responses.}, + author = {Bennett-Keki, Suzanne and Fowler, Emily K. and Folkes, Leighton and Moxon, Simon and Chapman, Tracey}, + doi = {10.1098/rspb.2022.2086}, + journal = {Proceedings of the Royal Society B: Biological Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, diet, fruitfly, lifespan, nutrient-sensing}, + month = {March}, + note = {Publisher: Royal Society}, + number = {1994}, + pages = {20222086}, + title = {Sex-biased gene expression in nutrient-sensing pathways}, + url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2022.2086}, + urldate = {2023-03-15}, + volume = {290}, + year = {2023} +} + +@article{bianconi_characterization_2024, + abstract = {Multidrug-resistant Escherichia coli, particularly carbapenemase producers, are a major source of concern. This study aims to investigate the long-term epidemiology of Verona integron-encoded metallo-β-lactamase (VIM)-producing E. coli in the health district of Bolzano, Northern Italy, by examining the phenotypic and genotypic characteristics of 26 isolates obtained during 2005–2020. Isolates were identified with matrix-assisted laser desorption/ionization time-of-flight, susceptibility testing was by Vitek 2, Sensititre, and Etest; carbapenemase activity was confirmed by Etest and Carbapenemase Inactivation Method (CIM) test; and the VIM-antigen was identified by the NG-Test CARBA 5. Genome sequencing was performed on an Illumina MiSeq platform. Carbapenem minimum inhibitory concentrations varied across methodologies, and overall category agreement between phenotypic methods was low. All 23 sequenced isolates contained blaVIM-1. Eleven (47.8\%) isolates belonged to the clonal lineage ST131, with fimH30 being the most common subclone. In Bolzano ST131-fimH30 was present as early as 2005. While the ST131 clonal lineage predominated for the first 10 years, various clonal lineages were present, especially in subsequent years, indicating the concurrent circulation of multiple clonal lineages. Future efforts should focus on the implementation of surveillance methods, including genomic analysis, as well as the use of updated infection control strategies and antibiotic stewardship programs to prevent the spread of these carbapenem-resistant strains.}, + author = {Bianconi, Irene and Spath, Manuela and Aschbacher, Richard and Pedron, Renato and Wieser, Stefanie and Pagani, Elisabetta}, + doi = {10.1089/mdr.2023.0197}, + issn = {1076-6294}, + journal = {Microbial Drug Resistance}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: Mary Ann Liebert, Inc., publishers}, + number = {2}, + pages = {91--100}, + title = {Characterization of {Verona} {Integron}-{Encoded} {Metallo}-β-{Lactamase}-{Type} {Carbapenemase}-{Producing} {Escherichia} coli {Isolates} {Collected} over a 16-{Year} {Period} in {Bolzano} ({Northern} {Italy})}, + url = {https://www.liebertpub.com/doi/abs/10.1089/mdr.2023.0197}, + urldate = {2024-04-28}, + volume = {30}, + year = {2024} +} + +@article{blacklock_examination_2022, + author = {Blacklock, Emily}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + title = {Examination of crustacean immune responses through {dsRNA}-nanoparticle injection and phylogenetic analysis}, + year = {2022} +} + +@article{blagitko-dorfs_combination_2018, + abstract = {DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2′-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi. Transcriptome analyses revealed that a combined treatment with DAC and the HDACi panobinostat or valproic acid affected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative methylome and transcriptome analyses showed that a massive downregulation of genes, including oncogenes (e.g., MYC) and epigenetic modifiers (e.g., KDM2B, SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatments, and for a better understanding of responses in trials where this approach is clinically tested.}, + author = {Blagitko-Dorfs, Nadja and Schlosser, Pascal and Greve, Gabriele and Pfeifer, Dietmar and Meier, Ruth and Baude, Annika and Brocks, David and Plass, Christoph and Lübbert, Michael}, + copyright = {2018 Springer Nature Limited}, + doi = {10.1038/s41375-018-0293-8}, + issn = {1476-5551}, + journal = {Leukemia}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + language = {En}, + month = {November}, + pages = {1}, + shorttitle = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors}, + title = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors: predominant synergistic gene downregulation associated with gene body demethylation}, url = {https://www.nature.com/articles/s41375-018-0293-8}, urldate = {2018-11-29}, year = {2018} @@ -450,6 +1237,42 @@ @article{blomberg_connecting_2020 year = {2020} } +@article{bode_catecholamine_2024, + abstract = {Catecholamines are commonly used as therapeutic drugs in intensive care medicine to maintain sufficient organ perfusion during shock. However, excessive or sustained adrenergic activation drives detrimental cardiac remodeling and may lead to heart failure. Whether catecholamine treatment in absence of heart failure causes persistent cardiac injury, is uncertain. In this experimental study, we assessed the course of cardiac remodeling and recovery during and after prolonged catecholamine treatment and investigated the molecular mechanisms involved.}, + author = {Bode, Christine and Preissl, Sebastian and Hein, Lutz and Lother, Achim}, + doi = {10.1186/s40635-024-00632-9}, + issn = {2197-425X}, + journal = {Intensive Care Medicine Experimental}, + keywords = {{\textgreater}UseGalaxy.eu, Adrenergic receptors, Cardiomyocyte, Endothelin, Gene expression, Intensive care medicine}, + month = {May}, + number = {1}, + pages = {48}, + title = {Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression}, + url = {https://doi.org/10.1186/s40635-024-00632-9}, + urldate = {2024-05-13}, + volume = {12}, + year = {2024} +} + +@incollection{boeckman_phage_2024, + abstract = {Bacteriophages, or more simply phages, are currently experiencing a renaissance in life science research for their roles in natural microbial communities, their potential use as antimicrobials, and biotechnological applications. In the modern era, one of the primary steps in phage characterization is obtaining the sequence of the complete genome; this information can be used to determine the relationship of the phage to known phages, predict phage lifestyle, and is a prerequisite for many downstream applications. This protocol describes methods for determining the complete sequence of a double-stranded DNA bacteriophage genome, including DNA extraction from a phage lysate, sending the DNA out to a sequencing service, assembly of the sequence raw reads, and completion of the genome sequence.}, + address = {New York, NY}, + author = {Boeckman, Justin and Liu, Mei and Ramsey, Jolene and Gill, Jason}, + booktitle = {Bacteriophages: {Methods} and {Protocols}}, + doi = {10.1007/978-1-0716-3549-0_8}, + editor = {Tumban, Ebenezer}, + isbn = {978-1-07-163549-0}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Bacteriophage, DNA sequence assembly, Genomics, Phage, Whole-genome sequencing}, + language = {en}, + pages = {125--144}, + publisher = {Springer US}, + series = {Methods in {Molecular} {Biology}}, + title = {Phage {DNA} {Extraction}, {Genome} {Assembly}, and {Genome} {Closure}}, + url = {https://doi.org/10.1007/978-1-0716-3549-0_8}, + urldate = {2023-11-18}, + year = {2024} +} + @article{bohlender_stable_2020, abstract = {Recombinantly produced proteins are indispensable tools for medical applications. Since the majority of them are glycoproteins, their N-glycosylation profiles are major determinants for their activity, structural properties and safety. For therapeutical applications, a glycosylation pattern adapted to product and treatment requirements is advantageous. Physcomitrium patens (Physcomitrella, moss) is able to perform highly homogeneous complex-type N-glycosylation. Additionally, it has been glyco-engineered to eliminate plant-specific sugar residues by knock-out of the β1,2-xylosyltransferase and α1,3-fucosyltransferase genes (Δxt/ft). Furthermore, Physcomitrella meets wide-ranging biopharmaceutical requirements such as GMP compliance, product safety, scalability and outstanding possibilities for precise genome engineering. However, all plants, in contrast to mammals, lack the capability to perform N-glycan sialylation. Since sialic acids are a common terminal modification on human N glycans, the property to perform N-glycan sialylation is highly desired within the plant-based biopharmaceutical sector. In this study, we present the successful achievement of protein N-glycan sialylation in stably transformed Physcomitrella. The sialylation ability was achieved in a Δxt/ft moss line by stable expression of seven mammalian coding sequences combined with targeted organelle-specific localization of the encoded enzymes responsible for the generation of β1,4 galactosylated acceptor N glycans as well as the synthesis, activation, transport and transfer of sialic acid. Production of free (Neu5Ac) and activated (CMP-Neu5Ac) sialic acid was proven. The glycosidic anchor for the attachment of terminal sialic acid was generated by the introduction of a chimeric human β1,4 galactosyltransferase gene under the simultaneous knock-out of the gene encoding the endogenous β1,3 galactosyltransferase. Functional complex-type N-glycan sialylation was confirmed via mass spectrometric analysis of a stably co-expressed recombinant human protein.}, author = {Bohlender, Lennard L. and Parsons, Juliana and Hoernstein, Sebastian N. W. and Rempfer, Christine and Ruiz-Molina, Natalia and Lorenz, Timo and Rodríguez Jahnke, Fernando and Figl, Rudolf and Fode, Benjamin and Altmann, Friedrich and Reski, Ralf and Decker, Eva L.}, @@ -466,6 +1289,20 @@ @article{bohlender_stable_2020 year = {2020} } +@article{bokharaie_analysis_2022, + abstract = {Alternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SK-MEL-239 melanoma cells and a BRAF inhibitor (vemurafenib)-resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib-resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib-resistant cells. This analysis shows that combining different AS analysis approaches produces reliable results and meaningful, biologically testable hypotheses.}, + author = {Bokharaie, Honey and Kolch, Walter and Krstic, Aleksandar}, + doi = {10.3390/biom12070993}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu}, + number = {7}, + title = {Analysis of {Alternative} {mRNA} {Splicing} in {Vemurafenib}-{Resistant} {Melanoma} {Cells}}, + url = {https://www.mdpi.com/2218-273X/12/7/993}, + volume = {12}, + year = {2022} +} + @article{boneva_3_2020, abstract = {This study aims to compare the potential of standard RNA-sequencing (RNA-Seq) and 3′ massive analysis of c-DNA ends (MACE) RNA-sequencing for the analysis of fresh tissue and describes transcriptome profiling of formalin-fixed paraffin-embedded (FFPE) archival human samples by MACE. To compare MACE to standard RNA-Seq on fresh tissue, four healthy conjunctiva from four subjects were collected during vitreoretinal surgery, halved and immediately transferred to RNA lysis buffer without prior fixation and then processed for either standard RNA-Seq or MACE RNA-Seq analysis. To assess the impact of FFPE preparation on MACE, a third part was fixed in formalin and processed for paraffin embedding, and its transcriptional profile was compared with the unfixed specimens analyzed by MACE. To investigate the impact of FFPE storage time on MACE results, 24 FFPE-treated conjunctival samples from 24 patients were analyzed as well. Nineteen thousand six hundred fifty-nine transcribed genes were detected by both MACE and standard RNA-Seq on fresh tissue, while 3251 and 2213 transcripts were identified explicitly by MACE or RNA-Seq, respectively. Standard RNA-Seq tended to yield longer detected transcripts more often than MACE technology despite normalization, indicating that the MACE technology is less susceptible to a length bias. FFPE processing revealed negligible effects on MACE sequencing results. Several quality-control measurements showed that long-term storage in paraffin did not decrease the diversity of MACE libraries. We noted a nonlinear relation between storage time and the number of raw reads with an accelerated decrease within the first 1000 days in paraffin, while the numbers remained relatively stable in older samples. Interestingly, the number of transcribed genes detected was independent on FFPE storage time. RNA of sufficient quality and quantity can be extracted from FFPE samples to obtain comprehensive transcriptome profiling using MACE technology. We thus present MACE as a novel opportunity for utilizing FFPE samples stored in histological archives.}, author = {Boneva, Stefaniya and Schlecht, Anja and Böhringer, Daniel and Mittelviefhaus, Hans and Reinhard, Thomas and Agostini, Hansjürgen and Auw-Haedrich, Claudia and Schlunck, Günther and Wolf, Julian and Lange, Clemens}, @@ -521,6 +1358,62 @@ @article{boneva_transcriptional_2020 year = {2020} } +@article{borchel_sex_2022, + abstract = {Salmon lice are ectoparasites on salmonids and feed on blood, mucus, and skin from their hosts. This causes high annual costs for treatment and control for the aquaculture industry. Salmon lice have a life cycle consisting of eight life stages. Sex determination by eye is only possible from the sixth stage onwards. A molecular sex determination has not been carried out so far, even though few individual sex-linked SNPs have been reported. In the present study, we used known sex-specific SNPs as a basis to sequence the complete sex-specific gene variants and used the sequence information to develop a sex determination assay. This assay could be used to determine the developmental speed of the two sexes already in the earliest life stages. Additionally, we sampled salmon lice in the nauplius II stage, determined the sex of each individual, pooled their RNA according to their sex, and used RNA sequencing to search for differences in gene expression and further sex-specific SNPs. We succeeded in developing a sex-determination assay that works on DNA or RNA from even the earliest larval stages of the salmon louse after hatching. At these early developmental stages, male salmon lice develop slightly quicker than females. We detected several previously unknown, sex-specific SNPs in our RNA-data seq, but only very few genes showed a differential expression between the sexes. Potential connections between SNPs, gene expression, and development are discussed.}, + author = {Borchel, Andreas and Komisarczuk, Anna Zofia and Nilsen, Frank}, + doi = {10.1371/journal.pone.0266022}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Eggs, Gene expression, Heterozygosity, Lice, Molting, Polymerase chain reaction, Sex ratio, Single nucleotide polymorphisms}, + language = {en}, + month = {March}, + note = {Publisher: Public Library of Science}, + number = {3}, + pages = {e0266022}, + shorttitle = {Sex differences in the early life stages of the salmon louse {Lepeophtheirus} salmonis ({Copepoda}}, + title = {Sex differences in the early life stages of the salmon louse {Lepeophtheirus} salmonis ({Copepoda}: {Caligidae})}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0266022}, + urldate = {2022-09-24}, + volume = {17}, + year = {2022} +} + +@article{bordel_genome_2023, + abstract = {Keratin-rich wastes, mainly in the form of feathers, are recalcitrant residues generated in high amounts as by-products in chicken farms and food industry. Polylactic acid (PLA) is the second most common biodegradable polymer found in commercial plastics, which is not easily degraded by microbial activity. This work reports the 3.8-Mb genome of Bacillus altitudinis B12, a highly efficient PLA- and keratin-degrading bacterium, with potential for environmental friendly biotechnological applications in the feed, fertilizer, detergent, leather, and pharmaceutical industries. The whole genome sequence of B. altitudinis B12 revealed that this strain (which had been previously misclassified as Bacillus pumilus B12) is closely related to the B. altitudinis strains ER5, W3, and GR-8. A total of 4056 coding sequences were annotated using the RAST server, of which 2484 are core genes of the pan genome of B. altitudinis and 171 are unique to this strain. According to the sequence analysis, B. pumilus B12 has a predicted secretome of 353 proteins, among which a keratinase and a PLA depolymerase were identified by sequence analysis. The presence of these two enzymes could explain the characterized PLA and keratin biodegradation capability of the strain.}, + author = {Bordel, Sergio and Martín-González, Diego and Muñoz, Raúl and Santos-Beneit, Fernando}, + doi = {10.1007/s00438-022-01989-w}, + issn = {1617-4623}, + journal = {Molecular Genetics and Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Bacillus altitudinis, Keratinases, Pan genome, Polyester biodegradation}, + language = {en}, + month = {March}, + number = {2}, + pages = {389--398}, + title = {Genome sequence analysis and characterization of {Bacillus} altitudinis {B12}, a polylactic acid- and keratin-degrading bacterium}, + url = {https://doi.org/10.1007/s00438-022-01989-w}, + urldate = {2023-10-28}, + volume = {298}, + year = {2023} +} + +@article{bordel_genome_2023, + abstract = {Keratin-rich wastes, mainly in the form of feathers, are recalcitrant residues generated in high amounts as by-products in chicken farms and food industry. Polylactic acid (PLA) is the second most common biodegradable polymer found in commercial plastics, which is not easily degraded by microbial activity. This work reports the 3.8-Mb genome of Bacillus altitudinis B12, a highly efficient PLA- and keratin-degrading bacterium, with potential for environmental friendly biotechnological applications in the feed, fertilizer, detergent, leather, and pharmaceutical industries. The whole genome sequence of B. altitudinis B12 revealed that this strain (which had been previously misclassified as Bacillus pumilus B12) is closely related to the B. altitudinis strains ER5, W3, and GR-8. A total of 4056 coding sequences were annotated using the RAST server, of which 2484 are core genes of the pan genome of B. altitudinis and 171 are unique to this strain. According to the sequence analysis, B. pumilus B12 has a predicted secretome of 353 proteins, among which a keratinase and a PLA depolymerase were identified by sequence analysis. The presence of these two enzymes could explain the characterized PLA and keratin biodegradation capability of the strain.}, + author = {Bordel, Sergio and Martín-González, Diego and Muñoz, Raúl and Santos-Beneit, Fernando}, + doi = {10.1007/s00438-022-01989-w}, + issn = {1617-4623}, + journal = {Molecular Genetics and Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Bacillus altitudinis, Keratinases, Pan genome, Polyester biodegradation}, + language = {en}, + month = {March}, + number = {2}, + pages = {389--398}, + title = {Genome sequence analysis and characterization of {Bacillus} altitudinis {B12}, a polylactic acid- and keratin-degrading bacterium}, + url = {https://doi.org/10.1007/s00438-022-01989-w}, + urldate = {2023-07-31}, + volume = {298}, + year = {2023} +} + @article{bose_trna_2020, abstract = {tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism.}, author = {Bose, Sreyashree and Suescún, Ana Victoria and Song, Jiarui and Castillo-González, Claudia and Aklilu, Behailu Birhanu and Branham, Erica and Lynch, Ryan and Shippen, Dorothy E.}, @@ -558,6 +1451,23 @@ @article{bossche_critical_2021 year = {2021} } +@article{boutigny_direct_2023, + abstract = {A targeted enrichment method was developed to sequence Xylella fastidiosa genomic DNA directly from plant samples. The method was evaluated on various plant species infected with different strains at different levels of contamination. After enrichment, X. fastidiosa genome coverage was above 99.9\% for all tested samples.}, + author = {Boutigny, Anne-Laure and Remenant, Benoit and Legendre, Bruno and Beven, Véronique and Rolland, Mathieu and Blanchard, Yannick and Cunty, Amandine}, + doi = {10.1016/j.mimet.2023.106719}, + issn = {0167-7012}, + journal = {Journal of Microbiological Methods}, + keywords = {{\textgreater}UseGalaxy.eu, Capture, Illumina sequencing, SureSelect, Whole genome}, + language = {en}, + month = {May}, + pages = {106719}, + title = {Direct {Xylella} fastidiosa whole genome sequencing from various plant species using targeted enrichment}, + url = {https://www.sciencedirect.com/science/article/pii/S0167701223000532}, + urldate = {2023-06-05}, + volume = {208}, + year = {2023} +} + @article{bovio_differential_2018, abstract = {The disruptor of telomeric silencing 1-like (DOT1L) mediates methylation of histone H3 at position lysine 79 (H3K79). Conditional knockout of Dot1l in mouse cerebellar granule cells (Dot1l-cKOAtoh1) led to a smaller external granular layer with fewer precursors of granule neurons. Dot1l-cKOAtoh1 mice had impaired proliferation and differentiation of granular progenitors, which resulted in a smaller cerebellum. Mutant mice showed mild ataxia in motor behavior tests. In contrast, Purkinje cell-specific conditional knockout mice showed no obvious phenotype. Genome-wide transcription analysis of Dot1l-cKOAtoh1 cerebella using microarrays revealed changes in genes that function in cell cycle, cell migration, axon guidance, and metabolism. To identify direct DOT1L target genes, we used genome-wide profiling of H3K79me2 and transcriptional analysis. Analysis of differentially methylated regions (DR) and differentially expressed genes (DE) revealed in total 12 putative DOT1L target genes in Dot1l-cKOAtoh1 affecting signaling (Tnfaip8l3, B3galt5), transcription (Otx1), cell migration and axon guidance (Sema4a, Sema5a, Robo1), cholesterol and lipid metabolism (Lss, Cyp51), cell cycle (Cdkn1a), calcium-dependent cell-adhesion or exocytosis (Pcdh17, Cadps2), and unknown function (Fam174b). Dysregulated expression of these target genes might be implicated in the ataxia phenotype observed in Dot1l-cKOAtoh1.}, author = {Bovio, Patrick Piero and Franz, Henriette and Heidrich, Stefanie and Rauleac, Tudor and Kilpert, Fabian and Manke, Thomas and Vogel, Tanja}, @@ -573,6 +1483,56 @@ @article{bovio_differential_2018 year = {2018} } +@misc{boyer_pulsar_2024, + abstract = {Recent evidence for the stochastic gravitational wave backgorund reported by the pulsar timing arrays (PTA) can be interpreted as a signal from the cosmological phase transition. We use up-to-date models of the gravitational wave power spectra to compare constraints on the parameters of the phase transition for the three different available PTA measurements and to work out a refined estimate of the cosmological magnetic field that should result from this transition. We find that the PTA data, combined with a constraint from the abundance of primordial black holes, are consistent with a possibility of a moderate strength first-order phase transition during quark confinement and yield a rather precise prediction for the initial parameters of the magnetic field, with the magnetic field energy density in near equipartition with photon energy density and correlation length close to one co-moving parsec.}, + author = {Boyer, T. and Neronov, A.}, + doi = {10.48550/arXiv.2405.07746}, + keywords = {{\textgreater}UseGalaxy.eu, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - High Energy Astrophysical Phenomena}, + month = {May}, + note = {arXiv:2405.07746 [astro-ph]}, + publisher = {arXiv}, + title = {Pulsar timing array constraints on the cosmological magnetic field from quark confinement epoch}, + url = {http://arxiv.org/abs/2405.07746}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{bozan_whole-genome_2022, + abstract = {Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98\% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.}, + author = {Bozan, Mahir and Popp, Denny and Kallies, Rene and da Rocha, Ulisses Nunes and Klähn, Stephan and Bühler, Katja}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Whole-genome sequence of the filamentous diazotrophic cyanobacterium {Tolypothrix} sp. {PCC} 7712 and its comparison with non-diazotrophic {Tolypothrix} sp. {PCC} 7601}, + url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1042437}, + urldate = {2023-07-31}, + volume = {13}, + year = {2022} +} + +@article{braga_detection_2023, + abstract = {Objectives +This study reports the genomic characterization of the multidrug resistant Salmonella Newport strain 195\_20 recovered from the diarrheic faeces of a foal in Brazil and co-harbouring the mcr-9, blaCMY-2 and qnrB19 antibiotic resistance genes. +Methods +Bacterial isolate positive for mobile colistin resistance gene (mcr-9) was submitted to antimicrobial susceptibility testing by disk diffusion and broth microdilution for colistin and polymyxin B. The isolate was submitted to whole genome sequencing by Illumina technology and Nanopore Sequencing. Conjugation assays, plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinIon long reads sequencing. +Results +Isolate 195\_20 was identified as sequence type ST45, resistant to penicillin and cephalosporins (ampicillin, ceftazidime, ceftriaxone and cefotaxime), aminoglycosides (streptomycin and gentamicin), phenicol (chloramphenicol), quinolones and fluoroquinolones (nalidixic acid, ciprofloxacin, and pefloxacin), folate pathway antagonists (sulfonamides and trimethoprim-sulfamethoxazole), and tetracycline. A transferable IncHI2/IncHI2A plasmid sized ca. 262kb was found to carry the mcr-9 gene in a module consisting of IS903-mcr-9-wbuC-IS26. In addition, an 174kb IncC and a 48kb IncN plasmid were also identified in the 195\_20 isolate, carrying blaCMY-2 and qnrB19, respectively. +Conclusions +Not surprisingly, isolate 195\_20 was susceptible to polymyxins, possibly due to absence of qseBC regulatory operon. Presence of mobile colistin resistance (mcr-9), third-generation cephalosporins (blaCMY-2) and quinolone (qnrB19) resistance determinants in zoonotic pathogens from animals in close contact with humans alerts for the possible route of transmission between these different reservoirs.}, + author = {Braga, Pollyana Rennó Campos and dos Santos, Carla Adriana and Bertani, Amanda Maria de Jesus and Vieira, Thais and Amarante, Ariadne Ferreira and Reis, Alex Domingos and Sacchi, Cláudio Tavares and Camargo, Carlos Henrique and Ribeiro, Marcio Garcia and Borges, Alexandre Secorun and Tiba-Casas, Monique Ribeiro}, + doi = {10.1016/j.jgar.2023.09.019}, + issn = {2213-7165}, + journal = {Journal of Global Antimicrobial Resistance}, + keywords = {{\textgreater}UseGalaxy.eu, Colistin, Illumina sequencing, Nanopore sequencing, Newport, Plasmids}, + month = {December}, + pages = {198--201}, + title = {Detection and genomic characterization of a multidrug-resistant {Salmonella} {Newport} co-harbouring {blaCMY}-2, {qnrB19} and mcr-9 from the diarrheic faeces of a foal}, + url = {https://www.sciencedirect.com/science/article/pii/S2213716523001662}, + urldate = {2023-12-28}, + volume = {35}, + year = {2023} +} + @article{bray_chemicaltoolbox_2020, abstract = {Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows may be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project. The ChemicalToolbox is hosted on the European Galaxy server and may be accessed via https://cheminformatics.usegalaxy.eu.}, author = {Bray, Simon A. and Lucas, Xavier and Kumar, Anup and Grüning, Björn A.}, @@ -591,19 +1551,23 @@ @article{bray_chemicaltoolbox_2020 year = {2020} } -@article{bray_galaxy_2021, - abstract = {We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 40000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.}, - author = {Bray, Simon and Dudgeon, Tim and Skyner, Rachael and Backofen, Rolf and Grüning, Björn and Delft, Frank von}, - doi = {10.26434/chemrxiv-2021-zr4xn}, - journal = {ChemRxiv}, - keywords = {+Galactic, +IsGalaxy, +Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu}, +@article{bray_galaxy_2022, + abstract = {We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.}, + author = {Bray, Simon and Dudgeon, Tim and Skyner, Rachael and Backofen, Rolf and Grüning, Björn and von Delft, Frank}, + doi = {10.1186/s13321-022-00588-6}, + issn = {1758-2946}, + journal = {Journal of Cheminformatics}, + keywords = {+UsePublic, {\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Chem-informatics, chemical compounds}, language = {en}, month = {December}, + number = {1}, + pages = {22}, shorttitle = {Galaxy workflows for fragment-based virtual screening}, title = {Galaxy workflows for fragment-based virtual screening: a case study on the {SARS}-{CoV}-2 main protease}, - url = {https://chemrxiv.org/engage/chemrxiv/article-details/61a621c1ceb7d316bd010728}, - urldate = {2021-12-07}, - year = {2021} + url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00588-6}, + urldate = {2022-04-14}, + volume = {14}, + year = {2022} } @article{bray_intuitive_2020, @@ -624,6 +1588,34 @@ @article{bray_intuitive_2020 year = {2020} } +@phdthesis{breidenbach_harmful_2023, + author = {Breidenbach, Joshua David}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + school = {University of Toledo}, + title = {Harmful {Algal} {Bloom} {Toxin} {Aerosol} {Exposure} and {Airway} {Inflammation}}, + url = {https://etd.ohiolink.edu/apexprod/rws_olink/r/1501/10?clear=10&p10_accession_num=mco1676650815957184}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{breidenbach_microcystin-lr_2022, + abstract = {Harmful algal blooms plague bodies of freshwater globally. These blooms are often composed of outgrowths of cyanobacteria capable of producing the heptapeptide Microcystin-LR (MC-LR) which is a well-known hepatotoxin. Recently, MC-LR has been detected in aerosols generated from lake water. However, the risk for human health effects due to MC-LR inhalation exposure have not been extensively investigated. In this study, we exposed a fully differentiated 3D human airway epithelium derived from 14 healthy donors to MC-LR-containing aerosol once a day for 3 days. Concentrations of MC-LR ranged from 100 pM to 1 µM. Although there were little to no detrimental alterations in measures of the airway epithelial function (i.e. cell survival, tissue integrity, mucociliary clearance, or cilia beating frequency), a distinct shift in the transcriptional activity was found. Genes related to inflammation were found to be upregulated such as C-C motif chemokine 5 (CCL5; log2FC = 0.57, p = 0.03) and C-C chemokine receptor type 7 (CCR7; log2FC = 0.84, p = 0.03). Functionally, conditioned media from MC-LR exposed airway epithelium was also found to have significant chemo-attractive properties for primary human neutrophils. Additionally, increases were found in the concentration of secreted chemokine proteins in the conditioned media such as CCL1 (log2FC = 5.07, p = 0.0001) and CCL5 (log2FC = 1.02, p = 0.046). These results suggest that MC-LR exposure to the human airway epithelium is capable of inducing an inflammatory response that may potentiate acute or chronic disease.}, + author = {Breidenbach, Joshua D. and French, Benjamin W. and Gordon, Tamiya T. and Kleinhenz, Andrew L. and Khalaf, Fatimah K. and Willey, James C. and Hammersley, Jeffrey R. and Mark Wooten, R. and Crawford, Erin L. and Modyanov, Nikolai N. and Malhotra, Deepak and Teeguarden, Justin G. and Haller, Steven T. and Kennedy, David J.}, + doi = {10.1016/j.envint.2022.107531}, + issn = {0160-4120}, + journal = {Environment International}, + keywords = {3D human airway epithelium, {\textgreater}UseGalaxy.eu, Aerosol, Algal bloom, Inflammation, Microcystin-LR}, + language = {en}, + month = {November}, + pages = {107531}, + title = {Microcystin-{LR} aerosol induces inflammatory responses in healthy human primary airway epithelium}, + url = {https://www.sciencedirect.com/science/article/pii/S0160412022004585}, + urldate = {2022-09-24}, + volume = {169}, + year = {2022} +} + @article{broche_genome-wide_2021, abstract = {Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90\% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.}, author = {Broche, Julian and Kungulovski, Goran and Bashtrykov, Pavel and Rathert, Philipp and Jeltsch, Albert}, @@ -641,6 +1633,49 @@ @article{broche_genome-wide_2021 year = {2021} } +@article{broche_genome-wide_2023, + abstract = {While cytosine-C5 methylation of DNA is an essential regulatory system in higher eukaryotes, the presence and relevance of 6-methyladenine (m6dA) in human cells is controversial. To study the role of m6dA in human DNA, we introduced it in human cells at a genome-wide scale at GANTC and GATC sites by expression of bacterial DNA methyltransferases and observed concomitant reductions in cell viability, in particular after global GANTC methylation. We identified several genes that are directly regulated by m6dA in a GANTC context. Upregulated genes showed m6dA-dependent reduction of H3K27me3 suggesting that the PRC2 complex is inhibited by m6dA. Genes downregulated by m6dA showed enrichment of JUN family transcription factor binding sites. JUN binds m6dA containing DNA with reduced affinity suggesting that m6dA can reduce the recruitment of JUN transcription factors to target genes. Our study documents that global introduction of m6dA in human DNA has physiological effects. Furthermore, we identified a set of target genes which are directly regulated by m6dA in human cells, and we defined two molecular pathways with opposing effects by which artificially introduced m6dA in GANTC motifs can directly control gene expression and phenotypes of human cells.}, + author = {Broche, Julian and Köhler, Anja R. and Kühnel, Fiona and Osteresch, Bernd and Chandrasekaran, Thyagarajan T. and Adam, Sabrina and Brockmeyer, Jens and Jeltsch, Albert}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s42003-023-04466-1}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, Epigenetics, Histone post-translational modifications, Transcriptional regulatory elements}, + language = {en}, + month = {February}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--12}, + title = {Genome-wide deposition of 6-methyladenine in human {DNA} reduces the viability of {HEK293} cells and directly influences gene expression}, + url = {https://www.nature.com/articles/s42003-023-04466-1}, + urldate = {2023-03-15}, + volume = {6}, + year = {2023} +} + +@article{bruck_ploidy_2023, + abstract = {Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12–14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.}, + author = {Brück, Patrik and Wasser, Daniel and Soppa, Jörg}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/genes14071437}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {\textit{Vibrio natriegens}, {\textgreater}UseGalaxy.eu, cell size, cell volume, chromosome copy number, dynamic regulation, growth curve, origin of replication, ploidy, polyploidy, terminus of replication}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {1437}, + shorttitle = {Ploidy in {Vibrio} natriegens}, + title = {Ploidy in {Vibrio} natriegens: {Very} {Dynamic} and {Rapidly} {Changing} {Copy} {Numbers} of {Both} {Chromosomes}}, + url = {https://www.mdpi.com/2073-4425/14/7/1437}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + @article{brunet_mass_2019, abstract = {Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame (ORF) annotation impose two arbitrary criteria: a minimum length of 100 codons and a single ORF per transcript. However, a growing number of studies report expression of proteins from allegedly non-coding regions, challenging the accuracy of current genome annotations. These novel proteins were found encoded either within non-coding RNAs, 5' or 3' untranslated regions (UTRs) of mRNAs, or overlapping a known coding sequence (CDS) in an alternative ORF. OpenProt is the first database that enforces a polycistronic model for eukaryotic genomes, allowing annotation of multiple ORFs per transcript. OpenProt is freely accessible and offers custom downloads of protein sequences across 10 species. Using OpenProt database for proteomic experiments enables novel proteins discovery and highlights the polycistronic nature of eukaryotic genes. The size of OpenProt database (all predicted proteins) is substantial and need be taken in account for the analysis. However, with appropriate false discovery rate (FDR) settings or the use of a restricted OpenProt database, users will gain a more realistic view of the proteomic landscape. Overall, OpenProt is a freely available tool that will foster proteomic discoveries.}, author = {Brunet, Marie A. and Roucou, Xavier}, @@ -657,6 +1692,38 @@ @article{brunet_mass_2019 year = {2019} } +@article{bruno_collisions_2023, + abstract = {DNA replication produces a global disorganization of chromatin structure that takes hours to be restored. However, how these chromatin rearrangements affect the regulation of gene expression and the maintenance of cell identity is not clear. Here, we use ChOR-seq and ChrRNA-seq experiments to analyze RNA polymerase II (RNAPII) activity and nascent RNA synthesis during the first hours after chromatin replication in human cells. We observe that transcription elongation is rapidly reactivated in nascent chromatin but that RNAPII abundance and distribution are altered, producing heterogeneous changes in RNA synthesis. Moreover, this first wave of transcription results in RNAPII blockages behind the replication fork, leading to changes in alternative splicing. Altogether, our results deepen our understanding of how transcriptional programs are regulated during cell division and uncover molecular mechanisms that explain why chromatin replication is an important source of gene expression variability.}, + author = {Bruno, Federica and Coronel-Guisado, Cristóbal and González-Aguilera, Cristina}, + doi = {10.1016/j.molcel.2023.11.036}, + issn = {1097-4164}, + journal = {Molecular Cell}, + keywords = {{\textgreater}UseGalaxy.eu, ChOR-seq, RNAPII, cell division, cell identity, chromatin, gene expression, replication, splicing, transcription, transcription-replication conflicts}, + language = {eng}, + month = {December}, + pages = {S1097--2765(23)01012--2}, + pmid = {38151016}, + title = {Collisions of {RNA} polymerases behind the replication fork promote alternative {RNA} splicing in newly replicated chromatin}, + year = {2023} +} + +@article{buchacher_pim_2023, + abstract = {The serine/threonine-specific Moloney murine leukemia virus (PIM) kinase family (i.e., PIM1, PIM2, and PIM3) has been extensively studied in tumorigenesis. PIM kinases are downstream of several cytokine signaling pathways that drive immune-mediated diseases. Uncontrolled T helper 17 (Th17) cell activation has been associated with the pathogenesis of autoimmunity. However, the detailed molecular function of PIMs in human Th17 cell regulation has yet to be studied. In the present study, we comprehensively investigated how the three PIMs simultaneously alter transcriptional gene regulation during early human Th17 cell differentiation. By combining PIM triple knockdown with bulk and scRNA-seq approaches, we found that PIM deficiency promotes the early expression of key Th17-related genes while suppressing Th1-lineage genes. Further, PIMs modulate Th cell signaling, potentially via STAT1 and STAT3. Overall, our study highlights the inhibitory role of PIMs in human Th17 cell differentiation, thereby suggesting their association with autoimmune phenotypes.}, + author = {Buchacher, Tanja and Shetty, Ankitha and Koskela, Saara A. and Smolander, Johannes and Kaukonen, Riina and Sousa, António G. G. and Junttila, Sini and Laiho, Asta and Rundquist, Olof and Lönnberg, Tapio and Marson, Alexander and Rasool, Omid and Elo, Laura L. and Lahesmaa, Riitta}, + doi = {10.1016/j.celrep.2023.113469}, + issn = {2211-1247}, + journal = {Cell Reports}, + keywords = {{\textgreater}UseGalaxy.eu, PIM kinases, T helper cell differentiation, Th1 cells, Th17 cells, bulk RNA sequencing, single-cell RNA sequencing, transcriptomics}, + month = {December}, + number = {12}, + pages = {113469}, + title = {{PIM} kinases regulate early human {Th17} cell differentiation}, + url = {https://www.sciencedirect.com/science/article/pii/S221112472301481X}, + urldate = {2023-12-02}, + volume = {42}, + year = {2023} +} + @article{buhl_prevotella_2020, abstract = {A strain of an obligately anaerobic, Gram-­stain-n­ egative rod-­shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879T was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-­length 16S rRNA gene and whole-­genome sequence) revealed the strain to belong to the genus Prevotella, but to be distant from recognized species, with the closest relationship to Prevotella veroralis. Unambiguous identification also proved possible by MALDI-­TOF MS. The genomic DNA G+C content was 41.5 mol\%. Strain A2879T was moderately saccharolytic and proteolytic. The most abundant cellular long-­chain fatty acids were anteiso-C­ 15 : 0 and iso-C­ 15 : 0. In view of these data, strain A2879T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella vespertina sp. nov. is proposed. The type strain is A2879T (=DSM 108027T=CCOS 1233T=CCUG72808T). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.}, author = {Buhl, Michael and Marschal, Matthias}, @@ -723,6 +1790,64 @@ @article{buttimer_isolation_2020 year = {2020} } +@article{camacho-beltran_complete_2024, + author = {Camacho-Beltrán, Erika and Morales-Aguilar, Juan José and López-Meyer, Melina and Rincón-Enríquez, Gabriel and Quiñones-Aguilar, Evangelina Esmeralda}, + doi = {10.1128/mra.00302-24}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00302--24}, + title = {Complete genome sequence of the {Microbacterium} enclense bacteriophage {phiMiGM15}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00302-24}, + urldate = {2024-05-06}, + volume = {0}, + year = {2024} +} + +@article{camargo_genomic_2023, + abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) are highly disseminated worldwide, and isolates co-resistant to other antimicrobial agents pose a threat to effective antimicrobial therapy. Therefore, evaluation of novel antimicrobial drugs is needed to identify potential treatments with better outcomes. We evaluated the in vitro activity of novel antimicrobial drugs/combinations against 97 KPC-producing Klebsiella pneumoniae isolates recovered from different hospitals in Brazil during 2021–2022. Clonality, resistance and virulence genes were detected by whole-genome sequencing. The majority of the isolates (54.6\%) were classified as extensively drug resistant or multidrug resistant (44.3\%); one isolate showed a pandrug resistance phenotype. The most active antimicrobial agents were meropenem-vaborbactam, cefiderocol, and ceftazidime-avibactam, with sensitivities higher than 90\%; resistance to ceftazidime-avibactam was associated with KPC-33 or KPC-44 variants. Colistin and polymyxin B were active against 58.6\% of the isolates. The 97 isolates were distributed into 17 different sequence types, with a predominance of ST11 (37.4\%). Although high in vitro susceptibility rates were detected for meropenem-vaborbactam and cefiderocol, only ceftazidime-avibactam is currently available in Brazil. Our findings showed limited susceptibility to antimicrobial drugs employed for infection treatment of carbapenem-resistant K. pneumoniae, underscoring the urgent need for stringent policies for antimicrobial stewardship to preserve the activity of such drugs.}, + author = {Camargo, Carlos Henrique and Yamada, Amanda Yaeko and de Souza, Andreia Rodrigues and Cunha, Marcos Paulo Vieira and Ferraro, Pedro Smith Pereira and Sacchi, Claudio Tavares and dos Santos, Marlon Benedito and Campos, Karoline Rodrigues and Tiba-Casas, Monique Ribeiro and Freire, Maristela Pinheiro and Barretti, Pasqual}, + copyright = {2023 Springer Nature Limited}, + doi = {10.1038/s41598-023-41903-x}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Clinical microbiology, Policy and public health in microbiology}, + language = {en}, + month = {September}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {14603}, + title = {Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against {KPC}-producing {Klebsiella} pneumoniae clinical isolates from {Brazilian} hospitals}, + url = {https://www.nature.com/articles/s41598-023-41903-x}, + urldate = {2023-09-10}, + volume = {13}, + year = {2023} +} + +@article{camargo_genomics_2023, + abstract = {Pseudomonas aeruginosa, an opportunistic pathogen causing infections in immunocompromised patients, usually shows pronounced antimicrobial resistance. In recent years, the frequency of carbapenemases in P. aeruginosa has decreased, which allows use of new beta-lactams/combinations in antimicrobial therapy. Therefore, the in vitro evaluation of these drugs in contemporary isolates is warranted. We evaluated the antimicrobial susceptibility and genomic aspects of 119 clinical P. aeruginosa isolates from 24 different hospitals in Brazil in 2021–2022. Identification was performed via MALDI-TOF-MS, and antimicrobial susceptibility was identified through broth microdilution, gradient tests, or disk diffusion. Whole-genome sequencing was carried out using NextSeq equipment. The most active drug was cefiderocol (100\%), followed by ceftazidime–avibactam (94.1\%), ceftolozane–tazobactam (92.4\%), and imipenem–relebactam (81.5\%). Imipenem susceptibility was detected in 59 isolates (49.6\%), and the most active aminoglycoside was tobramycin, to which 99 (83.2\%) isolates were susceptible. Seventy-one different sequence types (STs) were detected, including twelve new STs described herein. The acquired resistance genes blaCTX-M-2 and blaKPC-2 were identified in ten (8.4\%) and two (1.7\%) isolates, respectively. Several virulence genes (exoSTUY, toxA, aprA, lasA/B, plcH) were also identified. We found that new antimicrobials are effective against the diverse P. aeruginosa population that has been circulating in Brazilian hospitals in recent years.}, + author = {Camargo, Carlos Henrique and Yamada, Amanda Yaeko and Souza, Andreia Rodrigues de and Lima, Marisa de Jesus de Castro and Cunha, Marcos Paulo Vieira and Ferraro, Pedro Smith Pereira and Sacchi, Claudio Tavares and Santos, Marlon Benedito Nascimento dos and Campos, Karoline Rodrigues and Tiba-Casas, Monique Ribeiro and Freire, Maristela Pinheiro and Barretti, Pasqual}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/pathogens12070918}, + issn = {2076-0817}, + journal = {Pathogens}, + keywords = {{\textgreater}UseGalaxy.eu, CAZ-AVI, Illumina, MEM-VAR, MLST, cefiderocol, fosfomycin, polymyxin, whole genome sequencing}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {918}, + title = {Genomics and {Antimicrobial} {Susceptibility} of {Clinical} {Pseudomonas} aeruginosa {Isolates} from {Hospitals} in {Brazil}}, + url = {https://www.mdpi.com/2076-0817/12/7/918}, + urldate = {2023-07-11}, + volume = {12}, + year = {2023} +} + @misc{camargo_romera_isoform_2021, abstract = {Neuroblastoma (NB) is the most frequent extracranial solid tumour in childhood. The clinical diagnosis of NB is difficult due to the age of the patient and the vague appearance of the symptoms. Moreover, there are two groups of aggressive NBs, one with MYCN amplification and the other with an 11q deletion. Some genes could be a candidate suppressor for NB, e.g., the DLG2 gene that resides within the 11q-deleted region. The DLG2 gene has a large number of exons and multiple isoforms depending on the alternative splicing process. Moreover, these isoforms can include the L27 domain or not. This study aimed to analyse, by applying bioinformatic tools, if isoform 2, which does not have L27 domain, could be a candidate suppressor for this disease. RNA-seq samples from different human cell lines were collected from NCBI and a quality analysis was performed. The filtered samples were run in R and Python programs to do a visualization of the exon expression level and the prediction of Rsubread for exon-exon junctions. The results showed that isoform 2 of DLG2 gene was not expressed in the samples of NB, which is a promising result for being a candidate suppressor of NB. Furthermore, the prediction of exon-exon junctions by Rsubread was confirmed to be very accurate. In conclusion, this study shows that isoform 2 of DLG2 gene could be a candidate tumour suppressor in NB that could, in the future, be used as a target to help to detect earlier the presence of NB and increase the life expectancy of children who suffer from this disease.}, author = {Camargo Romera, Paula}, @@ -753,6 +1878,23 @@ @article{candeliere_draft_2020 year = {2020} } +@article{candeliere_genomic_2024, + abstract = {{\textless}p{\textgreater}Mucins are large glycoproteins whose degradation requires the expression of several glycosil hydrolases to catalyze the cleavage of the oligosaccharide chains and release monosaccharides that can be assimilated. In this study, we present a characterization on the strains {\textless}italic{\textgreater}Clostridium celatum{\textless}/italic{\textgreater} WC0700, {\textless}italic{\textgreater}Clostridium tertium{\textless}/italic{\textgreater} WC0709, and {\textless}italic{\textgreater}Paraclostridium bifermentans{\textless}/italic{\textgreater} WC0705. These three strains were previously isolated from enrichment cultures on mucin of fecal samples from healthy subjects and can use mucin as sole carbon and nitrogen source. Genome analysis and {\textless}italic{\textgreater}in vitro{\textless}/italic{\textgreater} functional analysis of these strains elucidated their physiological and biochemical features. {\textless}italic{\textgreater}C. celatum{\textless}/italic{\textgreater} WC0700 harbored the highest number of glycosyl hydrolases specific for mucin degradation, while {\textless}italic{\textgreater}P. bifermentans{\textless}/italic{\textgreater} WC0705 had the least. These predicted differences were confirmed growing the strains on 5 mucin-decorating monosaccharides (L-fucose, N-Acetylneuraminic acid, galactose, N-acetylgalactosamine, and N-acetylglucosamine) as only source of carbon. Fermenting mucin, they all produced formic, acetic, propionic, butyric, isovaleric, and lactic acids, and ethanol; acetic acid was the main primary metabolite. Further catabolic capabilities were investigated, as well as antibiotic susceptibility, biofilm formation, tolerance to oxygen and temperature. The potential pathogenicity of the strains was evaluated through {\textless}italic{\textgreater}in silico{\textless}/italic{\textgreater} research of virulence factors. The merge between comparative and functional genomics and biochemical/physiological characterization provided a comprehensive view of these mucin degraders, reassuring on the safety of these species and leaving ample scope for deeper investigations on the relationship with the host and for assessing if some relevant health-promoting effect could be ascribed to these SCFA producing species.{\textless}/p{\textgreater}}, + author = {Candeliere, Francesco and Musmeci, Eliana and Sola, Laura and Amaretti, Alberto and Raimondi, Stefano and Rossi, Maddalena}, + doi = {10.3389/fmicb.2024.1359726}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Clostridium celatum, Clostridium tertium, Functional Genomics, Paraclostridium bifermentans, human gut microbiota, mucin}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {Genomic and functional analysis of the mucinolytic species {Clostridium} celatum, {Clostridium} tertium, and {Paraclostridium} bifermentans}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1359726/full}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + @phdthesis{cantarella_insights_2020, abstract = {A large portion of the human genome is composed of repeated sequences, with Alu retrotransposons representing the most abundant repetitive elements. Alu sequences belong to the class of the Short Interspersed Nuclear Elements (SINEs) and depend on the Long Interspersed Nuclear Elements (LINEs) for their mobilization into the genome. The efficiency of Alu amplification during primate evolution suggests a positive driving force for their accumulation, bringing up to 1 million copies in the human genome. For unclear reasons, the majority of Alu sequences is repressed by tight epigenetic silencing, which is released in response to cell stresses such as virus infection and cancer progression. Adenovirus 5 (Ad5) is known to cause an increase of Alu transcription in HeLa, myelogenous leukemia and embryonic kidney cell lines, even though the virus factors that are responsible for this transcriptional enhancement have not been identified yet. Potential candidates could be represented by oncovirus proteins that induce a global remodeling of the host epigenetic landscape. For example, the Adenovirus early E1A protein interacts with the host tumor suppressor Rb, the lysine acetylase p300 and the p400 ATP-dependent chromatin remodeling complex, resulting in the induction of quiescent fibroblasts to enter the S-phase of the cell cycle. The exceptional success of Alu expansion and their retention even at the cost of a strong epigenetic silencing, which is released by virus infection, led us to investigate the molecular mechanism of Alus activation and their potential involvement in various cell processes. @@ -774,6 +1916,45 @@ @phdthesis{cantarella_insights_2020 year = {2020} } +@article{capitani_genome-based_2023, + abstract = {Providencia stuartii is a member of the Morganellaceae family, notorious for its intrinsic resistance to several antibiotics, including last-resort drugs such as colistin and tigecycline. Between February and March 2022, a four-patient outbreak sustained by P. stuartii occurred in a hospital in Rome. Phenotypic analyses defined these strains as eXtensively Drug-Resistant (XDR). Whole-genome sequencing was performed on the representative P. stuartii strains and resulted in fully closed genomes and plasmids. The genomes were highly related phylogenetically and encoded various virulence factors, including fimbrial clusters. The XDR phenotype was primarily driven by the presence of the blaNDM-1 metallo-β-lactamase alongside the rmtC 16S rRNA methyltransferase, conferring resistance to most β-lactams and every aminoglycoside, respectively. These genes were found on an IncC plasmid that was highly related to an NDM-IncC plasmid retrieved from a ST15 Klebsiella pneumoniae strain circulating in the same hospital two years earlier. Given its ability to acquire resistance plasmids and its intrinsic resistance mechanisms, P. stuartii is a formidable pathogen. The emergence of XDR P. stuartii strains poses a significant public health threat. It is essential to monitor the spread of these strains and develop new strategies for their control and treatment.}, + author = {Capitani, Valerio and Arcari, Gabriele and Oliva, Alessandra and Sacco, Federica and Menichincheri, Gaia and Fenske, Linda and Polani, Riccardo and Raponi, Giammarco and Antonelli, Guido and Carattoli, Alessandra}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12050943}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Enterobacterales}, \textit{Providencia stuartii}, \textit{bla}$_{\textrm{NDM}}$, {\textgreater}UseGalaxy.eu, IncC plasmid, antibiotic resistance, opportunistic pathogen, plasmid mediated resistance}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {943}, + shorttitle = {Genome-{Based} {Retrospective} {Analysis} of a {Providencia} stuartii {Outbreak} in {Rome}, {Italy}}, + title = {Genome-{Based} {Retrospective} {Analysis} of a {Providencia} stuartii {Outbreak} in {Rome}, {Italy}: {Broad} {Spectrum} {IncC} {Plasmids} {Spread} the {NDM} {Carbapenemase} within the {Hospital}}, + url = {https://www.mdpi.com/2079-6382/12/5/943}, + urldate = {2023-06-05}, + volume = {12}, + year = {2023} +} + +@article{capra_cpg_2023, + abstract = {During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions.}, + author = {Capra, Emanuele and Turri, F. and Lazzari, B. and Biffani, S. and Lange Consiglio, A. and Ajmone Marsan, P. and Stella, A. and Pizzi, F.}, + doi = {10.1186/s13072-023-00495-6}, + issn = {1756-8935}, + journal = {Epigenetics \& Chromatin}, + keywords = {{\textgreater}UseGalaxy.eu, Bull, Caput, Cauda, Chromatin integrity, Corpus, Epididymis, Methylation, Motility, Sperm, Sperm kinetics}, + month = {May}, + number = {1}, + pages = {20}, + title = {{CpG} {DNA} methylation changes during epididymal sperm maturation in bulls}, + url = {https://doi.org/10.1186/s13072-023-00495-6}, + urldate = {2023-06-03}, + volume = {16}, + year = {2023} +} + @article{carattoli_evolutionary_2021, author = {Carattoli, Alessandra and Arcari, Gabriele and Bibbolino, Giulia and Sacco, Federica and Tomolillo, Dario and Lella, Federica Maria Di and Trancassini, Maria and Faino, Luigi and Venditti, Mario and Antonelli, Guido and Raponi, Giammarco}, doi = {10.1128/aac.00574-21}, @@ -787,6 +1968,42 @@ @article{carattoli_evolutionary_2021 year = {2021} } +@techreport{carval_pangeo_2024, + author = {Carval, Thierry and Jossé, Marie and Detoc, Jérôme}, + doi = {10.5194/egusphere-egu24-6216}, + institution = {Copernicus Meetings}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + note = {Conference Name: EGU24}, + number = {EGU24-6216}, + title = {Pangeo environment in {Galaxy} {Earth} {System} supported by {Fair}-{Ease}}, + url = {https://meetingorganizer.copernicus.org/EGU24/EGU24-6216.html}, + urldate = {2024-04-28}, + year = {2024} +} + +@article{castellana_pannonibacter_2024, + abstract = {This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance.}, + author = {Castellana, Stefano and De Laurentiis, Vittoriana and Bianco, Angelica and Del Sambro, Laura and Grassi, Massimo and De Leonardis, Francesco and Derobertis, Anna Maria and De Carlo, Carmen and Sparapano, Eleonora and Mosca, Adriana and Stolfa, Stefania and Ronga, Luigi and Santacroce, Luigi and Chironna, Maria and Parisi, Michela and Capozzi, Loredana and Parisi, Antonio}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms12040799}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Pannonibacter, environmental bacteria, hospital acquired infections, putative novel species, whole-genome sequencing}, + language = {en}, + month = {April}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {799}, + title = {Pannonibacter anstelovis sp. nov. {Isolated} from {Two} {Cases} of {Bloodstream} {Infections} in {Paediatric} {Patients}}, + url = {https://www.mdpi.com/2076-2607/12/4/799}, + urldate = {2024-05-17}, + volume = {12}, + year = {2024} +} + @article{cermak_unexpected_2020, abstract = {In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.}, author = {Čermák, Vojtěch and Tyč, Dimitrij and Přibylová, Adéla and Fischer, Lukáš}, @@ -805,6 +2022,42 @@ @article{cermak_unexpected_2020 year = {2020} } +@article{ceylan_whole-genome_2024, + abstract = {Common sage (Salvia officinalis L.), the type species of the genus Salvia, is a historically acknowledged medicinal and aromatic plant that is utilized in several different industries for manufacturing diverse end products, including food, pharmaceuticals, cosmetics, personal hygiene products and insect repellants. The medical uses of sage essential oil terpenoids have made these secondary metabolites a focus of medical/pharmaceutical chemistry research. In the present work, the common sage genome was resequenced and assembled, and the protein-encoding gene content was annotated. The terpenoid biosynthesis gene repertoire, which includes 75 terpene synthase and 67 terpenoid backbone biosynthesis pathway genes, was predicted and located on assembly scaffolds, revealing tandem duplication blocks on the chromosomes. Variant analysis identified 188 variable single-nucleotide loci in the coding sequences of sage terpenoid biosynthesis genes. A total of 24,570 single-nucleotide polymorphisms were identified in the common sage total exome, representing a database of potential variable loci for targeted genotyping research. Given that terpene synthase activity is highly prone to modulation by point mutations and that the genotype plays an important role in the complex traits of terpenoid composition, single-nucleotide polymorphisms located in coding sequences constitute candidate functional markers that can be associated with terpenoid compositional traits in future research.}, + author = {Ceylan, Fatima and Uncu, Ayse Ozgur and Soyturk Patat, Aysenur and Uncu, Ali Tevfik}, + doi = {10.1007/s10722-024-01900-z}, + issn = {1573-5109}, + journal = {Genetic Resources and Crop Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Genome assembly, Lamiaceae, Mint, Secondary metabolite, Variant calling}, + language = {en}, + month = {February}, + title = {Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage ({Salvia} officinalis {L}.)}, + url = {https://doi.org/10.1007/s10722-024-01900-z}, + urldate = {2024-04-28}, + year = {2024} +} + +@article{chanama_comparative_2023, + abstract = {Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family Pseudonocardiaceae has abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently, Kutzneria chonburiensis SMC256T has been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256T (genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256T and other publicly available Kutzneria species. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256T is most closely related to Kutzneria sp. 744, Kutzneria kofuensis, Kutzneria sp. CA-103260 and Kutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among the Kutzneria genomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256Tgenome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific in Kutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome of Kutzneria chonburiensis contains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in the Kutzneria.}, + author = {Chanama, Manee and Prombutara, Pinidphon and Chanama, Suchart}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-36039-x}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Comparative genomics, Phylogenomics}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {8794}, + title = {Comparative genome features and secondary metabolite biosynthetic potential of {Kutzneria} chonburiensis and other species of the genus {Kutzneria}}, + url = {https://www.nature.com/articles/s41598-023-36039-x}, + urldate = {2023-06-05}, + volume = {13}, + year = {2023} +} + @article{chen_first_2021, author = {Chen, Dong-Bin and Zhang, Ru-Song and Jin, Xiang-Dong and Yang, Jian and Li, Peng and Liu, Yan-Qun}, doi = {10.1017/s0007485321000808}, @@ -831,6 +2084,68 @@ @article{chen_versatile_2018 year = {2018} } +@article{cheron_usp7maged1-mediated_2023, + abstract = {The risk of developing drug addiction is strongly influenced by the epigenetic landscape and chromatin remodeling. While histone modifications such as methylation and acetylation have been studied in the ventral tegmental area and nucleus accumbens (NAc), the role of H2A monoubiquitination remains unknown. Our investigations, initially focused on the scaffold protein melanoma-associated antigen D1 (Maged1), reveal that H2A monoubiquitination in the paraventricular thalamus (PVT) significantly contributes to cocaine-adaptive behaviors and transcriptional repression induced by cocaine. Chronic cocaine use increases H2A monoubiquitination, regulated by Maged1 and its partner USP7. Accordingly, Maged1 specific inactivation in thalamic Vglut2 neurons, or USP7 inhibition, blocks cocaine-evoked H2A monoubiquitination and cocaine locomotor sensitization. Additionally, genetic variations in MAGED1 and USP7 are linked to altered susceptibility to cocaine addiction and cocaine-associated symptoms in humans. These findings unveil an epigenetic modification in a non-canonical reward pathway of the brain and a potent marker of epigenetic risk factors for drug addiction in humans.}, + author = {Cheron, Julian and Beccari, Leonardo and Hagué, Perrine and Icick, Romain and Despontin, Chloé and Carusone, Teresa and Defrance, Matthieu and Bhogaraju, Sagar and Martin-Garcia, Elena and Capellan, Roberto and Maldonado, Rafael and Vorspan, Florence and Bonnefont, Jérôme and de Kerchove d’Exaerde, Alban}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-44120-2}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Addiction, Epigenetics in the nervous system}, + language = {en}, + month = {December}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {8481}, + shorttitle = {{USP7}/{Maged1}-mediated {H2A} monoubiquitination in the paraventricular thalamus}, + title = {{USP7}/{Maged1}-mediated {H2A} monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder}, + url = {https://www.nature.com/articles/s41467-023-44120-2}, + urldate = {2023-12-23}, + volume = {14}, + year = {2023} +} + +@article{cherrad_new_2023, + abstract = {Downy mildew is caused by Plasmopara viticola, an obligate oomycete plant pathogen, a devasting disease of grapevine. To protect plants from the disease, complex III inhibitors are among the fungicides widely used. They specifically target the mitochondrial cytochrome b (cytb) of the pathogen to block cellular respiration mechanisms. In the French vineyard, P. viticola has developed resistance against a first group of these fungicides, the Quinone outside Inhibitors (QoI), with a single amino acid substitution G143A in its cytb mitochondrial sequence. The use of QoI was limited and another type of fungicide, the Quinone inside Inhibitors, targeting the same gene and highly effective against oomycetes, was used instead. Recently however, less sensitive P. viticola populations were detected after treatments with some inhibitors, in particular ametoctradin and cyazofamid. By isolating single-sporangia P. viticola strains resistant to these fungicides, we characterized new variants in the cytb sequences associated with cyazofamid resistance: a point mutation (L201S) and more strikingly, two insertions (E203-DE-V204, E203-VE-V204). In parallel with the classical tools, pyrosequencing and qPCR, we then benchmarked short and long-reads NGS technologies (Ion Torrent, Illumina, Oxford Nanopore Technologies) to sequence the complete cytb with a view to detecting and assessing the proportion of resistant variants of P. viticola at the scale of a field population. Eighteen populations collected from French vineyard fields in 2020 were analysed: 12 showed a variable proportion of G143A, 11 of E203-DE-V204 and 7 populations of the S34L variant that confers resistance to ametoctradin. Interestingly, the long reads were able to identify variants, including SNPs, with confidence and to detect a small proportion of P. viticola with multiple variants along the same cytb sequence. Overall, NGS appears to be a promising method for assessing fungicide resistance of pathogens linked to cytb modifications at the field population level. This approach could rapidly become a robust decision support tool for resistance management in the future.}, + author = {Cherrad, Semcheddine and Gillet, Benjamin and Dellinger, Julien and Bellaton, Lalie and Roux, Pascale and Hernandez, Catalina and Steva, Hervé and Perrier, Lauriane and Vacher, Sébastien and Hughes, Sandrine}, + doi = {10.1371/journal.pone.0268385}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, DNA extraction, DNA isolation, Downy mildew, Fungicides, Gene sequencing, Leaves, Next-generation sequencing, Polymerase chain reaction}, + language = {en}, + month = {January}, + note = {Publisher: Public Library of Science}, + number = {1}, + pages = {e0268385}, + title = {New insights from short and long reads sequencing to explore cytochrome b variants in {Plasmopara} viticola populations collected from vineyards and related to resistance to complex {III} inhibitors}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0268385}, + urldate = {2023-03-15}, + volume = {18}, + year = {2023} +} + +@article{chetverikov_molecular_2024, + abstract = {Gall mites (Eriophyoidea) are cosmopolitan microscopic phytoparasites that often transmit viruses and induce gallogenesis. The tribe Calacarini is diagnosed by a set of plesiomorphic and homoplastic traits, including elimination of setae sc shared with other lineages of Eriophyoidea. We reviewed data on the generic diversity of calacarines, revised the concept of the type genus Calacarus Keifer 1940, and proposed three zones (MZ, SMZ, LZ) in the prodorsal shields of calacarines to simplify descriptions of their shield patterns. We describe three new calacarine species (Calacarus baviensisn. sp., C. burchelliaen. sp., and Viginticus searsiaen. sp.) from indigenous dicotyledonous trees from South Africa and Vietnam and report on new findings of Paracalacarus podocarpi Keifer in Brazil, Jiangsuacarus sp. in the USA, and Calacarus pusillus Pye in Latvia and Russia. The latter represents the new most northern locality of Calacarini. Reinvestigating the type species of Jaranasia Chandrapatya \& Boczek 2000 revealed that absence of setae l’’ II is the only character separating it from Jiangsuacarus Xue 2009. We proposed two new combinations: Jiangsuacarus sesleriae (Skoracka 2004) n. comb. (transferred from Jaranasia) and Procalacarus mussaendae (Keifer 1977) n. comb. (transferred from Calacarus). Partial sequences of Cox1 and 28S genes were obtained for six calacarines, some of them originating from old ethanol material kept at room temperature. Molecular phylogenetics revealed a stable cluster of “true” calacarine sequences comprising Calacarus, Jaranasia, Latitudo, and Viginticus and a polyphyletic group of erroneous sequences assigned to Calacarini in GenBank. All investigated females of calacarines have a pair of genital tubules associated with the vestibulum and hypothesized to participate in fertilization. This finding may contribute to resolving the question on how the fusion of gametes happens in gall mites.}, + author = {Chetverikov, Philipp E. and Craemer, Charnie and Gankevich, Vladimir D. and Le, Nhung Thi Tuyet and Nguyen, Viet Duc and Trinh, Hoat Xuan and Amrine, James}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/f15020329}, + issn = {1999-4907}, + journal = {Forests}, + keywords = {\textit{28S}, \textit{Calacarus}, \textit{Cox1}, {\textgreater}UseGalaxy.eu, Acari, arthropod structure, endemic, erroneous sequences, female genitalia, phytoparasite diversity, phytophagous mite, reproductive system}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {329}, + title = {Molecular {Phylogenetics} and {Light} {Microscopy} {Reveal} “{True}” and “{False}” {Calacarines} and {Novel} {Genital} {Structures} in {Gall} {Mites} ({Acariformes}, {Eriophyoidea})}, + url = {https://www.mdpi.com/1999-4907/15/2/329}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + @article{chiara_next_2020, author = {Chiara, Matteo and D'Erchia, Anna Maria and Gissi, Carmela and Manzari, Caterina and Parisi, Antonio and Resta, Nicoletta and Zambelli, Federico and Picardi, Ernesto and Pavesi, Giulio and Horner, David S. and Pesole, Graziano}, doi = {10.1093/bib/bbaa297}, @@ -861,6 +2176,38 @@ @article{chiara_next_2021 year = {2021} } +@article{choudalakis_repentools_2024, + abstract = {Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.}, + author = {Choudalakis, Michel and Bashtrykov, Pavel and Jeltsch, Albert}, + doi = {10.1186/s13100-024-00315-y}, + issn = {1759-8753}, + journal = {Mobile DNA}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin modification, Repeat element analysis, Repeat element enrichment, Repeat elements, UHRF1}, + month = {April}, + number = {1}, + pages = {6}, + shorttitle = {{RepEnTools}}, + title = {{RepEnTools}: an automated repeat enrichment analysis package for {ChIP}-seq data reveals {hUHRF1} {Tandem}-{Tudor} domain enrichment in young repeats}, + url = {https://doi.org/10.1186/s13100-024-00315-y}, + urldate = {2024-04-05}, + volume = {15}, + year = {2024} +} + +@article{cigana_monitoraggio_2023, + abstract = {La tesi ha come oggetto di analisi lo studio delle comunità microbiche associate ai bioreattori, individuando quelli che sono i parametri biotici e abiotici che possono influenzare la loro struttura e composizione. Per monitorare la comunità in questione, sono stati utilizzati approcci a coltura indipendente che richiedono il prelievo regolare di campioni dal bioreattore, l'estrazione del DNA dai campioni e sequenziamento avvenuto presso una ditta esterna. Successivamente sono stati analizzati i dati prodotti mediante l'utilizzo di software bioinformatici al fine di stimare la diversità microbica presente nel bioreattore e determinare i vari fattori ambientali che possano influenzarla.}, + author = {Cigana, Kevin {\textless}1994{\textgreater}}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {it}, + month = {March}, + note = {Accepted: 2023-02-19 +Publisher: Università Ca' Foscari Venezia}, + title = {Monitoraggio della comunità microbiologica durante un processo di fermentazione anaerobica di scarti vitivinicoli}, + url = {http://dspace.unive.it/handle/10579/23273}, + urldate = {2023-07-31}, + year = {2023} +} + @article{colin_whats_2022, author = {Colin, Luigi and Abed-Navandi, Daniel and Conde, Dalia A. and Craggs, Jamie and Silva, Rita da and Janse, Max and Källström, Björn and Pearce-Kelly, Alexander and Yesson, Chris}, doi = {10.1007/s12686-021-01250-3}, @@ -886,7 +2233,48 @@ @article{cordellier_next-generation_2021 year = {2021} } -@article{cova_helios_2021, +@article{corneo_proceedings_2023, + abstract = {Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The fungus infects only the flowers of camellias causing serious damage to the plant, particularly from an aesthetic point of view. The disease has been reported in almost all countries where camellia is grown for ornamental purposes, but there are not many studies on the variability of the population of this phytopathogen. The main objective of this study was to contribute to study the level of variability within the Italian population. More than 130 C. camelliae strains were collected from six localities distributed in five Italian regions and identified also based on molecular characterization of the ITS nucleotide sequences. The population variability was assessed by comparing the morphological characters. From a phenological point of view, 11 different colony morphotypes were identified, whose presence/absence and frequency are different in the various locations considered. The study of the taxonomically valid nucleotide sequences to differentiate fungi at the species level confirmed that the strains under study belong to a single species. To further investigate Italian population of C. camelliae we sequenced by a combination of long and short reads technologies the genome of a representative strain. This genome represents a worldwide reference for future C. cameliae diversity and pathogenicity studies.}, + author = {Corneo, Andrea}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + title = {Proceedings of 2023 {International} {Camellia} {Congress} in {Italy}}, + year = {2023} +} + +@article{cosenza-contreras_proteometabolomics_2023, + abstract = {There is an urgent need to better understand the mechanisms associated with the development, progression, and onset of recurrence after initial surgery in glioblastoma (GBM). The use of integrative phenotype-focused -omics technologies such as proteomics and lipidomics provides an unbiased approach to explore the molecular evolution of the tumor and its associated environment.We assembled a cohort of patient-matched initial (iGBM) and recurrent (rGBM) specimens of resected GBM. Proteome and metabolome composition were determined by mass spectrometry-based techniques. We performed neutrophil-GBM cell co-culture experiments to evaluate the behavior of rGBM-enriched proteins in the tumor microenvironment. ELISA-based quantitation of candidate proteins was performed to test the association of their plasma concentrations in iGBM with the onset of recurrence.Proteomic profiles reflect increased immune cell infiltration and extracellular matrix reorganization in rGBM. ASAH1, SYMN, and GPNMB were highly enriched proteins in rGBM. Lipidomics indicates the downregulation of ceramides in rGBM. Cell analyses suggest a role for ASAH1 in neutrophils and its localization in extracellular traps. Plasma concentrations of ASAH1 and SYNM show an association with time-to-recurrence.We describe the potential importance of ASAH1 in tumor progression and development of rGBM via metabolic rearrangement and showcase the feedback from the tumor microenvironment to plasma proteome profiles. We report the potential of ASAH1 and SYNM as plasma markers of rGBM progression. The published datasets can be considered as a resource for further functional and biomarker studies involving additional -omics technologies.}, + author = {Cosenza-Contreras, Miguel and Schäfer, Agnes and Sing, Justin and Cook, Lena and Stillger, Maren N and Chen, Chia-Yi and Hidalgo, Jose Villacorta and Pinter, Niko and Meyer, Larissa and Werner, Tilman and Bug, Darleen and Haberl, Zeno and Kübeck, Oliver and Zhao, Kai and Stei, Susanne and Gafencu, Anca Violeta and Ionita, Radu and Brehar, Felix M and Ferrer-Lozano, Jaime and Ribas, Gloria and Cerdá-Alberich, Leo and Martí-Bonmatí, Luis and Nimsky, Christopher and Van Straaten, Alexis and Biniossek, Martin L and Föll, Melanie and Cabezas-Wallscheid, Nina and Büscher, Jörg and Röst, Hannes and Arnoux, Armelle and Bartsch, Jörg W and Schilling, Oliver}, + doi = {10.1093/neuonc/noad208}, + issn = {1522-8517}, + journal = {Neuro-Oncology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + pages = {noad208}, + title = {Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism}, + url = {https://doi.org/10.1093/neuonc/noad208}, + urldate = {2023-10-31}, + year = {2023} +} + +@article{cosenza-contreras_proteometabolomics_2024, + abstract = {There is an urgent need to better understand the mechanisms associated with the development, progression, and onset of recurrence after initial surgery in glioblastoma (GBM). The use of integrative phenotype-focused -omics technologies such as proteomics and lipidomics provides an unbiased approach to explore the molecular evolution of the tumor and its associated environment.We assembled a cohort of patient-matched initial (iGBM) and recurrent (rGBM) specimens of resected GBM. Proteome and metabolome composition were determined by mass spectrometry-based techniques. We performed neutrophil-GBM cell coculture experiments to evaluate the behavior of rGBM-enriched proteins in the tumor microenvironment. ELISA-based quantitation of candidate proteins was performed to test the association of their plasma concentrations in iGBM with the onset of recurrence.Proteomic profiles reflect increased immune cell infiltration and extracellular matrix reorganization in rGBM. ASAH1, SYMN, and GPNMB were highly enriched proteins in rGBM. Lipidomics indicates the downregulation of ceramides in rGBM. Cell analyses suggest a role for ASAH1 in neutrophils and its localization in extracellular traps. Plasma concentrations of ASAH1 and SYNM show an association with time to recurrence.We describe the potential importance of ASAH1 in tumor progression and development of rGBM via metabolic rearrangement and showcase the feedback from the tumor microenvironment to plasma proteome profiles. We report the potential of ASAH1 and SYNM as plasma markers of rGBM progression. The published datasets can be considered as a resource for further functional and biomarker studies involving additional -omics technologies.}, + author = {Cosenza-Contreras, Miguel and Schäfer, Agnes and Sing, Justin and Cook, Lena and Stillger, Maren N and Chen, Chia-Yi and Villacorta Hidalgo, Jose and Pinter, Niko and Meyer, Larissa and Werner, Tilman and Bug, Darleen and Haberl, Zeno and Kübeck, Oliver and Zhao, Kai and Stei, Susanne and Gafencu, Anca Violeta and Ionita, Radu and Brehar, Felix M and Ferrer-Lozano, Jaime and Ribas, Gloria and Cerdá-Alberich, Leo and Martí-Bonmatí, Luis and Nimsky, Christopher and Van Straaten, Alexis and Biniossek, Martin L and Föll, Melanie and Cabezas-Wallscheid, Nina and Büscher, Jörg and Röst, Hannes and Arnoux, Armelle and Bartsch, Jörg W and Schilling, Oliver}, + doi = {10.1093/neuonc/noad208}, + issn = {1522-8517}, + journal = {Neuro-Oncology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {3}, + pages = {488--502}, + title = {Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism}, + url = {https://doi.org/10.1093/neuonc/noad208}, + urldate = {2024-05-17}, + volume = {26}, + year = {2024} +} + +@article{cova_helios_2021, author = {Cova, Giovanni and Taroni, Chiara and Deau, Marie-Céline and Cai, Qi and Mittelheisser, Vincent and Philipps, Muriel and Jung, Matthieu and Cerciat, Marie and Gras, Stéphanie Le and Thibault-Carpentier, Christelle and Jost, Bernard and Carlsson, Leif and Thornton, Angela M. and Shevach, Ethan M. and Kirstetter, Peggy and Kastner, Philippe and Chan, Susan}, doi = {10.1084/jem.20202317}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, @@ -899,6 +2287,24 @@ @article{cova_helios_2021 year = {2021} } +@article{crespo_pcid2_2024, + abstract = {HIV-1 latency results from tightly regulated molecular processes that act at distinct steps of HIV-1 gene expression. Here, we characterize PCI domain-containing 2 (PCID2) protein, a subunit of the transcription and export complex 2 (TREX2) complex, to enforce transcriptional repression and post-transcriptional blocks to HIV-1 gene expression during latency. PCID2 bound the latent HIV-1 LTR (long terminal repeat) and repressed transcription initiation during latency. Depletion of PCID2 remodeled the chromatin landscape at the HIV-1 promoter and resulted in transcriptional activation and latency reversal. Immunoprecipitation coupled to mass spectrometry identified PCID2-interacting proteins to include negative viral RNA (vRNA) splicing regulators, and PCID2 depletion resulted in over-splicing of intron-containing vRNA in cell lines and primary cells obtained from PWH. MCM3AP and DSS1, two other RNA-binding TREX2 complex subunits, also inhibit transcription initiation and vRNA alternative splicing during latency. Thus, PCID2 is a novel HIV-1 latency-promoting factor, which in context of the TREX2 sub-complex PCID2-DSS1-MCM3AP blocks transcription and dysregulates vRNA processing.}, + author = {Crespo, Raquel and Ne, Enrico and Reinders, Julian and Meier, Jenny I. J. and Li, Chengcheng and Jansen, Sanne and Górska, Alicja and Koçer, Selin and Kan, Tsung Wai and Doff, Wouter and Dekkers, Dick and Demmers, Jeroen and Palstra, Robert-Jan and Rao, Shringar and Mahmoudi, Tokameh}, + doi = {10.1016/j.isci.2024.109152}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Virology}, + language = {eng}, + month = {March}, + number = {3}, + pages = {109152}, + pmcid = {PMC10879814}, + pmid = {38384833}, + title = {{PCID2} dysregulates transcription and viral {RNA} processing to promote {HIV}-1 latency}, + volume = {27}, + year = {2024} +} + @article{dad_molecular_2020, abstract = {Recent studies support the assumption that mutation of the X-linked Pig-a gene is most likely responsible for the mutant phenotype of the cells deficient in glycosylphosphatidylinositol (GPI)-anchored proteins quantified in the rodent Pig-a gene mutation assay. In humans, however, mutations in both alleles of one of the 30 other genes involved in GPI-anchor synthesis, e.g., PIG-L and PIG-O, cause reduced expression of surface GPI-anchored proteins. Here, we investigated the possibility that the loss of the GPI-anchor detected by the rat Pig-a assay also could be caused by mutation in other GPI-biosynthesis genes. 31 samples were obtained from 8 inbred and outbred rat strains commonly used for genetic toxicology assays. In order to investigate possible sources of variation in the Pig-a assay, variant DNA sequences were evaluated in Cd59 and 24 GPI-biosynthesis genes. In some genes, such as Pig-n and Pig-u, homozygous variations occurred in all animals, suggesting that these variations are due to deviations in the reference genome. Heterozygous Pig-s, Pig-w, Pig-o, Pig-c, Pgap1, Pgap2, Pig-k and Pig-t variations were found, however, indicating that these genes could serve as targets for mutation in the assay. Protein alignment for these altered genes was conducted with possible human, mouse and rat phenotypic mutants from the literature; this analysis demonstrated that many of the variations that we detected were in non-conserved sequences and that no phenotypes for any of these variants could be inferred from known mutants from the literature. All heterozygous variants were in outbred rats. Overall, the findings of this study cannot totally rule out the possibility that mutations in GPI-biosynthesis genes other than Pig-a are detected in the Pig-a assay, but suggest that if it occurs, it must occur only rarely and therefore mutations in genes other than Pig-a have little impact on rat-based experiments.}, author = {Dad, Azra and Dobrovolsky, Vasily N. and Heflich, Robert H. and Revollo, Javier R.}, @@ -916,18 +2322,56 @@ @article{dad_molecular_2020 year = {2020} } +@article{darino_identification_2024, + abstract = {Fusarium Head Blight (FHB) is a destructive floral disease of different cereal crops. The Ascomycete fungus Fusarium graminearum (Fg) is one of the main causal agents of FHB in wheat and barley. The role(s) in virulence of Fg genes include genetic studies that involve the transformation of the fungus with different expression cassettes. We have observed in several studies where Fg genes functions were characterised that integration of expression cassettes occurred randomly. Random insertion of a cassette may disrupt gene expression and/or protein functions and hence the overall conclusion of the study. Target site integration (TSI) is an approach that consists of identifying a chromosomal region where the cassette can be inserted. The identification of a suitable locus for TSI in Fg would avert the potential risks of ectopic integration.}, + author = {Darino, Martin and Urban, Martin and Kaur, Navneet and Machado Wood, Ana and Grimwade-Mann, Mike and Smith, Dan and Beacham, Andrew and Hammond-Kosack, Kim}, + doi = {10.1186/s40694-024-00171-8}, + issn = {2054-3085}, + journal = {Fungal Biology and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Coleoptiles, Complementation, Confocal microscopy, Fungal transformation, Fusarium Head Blight, Fusarium graminearum, Genome sequence, Secretion, Target site integration, Wheat}, + language = {en}, + month = {February}, + number = {1}, + pages = {2}, + title = {Identification and functional characterisation of a locus for target site integration in {Fusarium} graminearum}, + url = {https://doi.org/10.1186/s40694-024-00171-8}, + urldate = {2024-04-28}, + volume = {11}, + year = {2024} +} + @article{darkow_small_2021, + abstract = {In search of more efficacious and safe pharmacological treatments for atrial fibrillation (AF), atria-selective antiarrhythmic agents have been promoted that target ion channels principally expressed in the atria. This concept allows one to engage antiarrhythmic effects in atria, but spares the ventricles from potentially proarrhythmic side effects. It has been suggested that cardiac small conductance Ca2+-activated K+ (SK) channels may represent an atria-selective target in mammals including humans. However, there are conflicting data concerning the expression of SK channels in different stages of AF, and recent findings suggest that SK channels are upregulated in ventricular myocardium when patients develop heart failure. To address this issue, RNA-sequencing was performed to compare expression levels of three SK channels (KCNN1, KCNN2, and KCNN3) in human atrial and ventricular tissue samples from transplant donor hearts (no cardiac disease), and patients with cardiac disease in sinus rhythm or with AF. In addition, for control purposes expression levels of several genes known to be either chamber-selective or differentially expressed in AF and heart failure were determined. In atria, as compared to ventricle from transplant donor hearts, we confirmed higher expression of KCNN1 and KCNA5, and lower expression of KCNJ2, whereas KCNN2 and KCNN3 were statistically not differentially expressed. Overall expression of KCNN1 was low compared to KCNN2 and KCNN3. Comparing atrial tissue from patients with AF to sinus rhythm samples we saw downregulation of KCNN2 in AF, as previously reported. When comparing ventricular tissue from heart failure patients to non-diseased samples, we found significantly increased ventricular expression of KCNN3 in heart failure, as previously published. The other channels showed no significant difference in expression in either disease. Our results add weight to the view that SK channels are not likely to be an atria-selective target, especially in failing human hearts, and modulators of these channels may prove to have less utility in treating AF than hoped. Whether targeting SK1 holds potential remains to be elucidated.}, author = {Darkow, Elisa and Nguyen, Thong T. and Stolina, Marina and Kari, Fabian A. and Schmidt, Constanze and Wiedmann, Felix and Baczkó, István and Kohl, Peter and Rajamani, Sridharan and Ravens, Ursula and Peyronnet, Rémi}, - doi = {10.3389/fphys.2021.650964}, + issn = {1664-042X}, + journal = {Frontiers in Physiology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - month = {April}, - note = {Publisher: Frontiers Media SA}, - title = {Small {Conductance} {Ca2} \${\textbackslash}mathplus\$-{Activated} {K}\${\textbackslash}mathplus\$ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}: {Comparison} {Between} {Donor}, {Atrial} {Fibrillation} and {Heart} {Failure} {Tissue}}, - url = {https://doi.org/10.3389/fphys.2021.650964}, + shorttitle = {Small {Conductance} {Ca2} +-{Activated} {K}+ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}}, + title = {Small {Conductance} {Ca2} +-{Activated} {K}+ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}: {Comparison} {Between} {Donor}, {Atrial} {Fibrillation} and {Heart} {Failure} {Tissue}}, + url = {https://www.frontiersin.org/article/10.3389/fphys.2021.650964}, + urldate = {2022-03-18}, volume = {12}, year = {2021} } +@article{davasaz_tabrizi_bioinformatic_2023, + abstract = {The Bioinformatics Resource Center (BRC) program was developed by the National Institute of Allergy and Infectious Diseases (NIAID) to assist researchers in analyzing the increasing amount of genomic sequences and other omics-related data. In this work, whole-genome sequences of prostate cancer and genitourinary diseases (WGS) were examined for genes utilizing the BV-BRC Bioinformatics Resource Center. using the Usegalaxy program to combine the plasma and gut microbiome sequences from prostate cancer patients. Following that, chromosomes, plasmids, and unclassified sequences were subjected to ARG analysis. As a result of comprehensive genomic analysis of all samples, the S2 sequences were of good quality compared to the other sequences. As for virulence factors, intracellular survival is one of the important virulence factors, a common gene of Salmonella, which was represented in the prostate cancer samples but not in the urine microbiome samples.}, + author = {Davasaz Tabrizi, Elmira and Sevil, Mushteba and Sajer Naser, Omar and Arican, Ercan}, + doi = {10.5281/zenodo.10029976}, + issn = {2610-7996}, + journal = {Revista Latinoamericana de Hipertensión}, + keywords = {{\textgreater}UseGalaxy.eu, Bioinformatic, Virulence factors, Antibiotic resistance gene, Prostate cancer}, + language = {eng}, + month = {October}, + number = {6}, + pages = {266--273}, + title = {Bioinformatic challenge on prostate cancer and urinary microbiome}, + url = {https://zenodo.org/records/10029976}, + urldate = {2023-12-28}, + volume = {18}, + year = {2023} +} + @article{davey_intrinsically_2019, abstract = {Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.}, author = {Davey, Norman E. and Babu, M. Madan and Blackledge, Martin and Bridge, Alan and Capella-Gutierrez, Salvador and Dosztanyi, Zsuzsanna and Drysdale, Rachel and Edwards, Richard J. and Elofsson, Arne and Felli, Isabella C. and Gibson, Toby J. and Gutmanas, Aleksandras and Hancock, John M. and Harrow, Jen and Higgins, Desmond and Jeffries, Cy M. and Le Mercier, Philippe and Mészáros, Balint and Necci, Marco and Notredame, Cedric and Orchard, Sandra and Ouzounis, Christos A. and Pancsa, Rita and Papaleo, Elena and Pierattelli, Roberta and Piovesan, Damiano and Promponas, Vasilis J. and Ruch, Patrick and Rustici, Gabriella and Romero, Pedro and Sarntivijai, Sirarat and Saunders, Gary and Schuler, Benjamin and Sharan, Malvika and Shields, Denis C. and Sussman, Joel L. and Tedds, Jonathan A. and Tompa, Peter and Turewicz, Michael and Vondrasek, Jiri and Vranken, Wim F. and Wallace, Bonnie Ann and Wichapong, Kanin and Tosatto, Silvio C. E.}, @@ -945,6 +2389,142 @@ @article{davey_intrinsically_2019 year = {2019} } +@article{de_andrade_whole_2023, + abstract = {Bacillus anthracis causes anthrax disease and can affect humans and other animals. This zoonotic disease has an impact on the economic and health aspects. B. anthracis population is divided into three major clades: A (with worldwide distribution), B, and C (restricted to specific regions). Anthrax is most common in agricultural regions of central and southwestern Asia, sub-Saharan Africa, Southern and Eastern Europe, the Caribbean, and Central and South America. Here, we sequenced by short and long reads technologies to generate a hybrid assembly of a lineage of B. anthracis recovered from animal source in the 1960s in Brazil. Isolate identification was confirmed by phenotypic/biochemical tests and MALDI-TOF MS. Antimicrobial susceptibility was performed by in-house broth microdilution. B. anthracis IAL52 was susceptible to penicillin, amoxicillin, doxycycline, levofloxacin, and tetracycline but non-susceptible to ciprofloxacin. IAL52 was classified as sequence type ST2, clade A.Br.069 (V770 group). Sequencing lineages of B. anthracis, especially from underrepresented regions, can help determine the evolution of this critical zoonotic and virulent pathogen.}, + author = {de Andrade, Tânia Sueli and Camargo, Carlos Henrique and Campos, Karoline Rodrigues and Reis, Alex Domingos and Santos, Marlon Benedito do Nascimento and Zanelatto, Vanessa Nieri and Takagi, Elizabeth Harummyy and Sacchi, Claudio Tavares}, + doi = {10.1016/j.cimid.2023.102027}, + issn = {0147-9571}, + journal = {Comparative Immunology, Microbiology and Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Anthrax, One health, WGS, Zoonotic disease}, + language = {en}, + month = {September}, + pages = {102027}, + title = {Whole genome sequencing of {Bacillus} anthracis isolated from animal in the 1960s, {Brazil}, belonging to the {South} {America} subclade}, + url = {https://www.sciencedirect.com/science/article/pii/S0147957123000851}, + urldate = {2023-07-31}, + volume = {100}, + year = {2023} +} + +@article{de_azevedo_genomic_2024, + author = {de Azevedo, Bruna Luiza and Queiroz, Victória Fulgêncio and de Aquino, Isabella Luiza Martins and Machado, Talita Bastos and de Assis, Felipe Lopes and Reis, Erik and Araújo Júnior, João Pessoa and Ullmann, Leila Sabrina and Colson, Philippe and Greub, Gilbert and Aylward, Frank and Rodrigues, Rodrigo Araújo Lima and Abrahão, Jônatas Santos}, + doi = {10.1128/jvi.00513-24}, + journal = {Journal of Virology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00513--24}, + title = {The genomic and phylogenetic analysis of {Marseillevirus} cajuinensis raises questions about the evolution of {Marseilleviridae} lineages and their taxonomical organization}, + url = {https://journals.asm.org/doi/full/10.1128/jvi.00513-24}, + urldate = {2024-06-07}, + volume = {0}, + year = {2024} +} + +@article{de_jesus_bertani_whole_2023, + abstract = {This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288\_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288\_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.}, + author = {de Jesus Bertani, Amanda Maria and Vieira, Thais and Reis, Alex Domingos and dos Santos, Carla Adriana and de Almeida, Elisabete Aparecida and Camargo, Carlos Henrique and Casas, Monique Ribeiro Tiba}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-29599-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobials, Microbiology}, + language = {en}, + month = {February}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {2299}, + title = {Whole genome sequence analysis of the first reported isolate of {Salmonella} {Agona} carrying {blaCTX}-{M}-55 gene in {Brazil}}, + url = {https://www.nature.com/articles/s41598-023-29599-5}, + urldate = {2023-03-15}, + volume = {13}, + year = {2023} +} + +@article{de_souza_mitochondrial_2024, + abstract = {Plant mitochondrial genomes are characterized by high homologous recombination, extensive intergenic spacers, conservation in DNA sequences, and gene content. The Hancornia genus belongs to the Apocynaceae family, with H. speciosa Gomes being the sole species in the genus. It is an siganificant commercial fruit crop; however, only a number of studies have been conducted. In this study, we present the mitochondrial genome of H. speciosa and compare it with other mitochondrial genomes within the Apocynaceae family.}, + author = {de Souza, Fernanda Danielle and Marques, André and Almeida, Cícero}, + doi = {10.1007/s11033-023-09184-9}, + issn = {1573-4978}, + journal = {Molecular Biology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Apocynaceae, Mangaba, Mitogenome}, + language = {en}, + month = {January}, + number = {1}, + pages = {132}, + shorttitle = {Mitochondrial genome of {Hancornia} speciosa gomes}, + title = {Mitochondrial genome of {Hancornia} speciosa gomes: intergenic regions containing retrotransposons and predicted genes}, + url = {https://doi.org/10.1007/s11033-023-09184-9}, + urldate = {2024-05-17}, + volume = {51}, + year = {2024} +} + +@article{de_souza_seeds_2024, + abstract = {Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes are unknown. To investigate the effects of increasing plant species richness on the diversity and composition of the seed microbiome, we made use of a well-established long-term biodiversity experiment in Germany (The Jena Experiment). We sampled seeds from different Plantago lanceolata blossoms in a plant diversity gradient ranging from monoculture to 16 species mixtures. The seeds were surface sterilized to remove seed surface-associated bacteria and subjected to a metabarcoding approach to assess bacterial community structure.}, + author = {de Souza, Yuri Pinheiro Alves and Schloter, Michael and Weisser, Wolfgang and Huang, Yuanyuan and Schulz, Stefanie}, + doi = {10.1186/s40793-024-00552-x}, + issn = {2524-6372}, + journal = {Environmental Microbiome}, + keywords = {{\textgreater}UseGalaxy.eu, Core microbiome, Plant diversity gradient, Plantago lanceolata, Seed microbiome}, + language = {en}, + month = {February}, + number = {1}, + pages = {11}, + title = {The seeds of {Plantago} lanceolata comprise a stable core microbiome along a plant richness gradient}, + url = {https://doi.org/10.1186/s40793-024-00552-x}, + urldate = {2024-04-28}, + volume = {19}, + year = {2024} +} + +@article{dehghanian_zfp982_2024, + abstract = {Background +Understanding the genetic underpinnings of protein networks conferring stemness is of broad interest for basic and translational research. +Methods +We used multi-omics analyses to identify and characterize stemness genes, and focused on the zinc finger protein 982 (Zfp982) that regulates stemness through the expression of Nanog, Zfp42, and Dppa3 in mouse embryonic stem cells (mESC). +Results +Zfp982 was expressed in stem cells, and bound to chromatin through a GCAGAGKC motif, for example near the stemness genes Nanog, Zfp42, and Dppa3. Nanog and Zfp42 were direct targets of ZFP982 that decreased in expression upon knockdown and increased upon overexpression of Zfp982. We show that ZFP982 expression strongly correlated with stem cell characteristics, both on the transcriptional and morphological levels. Zfp982 expression decreased with progressive differentiation into ecto-, endo- and mesodermal cell lineages, and knockdown of Zfp982 correlated with morphological and transcriptional features of differentiated cells. Zfp982 showed transcriptional overlap with members of the Hippo signaling pathway, one of which was Yap1, the major co-activator of Hippo signaling. Despite the observation that ZFP982 and YAP1 interacted and localized predominantly to the cytoplasm upon differentiation, the localization of YAP1 was not influenced by ZFP982 localization. +Conclusions +Together, our study identified ZFP982 as a transcriptional regulator of early stemness genes, and since ZFP982 is under the control of the Hippo pathway, underscored the importance of the context-dependent Hippo signals for stem cell characteristics.}, + author = {Dehghanian, Fariba and Bovio, Patrick Piero and Gather, Fabian and Probst, Simone and Naghsh-Nilchi, Amirhosein and Vogel, Tanja}, + doi = {10.1016/j.bbamcr.2024.119686}, + issn = {0167-4889}, + journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research}, + keywords = {{\textgreater}UseGalaxy.eu, Hippo pathway, Nanog, Pluripotency, Stemness, Yap1, ZFP982}, + month = {April}, + number = {4}, + pages = {119686}, + title = {{ZFP982} confers mouse embryonic stem cell characteristics by regulating expression of \textit{{Nanog}}, \textit{{Zfp42}}\textit{,} and \textit{{Dppa3}}}, + url = {https://www.sciencedirect.com/science/article/pii/S0167488924000296}, + urldate = {2024-05-17}, + volume = {1871}, + year = {2024} +} + +@article{delandre_long-read_2024, + abstract = {Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.}, + author = {Delandre, Océane and Lamer, Ombeline and Loreau, Jean-Marie and Papa Mze, Nasserdine and Fonta, Isabelle and Mosnier, Joel and Gomez, Nicolas and Javelle, Emilie and Pradines, Bruno}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/biology13020089}, + issn = {2079-7737}, + journal = {Biology}, + keywords = {\textit{Pf}3D7, \textit{Pf}W2, \textit{Plasmodium falciparum}, {\textgreater}UseGalaxy.eu, PromethION, genome assembly, long-read sequencing, nanopore}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {89}, + title = {Long-{Read} {Sequencing} and {De} {Novo} {Genome} {Assembly} {Pipeline} of {Two} {Plasmodium} falciparum {Clones} ({Pf3D7}, {PfW2}) {Using} {Only} the {PromethION} {Sequencer} from {Oxford} {Nanopore} {Technologies} without {Whole}-{Genome} {Amplification}}, + url = {https://www.mdpi.com/2079-7737/13/2/89}, + urldate = {2024-04-28}, + volume = {13}, + year = {2024} +} + @article{delroisse_photophore_2021, author = {Delroisse, Jérôme and Duchatelet, Laurent and Flammang, Patrick and Mallefet, Jérôme}, doi = {10.3389/fmars.2021.627045}, @@ -957,6 +2537,24 @@ @article{delroisse_photophore_2021 year = {2021} } +@article{deng_atlas_2024, + abstract = {Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.}, + author = {Deng, Lisa and Pollmeier, Luisa and Bednarz, Rebecca and Cao, Can and Laurette, Patrick and Wirth, Luisa and Mamazhakypov, Argen and Bode, Christine and Hein, Lutz and Gilsbach, Ralf and Lother, Achim}, + doi = {10.1126/sciadv.adj5101}, + issn = {2375-2548}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu, Animals, Ascomycota, Cardiovascular Diseases, Endothelial Cells, Enhancer Elements, Genetic, Gene Expression, Heart Failure, Hypertension, Mice, Receptors, Mineralocorticoid, Transcription Factors}, + language = {eng}, + month = {March}, + number = {10}, + pages = {eadj5101}, + pmcid = {PMC10917356}, + pmid = {38446896}, + title = {Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression}, + volume = {10}, + year = {2024} +} + @article{deng_gene_2020, abstract = {Endothelial cells take pivotal roles in the heart and the vascular system and their differentiation, subspecification and function is determined by gene expression. A stable, in vitro cardiac endothelial cell line could provide high cell numbers as needed for many epigenetic analyses and facilitate the understanding of molecular mechanisms involved in endothelial cell biology. To test their suitability for transcriptomic or epigenetic studies, we compared the transcriptome of cultured immortalized mouse cardiac endothelial cells (MCEC) to primary cardiac endothelial cells (pEC). Whole transcriptome comparison of MCEC and pEC showed a correlation of 0.75–0.77. Interestingly, correlation of gene expression declined in endothelial cell-typical genes. In MCEC, we found a broad downregulation of genes that are highly expressed in pEC, including well-described markers of endothelial cell differentiation. Accordingly, systematic analysis revealed a downregulation of genes associated with typical endothelial cell functions in MCEC, while genes related to mitotic cell cycle were upregulated when compared to pEC. In conclusion, the findings from this study suggest that primary cardiac endothelial cells should preferably be used for genome-wide transcriptome or epigenome studies. The suitability of in vitro cell lines for experiments investigating single genes or signaling pathways should be carefully validated before use.}, author = {Deng, Lisa and Pollmeier, Luisa and Zhou, Qian and Bergemann, Stella and Bode, Christoph and Hein, Lutz and Lother, Achim}, @@ -993,6 +2591,38 @@ @article{deng_lamp_2022 year = {2022} } +@article{deng_massively_2024, + abstract = {Performing saturation editing of chromosomal genes will enable the study of genetic variants in situ and facilitate protein and cell engineering. However, current in vivo editing of endogenous genes either lacks flexibility or is limited to discrete codons and short gene fragments, preventing a comprehensive exploration of genotype-phenotype relationships. To enable facile saturation editing of full-length genes, we used a protospacer adjacent motif–relaxed Cas9 variant and homology-directed repair to achieve above 60\% user-defined codon replacement efficiencies in Saccharomyces cerevisiae genome. Coupled with massively parallel DNA design and synthesis, we developed a saturation gene editing method termed CRISPR-Cas9– and homology-directed repair–assisted saturation editing (CHASE) and achieved highly saturated codon swapping of long genomic regions. By applying CHASE to massively edit a well-studied global transcription factor gene, we found known and unreported genetic variants affecting an industrially relevant microbial trait. The user-defined codon editing capability and wide targeting windows of CHASE substantially expand the scope of saturation gene editing.}, + author = {Deng, Lei and Zhou, Yi-Lian and Cai, Zhenkun and Zhu, Jie and Li, Zenan and Bao, Zehua}, + doi = {10.1126/sciadv.adj9382}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + note = {Publisher: American Association for the Advancement of Science}, + number = {20}, + pages = {eadj9382}, + title = {Massively parallel {CRISPR}-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast}, + url = {https://www.science.org/doi/full/10.1126/sciadv.adj9382}, + urldate = {2024-06-07}, + volume = {10}, + year = {2024} +} + +@misc{depari_long-read_2024, + abstract = {Abstract* Azadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbc L gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions.}, + author = {Depari, Efratenta Katherina and Wijayanto, Nurheni and Karlinasari, Lina and Rafi, Mohamad and Siregar, Iskandar Zulkarnaen}, + copyright = {http://creativecommons.org/licenses/by/4.0/}, + doi = {10.12688/f1000research.144155.1}, + keywords = {{\textgreater}UseGalaxy.eu, Azadirachta excelsa, chloroplast genome, gene marker, identification, identified seed stand, long-reads, phylogenetics}, + language = {en}, + month = {April}, + publisher = {F1000Research}, + title = {Long-read datasets of {Kayu} {Bawang} (\textit{{Azadirachta} excelsa} ({Jack}) {Jacobs}) from 3 different identified seed stands in {Bengkulu} ({Sumatra}), {Indonesia} and its phylogenetic relationships}, + url = {https://f1000research.com/articles/13-254}, + urldate = {2024-04-28}, + year = {2024} +} + @article{dhamija_pan-cancer_2020, abstract = {Nonstop or stop-loss mutations convert a stop into a sense codon, resulting in translation into the 3′ untranslated region as a nonstop extension mutation to the next in-frame stop codon or as a readthrough mutation into the poly-A tail. Nonstop mutations have been characterized in hereditary diseases, but not in cancer genetics. In a pan-cancer analysis, we curated and analysed 3,412 nonstop mutations from 62 tumour entities, generating a comprehensive database at http://NonStopDB.dkfz.de. Six different nonstop extension mutations affected the tumour suppressor SMAD4, extending its carboxy terminus by 40 amino acids. These caused rapid degradation of the SMAD4 mutants via the ubiquitin–proteasome system. A hydrophobic degron signal sequence of ten amino acids within the carboxy-terminal extension was required to induce complete loss of the SMAD4 protein. Thus, we discovered that nonstop mutations can be functionally important in cancer and characterize their loss-of-function impact on the tumour suppressor SMAD4.}, author = {Dhamija, Sonam and Yang, Chul Min and Seiler, Jeanette and Myacheva, Ksenia and Caudron-Herger, Maiwen and Wieland, Angela and Abdelkarim, Mahmoud and Sharma, Yogita and Riester, Marisa and Groß, Matthias and Maurer, Jochen and Diederichs, Sven}, @@ -1046,6 +2676,44 @@ @article{dias_pathogenicity_2022 year = {2022} } +@article{do_carmo_santos_proteomics_2023, + abstract = {Necrosis- and ethylene-inducing proteins are effector molecules of microorganisms able to induce cell death in plant tissues and/or ethylene biosynthesis. The fungus Moniliophthora perniciosa, which causes the witches' broom disease in Theobroma cacao, contains five genes that encode these proteins (MpNep1-5) in its genome. Among these, MpNep2 is the most expressed Nep during disease's development, especially in the necrotic phase. Although widely studied, little is known about the mechanisms by which these proteins induce cell death. In this perspective, the present study aimed to identify potential MpNEP2 target proteins in protein extracts of Theobroma cacao (genotype Catongo) and propose, from the results achieved, mechanisms by which MpNEP2 can induce the process of cell death. Molecular targets captured in vitro by rMpNEP2 immobilized on CNBr-Sepharose were identified by ms/ms. Candidate targets were identified as an Auxin Response Factor, Sphingosine Kinase and a Formin like protein. These proteins are known to participate in important processes in primary metabolism, molecular function and regulation of the plant's response. The targets:MpNEP2 interactions were validated in silico. We discussed the different signaling pathways, membrane modulation and cell cytoskeleton, by which MpNEP2 can act and induce responses in the plant that leads to necrosis.}, + author = {do Carmo Santos, Maria Luíza and dos Santos Lopes, Natasha and Ferreira, Monaliza Macedo and Amaral, Geiseane Velozo and Santos, Ariana Silva and Dias, Cristiano Villela and Pirovani, Carlos Priminho and Alvim, Fátima Cerqueira}, + doi = {10.1016/j.pmpp.2023.101946}, + issn = {0885-5765}, + journal = {Physiological and Molecular Plant Pathology}, + keywords = {{\textgreater}UseGalaxy.eu, Cell death, Molecular docking, NEP2 effector}, + language = {en}, + month = {March}, + pages = {101946}, + title = {Proteomics analysis reveals three potential cacao target that interacts with {Moniliophthora} perniciosa {NEP} during witches broom disease}, + url = {https://www.sciencedirect.com/science/article/pii/S0885576523000012}, + urldate = {2023-03-15}, + volume = {124}, + year = {2023} +} + +@article{donatova_changes_2024, + abstract = {Influenza type A virus (IAV) infection is a major cause of morbidity and mortality during influenza epidemics. Recently, a specific link between IAV infection and neurodegenerative disease progression has been established. The non-structural NS1 protein of IAV regulates viral replication during infection and antagonizes host antiviral responses, contributing to influenza virulence. In the present study, we have prepared a mouse lung-to-lung adapted to the NS1-truncated virus (NS80ad). Transcriptome analysis of the gene expression in the lungs revealed that infection with wild-type A/WSN/33 (WSN), NS80, and NS80ad viruses resulted in different regulation of genes involved in signaling pathways associated with the cell proliferation, inflammatory response, and development of neurodegenerative diseases. NS1 protein did not influence the genes involved in the RIG-I-like receptor signaling pathway in the brains. Lethal infection with IAVs dysregulated expression of proteins associated with the development of neurodegenerative diseases (CX3CL1/Fractalkine, Coagulation factor III, and CD105/Endoglin, CD54/ICAM-1, insulin-like growth factor-binding protein (IGFBP)-2, IGFBP-5, IGFBP-6, chitinase 3-like 1 (CHI3L1), Myeloperoxidase (MPO), Osteopontin (OPN), cystatin C, and LDL R). Transcription of GATA3 mRNA was decreased, and expression of MPO was inhibited in the brain infected with NS80 and NS80ad viruses. In addition, the truncation of NS1 protein led to reduced expression of IGFBP-2, CHI3L1, MPO, and LDL-R proteins in the brains. Our results indicate that the influenza virus influences the expression of proteins involved in brain function, and this might occur mostly through the NS1 protein. These findings suggest that the abovementioned proteins represent a promising target for the development of potentially effective immunotherapy against neurodegeneration.}, + author = {Donátová, Karin and Mladá, Miriam and Lopušná, Katarína and Baran, Filip and Betáková, Tatiana}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25052460}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, NS1 protein, adaptation, brain, immune response, inflammation, influenza virus, neurodegeneration}, + language = {en}, + month = {January}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {2460}, + title = {Changes in the {Expression} of {Proteins} {Associated} with {Neurodegeneration} in the {Brains} of {Mice} after {Infection} with {Influenza} {A} {Virus} with {Wild} {Type} and {Truncated} {NS1}}, + url = {https://www.mdpi.com/1422-0067/25/5/2460}, + urldate = {2024-05-17}, + volume = {25}, + year = {2024} +} + @article{dorn_linc00261_2020, abstract = {Pancreatic adenocarcinoma (PDAC) is one of the major causes of cancer-associated deaths worldwide, with a dismal prognosis that has not significantly changed over the last decades. Transcriptional analysis has provided valuable insights into pancreatic tumorigenesis. Specifically, pancreatic cancer subtypes were identified, characterized by specific mutations and gene expression changes associated with differences in patient survival. In addition to differentially regulated mRNAs, non-coding RNAs, including long non-coding RNAs (lncRNAs), were shown to have subtype-specific expression patterns. Hence, we aimed to characterize prognostic lncRNAs with deregulated expression in the squamous subtype of PDAC, which has the worst prognosis. Extensive in silico analyses followed by in vitro experiments identified long intergenic non-coding RNA 261 (LINC00261) as a downregulated lncRNA in the squamous subtype of PDAC, which is generally associated with transforming growth factor \β (TGF\β) signaling in human cancer cells. Its genomic neighbor, the transcription factor forkhead box protein A2 (FOXA2), regulated LINC00261 expression by direct binding of the LINC00261 promoter. CRISPR-mediated knockdown and promoter knockout validated the importance of LINC00261 in TGF\β-mediated epithelial\–mesenchymal transition (EMT) and established the epithelial marker E-cadherin, an important cell adhesion protein, as a downstream target of LINC00261. Consequently, depletion of LINC00261 enhanced motility and invasiveness of PANC-1 cells in vitro. Altogether, our data suggest that LINC00261 is an important tumor-suppressive lncRNA in PDAC that is involved in maintaining a pro-epithelial state associated with favorable disease outcome.}, author = {Dorn, Agnes and Glaß, Markus and Neu, Carolin T. and Heydel, Beate and Hüttelmaier, Stefan and Gutschner, Tony and Haemmerle, Monika}, @@ -1084,6 +2752,26 @@ @article{dorone_prion-like_2021 year = {2021} } +@article{dossmann_specific_2024, + abstract = {The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.}, + author = {Dossmann, Leonie and Emperle, Max and Dukatz, Michael and de Mendoza, Alex and Bashtrykov, Pavel and Jeltsch, Albert}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s42003-024-06252-z}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, Enzyme mechanisms, Transferases}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--12}, + title = {Specific {DNMT3C} flanking sequence preferences facilitate methylation of young murine retrotransposons}, + url = {https://www.nature.com/articles/s42003-024-06252-z}, + urldate = {2024-05-19}, + volume = {7}, + year = {2024} +} + @article{dugar_chromosomal_2022, author = {Dugar, Gaurav and Hofmann, Andreas and Heermann, Dieter W and Hamoen, Leendert W}, journal = {Nature Genetics}, @@ -1108,6 +2796,47 @@ @article{dvir_uncovering_2021 year = {2021} } +@article{dziuba_silent_2023, + abstract = {Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.}, + author = {Dziuba, M. V. and Paulus, A. and Schramm, L. and Awal, R. P. and Pósfai, M. and Monteil, C. L. and Fouteau, S. and Uebe, R. and Schüler, D.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41396-022-01348-y}, + issn = {1751-7370}, + journal = {The ISME Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial evolution, Bacterial genetics, Microbial ecology}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Nature Publishing Group}, + number = {3}, + pages = {326--339}, + title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium}, + url = {https://www.nature.com/articles/s41396-022-01348-y}, + urldate = {2023-07-31}, + volume = {17}, + year = {2023} +} + +@article{edet_genomic_2024, + abstract = {Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.}, + author = {Edet, Offiong Ukpong and Ubi, Benjamin Ewa and Ishii, Takayoshi}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-61062-x}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Computational biology and bioinformatics, Genetics, Molecular biology, Plant sciences}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {10654}, + title = {Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in {Vigna} unguiculata [{L}] {Walp}}, + url = {https://www.nature.com/articles/s41598-024-61062-x}, + urldate = {2024-05-17}, + volume = {14}, + year = {2024} +} + @article{eggenhofer_cmv_2018, abstract = {SummaryA standard method for the identification of novel RNAs or proteins is homology search via probabilistic models. One approach relies on the definition of families, which can be encoded as covariance models (CMs) or Hidden Markov Models (HMMs). While being powerful tools, their complexity makes it tedious to investigate them in their (default) tabulated form. This specifically applies to the interpretation of comparisons between multiple models as in family clans. The Covariance model visualization tools (CMV) visualize CMs or HMMs to: I) Obtain an easily interpretable representation of HMMs and CMs; II) Put them in context with the structural sequence alignments they have been created from; III) Investigate results of model comparisons and highlight regions of interest.AvailabilitySource code (http://www.github.com/eggzilla/cmv), web-service (http://rna.informatik.uni-freiburg.de/CMVS) Contactegg@informatik.uni-freiburg.de, choener@bioinf.uni-leipzig.deSupplementary informationSupplementary data available online.}, author = {Eggenhofer, Florian and Hofacker, Ivo L. and Backofen, Rolf and Höner zu Siederdissen, Christian and Valencia, Alfonso}, @@ -1122,6 +2851,63 @@ @informatik.uni-freiburg.de year = {2018} } +@incollection{eggenhofer_evolutionary_2024, + abstract = {Effective homology search for non-coding RNAs is frequently not possible via sequence similarity alone. Current methods leverage evolutionary information like structure conservation or covariance scores to identify homologs in organisms that are phylogenetically more distant. In this chapter, we introduce the theoretical background of evolutionary structure conservation and covariance score, and we show hands-on how current methods in the field are applied on example datasets.}, + address = {New York, NY}, + author = {Eggenhofer, Florian and Höner zu Siederdissen, Christian}, + booktitle = {{RNA} {Folding}: {Methods} and {Protocols}}, + doi = {10.1007/978-1-0716-3519-3_11}, + editor = {Lorenz, Ronny}, + isbn = {978-1-07-163519-3}, + keywords = {{\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, Covariance models, Multiple sequence alignment, RNA families, Secondary structure, Unsupervised model construction}, + language = {en}, + pages = {255--284}, + publisher = {Springer US}, + title = {Evolutionary {Structure} {Conservation} and {Covariance} {Scores}}, + url = {https://doi.org/10.1007/978-1-0716-3519-3_11}, + urldate = {2024-05-26}, + year = {2024} +} + +@article{ehle_downregulation_2024, + abstract = {The hepatic acute-phase response is characterized by a massive upregulation of serum proteins, such as haptoglobin and serum amyloid A, at the expense of liver homeostatic functions. Although the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has a well-established role in safeguarding liver function and its cistrome spans around 50\% of liver-specific genes, its role in the acute-phase response has received little attention so far. We demonstrate that HNF4A binds to and represses acute-phase genes under basal conditions. The reprogramming of hepatic transcription during inflammation necessitates loss of HNF4A function to allow expression of acute-phase genes while liver homeostatic genes are repressed. In a pre-clinical liver organoid model overexpression of HNF4A maintained liver functionality in spite of inflammation-induced cell damage. Conversely, HNF4A overexpression potently impaired the acute-phase response by retaining chromatin at regulatory regions of acute-phase genes inaccessible to transcription. Taken together, our data extend the understanding of dual HNF4A action as transcriptional activator and repressor, establishing HNF4A as gatekeeper for the hepatic acute-phase response.}, + author = {Ehle, Charlotte and Iyer-Bierhoff, Aishwarya and Wu, Yunchen and Xing, Shaojun and Kiehntopf, Michael and Mosig, Alexander S. and Godmann, Maren and Heinzel, Thorsten}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s42003-024-06288-1}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Hepatology, Transcription}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--14}, + title = {Downregulation of {HNF4A} enables transcriptomic reprogramming during the hepatic acute-phase response}, + url = {https://www.nature.com/articles/s42003-024-06288-1}, + urldate = {2024-05-19}, + volume = {7}, + year = {2024} +} + +@article{eisenhardt_genotyping_2022, + abstract = {Background: Synovial sarcoma (SS) is a malignant soft tissue tumor of mesenchymal origin that frequently occurs in young adults. Translocation of the SYT gene on chromosome 18 to the SSX genes on chromosome X leads to the formation of oncogenic fusion genes, which lead to initiation and proliferation of tumor cells. The detection and quantification of circulating tumor DNA (ctDNA) can serve as a non-invasive method for diagnostics of local or distant tumor recurrence, which could improve survival rates due to early detection. Methods: We developed a subtype-specific targeted next-generation sequencing (NGS) approach specifically targeting SS t(X;18)(p11;q11), which fuses SS18 (SYT) in chromosome 18 to SSX1 or SSX2 in chromosome x, and recurrent point mutations. In addition, patient-specific panels were designed from tumor exome sequencing. Both approaches were used to quantify ctDNA in patients’ plasma. Results: The subtype-specific assay allowed detection of somatic mutations from 25/25 tumors with a mean of 1.68 targetable mutations. The minimal limit of detection was determined at a variant allele frequency of 0.05\%. Analysis of 29 plasma samples from 15 tumor patients identified breakpoint ctDNA in 6 patients (sensitivity: 40\%, specificity 100\%). The addition of more mutations further increased assay sensitivity. Quantification of ctDNA in plasma samples (n = 11) from one patient collected over 3 years, with a patient-specific panel based on tumor exome sequencing, correlated with the clinical course, response to treatment and tumor volume. Conclusions: Targeted NGS allows for highly sensitive tumor profiling and non-invasive detection of ctDNA in SS patients, enabling non-invasive monitoring of tumor dynamics.}, + author = {Eisenhardt, Anja E. and Brugger, Zacharias and Lausch, Ute and Kiefer, Jurij and Zeller, Johannes and Runkel, Alexander and Schmid, Adrian and Bronsert, Peter and Wehrle, Julius and Leithner, Andreas and Liegl-Atzwanger, Bernadette and Giunta, Riccardo E. and Eisenhardt, Steffen U. and Braig, David}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cancers14092078}, + issn = {2072-6694}, + journal = {Cancers}, + keywords = {{\textgreater}UseGalaxy.eu, circulating tumor DNA, ctDNA, diagnostic biomarker, liquid biopsy, next-generation sequencing, soft tissue sarcoma, synovial sarcoma, targeted sequencing}, + language = {en}, + month = {January}, + number = {9}, + pages = {2078}, + title = {Genotyping of {Circulating} {Free} {DNA} {Enables} {Monitoring} of {Tumor} {Dynamics} in {Synovial} {Sarcomas}}, + url = {https://www.mdpi.com/2072-6694/14/9/2078}, + urldate = {2022-09-24}, + volume = {14}, + year = {2022} +} + @article{emperle_mutations_2019, abstract = {Abstract. Somatic DNMT3A mutations at R882 are frequently observed in AML patients including the very abundant R882H, but also R882C, R882P and R882S. Using de}, author = {Emperle, Max and Adam, Sabrina and Kunert, Stefan and Dukatz, Michael and Baude, Annika and Plass, Christoph and Rathert, Philipp and Bashtrykov, Pavel and Jeltsch, Albert}, @@ -1136,6 +2922,58 @@ @article{emperle_mutations_2019 year = {2019} } +@article{emser_mitochondrial_2023, + abstract = {Heterothermic thermoregulation requires intricate regulation of metabolic rate and activation of pro-survival factors. Eliciting these responses and coordinating the necessary energy shifts likely involves retrograde signalling by mitochondrial-derived peptides (MDPs). Members of the group were suggested before to play a role in heterothermic physiology, a key component of hibernation and daily torpor. Here we studied the mitochondrial single-nucleotide polymorphism (SNP) m.3017C{\textgreater}T that resides in the evolutionarily conserved gene MT-SHLP6. The substitution occurring in several mammalian orders causes truncation of SHLP6 peptide size from twenty to nine amino acids. Public mass spectrometric (MS) data of human SHLP6 indicated a canonical size of 20 amino acids, but not the use of alternative translation initiation codons that would expand the peptide. The shorter isoform of SHLP6 was found in heterothermic rodents at higher frequency compared to homeothermic rodents (p {\textless} 0.001). In heterothermic mammals it was associated with lower minimal body temperature (Tb, p {\textless} 0.001). In the thirteen-lined ground squirrel, brown adipose tissue—a key organ required for hibernation, showed dynamic changes of the steady-state transcript level of mt-Shlp6. The level was significantly higher before hibernation and during interbout arousal and lower during torpor and after hibernation. Our finding argues to further explore the mode of action of SHLP6 size isoforms with respect to mammalian thermoregulation and possibly mitochondrial retrograde signalling.}, + author = {Emser, Sarah V. and Spielvogel, Clemens P. and Millesi, Eva and Steinborn, Ralf}, + issn = {1664-042X}, + journal = {Frontiers in Physiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Mitochondrial polymorphism m.{3017C}{\textgreater}{T} of {SHLP6} relates to heterothermy}, + url = {https://www.frontiersin.org/articles/10.3389/fphys.2023.1207620}, + urldate = {2023-08-30}, + volume = {14}, + year = {2023} +} + +@article{ereqat_association_2022, + abstract = {Apolipoprotein E ({\textless}em{\textgreater}APOE{\textless}/em{\textgreater}) is a key regulator of lipoprotein metabolism, and consequently, affects the plasma and tissue lipid contents. The aim of the present study was to investigate the parallel effects of {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} genetic variants and promoter methylation levels of six CpGs on the risk of diabetic dyslipidemia. A total of 204 Palestinian type 2 diabetes (T2D) patients (mean age ± SD: 62.7±10.2) were enrolled in the present study (n=96 with dyslipidemia and n=108 without dyslipidemia). Next generation sequencing was performed to analyze five single nucleotide polymorphisms: Two variants rs7412 and rs429358 that determine {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} ε alleles, and three variants in the promoter region (rs769446, rs449647, and rs405509). For all subjects, the most common genotype was ε3/ε3 (79.4\%). No statistical differences were observed in the {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} ε polymorphisms and the three promoter variants among T2D patients with and without dyslipidemia (P\>0.05). A comparison of lipid parameters between ε3/ε3 subjects and ε4 carriers in both groups revealed no significant differences in the mean values of LDL‑C, HDL‑C, TG, and TC levels (P\>0.05). Six CpG sites in the {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} promoter on chromosome 19:44905755‑44906078 were identified, and differential DNA methylation in these CpGs were observed between the study groups. Logistic regression analysis revealed a significant association of DNA methylation level at the six CpGs with an increased risk of diabetic dyslipidemia (odds ratio, 1.038; 95\% confidence interval, 1.012‑1.064; P=0.004). In conclusion, the present study revealed that DNA methylation levels in six CpGs in the {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} promoter region was associated with the risk of diabetic dyslipidemia independently of the {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} ε4 variant which could be a potential therapeutic target to reverse the methylation of the {\textless}em{\textgreater}APOE{\textless}/em{\textgreater} promoter.}, + author = {Ereqat, Suheir and Cauchi, Stéphane and Eweidat, Khaled and Elqadi, Muawiyah and Ghatass, Manal and Sabarneh, Anas and Nasereddin, Abedelmajeed}, + doi = {10.3892/br.2022.1544}, + issn = {2049-9434}, + journal = {Biomedical Reports}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + month = {July}, + note = {Publisher: Spandidos Publications}, + number = {1}, + pages = {1--10}, + title = {Association of {DNA} methylation and genetic variations of the {\textless}em{\textgreater}{APOE}{\textless}/em{\textgreater} gene with the risk of diabetic dyslipidemia}, + url = {https://www.spandidos-publications.com/10.3892/br.2022.1544}, + urldate = {2022-09-24}, + volume = {17}, + year = {2022} +} + +@article{esha_exploring_2023, + abstract = {The present investigation utilized in silico methodologies to explore the diverse pharmacological activities, toxicity profiles, and chemical reactivity of a series of fluoro-flavonoid compounds (1–14), which are secondary metabolites of plants known for their broad range of biological effects. A comprehensive strategy is utilized, incorporating methods such as prediction of activity spectra for substances (PASS) prediction, absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessments, and density functional theory (B3LYP) calculations using three basis sets: 6-31G(d,p), 6-311G(d,p), and 6-311++G(d,p). Furthermore, the study employed molecular docking technique to identify target proteins, including HER2 (7JXH), EGFR (4UV7), FPPS (1YQ7), HPGDS (1V40), DCK (1P60), and KEAP1 on Nrf2 (1X2J), for the investigated compounds, with cianidanol and genistein serving as reference drugs for the docking process. The investigated fluoro-flavonoid compounds exhibited significantly greater binding affinities (ranging from −8.3 to −10.6 kcal mol−1) toward HER2, HPGDS, and KEAP1 compared to the reference drugs, cianidanol and genistein, which displayed binding affinities ranging from −8.4 to −9.4 kcal mol−1. Furthermore, molecular dynamics simulations were conducted to assess the stability of the protein-ligand interaction, using the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), Radius of gyration (Rg) parameters and principle component analysis (PCA). Among the tested fluoro-flavonoid analogs, analog 11 showed a RMSD value of .15 nm with the HER2 protein target, indicating a stable interaction. Based on in silico results, it appears that the fluoro-flavonoid compound 11 has the potential to serve as a targeted anti-lung cancer drug. However, additional in vivo and in vitro studies are necessary to confirm this hypothesis.}, + author = {Esha, Nusrat Jahan Ikbal and Quayum, Syeda Tasnim and Saif, Minhaz Zabin and Almatarneh, Mansour H. and Rahman, Shofiur and Alodhayb, Abdullah and Poirier, Raymond A. and Uddin, Kabir M.}, + copyright = {© 2023 Wiley Periodicals LLC.}, + doi = {10.1002/qua.27274}, + issn = {1097-461X}, + journal = {International Journal of Quantum Chemistry}, + keywords = {{\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, ADMET, DFT, MD simulation, PASS, fluoro-flavonoid, molecular docking}, + language = {en}, + month = {November}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.27274}, + number = {n/a}, + pages = {e27274}, + shorttitle = {Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents}, + title = {Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents: {DFT}, molecular docking, and molecular dynamics techniques}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.27274}, + urldate = {2023-11-14}, + volume = {n/a}, + year = {2023} +} + @article{espenshade_influence_2019, abstract = {The aerial surfaces of plants harbour diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterised the epiphytic microbial communities on leaves of Platanus x hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city centre compared to the natural site, and also more human-associated genera were found colonising the leaves from the city centre. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.}, author = {Espenshade, Jordan and Thijs, Sofie and Gawronski, Stanislaw and Bové, Hannelore and Weyens, Nele and Vangronsveld, Jaco}, @@ -1279,6 +3117,44 @@ @article{fallmann_rna_2019 year = {2019} } +@article{farias_basidin_2023, + abstract = {The fungus Moniliophthora perniciosa secretes protein effectors that manipulate the physiology of the host plant, but few effectors of this fungus have had their functions confirmed. We performed functional characterization of a promising candidate effector of M. perniciosa. The inoculation of rBASIDIN at 4 µmol L−1 in the mesophyll of leaflets of Solanum lycopersicum caused symptoms of shriveling within 6 h without the presence of necrosis. However, when sprayed on the plant at a concentration of 11 µmol L−1, it caused wilting symptoms only 2 h after application, followed by necrosis and cell death at 48 h. rBASIDIN applied to Theobroma cacao leaves at the same concentration caused milder symptoms. rBASIDIN caused hydrogen peroxide production in leaf tissue, damaging the leaf membrane and negatively affecting the photosynthetic rate of Solanum lycopersicum plants. Phylogenetic analysis indicated that BASIDIN has orthologs in other phytopathogenic basidiomycetes. Analysis of the transcripts revealed that BASIDIN and its orthologs are expressed in different fungal species, suggesting that this protein is differentially regulated in these basidiomycetes. Therefore, the results of applying BASIDIN allow the inference that it is an effector of the fungus M. perniciosa, with a strong potential to interfere in the defense system of the host plant.}, + author = {Farias, Keilane Silva and Ferreira, Monaliza Macêdo and Amaral, Geiseane Veloso and Zugaib, Maria and Santos, Ariana Silva and Gomes, Fábio Pinto and Rezende, Rachel Passos and Gramacho, Karina Peres and Aguiar, Eric Roberto Guimarães Rocha and Pirovani, Carlos Priminho}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms241411714}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Theobroma cacao}, {\textgreater}UseGalaxy.eu, basidiomycetes, effectors, hypersensitivity response, witche’s broom}, + language = {en}, + month = {January}, + note = {Number: 14 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {14}, + pages = {11714}, + title = {{BASIDIN} as a {New} {Protein} {Effector} of the {Phytopathogen} {Causing} {Witche}’s {Broom} {Disease} in {Cocoa}}, + url = {https://www.mdpi.com/1422-0067/24/14/11714}, + urldate = {2023-07-31}, + volume = {24}, + year = {2023} +} + +@article{farmiloe_structural_2023, + abstract = {Krüppel-associated box (KRAB) zinc finger proteins (KZNFs) recognize and repress transposable elements (TEs); TEs are DNA elements that are capable of replicating themselves throughout our genomes with potentially harmful consequences. However, genes from this family of transcription factors have a much wider potential for genomic regulation. KZNFs have become integrated into gene-regulatory networks through the control of TEs that function as enhancers and gene promoters; some KZNFs also bind directly to gene promoters, suggesting an additional, more direct layer of KZNF co-option into gene-regulatory networks. Binding site analysis of ZNF519, ZNF441, and ZNF468 suggests the structural evolution of KZNFs to recognize TEs can result in coincidental binding to gene promoters independent of TE sequences. We show a higher rate of sequence turnover in gene promoter KZNF binding sites than neighboring regions, implying a selective pressure is being applied by the binding of a KZNF. Through CRISPR/Cas9 mediated genetic deletion of ZNF519, ZNF441, and ZNF468, we provide further evidence for genome-wide co-option of the KZNF-mediated gene-regulatory functions; KZNF knockout leads to changes in expression of KZNF-bound genes in neuronal lineages. Finally, we show that the opposite can be established upon KZNF overexpression, further strengthening the support for the role of KZNFs as bona-fide gene regulators. With no eminent role for ZNF519 in controlling its TE target, our study may provide a snapshot into the early stages of the completed co-option of a KZNF, showing the lasting, multilayered impact that retrovirus invasions and host response mechanisms can have upon the evolution of our genomes.}, + author = {Farmiloe, Grace and van Bree, Elisabeth J and Robben, Stijn F and Janssen, Lara J M and Mol, Lisa and Jacobs, Frank M J}, + doi = {10.1093/gbe/evad184}, + issn = {1759-6653}, + journal = {Genome Biology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {November}, + number = {11}, + pages = {evad184}, + title = {Structural {Evolution} of {Gene} {Promoters} {Driven} by {Primate}-{Specific} {KRAB} {Zinc} {Finger} {Proteins}}, + url = {https://doi.org/10.1093/gbe/evad184}, + urldate = {2023-11-22}, + volume = {15}, + year = {2023} +} + @article{farmiloe_widespread_2020, abstract = {The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome.This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.}, author = {Farmiloe, Grace and Lodewijk, Gerrald A. and Robben, Stijn F. and van Bree, Elisabeth J. and Jacobs, Frank M. J.}, @@ -1296,6 +3172,43 @@ @article{farmiloe_widespread_2020 year = {2020} } +@article{farrell_detection_2022, + abstract = {Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA – the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that noninvasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g., biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.}, + author = {Farrell, Jessica A. and Whitmore, Liam and Mashkour, Narges and Rollinson Ramia, Devon R. and Thomas, Rachel S. and Eastman, Catherine B. and Burkhalter, Brooke and Yetsko, Kelsey and Mott, Cody and Wood, Larry and Zirkelbach, Bette and Meers, Lucas and Kleinsasser, Pat and Stock, Sharon and Libert, Elizabeth and Herren, Richard and Eastman, Scott and Crowder, Whitney and Bovery, Caitlin and Anderson, David and Godfrey, David and Condron, Nancy and Duffy, David J.}, + doi = {10.1111/1755-0998.13617}, + issn = {1755-0998}, + journal = {Molecular Ecology Resources}, + keywords = {{\textgreater}UseGalaxy.eu, ChHV5, endangered species, environmental DNA (eDNA), pathogens, population genetics/genomics, population monitoring, sea turtles}, + language = {en}, + number = {7}, + pages = {2471--2493}, + title = {Detection and population genomics of sea turtle species via noninvasive environmental {DNA} analysis of nesting beach sand tracks and oceanic water}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13617}, + urldate = {2022-09-24}, + volume = {22}, + year = {2022} +} + +@article{fatima_book_2023, + abstract = {The publication contains abstracts submitted to the\ 1st Colloquium on Bioinformatics Learning, Education and Training in the categories of oral presentations, poster presentations, keynote speeches and training workshops.}, + author = {Fatima, Ayesha and Khan, Mohammad Asif}, + copyright = {http://creativecommons.org/licenses/by/4.0/}, + doi = {10.7490/f1000research.1119358.1}, + journal = {F1000Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + note = {Number: 70 +Publisher: F1000 Research Limited}, + number = {70}, + pages = {70}, + title = {Book of {Abstracts} of the 1st {Colloquium} for {Bioinformatics} {Learning}, {Education}, and {Training}}, + url = {https://f1000research.com/documents/12-70}, + urldate = {2023-03-15}, + volume = {12}, + year = {2023} +} + @article{feldker_genome-wide_2020, abstract = {Abstract Invasion, metastasis and therapy resistance are the major cause of cancer-associated deaths, and the EMT-inducing transcription factor ZEB1 is a crucial stimulator of these processes. While work on ZEB1 has mainly focused on its role as a transcriptional repressor, it can also act as a transcriptional activator. To further understand these two modes of action, we performed a genome-wide ZEB1 binding study in triple-negative breast cancer cells. We identified ZEB1 as a novel interactor of the AP-1 factors FOSL1 and JUN and show that, together with the Hippo pathway effector YAP, they form a transactivation complex, predominantly activating tumour-promoting genes, thereby synergising with its function as a repressor of epithelial genes. High expression of ZEB1, YAP, FOSL1 and JUN marks the aggressive claudin-low subtype of breast cancer, indicating the translational relevance of our findings. Thus, our results link critical tumour-promoting transcription factors: ZEB1, AP-1 and Hippo pathway factors. Disturbing their molecular interaction may provide a promising treatment option for aggressive cancer types.}, author = {Feldker, Nora and Ferrazzi, Fulvia and Schuhwerk, Harald and Widholz, Sebastian A and Guenther, Kerstin and Frisch, Isabell and Jakob, Kathrin and Kleemann, Julia and Riegel, Dania and Bönisch, Ulrike and Lukassen, Sören and Eccles, Rebecca L and Schmidl, Christian and Stemmler, Marc P and Brabletz, Thomas and Brabletz, Simone}, @@ -1339,6 +3252,27 @@ @article{feng_scarless_2021 year = {2021} } +@article{feng_transcription_2022, + abstract = {In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which are specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, the precursors to the adult legs and ventral body regions, show that {\textasciitilde}8\% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, the homeodomain protein Distal-less (Dll) enhances Scr binding to a different subset of loci. These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors.}, + author = {Feng, Siqian and Rastogi, Chaitanya and Loker, Ryan and Glassford, William J. and Tomas Rube, H. and Bussemaker, Harmen J. and Mann, Richard S.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41467-022-31501-2}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Experimental organisms, Molecular biology}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {3808}, + title = {Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors}, + url = {https://www.nature.com/articles/s41467-022-31501-2}, + urldate = {2023-08-06}, + volume = {13}, + year = {2022} +} + @phdthesis{fernandes_guavadb_2020, author = {Fernandes, Miquéias}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, @@ -1349,6 +3283,87 @@ @phdthesis{fernandes_guavadb_2020 year = {2020} } +@article{fernandez-diaz_draft_2023, + abstract = {This study presents a draft genome sequence of a Newcastle disease virus (NDV) strain (VFAR-136) isolated from a fighting cock (Gallus gallus) in the south of Peru. Strain VFAR-136 is a new report of NDV genotype VII circulating in Peru.}, + author = {Fernández-Díaz, Manolo and Montalván-Avalos, Angela and Isasi-Rivas, Gisela and Villanueva-Pérez, Doris and Quiñones-Garcia, Stefany and Tataje-Lavanda, Luis and Rios-Matos, Dora and Lulo-Vargas, Milagros and Fernández-Sánchez, Manolo and Guevara-Sarmiento, Luis A. and Zimic, Mirko and Rojas-Neyra, Aldo and Calderón, Katherine}, + doi = {10.1128/mra.01293-22}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: American Society for Microbiology}, + number = {2}, + pages = {e01293--22}, + title = {Draft {Genome} {Sequence} of an {Isolate} of {Genotype} {VII} {Newcastle} {Disease} {Virus} {Isolated} from an {Outbreak} in {Fighting} {Cock} in {Peru}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01293-22}, + urldate = {2023-03-15}, + volume = {12}, + year = {2023} +} + +@article{ferreira_avaliacao_2023, + abstract = {Infertility is linked to different functions of male gametes, one of which is +caused by impaired motility due to anomalies in sperm flagella. Several genetic +defects culminate in the loss of fertility when viewed from an evolutionary +perspective, where sperm flagellar function is extremely conserved across all +kingdoms. The model moss Physcomitrium patens has genes copies homologous to +human that are related to the architecture of microtubules that enable sperm motility. +The moss P. patens has been an important model system for studying issues of +evolutionary and developmental biology, as well as being an excellent model for +studies of cellular reprogramming, in addition to collaborating with studies of +flagellated organisms from various domains of biodiversity. Although the genes +involved in the process of organogenesis of the reproductive structures of mosses +are still little explored, it is believed that these may be involved in the construction of +the motility of the flagellum and other elements of the architecture of the tissues and +organs involved in evolution. Based on this hypothesis, our objective is to identify the +genes responsible for the differentiation of reproductive structures and how these +can identify problems in the formation of Organs reproductive organs of mosses. To +achieve the objectives, a differential gene expression analysis was carried out with +the aid of data obtained in the RNA-Seq technique. The reads used were obtained +from the NCBI (National Center for Biotechnology Information) database, on the +Sequence Reads Archives (SRA) platform SRR19502729, SRR19502730, +SRR19502731, SRR19502732, SRR19502733, SRR19502734, SRR4454535 and +SRR9901085. The raw reads were filtered by size and quality (Phred-Score 28) and +then analyzed for transcript counts and differential gene expression analysis (DEGs) +using the Salmon tool. As a result, the genes Pp3c10\_9456v3.1, Pp3c17\_1640V3.1 +and Pp3c17\_13470V3.1 were identified as possible genes involved in the sexual +differentiation between sexual organs of moss, where these genes are +over-expressed when there is formation of antheridia and under-expressed when +there is formation of antheridia. archegoniums. Through the analysis of gene function +and ontology, it was observed that the Pp3c10\_9456v3.1 gene is responsible for the +determination of symmetry, morphogenesis of the anatomical structure, assembly of +cellular components and development of organs in P. patens, being an ideal target +for tests of gene knockout to validate its role in the differentiation of reproductive +organs in this plant.}, + author = {Ferreira, Tiego}, + copyright = {Acesso Aberto}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {por}, + month = {February}, + note = {Accepted: 2023-05-25T16:42:56Z +Publisher: Universidade Federal do Pampa}, + title = {Avaliação da expressão diferencial em {Physcomitrium} patens na busca das adaptações moleculares responsivas na arquitetura dos órgãos reprodutivos}, + url = {https://repositorio.unipampa.edu.br/jspui/handle/riu/8369}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{ferreira_tcserpin_2024, + abstract = {{\textless}p{\textgreater}In plants, serpins are a superfamily of serine and cysteine protease inhibitors involved in stress and defense mechanisms, with potential for controlling agricultural pests, making them important biotechnological tools. The objective of this study was to characterize a serpin from {\textless}italic{\textgreater}Theobroma cacao{\textless}/italic{\textgreater}, called TcSERPIN, to identify its endogenous targets and determine its function and biotechnological potential. TcSERPIN has 390 amino acid residues and shows conservation of the main active site, RCL. Cis-elements related to light, stress, hormones, anaerobic induction, cell cycle regulation and defense have been identified in the gene’s regulatory region. TcSERPIN transcripts are accumulated in different tissues of {\textless}italic{\textgreater}Theobroma cacao{\textless}/italic{\textgreater}. Furthermore, in plants infected with {\textless}italic{\textgreater}Moniliophtora perniciosa{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}Phytophthora palmivora{\textless}/italic{\textgreater}, the expression of TcSERPIN was positively regulated. The protein spectrum, rTcSERPIN, reveals a typical β-sheet pattern and is thermostable at pH 8, but loses its structure with temperature increases above 66°C at pH 7. At the molar ratios of 0.65 and 0.49, rTcSERPIN inhibited 55 and 28\% of the activity of papain from {\textless}italic{\textgreater}Carica papaya{\textless}/italic{\textgreater} and trypsin from {\textless}italic{\textgreater}Sus scrofa{\textless}/italic{\textgreater}, respectively. The protease trap containing immobilized rTcSERPIN captured endogenous defense proteins from cocoa extracts that are related to metabolic pathways, stress and defense. The evaluation of the biotechnological potential against geohelminth larvae showed that rTcSERPIN and rTcCYS4 ({\textless}italic{\textgreater}Theobroma cacao{\textless}/italic{\textgreater} cystatin 4) reduced the movement of larvae after 24 hours. The results of this work show that TcSERPIN has ideal biochemical characteristics for biotechnological applications, as well as potential for studies of resistance to phytopathogens of agricultural crops.{\textless}/p{\textgreater}}, + author = {Ferreira, Monaliza Macêdo and Farias, Keilane Silva and Zugaib, Maria and Alves, Akyla Maria Martins and Amaral, Geiseane Velozo and Santos, Maria Luíza do Carmo and Freitas, Andria dos Santos and Santana, Brenda Conceição Guimarães and dos Santos Júnior, Sérgio Liberato and Mora-Ocampo, Irma Yuliana and Santos, Ariana Silva and da Silva, Marcelo Fernandes and Andrade, Bruno Silva and Pirovani, Carlos Priminho}, + doi = {10.3389/fpls.2024.1337750}, + issn = {1664-462X}, + journal = {Frontiers in Plant Science}, + keywords = {{\textgreater}UseGalaxy.eu, Inglês (Estados Unidos) Inglês (Estados Unidos) Formatado: Inglês (Estados Unidos), Protease Inhibitors, Serpin, stress and defense Fonte: Itálico, theobroma cacao, thermostability}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {{TcSERPIN}, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens}, + url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1337750/full}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + @article{fiedler_taxonomic_2021, author = {Fiedler, Gregor and Herbstmann, Anna-Delia and Doll, Etienne and Wenning, Mareike and Brinks, Erik and Kabisch, Jan and Breitenwieser, Franziska and Lappann, Martin and Böhnlein, Christina and Franz, Charles M. A. P.}, doi = {10.3390/microorganisms9020246}, @@ -1363,6 +3378,75 @@ @article{fiedler_taxonomic_2021 year = {2021} } +@article{figiel_zinc_2023, + abstract = {Human protein Yin Yang 1 (YY1) controls the transcription of hundreds of genes both positively and negatively through interactions with a wide range of partner proteins. Results presented here from proteolytic sensitivity, calorimetry, circular dichroism, fluorescence, NMR, size-exclusion chromatography, SELEX, and EMSA show that purified YY1 forms dimers via its disordered N-terminal region with strong zinc-ion concentration dependence. The YY1 dimer is shown to bind tandem repeats of a canonical recognition DNA sequence with high affinity, and analysis of human YY1 regulatory sites shows that many contain repeats of its recognition elements. YY1 dimerization may compete with partner protein interactions, making control by zinc ion concentration a previously unrecognized factor affecting YY1 gene regulation. Indeed, YY1 is known to be important in many pathogenic processes, including neoplasia, in which zinc ion concentrations are altered. The present results incentivize studies in vivo or in vitro that explore the role of zinc ion concentration in YY1-mediated gene expression.}, + author = {Figiel, Małgorzata and Szubert, Filip and Luchinat, Enrico and Bonarek, Piotr and Baranowska, Anna and Wajda-Nikiel, Katarzyna and Wilamowski, Mateusz and Miłek, Piotr and Dziedzicka-Wasylewska, Marta and Banci, Lucia and Górecki, Andrzej}, + doi = {10.1016/j.bbagrm.2022.194905}, + issn = {1874-9399}, + journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, + keywords = {{\textgreater}UseGalaxy.eu, DNA binding, Dimerization, Intrinsically disordered protein, Yin Yang 1, Zinc-binding}, + language = {en}, + month = {March}, + number = {1}, + pages = {194905}, + title = {Zinc controls operator affinity of human transcription factor {YY1} by mediating dimerization via its {N}-terminal region}, + url = {https://www.sciencedirect.com/science/article/pii/S1874939922001201}, + urldate = {2023-03-15}, + volume = {1866}, + year = {2023} +} + +@article{fischer_expanding_2024, + abstract = {Recombinant adenoviruses are widely used in clinical and laboratory applications. Despite the wide variety of available sero- and genotypes, only a fraction is utilized in vivo. As adenoviruses are a large group of viruses, displaying many different tropisms, immune epitopes, and replication characteristics, the merits of translating these natural benefits into vector applications are apparent. This translation, however, proves difficult, since while research has investigated the application of these viruses, there are no universally applicable rules in vector design for non-classical adenovirus types. In this paper, we describe a generalized workflow that allows vectorization, rescue, and cloning of all adenoviral species to enable the rapid development of new vector variants. We show this using human and simian adenoviruses, further modifying a selection of them to investigate their gene transfer potential and build potential vector candidates for future applications.}, + author = {Fischer, Julian and Fedotova, Ariana and Bühler, Clara and Darriba, Laura and Schreiner, Sabrina and Ruzsics, Zsolt}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/v16050658}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, human adenoviruses, mutagenesis of viral genomes, replication-competent vectors, transgene insertion sites, viral bacmids}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {658}, + title = {Expanding the {Scope} of {Adenoviral} {Vectors} by {Utilizing} {Novel} {Tools} for {Recombination} and {Vector} {Rescue}}, + url = {https://www.mdpi.com/1999-4915/16/5/658}, + urldate = {2024-05-17}, + volume = {16}, + year = {2024} +} + +@article{fischer_peptide-mediated_2023, + abstract = {Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (kD = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.}, + author = {Fischer, Sabrina and Trinh, Van Tuan and Simon, Clara and Weber, Lisa M. and Forné, Ignasi and Nist, Andrea and Bange, Gert and Abendroth, Frank and Stiewe, Thorsten and Steinchen, Wieland and Liefke, Robert and Vázquez, Olalla}, + doi = {10.1016/j.chembiol.2023.05.012}, + issn = {2451-9456}, + journal = {Cell Chemical Biology}, + keywords = {{\textgreater}UseGalaxy.eu, EPOP, Elongin BC, VHL, apoptosis, cancer, peptide inhibition, proliferation, protein-protein interactions}, + language = {en}, + month = {July}, + number = {7}, + pages = {766--779.e11}, + title = {Peptide-mediated inhibition of the transcriptional regulator {Elongin} {BC} induces apoptosis in cancer cells}, + url = {https://www.sciencedirect.com/science/article/pii/S2451945623001551}, + urldate = {2023-07-31}, + volume = {30}, + year = {2023} +} + +@article{flores_orozco_evaluation_2024, + abstract = {Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50\% and MGEs by over 65\%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus), and Pseudomonadota (e.g., Acinetobacter, Comamonas) with these AMR elements. The decline in the abundance of aerobic and facultative anaerobes likely linked to hydrolytic functions was suggested as one of the main drivers of the changes in resistomes and mobilomes. The proximity of toxin-antitoxin systems and transposon structures to specific ARGs (e.g., Erm, tet, Ant(6)-la) was discovered, which could explain the persistence of such ARGs in digestates. The study of the effects of other manure treatments, such as aerobic storage in an open tank and solid-liquid separation, revealed that they are less efficient in reducing ARGs and MGEs from manures than AD. In this study, the high levels of ARGs and genes conferring resistance to heavy metals in a farm operating in an antibiotic-free environment suggested that other antimicrobials, such as foot bathing solutions, may be causing the indirect selection of ARGs. Overall, this research made several contributions to understanding AMR in the context of anaerobic digestion of animal manure that could be extrapolated to other manure treatments. These contributions not only bridge existing gaps in the literature but also pave the way for future research, providing valuable insights that can be used to inform the development of more effective strategies to mitigate the dissemination of AMR associated with manure management, application, and disposal.}, + author = {Flores Orozco, Daniel}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {May}, + title = {Evaluation of the long-term effects of anaerobic digestion on bovine manure resistomes and mobilomes and the molecular and microbial mechanisms involved}, + url = {http://hdl.handle.net/1993/38247}, + urldate = {2024-06-07}, + year = {2024} +} + @article{foll_accessible_2019, abstract = {AbstractBackground. Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial}, author = {Föll, Melanie Christine and Moritz, Lennart and Wollmann, Thomas and Stillger, Maren Nicole and Vockert, Niklas and Werner, Martin and Bronsert, Peter and Rohr, Karl and Grüning, Björn Andreas and Schilling, Oliver}, @@ -1404,6 +3488,24 @@ @article{foll_moving_2021 year = {2021} } +@article{formenti_gfastats_2022, + abstract = {With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.Gfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates.Supplementary data are available at Bioinformatics online.}, + author = {Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Cristóbal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D}, + doi = {10.1093/bioinformatics/btac460}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {17}, + pages = {4214--4216}, + shorttitle = {Gfastats}, + title = {Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs}, + url = {https://doi.org/10.1093/bioinformatics/btac460}, + urldate = {2022-09-24}, + volume = {38}, + year = {2022} +} + @article{forth_highly_2019, abstract = {Library preparation is a crucial step in next-generation sequencing workflows. Key determinants of successful library preparation are the available amount of input DNA and the efficiency of the conversion of this DNA into functional library molecules. While the standard blunt-end ligation protocol for Ion Torrent libraries has a theoretical maximum efficiency of 25\%, Y-adapters enable highly efficient library preparation by (i) sticky-end ligation and (ii) rendering both DNA strands functional for sequencing, hence resulting in a theoretical efficiency of up to 100\%. Moreover, the generation of adapter dimers is reduced. Therefore, we designed, optimized and validated Y-adapters compatible with Ion Torrent sequencing. These facilitate higher library yields combined with overall high sequencing performance regarding the key characteristics read-length, base quality, and library complexity.}, author = {Forth, Leonie F and Höper, Dirk}, @@ -1465,8 +3567,29 @@ @article{friedrich_tryptophan_2021 year = {2021} } -@article{gaafar_novel_2020, - abstract = {Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.}, +@article{frohlich_benchmarking_2022, + abstract = {Numerous software tools exist for data-independent acquisition (DIA) analysis of clinical samples, necessitating their comprehensive benchmarking. We present a benchmark dataset comprising real-world inter-patient heterogeneity, which we use for in-depth benchmarking of DIA data analysis workflows for clinical settings. Combining spectral libraries, DIA software, sparsity reduction, normalization, and statistical tests results in 1428 distinct data analysis workflows, which we evaluate based on their ability to correctly identify differentially abundant proteins. From our dataset, we derive bootstrap datasets of varying sample sizes and use the whole range of bootstrap datasets to robustly evaluate each workflow. We find that all DIA software suites benefit from using a gas-phase fractionated spectral library, irrespective of the library refinement used. Gas-phase fractionation-based libraries perform best against two out of three reference protein lists. Among all investigated statistical tests non-parametric permutation-based statistical tests consistently perform best.}, + author = {Fröhlich, Klemens and Brombacher, Eva and Fahrner, Matthias and Vogele, Daniel and Kook, Lucas and Pinter, Niko and Bronsert, Peter and Timme-Bronsert, Sylvia and Schmidt, Alexander and Bärenfaller, Katja and Kreutz, Clemens and Schilling, Oliver}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41467-022-30094-0}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Data processing, Mass spectrometry, Proteomics}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {2622}, + title = {Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity}, + url = {https://www.nature.com/articles/s41467-022-30094-0}, + urldate = {2022-11-06}, + volume = {13}, + year = {2022} +} + +@article{gaafar_novel_2020, + abstract = {Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.}, author = {Gaafar, Yahya Zakaria Abdou and Ziebell, Heiko}, doi = {10.7717/peerj.10096}, issn = {2167-8359}, @@ -1484,6 +3607,88 @@ @article{gaafar_novel_2020 year = {2020} } +@article{gains_identification_2023, + abstract = {Objective +The study aimed to investigate the role of the PGN2012 gene of the periodontitis contributing pathobiont Porphyromonas gingivalis. PGN2012 is a homolgue of TolC and is a gene our group previously showed was overexpressed in hyperinvasive cells. +Methods +The study used a combination of bioinformatics, knockout mutagenesis, growth experiments, biofilm assays and human cell invation assays to investigate PGN2012 function. +Results +Bioinformatics identified that PGN2012 is part of one of four TolC containing gene loci in P. gingivalis that we predicted may encode a metal resistance RND family tripartite pump, similar to those present in other Gram-negative bacteria, but which are not well understood in anaerobic bacteria. A ΔPGN2012 deletion displayed slightly reduced growth in liquid culture but did not effect biofilm formation or human cell invasion. When metal ions were included in the medium the mutant displayed significantly increased sensitivity to the divalent metal ions Zn2+ (500 μM), Co2+ (2 mM), and Cd2+(0.1 mM) but not Cu2+. +Conclusions +We propose to rename the PGN2012-2014 genes czcCBA, which we suggest plays a role in intracellular stress resistance where zinc is often employed by host cells in antibacterial defence with implications for chronic infection in humans.}, + author = {Gains, A. F. and Lambert, D. W. and Stafford, G. P.}, + doi = {10.1016/j.anaerobe.2023.102696}, + issn = {1075-9964}, + journal = {Anaerobe}, + keywords = {{\textgreater}UseGalaxy.eu, Efflux, Metal transport, Periodontitis}, + language = {en}, + month = {April}, + pages = {102696}, + title = {Identification of a {Czc}-like operon of the periodontal pathobiont {P}. gingivalis involved in metal ion efflux}, + url = {https://www.sciencedirect.com/science/article/pii/S1075996423000057}, + urldate = {2023-03-15}, + volume = {80}, + year = {2023} +} + +@article{galgano_pilot_2023, + abstract = {The indiscriminate use of antimicrobials in poultry farms is linked to the increase in multi-resistant bacteria. Accordingly, based on the antimicrobial properties of Thyme Essential Oil (TEO), the present study evaluated the effects of TEO on the reduction of common microbial contaminants and Salmonella on poultry litter. A litter bulk sample was collected in a broiler farm and qualitative/quantitative investigations identified Escherichia coli and Mammaliicoccus lentus. The experimental contamination with Salmonella Derby wild strain was also performed. All pathogens showed phenotypic and genotypic resistance to different classes of antibiotics. The litter, split in different units, was treated with aqueous solutions of TEO at different concentrations (5\% to 1.25\%), demonstrating its effectiveness in reducing the total number of bacteria. The strongest antibacterial action was observed at the lowest concentration against Enterobacteriaceae, with a growth reduction compared to the positive control of 73.3\% and 77.8\% against E. coli and Salmonella Derby, respectively, while towards M. lentus the reduction was 50\%. Our data confirm the antimicrobial activity of TEO and suggest its possible application for the treatment of poultry litter as an effective and natural approach for the prevention of diseases caused by the most common bacteria that colonize poultry farms, counteracting the onset of antibiotic resistance.}, + author = {Galgano, Michela and Pellegrini, Francesco and Fracchiolla, Giuseppe and Mrenoshki, Daniela and Zarea, Aya Attia Koraney and Bianco, Angelica and Del Sambro, Laura and Capozzi, Loredana and Schiavone, Antonella and Saleh, Medhat S. and Camero, Michele and Tempesta, Maria and Cirone, Francesco and Buonavoglia, Domenico and Pratelli, Annamaria and Buonavoglia, Alessio}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12030436}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Escherichia coli}, \textit{Mammaliicoccus lentus}, \textit{Salmonella} Derby, {\textgreater}UseGalaxy.eu, antimicrobial activity, essential oils, poultry farms}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {3}, + pages = {436}, + title = {Pilot {Study} on the {Action} of {Thymus} vulgaris {Essential} {Oil} in {Treating} the {Most} {Common} {Bacterial} {Contaminants} and {Salmonella} enterica subsp. enterica {Serovar} {Derby} in {Poultry} {Litter}}, + url = {https://www.mdpi.com/2079-6382/12/3/436}, + urldate = {2023-03-15}, + volume = {12}, + year = {2023} +} + +@article{gallus_fructobacillus_2022, + abstract = {A Fructobacillus strain was isolated from the flower of a nodding thistle (Carduus nutans) collected in Bavaria, Germany. The strain is Gram-positive, rod-shaped, non-motile, non-sporulating, catalase- and oxidase-negative, and facultatively anaerobic. Growth can be detected at 10–37 °C and pH 4 to 9. The genome size is about 1.56 Mbp and the G+C content is 43.76 mol\%. Assignment to the genus Fructobacillus was done by average nucleotide identity (ANI), 16S rRNA gene sequence and multilocus sequence analyses. Calculations of ANI and digital DNA–DNA hybridization values indicate a novel species with Fructobacillus tropaeoli DSM 23246T (93.58\% ANI and 57.9 \% dDDH) being its closest relative. Therefore, a new species named Fructobacillus cardui sp. nov. with TMW 2.2452T (=DSM 113480T=CECT 30515T) as type strain is proposed.,}, + author = {Gallus, Marion K. and Beer, Irina and Ivleva, Natalia P. and Ehrmann, Matthias A.YR 2022}, + doi = {10.1099/ijsem.0.005553}, + issn = {1466-5034,}, + journal = {International Journal of Systematic and Evolutionary Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + note = {Publisher: Microbiology Society,}, + number = {10}, + pages = {005553}, + title = {Fructobacillus cardui sp. nov., isolated from a thistle ({Carduus} nutans) flower}, + url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005553}, + urldate = {2022-11-06}, + volume = {72}, + year = {2022} +} + +@article{galvis_dimet_2024, + abstract = {MOTIVATION: Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics and downstream data analyses are widely used techniques for unraveling cells' metabolic activity to understand the altered functioning of metabolic pathways in the diseased state. While a number of bioinformatic solutions exist for the differential analysis of Stable Isotope-Resolved Metabolomics data, there is currently no available resource providing a comprehensive toolbox. +RESULTS: In this work, we present DIMet, a one-stop comprehensive tool for differential analysis of targeted tracer data. DIMet accepts metabolite total abundances, isotopologue contributions, and isotopic mean enrichment, and supports differential comparison (pairwise and multi-group), time-series analyses, and labeling profile comparison. Moreover, it integrates transcriptomics and targeted metabolomics data through network-based metabolograms. We illustrate the use of DIMet in real SIRM datasets obtained from Glioblastoma P3 cell-line samples. DIMet is open-source, and is readily available for routine downstream analysis of isotope-labeled targeted metabolomics data, as it can be used both in the command line interface or as a complete toolkit in the public Galaxy Europe and Workfow4Metabolomics web platforms. +AVAILABILITY: DIMet is freely available at https://github.com/cbib/DIMet, and through https://usegalaxy.eu and https://workflow4metabolomics.usegalaxy.fr. All the datasets are available at Zenodo https://zenodo.org/records/10925786. +SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, + author = {Galvis, Johanna and Guyon, Joris and Dartigues, Benjamin and Hecht, Helge and Grüning, Björn and Specque, Florian and Soueidan, Hayssam and Karkar, Slim and Daubon, Thomas and Nikolski, Macha}, + doi = {10.1093/bioinformatics/btae282}, + issn = {1367-4811}, + journal = {Bioinformatics (Oxford, England)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {April}, + pages = {btae282}, + pmid = {38656970}, + shorttitle = {{DIMet}}, + title = {{DIMet}: {An} open-source tool for {Differential} analysis of targeted {Isotope}-labeled {Metabolomics} data}, + year = {2024} +} + @article{gao_comprehensive_2020, abstract = {{\textless}p{\textgreater}Mammalian DNA methylation patterns are established by two \textit{de novo} DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.{\textless}/p{\textgreater}}, author = {Gao, Linfeng and Emperle, Max and Guo, Yiran and Grimm, Sara A. and Ren, Wendan and Adam, Sabrina and Uryu, Hidetaka and Zhang, Zhi-Min and Chen, Dongliang and Yin, Jiekai and Dukatz, Michael and Anteneh, Hiwot and Jurkowska, Renata Z. and Lu, Jiuwei and Wang, Yinsheng and Bashtrykov, Pavel and Wade, Paul A. and Wang, Gang Greg and Jeltsch, Albert and Song, Jikui}, @@ -1534,6 +3739,23 @@ @article{gao_pluripotency_2022 year = {2022} } +@article{garcia-fernandez_antibiotic_2024, + abstract = {{\textless}p{\textgreater}Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by {\textless}italic{\textgreater}Campylobacter jejuni{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}Campylobacter coli{\textless}/italic{\textgreater}, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin {\textless}italic{\textgreater}Campylobacter{\textless}/italic{\textgreater} spp. strains (102 {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} and 31 {\textless}italic{\textgreater}C. coli{\textless}/italic{\textgreater}) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} and ST-828 CC in {\textless}italic{\textgreater}C. coli{\textless}/italic{\textgreater}. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and {\textless}italic{\textgreater}tet{\textless}/italic{\textgreater}(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in {\textless}italic{\textgreater}C. coli{\textless}/italic{\textgreater} exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} exhibiting a higher abundance compared to {\textless}italic{\textgreater}C. coli{\textless}/italic{\textgreater}. Notably, specific {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} lineages. {\textless}italic{\textgreater}Campylobacter{\textless}/italic{\textgreater} spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among {\textless}italic{\textgreater}Campylobacter{\textless}/italic{\textgreater} spp. The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.{\textless}/p{\textgreater}}, + author = {Garcia-Fernandez, Aurora and Janowicz, Anna and Marotta, Francesca and Napoleoni, Maira and Arena, Sergio and Primavilla, Sara and Pitti, Monica and Romantini, Romina and Tomei, Fiorella and Garofolo, Giuliano and Villa, Laura}, + doi = {10.3389/fmicb.2023.1293666}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Virulence, antibiotic resistance (AMR), cgMLST, gyrA, pTet, pVir, tet(O)}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {Antibiotic resistance, plasmids, and virulence-associated markers in human strains of {Campylobacter} jejuni and {Campylobacter} coli isolated in {Italy}}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1293666/full}, + urldate = {2024-05-17}, + volume = {14}, + year = {2024} +} + @article{garrido_identification_2020, abstract = {Meiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.}, author = {Garrido, José and Aguilar, Miguel and Prieto, Pilar}, @@ -1555,6 +3777,20 @@ @article{garrido_identification_2020 year = {2020} } +@misc{gavalda-garcia_bio2byte_2024, + abstract = {We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics, incorporating predictors for backbone and sidechain dynamics, local secondary structure propensities, early folding, long disorder, beta-sheet aggregation and FUS-like phase separation. Our package significantly eases the integration and execution of these tools, enhancing accessibility for both computational and experimental researchers.}, + author = {Gavalda-Garcia, Jose and Diaz, Adrian and Vranken, Wim}, + doi = {10.48550/arXiv.2405.02136}, + keywords = {{\textgreater}UseGalaxy.eu, Quantitative Biology - Quantitative Methods}, + month = {May}, + note = {arXiv:2405.02136 [q-bio]}, + publisher = {arXiv}, + title = {{bio2Byte} {Tools} deployment as a {Python} package and {Galaxy} tool to predict protein biophysical properties}, + url = {http://arxiv.org/abs/2405.02136}, + urldate = {2024-05-17}, + year = {2024} +} + @article{gener_full-coverage_2019, abstract = {Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes. Methods: Fifteen HIV-1 strains were processed with Direct RNA Sequencing (SQK-RNA002) library kits and sequenced on MinION Mk1B devices with RevD flow cells (Oxford Nanopore Technologies (ONT), Oxford, UK). Raw reads were converted to FASTQ, aligned to reference sequences, and assembled into contigs. Multi-sequence alignments of the contigs were generated and used for cladistics analysis. Results: We sequenced full-length HIV-1 from the transcriptional start site to 39 LTR (100\% virion genome) in 3 out of 15 isolates (89.6, NLAD8, AD17), achieving majority coverage (defined as \> 50\%) in another 7 out of 15 isolates. Inspection of NLAD8 sequence alignments revealed splicing or deletion signatures. Despite the strong 3′ bias, read coverage was sufficient to evaluate single-nucleotide variants (SNVs), insertions and deletions in 9 isolates, and to assemble HIV-1 genomes directly from viral RNA, achieving a maximum of 94\% assembly coverage for NLAD8. Phylogenetic relationships were maintained at the level of contigs, as well as individual reads. Conclusions: ONT native RNA sequencing performed as expected, covering full-length HIV-1 RNA without PCR or cDNA sequencing. Native single-molecule RNA sequencing supported previous models of HIV-1 replication, and samples exhibited strain-specific transcriptional signals. We propose Context Dependency Variant Classification to describe variants occurring in information-dense regions of HIV. These data provide a rich resource for emerging RNA modification detection schemes. Future work will expand HIV-1 transcript profiling to infection models and clinical samples.}, author = {Gener, Alejandro R. and Kimata, Jason T.}, @@ -1650,6 +3886,27 @@ @article{gissi_13-gene_2019 year = {2019} } +@article{giufre_detection_2024, + abstract = {Background: Carbapenemase-producing Klebsiella pneumoniae (CP-KP) represents a global threat to public health, with limited antimicrobial therapeutic options. In this study, we analyzed a ceftazidime/avibactam (CAZ-AVI)-resistant K. pneumoniae isolate obtained from a patient previously exposed to CAZ-AVI expressing a novel K. pneumoniae carbapenemase (KPC)-3 variant. Methods: Antimicrobial susceptibility testing was performed using reference broth microdilution. Whole-genome sequencing (WGS) was performed using Illumina and Nanopore Technologies. Short- and long-reads were combined with Unicycler. Assemblies were investigated for multilocus sequence typing (MLST), antimicrobial resistance genes, porins, and plasmids. Results: The K. pneumoniae isolate (KP\_RM\_1) was resistant to CAZ-AVI, expanded-spectrum cephalosporins, amikacin, ertapenem, and cefiderocol (FDC) but was susceptible to tigecycline, colistin, trimethoprim/sulfamethoxazole, meropenem–vaborbactam, and imipenem–relebactam. WGS revealed that the KP\_RM\_1 genome is composed of a single chromosome of 5 Mbp and five circular plasmids. Further analysis showed the presence of novel blaKPC-216 located on a 72 kb plasmid. KPC-216 differs from KPC-3 by a Lysin (K) insertion at position 168 (+K168). Conclusions: We report the identification of a new KPC-3 variant associated with CAZ-AVI resistance. The KPC variants associated with CAZ-AVI resistance should be determined to promptly inform clinicians and start the appropriate antimicrobial therapy.}, + author = {Giufrè, Maria and Errico, Giulia and Del Grosso, Maria and Pagnotta, Michela and Palazzotti, Bernardetta and Ballardini, Milva and Pantosti, Annalisa and Meledandri, Marcello and Monaco, Monica}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13060507}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {{\textgreater}UseGalaxy.eu, ESKAPE, KPC-216, cefiderocol, ceftazidime-avibactam, cross-resistance}, + language = {en}, + month = {June}, + note = {Number: 6 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {6}, + pages = {507}, + title = {Detection of {KPC}-216, a {Novel} {KPC}-3 {Variant}, in a {Clinical} {Isolate} of {Klebsiella} pneumoniae {ST101} {Co}-{Resistant} to {Ceftazidime}-{Avibactam} and {Cefiderocol}}, + url = {https://www.mdpi.com/2079-6382/13/6/507}, + urldate = {2024-06-07}, + volume = {13}, + year = {2024} +} + @article{gjaltema_distal_2021, author = {Gjaltema, Rutger A. F. and Schwämmle, Till and Kautz, Pauline and Robson, Michael and Schöpflin, Robert and Lustig, Liat Ravid and Brandenburg, Lennart and Dunkel, Ilona and Vechiatto, Carolina and Ntini, Evgenia and Mutzel, Verena and Schmiedel, Vera and Marsico, Annalisa and Mundlos, Stefan and Schulz, Edda G.}, doi = {10.1101/2021.03.29.437476}, @@ -1661,6 +3918,23 @@ @article{gjaltema_distal_2021 year = {2021} } +@article{glaerum_postnatal_2024, + abstract = {Cajal-Retzius (CR) cells are a transient neuron type that populate the postnatal hippocampus. To understand how the persistence of CR cells influences the maturation of hippocampal circuits, we combined a specific transgenic mouse line with viral vector injection to selectively ablate CR cells from the postnatal hippocampus. We observed layer-specific changes in the dendritic complexity and spine density of CA1 pyramidal cells. In addition, transcriptomic analysis highlighted significant changes in the expression of synapse-related genes across development. Finally, we were able to identify significant changes in the expression levels of latrophilin 2, a postsynaptic guidance molecule known for its role in the entorhinal-hippocampal connectivity. These findings were supported by changes in the synaptic proteomic content in CA1 stratum lacunosum-moleculare. Our results reveal a crucial role for CR cells in the establishment of the hippocampal network.}, + author = {Glærum, Ingvild Lynneberg and Dunville, Keagan and Moan, Kristian and Krause, Maike and Montaldo, Nicola Pietro and Kirikae, Hinako and Nigro, Maximiliano Jose and Sætrom, Pål and van Loon, Barbara and Quattrocolo, Giulia}, + doi = {10.1242/dev.202236}, + issn = {0950-1991}, + journal = {Development}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {dev202236}, + title = {Postnatal persistence of hippocampal {Cajal}-{Retzius} cells has a crucial role in the establishment of the hippocampal circuit}, + url = {https://doi.org/10.1242/dev.202236}, + urldate = {2024-05-17}, + volume = {151}, + year = {2024} +} + @article{glaros_limited_2021, author = {Glaros, Vassilis and Rauschmeier, René and Artemov, Artem V. and Reinhardt, Annika and Ols, Sebastian and Emmanouilidi, Aikaterini and Gustafsson, Charlotte and You, Yuanyuan and Mirabello, Claudio and Björklund, Åsa K. and Perez, Laurent and King, Neil P. and Månsson, Robert and Angeletti, Davide and Loré, Karin and Adameyko, Igor and Busslinger, Meinrad and Kreslavsky, Taras}, doi = {10.1016/j.immuni.2021.08.017}, @@ -1675,6 +3949,43 @@ @article{glaros_limited_2021 year = {2021} } +@article{goossens_obligate_2023, + abstract = {Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34\% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.}, + author = {Goossens, Pim and Spooren, Jelle and Baremans, Kim C. M. and Andel, Annemiek and Lapin, Dmitry and Echobardo, Nakisa and Pieterse, Corné M. J. and Van den Ackerveken, Guido and Berendsen, Roeland L.}, + copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited}, + doi = {10.1038/s41564-023-01502-y}, + issn = {2058-5276}, + journal = {Nature Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Effectors in plant pathology, Microbe, Microbiome, Pathogens, Symbiosis}, + language = {en}, + month = {December}, + note = {Number: 12 +Publisher: Nature Publishing Group}, + number = {12}, + pages = {2349--2364}, + title = {Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in {Arabidopsis} thaliana}, + url = {https://www.nature.com/articles/s41564-023-01502-y}, + urldate = {2023-12-28}, + volume = {8}, + year = {2023} +} + +@article{gosch_spitting_2023, + abstract = {Forensic trace contextualization, i.e., assessing information beyond who deposited a biological stain, has become an issue of great and steadily growing importance in forensic genetic casework and research. The human transcriptome encodes a wide variety of information and thus has received increasing interest for the identification of biomarkers for different aspects of forensic trace contextualization over the past years. Massively parallel sequencing of reverse-transcribed RNA (“RNA sequencing”) has emerged as the gold standard technology to characterize the transcriptome in its entirety and identify RNA markers showing significant expression differences not only between different forensically relevant body fluids but also within a single body fluid between forensically relevant conditions of interest. Here, we analyze the quality and composition of four RNA sequencing datasets (whole transcriptome as well as miRNA sequencing) from two different research projects (the RNAgE project and the TrACES project), aiming at identifying contextualizing forensic biomarker from the forensically relevant body fluid saliva. We describe and characterize challenges of RNA sequencing of saliva samples arising from the presence of oral bacteria, the heterogeneity of sample composition, and the confounding factor of degradation. Based on these observations, we formulate recommendations that might help to improve RNA biomarker discovery from the challenging but forensically relevant body fluid saliva.}, + author = {Gosch, Annica and Banemann, Regine and Dørum, Guro and Haas, Cordula and Hadrys, Thorsten and Haenggi, Nadescha and Kulstein, Galina and Neubauer, Jacqueline and Courts, Cornelius}, + doi = {10.1007/s00414-023-03100-3}, + issn = {1437-1596}, + journal = {International Journal of Legal Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, Forensic RNA analysis, Massive parallel sequencing, Saliva}, + language = {en}, + month = {October}, + shorttitle = {Spitting in the wind?}, + title = {Spitting in the wind?—{The} challenges of {RNA} sequencing for biomarker discovery from saliva}, + url = {https://doi.org/10.1007/s00414-023-03100-3}, + urldate = {2023-12-28}, + year = {2023} +} + @article{greenfield_modification_2020, abstract = {Dysregulation of epigenetic processes is increasingly understood to play a role in the pathogenesis of myeloproliferative neoplasms (MPNs). Ruxolitinib, a JAK/STAT inhibitor, has proved a useful addition to the therapeutic arsenal for these disorders, but has limited disease modifying activity. We determined the effect of JAK inhibition on the histone landscape of MPN cells in cell line models of MPNs and validated using samples from the MAJIC randomised clinical trial of ruxolitinib in polycythaemia vera and essential thrombocythaemia. We demonstrated an epigenetic modifying effect of ruxolitinib using a histone modification assay. The majority of 21 histone H3 modifications were upregulated, with H3K27me3 and H3K36me2 significant in the combined cell line results. Chromatin immunoprecipitation and sequencing (CHIP-seq) for three marks of interest, H3K4me1, H3K4me3 and H3K27ac, was consistent with the histone modification assay showing a significant increase in H3K4me3 and H3K27ac peaks at promoter regions, both marks of active transcription. In contrast, RNA sequencing demonstrates a coordinated reduction in gene expression in a number of cell pathways including PI3K-AKT signalling, transcriptional misregulation in cancer and JAK-STAT signalling in spite of these histone changes. This highlights the complex mechanisms of transcriptional control within the cells which was reflected in analysis of the histone landscape in patient samples following ruxolitinib treatment.}, author = {Greenfield, Graeme and McPherson, Suzanne and Smith, James and Mead, Adam and Harrison, Claire and Mills, Ken and McMullin, Mary Frances}, @@ -1695,6 +4006,27 @@ @article{greenfield_modification_2020 year = {2020} } +@article{gress_transcriptomic_2024, + abstract = {Segmental instillation of lipopolysaccharide (LPS) by bronchoscopy safely induces transient airway inflammation in human lungs. This model enables investigation of pulmonary inflammatory mechanisms as well as pharmacodynamic analysis of investigational drugs. The aim of this work was to describe the transcriptomic profile of human segmental LPS challenge with contextualization to major respiratory diseases. Pre-challenge bronchoalveolar lavage (BAL) fluid and biopsies were sampled from 28 smoking, healthy participants, followed by segmental instillation of LPS and saline as control. Twenty-four hours post instillation, BAL and biopsies were collected from challenged lung segments. Total RNA of cells from BAL and biopsy samples were sequenced and analysed for differentially expressed genes (DEGs). After challenge with LPS compared with saline, 6316 DEGs were upregulated and 241 were downregulated in BAL, but only one DEG was downregulated in biopsy samples. Upregulated DEGs in BAL were related to molecular functions such as “Inflammatory response” or “chemokine receptor activity”, and upregulated pro-inflammatory pathways such as “Wnt-"/“Ras-"/“JAK-STAT” “-signaling pathway”. Furthermore, the segmental LPS challenge model resembled aspects of the five most prevalent respiratory diseases chronic obstructive pulmonary disease (COPD), asthma, pneumonia, tuberculosis and lung cancer and featured similarities with acute exacerbations in COPD (AECOPD) and community-acquired pneumonia. Overall, our study provides extensive information about the transcriptomic profile from BAL cells and mucosal biopsies following LPS challenge in healthy smokers. It expands the knowledge about the LPS challenge model providing potential overlap with respiratory diseases in general and infection-triggered respiratory insults such as AECOPD in particular.}, + author = {Gress, Christina and Litzenburger, Tobias and Schmid, Ramona and Xiao, Ke and Heissig, Florian and Muller, Meike and Gupta, Abhya and Hohlfeld, Jens M.}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-51547-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Biomarkers, Experimental models of disease, Gene regulation in immune cells, Inflammation, RNA sequencing}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1721}, + title = {Transcriptomic characterization of the human segmental endotoxin challenge model}, + url = {https://www.nature.com/articles/s41598-024-51547-0}, + urldate = {2024-01-23}, + volume = {14}, + year = {2024} +} + @article{greve_decitabine_2021, abstract = {Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3–1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3–1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group. Significance: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813 @@ -1774,6 +4106,55 @@ @article{guendel_group_2020 year = {2020} } +@article{guerler_fast_2023, + abstract = {Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein–protein interactions and produce high-quality multimeric structural models.}, + author = {Guerler, Aysam and Baker, Dannon and van den Beek, Marius and Gruening, Bjoern and Bouvier, Dave and Coraor, Nate and Shank, Stephen D. and Zehr, Jordan D. and Schatz, Michael C. and Nekrutenko, Anton}, + doi = {10.1186/s12859-023-05389-8}, + issn = {1471-2105}, + journal = {BMC Bioinformatics}, + keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Galaxy workflow, Protein–protein interactions, Structural modeling}, + language = {en}, + month = {June}, + number = {1}, + pages = {263}, + title = {Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using {Galaxy}}, + url = {https://doi.org/10.1186/s12859-023-05389-8}, + urldate = {2023-07-31}, + volume = {24}, + year = {2023} +} + +@article{guindo_tetragenococcus_2022, + abstract = {Tetragenococcus halophilus (T. halophilus) is a facultative anaerobic, coccus-shaped halophilic lactic acid-producing bacterium previously detected and cultured in various salty foods and credited for beneficial effects on human health. In this study, we investigated the presence of T. halophilus in human samples using a polyphasic approach including scanning electron microscopy, molecular biology methods and microbial culture. This unique investigation yielded the unprecedented presence of T. halophilus in human feces samples, thus enriching the repertoire of halophilic microorganisms colonizing the human gastrointestinal tract with the isolation and culture of T. halophilus for the first time in humans. Using the E-test strips, the MIC was assessed for T. halophilus strain CSURQ6002: rifampicin (MIC at 0.002 μg/mL), benzylpenicillin (MIC at 0.094 μg/mL), amoxicillin (MIC at 0.5 μg/mL), erythromycin (MIC at 2 μg/mL), clindamycin (MIC at 4 μg/mL), and vancomycin (MIC at 8 μg/mL). However, this strain showed a MIC up to 256 μg/mL for ciprofloxacin, fosfomycin, doxycyclin, imipenem, and colistin. In-silico profiling derived from whole genome sequencing (NCBI accession number: PRJNA780809), was confirmed. This discovery suggested that T. halophilus was part of the human digestive microbiota and that its potential role on human health should be considered.}, + author = {Guindo, Cheick Oumar and Morsli, Madjid and Bellali, Sara and Drancourt, Michel and Grine, Ghiles}, + doi = {10.1016/j.crmicr.2022.100112}, + issn = {2666-5174}, + journal = {Current Research in Microbial Sciences}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Human gut microbiota, Isolation and culture, Next-generation sequencing, Scanning electron microscopy}, + language = {en}, + month = {January}, + pages = {100112}, + title = {A {Tetragenococcus} halophilus human gut isolate}, + url = {https://www.sciencedirect.com/science/article/pii/S2666517422000098}, + urldate = {2022-02-21}, + volume = {3}, + year = {2022} +} + +@article{gussak_precision_2023, + abstract = {Streptococcussuis is an important zoonotic pathogen that causes severe invasive disease in pigs and humans. Current methods for genome engineering of S. suis rely on the insertion of antibiotic resistance markers, which is time-consuming and labor-intensive and does not allow the precise introduction of small genomic mutations. Here we developed a system for CRISPR-based genome editing in S. suis, utilizing linear DNA fragments for homologous recombination (HR) and a plasmid-based negative selection system for bacteria not edited by HR. To enable the use of this system in other bacteria, we engineered a broad-host-range replicon in the CRISPR plasmid. We demonstrated the utility of this system to rapidly introduce multiple gene deletions in successive rounds of genome editing and to make precise nucleotide changes in essential genes. Furthermore, we characterized a mechanism by which S. suis can escape killing by a targeted Cas9-sgRNA complex in the absence of HR. A characteristic of this new mechanism is the presence of very slow-growing colonies in a persister-like state that may allow for DNA repair or the introduction of mutations, alleviating Cas9 pressure. This does not impact the utility of CRISPR-based genome editing because the escape colonies are easily distinguished from genetically edited clones due to their small colony size. Our CRISPR-based editing system is a valuable addition to the genetic toolbox for engineering of S. suis, as it accelerates the process of mutant construction and simplifies the removal of antibiotic markers between successive rounds of genome editing.}, + author = {Gussak, Alex and Ferrando, Maria Laura and Schrama, Mels and van Baarlen, Peter and Wells, Jerry Mark}, + doi = {10.1021/acssynbio.3c00110}, + journal = {ACS Synthetic Biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Chemical Society}, + title = {Precision {Genome} {Engineering} in {Streptococcus} suis {Based} on a {Broad}-{Host}-{Range} {Vector} and {CRISPR}-{Cas9} {Technology}}, + url = {https://doi.org/10.1021/acssynbio.3c00110}, + urldate = {2023-08-24}, + year = {2023} +} + @article{haas_n-tp63_2019, abstract = {Mucociliary epithelia provide a first line of defense against pathogens. Impaired regeneration and remodeling of mucociliary epithelia are associated with dysregulated Wnt/β-catenin signaling in chronic airway diseases, but underlying mechanisms remain elusive, and studies yield seemingly contradicting results. Employing the Xenopus mucociliary epidermis, the mouse airway, and human airway Basal cells, we characterize the evolutionarily conserved roles of Wnt/β-catenin signaling in vertebrates. In multiciliated cells, Wnt is required for cilia formation during differentiation. In Basal cells, Wnt prevents specification of epithelial cell types by activating ΔN-TP63, a master transcription factor, which is necessary and sufficient to mediate the Wnt-induced inhibition of specification and is required to retain Basal cells during development. Chronic Wnt activation leads to remodeling and Basal cell hyperplasia, which are reversible in vivo and in vitro, suggesting Wnt inhibition as a treatment option in chronic lung diseases. Our work provides important insights into mucociliary signaling, development, and disease.}, author = {Haas, Maximilian and Gómez Vázquez, José Luis and Sun, Dingyuan Iris and Tran, Hong Thi and Brislinger, Magdalena and Tasca, Alexia and Shomroni, Orr and Vleminckx, Kris and Walentek, Peter}, @@ -1808,6 +4189,24 @@ @article{hahn_dna_2020 year = {2020} } +@article{hakkanen_molecular_2024, + abstract = {The aims of the study were to characterise the distribution of Cryptosporidium spp. and subtypes causing infections in Finland during 2021. This was carried out with 60 clinical samples from the hospital districts of Helsinki and Uusimaa, Vaasa, Kymenlaakso, South Karelia, and Central Finland, as well as with Finnish Infectious Diseases Register (FIDR) data. Additionally, the study aimed to explore the potential exposures related to Cryptosporidium mortiferum (Cryptosporidium chipmunk genotype I) infections via interview. Species identification was carried out with quantitative real-time PCR (qPCR) and 18S sequencing. Further typing was performed with gp60 subtyping. Over 70\% of the samples were identified as Cryptosporidium parvum and 20\% as C. mortiferum, which had not been identified in Finland before. Two cases of Cryptosporidium hominis were identified from patients reported to have travelled outside Europe. The C. parvum subtype IIaA15G2R1 and the C. mortiferum subtype XIVaA20G2T1 were the most common subtypes identified. The interviewed C. mortiferum cases did not report shared exposures such as contact with wild rodents. In conclusion, C. parvum and C. mortiferum were the major causes of cryptosporidiosis in the five studied Finnish hospital districts.}, + author = {Häkkänen, Tessa and Rimhanen-Finne, Ruska and Antikainen, Jenni and Ruotsalainen, Eeva and Vainio, Anni}, + doi = {10.1016/j.ijpara.2024.01.002}, + issn = {0020-7519}, + journal = {International Journal for Parasitology}, + keywords = {{\textgreater}UseGalaxy.eu, Cryptosporidiosis, Finland, GP60, chipmunk genotype I}, + month = {April}, + number = {5}, + pages = {225--231}, + shorttitle = {Molecular characteristics of \textit{{Cryptosporidium}} spp. in human cases in five {Finnish} hospital districts during 2021}, + title = {Molecular characteristics of \textit{{Cryptosporidium}} spp. in human cases in five {Finnish} hospital districts during 2021: first findings of \textit{{Cryptosporidium} mortiferum} (\textit{{Cryptosporidium}} chipmunk genotype {I}) in {Finland}}, + url = {https://www.sciencedirect.com/science/article/pii/S0020751924000134}, + urldate = {2024-05-17}, + volume = {54}, + year = {2024} +} + @article{hamprecht_candida_2019, author = {Hamprecht, Axel and Barber, Amelia E. and Mellinghoff, Sibylle C. and Thelen, Philipp and Walther, Grit and Yu, Yanying and Neurgaonkar, Priya and Dandekar, Thomas and Cornely, Oliver A. and Martin, Ronny and Kurzai, Oliver and {on behalf of the German Candida auris Study Group}}, doi = {10.3201/eid2509.190262}, @@ -1825,6 +4224,86 @@ @article{hamprecht_candida_2019 year = {2019} } +@article{han_dna-directed_2023, + author = {Han, Zhong and Moore, George A. and Mitter, Richard and Martinez, David Lopez and Wan, Li and Svejstrup, A. Barbara Dirac and Rueda, David S. and Svejstrup, Jesper Q.}, + doi = {10.1016/j.molcel.2023.08.007}, + issn = {1097-2765}, + journal = {Molecular Cell}, + keywords = {{\textgreater}UseGalaxy.eu, CPSF73, DSIF, RNA polymerase II, Rat1, Spt5, TFIIS, XRN2, intrinsic termination site, termination, torpedo}, + language = {English}, + month = {September}, + note = {Publisher: Elsevier}, + number = {18}, + pages = {3253--3267.e7}, + pmid = {37683646}, + title = {{DNA}-directed termination of {RNA} polymerase {II} transcription}, + url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(23)00644-5}, + urldate = {2023-11-18}, + volume = {83}, + year = {2023} +} + +@article{hardtner_comparative_2023, + abstract = {Background and aims +Atherosclerosis is a systemic and chronic inflammatory disease propagated by monocytes and macrophages. Yet, our knowledge on how transcriptome of these cells evolves in time and space is limited. We aimed at characterizing gene expression changes in site-specific macrophages and in circulating monocytes during the course of atherosclerosis. +Methods +We utilized apolipoprotein E-deficient mice undergoing one- and six-month high cholesterol diet to model early and advanced atherosclerosis. Aortic macrophages, peritoneal macrophages, and circulating monocytes from each mouse were subjected to bulk RNA-sequencing (RNA-seq). We constructed a comparative directory that profiles lesion- and disease stage-specific transcriptomic regulation of the three cell types in atherosclerosis. Lastly, the regulation of one gene, Gpnmb, whose expression positively correlated with atheroma growth, was validated using single-cell RNA-seq (scRNA-seq) of atheroma plaque from murine and human. +Results +The convergence of gene regulation between the three investigated cell types was surprisingly low. Overall 3245 differentially expressed genes were involved in the biological modulation of aortic macrophages, among which less than 1\% were commonly regulated by the remote monocytes/macrophages. Aortic macrophages regulated gene expression most actively during atheroma initiation. Through complementary interrogation of murine and human scRNA-seq datasets, we showcased the practicality of our directory, using the selected gene, Gpnmb, whose expression in aortic macrophages, and a subset of foamy macrophages in particular, strongly correlated with disease advancement during atherosclerosis initiation and progression. +Conclusions +Our study provides a unique toolset to explore gene regulation of macrophage-related biological processes in and outside the atheromatous plaque at early and advanced disease stages.}, + author = {Härdtner, Carmen and Kumar, Anup and Ehlert, Carolin A. and Vico, Tamara Antonela and Starz, Christopher and von Ehr, Alexander and Krebs, Katja and Dufner, Bianca and Hoppe, Natalie and Stachon, Peter and Heidt, Timo and Wolf, Dennis and von zur Mühlen, Constantin and Grüning, Björn and Robbins, Clinton S. and Maegdefessel, Lars and Westermann, Dirk and Dederichs, Tsai-Sang and Hilgendorf, Ingo}, + doi = {10.1016/j.atherosclerosis.2023.03.006}, + issn = {0021-9150}, + journal = {Atherosclerosis}, + keywords = {{\textgreater}UseGalaxy.eu, Atherosclerosis, Gpnmb, Macrophage, RNA-seq}, + language = {en}, + month = {April}, + pages = {1--13}, + title = {A comparative gene expression matrix in {Apoe}-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages}, + url = {https://www.sciencedirect.com/science/article/pii/S0021915023001041}, + urldate = {2023-06-05}, + volume = {371}, + year = {2023} +} + +@article{hassan_genome-wide_2023, + author = {Hassan, Zarqa and Abbas, Amjad and Shafique, Ikhlas}, + doi = {10.22194/pdc/3.1017}, + issn = {2957-5842}, + journal = {Phytopathogenomics and Disease Control}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + note = {Publisher: Journal of Global Innovations in Agricultural and Social Sciences (JGIASS)}, + number = {2}, + pages = {1--12}, + title = {Genome-wide identification and characterization of the plant defensins ({Pdfs}) gene family in selected {Leguminous} crops and their expression profiles in response to biotic and abiotic stresses}, + url = {http://dx.doi.org/10.22194/Pdc/3.1017}, + volume = {2}, + year = {2023} +} + +@article{hedhly_s-locus_2023, + abstract = {Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein—i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV).}, + author = {Hedhly, Afif and Guerra, María Engracia and Grimplet, Jerome and Rodrigo, Javier}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms24043932}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Prunus salicina}, \textit{S}-allele, \textit{S}-genotyping-by-sequencing, {\textgreater}UseGalaxy.eu, Japanese plum, self-incompatibility}, + language = {en}, + month = {January}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {3932}, + title = {S-{Locus} {Genotyping} in {Japanese} {Plum} by {High} {Throughput} {Sequencing} {Using} a {Synthetic} {S}-{Loci} {Reference} {Sequence}}, + url = {https://www.mdpi.com/1422-0067/24/4/3932}, + urldate = {2023-03-15}, + volume = {24}, + year = {2023} +} + @article{hering_eikenella_2021, author = {Hering, Silvio and Jansson, Moritz K. and Buhl, Michael E. J.}, doi = {10.1099/ijsem.0.004977}, @@ -1854,6 +4333,64 @@ @article{hernandez_design_2020 year = {2020} } +@article{herwibawa_association_2024, + abstract = {We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL groups; next, we focused on OsCUL3c, the third CUL3 of the CUL3 family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the OsCUL3c region, representing 79 haplotypes (haps), were found. Haplotyping revealed that group I (hap A and hap C) and group II (hap B1 and hap D) were different mutated variants, which showed their association with phenotypes under salt stress. These results were supported by cis-regulatory elements (CREs) and transcription factor binding sites (TFBSs) analyses. We found that LTR, MYC, [AP2; ERF], and NF-YB, which are related to salt stress, drought stress, and the response to abscisic acid (ABA), have distinct positions and numbers in the haplotypes of group I and group II. An RNA Seq analysis of the two predominant haplotypes from each group showed that the OsCUL3c expression of the group I representative was upregulated and that of group II was downregulated, which was confirmed by RT-qPCR. Promoter changes might affect the transcriptional responses to salt stress, leading to different regulatory mechanisms for the expression of different haplotypes. We speculate that OsCUL3c influences the regulation of salt-related responses, and haplotype variations play a role in this regulation.}, + author = {Herwibawa, Bagus and Lekklar, Chakkree and Chadchawan, Supachitra and Buaboocha, Teerapong}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25021040}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, CRE, SNP, TFBS, cullin, indel, phylogenetic}, + language = {en}, + month = {January}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {1040}, + title = {Association of a {Specific} {OsCULLIN3c} {Haplotype} with {Salt} {Stress} {Responses} in {Local} {Thai} {Rice}}, + url = {https://www.mdpi.com/1422-0067/25/2/1040}, + urldate = {2024-05-17}, + volume = {25}, + year = {2024} +} + +@article{hes_impact_2023, + abstract = {Chara braunii is a model for early land plant evolution and terrestrialization. Salt stress has a profound effect on water and ion transport activities, thereby interacting with many other processes, including inorganic carbon acquisition for photosynthesis. In this study, we analyzed the impact of salt stress (5 practical salt units, PSU) on the physiology and gene expression in C. braunii. Photosynthesis was only slightly affected 6 h after salt addition and returned to control levels after 48 h. Several organic compounds such as proline, glutamate, sucrose, and 2-aminobutyrate accumulated in salt-treated thalli and might contribute to osmotic potential acclimation, whereas the amount of K+ decreased. We quantified transcript levels for 17,387 genes, of which 95 were up-regulated and 44 down-regulated after salt addition. Genes encoding proteins of the functional groups ion/solute transport and cell wall synthesis/modulation were enriched among the up-regulated genes 24–48 h after salt stress, indicating their role in osmotic acclimation. However, a homolog to land plant ERD4 osmosensors was transiently upregulated after 6 h, and phylogenetic analyses suggested that these sensors evolved in Charophyceae. Down-regulated genes were mainly related to photosynthesis and carbon metabolism/fixation, consistent with the observed lowered growth after extended cultivation. The changed expression of genes encoding proteins for inorganic carbon acquisition might be related to the impact of salt on ionic relations and inorganic carbon uptake. The results indicate that C. braunii can tolerate enhanced salt concentrations in a defined acclimation process, including distinct gene expression changes to achieve new metabolic homeostasis.}, + author = {Heß, Daniel and Heise, Carolin M. and Schubert, Hendrik and Hess, Wolfgang R. and Hagemann, Martin}, + copyright = {© 2023 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.}, + doi = {10.1111/ppl.14123}, + issn = {1399-3054}, + journal = {Physiologia Plantarum}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14123}, + number = {6}, + pages = {e14123}, + title = {The impact of salt stress on the physiology and the transcriptome of the model streptophyte green alga {Chara} braunii}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14123}, + urldate = {2023-12-28}, + volume = {175}, + year = {2023} +} + +@article{hes_insight_2023, + abstract = {Charophyceae are the most complex streptophyte algae, possessing tissue-like structures, rhizoids and a cellulose-pectin-based cell wall akin to embryophytes. Together with the Zygnematophyceae and the Coleochaetophycae, the Charophyceae form a grade in which the Zygnematophyceae share a last common ancestor with land plants. The availability of genomic data, its short life cycle, and the ease of non-sterile cultivation in the laboratory have made the species Chara braunii an emerging model system for streptophyte terrestrialization and early land plant evolution. In this study, tissue containing nodal cells was prepared under the stereomicroscope, and an RNA-seq dataset was generated and compared to transcriptome data from whole plantlets. In both samples, transcript coverage was high for genes encoding ribosomal proteins and a homolog of the putative PAX3- and PAX7-binding protein 1. Gene ontology was used to classify the putative functions of the differently expressed genes. In the nodal cell sample, main upregulated molecular functions were related to protein, nucleic acid, ATP- and DNA binding. Looking at specific genes, several signaling-related genes and genes encoding sugar-metabolizing enzymes were found to be expressed at a higher level in the nodal cell sample, while photosynthesis-and chloroplast-related genes were expressed at a comparatively lower level. We detected the transcription of 21 different genes encoding DUF4360-containing cysteine-rich proteins. The data contribute to the growing understanding of Charophyceae developmental biology by providing a first insight into the transcriptome composition of Chara nodal cells.}, + author = {Heß, Daniel and Holzhausen, Anja and Hess, Wolfgang R.}, + doi = {10.1111/ppl.14025}, + issn = {1399-3054}, + journal = {Physiologia Plantarum}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14025}, + number = {5}, + pages = {e14025}, + title = {Insight into the nodal cells transcriptome of the streptophyte green alga {Chara} braunii {S276}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14025}, + urldate = {2023-09-26}, + volume = {175}, + year = {2023} +} + @article{hesse_proximity_2020, author = {Hesse, Michael and Bednarz, Rebecca and Carls, Esther and Becker, Cora and Bondareva, Olga and Lother, Achim and Geisen, Caroline and Dreßen, Martina and Krane, Markus and Roell, Wilhelm and Hein, Lutz and Fleischmann, Bernd K. and Gilsbach, Ralf}, doi = {10.1016/j.yjmcc.2020.11.012}, @@ -1931,6 +4468,25 @@ @article{hille_ultrastructural_2020 year = {2020} } +@article{hodzhev_analysis_2023, + abstract = {Pulmonary sarcoidosis is a complex inflammatory disease characterized by granulomas in the lung tissue, leading to breathing difficulties and chest pain. Its etiology remains not fully understood, with factors such as allergies, autoimmune responses and genetics playing a role. This study explores the potential of blood microbiome dysbiosis, defined as an imbalance in the microbial ecosystem, as a missing piece of the puzzle in understanding the etiology of the disease. Our objective was to apply a decision-tree supervised machine learning hierarchical model to distinguish potential patterns of microbiome dysbiosis in blood samples from patients with pulmonary sarcoidosis as compared to healthy age-matched controls. Blood microbiome analysis, being individually-specific and stable, offers a unique perspective. Utilizing 16S rRNA gene amplicon sequencing, we analyzed the blood microbiome composition characterized by non-normally distributed and sparse data. Because of the rarity of the disease in Bulgaria, we studied a relatively small patient group, n = 7. The findings were compared to 21 healthy age-matched controls. Bioinformatics and statistical analysis play a pivotal role in microbiome analysis, especially when discerning associations between taxonomic composition and disorders such as pulmonary sarcoidosis. By analyzing the microbial diversity, we identified alterations in the blood microbiome composition between healthy individuals and those with sarcoidosis, which potentially may trigger the disease. Advanced machine learning techniques provided additional power to the analysis, that might be overlooked by the usual group statistics, confirming the differentiation of the diversity within the studied microbiome.}, + author = {Hodzhev, Yordan}, + doi = {10.1080/13102818.2023.2283133}, + issn = {1310-2818}, + journal = {Biotechnology \& Biotechnological Equipment}, + keywords = {{\textgreater}UseGalaxy.eu, Pulmonary sarcoidosis, blood microbiome dysbiosis, classification, decision tree model}, + month = {December}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/13102818.2023.2283133}, + number = {1}, + pages = {2283133}, + title = {Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model}, + url = {https://doi.org/10.1080/13102818.2023.2283133}, + urldate = {2023-12-03}, + volume = {37}, + year = {2023} +} + @article{hofacker_engineering_2020, abstract = {Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.}, author = {Hofacker, Daniel and Broche, Julian and Laistner, Laura and Adam, Sabrina and Bashtrykov, Pavel and Jeltsch, Albert}, @@ -1949,6 +4505,22 @@ @article{hofacker_engineering_2020 year = {2020} } +@article{hoffmann_role_2024, + abstract = {RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNa...}, + author = {Hoffmann, Ute A. and Lichtenberg, Elisabeth and Rogh, Said N. and Bilger, Raphael and Reimann, Viktoria and Heyl, Florian and Backofen, Rolf and Steglich, Claudia and Hess, Wolfgang R. and Wilde, Annegret}, + copyright = {© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor \& Francis Group.}, + issn = {1547-6286}, + journal = {RNA Biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + note = {Publisher: Taylor \& Francis}, + title = {The role of the 5’ sensing function of ribonuclease {E} in cyanobacteria}, + url = {https://www.tandfonline.com/doi/abs/10.1080/15476286.2024.2328438}, + urldate = {2024-05-17}, + year = {2024} +} + @article{holper_genome-wide_2021, author = {Hölper, Julia E. and Grey, Finn and Baillie, John Kenneth and Regan, Tim and Parkinson, Nicholas J. and Höper, Dirk and Thamamongood, Thiprampai and Schwemmle, Martin and Pannhorst, Katrin and Wendt, Lisa and Mettenleiter, Thomas C. and Klupp, Barbara G.}, doi = {10.3390/v13081574}, @@ -1980,6 +4552,300 @@ @phdthesis{holthausen_bermejo_workflow-based_2019 year = {2019} } +@article{hossain_evaluation_2024, + abstract = {This investigation employed computational methodologies to assess the therapeutic potential of derivatives (1–16) of pyridoxal isonicotinoyl hydrazone (PIH) as potential treatments for tuberculosis. Various computational techniques, including molecular dynamics simulation, molecular docking, density functional theory, and global chemical descriptors, were employed to analyze the interactions between the ligands and target proteins. Docking results indicated that ligands 6, 7, 8, and rifampin exhibited binding affinities of −8.4, −7.4, −9.2, and − 7.2 kcal mol−1, respectively, against mycobacterium tuberculosis enoyl acyl carrier protein reductase (INHA), with ligand 8 demonstrating superior inhibition. Molecular dynamics (MD) simulations were utilized to assess the stability of protein-ligand interactions. Remarkably, the Root Mean Square Deviation (RMSD) of the INHA-ligand 8 complex remained minimal, with peak values at .40, .56, .37, and .50 nm at temperatures of 300, 305, 310, and 320 K, respectively. This suggests superior stability compared to the reference drug rifampin and INHA complex, which exhibited an RMSD range of .2 to .8 nm at 300 K. Furthermore, analysis using Frontier Molecular Orbital (FMO) revealed that the Egap value of ligand 8 (4.407 eV) is lower than all the reference drugs except rifampin. This comprehensive theoretical analysis positions ligand 8 as a promising candidate for anti-tuberculosis drug development, underscoring the need for further exploration through in vitro and in vivo studies.}, + author = {Hossain, Md. Shamim and Al Abbad, Sanaa S. and Alsunaidi, Zainab H. A. and Rahman, Shofiur and Alodhayb, Abdullah N. and Hossain, Md. Mainul and Poirier, Raymond A. and Uddin, Kabir M.}, + copyright = {© 2024 Wiley Periodicals LLC.}, + doi = {10.1002/qua.27381}, + issn = {1097-461X}, + journal = {International Journal of Quantum Chemistry}, + keywords = {{\textgreater}ChemicalToolbox, ADMET, DFT, MD simulation, PCA, PIH, molecular docking}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.27381}, + number = {9}, + pages = {e27381}, + shorttitle = {Evaluation of novel pyridoxal isonicotinoyl hydrazone ({PIH}) derivatives as potential anti-tuberculosis agents}, + title = {Evaluation of novel pyridoxal isonicotinoyl hydrazone ({PIH}) derivatives as potential anti-tuberculosis agents: {An} in silico investigation}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.27381}, + urldate = {2024-05-01}, + volume = {124}, + year = {2024} +} + +@article{hosseinzadeh_gene_2023, + abstract = {Heat stress in poultry houses, especially in warm areas, is one of the main environmental factors that restrict the growth of broilers or laying performance of layers, suppresses the immune system, and deteriorates egg quality and feed conversion ratio. The molecular mechanisms underlying the response of chicken to acute heat stress (AHS) have not been comprehensively elucidated. Therefore, the main object of the current work was to investigate the liver gene expression profile of chickens under AHS in comparison with their corresponding control groups, using four RNA-seq datasets. The meta-analysis, GO and KEGG pathway enrichment, WGCNA, machine-learning, and eGWAS analyses were performed. The results revealed 77 meta-genes that were mainly related to protein biosynthesis, protein folding, and protein transport between cellular organelles. In other words, under AHS, the expression of genes involving in the structure of rough reticulum membrane and in the process of protein folding was adversely influenced. In addition, genes related to biological processes such as “response to unfolded proteins,” “response to reticulum stress” and “ERAD pathway” were differentially regulated. We introduce here a couple of genes such as HSPA5, SSR1, SDF2L1, and SEC23B, as the most significantly differentiated under AHS, which could be used as bio-signatures of AHS. Besides the mentioned genes, the main findings of the current work may shed light to the identification of the effects of AHS on gene expression profiling of domestic chicken as well as the adaptive response of chicken to environmental stresses.}, + author = {Hosseinzadeh, Sevda and Hasanpur, Karim}, + issn = {1664-8021}, + journal = {Frontiers in Genetics}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress}, + url = {https://www.frontiersin.org/articles/10.3389/fgene.2023.1102136}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + +@article{hosseinzadeh_whole_2024, + abstract = {Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with {\textasciitilde} 8800 known lncRNAs and {\textasciitilde} 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb\_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb\_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value {\textless} 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.}, + author = {Hosseinzadeh, Sevda and Hasanpur, Karim}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-56757-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Animal breeding, Genetics}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {6544}, + title = {Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress}, + url = {https://www.nature.com/articles/s41598-024-56757-0}, + urldate = {2024-04-28}, + volume = {14}, + year = {2024} +} + +@article{howard_complete_2023, + author = {Howard, Mondraya and Maki, Joel J. and Connelly, Sara and Hardy, Dwight J. and Cameron, Andrew}, + doi = {10.1128/MRA.00293-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00293--23}, + title = {Complete genome sequence of a human bacteremia isolate of {Kalamiella} piersonii}, + url = {https://journals.asm.org/doi/10.1128/mra.00293-23}, + urldate = {2023-09-05}, + volume = {0}, + year = {2023} +} + +@article{huang_translational_2023, + abstract = {Ethylene plays essential roles in rice growth, development and stress adaptation. Translational control of ethylene signaling remains unclear in rice. Here, through analysis of an ethylene-response mutant mhz9, we identified a glycine-tyrosine-phenylalanine (GYF) domain protein MHZ9, which positively regulates ethylene signaling at translational level in rice. MHZ9 is localized in RNA processing bodies. The C-terminal domain of MHZ9 interacts with OsEIN2, a central regulator of rice ethylene signaling, and the N-terminal domain directly binds to the OsEBF1/2 mRNAs for translational inhibition, allowing accumulation of transcription factor OsEIL1 to activate the downstream signaling. RNA-IP seq and CLIP-seq analyses reveal that MHZ9 associates with hundreds of RNAs. Ribo-seq analysis indicates that MHZ9 is required for the regulation of {\textasciitilde} 90\% of genes translationally affected by ethylene. Our study identifies a translational regulator MHZ9, which mediates translational regulation of genes in response to ethylene, facilitating stress adaptation and trait improvement in rice.}, + author = {Huang, Yi-Hua and Han, Jia-Qi and Ma, Biao and Cao, Wu-Qiang and Li, Xin-Kai and Xiong, Qing and Zhao, He and Zhao, Rui and Zhang, Xun and Zhou, Yang and Wei, Wei and Tao, Jian-Jun and Zhang, Wan-Ke and Qian, Wenfeng and Chen, Shou-Yi and Yang, Chao and Yin, Cui-Cui and Zhang, Jin-Song}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-40429-0}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Plant hormones, Plant molecular biology, Translation}, + language = {en}, + month = {August}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {4674}, + title = {A translational regulator {MHZ9} modulates ethylene signaling in rice}, + url = {https://www.nature.com/articles/s41467-023-40429-0}, + urldate = {2023-11-18}, + volume = {14}, + year = {2023} +} + +@article{huszarik_external_2023, + abstract = {DNA metabarcoding is increasingly used to analyze the diet of arthropods, including spiders. However, high sensitivity to DNA contamination makes it difficult to apply to organisms obtained from mass-sampling methods such as pitfall traps. An alternative is to hand-sample spiders, but it is unclear how effectively this prevents external contamination, especially with new knowledge showing the wide spread of eDNA in the environment. Protocols using bleach to remove external DNA have been tested on several invertebrates, though testing with both mass-sampling methods and spiders is lacking. Here, we used wolf spiders (Lycosidae) to assess the risk of external DNA contamination from pitfall trapping and hand sampling, and the efficacy of bleach decontamination. We first conducted a contamination experiment where we placed spiders in pitfall traps containing trapping medium and a nonprey insect species to simulate external DNA contamination. We also compared sampling methods by collecting spiders using pitfall traps and hand sampling. Spiders from the contamination experiment and sampling method comparison were either bleached or untreated, then metabarcoded using multiple primer pairs. The contamination experiment resulted in the contamination of almost all spiders from pitfall traps, which was successfully eliminated with bleaching. Interestingly, there was no difference in the number of amplicon sequence variants (ASVs) detected per spider between pitfall trapping and hand sampling but bleaching resulted in significantly fewer ASV detections for both methods. Additionally, bleaching, but not sampling method, affected the taxonomic diet composition for both hand-sampled and pitfall-trapped spiders, indicating similar levels of external contamination. Our results are the first to confirm that DNA metabarcoding can be used together with bleaching for spiders sampled from pitfall traps, and that hand sampling does not necessarily exclude external DNA contamination. Thus, diet studies using metabarcoding should address the risk of external contamination with field-sampled arthropods, regardless of sampling method.}, + author = {Huszarik, Maike and Röder, Nina and Eberhardt, Linda and Kennedy, Susan and Krehenwinkel, Henrik and Schwenk, Klaus and Entling, Martin H.}, + copyright = {© 2023 The Authors. Environmental DNA published by John Wiley \& Sons Ltd.}, + doi = {10.1002/edn3.410}, + issn = {2637-4943}, + journal = {Environmental DNA}, + keywords = {{\textgreater}UseGalaxy.eu, Araneae, DNA metabarcoding, Lycosidae, gut content, hand sampling, pitfall trap}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.410}, + number = {3}, + pages = {540--550}, + title = {External {DNA} contamination and efficiency of bleach decontamination for arthropod diet analysis}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/edn3.410}, + urldate = {2023-06-05}, + volume = {5}, + year = {2023} +} + +@article{hwang_reduction_2024, + abstract = {A hallmark of fetal alcohol spectrum disorders (FASD) is neurobehavioral deficits that still do not have effective treatment. Here, we present that reduction of Apolipoprotein E (APOE) is critically involved in neurobehavioral deficits in FASD. We show that prenatal alcohol exposure (PAE) changes chromatin accessibility of Apoe locus, and causes reduction of APOE levels in both the brain and peripheral blood in postnatal mice. Of note, postnatal administration of an APOE receptor agonist (APOE-RA) mitigates motor learning deficits and anxiety in those mice. Several molecular and electrophysiological properties essential for learning, which are altered by PAE, are restored by APOE-RA. Our human genome-wide association study further reveals that the interaction of PAE and a single nucleotide polymorphism in the APOE enhancer which chromatin is closed by PAE in mice is associated with lower scores in the delayed matching-to-sample task in children. APOE in the plasma is also reduced in PAE children, and the reduced level is associated with their lower cognitive performance. These findings suggest that controlling the APOE level can serve as an effective treatment for neurobehavioral deficits in FASD.}, + author = {Hwang, Hye M. and Yamashita, Satoshi and Matsumoto, Yu and Ito, Mariko and Edwards, Alex and Sasaki, Junko and Dutta, Dipankar J. and Mohammad, Shahid and Yamashita, Chiho and Wetherill, Leah and Schwantes-An, Tae-Hwi and Abreu, Marco and Mahnke, Amanda H. and Mattson, Sarah N. and Foroud, Tatiana and Miranda, Rajesh C. and Chambers, Christina and Torii, Masaaki and Hashimoto-Torii, Kazue}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41380-024-02586-6}, + issn = {1476-5578}, + journal = {Molecular Psychiatry}, + keywords = {{\textgreater}UseGalaxy.eu, Biomarkers, Diseases, Neuroscience}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + pages = {1--17}, + title = {Reduction of {APOE} accounts for neurobehavioral deficits in fetal alcohol spectrum disorders}, + url = {https://www.nature.com/articles/s41380-024-02586-6}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{ilikkan_laktik_2023, + abstract = {Laktik asit bakterileri, endüstride starter kültür veya probiyotik olarak kullanılmaktadırlar. European Food Safety Authority (EFSA) tarafından 2021 yılında yayımlanan raporda gıdalarda kullanılacak bakterilerin tüm genom dizileri üzerinden risk değerlendirmesi yapılması gerekliliği vurgulanmıştır. Bu nedenle, laktik asit bakterilerinde dirençlilik geni araştırmaları önem kazanmıştır. Çünkü antibiyotik direnç genlerinin bağırsak sisteminde bulunan patojen bakterilere aktarılma olasılığı vardır ya da laktik asit bakterilerini barındıran gıdalar aracılığıyla alınmaları olasıdır. Bu nedenle, çalışmada, farklı fermente gıdalardan izole edilen dört laktik asit bakterisi (Lentilactobacillus buchneri Egmn17, Levilactobacillus brevis Atlas17, Levilactobacillus namurensis Ozge01, Lactiplantibacillus plantarum Gmze16) ve probiyotik bir bakteri olan Lactiplantibacillus plantarum 299v suşu kullanılmıştır. Çalışmada, laktik asit bakterileri arasında en yaygın antibiyotik dirençliliği gözlenen tetrasiklin seçilmiştir. 3 bakterinin tetrasiklin antibiyotiğine orta derecede dirençli (zon çapı 15-18 mm) (299v, Gmze16 ve Egmn17) ve 2 bakterinin duyarlı (zon çapı {\textgreater}19 mm) (Atlas17 ve Ozge01) olduğu belirlenmiştir. Laktik asit bakterilerinin tüm genom sekanslarının incelenmesi sonucu, orta dirençli bakterilerin tetrasikline bağlı antimikrobiyal direnç (AMR) genlerinden tetA (MFS dışa atım pompası) ve tetO’ya (ribozomal koruma proteini) sahip oldukları görülmüştür. Levilactobacillus brevis Atlas17’de ise TetA proteini mevcutken 322. aminoasit sekansında M → T değişimi gözlenmiştir. Ayrıca probiyotik bakteri olan Lactiplantibacillus plantarum 299v’nin direnç genlerine sahip olması bu genlerin bağırsaktaki patojenlere aktarılma riskini de arttırmaktadır. tetA genine sahip olduğu gözlenen Levilactobacillus brevis Atlas17 gibi fenotipi duyarlı olan türler de sessiz dirençlilik genlerine sahip olduklarında bunu diğer bakterilere aktarabilmeleri olasıdır. Bu nedenle genotip ve fenotip birlikte incelenmesi önemlidir}, + author = {Ilikkan, Özge}, + doi = {10.21597/jist.1233617}, + issn = {2536-4618}, + journal = {Journal of the Institute of Science and Technology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {tr}, + month = {June}, + note = {Number: 2 +Publisher: Igdir University}, + number = {2}, + pages = {932--940}, + title = {Laktik {Asit} {Bakterilerinde} {Tetrasiklin} {Direncinin} {Fenotipik} ve {Tüm} {Genom} {Dizilerinde} in silico {Genotipik} {Olarak} {Araştırılması}}, + url = {https://dergipark.org.tr/en/pub/jist/issue/77307/1233617}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + +@article{iniesta-pallares_changes_2023, + abstract = {The Doñana wetlands comprise an emblematic Mediterranean landscape protected as a UNESCO World Heritage Site. Some parts of these wetlands have been transformed into intensive rice cultivation areas, which are currently the most productive rice-growing areas in Europe. We examined the bacterial communities in these domesticated soils as they are key for plant health and productivity and have a strong influence on biochemical cycles. To identify the bacteria, we used metabarcoding analysis coupled with metabolic predictions and co-occurrence networks. This analysis was performed in the bulk and rhizosphere soils during different stages in the growing season. These soil compartments had a greater effect on the bacterial communities than the plant phenological stages. The diversity and richness of the bacterial population inhabiting the rhizosphere was much lower than that in the bulk soil, comprising taxa that were significantly more represented in this soil compartment, such as bacteria from the genus Hydrogenophaga, three genera from the order Rhizobiales, and unclassified genera from the families Desulfocapsaceae and Actinobacteria. Rhizosphere co-occurrence networks revealed a high number of negative connections, indicating unstable bacterial communities that may be highly influenced by biotic and abiotic factors. Rhizosphere networks mostly rely on two taxa belonging to the phyla Proteobacteria and Cyanobacteria, which are the predicted network hubs in this soil compartment. The bulk soil conserved high bacterial diversity and richness that was stable throughout the growth period of rice. Anaerobic bacteria from genera Marmoricola, the uncultured Gemmatimonadota bacteria SDR1034 terrestrial group, Anaerolinea, and the sulphur oxidizer, Thiobacillus were highly represented. This analysis provides valuable information for understanding bacterial diversity in the rhizosphere of rice cultivated in this region, which is critical for enhancing plant growth and productivity.}, + author = {Iniesta-Pallarés, Macarena and Brenes-Álvarez, Manuel and Lasa, Ana V. and Fernández-López, Manuel and Álvarez, Consolación and Molina-Heredia, Fernando P. and Mariscal, Vicente}, + doi = {10.1016/j.apsoil.2023.105013}, + issn = {0929-1393}, + journal = {Applied Soil Ecology}, + keywords = {16S rRNA, {\textgreater}UseGalaxy.eu, Bacterial potential functionality, Bacteriome, Co-occurrence networks, Metabarcoding, Rhizosphere}, + language = {en}, + month = {October}, + pages = {105013}, + title = {Changes in rice rhizosphere and bulk soil bacterial communities in the {Doñana} wetlands at different growth stages}, + url = {https://www.sciencedirect.com/science/article/pii/S0929139323002111}, + urldate = {2023-06-20}, + volume = {190}, + year = {2023} +} + +@article{ioos_harnessing_2023, + abstract = {Citrus crops are affected by many fungal diseases. Among them, Citrus Black Spot caused by the ascomycete Phyllosticta citricarpa is particularly economically damaging wherever it occurs. Many other species of Phyllosticta are described on Citrus, but only P. citricarpa is considered a quarantine pest on the European continent. In order to prevent the introduction of this species into Europe, it is essential to have a detection test which can reliably identify it, and not confuse it with other species present on citrus, notably P. paracitricarpa. The latter taxon has recently been described as very close to P. citricarpa, and most detection tests do not allow to distinguish the two species. In this work, we exploited the genomic data of 37 isolates of Phyllosticta spp. from citrus, firstly to assess their phylogenetic relationships, and secondly to search for genomic regions that allowed the definition of species-specific markers of P. citricarpa. Analysis of 51 concatenated genes separated P. citricarpa and P. paracitricarpa in two phylogenetic clades. A locus was selected to define a hydrolysis probe and primers combination that could be used in real-time PCR for the specific detection of the quarantine species, to the exclusion of all others present on Citrus. This test was then thoroughly validated on a set of strains covering a wide geographical diversity, and on numerous biological samples to demonstrate its reliability for regulatory control. The validation data highlighted the need to check the reliability of the test in advance, when a change of reagents was being considered.}, + author = {Ioos, Renaud and Puertolas, Alexandra and Renault, Camille and Ndiaye, Aida and Cerf-Wendling, Isabelle and Hubert, Jacqueline and Wang, Wen and Jiao, Chen and Li, Hongye and Armengol, Josep and Aguayo, Jaime}, + doi = {10.7717/peerj.16354}, + issn = {2167-8359}, + journal = {PeerJ}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + pages = {e16354}, + pmcid = {PMC10601906}, + pmid = {null}, + title = {Harnessing the power of comparative genomics to support the distinction of sister species within {Phyllosticta} and development of highly specific detection of {Phyllosticta} citricarpa causing citrus black spot by real-time {PCR}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10601906/}, + urldate = {2023-10-28}, + volume = {11}, + year = {2023} +} + +@article{ipoutcha_synthetic_2024, + author = {Ipoutcha, Thomas and Racharaks, Ratanachat and Huttelmaier, Stefanie and Wilson, Cole J. and Ozer, Egon A. and Hartmann, Erica M.}, + doi = {10.1128/spectrum.02897-23}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: American Society for Microbiology}, + number = {3}, + pages = {e02897--23}, + title = {A synthetic biology approach to assemble and reboot clinically relevant {Pseudomonas} aeruginosa tailed phages}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.02897-23}, + urldate = {2024-05-17}, + volume = {12}, + year = {2024} +} + +@article{ishola_comparative_2024, + abstract = {Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4\%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host’s environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome “dark matter” and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.}, + author = {Ishola, Oluwaseun A. and Kublik, Susanne and Durai Raj, Abilash Chakravarthy and Ohnmacht, Caspar and Schulz, Stefanie and Foesel, Bärbel U. and Schloter, Michael}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms12020255}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, auxiliary metabolic genes (AMGs), bacteriophages, metagenomics, murine models, prophages, virome}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {255}, + title = {Comparative {Metagenomic} {Analysis} of {Bacteriophages} and {Prophages} in {Gnotobiotic} {Mouse} {Models}}, + url = {https://www.mdpi.com/2076-2607/12/2/255}, + urldate = {2024-01-30}, + volume = {12}, + year = {2024} +} + +@article{izquierdo-lara_rise_2023, + abstract = {Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.}, + author = {Izquierdo-Lara, Ray W. and Heijnen, Leo and Oude Munnink, Bas B. and Schapendonk, Claudia M. E. and Elsinga, Goffe and Langeveld, Jeroen and Post, Johan and Prasad, Divyae K. and Carrizosa, Christian and Been, Frederic and van Beek, Janko and Schilperoort, Remy and Vriend, Rianne and Fanoy, Ewout and de Schepper, Evelien I. T. and Sikkema, Reina S. and Molenkamp, Richard and Aarestrup, Frank M. and Medema, Gertjan and Koopmans, Marion P. G. and de Graaf, Miranda}, + doi = {10.1016/j.scitotenv.2023.162209}, + issn = {0048-9697}, + journal = {Science of The Total Environment}, + keywords = {{\textgreater}UseGalaxy.eu, Next generation sequencing, RT-ddPCR, SARS-CoV-2, Single nucleotide variant, Viral diversity, Wastewater genomic surveillance}, + month = {May}, + pages = {162209}, + shorttitle = {Rise and fall of {SARS}-{CoV}-2 variants in {Rotterdam}}, + title = {Rise and fall of {SARS}-{CoV}-2 variants in {Rotterdam}: {Comparison} of wastewater and clinical surveillance}, + url = {https://www.sciencedirect.com/science/article/pii/S0048969723008252}, + urldate = {2023-10-28}, + volume = {873}, + year = {2023} +} + +@techreport{izzo_nucleophosmin_2023, + abstract = {Background The histone methyltransferase DOT1L catalyzes methylation of H3K79 and it is highly conserved in mammals. DOT1L plays a functional role in several biological processes including cell cycle regulation, DNA repair, RNA splicing and gene expression, suggesting a complex role in chromatin organization and regulation. Such a remarkable range of functions performed by DOT1L can be the result, at least partially, of its interaction with a plethora of proteins and presence in different complexes. +Results Here, we characterized the cooperation of DOT1L with the nucleolar protein NPM1 and the impact of both proteins on peri-nucleolar heterochromatin activity. We show that i) DOT1L interacts preferentially with monomeric NPM1 in the nucleus; ii) DOT1L acts in concert with NPM1 to maintain each other’s protein homeostasis; iii) NPM1 depletion results in H3K79me2 upregulation at chromatin remodeling genes but does not affect their expression; iv) DOT1L and NPM1 preserved DNA satellite expression at perinucleolar heterochromatin via epigenetic mechanisms dependent on H3K27me3. +Conclusions Our findings give insights into molecular mechanisms employed by DOT1L and NPM1 to regulate heterochromatin activities around the nucleoli and shed light on one aspect of the complex role of both proteins in chromatin dynamics.}, + author = {izzo, annalisa and akol, ipek and Villarreal, Alejandro and Garcia-Miralles, Marta and Bovio, Patrick and Heidrich, Stefanie and Vogel, Tanja}, + doi = {10.21203/rs.3.rs-2745386/v1}, + institution = {In Review}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + title = {Nucleophosmin 1 cooperates with the methyltransferase {DOT1L} to regulate {H3K79me2} levels and {DNA} satellites expression at peri-nucleolar heterochromatin}, + type = {preprint}, + url = {https://www.researchsquare.com/article/rs-2745386/v1}, + urldate = {2023-04-01}, + year = {2023} +} + +@article{jain_human_2024, + abstract = {Coronavirus disease (Covid-19) is an infectious disease which is caused by a virus named as SARS-COV. This virus belongs to the Coronavirus family that causes a variety of diseases including head and chest colds, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Metagenomics is the study of genetic material that is recuperated from the environmental samples directly. By examining and elucidating microbial genomes in healthy and infected samples, the metagenomics branch has allowed us to discover the significance of microbial genomes. The metagenomic approach used in the covid-19 infectious disease will serve as a prominent tool for explicating the relationship between host-associated microbial communities and host phenotype. European Nucleotide Archive (ENA) was used to retrieve the metagenome data of the Gut Microbiome of Covid-19 patients with the project id PRJDB12349. For metagenomics analyses, Galaxy server was used identification and classification of microbial communities furhter taxonomic analysis and functional analysis was also performed. Different tools from the galaxy like FastQC, MultiQC, Trim Galore, Megahit, Kraken 2, Convert Kraken, Krona Pie Chart and HUMANn2 were used for complete metagenomic analysis. Metagenomic Analysis shows that there is difference in the percentage and abundance of bacteria in all the covid-19 patients sample. The fungi that were commonly present in all the samples were identified as Eurotiales 78-93\% and Mycospaerellales 7-20\% and the other fungi that were not common but were observed are Dipodasceae 10\% and Sordariales 4-6\%. Further, the gene abundance and the families of the samples were also observed. This study highlights the metagenome of the Covid-19 infectious disease. The metagenomic analysis of the gut microbiome of the Covid-19 patients shows difference in the microbial community among all the samples}, + author = {Jain, Kashish and Yadav, Ruchi}, + copyright = {Copyright (c) 2024 Current Trends in Biotechnology and Pharmacy}, + doi = {10.5530/ctbp.2024.1.10}, + issn = {2230-7303}, + journal = {Current Trends in Biotechnology and Pharmacy}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19}, + language = {en}, + month = {March}, + note = {Number: 1}, + number = {1}, + pages = {1616--1628}, + title = {Human {Metagenome} {Analysis} with {COVID}-19 {Infectious} {Disease}}, + url = {https://abap.co.in/index.php/home/article/view/808}, + urldate = {2024-05-17}, + volume = {18}, + year = {2024} +} + +@article{jaki_total_2023, + abstract = {Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to the mAb cocktail REGN-COV in a kidney transplant patient with hypogammaglobulinemia. Following mAb treatment, the patient did not clear the infection. During viral persistence, SARS-CoV-2 acquired three novel spike mutations. Neutralization and mouse protection analyses demonstrate a complete viral escape from REGN-COV at the expense of ACE-2 binding. Final clearance of the virus occurred upon reduction of the immunosuppressive regimen and total IgG substitution. Serology suggests that the development of highly neutralizing IgM rather than IgG substitution aids clearance. Our findings emphasise that selection pressure by mAbs on SARS-CoV-2 can lead to development of escape variants in immunocompromised patients. Thus, modification of immunosuppressive therapy, if possible, might be preferable to control and clearance of the viral infection.}, + author = {Jaki, Lena and Weigang, Sebastian and Kern, Lisa and Kramme, Stefanie and Wrobel, Antoni G. and Grawitz, Andrea B. and Nawrath, Philipp and Martin, Stephen R. and Dähne, Theo and Beer, Julius and Disch, Miriam and Kolb, Philipp and Gutbrod, Lisa and Reuter, Sandra and Warnatz, Klaus and Schwemmle, Martin and Gamblin, Steven J. and Neumann-Haefelin, Elke and Schnepf, Daniel and Welte, Thomas and Kochs, Georg and Huzly, Daniela and Panning, Marcus and Fuchs, Jonas}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-37591-w}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Immune evasion, Outcomes research, SARS-CoV-2, Viral evolution, Viral infection}, + language = {en}, + month = {April}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1999}, + title = {Total escape of {SARS}-{CoV}-2 from dual monoclonal antibody therapy in an immunocompromised patient}, + url = {https://www.nature.com/articles/s41467-023-37591-w}, + urldate = {2023-06-05}, + volume = {14}, + year = {2023} +} + @article{jalili_galaxy_2020, abstract = {Abstract. Galaxy (https://galaxyproject.org) is a web-based computational workbench used by tens of thousands of scientists across the world to analyze large b}, author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton}, @@ -2000,25 +4866,235 @@ @article{jalili_galaxy_2020 year = {2020} } -@article{jude_draft_2019, - abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.}, - author = {Jude, Brooke A.}, - doi = {10.1128/MRA.00683-19}, - editor = {Dunning Hotopp, Julie C.}, - issn = {2576-098X}, - journal = {Microbiology Resource Announcements}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, +@article{jarvis_semi-automated_2022, + abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.}, + author = {Jarvis, Erich D. and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R. and Porubsky, David and Cheng, Haoyu and Asri, Mobin and Logsdon, Glennis A. and Carnevali, Paolo and Chaisson, Mark J. P. and Chin, Chen-Shan and Cody, Sarah and Collins, Joanna and Ebert, Peter and Escalona, Merly and Fedrigo, Olivier and Fulton, Robert S. and Fulton, Lucinda L. and Garg, Shilpa and Gerton, Jennifer L. and Ghurye, Jay and Granat, Anastasiya and Green, Richard E. and Harvey, William and Hasenfeld, Patrick and Hastie, Alex and Haukness, Marina and Jaeger, Erich B. and Jain, Miten and Kirsche, Melanie and Kolmogorov, Mikhail and Korbel, Jan O. and Koren, Sergey and Korlach, Jonas and Lee, Joyce and Li, Daofeng and Lindsay, Tina and Lucas, Julian and Luo, Feng and Marschall, Tobias and Mitchell, Matthew W. and McDaniel, Jennifer and Nie, Fan and Olsen, Hugh E. and Olson, Nathan D. and Pesout, Trevor and Potapova, Tamara and Puiu, Daniela and Regier, Allison and Ruan, Jue and Salzberg, Steven L. and Sanders, Ashley D. and Schatz, Michael C. and Schmitt, Anthony and Schneider, Valerie A. and Selvaraj, Siddarth and Shafin, Kishwar and Shumate, Alaina and Stitziel, Nathan O. and Stober, Catherine and Torrance, James and Wagner, Justin and Wang, Jianxin and Wenger, Aaron and Xiao, Chuanle and Zimin, Aleksey V. and Zhang, Guojie and Wang, Ting and Li, Heng and Garrison, Erik and Haussler, David and Hall, Ira and Zook, Justin M. and Eichler, Evan E. and Phillippy, Adam M. and Paten, Benedict and Howe, Kerstin and Miga, Karen H.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41586-022-05325-5}, + issn = {1476-4687}, + journal = {Nature}, + keywords = {{\textgreater}UseGalaxy.eu, Centromeres, Genetic variation, Genome assembly algorithms, Genomics}, language = {en}, - month = {August}, - number = {35}, - pages = {e00683--19, /mra/8/35/MRA.00683--19.atom}, - title = {Draft {Genome} {Sequence} of a {Chitinimonas} {Species} from {Hudson} {Valley} {Waterways} {That} {Expresses} {Violacein} {Pigment}}, - url = {http://genomea.asm.org/lookup/doi/10.1128/MRA.00683-19}, - urldate = {2019-09-20}, + month = {November}, + note = {Number: 7936 +Publisher: Nature Publishing Group}, + number = {7936}, + pages = {519--531}, + title = {Semi-automated assembly of high-quality diploid human reference genomes}, + url = {https://www.nature.com/articles/s41586-022-05325-5}, + urldate = {2022-12-03}, + volume = {611}, + year = {2022} +} + +@article{javed_unraveling_2023, + abstract = {The plant pathogen Magnaporthe oryzae poses a significant threat to global food security, and its management through the cultivation of resistant varieties and crop husbandry practices, including fungicidal sprays, has proven to be inadequate. To address this issue, we conducted small-RNA sequencing to identify the roles of miRNAs and their target genes in both resistant (PB1637) and susceptible (PB1) rice genotypes. We confirmed the expression of differentially expressed miRNAs using stem-loop qRT-PCR analysis and correlated them with rice patho-phenotypic and physio-biochemical responses. Our findings revealed several noteworthy differences between the resistant and susceptible genotypes. The resistant genotype exhibited reduced levels of total chlorophyll and carotenoids compared to the susceptible genotype. However, it showed increased levels of total protein, callose, H2O2, antioxidants, flavonoids, and total polyphenols. Additionally, among the defense-associated enzymes, guaiacol peroxidase and polyphenol oxidase responses were higher in the susceptible genotypes. In our comparative analysis, we identified 27 up-regulated and 43 down-regulated miRNAs in the resistant genotype, while the susceptible genotype exhibited 44 up-regulated and 62 down-regulated miRNAs. Furthermore, we discovered eight up-regulated and five down-regulated miRNAs shared between the resistant and susceptible genotypes. Notably, we also identified six novel miRNAs in the resistant genotype and eight novel miRNAs in the susceptible genotype. These novel miRNAs, namely Chr8\_26996, Chr12\_40110, and Chr12\_41899, were found to negatively correlate with the expression of predicted target genes, including Cyt-P450 monooxygenase, serine carboxypeptidase, and zinc finger A20 domain-containing stress-associated protein, respectively. The results of our study on miRNA and transcriptional responses provide valuable insights for the development of future rice lines that are resistant to blast disease. By understanding the roles of specific miRNAs and their target genes in conferring resistance, we can enhance breeding strategies and improve crop management practices to ensure global food security.}, + author = {Javed, Mohammed and Reddy, Bhaskar and Sheoran, Neelam and Ganesan, Prakash and Kumar, Aundy}, + doi = {10.1016/j.gene.2023.147718}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Biochemical, Blast, Physiological, Rice, Transcriptome, miRNA}, + month = {November}, + pages = {147718}, + title = {Unraveling the transcriptional network regulated by {miRNAs} in blast-resistant and blast-susceptible rice genotypes during {Magnaporthe} oryzae interaction}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111923005590}, + urldate = {2023-12-03}, + volume = {886}, + year = {2023} +} + +@article{jdeed_redistribution_2022, + abstract = {Therapeutic targets in cancer cells defective for the tumor suppressor ARID1A are fundamentals of synthetic lethal strategies. However, whether modulating ARID1A function in premalignant breast epithelial cells could be exploited to reduce carcinogenic potential remains to be elucidated. In search of chromatin-modulating mechanisms activated by anti-proliferative agents in normal breast epithelial (HME-hTert) cells, we identified a distinct pattern of genome-wide H3K27 histone acetylation marks characteristic for the combined treatment by the cancer preventive rexinoid bexarotene (Bex) and carvedilol (Carv). Among these marks, several enhancers functionally linked to TGF-β signaling were enriched for ARID1A and Brg1, subunits within the SWI/SNF chromatin-remodeling complex. The recruitment of ARID1A and Brg1 was associated with the suppression of TGFBR2, KLF4, and FoxQ1, and the induction of BMP6, while the inverse pattern ensued upon the knock-down of ARID1A. Bex+Carv treatment resulted in fewer cells expressing N-cadherin and dictated a more epithelial phenotype. However, the silencing of ARID1A expression reversed the ability of Bex and Carv to limit epithelial–mesenchymal transition. The nuclear levels of SMAD4, a canonical mediator of TGF-β action, were more effectively suppressed by the combination than by TGF-β. In contrast, TGF-β treatment exceeded the ability of Bex+Carv to lower nuclear FoxQ1 levels and induced markedly higher E-cadherin positivity, indicating a target-selective antagonism of Bex+Carv to TGF-β action. In summary, the chromatin-wide redistribution of ARID1A by Bex and Carv treatment is instrumental in the suppression of genes mediating TGF-β signaling, and, thus, the morphologic reprogramming of normal breast epithelial cells. The concerted engagement of functionally linked targets using low toxicity clinical agents represents an attractive new approach for cancer interception.}, + author = {Jdeed, Sham and Lengyel, Máté and Uray, Iván P.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cells11172633}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, ARID1A, FoxQ1, SWI/SNF, TGF-β, bexarotene, epithelial–mesenchymal transition}, + language = {en}, + month = {January}, + number = {17}, + pages = {2633}, + title = {Redistribution of the {SWI}/{SNF} {Complex} {Dictates} {Coordinated} {Transcriptional} {Control} over {Epithelial}–{Mesenchymal} {Transition} of {Normal} {Breast} {Cells} through {TGF}-β {Signaling}}, + url = {https://www.mdpi.com/2073-4409/11/17/2633}, + urldate = {2022-09-24}, + volume = {11}, + year = {2022} +} + +@article{jeon_tailored_2023, + abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been frequently reported in companion dogs and cats worldwide during the ongoing coronavirus disease. However, RT-qPCR methods developed for humans have been used for the diagnosis of SARS-CoV-2 infections in suspected companion dogs and cats owing to the lack of the companion animal-tailored methods. Therefore, we developed a multiplex RT-qPCR (mRT-qPCR) using newly designed primers and probes targeting RdRp and N genes of all currently circulating SARS-CoV-2 variants as well as the canine or feline 16S rRNA gene as an endogenous internal positive control (EIPC) for reliable diagnosis of SARS-CoV-2 infection from suspected dogs and cats. The developed mRT-qPCR assay specifically detected the target genes of SARS-CoV-2 but no other canine or feline pathogens. Furthermore, canine and feline EIPCs were stably amplified by mRT-qPCR in samples containing canine- or feline-origin cellular materials. This assay has high repeatability and reproducibility, with an optimal limit of detection ({\textless}10 RNA copies per reaction) and coefficients of variation ({\textless}1.0\%). The detection rate of SARS-CoV-2 of the developed mRT-qPCR was 6.6\% for canine and feline nasopharyngeal samples, which was consistent with that of a commercial mRT-qPCR kit for humans. Collectively, the newly developed mRT-qPCR with canine and feline EIPC can efficiently diagnose and evaluate the viral load in field specimens and will be a valuable tool for etiological diagnosis, epidemiological study, and controlling SARS-CoV-2 infections in canine and feline populations.}, + author = {Jeon, Gyu-Tae and Kim, Hye-Ryung and Kim, Jong-Min and Baek, Ji-Su and Shin, Yeun-Kyung and Kwon, Oh-Kyu and Kang, Hae-Eun and Cho, Ho-Seong and Cheon, Doo-Sung and Park, Choi-Kyu}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ani13040602}, + issn = {2076-2615}, + journal = {Animals}, + keywords = {\textit{N} gene, \textit{RdRp} gene, {\textgreater}UseGalaxy.eu, SARS-CoV-2, internal positive control, multiplex real-time RT-PCR}, + language = {en}, + month = {January}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {602}, + title = {Tailored {Multiplex} {Real}-{Time} {RT}-{PCR} with {Species}-{Specific} {Internal} {Positive} {Controls} for {Detecting} {SARS}-{CoV}-2 in {Canine} and {Feline} {Clinical} {Samples}}, + url = {https://www.mdpi.com/2076-2615/13/4/602}, + urldate = {2023-03-15}, + volume = {13}, + year = {2023} +} + +@article{jesudoss_chelladurai_comparative_2023, + abstract = {Dipylidium caninum (Linnaeus, 1758) is a common zoonotic cestode of dogs and cats worldwide. Previous studies have demonstrated the existence of largely host-associated canine and feline genotypes based on infection studies, differences at the 28S rDNA gene, and complete mitochondrial genomes. There have been no comparative genome-wide studies. Here, we sequenced the genomes of a dog and cat isolate of Dipylidium caninum from the United States using the Illumina platform at mean coverage depths of 45× and 26× and conducted comparative analyses with the reference draft genome. Complete mitochondrial genomes were used to confirm the genotypes of the isolates. Genomes of D. caninum canine and feline genotypes generated in this study, had an average identity of 98\% and 89\%, respectively, when compared to the reference genome. SNPs were 20 times higher in the feline isolate. Comparison and species delimitation using universally conserved orthologs and protein-coding mitochondrial genes revealed that the canine and feline isolates are different species. Data from this study build a base for future integrative taxonomy. Further genomic studies from geographically diverse populations are necessary to understand implications for taxonomy, epidemiology, veterinary clinical medicine, and anthelmintic resistance.}, + author = {Jesudoss Chelladurai, Jeba R. J. and Abraham, Aloysius and Quintana, Theresa A. and Ritchie, Deb and Smith, Vicki}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/pathogens12050675}, + issn = {2076-0817}, + journal = {Pathogens}, + keywords = {\textit{Dipylidium caninum}, {\textgreater}UseGalaxy.eu, cat and dog, cestode, flea tapeworm, genome comparison, species delimitation}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {675}, + shorttitle = {Comparative {Genomic} {Analysis} and {Species} {Delimitation}}, + title = {Comparative {Genomic} {Analysis} and {Species} {Delimitation}: {A} {Case} for {Two} {Species} in the {Zoonotic} {Cestode} {Dipylidium} caninum}, + url = {https://www.mdpi.com/2076-0817/12/5/675}, + urldate = {2023-06-05}, + volume = {12}, + year = {2023} +} + +@article{jhinjharia_high-throughput_2023, + abstract = {Diabetes mellitus is a metabolic disorder that persists as a global threat to the world. A G-protein coupled receptor (GPCR), free fatty acid receptor 4 (FFAR4), has emerged as a potential target for type 2 diabetes mellitus (T2DM) and obesity-related disorders. The current study has investigated the FFAR4, deploying 3-dimensional structure modeling, molecular docking, machine learning, and high-throughput virtual screening methods to unravel the receptor’s crucial and non-crucial binding site residues. We screened four lakh compounds and shortlisted them based on binding energy, stereochemical considerations, non-bonded interactions, and pharmacokinetic profiling. Out of the screened compounds, four compounds were selected for ligand-bound simulations. The molecular dynamic simulations were carried out for 1µs for native FFAR4 and 500 ns each for complexes of FFAR4 with compound 1, compound 2, compound 3, and compound 4. Our findings showed that in addition to reported binding site residues ARG99, ARG183, and VAL98 in known agonists like TUG-891, the amino acids ARG22, ARG24, THR23, TRP305, and GLU43 were also critical binding site residues. These amino acids impart stability to the FFAR4 complexes and contribute to the stronger binding affinity of the compounds. The study also indicated that aromatic residues like PHE211 are crucial for recognizing the active site’s pi-pi and C-C double bonds. Since FFAR4 is a membrane protein, the simulation studies give an insight into the mechanisms of the crucial protein-lipid and lipid-water interactions. The analysis of the molecular dynamics trajectories showed all four compounds as potential hit molecules that can be developed further into potential agonists for T2DM therapy. Amongst the four compounds, compound 4 showed relatively better binding affinity, stronger non-bonded interactions, and a stable complex. Communicated by Ramaswamy H. Sarma}, + author = {Jhinjharia, Divya and Kaushik, Aman Chandra and Sahi, Shakti}, + doi = {10.1080/07391102.2023.2280707}, + issn = {0739-1102}, + journal = {Journal of Biomolecular Structure and Dynamics}, + keywords = {{\textgreater}ChemicalToolbox, FFAR4, HTVS, diabetes, machine-learning, molecular dynamic simulations}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/07391102.2023.2280707}, + number = {0}, + pages = {1--21}, + pmid = {37978906}, + title = {A high-throughput structural dynamics approach for identification of potential agonists of {FFAR4} for type 2 diabetes mellitus therapy}, + url = {https://doi.org/10.1080/07391102.2023.2280707}, + urldate = {2023-11-22}, + volume = {0}, + year = {2023} +} + +@incollection{jia_salmonella_2024, + abstract = {Salmonella is a widespread pathogen that can cause a variety of disease syndromes, thereby having a tremendous impact on human health and animal husbandry. Currently, whole genome sequencing technology has been widely used to study the phylogenetic relationships of Salmonella, primarily using the Illumina short-read platform. Complete genome sequence data of Salmonella are rarely systematically analyzed in similar studies considering the relatively high cost currently. Therefore, here we collected the complete genome sequence data of 1819 Salmonella in GenBank and classified these strains into different subspecies, serovars, and STs by SISTR, Seqsero2, multilocus sequence typing (MLST), and other sophisticated software. In addition, we constructed and demonstrated different phylogenetic trees by four methods with high discriminatory power: core single-nucleotide polymorphism typing, core genome MLST (cgMLST), clustered regularly interspaced short palindromic repeat typing, and pan-genome typing. The different typing methods are systematically presented, along with a comparison of the characteristics of the four distinct typing methods used in this chapter. In conclusion, we have made a new attempt to use complete genome sequence datasets to study the phylogenetic relationships of Salmonella. Additional considerations regarding the time required to be consumed, the clustering effect, and the cgMLST method are also discussed.}, + author = {Jia, Chenghao and Zhou, Haiyang and Wang, Zining and Liu, Yuhao and Yue, Min}, + booktitle = {Phylogenomics}, + doi = {10.1016/B978-0-323-99886-4.00019-3}, + editor = {Mokrousov, Igor and Shitikov, Egor}, + isbn = {978-0-323-99886-4}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR typing, cgMLST, core SNP typing, pan-genome typing, phylogenomic analysis}, + month = {January}, + pages = {267--281}, + publisher = {Academic Press}, + title = {\textit{{Salmonella}} phylogenomics}, + url = {https://www.sciencedirect.com/science/article/pii/B9780323998864000193}, + urldate = {2024-06-07}, + year = {2024} +} + +@article{joshi_physicochemical_2024, + abstract = {Prostate cancer is the most common cancer among men which has major diagnosis in the United States in 2017. Among DYRK class II members, dual specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) is the functional target for prostate cancer treatment. Studies show that subfamilies of DYRKs are also capable to phosphorylate (tyrosine, serine, and threonine) residues, yet little research has been carried out for its inhibitors. In this article, conceptual density theory is used to estimate the physicochemical properties of 30 experimentally synthesized inhibitors targeting DYRK2. The HOMO–LUMO gap showed low reactivity and high chemical activity for the inhibitors. The biological efficacy of these 30 inhibitors is predicted by bioavailability, mutagenicity, and cardiotoxicity measures. The inhibitors showed low toxicity and no blood brain barrier permeability. Results indicated that the physiological actions of these inhibitors involve multiple target interactions. Since the experimental results of the DYRK2 protein showed great water solubility, favorable safety properties, and potential anti-prostate cancer activities for ligand 24, docking and molecular dynamics simulations from the Galaxy webserver using Gromacs open-source tools are also performed for (DYRK2-24) complex (PDB: 7EJV). (DYRK2-24) showed strong binding affinity and noncovalent interactions.}, + author = {Joshi, Sravani and Srivastava, Ruby}, + copyright = {© 2024 Vietnam Academy of Science and Technology and Wiley-VCH GmbH.}, + doi = {10.1002/vjch.202300313}, + issn = {2572-8288}, + journal = {Vietnam Journal of Chemistry}, + keywords = {{\textgreater}UseGalaxy.eu, diagnosis, drugs, dual specificity tyrosine phosphorylation-regulated kinase 2, phosphorylation, prostate cancer}, + language = {en}, + month = {April}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/vjch.202300313}, + number = {n/a}, + title = {Physicochemical properties and biological efficacy of 30 {DYRK2} {Inhibitors} for the treatment of prostate cancer}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/vjch.202300313}, + urldate = {2024-05-17}, + volume = {n/a}, + year = {2024} +} + +@article{joshi_tracing_2024, + abstract = {Pharmacological drugs targeting specific pathways involved in various diseases have seen recent advancement with newer and more efficient emerging drug targets but these drugs are limited in terms of their side effects and patient adherence. The potential of plant-based diets in the form of functional foods is increasingly being realized as an option to treat and/or prevent several diseases. In this work, we have selected flaxseed (Linum usitatissimum), also known as linseed to study its pharmacological efficacy and proposed mechanisms of action for medicinal purposes. The target genes of linseed with disease specificity index (DSI {\textgreater} 0.6) are compared to the associated genes of diabetes mellitus, decrease in appetite, addictive behavior, cardiovascular diseases, Inflammatory Bowel Diseases (IMD), Polycystic Ovary Syndrome (PCOS) and the selected genes are evaluation further using in silico methods. The binding affinity of flaxseed to three common target proteins family (CCDC28b, PDCD6IP and USP34) is assessed by docking and Molecular dynamics (MD) simulations. Results show that linseed is safe to use for mutagenic toxicity and other cardiotoxicity measures but linseed is unsafe for embryotoxicity, herG toxicity and cardiac failure. The protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis indicates that flaxseed can be used as a medicinal herb for diabetes mellitus, cardiovascular diseases, Inflammatory Bowel Diseases (IMD) and Polycystic Ovary Syndrome (PCOS).}, + author = {Joshi, Sravani and Srivastava, Ruby}, + doi = {10.3389/fchem.2023.1276052}, + issn = {2296-2646}, + journal = {Frontiers in Chemistry}, + keywords = {{\textgreater}UseGalaxy.eu, Flaxseed, Hypertension, addictions, cardiovascular, side effects}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools}, + url = {https://www.frontiersin.org/articles/10.3389/fchem.2023.1276052}, + urldate = {2024-05-17}, + volume = {11}, + year = {2024} +} + +@article{jovovic_novo_2024, + abstract = {Isopods are a diverse group of crustaceans, that inhabit various environments, including terrestrial, freshwater, and marine, both on the surface and in the underground. The biological mechanisms underlying their wide range of adaptations to diverse ecological niches remain elusive. In order to unravel the molecular basis of their adaptability, we generated a comprehensive RNAseq dataset comprising 11 isopod species belonging to the three different suborders: freshwater Asellota, marine, brackish and freshwater Sphaeromatidea, and terrestrial Oniscidea, with representatives from families Asellidae, Sphaeromatidae, and Trichoniscidae, respectively. Representatives of each family were collected from both cave and surface environments, representing at least three independent cave colonization events. Three biological replicates were sequenced from each species to ensure data robustness. The 11 high-quality RNAseq datasets will serve as a valuable resource for understanding cave-specific adaptations, comparative and functional genomics, ecological annotation as well as aid in conservation efforts of these non-model organisms. Importantly, transcriptomes of eight featured species have been made publicly accessible for the first time.}, + author = {Jovović, Lada and Bedek, Jana and Malard, Florian and Bilandžija, Helena}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41597-024-03393-y}, + issn = {2052-4463}, + journal = {Scientific Data}, + keywords = {{\textgreater}UseGalaxy.eu, Molecular ecology, Molecular evolution, Transcriptomics}, + language = {en}, + month = {June}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {595}, + shorttitle = {De novo transcriptomes of cave and surface isopod crustaceans}, + title = {De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders}, + url = {https://www.nature.com/articles/s41597-024-03393-y}, + urldate = {2024-06-08}, + volume = {11}, + year = {2024} +} + +@article{jude_draft_2019, + abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.}, + author = {Jude, Brooke A.}, + doi = {10.1128/MRA.00683-19}, + editor = {Dunning Hotopp, Julie C.}, + issn = {2576-098X}, + journal = {Microbiology Resource Announcements}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + number = {35}, + pages = {e00683--19, /mra/8/35/MRA.00683--19.atom}, + title = {Draft {Genome} {Sequence} of a {Chitinimonas} {Species} from {Hudson} {Valley} {Waterways} {That} {Expresses} {Violacein} {Pigment}}, + url = {http://genomea.asm.org/lookup/doi/10.1128/MRA.00683-19}, + urldate = {2019-09-20}, volume = {8}, year = {2019} } +@article{kahraman-ilikkan_comparative_2024, + abstract = {Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.}, + author = {Kahraman-Ilıkkan, Özge}, + doi = {10.1007/s00438-024-02129-2}, + issn = {1617-4623}, + journal = {Molecular Genetics and Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Identification, Lactic acid bacteria, Vitek MS (MALDI-TOF), Whole genome sequencing}, + language = {en}, + month = {March}, + number = {1}, + pages = {31}, + title = {Comparative genomics of four lactic acid bacteria identified with {Vitek} {MS} ({MALDI}-{TOF}) and whole-genome sequencing}, + url = {https://doi.org/10.1007/s00438-024-02129-2}, + urldate = {2024-05-17}, + volume = {299}, + year = {2024} +} + @article{kaiser_mutational_2021, author = {Kaiser, Vera B. and Talmane, Lana and Kumar, Yatendra and Semple, Fiona and MacLennan, Marie and FitzPatrick, David R. and Taylor, Martin S. and and, Colin A. Semple}, doi = {10.1101/2021.06.10.447556}, @@ -2048,6 +5124,103 @@ @article{kalmbach_genome-wide_2019 year = {2019} } +@article{kalnytska_sorcs2_2024, + abstract = {Sorting receptor SORCS2 is a stress-response factor protecting neurons from acute insults, such as during epilepsy. SORCS2 is also expressed in the pancreas, yet its action in this tissue remains unknown. Combining metabolic studies in SORCS2-deficient mice with ex vivo functional analyses and single-cell transcriptomics of pancreatic tissues, we identified a role for SORCS2 in protective stress response in pancreatic islets, essential to sustain insulin release. We show that SORCS2 is predominantly expressed in islet alpha cells. Loss of expression coincides with inability of these cells to produce osteopontin, a secreted factor that facilitates insulin release from stressed beta cells. In line with diminished osteopontin levels, beta cells in SORCS2-deficient islets show gene expression patterns indicative of aggravated cell stress, and exhibit defects in insulin granule maturation and a blunted glucose response. These findings corroborate a function for SORCS2 in protective stress response that extends to metabolism.}, + author = {Kalnytska, Oleksandra and Qvist, Per and Kunz, Séverine and Conrad, Thomas and Willnow, Thomas E. and Schmidt, Vanessa}, + doi = {10.1016/j.isci.2023.108725}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu, Biological sciences, Endocrinology, Natural sciences, Physiology}, + month = {January}, + number = {1}, + pages = {108725}, + title = {{SORCS2} activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells}, + url = {https://www.sciencedirect.com/science/article/pii/S258900422302802X}, + urldate = {2024-05-17}, + volume = {27}, + year = {2024} +} + +@article{kandinov_azithromycin_2023, + abstract = {The aim of this work was to study the resistance to macrolides (azithromycin) in the modern Russian population of N. gonorrhoeae with the analysis of genetic resistance determinants. Azithromycin is not used to treat gonococcal infection in Russia. However, among 162 isolates collected in 2020–2021, 22 isolates (13.6\%) were phenotypically resistant to azithromycin. Mutations in 23S rRNA genes were found only in two isolates; erm and mefA genes were absent. Azithromycin resistance was shown to be predominantly associated with mutations in the mtrR and mtrD genes of the MtrCDE efflux pump and their mosaic alleles which may have formed due to a horizontal transfer from N. meningitidis. A total of 30 types of mtrR alleles and 10 types of mtrD alleles were identified including mosaic variants. Matching between the mtrR and mtrD alleles was revealed to indicate the cooperative molecular evolution of these genes. A link between the mtrR and mtrD alleles and NG-MAST types was found only for NG-MAST 228 and 807, typical of N. gonorrhoeae in Russia. The high level of resistance to azithromycin in Russia may be related to the spread of multiple transferable resistance to antimicrobials regardless of their use in the treatment of gonococcal infection.}, + author = {Kandinov, Ilya and Shaskolskiy, Boris and Kravtsov, Dmitry and Vinokurova, Alexandra and Gorshkova, Sofya and Kubanov, Alexey and Solomka, Victoria and Shagabieva, Julia and Deryabin, Dmitry and Dementieva, Ekaterina and Gryadunov, Dmitry}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12010170}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Neisseria gonorrhoeae}, \textit{mtrR} and \textit{mtrD} alleles, {\textgreater}UseGalaxy.eu, azithromycin resistance, efflux pump, resistance determinants}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {170}, + title = {Azithromycin {Susceptibility} {Testing} and {Molecular} {Investigation} of {Neisseria} gonorrhoeae {Isolates} {Collected} in {Russia}, 2020–2021}, + url = {https://www.mdpi.com/2079-6382/12/1/170}, + urldate = {2023-03-15}, + volume = {12}, + year = {2023} +} + +@article{kandinov_emergence_2023, + abstract = {The goal of this work was to determine the factors affecting the emergence of azithromycin-resistant Neisseria gonorrhoeae isolates in Russia, where azithromycin was never recommended for the treatment of gonococcal infections. Clinical N. gonorrhoeae isolates collected in 2018–2021 (428 isolates) were analyzed. No azithromycin-resistant isolates were found in 2018–2019, but in 2020–2021, a significant increase in the ratio of azithromycin-resistant isolates was observed: 16.8\% and 9.3\%, respectively. A hydrogel DNA microarray was developed for the analysis of resistance determinants: mutations in the genes encoding the mtrCDE efflux system and in all four copies of the 23S rRNA gene (position 2611). A majority of the azithromycin-resistant Russian isolates belonged to the NG-MAST G12302 genogroup, and the resistance was associated with the presence of a mosaic structure of the mtrR gene promoter region with the −35 delA deletion, an Ala86Thr mutation in the mtrR gene, and a mosaic structure of the mtrD gene. A comparative phylogenetic study of modern Russian and European N. gonorrhoeae populations allowed us to conclude that the emergence of azithromycin resistance in Russia in 2020 was the result of the appearance and spread of European N. gonorrhoeae strains belonging to the G12302 genogroup due to possible cross-border transfer.}, + author = {Kandinov, Ilya and Dementieva, Ekaterina and Filippova, Marina and Vinokurova, Alexandra and Gorshkova, Sofya and Kubanov, Alexey and Solomka, Victoria and Shagabieva, Julia and Deryabin, Dmitry and Shaskolskiy, Boris and Gryadunov, Dmitry}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms11051226}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, G12302 genogroup, NG-MAST, azithromycin resistance, genetic determinants of antimicrobial resistance, phylogenetic analysis}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {1226}, + title = {Emergence of {Azithromycin}-{Resistant} {Neisseria} gonorrhoeae {Isolates} {Belonging} to the {NG}-{MAST} {Genogroup} 12302 in {Russia}}, + url = {https://www.mdpi.com/2076-2607/11/5/1226}, + urldate = {2023-07-31}, + volume = {11}, + year = {2023} +} + +@article{kandinov_mini-multilocus_2024, + abstract = {The increasing problem of antimicrobial resistance in N. gonorrhoeae necessitates the development of molecular typing schemes that are suitable for rapid and mass screening. The objective of this study was to design and validate a mini-MLST scheme for N. gonorrhoeae based on global pathogen population data. Using sequences of seven housekeeping genes of 21,402 isolates with known MLSTs from the PubMLST database, we identified eighteen informative polymorphisms and obtained mini-MLST nucleotide profiles to predict MLSTs of isolates. We proposed a new MLST grouping system for N. gonorrhoeae based on mini-MLST profiles. Phylogenetic analysis revealed that MLST genogroups are a stable characteristic of the N. gonorrhoeae global population. The proposed grouping system has been shown to bring together isolates with similar antimicrobial susceptibility, as demonstrated by the characteristics of major genogroups. Established MLST prediction algorithms based on nucleotide profiles are now publicly available. The mini-MLST scheme was evaluated using a MLST detection/prediction method based on the original hydrogel DNA microarray. The results confirmed a high predictive ability up to the MLST genogroup. The proposed holistic approach to gonococcal population analysis can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.}, + author = {Kandinov, Ilya and Shaskolskiy, Boris and Kravtsov, Dmitry and Filippova, Marina and Larkin, Anatoliy and Gryadunov, Dmitry}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25115781}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, antimicrobial resistance, genogroups, informative polymorphisms, multilocus sequence typing, oligonucleotide microarray, phylogenetic analysis}, + language = {en}, + month = {January}, + note = {Number: 11 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {11}, + pages = {5781}, + title = {Mini-{Multilocus} {Sequence} {Typing} {Scheme} for the {Global} {Population} of {Neisseria} gonorrhoeae}, + url = {https://www.mdpi.com/1422-0067/25/11/5781}, + urldate = {2024-06-07}, + volume = {25}, + year = {2024} +} + +@article{karthik_foremost_2023, + abstract = {Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN\_CUL\_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN\_CUL\_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.}, + author = {Karthik, Kumaragurubaran and Anbazhagan, Subbaiyan and Ananda Chitra, Murugesan and Ramya, Rajendran and Sridhar, Ramaswamy and Dhinakar Raj, Gopal}, + doi = {10.1016/j.gene.2023.147359}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, India, Pigeon, Vitek 2}, + language = {en}, + month = {May}, + pages = {147359}, + title = {Foremost report of the whole genome of {Spirabiliibacterium} mucosae from {India} and comparative genomics of the novel genus {Spirabiliibacterium}}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111923002007}, + urldate = {2023-07-31}, + volume = {867}, + year = {2023} +} + @article{katsanos_gene_2021, author = {Katsanos, Dimitris and Ferrando-Marco, Mar and Razzaq, Iqrah and Aughey, Gabriel and Southall, Tony D. and Barkoulas, Michalis}, doi = {10.1242/dev.199452}, @@ -2089,6 +5262,133 @@ @article{kavas_genome-wide_2021 year = {2021} } +@article{kavas_genome-wide_2022, + abstract = {The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. A comprehensive genome-wide analysis was performed in its genome to understand the role of DDP genes (DUF221) in the common bean (Phaseolus vulgaris L.). A total of 12 DDP genes were identified and distributed in 8 chromosomes in the common bean genome. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of DDP members were determined. Phylogenetically all PvDDPs were clustered into nine clades, subsequently supported by their gene structure and conserved motifs distribution. The PvDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. A total of 45 different cis-regulatory elements in the putative promoter regions of the PvDDPs were identified. ERE and ABRE were discovered to be present in all PvDDPs, indicating that they may be regulated by ethylene and ABA, both of which are strongly associated with biotic stress response in plant species. Additionally, PvDDPs were targeted by multiple miRNA gene families as well. In this context, the most targeted DDP family members are PvDD10 and PvDDP11. The miRNA target analysis showed that Pvu-miR2594, Pvu-miR169, Pvu-miR2584, Pvu-miR530, Pvu-miR156, and Pvu-miR2592 target these genes. There is a strong correlation between abiotic stress and PvDDPs expression in both leaf and root tissues. PvDDP11 is the unique and highest upregulated gene with hormone treatment and abiotic stress among all the members. Expression of the PvDDP11 gene indicated a strong correlation with drought and salt stress in the common bean roots and leaves, respectively. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in common bean.}, + author = {Kavas, Musa and Mostafa, Karam and Seçgin, Zafer and Yerlikaya, Bayram Ali and Yıldırım, Kubilay and Gökdemir, Gökhan}, + doi = {10.1007/s10722-022-01421-7}, + issn = {1573-5109}, + journal = {Genetic Resources and Crop Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, ABA, Abiotic stress, DUF221, IAA, RSN1\_7TM, miRNA}, + language = {en}, + month = {July}, + title = {Genome-wide analysis of {DUF221} domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response}, + url = {https://doi.org/10.1007/s10722-022-01421-7}, + urldate = {2022-09-24}, + year = {2022} +} + +@phdthesis{kefi_improving_2023, + abstract = {The Human Genome Annotation (HGA) file is a database where different features describing elements of the genome (genes, transcripts, etc) are stored. HGA is the process of identifying those elements, characterizing them and elucidating their roles. Currently, HGA is still incomplete because it suffers from missed annotation and mis-annotation. Mis-annotation happens when some elements are wrongly annotated or labeled. Missed annotation happens when some elements are absent from the annotation files due to the limitations of analytical and experimental procedures. On one hand, improved identification of novel genome elements is required to help solve the problem of missed annotation. On the other hand, to address the problem of mis-annotation, better classification methods are needed to characterize and validate the novel elements. This thesis addresses the problem of incomplete human genome annotation and proposes an improved identification and validation approach via integration of second and third generation of sequencing. We apply this integrative approach to detect novel mono-exonic genes (MNEGs) and confirm their transcription and translation. Up until recent studies, MNEGs were thought to be artifacts and were discarded. However, our integrative analysis provided additional evidence for the genuine existence of these genes. In the second part of this project, we used computational methods based on a deep learning framework to validate these findings by characterizing MNEG types and classifying them into either proteins coding RNAs (pcRNAs) or long non-coding RNAs (lncRNAs). Our results showed that the majority of MNEGs are classified as lncRNAs and further investigation suggested that some of them are circRNAs. Finally, this work provides an innovative approach and a unique computational framework to address the problem of incomplete HGA and could be adopted by the annotators in their pipelines. This study is an important step towards the completion and the improvement of the human genome annotation.}, + address = {Ann Arbor, United States}, + author = {Kefi, Amira}, + copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.}, + keywords = {{\textgreater}UseGalaxy.eu, Deep learning, Genome annotation, ISOseq, Machine learning, RNAseq, Ribo-seq}, + language = {Englisch}, + note = {ISBN: 9798379745967}, + title = {Improving the {Human} {Genome} {Annotation} {Using} {Integrative} {Analysis} and {Deep} {Learning} {Methods}}, + type = {Ph.{D}.}, + url = {https://www.proquest.com/docview/2830283170/abstract/B6B2BD2F6A44FF9PQ/1}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{khan_comparative_2023, + abstract = {Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. FAE (Fatty Acid Elongation) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS (Ketoacyl-CoA synthase) and ELO (Elongation Defective Elongase) sub-gene families. The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. Polyploidization has also increased the number of ELO genes in B. carinata (17) over its progenitors B. nigra (7) and B. oleracea (6). Based on comparative phylogenetics, KCS, and ELO proteins can be classified into eight and four major groups, respectively. The approximate date of divergence for duplicated KCS and ELO genes varied from 0.03 to 3.20 million years ago (MYA). Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO/KCS genes. The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, some KCS and ELO genes were found to be specifically expressed under heat stress, phosphorus starvation, and Xanthomonas campestris infection. The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance.}, + author = {Khan, Uzair Muhammad and Rana, Iqrar Ahmad and Shaheen, Nabeel and Raza, Qasim and Rehman, Hafiz Mamoon and Maqbool, Rizwana and Khan, Iqrar Ahmad and Atif, Rana Muhammad}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-28665-2}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Molecular biology, Plant sciences}, + language = {en}, + month = {March}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {3577}, + title = {Comparative phylogenomic insights of {KCS} and {ELO} gene families in {Brassica} species indicate their role in seed development and stress responsiveness}, + url = {https://www.nature.com/articles/s41598-023-28665-2}, + urldate = {2023-03-15}, + volume = {13}, + year = {2023} +} + +@article{khine_comparative_2023, + abstract = {In this study, genomic and plasmid characteristics of Escherichia coli were determined with the aim of deducing how mcr genes may have spread on a colistin withdrawn pig farm. Whole genome hybrid sequencing was applied to six mcr-positive E. coli (MCRPE) strains isolated from pigs, a farmworker and wastewater collected between 2017 and 2019. Among these, mcr-1.1 genes were identified on IncI2 plasmids from a pig and wastewater, and on IncX4 from the human isolate, whereas mcr-3 genes were found on plasmids IncFII and IncHI2 in two porcine strains. The MCRPE isolates exhibited genotypic and phenotypic multidrug resistance (MDR) traits as well as heavy metal and antiseptic resistance genes. The mcr-1.1-IncI2 and IncX4 plasmids carried only colistin resistance genes. Whereas, the mcr-3.5-IncHI2 plasmid presented MDR region, with several mobile genetic elements. Despite the MCRPE strains belonged to different E. coli lineages, mcr-carrying plasmids with high similarities were found in isolates from pigs and wastewater recovered in different years. This study highlighted that several factors, including the resistomic profile of the host bacteria, co-selection via adjunct antibiotic resistance genes, antiseptics, and/or disinfectants, and plasmid-host fitness adaptation may encourage the maintenance of plasmids carrying mcr genes in E. coli.}, + author = {Khine, Nwai Oo and Wongsurawat, Thidathip and Jenjaroenpun, Piroon and Hampson, David J. and Prapasarakul, Nuvee}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-32406-w}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Evolution, Genetics, Microbiology}, + language = {en}, + month = {March}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {5124}, + title = {Comparative genomic analysis of {Colistin} resistant {Escherichia} coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm}, + url = {https://www.nature.com/articles/s41598-023-32406-w}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + +@article{kim_complete_2022, + abstract = {Metabacillus litoralis is part of the newly proposed genus Metabacillus. The bacterium was first isolated from a Yellow Sea tidal flat in 2005. As of May 2022, there are five genomic assemblies deposited in GenBank. We report the 5.2-Mbp genome sequence of M. litoralis strain NCTR108, from commercial tattoo ink.}, + author = {Kim, Sung Guk and Summage-West, Christine V. and Reyna, Mariela and Kim, Seong-Jae and Foley, Steven L.}, + doi = {10.1128/mra.00794-22}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00794--22}, + title = {Complete {Genome} {Sequence} of {Metabacillus} litoralis {Strain} {NCTR108}, {Isolated} from {Commercial} {Tattoo} {Ink}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00794-22}, + urldate = {2022-11-06}, + volume = {0}, + year = {2022} +} + +@article{kim_complete_2022-1, + abstract = {Terrisporobacter glycolicus is an emerging obligate anaerobic pathogen. We report the 3.9-Mbp genome sequence of T. glycolicus strain WW3900, which was isolated from wastewater at a research center with laboratory animal facilities. The genome sequence predicted a biosynthetic gene cluster encoding an S-adenosylmethionine enzyme and other synthetic genes associated with potential antimicrobial producers.}, + author = {Kim, Sung Guk and Summage-West, Christine V. and Reyna, Mariela and Feye, Kristina M. and Foley, Steven L.}, + doi = {10.1128/mra.00859-22}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00859--22}, + title = {Complete {Genome} {Sequence} of {Terrisporobacter} glycolicus {Strain} {WW3900}, {Isolated} from {Influent} {Wastewater} at a {Research} {Center} with {Multiple}-{Species} {Research} {Animal} {Facilities}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00859-22}, + urldate = {2022-11-06}, + volume = {0}, + year = {2022} +} + +@article{kimura_overexpression_2021, + abstract = {An amino acid exchange (P209L) in the HSPB8 binding site of the human co-chaperone BAG3 gives rise to severe childhood cardiomyopathy. To phenocopy the disease in mice and gain insight into its mechanisms, we generated humanized transgenic mouse models. Expression of human BAG3P209L-eGFP in mice caused Z-disc disintegration and formation of protein aggregates. This was accompanied by massive fibrosis resulting in early-onset restrictive cardiomyopathy with increased mortality as observed in patients. RNA-Seq and proteomics revealed changes in the protein quality control system and increased autophagy in hearts from hBAG3P209L-eGFP mice. The mutation renders hBAG3P209L less soluble in vivo and induces protein aggregation, but does not abrogate hBAG3 binding properties. In conclusion, we report a mouse model mimicking the human disease. Our data suggest that the disease mechanism is due to accumulation of hBAG3P209L and mouse Bag3, causing sequestering of components of the protein quality control system and autophagy machinery leading to sarcomere disruption.}, + author = {Kimura, Kenichi and Ooms, Astrid and Graf-Riesen, Kathrin and Kuppusamy, Maithreyan and Unger, Andreas and Schuld, Julia and Daerr, Jan and Lother, Achim and Geisen, Caroline and Hein, Lutz and Takahashi, Satoru and Li, Guang and Röll, Wilhelm and Bloch, Wilhelm and van der Ven, Peter F. M. and Linke, Wolfgang A. and Wu, Sean M. and Huesgen, Pitter F. and Höhfeld, Jörg and Fürst, Dieter O. and Fleischmann, Bernd K. and Hesse, Michael}, + copyright = {2021 The Author(s)}, + doi = {10.1038/s41467-021-23858-7}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Cardiomyopathies, Experimental models of disease, Gene therapy}, + language = {en}, + month = {June}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {3575}, + title = {Overexpression of human {BAG3P209L} in mice causes restrictive cardiomyopathy}, + url = {https://www.nature.com/articles/s41467-021-23858-7}, + urldate = {2023-06-05}, + volume = {12}, + year = {2021} +} + @article{king_resistome_2021, author = {King, T. L. and Schmidt, S. and Thakur, S. and Fedorka-Cray, P. and Keelara, S. and Harden, L. and Essack, S. Y.}, doi = {10.1016/j.jgar.2021.01.004}, @@ -2102,6 +5402,24 @@ @article{king_resistome_2021 year = {2021} } +@article{klaas_olfactomedin-4_2022, + abstract = {Olfactomedin-4 (OLFM4) is an olfactomedin-domain-containing glycoprotein, which regulates cell adhesion, proliferation, gastrointestinal inflammation, innate immunity and cancer metastasis. In the present study we investigated its role in skin regeneration. We found that OLFM4 expression is transiently upregulated in the proliferative phase of cutaneous wound healing in humans as well as in mice. Moreover, a significant increase in OLFM4 expression was detected in the skin of lesional psoriasis, a chronic inflammatory disease characterized by keratinocyte hyperproliferation. In vitro experiments demonstrated that OLFM4 selectively stimulated keratinocyte proliferation and increased both keratinocyte and fibroblast migration. Using proteotranscriptomic pathway analysis we revealed that transcription factors POU5F1/OCT4 and ESR1 acted as hubs for OLFM4-induced signalling in keratinocytes. In vivo experiments utilizing mouse splinted full-thickness cutaneous wound healing model showed that application of recombinant OLFM4 protein can significantly improve wound healing efficacy. Taken together, our results suggest that OLFM4 acts as a transiently upregulated inflammatory signal that promotes wound healing by regulating both dermal and epidermal cell compartments of the skin.}, + author = {Klaas, Mariliis and Mäemets-Allas, Kristina and Heinmäe, Elizabeth and Lagus, Heli and Arak, Terje and Eller, Mart and Kingo, Külli and Kankuri, Esko and Jaks, Viljar}, + doi = {10.1007/s00018-022-04202-8}, + issn = {1420-9071}, + journal = {Cellular and Molecular Life Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Keratinocytes, Olfactomedin-4, Psoriasis, Skin burns, Skin regeneration, Wound healing}, + language = {en}, + month = {February}, + number = {3}, + pages = {157}, + title = {Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through {POU5F1}/{OCT4} and {ESR1} signalling cascades}, + url = {https://doi.org/10.1007/s00018-022-04202-8}, + urldate = {2022-09-24}, + volume = {79}, + year = {2022} +} + @article{klein_pruriception_2021, author = {Klein, Amanda and Solinski, Hans Jürgen and Malewicz, Nathalie M. and Ieong, Hada Fong-ha and Sypek, Elizabeth I. and Shimada, Steven G. and Hartke, Timothy V. and Wooten, Matthew and Wu, Gang and Dong, Xinzhong and Hoon, Mark A. and LaMotte, Robert H. and Ringkamp, Matthias}, doi = {10.7554/elife.64506}, @@ -2114,6 +5432,39 @@ @article{klein_pruriception_2021 year = {2021} } +@article{kmeli_genome-wide_2023, + abstract = {MCM1-AGAMOUS-DEFICIENS-SRF (MADS)-box transcription factors (TFs) regulate a variety of plant developmental processes, particularly floral organ identity and fruit ripening. However, little is known about the MADS-box TF family in the common fig (Ficus carica L.), a vital fruit crop of Mediterranean countries. Here, we report a comprehensive overview of the MADS-box genes and their TF products in fig, describing their classification, physicochemical properties, protein and gene architectures, phylogenetic relationships, selection mode and differential expression during fruit development. A total of 64 MADS-box members were identified in F. carica and phylogenetically categorized as either type I (30) or type II (34). Type I MADS-box TFs were divided into three families (Mα, Mβ and Mγ, with 16, 4 and 10 members, respectively), whereas type II TFs were classified into two families (MIKCC and MIKC*, with 29 and 5 members, respectively). MIKCC TFs could be further classified into 12 subfamilies. Most FcMADS genes within the same clade were characterized by similar exon–intron organizations and motif compositions. Comparative phylogenetic analysis using mulberry (Morus notabilis) identified 24 (18 type II and 6 type I) orthologs between F. carica and M. notabilis. In addition, 11 paralogous MADS-box gene pairs were identified in F. carica, which evolved under purifying selection, except for two recent paralogs from the TM3 (SOC1) subfamily. RNA-seq results indicated that 28 and 34 FcMADS genes were differentially expressed in fruit peel and female flowers, respectively, during six successive stages of fruit development. According to their expression profiles, genes were grouped into four clusters (I, II, III and IV) in both tissues. FcMADS genes from fruit peel expression cluster IV (FcMADS13, -23, -32, -40 and -60) and female flower expression cluster III (FcMADS9, -49 and -58) were upregulated during fruit ripening in the corresponding tissues, suggesting a potential, tissue-specific role of these candidate genes in fruit ripening. Our findings provide the first genome-wide extended characterization of the MADS-box TF family in F. carica, laying the groundwork for future research on its molecular roles in fruit ripening.}, + author = {Kmeli, Narjes and Hamdi, Jihen and Bouktila, Dhia}, + doi = {10.1007/s13580-022-00478-8}, + issn = {2211-3460}, + journal = {Horticulture, Environment, and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Common fig, Comparative phylogeny, Expression profiling, Fruit ripening, In silico analysis, MADS-box}, + language = {en}, + month = {January}, + title = {Genome-wide characterization of {Ficus} carica {MADS}-box transcription factors with a focus on their roles during fruit development}, + url = {https://doi.org/10.1007/s13580-022-00478-8}, + urldate = {2023-03-15}, + year = {2023} +} + +@article{kocsmar_proteome_2023, + abstract = {Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography–tandem mass spectrometry (LC–MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.}, + author = {Kocsmár, Éva and Schmid, Marlene and Cosenza-Contreras, Miguel and Kocsmár, Ildikó and Föll, Melanie and Krey, Leah and Barta, Bálint András and Rácz, Gergely and Kiss, András and Werner, Martin and Schilling, Oliver and Lotz, Gábor and Bronsert, Peter}, + doi = {10.1007/s00018-023-04754-3}, + issn = {1420-9071}, + journal = {Cellular and Molecular Life Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Autopsy, Degradation, Proteomics}, + language = {en}, + month = {April}, + number = {5}, + pages = {117}, + title = {Proteome alterations in human autopsy tissues in relation to time after death}, + url = {https://doi.org/10.1007/s00018-023-04754-3}, + urldate = {2023-06-05}, + volume = {80}, + year = {2023} +} + @article{koeppel_sars-cov-2_2022, author = {Koeppel, Katja Natalie and Mendes, Adriano and Strydom, Amy and Rotherham, Lia and Mulumba, Misheck and Venter, Marietjie}, doi = {10.3390/v14010120}, @@ -2129,6 +5480,25 @@ @article{koeppel_sars-cov-2_2022 year = {2022} } +@article{kohler_msstatsshiny_2023, + abstract = {Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is a versatile technology for identifying and quantifying proteins in complex biological mixtures. Postidentification, analysis of changes in protein abundances between conditions requires increasingly complex and specialized statistical methods. Many of these methods, in particular the family of open-source Bioconductor packages MSstats, are implemented in a coding language such as R. To make the methods in MSstats accessible to users with limited programming and statistical background, we have created MSstatsShiny, an R-Shiny graphical user interface (GUI) integrated with MSstats, MSstatsTMT, and MSstatsPTM. The GUI provides a point and click analysis pipeline applicable to a wide variety of proteomics experimental types, including label-free data-dependent acquisitions (DDAs) or data-independent acquisitions (DIAs), or tandem mass tag (TMT)-based TMT-DDAs, answering questions such as relative changes in the abundance of peptides, proteins, or post-translational modifications (PTMs). To support reproducible research, the application saves user’s selections and builds an R script that programmatically recreates the analysis. MSstatsShiny can be installed locally via Github and Bioconductor, or utilized on the cloud at www.msstatsshiny.com. We illustrate the utility of the platform using two experimental data sets (MassIVE IDs MSV000086623 and MSV000085565).}, + author = {Kohler, Devon and Kaza, Maanasa and Pasi, Cristina and Huang, Ting and Staniak, Mateusz and Mohandas, Dhaval and Sabido, Eduard and Choi, Meena and Vitek, Olga}, + doi = {10.1021/acs.jproteome.2c00603}, + issn = {1535-3893}, + journal = {Journal of Proteome Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Chemical Society}, + number = {2}, + pages = {551--556}, + shorttitle = {{MSstatsShiny}}, + title = {{MSstatsShiny}: {A} {GUI} for {Versatile}, {Scalable}, and {Reproducible} {Statistical} {Analyses} of {Quantitative} {Proteomic} {Experiments}}, + url = {https://doi.org/10.1021/acs.jproteome.2c00603}, + urldate = {2023-03-15}, + volume = {22}, + year = {2023} +} + @article{kolosov_malpighian_2019, abstract = {Skip to Next Section The Malpighian tubules (MTs) and hindgut constitute the functional kidney of insects. MTs are outpouchings of the gut and in most insects demonstrate proximodistal heterogeneity in function. In most insects, such heterogeneity is confined to ion/fluid secretion in the distal portion and ion/fluid reabsorption in the proximal portion. In contrast, MTs of larval Lepidoptera (caterpillars of butterflies and moths) are composed of five regions that differ in their association with the gut, their structure and ion/fluid transport function. Recent studies have shown that several regions can rapidly and reversibly switch between ion secretion and reabsorption. The present study employed RNAseq, pharmacology and electrophysiology to characterize four distinct regions of the MT in larval Trichoplusia ni. Luminal microelectrode measurements indicate changes in [K+], [Na+] and pH as fluid passes through different regions of the tubule. In addition, the regions examined differ in gene ontology enrichment, and demonstrate robust gradients in expression of ion transporters and endocrine ligand receptors. Lastly, the study provides evidence for direct involvement of voltage- and ligand-gated ion channels in epithelial ion transport of insect MTs.}, @@ -2160,6 +5530,77 @@ @phdthesis{konovalovas_molecular_2018 year = {2018} } +@misc{kostrykin_enhancing_2024, + abstract = {Project 6 during the 2023 BioHackathon Europe in Barcelona focused on "Enhancing the image analysis community in Galaxy." Despite Galaxy's strong presence in genomics and proteomics, its image analysis tools and workflows are currently scattered. This project aimed to gather efforts in image analysis across fields to build a robust interdisciplinary community.}, + author = {Kostrykin, Leonid and Woller, Tatiana and Kalaš, Matúš and Özdemir, Bugra and Buono, Rafael Andrade and Sun, Yi and Kumar, Anup and Goué, Nadia and Grüning, Björn and Serrano-Solano, Beatriz and Fouilloux, Anne}, + doi = {10.37044/osf.io/w8dsz}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en-us}, + month = {April}, + publisher = {OSF}, + title = {Enhancing the image analysis community in {Galaxy}}, + url = {https://osf.io/w8dsz}, + urldate = {2024-04-28}, + year = {2024} +} + +@article{kowalski_eplerenone_2021, + abstract = {Download figureDownload PowerPoint}, + author = {Kowalski, Jessica and Deng, Lisa and Suennen, Chiara and Koca, Duygu and Meral, David and Bode, Christoph and Hein, Lutz and Lother, Achim}, + doi = {10.1161/HYPERTENSIONAHA.120.16196}, + journal = {Hypertension}, + keywords = {{\textgreater}UseGalaxy.eu, aldosterone, cardiovascular disease, endothelial cells, mineralocorticoid receptor, pulmonary hypertension}, + month = {August}, + note = {Publisher: American Heart Association}, + number = {2}, + pages = {456--465}, + title = {Eplerenone {Improves} {Pulmonary} {Vascular} {Remodeling} and {Hypertension} by {Inhibition} of the {Mineralocorticoid} {Receptor} in {Endothelial} {Cells}}, + url = {https://www.ahajournals.org/doi/10.1161/HYPERTENSIONAHA.120.16196}, + urldate = {2023-06-05}, + volume = {78}, + year = {2021} +} + +@article{kruse_synaptopodin_2024, + abstract = {Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. The molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions, however, are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in learning and memory formation. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, CA3-PCs and their direct synaptic connections, as revealed by paired recordings (dGC-to-CA3-PC). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-regulating protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and synaptopodin are related to ribosomes in close proximity to synaptic sites and reveal a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.}, + author = {Kruse, Pia and Brandes, Gudrun and Hemeling, Hanna and Huang, Zhong and Wrede, Christoph and Hegermann, Jan and Vlachos, Andreas and Lenz, Maximilian}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cells13020114}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, + language = {en}, + month = {January}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {114}, + title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, + url = {https://www.mdpi.com/2073-4409/13/2/114}, + urldate = {2024-01-14}, + volume = {13}, + year = {2024} +} + +@article{kumar_accessible_2022, + abstract = {BACKGROUND: Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU cores and GPUs. JupyterLab provides an excellent framework for developing AI programs, but it needs to be hosted on such an infrastructure to enable faster training of AI programs using parallel computing. +FINDINGS: An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe consisting of thousands of CPU cores, many GPUs, and several petabytes of storage to rapidly prototype and develop end-to-end AI projects. Using a JupyterLab notebook, long-running AI model training programs can also be executed remotely to create trained models, represented in open neural network exchange (ONNX) format, and other output datasets in Galaxy. Other features include Git integration for version control, the option of creating and executing pipelines of notebooks, and multiple dashboards and packages for monitoring compute resources and visualization, respectively. +CONCLUSIONS: These features make JupyterLab in Galaxy Europe highly suitable for creating and managing AI projects. A recent scientific publication that predicts infected regions in COVID-19 computed tomography scan images is reproduced using various features of JupyterLab on Galaxy Europe. In addition, ColabFold, a faster implementation of AlphaFold2, is accessed in JupyterLab to predict the 3-dimensional structure of protein sequences. JupyterLab is accessible in 2 ways-one as an interactive Galaxy tool and the other by running the underlying Docker container. In both ways, long-running training can be executed on Galaxy's compute infrastructure. Scripts to create the Docker container are available under MIT license at https://github.com/usegalaxy-eu/gpu-jupyterlab-docker.}, + author = {Kumar, Anup and Cuccuru, Gianmauro and Grüning, Björn and Backofen, Rolf}, + doi = {10.1093/gigascience/giad028}, + issn = {2047-217X}, + journal = {GigaScience}, + keywords = {{\textgreater}UseGalaxy.eu, CUDA, Elyra AI, GPU, Galaxy Europe, JupyterLab, ONNX, artificial intelligence, remote model training}, + language = {eng}, + month = {December}, + pages = {giad028}, + pmcid = {PMC10132306}, + pmid = {37099385}, + title = {An accessible infrastructure for artificial intelligence using a {Docker}-based {JupyterLab} in {Galaxy}}, + volume = {12}, + year = {2022} +} + @article{kumar_community_2020, abstract = {Citizen Science has come up to perform analytics over the SARS-CoV-2 genome. Public GALAXY servers provide an automated platform for genomics analysis. Study includes design of GALAXY workflows for RNASEQ assembly and annotation as well as genomic variant discovery and perform analysis across four samples of SARS-CoV-2 infected humans obtained from the local population of Wuhan, China. It provides information about transcriptomics and genomic variants across the SARS-CoV-2 genome. Study can be extended to perform evolutionary and comparative study across each species of coronaviruses. Augmented and integrated study with cheminformatics and immunoinformatics will be a way forward for drug discovery and vaccine development.}, author = {Kumar, Ambarish and Bangash, Ali Haider and Gruening, Bjoern}, @@ -2272,6 +5713,41 @@ @article{kumaran_vitro_2022 year = {2022} } +@article{kumarhalder_oxa-376_2022, + author = {Kumar Halder, Sajal and Mulla Mim, Maria and Hassan Alif, Md Meharab and Fardous Shathi, Jannatul and Alam, Nuhu and Shil, Aparna and Kabir Himel, Mahbubul}, + doi = {10.1039/D2RA02939A}, + journal = {RSC Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Publisher: Royal Society of Chemistry}, + number = {37}, + pages = {24319--24338}, + shorttitle = {Oxa-376 and {Oxa}-530 variants of β-lactamase}, + title = {Oxa-376 and {Oxa}-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of {Acinetobacter} baumannii}, + url = {https://pubs.rsc.org/en/content/articlelanding/2022/ra/d2ra02939a}, + urldate = {2022-09-24}, + volume = {12}, + year = {2022} +} + +@article{kumawat_association_2024, + abstract = {Knowledge of variability in phenological traits is of utmost importance in breeding new almond cultivars in the context of impending climate change. The Northwestern Himalayan region is characterized by extreme winters, and phenological studies of fruit crops in relation to environmental variables in this region are scant. Flowering time being an important trait governing agricultural productivity, the objectives of this study were the evaluation of local and exotic almond cultivars for blooming initiation and other associated parameters. This study also aimed at deciphering the association between bloom dates in almonds and prevailing temperatures. Field phenological observations were performed during seven growing seasons (2012–2018) in Kashmir. Phenological traits like endodormancy breaking were estimated using the correlation model. The heat requirements for blooming were estimated using the growing degree days (GDD) method. The association between average temperatures and days to flowering was studied using partial least squares (PLS) regression. Local cultivars ‘Makhdoom’ and ‘Shalimar’ were earliest to bloom within 80 days, while the exotic cultivars were late bloomers, requiring 87 days. Cultivars ‘Makhdoom’, ‘Shalimar’, ‘Drake’ and ‘Pranyaj’ broke their endodormancy on the same date, i.e. December 26, although another group including ‘Waris’, ‘California Paper Shell’ and ‘Merced’ exhibited endo- to ecodormancy transition on January 21. In general, Himalayan-origin almond cultivars revealed low heat requirements for flowering compared to the exotic ones. PLS regression analysis identified four major periods in which average temperatures successfully explained variation in days to blooming in almonds. In conclusion, a phenological prediction model is presented here that explains variation in blooming dates in almond cultivars as a function of average temperatures. This model addresses the almond cultivars growing in the Himalayan region and is expected to be of great practical utility to the farming community to efficiently plan their orchard management practices.}, + author = {Kumawat, Kishan Lal and Raina, Susheel Kumar and Kumar, Dinesh and Verma, Mahendra Kumar and Singh, Deshbeer and Mir, Javid Iqbal and Sultan, Sheikh M. and Sharma, Om Chand}, + doi = {10.1007/s10341-023-00991-9}, + issn = {2948-2631}, + journal = {Applied Fruit Science}, + keywords = {{\textgreater}UseGalaxy.eu, Endodormancy, Flowering, Growing degree days, Kashmir, PLS regression}, + language = {en}, + month = {April}, + number = {2}, + pages = {581--588}, + title = {Association of {Reproductive} {Phenology} with {Air} {Temperature} in {Almond} ({Prunus} dulcis [{Mill}.] {D}.{A}. {Webb}) {Cultivars} {Under} {Northwestern} {Himalayan} {Conditions}}, + url = {https://doi.org/10.1007/s10341-023-00991-9}, + urldate = {2024-05-17}, + volume = {66}, + year = {2024} +} + @article{lahm_congenital_2020, author = {Lahm, Harald and Jia, Meiwen and Dreßen, Martina and Wirth, Felix F. M. and Puluca, Nazan and Gilsbach, Ralf and Keavney, Bernard and Cleuziou, Julie and Beck, Nicole and Bondareva, Olga and Dzilic, Elda and Burri, Melchior and König, Karl C. and Ziegelmüller, Johannes A. and Abou-Ajram, Claudia and Neb, Irina and Zhang, Zhong and Doppler, Stefanie A. and Mastantuono, Elisa and Lichtner, Peter and Eckstein, Gertrud and Hörer, Jürgen and Ewert, Peter and Priest, James R. and Hein, Lutz and Lange, Rüdiger and Meitinger, Thomas and Cordell, Heather J. and Müller-Myhsok, Bertram and Krane, Markus}, doi = {10.1172/JCI141837}, @@ -2306,6 +5782,23 @@ @article{lahm_genome-wide_2020 year = {2020} } +@article{lamas_whole_2023, + abstract = {Whole Genome Sequencing (WGS) implementation in food safety laboratories is a significant advancement in food pathogen control and outbreak tracking. However, the initial investment for acquiring next-generation sequencing platforms and the need for bioinformatic ...}, + author = {Lamas, Alexandre and Garrido-Maestu, Alejandro and Prieto, Alberto and Cepeda, Alberto and Franco, Carlos Manuel}, + doi = {10.3389/fmicb.2023.1254692}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + language = {en}, + note = {Publisher: Frontiers Media SA}, + pmid = {38107857}, + shorttitle = {Whole genome sequencing in the palm of your hand}, + title = {Whole genome sequencing in the palm of your hand: how to implement a {MinION} {Galaxy}-based workflow in a food safety laboratory for rapid {Salmonella} spp. serotyping, virulence, and antimicrobial resistance gene identification}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722185/}, + urldate = {2023-12-28}, + volume = {14}, + year = {2023} +} + @article{lambrecht_interplay_2019, abstract = {The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.}, author = {Lambrecht, S. Joke and Kanesaki, Yu and Fuss, Janina and Huettel, Bruno and Reinhardt, Richard and Steglich, Claudia}, @@ -2344,6 +5837,58 @@ @article{lange_expression_2020 year = {2020} } +@article{lapadula_ribosome_2023, + abstract = {Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolving under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.}, + author = {Lapadula, Walter J. and Juri Ayub, Maximiliano}, + doi = {10.1016/j.gene.2023.147547}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Horizontal Gene Transfer, Immune effectors, Insects, RNA -glycosidase, Ribosome Inactivating Proteins}, + language = {en}, + month = {August}, + pages = {147547}, + shorttitle = {Ribosome inactivating proteins in insects}, + title = {Ribosome inactivating proteins in insects: {HGT}, gene expression, and functional implications}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111923003888}, + urldate = {2023-07-31}, + volume = {877}, + year = {2023} +} + +@article{lapp_transcriptional_2024, + abstract = {PURPOSE Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and pathogen-specific molecular and cellular mechanisms during human corneal infection. METHODS Clinical diagnoses of herpes simplex virus (HSV) (n=5) and bacterial/fungal (n=5) keratitis were confirmed by histology. Healthy corneas (n=7) and keratoconus (n=4) samples served as controls. Formalin-fixed, paraffin-embedded (FFPE) human corneal specimens were analyzed using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE RNA-seq). The cellular host response was investigated using comprehensive bioinformatic deconvolution (xCell and CYBERSORTx) analyses and by integration with published single cell RNA-seq data of the human cornea. RESULTS Our analysis identified 216 and 561 genes, that were specifically overexpressed in viral or bacterial/fungal keratitis, respectively, and allowed to distinguish the two etiologies. The virus-specific host response was driven by adaptive immunity and associated molecular signaling pathways, whereas the bacterial/fungal-specific host response mainly involved innate immunity signaling pathways and cell types. We identified several genes and pathways involved in the host response to infectious keratitis, including CXCL9, CXCR3, and MMP9 for viral, and S100A8/A9, MMP9, and the IL17 pathway for bacterial/fungal keratitis. CONCLUSIONS High-resolution molecular profiling provides new insights into the human corneal host response to viral and bacterial/fungal infection. Pathogen-specific molecular profiles may provide the foundation for novel diagnostic biomarker and therapeutic approaches that target inflammation-induced damage to corneal host cells with the goal to improve the outcome of infectious keratitis.}, + author = {Lapp, Thabo and Kammrath Betancor, Paola and Schlunck, Günther and Auw-Hädrich, Claudia and Maier, Philip and Lange, Clemens and Reinhard, Thomas and Wolf, Julian}, + doi = {10.3389/fcimb.2023.1285676}, + issn = {2235-2988}, + journal = {Frontiers in Cellular and Infection Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial keratitis, FFPE (formalin fixed paraffin embedded), Infectious keratitis, Keratoplasty, RNA sequencing, Viral keratitis, host response, human}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis}, + url = {https://www.frontiersin.org/articles/10.3389/fcimb.2023.1285676}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + +@article{lariviere_scalable_2024, + author = {Larivière, Delphine and Abueg, Linelle and Brajuka, Nadolina and Gallardo-Alba, Cristóbal and Grüning, Bjorn and Ko, Byung June and Ostrovsky, Alex and Palmada-Flores, Marc and Pickett, Brandon D. and Rabbani, Keon and Antunes, Agostinho and Balacco, Jennifer R. and Chaisson, Mark J. P. and Cheng, Haoyu and Collins, Joanna and Couture, Melanie and Denisova, Alexandra and Fedrigo, Olivier and Gallo, Guido Roberto and Giani, Alice Maria and Gooder, Grenville MacDonald and Horan, Kathleen and Jain, Nivesh and Johnson, Cassidy and Kim, Heebal and Lee, Chul and Marques-Bonet, Tomas and O’Toole, Brian and Rhie, Arang and Secomandi, Simona and Sozzoni, Marcella and Tilley, Tatiana and Uliano-Silva, Marcela and van den Beek, Marius and Williams, Robert W. and Waterhouse, Robert M. and Phillippy, Adam M. and Jarvis, Erich D. and Schatz, Michael C. and Nekrutenko, Anton and Formenti, Giulio}, + copyright = {2024 The Author(s), under exclusive licence to Springer Nature America, Inc.}, + doi = {10.1038/s41587-023-02100-3}, + issn = {1546-1696}, + journal = {Nature Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Computational platforms and environments, Genome assembly algorithms}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + pages = {1--4}, + title = {Scalable, accessible and reproducible reference genome assembly and evaluation in {Galaxy}}, + url = {https://www.nature.com/articles/s41587-023-02100-3}, + urldate = {2024-01-26}, + year = {2024} +} + @article{larsen_identification_2019, abstract = {C-type lectin-like domain containing proteins (CTLDcps) mainly bind carbohydrate-based ligands, but also other ligands. CTLDcps are involved in several biological processes including cell adhesion, cell-cell interactions, and pathogen recognition. Pathogen recognition by myeloid cells, e.g. dendritic cells (DCs), can be facilitated through cell surface expressed CTLDcps. Cell surface expressed CTLDcps have been exploited in vaccine designs for specific targeting of human and mouse DCs using antibodies. In recent years, however, DC targeting using carbohydrate-based vaccines has gained interest due to low production cost, limited immunogenicity, and possibility of multivalent adjustment. In chicken, however, only a few CTLDcps have been identified. Identifying and annotating additional chicken CTLDcps (chCTLDcps) is needed to exploit carbohydrate-mediated DC targeting in chicken. Therefore, we searched the chicken GRCg6a assembly for novel chCTLDcps. We identified 28 chCTLDcps of which 10 had previously been described and also experimentally validated. RNA-seq and RT-qPCR confirmed mRNA expression of the remaining 18 identified chCTLDcps. A group of highly related chCTLDcps, moreover, was shown to be avian-specific and comprise novel members mapped to the proposed chicken natural killer gene complex. Two chCTLDcps, chCLEC17AL-A and chCLEC17AL-B, were found to share a recent common ancestor with CLEC17A. Putative mannose or fucose-binding sequence motifs, EPN and WND, were found in the CTLD of chCLEC17AL-A. Both contained intracellular internalisation and signalling sequence motifs. In conclusion, several chCTLDcps were identified and their expression confirmed. Both chCLEC17AL-A and -B showed promise as potential targets in carbohydrate-based chicken vaccine strategies. Determination of DC-specific expression of chCLEC17AL-A and -B, thus, might prove useful in chicken vaccinology.}, author = {Larsen, Frederik T. and Bed’Hom, Bertrand and Guldbrandtsen, Bernt and Dalgaard, Tina S.}, @@ -2360,7 +5905,27 @@ @article{larsen_identification_2019 year = {2019} } -@article{lastic_entropic_2020, +@article{lasolle_dual_2024, + abstract = {Thyroid cancer is the most common endocrine malignancy and several genetic events have been described to promote the development of thyroid carcinogenesis. Besides the effects of specific mutations on thyroid cancer development, the molecular mechanisms controlling tumorigenesis, tumor behavior, and drug resistance are still largely unknown. Cancer organoids have been proposed as a powerful tool to study aspects related to tumor development and progression and appear promising to test individual responses to therapies. Here, using mESC-derived thyroid organoids, we developed a BrafV637E-inducible model able to recapitulate the features of papillary thyroid cancer in vitro. Overexpression of the murine BrafV637E mutation, equivalent to BrafV600E in humans, rapidly triggers to MAPK activation, cell dedifferentiation, and disruption of follicular organization. BrafV637E-expressing organoids show a transcriptomic signature for p53, focal adhesion, ECM-receptor interactions, EMT, and inflammatory signaling pathways. Finally, PTC-like thyroid organoids were used for drug screening assays. The combination of MAPK and PI3K inhibitors reversed BrafV637E oncogene-promoted cell dedifferentiation while restoring thyroid follicle organization and function in vitro. Our results demonstrate that pluripotent stem cells-derived thyroid cancer organoids can mimic tumor development and features while providing an efficient tool for testing novel targeted therapies.}, + author = {Lasolle, Hélène and Schiavo, Andrea and Tourneur, Adrien and Gillotay, Pierre and de Faria da Fonseca, Bárbara and Ceolin, Lucieli and Monestier, Olivier and Aganahi, Benilda and Chomette, Laura and Kizys, Marina Malta Letro and Haenebalcke, Lieven and Pieters, Tim and Goossens, Steven and Haigh, Jody and Detours, Vincent and Maia, Ana Luiza Silva and Costagliola, Sabine and Romitti, Mírian}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41388-023-02889-y}, + issn = {1476-5594}, + journal = {Oncogene}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Phenotypic screening}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + number = {3}, + pages = {155--170}, + title = {Dual targeting of {MAPK} and {PI3K} pathways unlocks redifferentiation of {Braf}-mutated thyroid cancer organoids}, + url = {https://www.nature.com/articles/s41388-023-02889-y}, + urldate = {2024-05-17}, + volume = {43}, + year = {2024} +} + +@article{lastic_entropic_2020, abstract = {Background: Traditional omic analysis relies on p-value and fold change as selection criteria. There is an ongoing debate on their effectiveness in delivering systemic and robust interpretation, due to their dependence on assumptions of conformity with various parametric distributions.Here, we propose a threshold-free selection method based on robust, non-parametric statistics, ensuring independence from the statistical distribution properties and broad applicability. Such methods could adapt to different initial data distributions, contrary to statistical techniques based on fixed thresholds. Methods: Our work extends the Rank Products methodology with a neutral selection method of high information-extraction capacity. We introduce the calculation of the RP distribution\’s entropy to isolate the features of interest by their contribution to the distribution\’s information content. The aim is a methodology performing threshold-free identification of the differentially expressed features, which are highly informative about the phenomenon under scrutiny. Conclusions: Applying the proposed method on microarray (transcriptomic and DNA methylation) and RNAseq count data of varying sizes and noise presence, we observe robust convergence for the different parameterisations to stable cutoff points. Functional analysis through BioInfoMiner and EnrichR was used to evaluate the information potency of the resulting feature lists. Overall, the derived functional terms provide a systemic description highly compatible with the results of traditional statistical hypothesis testing techniques. The methodology behaves consistently across different data types. The feature lists are compact and information-rich, indicating phenotypic aspects specific to the tissue and biological phenomenon i nvestigated. Selection by information content measures efficiently addresses problems, emerging from arbitrary thresholding, thus facilitating the full automation of the analysis.}, author = {Lastic, Hector-Xavier de and Liampa, Irene and Georgakilas, Alexandros G. and Zervakis, Michalis and Chatziioannou, Aristotelis}, doi = {10.20944/preprints202009.0424.v1}, @@ -2376,6 +5941,109 @@ @article{lastic_entropic_2020 year = {2020} } +@article{latif_nfatc1_2022, + abstract = {Objectives Non-alcoholic fatty liver disease (NAFLD) can persist in the stage of simple hepatic steatosis or progress to steatohepatitis (NASH) with an increased risk for cirrhosis and cancer. We examined the mechanisms controlling the progression to severe NASH in order to develop future treatment strategies for this disease. +Design NFATc1 activation and regulation was examined in livers from patients with NAFLD, cultured and primary hepatocytes and in transgenic mice with differential hepatocyte-specific expression of the transcription factor (Alb-cre, NFATc1c.a. and NFATc1Δ/Δ). Animals were fed with high-fat western diet (WD) alone or in combination with tauroursodeoxycholic acid (TUDCA), a candidate drug for NAFLD treatment. NFATc1-dependent ER stress-responses, NLRP3 inflammasome activation and disease progression were assessed both in vitro and in vivo. +Results NFATc1 expression was weak in healthy livers but strongly induced in advanced NAFLD stages, where it correlates with liver enzyme values as well as hepatic inflammation and fibrosis. Moreover, high-fat WD increased NFATc1 expression, nuclear localisation and activation to promote NAFLD progression, whereas hepatocyte-specific depletion of the transcription factor can prevent mice from disease acceleration. Mechanistically, NFATc1 drives liver cell damage and inflammation through ER stress sensing and activation of the PERK-CHOP unfolded protein response (UPR). Finally, NFATc1-induced disease progression towards NASH can be blocked by TUDCA administration. +Conclusion NFATc1 stimulates NAFLD progression through chronic ER stress sensing and subsequent activation of terminal UPR signalling in hepatocytes. Interfering with ER stress-responses, for example, by TUDCA, protects fatty livers from progression towards manifest NASH.}, + author = {Latif, Muhammad Umair and Schmidt, Geske Elisabeth and Mercan, Sercan and Rahman, Raza and Gibhardt, Christine Silvia and Stejerean-Todoran, Ioana and Reutlinger, Kristina and Hessmann, Elisabeth and Singh, Shiv K. and Moeed, Abdul and Rehman, Abdul and Butt, Umer Javed and Bohnenberger, Hanibal and Stroebel, Philipp and Bremer, Sebastian Christopher and Neesse, Albrecht and Bogeski, Ivan and Ellenrieder, Volker}, + copyright = {© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.. http://creativecommons.org/licenses/by-nc/4.0/This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.}, + doi = {10.1136/gutjnl-2021-325013}, + issn = {0017-5749, 1468-3288}, + journal = {Gut}, + keywords = {{\textgreater}UseGalaxy.eu, fatty liver, hepatic fibrosis, inflammation, nonalcoholic steatohepatitis}, + language = {en}, + month = {March}, + note = {Publisher: BMJ Publishing Group +Section: Hepatology}, + pmid = {35365570}, + title = {{NFATc1} signaling drives chronic {ER} stress responses to promote {NAFLD} progression}, + url = {https://gut.bmj.com/content/early/2022/03/31/gutjnl-2021-325013}, + urldate = {2022-09-24}, + year = {2022} +} + +@article{le_corre_mechanism-based_2023, + abstract = {Hydrogen sulfide (H2S) is a gaseous signaling molecule that participates in various signaling functions in health and diseases. The tetrameric cystathionine γ-lyase (CSE) contributes to H2S biogenesis and several investigations provide evidence on the pharmacological modulation of CSE as a potential target for the treatment of a multitude of conditions. D-penicillamine (D-pen) has recently been reported to selectively impede CSE-catalyzed H2S production but the molecular bases for such inhibitory effect have not been investigated. In this study, we report that D-pen follows a mixed-inhibition mechanism to inhibit both cystathionine (CST) cleavage and H2S biogenesis by human CSE. To decipher the molecular mechanisms underlying such a mixed inhibition, we performed docking and molecular dynamics (MD) simulations. Interestingly, MD analysis of CST binding reveals a likely active site configuration prior to gem-diamine intermediate formation, particularly H-bond formation between the amino group of the substrate and the O3′ of PLP. Similar analyses realized with both CST and D-pen identified three potent interfacial ligand-binding sites for D-pen and offered a rational for D-pen effect. Thus, inhibitor binding not only induces the creation of an entirely new interacting network at the vicinity of the interface between enzyme subunits, but it also exerts long range effects by propagating to the active site. Overall, our study paves the way for the design of new allosteric interfacial inhibitory compounds that will specifically modulate H2S biogenesis by cystathionine γ-lyase.}, + author = {Le Corre, Laurent and Padovani, Dominique}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-34405-3}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Biochemistry, Chem-informatics, Enzyme mechanisms, Enzymes, Mechanism of action, Small molecules, chemicaltoolbox}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {7287}, + shorttitle = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition}, + title = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition}, + url = {https://www.nature.com/articles/s41598-023-34405-3}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + +@article{leavitt_acute_2024, + abstract = {Purpose +Tumor hypoxia is a major cause of treatment resistance, especially to radiation therapy at conventional dose rate (CONV), and we wanted to assess whether hypoxia does alter tumor sensitivity to FLASH. +Methods and Materials +We engrafted several tumor types (glioblastoma [GBM], head and neck cancer, and lung adenocarcinoma) subcutaneously in mice to provide a reliable and rigorous way to modulate oxygen supply via vascular clamping or carbogen breathing. We irradiated tumors using a single 20-Gy fraction at either CONV or FLASH, measured oxygen tension, monitored tumor growth, and sampled tumors for bulk RNAseq and pimonidazole analysis. Next, we inhibited glycolysis with trametinib in GBM tumors to enhance FLASH efficacy. +Results +Using various subcutaneous tumor models, and in contrast to CONV, FLASH retained antitumor efficacy under acute hypoxia. These findings show that in addition to normal tissue sparing, FLASH could overcome hypoxia-mediated tumor resistance. Follow-up molecular analysis using RNAseq profiling uncovered a FLASH-specific profile in human GBM that involved cell-cycle arrest, decreased ribosomal biogenesis, and a switch from oxidative phosphorylation to glycolysis. Glycolysis inhibition by trametinib enhanced FLASH efficacy in both normal and clamped conditions. +Conclusions +These data provide new and specific insights showing the efficacy of FLASH in a radiation-resistant context, proving an additional benefit of FLASH over CONV.}, + author = {Leavitt, Ron J. and Almeida, Aymeric and Grilj, Veljko and Montay-Gruel, Pierre and Godfroid, Céline and Petit, Benoit and Bailat, Claude and Limoli, Charles L. and Vozenin, Marie-Catherine}, + doi = {10.1016/j.ijrobp.2024.02.015}, + issn = {0360-3016}, + journal = {International Journal of Radiation Oncology*Biology*Physics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + title = {Acute {Hypoxia} {Does} {Not} {Alter} {Tumor} {Sensitivity} to {FLASH} {Radiation} {Therapy}}, + url = {https://www.sciencedirect.com/science/article/pii/S0360301624003201}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{lee_genomic_2022, + abstract = {The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic since 2019. Variants of concern (VOCs) declared by the World Health Organization require continuous monitoring because of their possible changes in transmissibility, virulence, and antigenicity. The Omicron variant, a VOC, has become the dominant variant worldwide since November 2021. In the Republic of Korea (South Korea), the number of confirmed cases increased rapidly after the detection of Omicron VOC on November 24, 2021. In this study, we estimated the underlying epidemiological processes of Omicron VOC in South Korea using time-scaled phylodynamic analysis. Three distinct phylogenetic subgroups (Kor-O1, Kor-O2, and Kor-O3) were detected in South Korea. The Kor-O1 subgroup circulated in the Daegu region, whereas Kor-O2 and Kor-O3 circulated in Incheon and Jeollanam-do, respectively. The viral population size and case number of the Kor-O1 subgroup increased more rapidly than those of the other subgroups, indicating the rapid spread of the virus. The results indicated the multiple introductions of Omicron sub-lineages into South Korea and their subsequent co-circulation. The evolution and transmission of SARS-CoV-2 should be continuously monitored, and control strategies need to be improved to control the multiple variants.}, + author = {Lee, Dong-Wook and Kim, Jeong-Min and Park, Ae Kyung and Kim, Da-Won and Kim, Ji-Yun and Lim, Noori and Lee, Hyeokjin and Kim, Il-Hwan and Kim, Jeong-Ah and Lee, Chae young and Kwon, Jung-Hoon and Kim, Eun-Jin}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41598-022-26803-w}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Infectious diseases, SARS-CoV-2, Viral epidemiology, Virology}, + language = {en}, + month = {December}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {22414}, + title = {Genomic epidemiology of {SARS}- {CoV}-2 {Omicron} variants in the {Republic} of {Korea}}, + url = {https://www.nature.com/articles/s41598-022-26803-w}, + urldate = {2023-08-06}, + volume = {12}, + year = {2022} +} + +@article{lee_global_2023, + abstract = {Ciliates assemble numerous microtubular structures into complex cortical patterns. During ciliate division, the pattern is duplicated by intracellular segmentation that produces a tandem of daughter cells. In Tetrahymena thermophila, the induction and positioning of the division boundary involves two mutually antagonistic factors: posterior CdaA (cyclin E) and anterior CdaI (Hippo kinase). Here, we characterized the related cdaH-1 allele, which confers a pleiotropic patterning phenotype including an absence of the division boundary and an anterior–posterior mispositioning of the new oral apparatus. CdaH is a Fused or Stk36 kinase ortholog that localizes to multiple sites that correlate with the effects of its loss, including the division boundary and the new oral apparatus. CdaH acts downstream of CdaA to induce the division boundary and drives asymmetric cytokinesis at the tip of the posterior daughter. CdaH both maintains the anterior–posterior position of the new oral apparatus and interacts with CdaI to pattern ciliary rows within the oral apparatus. Thus, CdaH acts at multiple scales, from induction and positioning of structures on the cell-wide polarity axis to local organelle-level patterning.}, + author = {Lee, Chinkyu and Maier, Wolfgang and Jiang, Yu-Yang and Nakano, Kentaro and Lechtreck, Karl F. and Gaertig, Jacek}, + doi = {10.1242/jcs.261256}, + issn = {0021-9533}, + journal = {Journal of Cell Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {5}, + pages = {jcs261256}, + title = {Global and local functions of the {Fused} kinase ortholog {CdaH} in intracellular patterning in {Tetrahymena}}, + url = {https://doi.org/10.1242/jcs.261256}, + urldate = {2024-05-17}, + volume = {137}, + year = {2023} +} + @article{lengfelder_complex_2019, abstract = {Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10-/-) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10-/- mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (∆eutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10-/- mice. However, replacement of the E. faecalis wild type bacteria by a ∆eutVW mutant in SIHUMI-colonized IL-10-/- mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10-/- mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis towards a protective function.}, author = {Lengfelder, Isabella and Sava, Irina G. and Hansen, Jonathan J. and Kleigrewe, Karin and Herzog, Jeremy and Neuhaus, Klaus and Hofmann, Thomas and Sartor, R. Balfour and Haller, Dirk}, @@ -2391,6 +6059,45 @@ @article{lengfelder_complex_2019 year = {2019} } +@article{lenz_amyloid_2023, + abstract = {The perforant path provides the primary cortical excitatory input to the hippocampus. Because of its important role in information processing and coding, entorhinal projections to the dentate gyrus have been studied in considerable detail. Nevertheless, synaptic transmission between individual connected pairs of entorhinal stellate cells and dentate granule cells remains to be characterized. Here, we have used mouse organotypic entorhino-hippocampal tissue cultures of either sex, in which the entorhinal cortex (EC) to dentate granule cell (GC; EC–GC) projection is present, and EC–GC pairs can be studied using whole-cell patch-clamp recordings. By using cultures of wild-type mice, the properties of EC–GC synapses formed by afferents from the lateral and medial entorhinal cortex were compared, and differences in short-term plasticity were identified. As the perforant path is severely affected in Alzheimer's disease, we used tissue cultures of amyloid precursor protein (APP)–deficient mice to examine the role of APP at this synapse. APP deficiency altered excitatory neurotransmission at medial perforant path synapses, which was accompanied by transcriptomic and ultrastructural changes. Moreover, presynaptic but not postsynaptic APP deletion through the local injection of Cre-expressing adeno-associated viruses in conditional APPflox/flox tissue cultures increased the neurotransmission efficacy at perforant path synapses. In summary, these data suggest a physiological role for presynaptic APP at medial perforant path synapses that may be adversely affected under altered APP processing conditions. +SIGNIFICANCE STATEMENT The hippocampus receives input from the entorhinal cortex via the perforant path. These projections to hippocampal dentate granule cells are of utmost importance for learning and memory formation. Although there is detailed knowledge about perforant path projections, the functional synaptic properties at the level of individual connected pairs of neurons are not well understood. In this study, we investigated the role of APP in mediating functional properties and transmission rules in individually connected neurons using paired whole-cell patch-clamp recordings and genetic tools in organotypic tissue cultures. Our results show that presynaptic APP expression limits excitatory neurotransmission via the perforant path, which could be compromised in pathologic conditions such as Alzheimer's disease.}, + author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Galanis, Christos and Kleidonas, Dimitrios and Andrieux, Geoffroy and Boerries, Melanie and Jedlicka, Peter and Müller, Ulrike and Deller, Thomas and Vlachos, Andreas}, + copyright = {Copyright © 2023 the authors. SfN exclusive license.}, + doi = {10.1523/JNEUROSCI.1824-22.2023}, + issn = {0270-6474, 1529-2401}, + journal = {Journal of Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, amyloid precursor protein, dentate gyrus, entorhinal cortex, hilar mossy cell, perforant path, stellate cells}, + language = {en}, + month = {July}, + note = {Publisher: Society for Neuroscience +Section: Research Articles}, + number = {29}, + pages = {5290--5304}, + pmid = {37369586}, + title = {The {Amyloid} {Precursor} {Protein} {Regulates} {Synaptic} {Transmission} at {Medial} {Perforant} {Path} {Synapses}}, + url = {https://www.jneurosci.org/content/43/29/5290}, + urldate = {2023-07-31}, + volume = {43}, + year = {2023} +} + +@article{lenz_denervated_2023, + abstract = {Structural, functional, and molecular reorganization of denervated neural networks is often observed in neurological conditions. The loss of input is accompanied by homeostatic synaptic adaptations, which can affect the reorganization process. A major ...}, + author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Stöhr, Phyllis and Kleidonas, Dimitrios and Galanis, Christos and Lu, Han and Vlachos, Andreas}, + doi = {10.3389/fnmol.2023.1148219}, + journal = {Frontiers in Molecular Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Publisher: Frontiers Media SA}, + pmid = {37122623}, + title = {Denervated mouse {CA1} pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10130538/}, + urldate = {2023-06-05}, + volume = {16}, + year = {2023} +} + @article{lezameta_draft_2020, abstract = {Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.}, author = {Lezameta, Lizet and Cuicapuza, Diego and Dávila-Barclay, Alejandra and Torres, Susan and Salvatierra, Guillermo and Tsukayama, Pablo and Tamariz, Jesús}, @@ -2426,6 +6133,25 @@ @article{li_mitochondrial_2021 year = {2021} } +@article{li_proteogenomic_2023, + author = {Li, Yize and Dou, Yongchao and Leprevost, Felipe Da Veiga and Geffen, Yifat and Calinawan, Anna P. and Aguet, François and Akiyama, Yo and Anand, Shankara and Birger, Chet and Cao, Song and Chaudhary, Rekha and Chilappagari, Padmini and Cieslik, Marcin and Colaprico, Antonio and Zhou, Daniel Cui and Day, Corbin and Domagalski, Marcin J. and Selvan, Myvizhi Esai and Fenyö, David and Foltz, Steven M. and Francis, Alicia and Gonzalez-Robles, Tania and Gümüş, Zeynep H. and Heiman, David and Holck, Michael and Hong, Runyu and Hu, Yingwei and Jaehnig, Eric J. and Ji, Jiayi and Jiang, Wen and Katsnelson, Lizabeth and Ketchum, Karen A. and Klein, Robert J. and Lei, Jonathan T. and Liang, Wen-Wei and Liao, Yuxing and Lindgren, Caleb M. and Ma, Weiping and Ma, Lei and MacCoss, Michael J. and Rodrigues, Fernanda Martins and McKerrow, Wilson and Nguyen, Ngoc and Oldroyd, Robert and Pilozzi, Alexander and Pugliese, Pietro and Reva, Boris and Rudnick, Paul and Ruggles, Kelly V. and Rykunov, Dmitry and Savage, Sara R. and Schnaubelt, Michael and Schraink, Tobias and Shi, Zhiao and Singhal, Deepak and Song, Xiaoyu and Storrs, Erik and Terekhanova, Nadezhda V. and Thangudu, Ratna R. and Thiagarajan, Mathangi and Wang, Liang-Bo and Wang, Joshua M. and Wang, Ying and Wen, Bo and Wu, Yige and Wyczalkowski, Matthew A. and Xin, Yi and Yao, Lijun and Yi, Xinpei and Zhang, Hui and Zhang, Qing and Zuhl, Maya and Getz, Gad and Ding, Li and Nesvizhskii, Alexey I. and Wang, Pei and Robles, Ana I. and Zhang, Bing and Payne, Samuel H. and Lazar, Alexander J. and Paulovich, Amanda G. and Colaprico, Antonio and Iavarone, Antonio and Chinnaiyan, Arul M. and Druker, Brian J. and Kumar-Sinha, Chandan and Newton, Chelsea J. and Huang, Chen and Mani, D. R. and Smith, Richard D. and Huntsman, Emily and Schadt, Eric E. and An, Eunkyung and Petralia, Francesca and Hostetter, Galen and Omenn, Gilbert S. and Cho, Hanbyul and Rodriguez, Henry and Zhang, Hui and Kolodziejczak, Iga and Johnson, Jared L. and Bavarva, Jasmin and Tan, Jimin and Rodland, Karin D. and Clauser, Karl R. and Krug, Karsten and Cantley, Lewis C. and Wiznerowicz, Maciej and Ellis, Matthew J. and Anurag, Meenakshi and Mesri, Mehdi and Gillette, Michael A. and Birrer, Michael J. and Ceccarelli, Michele and Dhanasekaran, Saravana M. and Edwards, Nathan and Tignor, Nicole and Babur, Özgün and Pugliese, Pietro and Gosline, Sara J. C. and Jewell, Scott D. and Satpathy, Shankha and Chowdhury, Shrabanti and Schürer, Stephan and Carr, Steven A. and Liu, Tao and Hiltke, Tara and Yaron, Tomer M. and Stathias, Vasileios and Liu, Wenke and Zhang, Xu and Song, Yizhe and Zhang, Zhen and Chan, Daniel W.}, + doi = {10.1016/j.ccell.2023.06.009}, + issn = {1535-6108, 1878-3686}, + journal = {Cancer Cell}, + keywords = {{\textgreater}UseGalaxy.eu, CPTAC, data harmonization, multi-omics, open data, pan-cancer, proteogenomics}, + language = {English}, + month = {August}, + note = {Publisher: Elsevier}, + number = {8}, + pages = {1397--1406}, + pmid = {37582339}, + title = {Proteogenomic data and resources for pan-cancer analysis}, + url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(23)00219-2}, + urldate = {2023-12-03}, + volume = {41}, + year = {2023} +} + @article{liang_reciprocal_2020, abstract = {Podocyte maintenance and stress resistance are exquisitely based on high basal rates of autophagy making these cells a unique model to unravel mechanisms of autophagy regulation. Polyamines have key cellular functions such as proliferation, nucleic acid biosynthesis and autophagy. Here we test whether endogenous spermidine signaling is a driver of basal and dynamic autophagy in podocytes by using genetic and pharmacologic approaches to interfere with different steps of polyamine metabolism. Translational studies revealed altered spermidine signaling in focal segmental glomerulosclerosis in vivo and in vitro. Exogenous spermidine supplementation emerged as new treatment strategy by successfully activating autophagy in vivo via inhibition of EP300, a protein with an essential role in controlling cell growth, cell division and prompting cells to differentiate to take on specialized functions. Surprisingly, gas chromatography-mass spectroscopy based untargeted metabolomics of wild type and autophagy deficient primary podocytes revealed a positive feed-back mechanism whereby autophagy itself maintains polyamine metabolism and spermidine synthesis. The transcription factor MAFB acted as an upstream regulator of polyamine metabolism. Thus, our data highlight a novel positive feedback loop of autophagy and spermidine signaling allowing maintenance of high basal levels of autophagy as a key mechanism to sustain the filtration barrier. Hence, spermidine supplementation may emerge as a new therapeutic to restore autophagy in glomerular disease.}, author = {Liang, Wei and Yamahara, Kosuke and Hernando-Erhard, Camila and Lagies, Simon and Wanner, Nicola and Liang, Huan and Schell, Christoph and Kammerer, Bernd and Huber, Tobias B. and Bork, Tillmann}, @@ -2441,15 +6167,59 @@ @article{liang_reciprocal_2020 year = {2020} } +@phdthesis{link_characterization_2024, + abstract = {{\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} are key players in the fermentation of lupine moromi. Comparative genomic analyses and transcriptomic profiling of {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains isolated from lupine moromi led to the identification of genes beneficial in this environment. Further, the competitiveness of isolated {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains in a lupine moromi model fermentation was investigated. The {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} strain that dominated the lupine moromi fermentation was fully sequenced and genomically analyzed.}, + author = {Link, Tobias}, + keywords = {{\textgreater}UseGalaxy.eu}, + school = {Technische Universität München}, + title = {Characterization and habitat adaptation of {\textless}em{\textgreater}{Tetragenococcus} halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}{Debaryomyces} hansenii{\textless}/em{\textgreater} from a lupine seasoning sauce fermentation}, + url = {https://mediatum.ub.tum.de/1713925}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{liu_comparative_2022, + abstract = {In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The phages used in the initial treatment are related, T4-like myophages. Analysis of 19 A. baumannii isolates collected before and during phage treatment shows that resistance to the T4-like phages appeared two days following the start of treatment. We generate complete genomic sequences for three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment, supporting a clonal relationship. Furthermore, we use strain TP1 to select for increased resistance to five of the phages in vitro, and identify mutations that are also found in phage-insensitive isolates TP2 and TP3 (which evolved in vivo during phage treatment). These results support that in vitro investigations can produce results that are relevant to the in vivo environment.}, + author = {Liu, Mei and Hernandez-Morales, Adriana and Clark, James and Le, Tram and Biswas, Biswajit and Bishop-Lilly, Kimberly A. and Henry, Matthew and Quinones, Javier and Voegtly, Logan J. and Cer, Regina Z. and Hamilton, Theron and Schooley, Robert T. and Salka, Scott and Young, Ry and Gill, Jason J.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41467-022-31455-5}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bacterial infection, Bacteriophages, Clinical microbiology}, + language = {en}, + month = {June}, + number = {1}, + pages = {3776}, + title = {Comparative genomics of {Acinetobacter} baumannii and therapeutic bacteriophages from a patient undergoing phage therapy}, + url = {https://www.nature.com/articles/s41467-022-31455-5}, + urldate = {2022-09-24}, + volume = {13}, + year = {2022} +} + +@article{liu_comprehensive_2023, + abstract = {Precisely calling chromatin loops has profound implications for further analysis of gene regulation and disease mechanisms. Technological advances in chromatin conformation capture (3C) assays make it possible to identify chromatin loops in the genome. However, a variety of experimental protocols have resulted in different levels of biases, which require distinct methods to call true loops from the background. Although many bioinformatics tools have been developed to address this problem, there is still a lack of special introduction to loop-calling algorithms. This review provides an overview of the loop-calling tools for various 3C-based techniques. We first discuss the background biases produced by different experimental techniques and the denoising algorithms. Then, the completeness and priority of each tool are categorized and summarized according to the data source of application. The summary of these works can help researchers select the most appropriate method to call loops and further perform downstream analysis. In addition, this survey is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.}, + author = {Liu, Li and Han, Kaiyuan and Sun, Huimin and Han, Lu and Gao, Dong and Xi, Qilemuge and Zhang, Lirong and Lin, Hao}, + doi = {10.1093/bib/bbad072}, + issn = {1477-4054}, + journal = {Briefings in Bioinformatics}, + keywords = {{\textgreater}HiCExplorer, {\textgreater}UseGalaxy.eu}, + month = {March}, + pages = {bbad072}, + title = {A comprehensive review of bioinformatics tools for chromatin loop calling}, + url = {https://doi.org/10.1093/bib/bbad072}, + urldate = {2023-03-15}, + year = {2023} +} + @article{liu_denovoprofiling_2021, abstract = {With the advances of deep learning techniques, various architectures for molecular generation have been proposed for de novo drug design. Successful cases from academia and industrial demonstrated that the deep learning-based de novo molecular design could efficiently accelerate the drug discovery process. The flourish of the de novo molecular generation methods and applications created a great demand for the visualization and functional profiling for the de novo generated molecules. The rising of publicly available chemogenomic databases lays good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification \&amp; visualization, (2) chemical space, (3) scaffold analysis, (4) molecular alignment, (5) drugs mapping, and (6) target \&amp; pathway. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target \&amp; pathway information. The comprehensive annotated information could give users a clear picture of their de novo library and could guide the further selection of candidates for synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.}, author = {Liu, Zhihong and Du, Jiewen and Liu, Bingdong and Cui, Zongbin and Fang, Jiansong and Xie, Liwei}, doi = {10.21203/rs.3.rs-142605/v2}, + issn = {2693-5015}, journal = {Research Square}, keywords = {+RefPublic, {\textgreater}ChemicalToolbox}, month = {August}, - note = {ISSN: 2693-5015 -Type: article}, shorttitle = {{DenovoProfiling}}, title = {{DenovoProfiling}: a webserver for de novo generated molecule library profiling}, url = {https://www.researchsquare.com/article/rs-142605/v2}, @@ -2457,6 +6227,24 @@ @article{liu_denovoprofiling_2021 year = {2021} } +@article{livingstone_novo_2023, + abstract = {Here, we report the complete genome sequences of Pasteurella multocida strains P504190 and P504188/1, which were isolated from the diseased lungs of a sow and her piglet, respectively. Despite the unusual clinical presentation, whole-genome sequence typing revealed both strains to be capsular type D and lipopolysaccharide (LPS) group 6, commonly found in pigs.}, + author = {Livingstone, Morag and Jorgensen, Pernille and McCall, Margaret and Thomson, Jill and Longbottom, David}, + doi = {10.1128/mra.00098-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + note = {Publisher: American Society for Microbiology}, + number = {5}, + pages = {e00098--23}, + shorttitle = {De {Novo} {Whole}-{Genome} {Sequencing} of {Two} {Pathogenic} {Pasteurella} multocida {Type} {D}}, + title = {De {Novo} {Whole}-{Genome} {Sequencing} of {Two} {Pathogenic} {Pasteurella} multocida {Type} {D}:6 {Strains} {Isolated} from {Pigs}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00098-23}, + urldate = {2023-06-05}, + volume = {12}, + year = {2023} +} + @article{lodewijk_evolution_2020, abstract = {Summary. Ever since the availability of genomes from Neanderthals, Denisovans and ancient humans, the field of evolutionary genomics has been searching for pro}, author = {Lodewijk, Gerrald A. and Fernandes, Diana P. and Vretzakis, Iraklis and Savage, Jeanne E. and Jacobs, Frank M. J.}, @@ -2486,6 +6274,41 @@ @article{lopez-delisle_pygenometracks_2020 year = {2020} } +@article{lopez-santamarina_evaluation_2022, + abstract = {Until now, although different studies have shown the potential prebiotic effect of seaweed carbohydrates, no studies with the whole seaweeds have been carried out. In addition, the prebiotic effect throughput sequencing remains poorly investigated since most of the published works used qPCR or FISH to estimate bacterial changes. In this work, an in vitro model of the human distal colon was used to determine, for the first time, the potential prebiotic effect of a brown whole seaweed Himanthalia elongata. The whole seaweed was characterized in basis of its nutritional and mineral composition and submitted to the entire gastrointestinal digestion. The prebiotic effect was evaluated by the microbial modulation through 16S rRNA amplicon sequencing, qPCR and short-chain fatty acid analysis. The obtained results indicated that the colonic fraction of H. elongata was used selectively by the Bacteroides genus, more specifically by the specie Bacteoides ovatus, whereas inulin was used mainly by the Parabacteroides genus, being Parabacteroides distasonis the most abundant identified specie. Selective use of inulin by P. distasonis is, therefore, reported by the first time. qPCR analysis shown no significative differences in Bifidobacterium population and a decrease in Lactobacillus along the fermentation assays with both substrates. Regarding to the short-fatty acid production, maximal concentration, 56.11 ± 20.48 mM, was achieved for H. elongata, at 24 h of fermentation whereas for inulin total acid production was 93.66 ± 21.82 mM at 48 h of assay. The metabolic pathways associated with bacterial genera were not significantly different between the two tested substrates. Although more studies are necessary to elucidate the prebiotic character of H. elongata, the results presented in this work are promissory and could open new opportunities of research and application in the area of Nutrition and Food Chemistry.}, + author = {Lopez-Santamarina, Aroa and Cardelle-Cobas, Alejandra and del Carmen Mondragon, Alicia and Sinisterra-Loaiza, Laura and Miranda, Jose Manuel and Cepeda, Alberto}, + doi = {10.1016/j.foodres.2022.111156}, + issn = {0963-9969}, + journal = {Food Research International}, + keywords = {16S rRNA, {\textgreater}UseGalaxy.eu, Algae, Digestion, Fermentation, Fibre, Gut microbiota}, + language = {en}, + month = {June}, + pages = {111156}, + title = {Evaluation of the potential prebiotic effect of {Himanthalia} elongata, an {Atlantic} brown seaweed, in an in vitro model of the human distal colon}, + url = {https://www.sciencedirect.com/science/article/pii/S0963996922002137}, + urldate = {2022-12-03}, + volume = {156}, + year = {2022} +} + +@article{lopez_epigenomic_2024, + abstract = {In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction.}, + author = {López, María-Estefanía and Denoyes, Béatrice and Bucher, Etienne}, + doi = {10.1186/s12870-024-05093-6}, + issn = {1471-2229}, + journal = {BMC Plant Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Asexual, Epigenetic, Fragaria, Memory, Plant, Reproduction, Stress}, + language = {en}, + month = {May}, + number = {1}, + pages = {405}, + title = {Epigenomic and transcriptomic persistence of heat stress memory in strawberry ({Fragaria} vesca)}, + url = {https://doi.org/10.1186/s12870-024-05093-6}, + urldate = {2024-06-07}, + volume = {24}, + year = {2024} +} + @article{lother_diabetes_2020, abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}h3{\textgreater}Background{\textless}/h3{\textgreater}{\textless}p{\textgreater}Diabetes mellitus is a worldwide epidemic that causes high mortality due to cardiovascular complications, in particular heart failure. Diabetes is associated with profound pathophysiological changes in the heart. The aim of this study was to investigate the impact of diabetes on gene expression and DNA methylation in cardiac cells.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and results{\textless}/h3{\textgreater}{\textless}p{\textgreater}Transcriptome analysis of heart tissue from mice with streptozotocin-induced diabetes revealed only 39 genes regulated, whereas cell type-specific analysis of the diabetic heart was more sensitive and more specific than heart tissue analysis and revealed a total of 3205 differentially regulated genes in five cell types. Whole genome DNA methylation analysis with basepair resolution of distinct cardiac cell types identified highly specific DNA methylation signatures of genic and regulatory regions. Interestingly, despite marked changes in gene expression, DNA methylation remained stable in streptozotocin-induced diabetes. Integrated analysis of cell type-specific gene expression enabled us to assign the particular contribution of single cell types to the pathophysiology of the diabetic heart. Finally, analysis of gene regulation revealed ligand-receptor pairs as potential mediators of heterocellular interaction in the diabetic heart, with fibroblasts and monocytes showing the highest degree of interaction.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusion{\textless}/h3{\textgreater}{\textless}p{\textgreater}In summary, cell type-specific analysis reveals differentially regulated gene programs that are associated with distinct biological processes in diabetes. Interestingly, despite these changes in gene expression, cell type-specific DNA methylation signatures of genic and regulatory regions remain stable in diabetes. Analysis of heterocellular interactions in the diabetic heart suggest that the interplay between fibroblasts and monocytes is of pivotal importance.{\textless}/p{\textgreater}}, author = {Lother, Achim and Bondareva, Olga and Saadatmand, Ali R. and Pollmeier, Luisa and Härdtner, Carmen and Hilgendorf, Ingo and Weichenhan, Dieter and Eckstein, Volker and Plass, Christoph and Bode, Christoph and Backs, Johannes and Hein, Lutz and Gilsbach, Ralf}, @@ -2591,6 +6414,22 @@ @article{macnee_simtext_2021 year = {2021} } +@article{maffei_complete_2024, + author = {Maffei, Enea and Manner, Christina and Jenal, Urs and Harms, Alexander}, + doi = {10.1128/mra.01174-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {4}, + pages = {e01174--23}, + title = {Complete genome sequence of {Pseudomonas} aeruginosa phage {Knedl}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01174-23}, + urldate = {2024-04-28}, + volume = {13}, + year = {2024} +} + @article{maier_freely_2021, abstract = {{\textless}p{\textgreater}The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.{\textless}/p{\textgreater}}, author = {Maier, Wolfgang and Bray, Simon and Beek, Marius van den and Bouvier, Dave and Coraor, Nathaniel and Miladi, Milad and Singh, Babita and Argila, Jordi Rambla De and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren and Lonie, Andrew and Gruning, Bjorn and Pond, Sergei Kosakovsky and Nekrutenko, Anton}, @@ -2631,6 +6470,40 @@ @article{maier_ready--use_2021 year = {2021} } +@article{maki_species_2023, + abstract = {Campylobacter ureolyticus is an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates. We reviewed the epidemiology of clinical C. ureolyticus cultured by our institution over the past 10 years. Fifty-one unique C. ureolyticus isolates were identified between January 2010 and August 2022, mostly originating from abscesses and blood cultures. To clarify the taxonomic relationships between isolates and to attribute specific genes with different clinical manifestations, we sequenced 19 available isolates from a variety of clinical specimen types and conducted a pangenomic analysis with publicly available C. ureolyticus genomes. Digital DNA:DNA hybridization suggested that these C. ureolyticus comprised a species complex of 10 species clusters (SCs) and several subspecies clusters. Although some orthologous genes or gene functions were enriched in isolates found in different SCs and clinical specimens, no association was significant. Nearly a third of the isolates possessed antimicrobial resistance genes, including the ermA resistance gene, potentially conferring resistance to macrolides, the treatment of choice for severe human campylobacteriosis. This work effectively doubles the number of publicly available C. ureolyticus genomes, provides further clarification of taxonomic relationships within this bacterial complex, and identifies target SCs for future analysis.}, + author = {Maki, Joel J. and Howard, Mondraya and Connelly, Sara and Pettengill, Matthew A. and Hardy, Dwight J. and Cameron, Andrew}, + doi = {10.1128/jcm.00046-23}, + journal = {Journal of Clinical Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + note = {Publisher: American Society for Microbiology}, + number = {5}, + pages = {e00046--23}, + title = {Species {Delineation} and {Comparative} {Genomics} within the {Campylobacter} ureolyticus {Complex}}, + url = {https://journals.asm.org/doi/full/10.1128/jcm.00046-23}, + urldate = {2023-06-05}, + volume = {61}, + year = {2023} +} + +@article{manna_endosomal_2023, + abstract = {Contractile vacuoles (CVs), enigmatic osmoregulatory organelles, share common characteristics, such as a requirement for RAB11 and high levels of V-ATPase. These commonalities suggest a conserved evolutionary origin for the CVs with implications for understanding of the last common ancestor of eukaryotes and eukaryotic diversification more broadly. A taxonomically broader sampling of CV-associated machinery is required to address this question further. We used a transcriptomics-based approach to identify CV-associated gene products in Dictyostelium discoideum. This approach was first validated by assessing a set of known CV-associated gene products, which were significantly upregulated following hypo-osmotic exposure. Moreover, endosomal and vacuolar gene products were enriched in the upregulated gene set. An upregulated SNARE protein (NPSNB) was predominantly plasma membrane localised and enriched in the vicinity of CVs, supporting the association with this organelle found in the transcriptomic analysis. We therefore confirm that transcriptomic approaches can identify known and novel players in CV function, in our case emphasizing the role of endosomal vesicle fusion machinery in the D. discoideum CV and facilitating future work to address questions regarding the deep evolution of eukaryotic organelles.}, + author = {Manna, Paul T. and Barlow, Lael D. and Ramirez-Macias, Inmaculada and Herman, Emily K. and Dacks, Joel B.}, + doi = {10.1242/jcs.260477}, + issn = {0021-9533}, + journal = {Journal of Cell Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {2}, + pages = {jcs260477}, + title = {Endosomal vesicle fusion machinery is involved with the contractile vacuole in {Dictyostelium} discoideum}, + url = {https://doi.org/10.1242/jcs.260477}, + urldate = {2023-03-15}, + volume = {136}, + year = {2023} +} + @article{marisaldi_novo_2021, abstract = {In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length ({\textgreater}80\% coverage), with an Ex90N50 of 3061 bp and 76\% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1\% of tuna transcripts were included in orthogroups with other species and 5.1\% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.}, author = {Marisaldi, Luca and Basili, Danilo and Gioacchini, Giorgia and Canapa, Adriana and Carnevali, Oliana}, @@ -2706,6 +6579,62 @@ @article{marzoli_next_2020 year = {2020} } +@article{mathlouthi_colorectal_2023, + abstract = {Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral (n = 33) and healthy mucosa (n = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33\% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in Halobacteria in the tumor tissues, while the correlation analysis revealed a significant association between the Halobacteria and the tumor mucosa (p {\textless} 0.05). We reported a strong correlation between Natrialba magadii, Sulfolobus acidocaldarius, and tumor tissues, and a weak correlation between Methanococcus voltae and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between Halobacteria and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients’ gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of Halobacteria, especially Natrialba magadii, in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including Sulfolobus acidocaldarius and Methanococcus voltae, which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues.}, + author = {Mathlouthi, Nour El Houda and Oumarou Hama, Hamadou and Belguith, Imen and Charfi, Slim and Boudawara, Tahya and Lagier, Jean-Christophe and Ammar Keskes, Leila and Grine, Ghiles and Gdoura, Radhouane}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cimb45090477}, + issn = {1467-3045}, + journal = {Current Issues in Molecular Biology}, + keywords = {\textit{Halobacteria}, \textit{Natrialba magadii}, {\textgreater}UseGalaxy.eu, archaeome, colorectal cancer, formalin-fixed paraffin embedded tissues, gut microbiome, metagenomic, prognosis}, + language = {en}, + month = {September}, + note = {Number: 9 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {9}, + pages = {7572--7581}, + shorttitle = {Colorectal {Cancer} {Archaeome}}, + title = {Colorectal {Cancer} {Archaeome}: {A} {Metagenomic} {Exploration}, {Tunisia}}, + url = {https://www.mdpi.com/1467-3045/45/9/477}, + urldate = {2023-09-23}, + volume = {45}, + year = {2023} +} + +@article{mathura_characterization_2023, + abstract = {Abscisic acid (ABA) signaling in plants is essential to several aspects of plant development, such as tolerance to environmental stresses and growth. ABA signaling is also important for storage organ formation in crops, such as sweet potato. However, the repertoire of I. batatas ABA signaling gene families has not yet been fully characterized, so that it is unclear which members of these families are necessary for tuberization. Therefore, genome-wide identification of the sweet potato ABF/ AREB/ ABI5, SnRK2, and PYL gene families was performed, along with phylogenetic, motif, cis-regulatory element (CRE), and expression analyses. Nine ABF, eight SnRK2, and eleven PYL gene family members were identified, and there was high sequence conservation among these proteins that were revealed by phylogenetic and motif analyses. The promoter sequences of these genes had multiple CREs that were involved in hormone responses and stress responses. In silico and qRT-PCR expression analyses revealed that these genes were expressed in various tissues and that IbABF3, IbABF4, IbDPBF3, IbDPBF4, IbPYL4, IbSnRK2.1, and IbSnRK2.2 were significantly expressed during storage root development. These results are an important reference that can be used for functional validation studies to better understand how ABA signaling elicits storage root formation at the molecular level.}, + author = {Mathura, Sarah R. and Sutton, Fedora and Bowrin, Valerie}, + doi = {10.1371/journal.pone.0288481}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Potato, Protein interaction networks, Sequence motif analysis, Signaling networks, Stress signaling cascade, Sweet potato, Tubers}, + language = {en}, + month = {March}, + note = {Publisher: Public Library of Science}, + number = {11}, + pages = {e0288481}, + title = {Characterization and expression analysis of {SnRK2}, {PYL}, and {ABF}/ {AREB}/ {ABI5} gene families in sweet potato}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288481}, + urldate = {2023-11-11}, + volume = {18}, + year = {2023} +} + +@article{mathura_genome-wide_2023, + abstract = {Auxin is a plant phytohormone that is essential for the initiation of tuberization in sweet potato (Ipomoea batatas (L.) Lam.). Auxin exerts these effects via polar auxin transport facilitated by various auxin influx and efflux carriers. It is unclear which members of the auxin transporter families: PIN, PILS, Aux/LAX, and ABCB, are involved in sweet potato tuber initiation and development. Therefore, a genome-wide analysis of the I. batatas auxin transporter genes was conducted, and their expression patterns during storage root initiation and development were analyzed. Five IbLAX, 16 IbPIN, 12 IbPILS, and 34 IbABCB family members were identified. These genes showed high conservation among families based on their intron-exon structure, motif composition, and phylogenetic analysis. Additionally, the promoter regions of these genes had various cis-acting regulatory elements involved in hormone, light, and developmental responses. The auxin transporter genes were expressed in various sweet potato tissues, and many were differentially expressed during storage root development. IbLAX1, IbPIN13, IbPILS7, IbABCB1, and IbABCB14 showed up-regulated expression during tuber initiation. This study characterizes these auxin transporter gene families for the first time. These results are an important reference for validation studies to determine the specific functions of these genes and their auxin transporting capability.}, + author = {Mathura, Sarah R. and Sutton, Fedora and Bowrin, Valerie}, + doi = {10.1007/s12042-023-09333-1}, + issn = {1935-9764}, + journal = {Tropical Plant Biology}, + keywords = {{\textgreater}UseGalaxy.eu, ABCB, Aux/LAX, Ipomoea batatas, PILS, PIN}, + language = {en}, + month = {June}, + title = {Genome-wide {Identification} of the {Auxin} {Transporter} {Gene} {Families} in {Sweet} {Potato} ({Ipomoea} batatas) and their {Expression} {During} {Tuberization}}, + url = {https://doi.org/10.1007/s12042-023-09333-1}, + urldate = {2023-07-31}, + year = {2023} +} + @article{mauer_genomics_2021, author = {Mauer, Katharina M. and Schmidt, Hanno and Dittrich, Marco and Fröbius, Andreas C. and Hellmann, Sören Lukas and Zischler, Hans and Hankeln, Thomas and Herlyn, Holger}, doi = {10.1186/s12864-021-07857-y}, @@ -2719,6 +6648,37 @@ @article{mauer_genomics_2021 year = {2021} } +@article{mccluskey_predicting_2024, + author = {McCluskey, Kevin and Brown, Daren and Bredeweg, Erin and Baker, Scott}, + doi = {10.4148/1941-4765.2183}, + issn = {1941-4765}, + journal = {Fungal Genetics Reports}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + number = {1}, + title = {Predicting the {Identities} of su(met-2) and met-3 in {Neurospora} crassa by {Genome} {Resequencing}}, + url = {https://newprairiepress.org/fgr/vol67/iss1/3}, + volume = {67}, + year = {2024} +} + +@article{mcdonald_ultraviolet_2022, + abstract = {Stomatopod crustaceans have among the most complex eyes in the animal kingdom, with up to 12 different color detection channels. The capabilities of these unique eyes include photoreception of ultraviolet (UV) wavelengths (\<400 nm). UV vision has been well characterized in adult stomatopods but has not been previously demonstrated in the comparatively simpler larval eye. Larval stomatopod eyes are developmentally distinct from their adult counterpart and have been described as lacking the visual pigment diversity and morphological specializations found in adult eyes. However, recent studies have provided evidence that larval stomatopod eyes are more complex than previously thought and warrant closer investigation. Using electroretinogram recordings in live animals we found physiological evidence of blue- and UV-sensitive photoreceptors in larvae of the Caribbean stomatopod species Neogonodactylus oerstedii. Transcriptomes of individual larvae were used to identify the expression of three distinct UV opsin mRNA transcripts, which may indicate the presence of multiple UV spectral channels. This is the first paper to document UV vision in any larval stomatopod, expanding our understanding of the importance of UV sensitivity in plankton. Larval stomatopod eyes are more complex and more similar to adult eyes than expected, showing previously uncharacterized molecular diversity and physiological functions.}, + author = {McDonald, Marisa S. and Palecanda, Sitara and Cohen, Jonathan H. and Porter, Megan L.}, + doi = {10.1242/jeb.243256}, + issn = {0022-0949}, + journal = {Journal of Experimental Biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + number = {3}, + pages = {jeb243256}, + title = {Ultraviolet vision in larval {Neogonodactylus} oerstedii}, + url = {https://doi.org/10.1242/jeb.243256}, + urldate = {2022-09-24}, + volume = {225}, + year = {2022} +} + @article{mcdonald_ultraviolet_2022, author = {McDonald, Marisa S. and Palecanda, Sitara and Cohen, Jonathan H. and Porter, Megan L.}, doi = {10.1242/jeb.243256}, @@ -2783,6 +6743,20 @@ @article{mcgowan_multi-omics_2020 year = {2020} } +@article{meem_exploring_2024, + abstract = {This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of −7.6, −7.9, −7.5, and −7.8 kcal mol−1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85\%. Convergence was confirmed by the eigenvector’s cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.}, + author = {Meem, Mehnaz Hossain and Yusuf, Sumaiya Binte and Al Abbad, Sanaa S. and Rahman, Shofiur and Al-Gawati, Mahmoud and Albrithen, Hamad and Alodhayb, Abdullah N. and Uddin, Kabir M.}, + issn = {2296-2646}, + journal = {Frontiers in Chemistry}, + keywords = {{\textgreater}UseGalaxy.eu}, + shorttitle = {Exploring the anticancer and antibacterial potential of naphthoquinone derivatives}, + title = {Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation}, + url = {https://www.frontiersin.org/articles/10.3389/fchem.2024.1351669}, + urldate = {2024-02-24}, + volume = {12}, + year = {2024} +} + @article{mehta_asaim-mt_2021, abstract = {The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.}, author = {Mehta, Subina and Crane, Marie and Leith, Emma and Batut, Bérénice and Hiltemann, Saskia and Arntzen, Magnus Ø and Kunath, Benoit J. and Delogu, Francesco and Sajulga, Ray and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -2801,6 +6775,43 @@ @article{mehta_asaim-mt_2021 year = {2021} } +@article{mehta_catching_2022, + abstract = {The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in a major health crisis worldwide with its continuously emerging new strains, resulting in new viral variants that drive "waves" of infection. PCR or antigen detection assays have been routinely used to detect clinical infections; however, the emergence of these newer strains has presented challenges in detection. One of the alternatives has been to detect and characterize variant-specific peptide sequences from viral proteins using mass spectrometry (MS)-based methods. MS methods can potentially help in both diagnostics and vaccine development by understanding the dynamic changes in the viral proteome associated with specific strains and infection waves. In this study, we developed an accessible, flexible, and shareable bioinformatics workflow that was implemented in the Galaxy Platform to detect variant-specific peptide sequences from MS data derived from the clinical samples. We demonstrated the utility of the workflow by characterizing published clinical data from across the world during various pandemic waves. Our analysis identified six SARS-CoV-2 variant-specific peptides suitable for confident detection by MS in commonly collected clinical samples.}, + author = {Mehta, Subina and Carvalho, Valdemir M. and Rajczewski, Andrew T. and Pible, Olivier and Grüning, Björn A. and Johnson, James E. and Wagner, Reid and Armengaud, Jean and Griffin, Timothy J. and Jagtap, Pratik D.}, + doi = {10.3390/v14102205}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Humans, Peptides, Proteome, SARS-CoV-2, Viral Proteins, mass-spectrometry, strain-specific, variant detection}, + language = {eng}, + month = {October}, + number = {10}, + pages = {2205}, + pmcid = {PMC9609567}, + pmid = {36298760}, + shorttitle = {Catching the {Wave}}, + title = {Catching the {Wave}: {Detecting} {Strain}-{Specific} {SARS}-{CoV}-2 {Peptides} in {Clinical} {Samples} {Collected} during {Infection} {Waves} from {Diverse} {Geographical} {Locations}}, + volume = {14}, + year = {2022} +} + +@article{mehta_galaxy_2023, + author = {Mehta, Subina and Bernt, Matthias and Chambers, Matthew and Fahrner, Matthias and Föll, Melanie Christine and Gruening, Bjoern and Horro, Carlos and Johnson, James E. and Loux, Valentin and Rajczewski, Andrew T. and Schilling, Oliver and Vandenbrouck, Yves and Gustafsson, Ove Johan Ragnar and Thang, W. C. Mike and Hyde, Cameron and Price, Gareth and Jagtap, Pratik D. and Griffin, Timothy J.}, + doi = {10.1080/14789450.2023.2265062}, + issn = {1478-9450}, + journal = {Expert Review of Proteomics}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Bioinformatics, Galaxy platform, computational workflows, mass spectrometry, multi-omics, proteomics, reproducibility}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/14789450.2023.2265062}, + number = {0}, + pages = {1--16}, + pmid = {37787106}, + title = {A {Galaxy} of informatics resources for {MS}-based proteomics}, + url = {https://doi.org/10.1080/14789450.2023.2265062}, + urldate = {2023-10-12}, + volume = {0}, + year = {2023} +} + @article{mehta_precursor_2020, abstract = {For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and multi-omics studies such as metaproteomics (analyzing taxon-specific microbial peptides) and proteogenomics (analyzing non-canonical sequences). Bioinformatics workflows accessible via the Galaxy platform have proven useful for analysis of such complex multi-omic studies. However, workflows within the Galaxy platform have lacked well-tested LFQ tools. In this study, we have evaluated moFF and FlashLFQ, two open-source LFQ tools, and implemented them within the Galaxy platform to offer access and use via established workflows. Through rigorous testing and communication with the tool developers, we have optimized the performance of each tool. Software features evaluated include: (a) match-between-runs (MBR); (b) using multiple file-formats as input for improved quantification; (c) use of containers and/or conda packages; (d) parameters needed for analyzing large datasets; and (e) optimization and validation of software performance. This work establishes a process for software implementation, optimization, and validation, and offers access to two robust software tools for LFQ-based analysis within the Galaxy platform.}, author = {Mehta, Subina and Easterly, Caleb W. and Sajulga, Ray and Millikin, Robert J. and Argentini, Andrea and Eguinoa, Ignacio and Martens, Lennart and Shortreed, Michael R. and Smith, Lloyd M. and McGowan, Thomas and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -2836,6 +6847,99 @@ @article{mehta_updates_2021 year = {2021} } +@article{meier_antileukemic_2022, + abstract = {The prognosis of AML patients with adverse genetics, such as a complex, monosomal karyotype and TP53 lesions, is still dismal even with standard chemotherapy. DNA-hypomethylating agent monotherapy induces an encouraging response rate in these patients. When combined with decitabine (DAC), all-trans retinoic acid (ATRA) resulted in an improved response rate and longer overall survival in a randomized phase II trial (DECIDER; NCT00867672). The molecular mechanisms governing this in vivo synergism are unclear. We now demonstrate cooperative antileukemic effects of DAC and ATRA on AML cell lines U937 and MOLM-13. By RNA-sequencing, derepression of {\textgreater}1200 commonly regulated transcripts following the dual treatment was observed. Overall chromatin accessibility (interrogated by ATAC-seq) and, in particular, at motifs of retinoic acid response elements were affected by both single-agent DAC and ATRA, and enhanced by the dual treatment. Cooperativity regarding transcriptional induction and chromatin remodeling was demonstrated by interrogating the HIC1, CYP26A1, GBP4, and LYZ genes, in vivo gene derepression by expression studies on peripheral blood blasts from AML patients receiving DAC + ATRA. The two drugs also cooperated in derepression of transposable elements, more effectively in U937 (mutated TP53) than MOLM-13 (intact TP53), resulting in a “viral mimicry” response. In conclusion, we demonstrate that in vitro and in vivo, the antileukemic and gene-derepressive epigenetic activity of DAC is enhanced by ATRA.}, + author = {Meier, Ruth and Greve, Gabriele and Zimmer, Dennis and Bresser, Helena and Berberich, Bettina and Langova, Ralitsa and Stomper, Julia and Rubarth, Anne and Feuerbach, Lars and Lipka, Daniel B. and Hey, Joschka and Grüning, Björn and Brors, Benedikt and Duyster, Justus and Plass, Christoph and Becker, Heiko and Lübbert, Michael}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41408-022-00715-4}, + issn = {2044-5385}, + journal = {Blood Cancer Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Acute myeloid leukaemia, Cancer models, Preclinical research}, + language = {en}, + month = {August}, + number = {8}, + pages = {1--13}, + shorttitle = {The antileukemic activity of decitabine upon {PML}/{RARA}-negative {AML} blasts is supported by all-trans retinoic acid}, + title = {The antileukemic activity of decitabine upon {PML}/{RARA}-negative {AML} blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation}, + url = {https://www.nature.com/articles/s41408-022-00715-4}, + urldate = {2022-08-29}, + volume = {12}, + year = {2022} +} + +@article{merida-cerro_rat1_2024, + abstract = {Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.}, + author = {Mérida-Cerro, José Antonio and Maraver-Cárdenas, Pablo and Rondón, Ana G and Aguilera, Andrés}, + doi = {10.1093/nar/gkae033}, + issn = {0305-1048}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + number = {7}, + pages = {3623--3635}, + title = {Rat1 promotes premature transcription termination at {R}-loops}, + url = {https://doi.org/10.1093/nar/gkae033}, + urldate = {2024-04-28}, + volume = {52}, + year = {2024} +} + +@article{merz_characterization_2024, + abstract = {Autolysis by cellular peptidoglycan hydrolases (PGH) is a well-known phenomenon in bacteria. During food fermentation, autolysis of starter cultures can exert an accelerating effect, as described in many studies on cheese ripening. In contrast, very little is known about autolysis of starter cultures used in other fermentations. Staphylococcus (S.) carnosus is often used in raw sausage fermentations, contributing to nitrate reduction and flavor formation. In this study, we analyzed the influence of PGHs of the strains S. carnosus TMW 2.146 and S. carnosus TMW 2.2525 on their autolytic behavior. The staphylococcal major autolysin (Atl), a bifunctional enzyme with an N-acetylmuramoyl-L-alanine amidase and a glucosaminidase as an active site, is assumed to be the enzyme by which autolysis is mainly mediated.}, + author = {Merz, Maximilian and Schiffer, Carolin J. and Klingl, Andreas and Ehrmann, Matthias A.}, + doi = {10.1186/s12866-024-03231-6}, + issn = {1471-2180}, + journal = {BMC Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, AtlC, Autolysis, Knockout mutant, Staphylococcus carnosus}, + language = {en}, + month = {March}, + number = {1}, + pages = {77}, + title = {Characterization of the major autolysin ({AtlC}) of {Staphylococcus} carnosus}, + url = {https://doi.org/10.1186/s12866-024-03231-6}, + urldate = {2024-05-17}, + volume = {24}, + year = {2024} +} + +@article{metris_aircraft_2023, + abstract = {Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.}, + author = {Métris, Kimberly L. and Métris, Jérémy}, + doi = {10.7717/peerj.15171}, + issn = {2167-8359}, + journal = {PeerJ}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Publisher: PeerJ Inc.}, + pages = {e15171}, + shorttitle = {Aircraft surveys for air {eDNA}}, + title = {Aircraft surveys for air {eDNA}: probing biodiversity in the sky}, + url = {https://peerj.com/articles/15171}, + urldate = {2023-04-18}, + volume = {11}, + year = {2023} +} + +@article{mevada_variant_2022, + abstract = {SARS-CoV-2 is an RNA coronavirus responsible for Acute Respiratory Syndrome (COVID-19). In January 2021, the re-occurrence of COVID-19 infection was at its peak, considered the second wave of epidemics. In the initial stage, it was considered a double mutant strain due to two significant mutations observed in their Spike protein (E484Q and L452R). Although it was first detected in India later on, it was spread to several countries worldwide, causing high fatality due to this strain. In the present study, we investigated the spreading of B.1.617 strain worldwide through 822 genome sequences submitted in GISAID on 21 April 2021. All genome sequences were analyzed for variations in genome sequences based on their effects due to changes in nucleotides. At Allele frequency 0.05, there were a total of 47 variations in ORF1ab, 22 in Spike protein gene, 6 variations in N gene, 5 in ORF8 and M gene, four mutations in Orf7a, and one nucleotide substitution observed for ORF3a, ORF6 and ORF7b gene. The clustering for similar mutations mentioned B.1.617 sub-lineages. The outcome of this study established relative occurrence and spread worldwide. The study’s finding represented that “double mutant” strain is not only spread through traveling but it is also observed to evolve naturally with different mutations observed in B.1.617 lineage. The information extracted from the study helps to understand viral evolution and genome variations of B.1.617 lineage. The results support the need of separating B.1.617 into sub-lineages.}, + author = {Mevada, Vishal and Patel, Rajesh and Dudhagara, Pravin and Gandhi, Himani and Beladiya, Urvisha and Vaghamshi, Nilam and Godhaniya, Manoj and Ghelani, Anjana}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/covid2050038}, + issn = {2673-8112}, + journal = {COVID}, + keywords = {{\textgreater}UseGalaxy.eu, B.1.617, double mutant strain of SARS-CoV-2, variant analysis}, + language = {en}, + month = {May}, + number = {5}, + pages = {513--531}, + title = {Variant {Analysis} and {Strategic} {Clustering} to {Sub}-{Lineage} of {Double} {Mutant} {Strain} {B}.1.617 of {SARS}-{CoV}-2}, + url = {https://www.mdpi.com/2673-8112/2/5/38}, + urldate = {2022-09-24}, + volume = {2}, + year = {2022} +} + @article{miao_putative_2020, abstract = {We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The feature genes, which are differentially expressed in the particular cell group, jointly discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterised by the feature genes as markers. To benchmark this approach, we use expert-annotated scRNA-seq datasets from a range of experiments, as well as comparing to existing cell annotation methods, which are all based on a pre-existing reference. We show that our method automatically identifies the 'ground truth' cell assignments with high accuracy. Moreover, our method, Single Cell Clustering Assessment Framework (SCCAF) predicts new putative biologically meaningful cell-states in published data on haematopoiesis and the human cortex. SCCAF is available as an open-source software package on GitHub (https://github.com/SCCAF/sccaf) and as a Python package index and has also been implemented as a Galaxy tool in the Human Cell Atlas.}, author = {Miao, Zhichao and Moreno, Pablo and Huang, Ni and Papatheodorou, Irene and Brazma, Alvis and Teichmann, Sarah A.}, @@ -2863,6 +6967,81 @@ @article{migur_temperature-regulated_2021 year = {2021} } +@article{miranda_assessment_2024, + abstract = {Apples (Malus × domestica Borkh.) and pears (Pyrus communis L.) are valuable crops closely related within the Rosaceae family with reported nutraceutical properties derived from secondary metabolites including phloridzin and arbutin, which are distinctive phenolic metabolites characterizing apples and pears, respectively. Here, we generated a de novo transcriptome assembly of an intergeneric hybrid between apple and pear, accumulating intermediate levels of phloridzin and arbutin. Combining RNA-seq, in silico functional annotation prediction, targeted gene expression analysis, and expression–metabolite correlations, we identified candidate genes for functional characterization, resulting in the identification of active arbutin synthases in the hybrid and parental genotypes. Despite exhibiting an active arbutin synthase in vitro, the natural lack of arbutin in apples is reasoned by the absence of the substrate and broad substrate specificity. Altogether, our study serves as the basis for future assessment of potential physiological roles of identified genes by genome editing of hybrids and pears.}, + author = {Miranda, Simón and Koop, Marion and Angeli, Andrea and Lagrèze, Jorge and Malnoy, Mickael and Martens, Stefan}, + doi = {10.1021/acs.jafc.4c01006}, + issn = {0021-8561}, + journal = {Journal of Agricultural and Food Chemistry}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + note = {Publisher: American Chemical Society}, + title = {Assessment and {Partial} {Characterization} of {Candidate} {Genes} in {Dihydrochalcone} and {Arbutin} {Biosynthesis} in an {Apple}–{Pear} {Hybrid} by {De} {Novo} {Transcriptome} {Assembly}}, + url = {https://doi.org/10.1021/acs.jafc.4c01006}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{mitrofanov_crisprtracrrna_2022, + abstract = {The CRISPR-Cas9 system is a Type II CRISPR system that has rapidly become the most versatile and widespread tool for genome engineering. It consists of two components, the Cas9 effector protein, and a single guide RNA that combines the spacer (for identifying the target) with the tracrRNA, a trans-activating small RNA required for both crRNA maturation and interference. While there are well-established methods for screening Cas effector proteins and CRISPR arrays, the detection of tracrRNA remains the bottleneck in detecting Class 2 CRISPR systems.We introduce a new pipeline CRISPRtracrRNA for screening and evaluation of tracrRNA candidates in genomes. This pipeline combines evidence from different components of the Cas9-sgRNA complex. The core is a newly developed structural model via covariance models from a sequence-structure alignment of experimentally validated tracrRNAs. As additional evidence, we determine the terminator signal (required for the tracrRNA transcription) and the RNA–RNA interaction between the CRISPR array repeat and the 5′-part of the tracrRNA. Repeats are detected via an ML-based approach (CRISPRidenify). Providing further evidence, we detect the cassette containing the Cas9 (Type II CRISPR systems) and Cas12 (Type V CRISPR systems) effector protein. Our tool is the first for detecting tracrRNA for Type V systems.The implementation of the CRISPRtracrRNA is available on GitHub upon requesting the access permission, (https://github.com/BackofenLab/CRISPRtracrRNA). Data generated in this study can be obtained upon request to the corresponding person: Rolf Backofen (backofen@informatik.uni-freiburg.de).Supplementary data are available at Bioinformatics online.}, + author = {Mitrofanov, Alexander and Ziemann, Marcus and Alkhnbashi, Omer S and Hess, Wolfgang R and Backofen, Rolf}, + doi = {10.1093/bioinformatics/btac466}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {Supplement\_2}, + pages = {ii42--ii48}, + shorttitle = {{CRISPRtracrRNA}}, + title = {{CRISPRtracrRNA}: robust approach for {CRISPR} {tracrRNA} detection}, + url = {https://doi.org/10.1093/bioinformatics/btac466}, + urldate = {2022-09-23}, + volume = {38}, + year = {2022} +} + +@article{mohamed_candidate_2023, + abstract = {Rice tungro disease (RTD), caused by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causing a series of outbreaks over the years after being first reported in International Rice Research Institute (IRRI), Philippines, in 1963. One of the effective ways to combat viruses is through RNA silencing. microRNA is an important player in the RNA silencing mechanism. Genome sequences analysis shows RTBV-SP isolate (8 Kb) is composed of four open reading frames (ORF 1, ORF 2, ORF 3, and ORF 4), meanwhile, RTSV-SP (12 Kb) consists of one open reading frame encoded by seven different polyproteins (P1, CP1, CP2, CP3, NTP, Pro, and Rep). Therefore, this study investigated possible rice-encoded miRNAs targeted on RTBV and RTSV using in silico analysis. Five bioinformatics tools were employed using five different prediction algorithms: miRanda, RNA22, RNAhybrid, Tapirhybrid, and psRNATarget. The results revealed each RTBV and RTSV can be silenced by three potentially best candidate rice-encoded miRNA. For RTBV, osa-miR5510 (accession no. MIMAT0022143), osa-miR3980a-3p (accession no. MIMAT0019676), and osa-miR3980b-3p (accession no. MIMAT0019678) are being predicted by all five algorithms. Meanwhile, for RTSV, three miRNAs predicted are osa-miR414 (accession no. MIMAT0001330), osa-miR5505 (accession no. MIMAT00221138) and osa-miR167a-3p (accession no. MIMAT0006780). The predicted data provide useful material for developing RTBV and RTSV-resistant rice varieties.}, + author = {Mohamed, Noor Amni and Ngah, Nik Muhammad Faris Nazmie Che and Abas, Azlan and Talip, Noraini and Sarian, Murni Nazira and Hamezah, Hamizah Shahirah and Harun, Sarahani and Bunawan, Hamidun}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/agriculture13030651}, + issn = {2077-0472}, + journal = {Agriculture}, + keywords = {\textit{Oryza sativa}, {\textgreater}UseGalaxy.eu, bioinformatics, miRNA, rice tungro disease}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {3}, + pages = {651}, + title = {Candidate {miRNAs} from {Oryza} sativa for {Silencing} the {Rice} {Tungro} {Viruses}}, + url = {https://www.mdpi.com/2077-0472/13/3/651}, + urldate = {2023-03-15}, + volume = {13}, + year = {2023} +} + +@article{mohebifar_construction_2023, + abstract = {Breast cancer (BC) is one of the leading causes of cancer-related deaths in women. The present study explored the potential role of pseudogenes in BC via construction and analysis of a competing endogenous RNA (ceRNA) network through a three-step process. First, we screened differentially expressed genes in nine BC datasets. Then the gene-pseudogenes pairs (nine hub genes) were selected according to the functional enrichment and correlation analysis. Second, the candidate hub genes and interacting miRNAs were used to construct the ceRNA network. Further analysis of the ceRNA network revealed a crucial ceRNA module with two genes-pseudogene pairs and two miRNAs. The in-depth analysis identified the GBP1/hsa-miR-30d-5p/GBP1P1 axis as a potential tumorigenic axis in BC patients. In the third step, the GBP1/hsa-miR-30d-5p/GBP1P1 axis expression level was assessed in 40 tumor/normal BC patients and MCF-7 cell lines. The expression of GBP1 and GBP1P1 was significantly higher in the tumor compared to the normal tissue. However, the expression of hsa-miR-30d-5p was lower in tumor samples. Then, we introduced the GBP1P1 pseudogene into the MCF-7 cell line to evaluate its effect on GBP1 and hsa-miR-30d-5p expression. As expected, the GBP1 level increased while the hsa-miR-30d-5p level decreased in the GBP1P1-overexprsssing cell line. In addition, the oncogenic properties of MCF-7 (cell viability, clonogenicity, and migration) were improved after GBP1P1 overexpression. In conclusion, we report a ceRNA network that may provide new insight into the role of pseudogenes in BC development.}, + author = {Mohebifar, Hossein and Sabbaghian, Amir and Farazmandfar, Touraj and Golalipour, Masoud}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-49110-4}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Breast cancer, Long non-coding RNAs}, + language = {en}, + month = {December}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {21874}, + title = {Construction and analysis of pseudogene-related {ceRNA} network in breast cancer}, + url = {https://www.nature.com/articles/s41598-023-49110-4}, + urldate = {2023-12-14}, + volume = {13}, + year = {2023} +} + @article{mootapally_sediment_2021, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, author = {Mootapally, Chandrashekar and Mahajan, Mayur S. and Nathani, Neelam M.}, @@ -2929,6 +7108,45 @@ @article{moreno_user-friendly_2021 year = {2021} } +@article{moris_intrasexual_2023, + abstract = {Cuticular hydrocarbons (CHCs) cover the cuticle of insects and serve as desiccation barrier and as semiochemicals. While the main enzymatic steps of CHC biosynthesis are well understood, few of the underlying genes have been identified. Here we show how exploitation of intrasexual CHC dimorphism in a mason wasp, Odynerus spinipes, in combination with whole-genome sequencing and comparative transcriptomics facilitated identification of such genes. RNAi-mediated knockdown of twelve candidate gene orthologs in the honey bee, Apis mellifera, confirmed nine genes impacting CHC profile composition. Most of them have predicted functions consistent with current knowledge of CHC metabolism. However, we found first-time evidence for a fatty acid amide hydrolase also influencing CHC profile composition. In situ hybridization experiments furthermore suggest trophocytes participating in CHC biosynthesis. Our results set the base for experimental CHC profile manipulation in Hymenoptera and imply that the evolutionary origin of CHC biosynthesis predates the arthropods’ colonization of land.}, + author = {Moris, Victoria C. and Podsiadlowski, Lars and Martin, Sebastian and Oeyen, Jan Philip and Donath, Alexander and Petersen, Malte and Wilbrandt, Jeanne and Misof, Bernhard and Liedtke, Daniel and Thamm, Markus and Scheiner, Ricarda and Schmitt, Thomas and Niehuis, Oliver}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s42003-022-04370-0}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Phylogenetics, RNAi}, + language = {en}, + month = {February}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--15}, + title = {Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in {Hymenoptera}}, + url = {https://www.nature.com/articles/s42003-022-04370-0}, + urldate = {2023-03-15}, + volume = {6}, + year = {2023} +} + +@article{moris_ionizing_2024, + abstract = {The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species.}, + author = {Moris, Victoria C. and Bruneau, Lucie and Berthe, Jérémy and Heuskin, Anne-Catherine and Penninckx, Sébastien and Ritter, Sylvia and Weber, Uli and Durante, Marco and Danchin, Etienne G. J. and Hespeels, Boris and Doninck, Karine Van}, + doi = {10.1186/s12915-023-01807-8}, + issn = {1741-7007}, + journal = {BMC Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Antioxidants, Bdelloid rotifers, DNA repair, Desiccation, Radiation}, + language = {en}, + month = {January}, + number = {1}, + pages = {11}, + title = {Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer {Adineta} vaga}, + url = {https://doi.org/10.1186/s12915-023-01807-8}, + urldate = {2024-05-17}, + volume = {22}, + year = {2024} +} + @article{morsli_direct_2021, abstract = {The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81\% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.}, author = {Morsli, Madjid and Zandotti, Christine and Morand, Aurelie and Colson, Philippe and Drancourt, Michel}, @@ -2949,6 +7167,42 @@ @article{morsli_direct_2021 year = {2021} } +@article{mossad_gut_2022, + abstract = {Microglial function declines during aging. The interaction of microglia with the gut microbiota has been well characterized during development and adulthood but not in aging. Here, we compared microglial transcriptomes from young-adult and aged mice housed under germ-free and specific pathogen-free conditions and found that the microbiota influenced aging associated-changes in microglial gene expression. The absence of gut microbiota diminished oxidative stress and ameliorated mitochondrial dysfunction in microglia from the brains of aged mice. Unbiased metabolomic analyses of serum and brain tissue revealed the accumulation of N6-carboxymethyllysine (CML) in the microglia of the aging brain. CML mediated a burst of reactive oxygen species and impeded mitochondrial activity and ATP reservoirs in microglia. We validated the age-dependent rise in CML levels in the sera and brains of humans. Finally, a microbiota-dependent increase in intestinal permeability in aged mice mediated the elevated levels of CML. This study adds insight into how specific features of microglia from aged mice are regulated by the gut microbiota.}, + author = {Mossad, Omar and Batut, Bérénice and Yilmaz, Bahtiyar and Dokalis, Nikolaos and Mezö, Charlotte and Nent, Elisa and Nabavi, Lara Susann and Mayer, Melanie and Maron, Feres José Mocayar and Buescher, Joerg M. and de Agüero, Mercedes Gomez and Szalay, Antal and Lämmermann, Tim and Macpherson, Andrew J. and Ganal-Vonarburg, Stephanie C. and Backofen, Rolf and Erny, Daniel and Prinz, Marco and Blank, Thomas}, + copyright = {2022 The Author(s), under exclusive licence to Springer Nature America, Inc.}, + doi = {10.1038/s41593-022-01027-3}, + issn = {1546-1726}, + journal = {Nature Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Ageing, Microbiology, Microglia}, + language = {en}, + month = {March}, + pages = {1--11}, + title = {Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite {N6}-carboxymethyllysine}, + url = {https://www.nature.com/articles/s41593-022-01027-3}, + urldate = {2022-03-07}, + year = {2022} +} + +@article{mostafa_genome-wide_2024, + abstract = {Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.}, + author = {Mostafa, Karam and Yerlikaya, Bayram Ali and Abdulla, Mohamed Farah and Aydin, Abdullah and Yerlikaya, Seher and Kavas, Musa}, + copyright = {© 2024 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.}, + doi = {10.1002/tpg2.20432}, + issn = {1940-3372}, + journal = {The Plant Genome}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.20432}, + number = {1}, + pages = {e20432}, + title = {Genome-wide analysis of {PvMADS} in common bean and functional characterization of {PvMADS31} in {Arabidopsis} thaliana as a player in abiotic stress responses}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tpg2.20432}, + urldate = {2024-04-28}, + volume = {17}, + year = {2024} +} + @article{muller-ruch_glp_2020, abstract = {In biomedical research, enormous progress is being made and new candidates for putative medicinal products emerge. However, most published preclinical data are not conducted according to the standard Good Laboratory Practice (GLP). GLP is mandatory for preclinical analysis of Advanced Therapy Medicinal Products (ATMP) and thereby a prerequisite for planning and conduction of clinical trials. Not inconsiderable numbers of clinical trials are terminated earlier or fail – do inadequate testing strategies or missing specialized assays during the preclinical development contribute to this severe complex of problems? Unfortunately, there is also a lack of access to GLP testing results and OECD (Organisation for Economic Co-operation and Development) GLP guidelines are not yet adjusted to ATMP specialties. Ultimately, GLP offers possibilities to generate reliable and reproducible data. Therefore, this review elucidates different GLP aspects in drug development, speculates on reasons of putative low GLP acceptance in the scientific community and mentions solution proposals.}, author = {Müller-Ruch, Ulrike and Skorska, Anna and Lemcke, Heiko and Steinhoff, Gustav and David, Robert}, @@ -3003,26 +7257,30 @@ @article{musmeci_draft_2021 year = {2021} } +@article{myacheva_crispri_2023, + abstract = {Since lung cancer remains the leading cause of cancer death globally, there is an urgent demand for novel therapeutic targets. We carried out a CRISPR interference (CRISPRi) loss-of-function screen for human lung adenocarcinoma (LUAD) targeting 2098 deregulated genes using a customized algorithm to comprehensively probe the functionality of every resolvable transcriptional start site (TSS). CASP8AP2 was identified as the only hit that significantly affected the viability of all eight screened LUAD cell lines while the viability of non-transformed lung cells was only moderately impacted. Knockdown (KD) of CASP8AP2 induced both autophagy and apoptotic cell death pathways. Systematic expression profiling linked the AP-1 transcription factor to the CASP8AP2 KD-induced cancer cell death. Furthermore, inhibition of AP-1 reverted the CASP8AP2 silencing-induced phenotype. Overall, the tailored CRISPRi screen profiled the impact of over 2000 genes on the survival of eight LUAD cell lines and identified the CASP8AP2 – AP-1 axis mediating lung cancer viability.}, + author = {Myacheva, Ksenia and Walsh, Andrew and Riester, Marisa and Pelos, Giulia and Carl, Jane and Diederichs, Sven}, + doi = {10.1016/j.canlet.2022.215958}, + issn = {0304-3835}, + journal = {Cancer Letters}, + keywords = {{\textgreater}UseGalaxy.eu, Autophagy, CRISPR, Caspase, FLASH, Lung adenocarcinoma, NSCLC}, + language = {en}, + month = {January}, + pages = {215958}, + title = {{CRISPRi} screening identifies {CASP8AP2} as an essential viability factor in lung cancer controlling tumor cell death via the {AP}-1 pathway}, + url = {https://www.sciencedirect.com/science/article/pii/S0304383522004451}, + urldate = {2022-11-06}, + volume = {552}, + year = {2023} +} + @article{nagy_draft_2021, + abstract = {The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring.}, author = {Nagy, Nikoletta A. and Rácz, Rita and Rimington, Oliver and Póliska, Szilárd and Orozco-terWengel, Pablo and Bruford, Michael W. and Barta, Zoltán}, doi = {10.1186/s12864-021-07627-w}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - month = {April}, - note = {Publisher: Springer Science and Business Media LLC}, - number = {1}, - title = {Draft genome of a biparental beetle species, {Lethrus} apterus}, - url = {https://doi.org/10.1186/s12864-021-07627-w}, - volume = {22}, - year = {2021} -} - -@article{nagy_draft_2021, - abstract = {The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring.}, - author = {Nagy, Nikoletta A. and Rácz, Rita and Rimington, Oliver and Póliska, Szilárd and Orozco-terWengel, Pablo and Bruford, Michael W. and Barta, Zoltán}, - doi = {10.1186/s12864-021-07627-w}, - issn = {1471-2164}, - journal = {BMC Genomics}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Coleoptera, Genome assembly, Geotrupidae, Parental behaviour}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Coleoptera, Genome assembly, Geotrupidae, Parental behaviour}, month = {April}, number = {1}, pages = {301}, @@ -3051,6 +7309,60 @@ @article{naimi_direct_2021 year = {2021} } +@article{napoli_absence_2022, + abstract = {Despite the increasing interest in using microbial-based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non-Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars-like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE-R2 facility installed outside the International Space Station. Genomic alterations were determined in a space-derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space-exposed cells. Comparative analysis of whole-genome sequences showed no increased variant numbers in the space-derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria-based technologies to support human space exploration.}, + author = {Napoli, Alessandro and Micheletti, Diego and Pindo, Massimo and Larger, Simone and Cestaro, Alessandro and de Vera, Jean-Pierre and Billi, Daniela}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41598-022-12631-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Astrobiology, Genome informatics}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {8437}, + title = {Absence of increased genomic variants in the cyanobacterium {Chroococcidiopsis} exposed to {Mars}-like conditions outside the space station}, + url = {https://www.nature.com/articles/s41598-022-12631-5}, + urldate = {2022-12-03}, + volume = {12}, + year = {2022} +} + +@article{nasereddin_concurrent_2022, + abstract = {Phlebotomine sand flies are vectors of Leishmania parasites, which are the causative agents of leishmaniasis. Herein, we developed an amplicon-based next-generation sequencing (Amp-NGS) to characterize sand flies and Leishmania parasites simultaneously targeting partial fragments of 18S rDNA and ITS1 genes, respectively.}, + author = {Nasereddin, Abedelmajeed and Ereqat, Suheir and Al-Jawabreh, Amer and Taradeh, Mohamad and Abbasi, Ibrahim and Al-Jawabreh, Hanan and Sawalha, Samer and Abdeen, Ziad}, + doi = {10.1186/s13071-022-05388-3}, + issn = {1756-3305}, + journal = {Parasites \& Vectors}, + keywords = {{\textgreater}UseGalaxy.eu, Amp-NGS, Leishmania, Phlebotomine sand flies, Taxonomy}, + month = {July}, + number = {1}, + pages = {262}, + title = {Concurrent molecular characterization of sand flies and {Leishmania} parasites by amplicon-based next-generation sequencing}, + url = {https://doi.org/10.1186/s13071-022-05388-3}, + urldate = {2022-09-24}, + volume = {15}, + year = {2022} +} + +@article{nasereddin_identification_2022, + author = {Nasereddin, Abdelmajeed and Golan Berman, Hadar and Wolf, Dana G. and Oiknine-Djian, Esther and Adar, Sheera}, + doi = {10.1128/spectrum.00736-22}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {June}, + note = {Publisher: American Society for Microbiology}, + number = {4}, + pages = {e00736--22}, + title = {Identification of {SARS}-{CoV}-2 {Variants} of {Concern} {Using} {Amplicon} {Next}-{Generation} {Sequencing}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.00736-22}, + urldate = {2022-09-24}, + volume = {10}, + year = {2022} +} + @article{nekrutenko_biology_2018, abstract = {Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg; Biology needs evolutionary software tools: Let’s build them right, Molecular Bi}, author = {Nekrutenko, Anton and Team, Galaxy and Goecks, Jeremy and Taylor, James and Blankenberg, Daniel}, @@ -3066,6 +7378,68 @@ @article{nekrutenko_biology_2018 year = {2018} } +@article{ngo_histone_2022, + abstract = {Background + +Epigenetic modulators have been proposed as promising new drug targets to treat adverse remodeling in heart failure. Here, we evaluated the potential of 4 epigenetic drugs, including the recently developed histone deacetylase 6 (HDAC6) inhibitor JS28, to prevent endothelin‐1 induced pathological gene expression in cardiac myocytes and analyzed the chromatin binding profile of the respective inhibitor targets. + +Methods and Results + +Cardiac myocytes were differentiated and puromycin‐selected from mouse embryonic stem cells and treated with endothelin‐1 to induce pathological gene expression (938 differentially expressed genes, q{\textless}0.05). Dysregulation of gene expression was at least in part prevented by epigenetic inhibitors, including the pan‐BRD (bromodomain‐containing protein) inhibitor bromosporine (290/938 genes), the BET (bromodomain and extraterminal) inhibitor JQ1 (288/938), the broad‐spectrum HDAC inhibitor suberoylanilide hydroxamic acid (227/938), and the HDAC6 inhibitor JS28 (210/938). Although the 4 compounds were similarly effective toward pathological gene expression, JS28 demonstrated the least adverse effects on physiological gene expression. Genome‐wide chromatin binding profiles revealed that HDAC6 binding sites were preferentially associated with promoters of genes involved in RNA processing. In contrast, BRD4 binding was associated with genes involved in core cardiac myocyte functions, for example, myocyte contractility, and showed enrichment at enhancers and intronic regions. These distinct chromatin binding profiles of HDAC6 and BRD4 might explain the different effects of their inhibitors on pathological versus physiological gene expression. + +Conclusions + +In summary, we demonstrated, that the HDAC6 inhibitor JS28 effectively prevented the adverse effects of endothelin‐1 on gene expression with minor impact on physiological gene expression in cardiac myocytes. Selective HDAC6 inhibition by JS28 appears to be a promising strategy for future evaluation in vivo and potential translation into clinical application.}, + author = {Ngo, Vivien and Fleischmann, Bernd K. and Jung, Manfred and Hein, Lutz and Lother, Achim}, + doi = {10.1161/JAHA.122.025857}, + journal = {Journal of the American Heart Association}, + keywords = {{\textgreater}UseGalaxy.eu, bromodomain‐containing protein, cardiac myocyte, epigenetics, heart, heart failure, histone deacetylase}, + month = {June}, + note = {Publisher: American Heart Association}, + number = {12}, + pages = {e025857}, + title = {Histone {Deacetylase} 6 {Inhibitor} {JS28} {Prevents} {Pathological} {Gene} {Expression} in {Cardiac} {Myocytes}}, + url = {https://www.ahajournals.org/doi/full/10.1161/JAHA.122.025857}, + urldate = {2022-11-06}, + volume = {11}, + year = {2022} +} + +@article{nicholson_contribution_2024, + abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Bordetella bronchiseptica{\textless}/italic{\textgreater} is a highly contagious respiratory bacterial veterinary pathogen. In this study the contribution of the transcriptional regulators BvgR, RisA, RisS, and the phosphorylation of RisA to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation were evaluated. Next Generation Sequencing (RNASeq) was used to differentiate the global gene regulation of both virulence-activated and virulence-repressed genes by each of these factors. The BvgAS system, along with BvgR, RisA, and the phosphorylation of RisA served in cyclic-di-GMP degradation. BvgR and unphosphorylated RisA were found to temporally regulate motility. Additionally, BvgR, RisA, and RisS were found to be required for biofilm formation.{\textless}/p{\textgreater}}, + author = {Nicholson, Tracy L. and Waack, Ursula and Fleming, Damarius S. and Chen, Qing and Miller, Laura C. and Merkel, Tod J. and Stibitz, Scott}, + doi = {10.3389/fmicb.2024.1305097}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bordetella bronchiseptica, RNA-Seq, and biofilm, cyclic-di-GMP, motility}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {The contribution of {BvgR}, {RisA}, and {RisS} to global gene regulation, intracellular cyclic-di-{GMP} levels, motility, and biofilm formation in {Bordetella} bronchiseptica}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305097/full}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + +@article{nielsen_delayed_2023, + author = {Nielsen, Carolyn M. and Barrett, Jordan R. and Davis, Christine and Fallon, Jonathan K. and Goh, Cyndi and Michell, Ashlin R. and Griffin, Catherine and Kwok, Andrew and Loos, Carolin and Darko, Samuel and Laboune, Farida and Tekman, Mehmet and Diouf, Ababacar and Miura, Kazutoyo and Francica, Joseph R. and Ransier, Amy and Long, Carole A. and Silk, Sarah E. and Payne, Ruth O. and Minassian, Angela M. and Lauffenburger, Douglas A. and Seder, Robert A. and Douek, Daniel C. and Alter, Galit and Draper, Simon J.}, + doi = {10.1172/jci.insight.163859}, + issn = {0021-9738}, + journal = {JCI Insight}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + language = {en}, + month = {January}, + note = {Publisher: American Society for Clinical Investigation}, + number = {2}, + pmid = {0}, + title = {Delayed boosting improves human antigen-specific {Ig} and {B} cell responses to the {RH5}.1/{AS01}$_{\textrm{{B}}}$ malaria vaccine}, + url = {https://insight.jci.org/articles/view/163859}, + urldate = {2023-01-28}, + volume = {8}, + year = {2023} +} + @article{niemoller_bisulfite-free_2021, abstract = {Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single acute myeloid leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between cell lines based on the DNA methylation and genetic profiles.}, author = {Niemöller, Christoph and Wehrle, Julius and Riba, Julian and Claus, Rainer and Renz, Nathalie and Rhein, Janika and Bleul, Sabine and Stosch, Juliane M. and Duyster, Justus and Plass, Christoph and Lutsik, Pavlo and Lipka, Daniel B. and Lübbert, Michael and Becker, Heiko}, @@ -3093,6 +7467,77 @@ @article{niemoller_bisulfite-free_2021 year = {2021} } +@misc{noauthor_candidatus_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + title = {Candidatus {Methanosphaera} massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos {\textbar} {Microbiology} {Spectrum}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.05141-22}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{noauthor_characterization_2023, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterization of the {Italian} population of {Ciborinia} camelliae}, + url = {https://air.unimi.it/handle/2434/980235}, + urldate = {2023-07-31}, + year = {2023} +} + +@misc{noauthor_effect_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + title = {Effect of {Anti}‐{S100A4} {Monoclonal} {Antibody} {Treatment} on {Experimental} {Skin} {Fibrosis} and {Systemic} {Sclerosis}–{Specific} {Transcriptional} {Signatures} in {Human} {Skin} - {Trinh}‐{Minh} - 2024 - {Arthritis} \& {Rheumatology} - {Wiley} {Online} {Library}}, + url = {https://acrjournals.onlinelibrary.wiley.com/doi/10.1002/art.42781}, + urldate = {2024-06-07}, + year = {2024} +} + +@misc{noauthor_importance_2020, + abstract = {Background: Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that...}, + doi = {10.21203/rs.3.rs-18225/v1}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + title = {The importance of incorporating transcript information in {CLIP}-seq data analysis}, + url = {https://www.researchsquare.com}, + urldate = {2023-12-28}, + year = {2020} +} + +@misc{noauthor_nutrients_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + title = {Nutrients {\textbar} {Free} {Full}-{Text} {\textbar} {A} 14-{Day} {Double}-{Blind}, {Randomized}, {Controlled} {Crossover} {Intervention} {Study} with {Anti}-{Bacterial} {Benzyl} {Isothiocyanate} from {Nasturtium} ({Tropaeolum} majus) on {Human} {Gut} {Microbiome} and {Host} {Defense}}, + url = {https://www.mdpi.com/2072-6643/16/3/373}, + urldate = {2024-06-07}, + year = {2024} +} + +@article{noauthor_proceedings_2023, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Proceedings of the {Joint} 3rd {International} {Conference} on {Bioinformatics} and {Data} {Science} ({ICBDS} 2022), {ISBN} 9789464631630 - {Better} {Read} {Than} {Dead} {Bookstore} {Newtown}}, + url = {https://www.betterread.com.au/book/proceedings-of-the-joint-3rd-international-conference-on-bioinformatics-and-data-science-icbds-2022.do}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{nugroho_transcriptome_2024, + abstract = {Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15\% were 5′prime\_partial, 8.15\% were 3′prime\_partial, 8.5\% were internal, and 49.14\% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.}, + author = {Nugroho, Aditya and Siregar, Iskandar Zulkarnaen and Matra, Deden Derajat and Siregar, Ulfah Juniarti}, + doi = {10.1016/j.dib.2023.109919}, + issn = {2352-3409}, + journal = {Data in Brief}, + keywords = {{\textgreater}UseGalaxy.eu, Long-read sequencing, Plant defense, Resistance, Sengon}, + month = {February}, + pages = {109919}, + title = {Transcriptome dataset of gall-rust infected {Sengon} (\textit{{Falcataria} falcata}) seedlings using long-read {PCR}-{cDNA} sequencing}, + url = {https://www.sciencedirect.com/science/article/pii/S2352340923009587}, + urldate = {2024-05-17}, + volume = {52}, + year = {2024} +} + @article{nuhrenberg_impact_2022, author = {Nührenberg, Thomas G. and Stöckle, Jasmin and Marini, Federico and Zurek, Mark and Grüning, Björn A. and Benes, Vladimir and Hein, Lutz and Neumann, Franz-Josef and Stratz, Christian and Cederqvist, Marco and Hochholzer, Willibald}, doi = {10.1371/journal.pone.0260222}, @@ -3129,6 +7574,44 @@ @article{nunez-sanchez_characterizing_2020 year = {2020} } +@article{nwankwo_metagenomic_2024, + abstract = {Soil contains a great diversity of microorganisms, including bacteria which are known to be drivers of soil ecosystem functions. This study was aimed at investigating the bacterial communities in bulk and rhizosphere soil of Fusarium wilt-infected plantain (Musa paradisiaca). Physicochemical analysis revealed that electrical conductivity (312 µS/cm), cation exchange capacity (15.62 meq/100g), phosphate (0.16 mg/kg), nitrogen (1.53 mg/kg), moisture (19.45 mg/kg), potassium (1.39 mg/kg), magnesium (0.61 mg/kg), clay (60 \%), and silt (35\%) were higher in bulk soil than rhizosphere soil. The 16S rRNA metagenomic sequences quantified a total of 89341 bacterial taxonomic units from bulk soil which consist of 10 phyla, 13 classes, 16 orders, 18 families, 21 genera, and 19 species. A total of 88034 bacterial taxonomic units which comprised of 9 phyla, 13 classes, 23 orders, 22 families, 26 genera, and 25 species, were found in rhizosphere soil. The most abundant phyla in bulk soil are Actinobacteria (31\%), Proteobacteria (26\%), and Gemmatimonadetes (17\%) Acidobacteria (17\%) and Planctomycetes (3\%) while the prominent phyla in rhizosphere soil are Actinobacteria (63\%) Proteobacteria (24\%), Acidobacteria (7\%) and Planctomycetes (3\%). The major functional profiles of bacterial communities in both bulk and rhizosphere soils are metabolism of amino acids, carbohydrates, terpenoids, polyketides, cofactors, and xenobiotic degradation. Alpha diversities among the bacterial community were higher in Simpson’s reciprocal index for both bulk and rhizosphere soils. This study opens up new frontiers in expanding metagenomics studies on environmental samples which would capture and contribute to the identification of soil bacteria useful to ecosystem functions.}, + author = {Nwankwo, C. C. and Ezeonuegbu, B. A. and Oranusi, E. C.}, + doi = {10.9734/jamb/2024/v24i4817}, + issn = {2456-7116}, + journal = {Journal of Advances in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Num Pages: 17 +Number: 4}, + number = {4}, + pages = {77--93}, + title = {Metagenomic {Study} of {Bacteria} {Diversity} and {Functional} {Profile} in {Bulk} and {Rhizosphere} {Soils} of {Fusarium}-{Wilt} {Infected} {Plantain} ({Musa} paradisiaca)}, + url = {https://doi.org/10.9734/jamb/2024/v24i4817}, + urldate = {2024-05-17}, + volume = {24}, + year = {2024} +} + +@article{oakes_building_2024, + abstract = {Domain experts are increasingly employing machine learning to solve their domain-specific problems. This article presents to software engineering researchers the six key challenges that a domain expert faces in addressing their problem with a computational workflow, and the underlying executable implementation. These challenges arise out of our conceptual framework which presents the “route” of transformations that a domain expert may choose to take while developing their solution. To ground our conceptual framework in the state of the practice, this article discusses a selection of available textual and graphical workflow systems and their support for the transformations described in our framework. Example studies from the literature in various domains are also examined to highlight the tools used by the domain experts as well as a classification of the domain specificity and machine learning usage of their problem, workflow, and implementation. The state of the practice informs our discussion of the six key challenges, where we identify which challenges and transformations are not sufficiently addressed by available tools. We also suggest possible research directions for software engineering researchers to increase the automation of these tools and disseminate best-practice techniques between software engineering and various scientific domains.}, + author = {Oakes, Bentley James and Famelis, Michalis and Sahraoui, Houari}, + doi = {10.1145/3638243}, + issn = {1049-331X}, + journal = {ACM Transactions on Software Engineering and Methodology}, + keywords = {{\textgreater}UseGalaxy.eu, Computational workflow, domain experts, machine learning, machine learning pipelines, software engineering framework, workflow composition}, + month = {April}, + number = {4}, + pages = {91:1--91:50}, + shorttitle = {Building {Domain}-{Specific} {Machine} {Learning} {Workflows}}, + title = {Building {Domain}-{Specific} {Machine} {Learning} {Workflows}: {A} {Conceptual} {Framework} for the {State} of the {Practice}}, + url = {https://dl.acm.org/doi/10.1145/3638243}, + urldate = {2024-05-17}, + volume = {33}, + year = {2024} +} + @article{oeyen_sawfly_2020, abstract = {Abstract. The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (}, author = {Oeyen, Jan Philip and Baa-Puyoulet, Patrice and Benoit, Joshua B. and Beukeboom, Leo W. and Bornberg-Bauer, Erich and Buttstedt, Anja and Calevro, Federica and Cash, Elizabeth I. and Chao, Hsu and Charles, Hubert and Chen, Mei-Ju May and Childers, Christopher and Cridge, Andrew G. and Dearden, Peter and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Dolan, Amanda and Donath, Alexander and Dowling, Daniel and Dugan, Shannon and Duncan, Elizabeth and Elpidina, Elena N. and Friedrich, Markus and Geuverink, Elzemiek and Gibson, Joshua D. and Grath, Sonja and Grimmelikhuijzen, Cornelis J. P. and Große-Wilde, Ewald and Gudobba, Cameron and Han, Yi and Hansson, Bill S. and Hauser, Frank and Hughes, Daniel S. T. and Ioannidis, Panagiotis and Jacquin-Joly, Emmanuelle and Jennings, Emily C. and Jones, Jeffery W. and Klasberg, Steffen and Lee, Sandra L. and Lesný, Peter and Lovegrove, Mackenzie and Martin, Sebastian and Martynov, Alexander G. and Mayer, Christoph and Montagné, Nicolas and Moris, Victoria C. and Munoz-Torres, Monica and Murali, Shwetha Canchi and Muzny, Donna M. and Oppert, Brenda and Parisot, Nicolas and Pauli, Thomas and Peters, Ralph S. and Petersen, Malte and Pick, Christian and Persyn, Emma and Podsiadlowski, Lars and Poelchau, Monica F. and Provataris, Panagiotis and Qu, Jiaxin and Reijnders, Maarten J. M. F. and von Reumont, Björn Marcus and Rosendale, Andrew J. and Simao, Felipe A. and Skelly, John and Sotiropoulos, Alexandros G. and Stahl, Aaron L. and Sumitani, Megumi and Szuter, Elise M. and Tidswell, Olivia and Tsitlakidis, Evangelos and Vedder, Lucia and Waterhouse, Robert M. and Werren, John H. and Wilbrandt, Jeanne and Worley, Kim C. and Yamamoto, Daisuke S. and van de Zande, Louis and Zdobnov, Evgeny M. and Ziesmann, Tanja and Gibbs, Richard A. and Richards, Stephen and Hatakeyama, Masatsugu and Misof, Bernhard and Niehuis, Oliver}, @@ -3147,6 +7630,96 @@ @article{oeyen_sawfly_2020 year = {2020} } +@article{oger_-cellspecific_2023, + abstract = {The loss of pancreatic β-cell identity has emerged as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cell-autonomous role of the cell-cycle regulator and transcription factor E2F1 in the maintenance of β-cell identity, insulin secretion, and glucose homeostasis. We show that the β-cell–specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, altered endocrine cell mass, downregulation of many β-cell genes, and concomitant increase of non–β-cell markers. Mechanistically, epigenomic profiling of the promoters of these non–β-cell upregulated genes identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, promoters of downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that specific E2f1 transcriptional, cistromic, and epigenomic signatures are associated with these β-cell dysfunctions, with E2F1 directly regulating several β-cell genes at the chromatin level. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of β-cell identity genes. Our data suggest that E2F1 is critical for maintaining β-cell identity and function through sustained control of β-cell and non–β-cell transcriptional programs.β-Cell–specific E2f1 deficiency in mice impairs glucose tolerance.Loss of E2f1 function alters the ratio of α- to β-cells but does not trigger β-cell conversion into α-cells.Pharmacological inhibition of E2F activity inhibits glucose-stimulated insulin secretion and alters β- and α-cell gene expression in human islets.E2F1 maintains β-cell function and identity through control of transcriptomic and epigenetic programs.}, + author = {Oger, Frédérik and Bourouh, Cyril and Friano, Marika Elsa and Courty, Emilie and Rolland, Laure and Gromada, Xavier and Moreno, Maeva and Carney, Charlène and Rabhi, Nabil and Durand, Emmanuelle and Amanzougarene, Souhila and Berberian, Lionel and Derhourhi, Mehdi and Blanc, Etienne and Hannou, Sarah Anissa and Denechaud, Pierre-Damien and Benfodda, Zohra and Meffre, Patrick and Fajas, Lluis and Kerr-Conte, Julie and Pattou, François and Froguel, Philippe and Pourcet, Benoit and Bonnefond, Amélie and Collombat, Patrick and Annicotte, Jean-Sébastien}, + doi = {10.2337/db22-0604}, + issn = {0012-1797}, + journal = {Diabetes}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + number = {8}, + pages = {1112--1126}, + title = {β-{Cell}–{Specific} {E2f1} {Deficiency} {Impairs} {Glucose} {Homeostasis}, β-{Cell} {Identity}, and {Insulin} {Secretion}}, + url = {https://doi.org/10.2337/db22-0604}, + urldate = {2023-07-31}, + volume = {72}, + year = {2023} +} + +@incollection{ohta_hybrid_2023, + abstract = {Galaxy is a web browser-based data analysis platform that is widely used in biology. Public Galaxy instances allow the analysis of data and interpretation of results without requiring software installation. NanoGalaxy is a public Galaxy instance with tools and workflows for nanopore data analysis. This chapter describes the steps involved in performing genome assembly using short and long reads in NanoGalaxy.}, + address = {New York, NY}, + author = {Ohta, Tazro and Shiwa, Yuh}, + booktitle = {Nanopore {Sequencing}: {Methods} and {Protocols}}, + doi = {10.1007/978-1-0716-2996-3_2}, + editor = {Arakawa, Kazuharu}, + isbn = {978-1-07-162996-3}, + keywords = {{\textgreater}UseGalaxy.eu, Galaxy, Hybrid genome assembly, Long-read sequencing, Nanopore sequencing, Visualizations, Workflow}, + language = {en}, + pages = {15--30}, + publisher = {Springer US}, + series = {Methods in {Molecular} {Biology}}, + title = {Hybrid {Genome} {Assembly} of {Short} and {Long} {Reads} in {Galaxy}}, + url = {https://doi.org/10.1007/978-1-0716-2996-3_2}, + urldate = {2023-02-16}, + year = {2023} +} + +@article{olagoke_rps6_2023, + abstract = {The use of insects to model molecular events that characterize degenerative conditions was originally met with scepticism. However, the discovery of insect insulin-like peptides in the 1970's and the demonstration of evolutionary conservation of insulin-related signalling from insects to mammals have highlighted the importance and reduced cost of insect models in biomedical research. Here, we expand on our earlier described modelling of streptozotocin-induced brain glucose metabolic disruption in Nauphoeta cinerea, using RNA-sequencing analysis to study the transcriptional and genetic signatures of degeneration and stress signalling when glucose levels are elevated in the brain of the lobster cockroach. Nymphs were randomly divided into three groups: Control (0.8\% NaCl), and two single streptozotocin injection doses (74 nmol and 740 nmol). The transcriptional analyses featured a dysregulation of 226 genes at high dose STZ treatment and 278 genes at the low dose. Our mRNA-sequencing data showed that ribosomal protein genes were the most upregulated genes at both 74 and 740 nmol STZ treatment. We therefore used RT-qPCR and relative transcriptional methods to validate our proposed mechanism of brain glucose toxicity-induced degeneration in Nauphoeta cinerea, which involved the upregulation of ribosomal proteins and rpS6 regulators (mTORC1, protein kinases, casein kinase 1 and Death-associated protein kinase), the upregulation of MAPK cascades (RAS, ERK, P38 and JNK), alongside the downregulation of the PI3K/AKT cascade. Taken together, this study highlights the remarkable opportunity for Nauphoeta cinerea use as an experimental organism in hyperglycaemia, degeneration, and stress signalling.}, + author = {Olagoke, Olawande C. and Segatto, Ana L. A. and Afolabi, Blessing A. and Ardisson-Araujo, Daniel and Aschner, Michael and Rocha, João B. T.}, + doi = {10.1016/j.cbpb.2022.110785}, + issn = {1096-4959}, + journal = {Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Gene ontology, RNA-seq, Ribosomal protein, cascade, signalling}, + language = {en}, + month = {January}, + pages = {110785}, + title = {{RPS6} transcriptional modulation in neural tissues of {Nauphoeta} cinerea during streptozotocin-associated sugar metabolism impairment.}, + url = {https://www.sciencedirect.com/science/article/pii/S1096495922000732}, + urldate = {2023-03-15}, + volume = {263}, + year = {2023} +} + +@misc{oliveira_cocoa_2023, + abstract = {The apoplast performs important functions in the plant, such as defense against stress, and compounds present form the apoplastic washing fluid (AWF). The fungus Moniliophthora perniciosa, the causal agent of witches' broom disease (WBD) in Theobroma cacao L., initially colonizes the apoplast in its biotrophic phase. In this period, the fungus can remain for approximately 60 days, until it changes to its second phase, causing tissue death and consequently large loss in the production of beans. To better understand the importance of the apoplast in the T. cacao-M. perniciosa interaction, we performed the first apoplastic proteomic mapping of two contrasting genotypes for WBD resistance (CCN51 - resistant and Catongo-susceptible). Based on two-dimensional gel analysis, we identified 36 proteins in CCN-51 and 15 in Catongo. We highlight PR-proteins, such as peroxidases, β-1, 3-glucanases and chitinases. A possible candidate for a resistance marker of the CCN-51 genotype, osmotin, was identified. The antioxidative metabolism of the superoxide dismutase (SOD) enzyme showed a significant increase (p{\textless}0.05) in the AWF of the two genotypes under field conditions (FD). T. cacao AWF inhibited the germination of M. perniciosa basidiospores ({\textgreater}80\%), in addition to causing morphological changes. Our results shed more light on the nature of the plant's defense performed by the apoplast in the T. cacao-M. perniciosa interaction in the initial (biotrophic) phase of fungal infection, and therefore make it possible to expand WBD control strategies based on the identification of potential targets for resistance markers and advance scientific knowledge of the disease.}, + author = {Oliveira, Ms Ivina Barbosa de and Moura, Mr Igor Moutinho and Santana, Dr Juliano Oliveira and Gramacho, Dr Karina Peres and Alves, Ms Saline dos Santos and Ferreira, Dr Monaliza Macêdo and Santos, Dr Ariana Silva and Novais, Prof Diogo Pereira Silva de and Pirovani, Dr Carlos Priminho}, + doi = {10.1094/PHYTO-03-23-0101-R}, + journal = {https://doi.org/10.1094/PHYTO-03-23-0101-R}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + note = {Archive Location: world}, + title = {Cocoa apoplastome contains defense proteins against pathogens}, + type = {research-article}, + url = {https://apsjournals.apsnet.org/doi/10.1094/PHYTO-03-23-0101-R}, + urldate = {2023-12-03}, + year = {2023} +} + +@article{oliveira_integrated_2024, + abstract = {During the COVID-19 pandemic, RNA-seq datasets were produced to investigate the virus–host relationship. However, much of these data remains underexplored. To improve the search for molecular targets and biomarkers, we performed an integrated analysis of multiple RNA-seq datasets, expanding the cohort and including patients from different countries, encompassing severe and mild COVID-19 patients. Our analysis revealed that severe COVID-19 patients exhibit overexpression of genes coding for proteins of extracellular exosomes, endomembrane system, and neutrophil granules (e.g., S100A9, LY96, and RAB1B), which may play an essential role in the cellular response to infection. Concurrently, these patients exhibit down-regulation of genes encoding components of the T cell receptor complex and nucleolus, including TP53, IL2RB, and NCL. Finally, SPI1 may emerge as a central transcriptional factor associated with the up-regulated genes, whereas TP53, MYC, and MAX were associated with the down-regulated genes during COVID-19. This study identified targets and transcriptional factors, lighting on the molecular pathophysiology of syndrome coronavirus 2 infection.}, + author = {Oliveira, Thais Teixeira and Freitas, Júlia Firme and Medeiros, Viviane Priscila Barros de and Xavier, Thiago Jesus da Silva and Agnez-Lima, Lucymara Fassarella}, + copyright = {© 2024 Oliveira et al.. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).}, + doi = {10.26508/lsa.202302358}, + issn = {2575-1077}, + journal = {Life Science Alliance}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Publisher: Life Science Alliance +Section: Research Articles}, + number = {4}, + pmid = {38262689}, + title = {Integrated analysis of {RNA}-seq datasets reveals novel targets and regulators of {COVID}-19 severity}, + url = {https://www.life-science-alliance.org/content/7/4/e202302358}, + urldate = {2024-05-17}, + volume = {7}, + year = {2024} +} + @article{oselusi_cheminformatic_2021, author = {Oselusi, Samson Olaitan and Christoffels, Alan and Egieyeh, Samuel Ayodele}, doi = {10.3390/molecules26133970}, @@ -3161,6 +7734,23 @@ @article{oselusi_cheminformatic_2021 year = {2021} } +@article{ostenfeld_hybrid_2024, + abstract = {{\textless}p{\textgreater}Flagellotropic bacteriophages are interesting candidates as therapeutics against pathogenic bacteria dependent on flagellar motility for colonization and causing disease. Yet, phage resistance other than loss of motility has been scarcely studied. Here we developed a soft agar assay to study flagellotropic phage F341 resistance in motile {\textless}italic{\textgreater}Campylobacter jejuni{\textless}/italic{\textgreater}. We found that phage adsorption was prevented by diverse genetic mutations in the lipooligosaccharides forming the secondary receptor of phage F341. Genome sequencing showed phage F341 belongs to the {\textless}italic{\textgreater}Fletchervirus{\textless}/italic{\textgreater} genus otherwise comprising capsular-dependent {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} phages. Interestingly, phage F341 encodes a hybrid receptor binding protein (RBP) predicted as a short tail fiber showing partial similarity to RBP1 encoded by capsular-dependent {\textless}italic{\textgreater}Fletchervirus{\textless}/italic{\textgreater}, but with a receptor binding domain similar to tail fiber protein H of {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} CJIE1 prophages. Thus, {\textless}italic{\textgreater}C. jejuni{\textless}/italic{\textgreater} prophages may represent a genetic pool from where lytic {\textless}italic{\textgreater}Fletchervirus{\textless}/italic{\textgreater} phages can acquire new traits like recognition of new receptors.{\textless}/p{\textgreater}}, + author = {Ostenfeld, Line Jensen and Sørensen, Anders Nørgaard and Neve, Horst and Vitt, Amira and Klumpp, Jochen and Sørensen, Martine Camilla Holst}, + doi = {10.3389/fmicb.2024.1358909}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Flagella, Fletchervirus, Phage, Receptor binding protein, flagellotropic phage, phage receptor, phage resistance}, + language = {English}, + month = {February}, + note = {Publisher: Frontiers}, + title = {A hybrid receptor binding protein enables phage {F341} infection of {Campylobacter} by binding to flagella and lipooligosaccharides}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1358909/full}, + urldate = {2024-03-30}, + volume = {15}, + year = {2024} +} + @article{ostrovsky_using_2021, abstract = {Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density Basic Protocol 2: Calling peaks for ChIP-seq data Basic Protocol 3: Compare datasets using genomic coordinates Basic Protocol 4: Working with multiple alignments Basic Protocol 5: Single cell RNA-seq}, author = {Ostrovsky, Alexander and Hillman‐Jackson, Jennifer and Bouvier, Dave and Clements, Dave and Afgan, Enis and Blankenberg, Daniel and Schatz, Michael C. and Nekrutenko, Anton and Taylor, James and Team, the Galaxy and Lariviere, Delphine}, @@ -3198,6 +7788,23 @@ @article{owen_rna-sequencing_2019 year = {2019} } +@article{pachanon_genomic_2024, + abstract = {Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates. All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried blaSHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same blaOXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the blaOXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.}, + author = {Pachanon, Ruttana and Khine, Nwai Oo and Phumthanakorn, Nathita and Wongsurawat, Thidathip and Niyomtham, Waree and Chatsuwan, Tanittha and Hampson, David J. and Prapasarakul, Nuvee}, + doi = {10.3389/fvets.2024.1386496}, + issn = {2297-1769}, + journal = {Frontiers in Veterinary Science}, + keywords = {{\textgreater}UseGalaxy.eu, Carbapenem resistance, Colistin resistance, Klebsiella pneumoniae, Plasmidmediated resistance, whole genome analysis}, + language = {English}, + month = {May}, + note = {Publisher: Frontiers}, + title = {Genomic characterization of carbapenem and colistin-resistant {Klebsiella} pneumoniae isolates from humans and dogs}, + url = {https://www.frontiersin.org/articles/10.3389/fvets.2024.1386496}, + urldate = {2024-06-07}, + volume = {11}, + year = {2024} +} + @article{page-karjian_fibropapillomatosis_2021, author = {Page-Karjian, Annie and Whitmore, Liam and Stacy, Brian A. and Perrault, Justin R. and Farrell, Jessica A. and Shaver, Donna J. and Walker, J. Shelby and Frandsen, Hilary R. and Rantonen, Elina and Harms, Craig A. and Norton, Terry M. and Innis, Charles and Yetsko, Kelsey and Duffy, David J.}, doi = {10.3390/ani11113076}, @@ -3213,6 +7820,61 @@ @article{page-karjian_fibropapillomatosis_2021 year = {2021} } +@article{palacios-rodriguez_antimicrobial_2024, + abstract = {Worldwide, bacterial resistance is one of the most severe public health problems. Currently, the failure of antibiotics to counteract superbugs highlights the need to search for new molecules with antimicrobial potential to combat them. The objective of this research was to evaluate the antimicrobial activity of Bacillus amyloliquefaciens BS4 against Gram-negative bacteria. Thirty yeasts and thirty-two Bacillus isolates were tested following the agar well-diffusion method. Four Bacillus sp. strains (BS3, BS4, BS17, and BS21) showed antagonistic activity against E. coli ATCC 25922 using bacterial culture (BC) and the cell-free supernatant (CFS), where the BS4 strain stood out, showing inhibitory values of 20.50 ± 0.70 mm and 19.67 ± 0.58 mm for BC and CFS, respectively. The Bacillus sp. BS4 strain can produce antioxidant, non-hemolytic, and antimicrobial metabolites that exhibit activity against several microorganisms such as Salmonella enterica, Klebsiella pneumoniae, Shigella flexneri, Enterobacter aerogenes, Proteus vulgaris, Yersinia enterocolitica, Serratia marcescens, Aeromonas sp., Pseudomonas aeruginosa, Candida albicans, and Candida tropicalis. According to the characterization of the supernatant, the metabolites could be proteinaceous. The production of these metabolites is influenced by carbon and nitrogen sources. The most suitable medium to produce antimicrobial metabolites was TSB broth. The one-factor-at-a-time method was used to standardize parameters such as pH, agitation, temperature, carbon source, nitrogen source, and salts, resulting in the best conditions of pH 7, 150 rpm, 28 °C, starch (2.5 g/L), tryptone (20 g/L), and magnesium sulfate (0.2 g/L), respectively. Moreover, the co-culture was an excellent strategy to improve antimicrobial activity, achieving maximum antimicrobial activity with an inhibition zone of 21.85 ± 1.03 mm. These findings position the Bacillus amyloliquefaciens BS4 strain as a promising candidate for producing bioactive molecules with potential applications in human health.}, + author = {Palacios-Rodriguez, Ana Paula and Espinoza-Culupú, Abraham and Durán, Yerson and Sánchez-Rojas, Tito}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13040304}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Bacillus amyloliquefaciens} BS4, {\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, antimicrobial activity, broad-spectrum metabolites, culture conditions}, + language = {en}, + month = {April}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {304}, + title = {Antimicrobial {Activity} of {Bacillus} amyloliquefaciens {BS4} against {Gram}-{Negative} {Pathogenic} {Bacteria}}, + url = {https://www.mdpi.com/2079-6382/13/4/304}, + urldate = {2024-04-08}, + volume = {13}, + year = {2024} +} + +@article{palecanda_increasing_2023, + abstract = {Stomatopods are well studied for their unique visual systems, which can consist of up to 16 different photoreceptor types and 33 opsin proteins expressed in the adults of some species. The light-sensing abilities of larval stomatopods are comparatively less well understood with limited information about the opsin repertoire of these early-life stages. Early work has suggested that larval stomatopods may not possess the extensive light detection abilities found in their adult counterparts. However, recent studies have shown that these larvae may have more complex photosensory systems than previously thought. To examine this idea at the molecular level, we characterized the expression of putative light-absorbing opsins across developmental stages, from embryo to adult, in the stomatopod species Pullosquilla thomassini using transcriptomic methods with a special focus on ecological and physiological transition periods. Opsin expression during the transition from the larval to the adult stage was further characterized in the species Gonodactylaceus falcatus. Opsin transcripts from short, middle, and long wavelength-sensitive clades were found in both species, and analysis of spectral tuning sites suggested differences in absorbance within these clades. This is the first study to document the changes in opsin repertoire across development in stomatopods, providing novel evidence for light detection across the visual spectrum in larvae.}, + author = {Palecanda, Sitara and Steck, Mireille and Porter, Megan L.}, + copyright = {© 2023 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.}, + doi = {10.1002/ece3.10121}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, crustacean, larval development, opsin, transcriptomics, vision}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.10121}, + number = {5}, + pages = {e10121}, + title = {Increasing complexity of opsin expression across stomatopod development}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.10121}, + urldate = {2023-06-05}, + volume = {13}, + year = {2023} +} + +@article{palecanda_molecular_2023, + abstract = {Investigations of the molecular mechanisms behind detection of short, and particularly ultraviolet, wavelengths in arthropods have relied heavily on studies from insects due to the relative ease of heterologous expression of modified opsin proteins in model organisms like Drosophila. However, species outside of the Insecta can provide information on mechanisms for spectral tuning as well as the evolutionary history of pancrustacean visual pigments. Here we investigate the basis of spectral tuning in malacostracan short wavelength sensitive (SWS) opsins using phylogenetic comparative methods. Tuning sites that may be responsible for the difference between ultraviolet (UV) and violet visual pigment absorbance in the Malacostraca are identified, and the idea that an amino acid polymorphism at a single site is responsible for this shift is shown to be unlikely. Instead, we suggest that this change in absorbance is accomplished through multiple amino acid substitutions. On the basis of our findings, we conducted further surveys to identify spectral tuning mechanisms in the order Stomatopoda where duplication of UV opsins has occurred. Ancestral state reconstructions of stomatopod opsins from two main clades provide insight into the amino acid changes that lead to differing absorption by the visual pigments they form, and likely contribute the basis for the wide array of UV spectral sensitivities found in this order.}, + author = {Palecanda, Sitara and Madrid, Elizabeth and Porter, Megan L.}, + doi = {10.1007/s00239-023-10137-w}, + issn = {1432-1432}, + journal = {Journal of Molecular Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Arthropod, Opsin, Spectral tuning, Stomatopod, Ultraviolet, Vision}, + language = {en}, + month = {November}, + title = {Molecular {Evolution} of {Malacostracan} {Short} {Wavelength} {Sensitive} {Opsins}}, + url = {https://doi.org/10.1007/s00239-023-10137-w}, + urldate = {2023-12-03}, + year = {2023} +} + @article{pallares-vega_temperature_2021, author = {Pallares-Vega, Rebeca and Macedo, Gonçalo and Brouwer, Michael S. M. and Leal, Lucia Hernandez and Maas, Peter van der and Loosdrecht, Mark C. M. van and Weissbrodt, David G. and Heederik, Dick and Mevius, Dik and Schmitt, Heike}, doi = {10.3389/fmicb.2021.656250}, @@ -3225,6 +7887,27 @@ @article{pallares-vega_temperature_2021 year = {2021} } +@article{pannhorst_non-classical_2023, + abstract = {African swine fever virus (ASFV) is a lethal animal pathogen that enters its host cells through endocytosis. So far, host factors specifically required for ASFV replication have been barely identified. In this study a genome-wide CRISPR/Cas9 knockout screen in porcine cells indicated that the genes RFXANK, RFXAP, SLA-DMA, SLA-DMB, and CIITA are important for productive ASFV infection. The proteins encoded by these genes belong to the major histocompatibility complex II (MHC II), or swine leucocyte antigen complex II (SLA II). RFXAP and CIITA are MHC II-specific transcription factors, whereas SLA-DMA/B are subunits of the non-classical MHC II molecule SLA-DM. Targeted knockout of either of these genes led to severe replication defects of different ASFV isolates, reflected by substantially reduced plating efficiency, cell-to-cell spread, progeny virus titers and viral DNA replication. Transgene-based reconstitution of SLA-DMA/B fully restored the replication capacity demonstrating that SLA-DM, which resides in late endosomes, plays a crucial role during early steps of ASFV infection.}, + author = {Pannhorst, Katrin and Carlson, Jolene and Hölper, Julia E. and Grey, Finn and Baillie, John Kenneth and Höper, Dirk and Wöhnke, Elisabeth and Franzke, Kati and Karger, Axel and Fuchs, Walter and Mettenleiter, Thomas C.}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-36788-9}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, High-throughput screening, Virus–host interactions}, + language = {en}, + month = {August}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {10342}, + title = {The non-classical major histocompatibility complex {II} protein {SLA}-{DM} is crucial for {African} swine fever virus replication}, + url = {https://www.nature.com/articles/s41598-023-36788-9}, + urldate = {2023-08-24}, + volume = {13}, + year = {2023} +} + @article{papatheodorou_expression_2019, author = {Papatheodorou, Irene and Moreno, Pablo and Manning, Jonathan and Fuentes, Alfonso Muñoz-Pomer and George, Nancy and Fexova, Silvie and Fonseca, Nuno A. and Füllgrabe, Anja and Green, Matthew and Huang, Ni and Huerta, Laura and Iqbal, Haider and Jianu, Monica and Mohammed, Suhaib and Zhao, Lingyun and Jarnuczak, Andrew F. and Jupp, Simon and Marioni, John and Meyer, Kerstin and Petryszak, Robert and Medina, Cesar Augusto Prada and Talavera-López, Carlos and Teichmann, Sarah and Vizcaino, Juan Antonio and Brazma, Alvis}, doi = {10.1093/nar/gkz947}, @@ -3255,6 +7938,55 @@ @article{parenti_mau2_2020 year = {2020} } +@article{patat_construction_2022, + abstract = {Garden cress (Lepidium sativum L.) is a Brassicaceae crop recognized as a healthy vegetable and a medicinal plant. Lepidium is one of the largest genera in Brassicaceae, yet, the genus has not been a focus of extensive genomic research. In the present work, garden cress genome was sequenced using the long read high-fidelity sequencing technology. A de novo, draft genome assembly that spans 336.5 Mb was produced, corresponding to 88.6\% of the estimated genome size and representing 90\% of the evolutionarily expected orthologous gene content. Protein coding gene content was structurally predicted and functionally annotated, resulting in the identification of 25,668 putative genes. A total of 599 candidate disease resistance genes were identified by predicting resistance gene domains in gene structures, and 37 genes were detected as orthologs of heavy metal associated protein coding genes. In addition, 4289 genes were assigned as “transcription factor coding.” Six different machine learning algorithms were trained and tested for their performance in classifying miRNA coding genomic sequences. Logistic regression proved the best performing trained algorithm, thus utilized for pre-miRNA coding loci identification in the assembly. Repetitive DNA analysis involved the characterization of transposable element and microsatellite contents. L. sativum chloroplast genome was also assembled and functionally annotated. Data produced in the present work is expected to constitute a foundation for genomic research in garden cress and contribute to genomics-assisted crop improvement and genome evolution studies in the Brassicaceae family.}, + author = {Patat, Aysenur Soyturk and Sen, Fatima and Erdogdu, Behic Selman and Uncu, Ali Tevfik and Uncu, Ayse Ozgur}, + doi = {10.1007/s10142-022-00866-4}, + issn = {1438-7948}, + journal = {Functional \& Integrative Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, De novo assembly, Heavy metal–associated protein, R gene, Transcription factor, Transposable element, miRNA}, + language = {en}, + month = {May}, + title = {Construction and characterization of a de novo draft genome of garden cress ({Lepidium} sativum {L}.)}, + url = {https://doi.org/10.1007/s10142-022-00866-4}, + urldate = {2022-09-24}, + year = {2022} +} + +@article{patel_bioprospecting_2023, + abstract = {The persistent spread of highly contagious COVID-19 disease is one of the deadliest occurrences in the history of mankind. Despite the distribution of numerous efficacious vaccines and their extensive usage, the perpetual effectiveness of immunization is being catechized. Therefore, discovering an alternative therapy to control and prevent COVID-19 infections has become a top priority. The main protease (Mpro) plays a key role in viral replication, making it an intriguing pharmacological target for SARS-CoV-2.}, + author = {Patel, Unnati and Desai, Krishna and Dabhi, Ranjitsinh C. and Maru, Jayesh J. and Shrivastav, Pranav S.}, + doi = {10.1007/s00894-023-05569-6}, + issn = {0948-5023}, + journal = {Journal of Molecular Modeling}, + keywords = {{\textgreater}UseGalaxy.eu, ADMET, Drug-likeness study, Molecular docking, Molecular dynamics, Rosmarinus officinalis L., SARS-CoV-2 Mpro}, + language = {en}, + month = {April}, + number = {5}, + pages = {161}, + shorttitle = {Bioprospecting phytochemicals of {Rosmarinus} officinalis {L}. for targeting {SARS}-{CoV}-2 main protease ({Mpro})}, + title = {Bioprospecting phytochemicals of {Rosmarinus} officinalis {L}. for targeting {SARS}-{CoV}-2 main protease ({Mpro}): a computational study}, + url = {https://doi.org/10.1007/s00894-023-05569-6}, + urldate = {2023-07-31}, + volume = {29}, + year = {2023} +} + +@article{pazoki_elucidating_2024, + abstract = {Genetic abnormalities like Y chromosome microdeletions are implicated in male infertility. This study investigated the association of azoospermia factor (AZF) region microdeletions with unsuccessful assisted reproductive techniques (ART), including in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI).This cross-sectional analysis study examined 80 Iranian oligospermic men (mean age 34 years) with prior failed ICSI and IVF cycles (IR.IAU.TNB.REC.1401.041). Semen analysis evaluated quantity/quality parameters based on World Health Organization guidelines. Participants were stratified by sperm DNA fragmentation (SDF) levels into: control (SDF \< 15\%, n = 20), mild elevation (15\% ≤ SDF ≤ 30\%, n = 60), and high (SDF \> 30\%, n = 20). Multiplex PCR mapped AZF microdeletions in the high SDF group. The AZF-associated genes were selected by RNA Seq analysis, and the candidate genes were checked for expression level by real-time PCR.High SDF individuals exhibited poorer semen metrics, including 69\% lower sperm concentration (P = 0.04) than those without SDF. Of this subset, 45\% (9/20 men) harboured predominately AZF microdeletions. Men with AZF microdeletions showed higher SDF (32\% vs 21\%, P = 0.02) and altered AZF-associated genes expression. As USP9Y 3-fold, UTY 1.3-fold, and BPY2 1-fold revealed up-regulation, while IQCF1 8-fold, CDY 6.5-fold, DAZ 6-fold, and DDX3Y 1-fold underwent down-regulation. The PAWP gene was also down-regulated (5.7-fold, P = 0.029) in the IVF/ICSI failure group.AZF microdeletions significantly impact male infertility and ART outcomes. High SDF individuals exhibited poorer semen metrics, with 45\% AZF microdeletions. These microdeletions altered AZF-associated genes expression, affecting fertility mediator PAWP independently. Dual AZF and SDF screening enables personalized management in severe male infertility, potentially explaining IVF/ICSI failures.}, + author = {Pazoki, Nasrin and Salehi, Mitra and Angaji, Seyed Abdolhamid and Abdollahpour-Alitappeh, Meghdad}, + doi = {10.1093/hmg/ddae086}, + issn = {0964-6906}, + journal = {Human Molecular Genetics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + pages = {ddae086}, + title = {Elucidating the impact of {Y} chromosome microdeletions and altered gene expression on male fertility in assisted reproduction}, + url = {https://doi.org/10.1093/hmg/ddae086}, + urldate = {2024-06-07}, + year = {2024} +} + @article{pelletier_standardized_2021, author = {Pelletier, Dominique and Roos, David and Bouchoucha, Marc and Schohn, Thomas and Roman, William and Gonson, Charles and Bockel, Thomas and Carpentier, Liliane and Preuss, Bastien and Powell, Abigail and Garcia, Jessica and Gaboriau, Matthias and Cadé, Florent and Royaux, Coline and Bras, Yvan Le and Reecht, Yves}, doi = {10.3389/fmars.2021.689280}, @@ -3267,6 +7999,41 @@ @article{pelletier_standardized_2021 year = {2021} } +@article{pelos_fast_2023, + abstract = {Non-small cell lung cancer (NSCLC) patients are often elderly or unfit and thus cannot tolerate standard aggressive therapy regimes. In our study, we test the efficacy of the DNA-hypomethylating agent decitabine (DAC) in combination with all-trans retinoic acid (ATRA), which has been shown to possess little systemic adverse effects. Screening a broad panel of 56 NSCLC cell lines uncovered a decrease in cell viability after the combination treatment in 77\% of the cell lines. Transcriptomics, proteomics, proliferation and migration profiling revealed that fast proliferating and slowly migrating cell lines were more sensitive to the drug combination. The comparison of mutational profiles found oncogenic KRAS mutations only in sensitive cells. Additionally, different cell lines showed a heterogeneous gene expression response to the treatment pointing to diverse mechanisms of action. Silencing KRAS, RIG-I or RARB partially reversed the sensitivity of KRAS-mutant NCI-H460 cells. To study resistance, we generated two NCI-H460 cell populations resistant to ATRA and DAC, which migrated faster and proliferated slower than the parental sensitive cells and showed signs of senescence. In summary, this comprehensive dataset uncovers a broad sensitivity of NSCLC cells to the combinatorial treatment with DAC and ATRA and indicates that migration and proliferation capacities correlate with and could thus serve as determinants for drug sensitivity in NSCLC.}, + author = {Pelos, Giulia and Riester, Marisa and Pal, Jagriti and Myacheva, Ksenia and Moneke, Isabelle and Rotondo, John Charles and Lübbert, Michael and Diederichs, Sven}, + doi = {10.1002/ijc.34783}, + issn = {1097-0215}, + journal = {International Journal of Cancer}, + keywords = {{\textgreater}UseGalaxy.eu, NCI-H460, NSCLC, drug resistance, epigenetic drugs, senescence}, + language = {eng}, + month = {November}, + pmid = {37947765}, + title = {Fast proliferating and slowly migrating non-small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment}, + year = {2023} +} + +@article{perez-schindler_characterization_2022, + abstract = {Non-alcoholic fatty liver disease is a continuum of disorders among which non-alcoholic steatohepatitis (NASH) is particularly associated with a negative prognosis. Hepatocyte lipotoxicity is one of the main pathogenic factors of liver fibrosis and NASH. However, the molecular mechanisms regulating this process are poorly understood. The main aim of this study was to dissect transcriptional mechanisms regulated by lipotoxicity in hepatocytes. We achieved this aim by combining transcriptomic, proteomic and chromatin accessibility analyses from human liver and mouse hepatocytes. This integrative approach revealed several transcription factor networks deregulated by NASH and lipotoxicity. To validate these predictions, genetic deletion of the transcription factors MAFK and TCF4 was performed, resulting in hepatocytes that were better protected against saturated fatty acid oversupply. MAFK- and TCF4-regulated gene expression profiles suggest a mitigating effect against cell stress, while promoting cell survival and growth. Moreover, in the context of lipotoxicity, some MAFK and TCF4 target genes were to the corresponding differentially regulated transcripts in human liver fibrosis. Collectively, our findings comprehensively profile the transcriptional response to lipotoxicity in hepatocytes, revealing new molecular insights and providing a valuable resource for future endeavours to tackle the molecular mechanisms of NASH.}, + author = {Pérez-Schindler, Joaquín and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Handschin, Christoph}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41598-022-15731-4}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Genetics, Molecular biology, Molecular medicine}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {11477}, + title = {Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity}, + url = {https://www.nature.com/articles/s41598-022-15731-4}, + urldate = {2023-08-06}, + volume = {12}, + year = {2022} +} + @article{perez-schindler_discovery_2021, author = {Pérez-Schindler, Joaquín and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Handschin, Christoph}, doi = {10.1101/2021.03.24.436772}, @@ -3292,6 +8059,27 @@ @article{perez-schindler_rna-bound_2021 year = {2021} } +@article{perez-sisques_intellectual_2024, + abstract = {The histone lysine demethylase KDM5B is implicated in recessive intellectual disability disorders, and heterozygous, protein-truncating variants in KDM5B are associated with reduced cognitive function in the population. The KDM5 family of lysine demethylases has developmental and homeostatic functions in the brain, some of which appear to be independent of lysine demethylase activity. To determine the functions of KDM5B in hippocampus-dependent learning and memory, we first studied male and female mice homozygous for a Kdm5bΔARID allele that lacks demethylase activity. Kdm5bΔARID/ΔARID mice exhibited hyperactivity and long-term memory deficits in hippocampus-dependent learning tasks. The expression of immediate early, activity-dependent genes was downregulated in these mice and hyperactivated upon a learning stimulus compared with wild-type (WT) mice. A number of other learning-associated genes were also significantly dysregulated in the Kdm5bΔARID/ΔARID hippocampus. Next, we knocked down Kdm5b specifically in the adult, WT mouse hippocampus with shRNA. Kdm5b knockdown resulted in spontaneous seizures, hyperactivity, and hippocampus-dependent long-term memory and long-term potentiation deficits. These findings identify KDM5B as a critical regulator of gene expression and synaptic plasticity in the adult hippocampus and suggest that at least some of the cognitive phenotypes associated with KDM5B gene variants are caused by direct effects on memory consolidation mechanisms.}, + author = {Pérez-Sisqués, Leticia and Bhatt, Shail U. and Matuleviciute, Rugile and Gileadi, Talia E. and Kramar, Eniko and Graham, Andrew and Garcia, Franklin G. and Keiser, Ashley and Matheos, Dina P. and Cain, James A. and Pittman, Alan M. and Andreae, Laura C. and Fernandes, Cathy and Wood, Marcelo A. and Giese, K. Peter and Basson, M. Albert}, + copyright = {Copyright © 2024 Perez-Sisques et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.}, + doi = {10.1523/JNEUROSCI.1544-23.2024}, + issn = {0270-6474, 1529-2401}, + journal = {Journal of Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, KDM5B, chromatin, hippocampus, histone lysine demethylase, learning, memory, mouse}, + language = {en}, + month = {May}, + note = {Publisher: Society for Neuroscience +Section: Research Articles}, + number = {19}, + pmid = {38575342}, + title = {The {Intellectual} {Disability} {Risk} {Gene} {Kdm5b} {Regulates} {Long}-{Term} {Memory} {Consolidation} in the {Hippocampus}}, + url = {https://www.jneurosci.org/content/44/19/e1544232024}, + urldate = {2024-05-17}, + volume = {44}, + year = {2024} +} + @article{perezriverol_scalable_2019, abstract = {The recent improvements in mass spectrometry instruments and new analytical methods are increasing the intersection between proteomics and big data science. In addition, bioinformatics analysis is becoming increasingly complex and convoluted, involving multiple algorithms and tools. A wide variety of methods and software tools have been developed for computational proteomics and metabolomics during recent years, and this trend is likely to continue. However, most of the computational proteomics and metabolomics tools are designed as single-tiered software application where the analytics tasks can't be distributed, limiting the scalability and reproducibility of the data analysis. In this paper we summarise the key steps of metabolomics and proteomics data processing, including the main tools and software used to perform the data analysis. We discuss the combination of software containers with workflows environments for large scale metabolomics and proteomics analysis. Finally, we introduce to the proteomics and metabolomics communities a new approach for reproducible and large-scale data analysis based on BioContainers and two of the most popular workflow environments: Galaxy and Nextflow. This article is protected by copyright. All rights reserved}, author = {Perez‐Riverol, Yasset and Moreno, Pablo}, @@ -3311,6 +8099,47 @@ @article{perezriverol_scalable_2019 year = {2019} } +@phdthesis{peschel_molekulare_2023, + abstract = {Metastasierung und Therapieresistenz stellen die wesentlichen Hindernisse bei der kurativen Behandlung des Kolorektalkarzinoms (KRK) dar und sind Hauptursache für die krebsbedingte Sterblichkeit. Bei etwa einem Viertel der KRK-Patient*innen liegen bei Erstdiagnose Fernmetastasen vor, bei ca. der Hälfte der Erkrankten treten im Verlauf Fernmetastasen auf (Kumbrink et al., 2021; Van Cutsem \& Oliveira, 2009; Vatandoust et al., 2015). +Fluoropyrimidin-basierte Chemotherapieregime sind das Grundgerüst der systemischen KRK-Therapie, welche durch weitere klassische Zytostatika sowie Antikörper-basierte Wirkstoffe erweitert werden kann. Das Kombinationsschema bestehend aus 5-Fluoruracil, Irinotecan und Leucovorin – syn. FOLFIRI – wird bei metastasiertem KRK (mKRK) als Erst- oder Zweitlinientherapie eingesetzt (Leitlinienprogramm Onkologie (Deutsche Krebsgesellschaft, 2019). Trotz der Wirksamkeit dieser Kombinationsbehandlung, durch die die Überlebensrate deutlich verbessert werden konnte, führen intrinsische und erworbene Resistenzmechanismen zur Progression der Krankheit (Jensen et al., 2015; Lyskjær et al., 2019). + +Um molekularen Mechanismen und Biomarker der FOLFIRI-Resistenz auf Transkriptomebene zu identifizieren, wurden aus den KRK -Zelllinien Colo205, HT29 und SW480 drei FOLFIRI-resistente Subzelllinien durch kontinuierliche Behandlung mit steigenden FOLFIRI-Konzentrationen hergestellt. Als biologische Effekte der FOLFIRI-Resistenz konnten Änderungen in der Genexpression, morphologische Veränderungen sowie Anpassung des Zellzyklus und Zelltod-Resistenz beobachtet werden. + +Zur Identifikation von resistenz-assoziierten Expressionssignaturen oder potentiell prognostischen Biomarkern wurde eine RNA-Sequenzierung der parentalen sowie der resistenten Zelllinien durchgeführt. +Insgesamt 284 differentiell exprimierte Gene (DEGs) wurden nach der bioinformatischen Analyse der RNA-Sequenzierung von 24 Proben ermittelt (Colo205: 222 Gene, HT29: 47 Gene, SW480: 30 Gene). Anschließend wurden diese DEGs miteinander abgeglichen und 12 DEGs identifiziert, die in zwei oder allen drei Zelllinien konsistent dysreguliert waren. Mittels Kaplan-Meier (KM-) Überlebenszeitanalyse des Kolon-Adenokarzinom-Datensatz (COAD) des Krebsgenomatlas (The Cancer Genome Atlas, TCGA, PanCancer Atlas Datenset ) wurden hieraus drei prognostisch relevante Gene (TACSTD2, PERP und CAV2) identifiziert, die sich signifikant mit kürzerem Überleben bei KRK assoziiert zeigten. +Diese Ergebnisse wurden mit den Ergebnissen einer klinischen Studie (GSE62322) abgeglichen. In dieser Studie wurden von 21 Chemotherapie-naiven KRK-Patient*innen Tumorproben entnommen, worauf eine postoperative Chemotherapie mit FOLFIRI folgte. Um eine Gensignatur zu identifizieren, die das Ansprechen auf FOLFIRI vorhersagen soll, wurden im nächsten Schritt die Expressionsdaten der auf FOLFIRI ansprechenden Patient*innen mit denen der nicht auf FOLFIRI ansprechenden Patient*innen verglichen. +Im Abgleich mit diesen Expressionsdaten konnten die drei Gene TACSTD2, PERP und CAV2 nicht als signifikant dysreguliert bzw. als Teil der Gensignatur nachgewiesen werden. Jedoch konnten die Gene SERPINE2 und TNC aus der Liste aller 284 DEGs in den klinischen Tumorproben ebenfalls als signifikant differentiell exprimiert nachgewiesen werden und mittels KM-Überlebenszeitanalyse als prognostisch relevant eingestuft werden. +Diese drei bzw. fünf identifizierten Gene können nun Grundlage für weitere experimentelle Schritte sein, um neue diagnostische und prognostische Biomarker für die klinische Praxis zu etablieren.}, + author = {Peschel, Christiane}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {March}, + school = {Ludwig-Maximilians-Universität München}, + title = {Molekulare {Mechanismen} der pharmakologischen {Resistenz} kolorektaler {Karzinomzelllinien} gegen das {Chemotherapieregime} {FOLFIRI}}, + type = {Text.{PhDThesis}}, + url = {https://edoc.ub.uni-muenchen.de/31524/}, + urldate = {2023-07-31}, + year = {2023} +} + +@article{pessoa_rodrigues_histone_2021, + abstract = {Noncommunicable diseases (NCDs) account for over 70\% of deaths world-wide. Previous work has linked NCDs such as type 2 diabetes (T2D) to disruption of chromatin regulators. However, the exact molecular origins of these chronic conditions remain elusive. Here, we identify the H4 lysine 16 acetyltransferase MOF as a critical regulator of central carbon metabolism. High-throughput metabolomics unveil a systemic amino acid and carbohydrate imbalance in Mof deficient mice, manifesting in T2D predisposition. Oral glucose tolerance testing (OGTT) reveals defects in glucose assimilation and insulin secretion in these animals. Furthermore, Mof deficient mice are resistant to diet-induced fat gain due to defects in glucose uptake in adipose tissue. MOF-mediated H4K16ac deposition controls expression of the master regulator of glucose metabolism, Pparg and the entire downstream transcriptional network. Glucose uptake and lipid storage can be reconstituted in MOF-depleted adipocytes in vitro by ectopic Glut4 expression, PPARγ agonist thiazolidinedione (TZD) treatment or SIRT1 inhibition. Hence, chronic imbalance in H4K16ac promotes a destabilisation of metabolism triggering the development of a metabolic disorder, and its maintenance provides an unprecedented regulatory epigenetic mechanism controlling diet-induced obesity.}, + author = {Pessoa Rodrigues, Cecilia and Chatterjee, Aindrila and Wiese, Meike and Stehle, Thomas and Szymanski, Witold and Shvedunova, Maria and Akhtar, Asifa}, + doi = {10.1038/s41467-021-26277-w}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Acetylation, Adipocytes, Adipose Tissue, Amino Acids, Animals, Carbon, Diabetes Mellitus, Type 2, Diet, High-Fat, Gene Expression Regulation, Genetic Predisposition to Disease, Glucose, Glucose Transporter Type 4, Haploinsufficiency, Histone Acetyltransferases, Histones, Lipid Metabolism, Lysine, Mice, Obesity, PPAR gamma}, + language = {eng}, + month = {October}, + number = {1}, + pages = {6212}, + pmcid = {PMC8551339}, + pmid = {34707105}, + title = {Histone {H4} lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice}, + volume = {12}, + year = {2021} +} + @article{peters_metabolic_2021, author = {Peters, Kristian and Herman, Stephanie and Khoonsari, Payam Emami and Burman, Joachim and Neumann, Steffen and Kultima, Kim}, doi = {10.1038/s41598-021-97491-1}, @@ -3324,6 +8153,27 @@ @article{peters_metabolic_2021 year = {2021} } +@article{pfaffle_14-day_2024, + abstract = {Despite substantial heterogeneity of studies, there is evidence that antibiotics commonly used in primary care influence the composition of the gastrointestinal microbiota in terms of changing their composition and/or diversity. Benzyl isothiocyanate (BITC) from the food and medicinal plant nasturtium (Tropaeolum majus) is known for its antimicrobial activity and is used for the treatment of infections of the draining urinary tract and upper respiratory tract. Against this background, we raised the question of whether a 14 d nasturtium intervention (3 g daily, N = 30 healthy females) could also impact the normal gut microbiota composition. Spot urinary BITC excretion highly correlated with a weak but significant antibacterial effect against Escherichia coli. A significant increase in human beta defensin 1 as a parameter for host defense was seen in urine and exhaled breath condensate (EBC) upon verum intervention. Pre-to-post analysis revealed that mean gut microbiome composition did not significantly differ between groups, nor did the circulating serum metabolome. On an individual level, some large changes were observed between sampling points, however. Explorative Spearman rank correlation analysis in subgroups revealed associations between gut microbiota and the circulating metabolome, as well as between changes in blood markers and bacterial gut species.}, + author = {Pfäffle, Simon P. and Herz, Corinna and Brombacher, Eva and Proietti, Michele and Gigl, Michael and Hofstetter, Christoph K. and Mittermeier-Kleßinger, Verena K. and Claßen, Sophie and Tran, Hoai T. T. and Dawid, Corinna and Kreutz, Clemens and Günther, Stefan and Lamy, Evelyn}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/nu16030373}, + issn = {2072-6643}, + journal = {Nutrients}, + keywords = {\textit{Escherichia coli}, {\textgreater}UseGalaxy.eu, BITC, antimicrobial, gut microbiome, human beta defensin 1, metabolome, nasturtium}, + language = {en}, + month = {January}, + note = {Number: 3 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {3}, + pages = {373}, + title = {A 14-{Day} {Double}-{Blind}, {Randomized}, {Controlled} {Crossover} {Intervention} {Study} with {Anti}-{Bacterial} {Benzyl} {Isothiocyanate} from {Nasturtium} ({Tropaeolum} majus) on {Human} {Gut} {Microbiome} and {Host} {Defense}}, + url = {https://www.mdpi.com/2072-6643/16/3/373}, + urldate = {2024-05-17}, + volume = {16}, + year = {2024} +} + @article{phan_transcriptome_2021, author = {Phan, Isabelle Q. and Rice, Christopher A. and Craig, Justin and Noorai, Rooksana E. and McDonald, Jacquelyn R. and Subramanian, Sandhya and Tillery, Logan and Barrett, Lynn K. and Shankar, Vijay and Morris, James C. and Voorhis, Wesley C. Van and Kyle, Dennis E. and Myler, Peter J.}, doi = {10.1038/s41598-021-99903-8}, @@ -3338,6 +8188,84 @@ @article{phan_transcriptome_2021 year = {2021} } +@article{phillip_molecular_2023, + abstract = {Background: There is a growing body of evidence on the potential involvement of coagulase-negative Staphylococci (CoNS) in causing urinary tract infections (UTIs). The aim of this study was to delineate virulence potential, antimicrobial resistance genes, and sequence types of CoNS isolated from patients with UTI symptoms and pyuria in Tanzania. Methods: CoNS from patients with UTI symptoms and more than 125 leucocytes/μL were retrieved, subcultured, and whole-genome sequenced. Results: Out of 65 CoNS isolates, 8 species of CoNS were identified; Staphylococcus haemolyticus, n = 27 (41.5\%), and Staphylococcus epidermidis, n = 24 (36.9\%), were predominant. The majority of S. haemolyticus were sequence type (ST) 30, with 8 new ST138-145 reported, while the majority of S. epidermidis were typed as ST490 with 7 new ST1184-1190 reported. Sixty isolates (92.3\%) had either one or multiple antimicrobial resistance genes. The most frequently detected resistance genes were 53 (21\%) dfrG, 32 (12.9\%) blaZ, and 26 (10.5\%) mecA genes conferring resistance to trimethoprim, penicillin, and methicillin, respectively. Out of 65 isolates, 59 (90.8\%) had virulence genes associated with UTI, with a predominance of the icaC 47 (46.5\%) and icaA 14 (13.9\%) genes. Conclusion:S. haemolyticus and S. epidermidis harboring icaC, dfrG, blaZ, and mecA genes were the predominant CoNS causing UTI in Tanzania. Laboratories should carefully interpret the significant bacteriuria due to CoNS in relation to UTI symptoms and pyuria before labeling them as contaminants. Follow-up studies to document the outcome of the treated patients is needed to add more evidence that CoNS are UTI pathogens.}, + author = {Phillip, Shukrani and Mushi, Martha F. and Decano, Arun Gonzales and Seni, Jeremiah and Mmbaga, Blandina T. and Kumburu, Happiness and Konje, Eveline T. and Mwanga, Joseph R. and Kidenya, Benson R. and Msemwa, Betrand and Gillespie, Stephen and Maldonado-Barragan, Antonio and Sandeman, Alison and Sabiti, Wilber and Holden, Mathew T. G. and Mshana, Stephen E.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/pathogens12020180}, + issn = {2076-0817}, + journal = {Pathogens}, + keywords = {\textit{S. epidermidis}, \textit{S. haemolyticus}, {\textgreater}UseGalaxy.eu, genes for AMR, icaC virulence genes}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {180}, + shorttitle = {Molecular {Characterizations} of the {Coagulase}-{Negative} {Staphylococci} {Species} {Causing} {Urinary} {Tract} {Infection} in {Tanzania}}, + title = {Molecular {Characterizations} of the {Coagulase}-{Negative} {Staphylococci} {Species} {Causing} {Urinary} {Tract} {Infection} in {Tanzania}: {A} {Laboratory}-{Based} {Cross}-{Sectional} {Study}}, + url = {https://www.mdpi.com/2076-0817/12/2/180}, + urldate = {2023-03-15}, + volume = {12}, + year = {2023} +} + +@article{pick_complete_2024, + author = {Pick, Kat and Stothard, Paul and Raivio, Tracy L.}, + doi = {10.1128/mra.01216-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01216--23}, + title = {Complete genome sequence of {Escherichia} coli {MP1}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01216-23}, + urldate = {2024-03-17}, + volume = {0}, + year = {2024} +} + +@article{pilliol_methanobrevibacter_2024, + abstract = {Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1–2-µm-long and 0.6–0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3\% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9\% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.}, + author = {Pilliol, Virginie and Beye, Mamadou and Terlier, Laureline and Balmelle, Julien and Kacel, Idir and Lan, Romain and Aboudharam, Gérard and Grine, Ghiles and Terrer, Elodie}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms12010215}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {\textit{Archaea}, \textit{Methanobrevibacter massiliense}, \textit{Pyramidobacter piscolens}, \textit{Synergistetes}, {\textgreater}UseGalaxy.eu, dental pulp, hydrogen-free culture, methanogen}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {215}, + title = {Methanobrevibacter massiliense and {Pyramidobacter} piscolens {Co}-{Culture} {Illustrates} {Transkingdom} {Symbiosis}}, + url = {https://www.mdpi.com/2076-2607/12/1/215}, + urldate = {2024-04-28}, + volume = {12}, + year = {2024} +} + +@article{pimentel_description_2023, + abstract = {The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.}, + author = {Pimentel, Luiz Guilherme Pereira and da Silva, Iuri Batista and Rodrigues-Oliveira, Igor Henrique and Pasa, Rubens and Menegídio, Fabiano Bezerra and Kavalco, Karine Frehner}, + doi = {10.5808/gi.23059}, + issn = {1598-866X}, + journal = {Genomics \& Informatics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + number = {4}, + pages = {e51}, + pmcid = {PMC10788360}, + pmid = {38224718}, + title = {Description of eight new mitochondrial genomes for the genus {Neoarius} and phylogenetic considerations for the family {Ariidae} ({Siluriformes})}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10788360/}, + urldate = {2024-01-20}, + volume = {21}, + year = {2023} +} + @article{pinter_functional_2021, abstract = {The lysine specific demethylase 1 (LSD1) plays a pivotal role in cellular differentiation by regulating the expression of key developmental genes in concert with different coregulatory proteins. This process is impaired in different cancer types and incompletely understood. To comprehensively identify functional coregulators of LSD1, we established a novel tractable fluorescent reporter system to monitor LSD1 activity in living cells. Combining this reporter system with a state-of-the-art multiplexed RNAi screen, we identify the DEAD-box helicase 19A (DDX19A) as a novel coregulator and demonstrate that suppression of Ddx19a results in an increase of R-loops and reduced LSD1-mediated gene silencing. We further show that DDX19A binds to tri-methylated lysine 27 of histone 3 (H3K27me3) and it regulates gene expression through the removal of transcription promoting R-loops. Our results uncover a novel transcriptional regulatory cascade where the downregulation of genes is dependent on the LSD1 mediated demethylation of histone H3 lysine 4 (H3K4). This allows the polycomb repressive complex 2 (PRC2) to methylate H3K27, which serves as a binding site for DDX19A. Finally, the binding of DDX19A leads to the efficient removal of R-loops at active promoters, which further de-represses LSD1 and PRC2, establishing a positive feedback loop leading to a robust repression of the target gene.}, author = {Pinter, Sabine and Knodel, Franziska and Choudalakis, Michel and Schnee, Philipp and Kroll, Carolin and Fuchs, Marina and Broehm, Alexander and Weirich, Sara and Roth, Mareike and Eisler, Stephan A and Zuber, Johannes and Jeltsch, Albert and Rathert, Philipp}, @@ -3355,7 +8283,102 @@ @article{pinter_functional_2021 year = {2021} } -@article{poulose_vprbp_2021, +@article{pinter_maxquant_2022, + abstract = {Quantitative mass spectrometry-based proteomics has become a high-throughput technology for the identification and quantification of thousands of proteins in complex biological samples. Two frequently used tools, MaxQuant and MSstats, allow for the analysis of raw data and finding proteins with differential abundance between conditions of interest. To enable accessible and reproducible quantitative proteomics analyses in a cloud environment, we have integrated MaxQuant (including TMTpro 16/18plex), Proteomics Quality Control (PTXQC), MSstats, and MSstatsTMT into the open-source Galaxy framework. This enables the web-based analysis of label-free and isobaric labeling proteomics experiments via Galaxy’s graphical user interface on public clouds. MaxQuant and MSstats in Galaxy can be applied in conjunction with thousands of existing Galaxy tools and integrated into standardized, sharable workflows. Galaxy tracks all metadata and intermediate results in analysis histories, which can be shared privately for collaborations or publicly, allowing full reproducibility and transparency of published analysis. To further increase accessibility, we provide detailed hands-on training materials. The integration of MaxQuant and MSstats into the Galaxy framework enables their usage in a reproducible way on accessible large computational infrastructures, hence realizing the foundation for high-throughput proteomics data science for everyone.}, + author = {Pinter, Niko and Glätzer, Damian and Fahrner, Matthias and Fröhlich, Klemens and Johnson, James and Grüning, Björn Andreas and Warscheid, Bettina and Drepper, Friedel and Schilling, Oliver and Föll, Melanie Christine}, + doi = {10.1021/acs.jproteome.2c00051}, + issn = {1535-3893}, + journal = {Journal of Proteome Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + note = {Publisher: American Chemical Society}, + title = {{MaxQuant} and {MSstats} in {Galaxy} {Enable} {Reproducible} {Cloud}-{Based} {Analysis} of {Quantitative} {Proteomics} {Experiments} for {Everyone}}, + url = {https://doi.org/10.1021/acs.jproteome.2c00051}, + urldate = {2022-05-04}, + year = {2022} +} + +@article{pinto_rescue_2024, + abstract = {Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.}, + author = {Pinto, Daniela and Themudo, Gonçalo and Pereira, André C. and Botelho, Ana and Cunha, Mónica V.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25073869}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Mycobacterium bovis}, {\textgreater}UseGalaxy.eu, animal tuberculosis, computational biology, mixed infection, whole genome amplification, whole genome sequencing}, + language = {en}, + month = {January}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {3869}, + shorttitle = {Rescue of {Mycobacterium} bovis {DNA} {Obtained} from {Cultured} {Samples} during {Official} {Surveillance} of {Animal} {TB}}, + title = {Rescue of {Mycobacterium} bovis {DNA} {Obtained} from {Cultured} {Samples} during {Official} {Surveillance} of {Animal} {TB}: {Key} {Steps} for {Robust} {Whole} {Genome} {Sequence} {Data} {Generation}}, + url = {https://www.mdpi.com/1422-0067/25/7/3869}, + urldate = {2024-04-02}, + volume = {25}, + year = {2024} +} + +@article{pirnay_personalized_2024, + abstract = {In contrast to the many reports of successful real-world cases of personalized bacteriophage therapy (BT), randomized controlled trials of non-personalized bacteriophage products have not produced the expected results. Here we present the outcomes of a retrospective observational analysis of the first 100 consecutive cases of personalized BT of difficult-to-treat infections facilitated by a Belgian consortium in 35 hospitals, 29 cities and 12 countries during the period from 1 January 2008 to 30 April 2022. We assessed how often personalized BT produced a positive clinical outcome (general efficacy) and performed a regression analysis to identify functional relationships. The most common indications were lower respiratory tract, skin and soft tissue, and bone infections, and involved combinations of 26 bacteriophages and 6 defined bacteriophage cocktails, individually selected and sometimes pre-adapted to target the causative bacterial pathogens. Clinical improvement and eradication of the targeted bacteria were reported for 77.2\% and 61.3\% of infections, respectively. In our dataset of 100 cases, eradication was 70\% less probable when no concomitant antibiotics were used (odds ratio = 0.3; 95\% confidence interval = 0.127–0.749). In vivo selection of bacteriophage resistance and in vitro bacteriophage–antibiotic synergy were documented in 43.8\% (7/16 patients) and 90\% (9/10) of evaluated patients, respectively. We observed a combination of antibiotic re-sensitization and reduced virulence in bacteriophage-resistant bacterial isolates that emerged during BT. Bacteriophage immune neutralization was observed in 38.5\% (5/13) of screened patients. Fifteen adverse events were reported, including seven non-serious adverse drug reactions suspected to be linked to BT. While our analysis is limited by the uncontrolled nature of these data, it indicates that BT can be effective in combination with antibiotics and can inform the design of future controlled clinical trials. BT100 study, ClinicalTrials.gov registration: NCT05498363.}, + author = {Pirnay, Jean-Paul and Djebara, Sarah and Steurs, Griet and Griselain, Johann and Cochez, Christel and De Soir, Steven and Glonti, Tea and Spiessens, An and Vanden Berghe, Emily and Green, Sabrina and Wagemans, Jeroen and Lood, Cédric and Schrevens, Eddie and Chanishvili, Nina and Kutateladze, Mzia and de Jode, Mathieu and Ceyssens, Pieter-Jan and Draye, Jean-Pierre and Verbeken, Gilbert and De Vos, Daniel and Rose, Thomas and Onsea, Jolien and Van Nieuwenhuyse, Brieuc and Soentjens, Patrick and Lavigne, Rob and Merabishvili, Maya}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41564-024-01705-x}, + issn = {2058-5276}, + journal = {Nature Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bacterial genetics, Bacterial infection, Bacteriophages}, + language = {en}, + month = {June}, + note = {Publisher: Nature Publishing Group}, + number = {6}, + pages = {1434--1453}, + shorttitle = {Personalized bacteriophage therapy outcomes for 100 consecutive cases}, + title = {Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study}, + url = {https://www.nature.com/articles/s41564-024-01705-x}, + urldate = {2024-06-07}, + volume = {9}, + year = {2024} +} + +@article{plaza_genomic_2023, + author = {Plaza, David Fernando and Zerebinski, Julia and Broumou, Ioanna and Lautenbach, Maximilian Julius and Ngasala, Billy and Sundling, Christopher and Färnert, Anna}, + doi = {10.1016/j.crmeth.2023.100574}, + issn = {2667-2375}, + journal = {Cell Reports Methods}, + keywords = {{\textgreater}UseGalaxy.eu, CP: Biotechnology, CP: Microbiology, antigen discovery, circumsporozoite protein, genomic surveillance, glutamate-rich protein, long-read sequencing, malaria epidemiology, merozoite surface protein 1, merozoite surface protein 2}, + language = {English}, + month = {August}, + note = {Publisher: Elsevier}, + number = {0}, + title = {A genomic platform for surveillance and antigen discovery in {Plasmodium} spp. using long-read amplicon sequencing}, + url = {https://www.cell.com/cell-reports-methods/abstract/S2667-2375(23)00218-7}, + urldate = {2023-09-14}, + volume = {0}, + year = {2023} +} + +@article{potgieter_metanovo_2023, + abstract = {Background Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines. Results We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database—but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation. Conclusions By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.}, + author = {Potgieter, Matthys G. and Nel, Andrew J. M. and Fortuin, Suereta and Garnett, Shaun and Wendoh, Jerome M. and Tabb, David L. and Mulder, Nicola J. and Blackburn, Jonathan M.}, + doi = {10.1371/journal.pcbi.1011163}, + issn = {1553-7358}, + journal = {PLOS Computational Biology}, + keywords = {{\textgreater}UseGalaxy.eu, BLAST algorithm, Database searching, Metagenomics, Microbiome, Open source software, Proteomes, Sequence databases, Taxonomy}, + language = {en}, + month = {June}, + note = {Publisher: Public Library of Science}, + number = {6}, + pages = {e1011163}, + shorttitle = {{MetaNovo}}, + title = {{MetaNovo}: {An} open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets}, + url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011163}, + urldate = {2023-07-31}, + volume = {19}, + year = {2023} +} + +@article{poulose_vprbp_2021, author = {Poulose, Ninu and Polonski, Adam and Forsythe, Nicholas and Gregg, Gemma and Maguire, Sarah and Fuchs, Marc and Minner, Sarah and McDade, Simon S. and Mills, Ian G.}, doi = {10.1101/2021.02.28.433236}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, @@ -3381,6 +8404,63 @@ @article{prislan_proof_2019 year = {2019} } +@article{pustam_comparative_2023, + abstract = {Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.}, + author = {Pustam, Aarti and Jayaraman, Jayaraj and Ramsubhag, Adesh}, + doi = {10.1371/journal.pone.0283583}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial pathogens, Caribbean, Genomics, Klebsiella pneumoniae, Mobile genetic elements, Pathogenesis, Secretion systems, Virulence factors}, + language = {en}, + month = {October}, + note = {Publisher: Public Library of Science}, + number = {7}, + pages = {e0283583}, + title = {Comparative genomics and virulome analysis reveal unique features associated with clinical strains of {Klebsiella} pneumoniae and {Klebsiella} quasipneumoniae from {Trinidad}, {West} {Indies}}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0283583}, + urldate = {2023-07-13}, + volume = {18}, + year = {2023} +} + +@article{pustam_whole_2024, + abstract = {Objectives +Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. +Methods +Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of ten clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. +Results +The results of the study revealed the presence of a complex antibiotic-resistant armory among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6′)-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. +Conclusion +This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.}, + author = {Pustam, Aarti and Jayaraman, Jayaraj and Ramsubhag, Adesh}, + doi = {10.1016/j.jgar.2024.03.019}, + issn = {2213-7165}, + journal = {Journal of Global Antimicrobial Resistance}, + keywords = {{\textgreater}UseGalaxy.eu, ESBL, carbapenem, multiple-drug resistant, resistome}, + month = {April}, + title = {Whole genome sequencing reveals complex resistome features of \textit{{Klebsiella} pneumoniae} isolated from patients at major hospitals in {Trinidad}, {West} {Indies}}, + url = {https://www.sciencedirect.com/science/article/pii/S2213716524000730}, + urldate = {2024-04-13}, + year = {2024} +} + +@article{pyles_altered_2024, + abstract = {Patients who suffer a traumatic brain injury (TBI) often experience chronic and sometimes debilitating sequelae. Recent reports have illustrated both acute and long-term dysbiosis of the gastrointestinal microbiome with significant alterations in composition and predicted functional consequences. Working with participants from past research, metagenomic stability of the TBIassociated fecal microbiome (FMB) was evaluated by custom qPCR array comparing a fecal sample from 2015 to one collected in 2020. A remarkably stable FMB metagenome with significant similarity (two-tail Spearman nonparametric correlation p80\% of the samples in only one of the cohorts (binary distinction). Functional differences included amino acid metabolism, energy and carbon source usage, fatty acid metabolism, bacterial cell wall component production and nucleic acid synthesis and processing pathways. Together these data shed light on the functional consequences of the dysbiotic TBI FMB decades after injury.}, + author = {Pyles, Richard B. and Miller, Aaron L. and Urban, Randall J. and Sheffield-Moore, Melinda and Wright, Traver J. and Maxwell, Carrie A. and Randolph, Kathleen M. and Danesi, Christopher P. and McGovern, Kristen A. and Vargas, Jayson and Armstrong, Peyton and Kreber, Lisa and Cumpa, Giuliana and Randall, Kevin and Morrison, Melissa and Masel, Brent E.}, + doi = {10.3389/fnmol.2024.1341808}, + issn = {1662-5099}, + journal = {Frontiers in Molecular Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, BIAFAC, Traumatic Brain Injury, fecal microbiome, metatranscriptome, microbiome}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {The altered {TBI} fecal microbiome is stable and functionally distinct}, + url = {https://www.frontiersin.org/articles/10.3389/fnmol.2024.1341808}, + urldate = {2024-05-17}, + volume = {17}, + year = {2024} +} + @article{qi_secreted_2020, abstract = {{\textless}p{\textgreater}Multicellular organisms coordinate tissue specific response to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, secreted small RNAs have recently been reported to regulate gene expression across tissue boundaries. Here we show that the conserved poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature in C. elegans. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 transmits environmental information across tissue boundaries and contributes to maintenance of stem cell immortality probably via retaining a stem cell specific program of gene expression.{\textless}/p{\textgreater}}, author = {Qi, Wenjing and Gromoff, Erika D. v and Xu, Fan and Zhao, Qian and Yang, Wei and Pfeifer, Dietmar and Maier, Wolfgang and Long, Lijiang and Baumeister, Ralf}, @@ -3399,6 +8479,22 @@ @article{qi_secreted_2020 year = {2020} } +@article{qiu_smcyp71d373_2024, + abstract = {Salvia miltiorrhiza is one of the most commonly used Chinese medicinal herbs. Tanshinone I and tanshinone IIB with anti-inflammatory, anti-bacterial, anti-oxidative, anti-neoplastic, neuron protective, and heart protective properties are valuable active components in it. However, the biosynthetic pathway of tanshinone IIB and tanshinone I has not been completely elucidated. Here, we identified a tanshinone IIA 19-hydroxylase from S. miltiorrhiza. In vitro and in vivo analyses showed that SmCYP71D373 could hydroxylate tanshinone IIA at C-19 position to produce tanshinone IIB. Reaction conditions optimization demonstrated that the catalytic efficiency of SmCYP71D373 was the highest using the substrate-feeding method under the following conditions, fed the tanshinone IIA into the Saccharomyces cerevisiae expressing codon-optimized SmCYP71D373 at 28℃ for 24 hours. And the yield of tanshinone IIB was up to 6.38\%. Furthermore, N121 and S210 of SmCYP71D373 were verified as the key amino acid residues responsible for its catalytic activity for tanshinone IIA by molecular docking and site-directed mutagenesis. The results not only lay a foundation for the elucidation of tanshinone I synthesis pathway, but also provide the theoretical support to improve the catalytic efficiency of SmCYP71D373 for tanshinone IIB production.}, + author = {Qiu, Xiaoping and Zhang, Yi and Luo, Yinggang and Zhang, Yongmei}, + doi = {10.1016/j.indcrop.2024.118323}, + issn = {0926-6690}, + journal = {Industrial Crops and Products}, + keywords = {{\textgreater}UseGalaxy.eu, Biosynthesis pathway, CYP450, Hydroxylation, Tanshinone IIB}, + month = {June}, + pages = {118323}, + title = {{SmCYP71D373} of \textit{{Salvia} miltiorrhiza} catalyzes the methyl oxidation reaction of tanshinone {IIA}-19 position}, + url = {https://www.sciencedirect.com/science/article/pii/S0926669024003005}, + urldate = {2024-05-17}, + volume = {212}, + year = {2024} +} + @article{ragot_edna_2022, author = {Ragot, Rose and Villemur, Richard}, journal = {Environmental monitoring and assessment}, @@ -3411,6 +8507,23 @@ @article{ragot_edna_2022 year = {2022} } +@article{rahman_mobilisation_2024, + abstract = {The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.}, + author = {Rahman, Nadim and O'Cathail, Colman and Zyoud, Ahmad and Sokolov, Alexey and Oude Munnink, Bas and Grüning, Björn and Cummins, Carla and Amid, Clara and Nieuwenhuijse, David F. and Visontai, Dávid and Yuan, David Yu and Gupta, Dipayan and Prasad, Divyae K. and Gulyás, Gábor Máté and Rinck, Gabriele and McKinnon, Jasmine and Rajan, Jeena and Knaggs, Jeff and Skiby, Jeffrey Edward and Stéger, József and Szarvas, Judit and Gueye, Khadim and Papp, Krisztián and Hoek, Maarten and Kumar, Manish and Ventouratou, Marianna A. and Bouquieaux, Marie-Catherine and Koliba, Martin and Mansurova, Milena and Haseeb, Muhammad and Worp, Nathalie and Harrison, Peter W. and Leinonen, Rasko and Thorne, Ross and Selvakumar, Sandeep and Hunt, Sarah and Venkataraman, Sundar and Jayathilaka, Suran and Cezard, Timothée and Maier, Wolfgang and Waheed, Zahra and Iqbal, Zamin and Aarestrup, Frank Møller and Csabai, Istvan and Koopmans, Marion and Burdett, Tony and Cochrane, Guy}, + doi = {10.1099/mgen.0.001188}, + issn = {2057-5858}, + journal = {Microbial Genomics}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Publisher: Microbiology Society,}, + number = {2}, + pages = {001188}, + title = {Mobilisation and analyses of publicly available {SARS}-{CoV}-2 data for pandemic responses}, + url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001188}, + urldate = {2024-02-16}, + volume = {10}, + year = {2024} +} + @article{rajczewski_rigorous_2021, abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.}, author = {Rajczewski, Andrew T. and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James E. and McGowan, Thomas and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -3428,6 +8541,21 @@ @article{rajczewski_rigorous_2021 year = {2021} } +@article{ramos_mobilome_2024, + abstract = {Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.}, + author = {Ramos, Beatriz and Cunha, Mónica V.}, + doi = {10.1016/j.envpol.2024.124241}, + issn = {0269-7491}, + journal = {Environmental Pollution}, + keywords = {{\textgreater}UseGalaxy.eu, antimicrobial resistance, cgMLST, mobile genetic element, wildlife}, + month = {May}, + pages = {124241}, + title = {The mobilome of \textit{{Staphylococcus} aureus} from wild ungulates reveals epidemiological links at the animal-human interface}, + url = {https://www.sciencedirect.com/science/article/pii/S0269749124009552}, + urldate = {2024-06-04}, + year = {2024} +} + @article{ranchou-peyruse_microbial_2021, author = {Ranchou-Peyruse, Magali and Guignard, Marion and Casteran, Franck and Abadie, Maïder and Defois, Clémence and Peyret, Pierre and Dequidt, David and Caumette, Guilhem and Chiquet, Pierre and Cézac, Pierre and Ranchou-Peyruse, Anthony}, doi = {10.3389/fmicb.2021.688929}, @@ -3440,6 +8568,40 @@ @article{ranchou-peyruse_microbial_2021 year = {2021} } +@article{rapp_oncostatin_2024, + abstract = {Continuous vision loss due to vasoproliferative eye disease still represents an unsolved issue despite anti-vascular endothelial growth factor (VEGF) therapy. The impact of signal transducer and activator of transcription 3 (STAT3) signaling on retinal angiogenesis and its potential use as a therapeutic target remain controversial. In vitro, oncostatin M (OSM), as a strong STAT3 activator, possesses robust proangiogenic activity. This study investigated to what extent the proangiogenic effects of OSM translate to the in vivo setting of vasoproliferative eye disease. The in vitro effect of OSM on endothelial cells was investigated in the spheroid sprouting assay and through RNA sequencing. The mouse model for oxygen-induced retinopathy (OIR) was used to evaluate the impact of OSM in vivo. Signaling patterns were measured by western blot and retinal cryosections. Primary Müller cell cultures were used to evaluate the effect of OSM on the Müller cell secretome. Murine retinal vascular endothelial cells were isolated from OIR retinas using fluorescence-activated cell sorting (FACS) and were used for RNA sequencing. Although OSM induced pro-angiogenic responses in vitro, in the OIR model intravitreal injection of OSM reduced retinal neovascularization by 65.2\% and vaso-obliteration by 45.5\% in Müller cells. Injecting OSM into the vitreous activated the STAT3 signaling pathway in multiple retinal cell types, including Müller cells. In vitro, OSM treatment increased CXCL10 secretion. RNA sequencing of sorted vascular endothelial cells at OIR P17 following OSM treatment indicated downregulation of angiogenesis- and mitosis-associated genes. In vivo, OSM reveals a beneficial angiomodulatory effect by activating Müller cells and changing their secretome. The data highlight contradictions between cytokine-induced effects in vitro and in vivo depending on the cell types mediating the effect.}, + author = {Rapp, Julian and Hospach, Alban and Liang, Paula and Schwämmle, Melanie and Renz, Lisa and Agostini, Hansjürgen and Schlunck, Günther and Bucher, Felicitas}, + doi = {10.1167/iovs.65.1.22}, + issn = {1552-5783}, + journal = {Investigative Ophthalmology \& Visual Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {22}, + title = {Oncostatin {M} {Reduces} {Pathological} {Neovascularization} in the {Retina} {Through} {Müller} {Cell} {Activation}}, + url = {https://doi.org/10.1167/iovs.65.1.22}, + urldate = {2024-04-28}, + volume = {65}, + year = {2024} +} + +@article{rapp_stat3_2023, + abstract = {Aberrant angiogenesis is a hallmark of cardiovascular and retinal neovascular disease. The STAT3 signaling pathway represents a potential pharmacological target for these diseases due to its impact on angiogenesis. Surprisingly, some STAT3 activators, such as the IL-6 cytokine family member oncostatin M (OSM), enhance angiogenesis, whereas others, such as ciliary neurotropic factor (CNTF), reduce it. This study aimed to clarify these conflicting effects. In contrast to the anti-angiogenic cytokine CNTF, the pro-angiogenic cytokine OSM was able to activate intracellular signaling pathways beyond the STAT3 pathway, including the ERK and AKT pathways. These differences translated into transcriptomic and metabolic shifts. siRNA-mediated STAT3 knockdown experiments showed a decrease in VEGF-induced endothelial migration and sprouting, enhancing the pro-angiogenic drive of OSM and switching the CNTF response from anti-angiogenic to pro-angiogenic. These effects correlated with a transcriptomic shift representing enhanced STAT1 and ERK activity following STAT3 knockdown, including a compensatory prolonged phosphorylated STAT1 activity. In conclusion, the angiogenic effect of STAT3 appears to be determined by cytokine-induced STAT3 specificity and simultaneous activity of other intracellular signaling pathways, whereas the STAT3 pathway, predominantly recognized for its pro-angiogenic phenotypes, reveals novel anti-angiogenic potential.}, + author = {Rapp, Julian and Jung, Malte and Klar, Rhena F. U. and Wolf, Julian and Arnold, Jakob and Gorka, Oliver and Groß, Olaf and Lange, Clemens and Agostini, Hansjürgen and Schlunck, Günther and Bucher, Felicitas}, + doi = {10.1242/jcs.260182}, + issn = {0021-9533}, + journal = {Journal of Cell Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {jcs260182}, + title = {{STAT3} signaling induced by the {IL}-6 family of cytokines modulates angiogenesis}, + url = {https://doi.org/10.1242/jcs.260182}, + urldate = {2023-03-15}, + volume = {136}, + year = {2023} +} + @article{rasche_galactic_2020, abstract = {AbstractBackground. Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the f}, author = {Rasche, Helena and Hiltemann, Saskia}, @@ -3526,6 +8688,26 @@ @article{rauschmeier_cell-intrinsic_2021 year = {2021} } +@phdthesis{rehm_analyse_2023, + abstract = {Humane Papillomviren (HPV) infizieren Keratinozyten der Haut- und Schleimhaut. Die Hochrisiko-Typen (HR) der alpha-Gattung verursachen dadurch anogenitalen- und oropharyngalen-Krebs. Vorherrschend dabei ist das Zervixkarzinom, welches zu 70 \% von HPV16 und HPV18 ausgelöst wird. Im Gegensatz dazu sind die onkogenen Eigenschaften der beta-HPV Gattung weniger gut erforscht. Bei Patienten mit der seltenen Erbkrankheit Epidermodysplasia Verruciformis (EV) und Organtransplantatempfängern (OTRs) wird ein Zusammenhang zwischen beta-HPV-Infektionen und der Entstehung von kutanen Plattenepithelkarzinomen vermutet. Bisher wurden die Eigenschaften von beta-HPV vor allem durch retrovirale Expression der E6 und E7 Onkogene in Keratinozyten, durch Transfektion der Osteosarkomzelllinie U2OS mit beta-HPV Genomen und in transgenen Mausmodellen untersucht, aber nicht mit vollständigen viralen Genomen in normalen humanen Keratinozyten (NHK), den natürlichen Zielzellen. Im Rahmen meiner Dissertation konnte ich zeigen, dass HPV8-, 38- und 49-Genome in humanen Keratinozyten mindestens neun Tage lang transkriptionell aktiv sind und replizieren. Durch Inaktivierung des viralen E8{\textasciicircum}E2 Repressors (E8-/E8{\textasciicircum}E2-) erhält das HPV49 Genom die Fähigkeit NHK zu immortalisieren. Die immortalisierten HPV49 E8- Zelllinien enthalten große Mengen an episomalen Virusgenomen und viralen Transkripten und behalten diese in Kultur über einen langen Zeitraum. Nicht nur der Verlust der E6 und E7 Onkogene, sondern auch eine Inaktivierung der E1 oder E2 Replikationsgene verhindern die Immortalisierung. Die E8-/E1- und E8-/E2- Genome zeigen deutlich niedrigere E6 und E7 Transkriptmengen in transienten Experimenten. Dies legt nahe, dass für die Immortalisierung eine starke E6 und E7 Expression von extrachromosomalen Virusgenomen erforderlich ist. Die Notwendigkeit für eine Inaktivierung von E8 im Kontext von intakten E1 und E2 Genen für die Immortalisierung von NHK zeigt, dass E8{\textasciicircum}E2 eine wichtige Rolle bei der Kontrolle der Onkogenität von beta-HPV spielen könnte, und weist auf grundlegende Unterschiede zwischen HPV49 und HR-HPV Genomen hin. +Durch RNA-Sequenzierung der HPV49 E8- positiven Zelllinien konnten bekannte Spleißverknüpfungen bestätigt, das frühe Polyadenylierungssignal lokalisiert und Hinweise auf unterschiedliche virale Promotoren erhalten werden. Außerdem wurden neue Spleißverbindungen kartiert und ein neuer Spleißdonor im E6 Gen funktionell untersucht. Dieser beeinflusst die Menge an E6 Protein und vermutlich dadurch die Immortalisierung durch das HPV49 E8- Genom. +Bei HPV8 und 38 konnten auch durch Inaktivierung von E8{\textasciicircum}E2 keine immortalisierten Zelllinien erzeugt werden, obwohl ähnliche Mengen an Transkripten für die E6 und E7 Onkogene wie bei HPV49 E8- Genomen transkribiert wurden. Dies legt nahe, dass beta-HPV Genome unterschiedliche onkogene Eigenschaften besitzen. Die Inaktivierung der Replikationsgene E1 und E2 reduzierte die Transkription aller untersuchten beta-HPV in NHK, was nahelegt, dass auch WT Genome aktiv replizieren. Die Kultivierung von HPV8- oder 38-transfizierten NHKs in organotypischen Modellen, die die Analyse des produktiven Replikationszyklus von HR-HPV ermöglichen, induziert Transkripte für das L1 Kapsidgen, was nahelegt, dass der produktive Lebenszyklus eingeleitet wurde. Außerdem ähnelt das HPV8-Transkriptionsmuster in organotypischen Kulturen dem einer HPV8-positiven EV-Läsion. +Zusammengefasst bedeutet dies, dass NHK ein physiologisch relevantes System sind, um die Replikation und onkogenen Eigenschaften von beta-HPV zu untersuchen.}, + author = {Rehm, Tina Melanie}, + copyright = {http://tobias-lib.uni-tuebingen.de/doku/lic\_ohne\_pod.php?la=de}, + doi = {10.15496/publikation-80519}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {April}, + note = {Accepted: 2023-04-13T10:45:38Z}, + school = {Universität Tübingen}, + title = {Analyse des {Replikationszyklus} von nicht-melanozytären {Hautkrebs}-assoziierten beta-humanen {Papillomviren} in humanen {Keratinozyten}}, + type = {Dissertation}, + url = {https://publikationen.uni-tuebingen.de/xmlui/handle/10900/139172}, + urldate = {2023-07-31}, + year = {2023} +} + @article{retamal-morales_draft_2018, abstract = {Biosurfactants are amphipathic molecules with relevance in biotechnology due to their structural diversity, low toxicity and biodegradability. The genus Rhodococcus has extensively been studied because of its capacity to produce trehalose-containing surfactants as well as trehalose lipids as potential pathogenic factor. Here we present the draft genome sequence of Rhodococcus erythropolis B7g isolated with toluene from fuel-contaminated soil. The genome comprises 7,175,690 bp in 121 contigs, a G + C content of 62,4\% and 7,153 coding DNA sequences (CDSs), and it contains genes for trehalose biosynthesis and surfactant production. Additionally, genes for the production of trehalose-tetraester biosurfactant were identified, whose function was experimentally verified making the strain B7g a potential candidate for use in bioremediation applications or in biosurfactant exploration.}, author = {Retamal-Morales, Gerardo and Heine, Thomas and Tischler, Judith S. and Erler, Beate and Gröning, Janosch A. D. and Kaschabek, Stefan R. and Schlömann, Michael and Levicán, Gloria and Tischler, Dirk}, @@ -3542,6 +8724,19 @@ @article{retamal-morales_draft_2018 year = {2018} } +@article{reyes_characterization_2023, + abstract = {IntroductionTheobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.MethodsHerein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.ResultsOur data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.DiscussionTo the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.}, + author = {Reyes, Brayan Maudiel Diaz and Fonseca, Paula Luize Camargos and Heming, Neander Marcel and Conceição, Lucas Barbosa de Amorim and Nascimento, Katiucia Ticila de Souza and Gramacho, Karina Peres and Arevalo-Gardini, Enrique and Pirovani, Carlos Priminho and Aguiar, Eric Roberto Guimarães Rocha}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterization of the microbiota dynamics associated with {Moniliophthora} roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species}, + url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1053562}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + @article{riediger_analysis_2020, author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.}, doi = {10.1093/plcell/koaa017}, @@ -3556,6 +8751,59 @@ @article{riediger_analysis_2020 year = {2020} } +@article{ristinmaa_resin_2023, + abstract = {The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.}, + author = {Ristinmaa, Amanda Sörensen and Tafur Rangel, Albert and Idström, Alexander and Valenzuela, Sebastian and Kerkhoven, Eduard J. and Pope, Phillip B. and Hasani, Merima and Larsbrink, Johan}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-43867-y}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Environmental microbiology, Metagenomics, Microbiome}, + language = {en}, + month = {December}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {8171}, + title = {Resin acids play key roles in shaping microbial communities during degradation of spruce bark}, + url = {https://www.nature.com/articles/s41467-023-43867-y}, + urldate = {2023-12-28}, + volume = {14}, + year = {2023} +} + +@article{robson_environmental_2023, + abstract = {Formation of functional pollen and successful fertilisation relies upon the spatial and temporal regulation of anther and pollen development. This process responds to environmental cues to maintain optimal fertility despite climatic changes. Arabidopsis transcription factors bHLH10,-89,-91 were previously thought to be functionally redundant in their control of male reproductive development, however here we show that they play distinct roles in the integration of light signals to maintain pollen development under different environmental conditions. Combinations of the double and triple bHLH10,-89,-91 mutants were analysed under normal (200μmol/m2/s) and low (50μmol/m2/s) light conditions to determine the impact on fertility. Transcriptomic analysis of a new conditionally sterile bhlh89,91 double mutant shows differential regulation of genes related to sexual reproduction, hormone signal transduction and lipid storage and metabolism under low-light. Here we have shown that bHLH89 and bHLH91 play a role in regulating fertility in response to light, suggesting they function in mitigating environmental variation to ensure fertility is maintained under environmental stress.}, + author = {Robson, Jordan K and Tidy, Alison C and Thomas, Stephen G and Wilson, Zoe A}, + doi = {10.1093/jxb/erad480}, + issn = {0022-0957}, + journal = {Journal of Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + pages = {erad480}, + title = {Environmental regulation of male fertility is mediated through {Arabidopsis} {bHLH89}, 91 and 10}, + url = {https://doi.org/10.1093/jxb/erad480}, + urldate = {2023-12-28}, + year = {2023} +} + +@article{robson_environmental_2024, + abstract = {Formation of functional pollen and successful fertilization rely on the spatial and temporal regulation of anther and pollen development. This process responds to environmental cues to maintain optimal fertility despite climatic changes. Arabidopsis transcription factors basic helix–loop–helix (bHLH) 10, 89, and 91 were previously thought to be functionally redundant in their control of male reproductive development, however here we show that they play distinct roles in the integration of light signals to maintain pollen development under different environmental conditions. Combinations of the double and triple bHLH10,89,91 mutants were analysed under normal (200 μmol m–2 s–1) and low (50 μmol m–2 s–1) light conditions to determine the impact on fertility. Transcriptomic analysis of a new conditionally sterile bhlh89,91 double mutant shows differential regulation of genes related to sexual reproduction, hormone signal transduction, and lipid storage and metabolism under low light. Here we have shown that bHLH89 and bHLH91 play a role in regulating fertility in response to light, suggesting that they function in mitigating environmental variation to ensure fertility is maintained under environmental stress.}, + author = {Robson, Jordan K and Tidy, Alison C and Thomas, Stephen G and Wilson, Zoe A}, + doi = {10.1093/jxb/erad480}, + issn = {0022-0957}, + journal = {Journal of Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {7}, + pages = {1934--1947}, + title = {Environmental regulation of male fertility is mediated through {Arabidopsis} transcription factors {bHLH89}, 91, and 10}, + url = {https://doi.org/10.1093/jxb/erad480}, + urldate = {2024-05-17}, + volume = {75}, + year = {2024} +} + @article{rogg_srgap1_2021, author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph}, doi = {10.1681/asn.2020081126}, @@ -3611,6 +8859,98 @@ @article{roquis_genomic_2021 year = {2021} } +@article{roux_dna_2023, + abstract = {Unintegrated HIV DNA represents between 20\% and 35\% of the total viral DNA in infected patients. Only the linear forms (unintegrated linear DNAs [ULDs]) can be substrates for integration and for the completion of a full viral cycle. In quiescent cells, these ULDs may be responsible for pre-integrative latency. However, their detection remains difficult due to the lack of specificity and sensitivity of existing techniques. We developed an ultra-sensitive, specific, and high-throughput technology for ULD quantification called DUSQ (DNA ultra-sensitive quantification) combining linker-mediated PCR and next-generation sequencing (NGS) using molecular barcodes. Studying cells with different activity levels, we determined that the ULD half-life goes up to 11 days in resting CD4+ T cells. Finally, we were able to quantify ULDs in samples from patients infected with HIV-1, providing a proof of concept for the use of DUSQ in vivo to track pre-integrative latency. DUSQ can be adapted to the detection of other rare DNA molecules.}, + author = {Roux, Hélène Marie and Figueiredo, Suzanne and Sareoua, Lucas and Salmona, Maud and Hamroune, Juliette and Adoux, Lucie and Migraine, Julie and Hance, Allan and Clavel, François and Cheynier, Rémi and Dutrieux, Jacques}, + doi = {10.1016/j.crmeth.2023.100443}, + issn = {2667-2375}, + journal = {Cell Reports Methods}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + number = {4}, + pages = {100443}, + title = {{DNA} ultra-sensitive quantification, a technology for studying {HIV} unintegrated linear {DNA}}, + url = {https://www.sciencedirect.com/science/article/pii/S2667237523000589}, + urldate = {2023-07-31}, + volume = {3}, + year = {2023} +} + +@article{royaux_genetic_2024, + abstract = {Thirteen new freshwater populations of the copepod genus BoeckellaDe Guerne \& Richard, 1889 were found during three expeditions to New Caledonia (‘La Planète Revisitée,’ 2016-2018). The 12 populations from the Plaine des Lacs, which show remarkable genetic diversity among themselves, were identified as B. spinogibbaDefaye, 1998, the only species of its genus known from New Caledonia until now. The sole exception, the population from Mont-Dore 22 km further east, appeared genetically and morphologically distinct from the others and is described herein as a new species. The two species are distinguished from each other by the shapes of the male and female P5, female Th5, and body colour. A previously published key is amended to separate the species. Our concatenated COI+28S phylogeny places the two New Caledonia species as a new branch within Boeckella, distinct from the branches consisting of South American, Antarctic and Australasian species. All 13 Boeckella populations inhabit the extreme south of New Caledonia, an area known for endemism and high heavy metal concentrations in the soil. Extensive mining activity in this metal-rich area, begun in 1873, is now leading to conflict with conservation goals. By using aerial photographs to trace the fate of the pond that is the type locality of B. spinogibba, we confirmed that it disappeared between 2007 and 2014 as a result of the expansion of the Goro nickel mine.}, + author = {Royaux, Coline and Charpin, Nicolas and Rabet, Nicolas}, + doi = {10.1093/jcbiol/ruae001}, + issn = {0278-0372}, + journal = {Journal of Crustacean Biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {1}, + pages = {ruae001}, + shorttitle = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}}, + title = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}: {Calanoida}), with the description of a new species}, + url = {https://doi.org/10.1093/jcbiol/ruae001}, + urldate = {2024-06-07}, + volume = {44}, + year = {2024} +} + +@article{royaux_genetic_2024, + abstract = {Thirteen new freshwater populations of the copepod genus BoeckellaDe Guerne \& Richard, 1889 were found during three expeditions to New Caledonia (‘La Planète Revisitée,’ 2016-2018). The 12 populations from the Plaine des Lacs, which show remarkable genetic diversity among themselves, were identified as B. spinogibbaDefaye, 1998, the only species of its genus known from New Caledonia until now. The sole exception, the population from Mont-Dore 22 km further east, appeared genetically and morphologically distinct from the others and is described herein as a new species. The two species are distinguished from each other by the shapes of the male and female P5, female Th5, and body colour. A previously published key is amended to separate the species. Our concatenated COI+28S phylogeny places the two New Caledonia species as a new branch within Boeckella, distinct from the branches consisting of South American, Antarctic and Australasian species. All 13 Boeckella populations inhabit the extreme south of New Caledonia, an area known for endemism and high heavy metal concentrations in the soil. Extensive mining activity in this metal-rich area, begun in 1873, is now leading to conflict with conservation goals. By using aerial photographs to trace the fate of the pond that is the type locality of B. spinogibba, we confirmed that it disappeared between 2007 and 2014 as a result of the expansion of the Goro nickel mine.}, + author = {Royaux, Coline and Charpin, Nicolas and Rabet, Nicolas}, + doi = {10.1093/jcbiol/ruae001}, + issn = {0278-0372}, + journal = {Journal of Crustacean Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Ecology}, + month = {March}, + number = {1}, + pages = {ruae001}, + shorttitle = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}}, + title = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}: {Calanoida}), with the description of a new species}, + url = {https://doi.org/10.1093/jcbiol/ruae001}, + urldate = {2024-01-27}, + volume = {44}, + year = {2024} +} + +@article{sabala_carbapenem_2024, + abstract = {Background +Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great public health problem and is associated with many disease outbreaks and high mortality rates. Alarmingly, K. pneumoniae has been isolated from food in several recent studies. This study aimed to investigate the prevalence and characteristics of CRKP in food samples from Egypt. +Methods +A total of 311 food samples (including 116 minced meat, 92 chicken meat, 75 diced meat, and 28 mutton) were collected from local markets in Egypt and were screened for CRKP with the determination of their antimicrobial resistance profiles. The whole genome sequence was done for 23 CRKP isolates to clarify the relationship between CRKP from food and human cases in Egypt using the SNP core genome. The conjugation probability of the blaNDM-5 harboring plasmid was identified using oriTfinder +Results +CRKP was isolated from 11\% (35/311) of the samples, with 45.71\% (16/35) of them showing resistance to colistin, one of the last-resort options for treating CRKP-mediated infections. In addition to the carbapenem and colistin resistance, the CRKP isolates frequently exhibited resistance to multiple antimicrobials including β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and chloramphenicol. In addition, most of the CRKP were potentially hypervirulent K. pneumoniae (HvKP) identified as phylogroup Kp1 and of high-risk groups as detected in STs reported in many human outbreaks globally, such as ST383 and ST147. The core-genome phylogeny showed similarities between the isolates from this study and those previously isolated from clinical human samples in Egypt. In addition, analysis of the plasmid on which blaNDM is encoded revealed that several antimicrobial resistance genes such as blaOXA-9, blaCTX-M-15, aac(6′)-Ib, qnrS1, and several virulence genes are encoded on the same plasmid. +Conclusions +This study is significant for food safety and public health and is important to further identify the change in the epidemiology of CRKP infections, especially the consumption of contaminated food products.}, + author = {Sabala, Rana Fahmi and Fukuda, Akira and Nakajima, Chie and Suzuki, Yasuhiko and Usui, Masaru and Elhadidy, Mohamed}, + doi = {10.1016/j.jiph.2024.04.010}, + issn = {1876-0341}, + journal = {Journal of Infection and Public Health}, + keywords = {{\textgreater}UseGalaxy.eu, CRKP, Colistin, Food safety, HvKP, NDM, Retail meat}, + month = {June}, + number = {6}, + pages = {1037--1046}, + shorttitle = {Carbapenem and colistin-resistant hypervirulent \textit{{Klebsiella} pneumoniae}}, + title = {Carbapenem and colistin-resistant hypervirulent \textit{{Klebsiella} pneumoniae}: {An} emerging threat transcending the egyptian food chain}, + url = {https://www.sciencedirect.com/science/article/pii/S1876034124001230}, + urldate = {2024-04-28}, + volume = {17}, + year = {2024} +} + +@article{sabbaghian_panel_2022, + abstract = {Introduction: MicroRNAs have a significant role in the regulation of the transcriptome. Several miRNAs have been proposed as potential biomarkers in different malignancies. However, contradictory results have been reported on the capability of miRNA biomarkers in cancer detection. The human biological clock involves molecular mechanisms that regulate several genes over time. Therefore, the sampling time becomes one of the significant factors in gene expression studies.Method: In the present study, we have tried to find miRNAs with minimum fluctuation in expression levels at different time points that could be more accurate candidates as diagnostic biomarkers. The small RNA-seq raw data of ten healthy individuals across nine-time points were analyzed to identify miRNAs with stable expression.Results: We have found five oscillation patterns. The stable miRNAs were investigated in 779 small-RNA-seq datasets of eleven cancer types. All miRNAs with the highest differential expression were selected for further analysis. The selected miRNAs were explored for functional pathways. The predominantly enriched pathways were miRNA in cancer and the P53-signaling pathway. Finally, we have found seven miRNAs, including miR-142-3p, miR-199a-5p, miR-223-5p, let-7d-5p, miR-148b-3p, miR-340-5p, and miR-421. These miRNAs showed minimum fluctuation in healthy blood and were dysregulated in the blood of eleven cancer types. Conclusion: We have found a signature of seven stable miRNAs which dysregulate in several cancer types and may serve as potential pan-cancer biomarkers.}, + author = {Sabbaghian, Amir and Mussack, Veronika and Kirchner, Benedikt and Bui, Maria L. U. and Kalani, Mohammad Reza and Pfaffl, Michael W. and Golalipour, Masoud}, + issn = {2296-889X}, + journal = {Frontiers in Molecular Biosciences}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A panel of blood-derived {miRNAs} with a stable expression pattern as a potential pan-cancer detection signature}, + url = {https://www.frontiersin.org/articles/10.3389/fmolb.2022.1030749}, + urldate = {2023-05-20}, + volume = {9}, + year = {2022} +} + @phdthesis{sabrina_statistical_2020, abstract = {Protein-RNA interactions play an important role in all post-transcriptional regulatory processes. High throughput detection of protein-RNA interactions has been facilitated by the emerging CLIP-seq (crosslinking and immunoprecipitation combined with high-throughput sequencing) techniques. Enrichments in mapped reads as well as base transitions or deletions at crosslink sites can be used to infer binding regions. Single-nucleotide resolution techniques (iCLIP and eCLIP) have been achieved by capturing high fractions of cDNAs which are truncated at protein-RNA crosslink sites. Increasing numbers of datasets and derivatives of these protocols have been published in recent years, requiring tailored computational analyses. Existing methods unfortunately do not explicitly model the specifics of truncation patterns and possible biases caused by background binding or crosslinking sequence preferences. We present PureCLIP, a hidden Markov model based approach, which simultaneously performs peak calling and individual crosslink site detection. It is capable of incorporating external data to correct for non-specific background signals and, for the first time, for the crosslinking biases. We devised a comprehensive evaluation based on three strategies. Firstly, we developed a workflow to simulate iCLIP data, which starts from real RNA-seq data and known binding regions and then mimics the experimental steps of the iCLIP protocol, including the generation of background signals. Secondly, we used experimental iCLIP and eCLIP datasets, using the proteins’ known predominant binding regions. And thirdly, we assessed the agreement of called sites between replicates, assuming target-specific signals are reproducible between replicates. @@ -3627,6 +8967,42 @@ @phdthesis{sabrina_statistical_2020 year = {2020} } +@article{sacco_outbreak_2022, + abstract = {The spread of extremely-drug-resistant Klebsiella pneumoniae has become a major health threat worldwide. This is largely mediated by certain lineages, recognized as high-risk clones dispersed throughout the world. Analysis of an outbreak of nine ST15, NDM-1 metallo-β-lactamase-producing K. pneumoniae was performed. An IncC plasmid carrying the blaNDM-1 gene also carried the rare rmtC gene, encoding for 16S rRNA methyltransferases (16RMTases), conferring resistance to all aminoglycosides. The global spread of New Delhi metallo (NDM) variants and their association with the 16RMTases among K. pneumoniae complete genomes available in GenBank was studied, and a complete overview of the association of 16RMTases and NDM in K. pneumoniae genomics was produced. NDM is often associated with16RMTases, and both are spreading in K. pneumoniae, conferring resistance to all beta-lactams and aminoglycosides. This analysis suggests that aminoglycosides have a limited future as a second-line treatment against NDM-producing K. pneumoniae.}, + author = {Sacco, Federica and Raponi, Giammarco and Oliva, Alessandra and Bibbolino, Giulia and Mauro, Vera and Di Lella, Federica Maria and Volpicelli, Lorenzo and Antonelli, Guido and Venditti, Mario and Carattoli, Alessandra and Arcari, Gabriele}, + doi = {10.1016/j.ijantimicag.2022.106615}, + issn = {0924-8579}, + journal = {International Journal of Antimicrobial Agents}, + keywords = {{\textgreater}UseGalaxy.eu, Aminoglycosides, Antimicrobial resistance, Metallo-beta lactamase, Neoglycosides, armA, rmtC}, + language = {en}, + month = {August}, + number = {2}, + pages = {106615}, + shorttitle = {An outbreak sustained by {ST15} {Klebsiella} pneumoniae carrying {16S} {rRNA} methyltransferases and {blaNDM}}, + title = {An outbreak sustained by {ST15} {Klebsiella} pneumoniae carrying {16S} {rRNA} methyltransferases and {blaNDM}: evaluation of the global dissemination of these resistance determinants}, + url = {https://www.sciencedirect.com/science/article/pii/S0924857922001273}, + urldate = {2022-09-24}, + volume = {60}, + year = {2022} +} + +@article{sageman-furnas_detailing_2024, + abstract = {Shoot growth directly impacts plant productivity. Plants adjust their shoot growth in response to varying environments to maximize resource capture and stress resilience. While several factors controlling shoot growth are known, the complexity of the regulation and the input of the environment are not fully understood. We have investigated shoot growth repression induced by low ambient temperatures in hybrids of Arabidopsis thaliana Kro-0 and BG-5 accessions. To continue our previous studies, we confirmed that the Kro-0 allele of DYNAMIN-RELATED PROTEIN 3B causes stunted shoot growth in the BG-5 background. We also found that shoot growth repression was most pronounced near the apex at a lower temperature and that the cells in the hybrid stem failed to elongate correctly. Furthermore, we observed that shoot growth repression in hybrids depended on light availability. Global gene expression analysis indicated the involvement of hormones, especially strigolactone, associated with the dwarf phenotype. Altogether, this study enhances our knowledge on the genetic, physiological and environmental factors associated with shoot growth regulation.}, + author = {Sageman-Furnas, Katelyn and Duarte, Gustavo T and Laitinen, Roosa A E}, + doi = {10.1093/pcp/pcad167}, + issn = {1471-9053}, + journal = {Plant and Cell Physiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {3}, + pages = {420--427}, + title = {Detailing {Early} {Shoot} {Growth} {Arrest} in {Kro}-0 x {BG}-5 {Hybrids} of {Arabidopsis} thaliana}, + url = {https://doi.org/10.1093/pcp/pcad167}, + urldate = {2024-05-17}, + volume = {65}, + year = {2024} +} + @article{sajulga_survey_2020, abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.}, author = {Sajulga, Ray and Easterly, Caleb and Riffle, Michael and Mesuere, Bart and Muth, Thilo and Mehta, Subina and Kumar, Praveen and Johnson, James and Gruening, Bjoern Andreas and Schiebenhoefer, Henning and Kolmeder, Carolin A. and Fuchs, Stephan and Nunn, Brook L. and Rudney, Joel and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -3646,6 +9022,58 @@ @article{sajulga_survey_2020 year = {2020} } +@article{sakamoto_detection_2023, + abstract = {The novel domestic cat hepadnavirus (DCH), a member of the +Hepadnaviridae, was first detected in Australia and has recently been +identified in more countries. In this study, we explored the DCH genome using +next-generation sequencing of a plasma sample from a cat with a fever of unknown cause. +Nucleotide sequence analysis showed the virus to be relatively genetically distant from +the first reported DCH in Australia, showing 89\% homology. Then we conducted an +epidemiological survey by PCR of plasma samples collected from 203 cats that visited a +veterinary hospital for diagnosis and treatment. Two of the 203 surveyed cats a were +positive for DCH. One of the two positive cases had elevated liver enzymes of unknown +etiology, and the other had hepatocellular adenoma. Our study indicated that DCH infection +was observed in domestic cats in the Tokyo area of Japan as well as other reported areas +in the world. Further investigations are needed to define the clinical importance of +DCH.}, + author = {SAKAMOTO, Haruka and ITO, Genta and GOTO-KOSHINO, Yuko and SAKAMOTO, Megumi and NISHIMURA, Ryohei and MOMOI, Yasuyuki}, + doi = {10.1292/jvms.22-0439}, + issn = {0916-7250}, + journal = {The Journal of Veterinary Medical Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {June}, + number = {6}, + pages = {642--646}, + pmcid = {PMC10315552}, + pmid = {37183016}, + title = {Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in {Japan}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10315552/}, + urldate = {2023-10-07}, + volume = {85}, + year = {2023} +} + +@article{salapa_hnrnp_2024, + abstract = {Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.}, + author = {Salapa, Hannah E. and Thibault, Patricia A. and Libner, Cole D. and Ding, Yulian and Clarke, Joseph-Patrick W. E. and Denomy, Connor and Hutchinson, Catherine and Abidullah, Hashim M. and Austin Hammond, S. and Pastushok, Landon and Vizeacoumar, Frederick S. and Levin, Michael C.}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41467-023-44658-1}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, CLIP-seq, Multiple sclerosis, RNA metabolism}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {356}, + title = {{hnRNP} {A1} dysfunction alters {RNA} splicing and drives neurodegeneration in multiple sclerosis ({MS})}, + url = {https://www.nature.com/articles/s41467-023-44658-1}, + urldate = {2024-01-11}, + volume = {15}, + year = {2024} +} + @incollection{saleh_nascent_2021, author = {Saleh, Omar and Dwiani, Sarlita and Rott, Julia and Kühn, Kristina}, booktitle = {Methods in {Molecular} {Biology}}, @@ -3659,6 +9087,27 @@ @incollection{saleh_nascent_2021 year = {2021} } +@article{sanchez-leon_heteroresistance_2023, + abstract = {Heteroresistance to colistin can be defined as the presence of resistant subpopulations in an isolate that is susceptible to this antibiotic. Colistin resistance in Gram-negative bacteria is more frequently related to chromosomal mutations and insertions. This work aimed to study heteroresistance in nine clinical isolates of Klebsiella pneumoniae producing OXA-48 and to describe genomic changes in mutants with acquired resistance in vitro. Antimicrobial susceptibility was determined by broth microdilution (BMD) and heteroresistance by population analysis profiling (PAP). The proteins related to colistin resistance were analyzed for the presence of mutations. Additionally, PCR of the mgrB gene was performed to identify the presence of insertions. In the nine parental isolates, the PAP method showed colistin heteroresistance of colonies growing on plates with concentrations of up to 64 mg/L, corresponding to stable mutant subpopulations. The MICs of some mutants from the PAP plate containing 4×MIC of colistin had absolute values of ≤2 mg/L that were higher than the parental MICs and were defined as persistent variants. PCR of the mgrB gene identified an insertion sequence that inactivated the gene in 21 mutants. Other substitutions in the investigated mutants were found in PhoP, PhoQ, PmrB, PmrC, CrrA and CrrB proteins. Colistin heteroresistance in K. pneumoniae isolates was attributed mainly to insertions in the mgrB gene and point mutations in colistin resistance proteins. The results of this study will improve understanding regarding the mechanisms of colistin resistance in mutants of K. pneumoniae producing OXA-48.}, + author = {Sánchez-León, Irene and García-Martínez, Teresa and Diene, Seydina M. and Pérez-Nadales, Elena and Martínez-Martínez, Luis and Rolain, Jean-Marc}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12071111}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Klebsiella pneumoniae} producing OXA-48, \textit{mgr}B, {\textgreater}UseGalaxy.eu, heteroresistance to colistin}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {1111}, + title = {Heteroresistance to {Colistin} in {Clinical} {Isolates} of {Klebsiella} pneumoniae {Producing} {OXA}-48}, + url = {https://www.mdpi.com/2079-6382/12/7/1111}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + @article{sanchez_pathwaymatcher_2019, abstract = {AbstractBackground. Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., g}, author = {Sánchez, Luis Francisco Hernández and Burger, Bram and Horro, Carlos and Fabregat, Antonio and Johansson, Stefan and Njølstad, Pål Rasmus and Barsnes, Harald and Hermjakob, Henning and Vaudel, Marc}, @@ -3677,6 +9126,25 @@ @article{sanchez_pathwaymatcher_2019 year = {2019} } +@article{saragih_potential_2022, + abstract = {Bacterial key species (BKS) is unique and found only in peat secondary forest, but not in converted peat areas. Its presence helps in biomonitoring of peatland quality. BKS candidates were detected based on the 16S rRNA gene sequence using the Next Generation Sequencing method. The 16S rRNA gene sequencing data were obtained from DNA isolated from peat soil of the secondary forest (SF), acacia plantations (AP), and rubber plantations (RP) in the Giam Siak Kecil - Bukit Batu (GSK-BB) Biosphere Reserve, Riau. The natural vegetation of peat swamp forest dominates the SF, which was relatively heterogeneous with anaerobic conditions and water level at 60-120 cm. The RP locations were planted with 6-7 year old rubber, water level was 20 cm, and the garden was not maintained. The AP locations were planted with A. crassicarpa and peat thickness was 9 m. The peat soil was sampled in August 2019. BKS candidates were selected based on a phylogenetic tree using MEGA 6.06 by observing the grouping of DNA sequences obtained only from secondary forests. Furthermore, the selection was also conducted using BLASTn: Align Two or More Sequence analysis to determine the similarity between selected BKS candidates. Based on the detected BKS candidate, a specific primer was designed to amplify the BKS sequence, and the specificity was tested in silico with FastPCR to detect that the primer was only for the amplification of the BKS target. Two BKS candidates with the same sequence length of 455 bp were discovered in the secondary forests and there were successfully amplified by 2 pairs of specific primers. The 16S rRNA gene sequences of the two BKS candidates could be used to monitor the peat quality that has been converted into plantation areas molecularly.}, + author = {Saragih, F. A. S. and {Nelvia} and Pratiwi, N. W. and Zul, D.}, + doi = {10.1088/1755-1315/1025/1/012007}, + issn = {1755-1315}, + journal = {IOP Conference Series: Earth and Environmental Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {May}, + note = {Publisher: IOP Publishing}, + number = {1}, + pages = {012007}, + title = {The potential of bacterial key species as a tool for monitoring peatland quality}, + url = {https://doi.org/10.1088/1755-1315/1025/1/012007}, + urldate = {2022-09-24}, + volume = {1025}, + year = {2022} +} + @article{sauriol_modeling_2020, abstract = {Cancer cell lines are amongst the most important pre-clinical models. In the context of epithelial ovarian cancer, a highly heterogeneous disease with diverse subtypes, it is paramount to study a wide panel of models in order to draw a representative picture of the disease. As this lethal gynaecological malignancy has seen little improvement in overall survival in the last decade, it is all the more pressing to support future research with robust and diverse study models. Here, we describe ten novel spontaneously immortalized patient-derived ovarian cancer cell lines, detailing their respective mutational profiles and gene/biomarker expression patterns, as well as their in vitro and in vivo growth characteristics. Eight of the cell lines were classified as high-grade serous, while two were determined to be of the rarer mucinous and clear cell subtypes, respectively. Each of the ten cell lines presents a panel of characteristics reflective of diverse clinically relevant phenomena, including chemotherapeutic resistance, metastatic potential, and subtype-associated mutations and gene/protein expression profiles. Importantly, four cell lines formed subcutaneous tumors in mice, a key characteristic for pre-clinical drug testing. Our work thus contributes significantly to the available models for the study of ovarian cancer, supplying additional tools to better understand this complex disease.}, author = {Sauriol, Alexandre and Simeone, Kayla and Portelance, Lise and Meunier, Liliane and Leclerc-Desaulniers, Kim and de Ladurantaye, Manon and Chergui, Meriem and Kendall-Dupont, Jennifer and Rahimi, Kurosh and Carmona, Euridice and Provencher, Diane M. and Mes-Masson, Anne-Marie}, @@ -3712,6 +9180,24 @@ @article{schafer_glassgo_2020 year = {2020} } +@article{schiml_integrative_2023, + abstract = {‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omics”, they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.}, + author = {Schiml, Valerie C. and Delogu, Francesco and Kumar, Praveen and Kunath, Benoit and Batut, Bérénice and Mehta, Subina and Johnson, James E. and Grüning, Björn and Pope, Phillip B. and Jagtap, Pratik D. and Griffin, Timothy J. and Arntzen, Magnus Ø.}, + doi = {10.1186/s40793-023-00514-9}, + issn = {2524-6372}, + journal = {Environmental Microbiome}, + keywords = {{\textgreater}UseGalaxy.eu, Bioinformatics, Galaxy, Integrated meta-omics, Metagenomics, Metaproteomics, Metatrascriptomics}, + language = {en}, + month = {July}, + number = {1}, + pages = {56}, + title = {Integrative meta-omics in {Galaxy} and beyond}, + url = {https://doi.org/10.1186/s40793-023-00514-9}, + urldate = {2023-07-31}, + volume = {18}, + year = {2023} +} + @article{schlecht_transcriptomic_2020, abstract = {Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) in body donor eyes with neovascular age-related macular degeneration (nAMD) and were thus limited by the time span from death to preservation and the associated 5'-RNA degradation. Therefore, this study used CNV and control specimens which had been formalin-fixed and paraffin-embedded immediately after surgical extraction and analyzed them using a 3’ RNA sequencing approach. Transcriptome profiles were analyzed and used to estimate content of immune and stromal cells and to define disease-associated gene signatures using statistical and bioinformatic methods. We identified 158 differentially-expressed genes (DEG) that were significantly increased in CNV compared to control tissue. Cell type enrichment analysis revealed a diverse cellular landscape with an enrichment of immune and stroma cell types in CNV including endothelial cells, macrophages, T cells and NKT cells. Gene ontology enrichment analysis demonstrated that DEG contributed to Blood Vessel Development, Extracellular Structure Organization, Response to Wounding and several immune-related terms. The S100 calcium-binding protein A8 (S100A8) and S100A9 emerged among the top DEG, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples. This study provides a high-resolution RNA-sequencing-based transcriptional signature of human CNV, characterizes its compositional pattern of immune and stromal cells and reveals S100A8/A9 as a novel biomarker and promising target for AMD-directed therapeutics and diagnostics.}, author = {Schlecht, Anja and Boneva, Stefaniya and Gruber, Markus and Zhang, Peipei and Horres, Ralf and Bucher, Felicitas and Auw-Haedrich, Claudia and Hansen, Lutz and Stahl, Andreas and Hilgendorf, Ingo and Agostini, Hansjürgen and Wieghofer, Peter and Schlunck, Günther and Wolf, Julian and Lange, Clemens AK.}, @@ -3727,6 +9213,142 @@ @article{schlecht_transcriptomic_2020 year = {2020} } +@article{schmidt_practical_2024, + abstract = {Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data-driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well-established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging – Society for Microscopy and Image Analysis (GerBI-GMB), cross-institutional working groups and third-party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.}, + author = {Schmidt, Christian and Boissonnet, Tom and Dohle, Julia and Bernhardt, Karen and Ferrando-May, Elisa and Wernet, Tobias and Nitschke, Roland and Kunis, Susanne and Weidtkamp-Peters, Stefanie}, + doi = {10.1111/jmi.13317}, + issn = {1365-2818}, + journal = {Journal of Microscopy}, + keywords = {{\textgreater}UseGalaxy.eu, FAIR, OMERO, bioimaging, data stewardship, research data management}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.13317}, + number = {3}, + pages = {350--371}, + title = {A practical guide to bioimaging research data management in core facilities}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13317}, + urldate = {2024-06-07}, + volume = {294}, + year = {2024} +} + +@article{schoof_mouse_2023, + abstract = {Pediatric high-grade gliomas of the subclass MYCN (HGG-MYCN) are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. Due to their rarity, such tumors have only recently been identified as a distinct entity, and biological as well as clinical characteristics have not been addressed specifically. To gain insights into tumorigenesis and molecular profiles of these tumors, and to ultimately suggest alternative treatment options, we generated a genetically engineered mouse model by breeding hGFAP-cre::Trp53Fl/Fl::lsl-MYCN mice. All mice developed aggressive forebrain tumors early in their lifetime that mimic human HGG-MYCN regarding histology, DNA methylation, and gene expression. Single-cell RNA sequencing revealed a high intratumoral heterogeneity with neuronal and oligodendroglial lineage signatures. High-throughput drug screening using both mouse and human tumor cells finally indicated high efficacy of Doxorubicin, Irinotecan, and Etoposide as possible therapy options that children with HGG-MYCN might benefit from.}, + author = {Schoof, Melanie and Godbole, Shweta and Albert, Thomas K. and Dottermusch, Matthias and Walter, Carolin and Ballast, Annika and Qin, Nan and Olivera, Marlena Baca and Göbel, Carolin and Neyazi, Sina and Holdhof, Dörthe and Kresbach, Catena and Peter, Levke-Sophie and Epplen, Gefion Dorothea and Thaden, Vanessa and Spohn, Michael and Blattner-Johnson, Mirjam and Modemann, Franziska and Mynarek, Martin and Rutkowski, Stefan and Sill, Martin and Varghese, Julian and Afflerbach, Ann-Kristin and Eckhardt, Alicia and Münter, Daniel and Verma, Archana and Struve, Nina and Jones, David T. W. and Remke, Marc and Neumann, Julia E. and Kerl, Kornelius and Schüller, Ulrich}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-43564-w}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Oncogenesis}, + language = {en}, + month = {November}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {7717}, + title = {Mouse models of pediatric high-grade gliomas with {MYCN} amplification reveal intratumoral heterogeneity and lineage signatures}, + url = {https://www.nature.com/articles/s41467-023-43564-w}, + urldate = {2023-11-28}, + volume = {14}, + year = {2023} +} + +@article{schule_eomes_2023, + author = {Schüle, Katrin M. and Weckerle, Jelena and Probst, Simone and Wehmeyer, Alexandra E. and Zissel, Lea and Schröder, Chiara M. and Tekman, Mehmet and Kim, Gwang-Jin and Schlägl, Inga-Marie and Sagar and Arnold, Sebastian J.}, + doi = {10.1016/j.devcel.2023.07.023}, + issn = {1534-5807}, + journal = {Developmental Cell}, + keywords = {{\textgreater}UseGalaxy.eu, Brachyury, Eomes, T-box transcription factors, chromatin accessibility, endoderm, lineage specification, mesoderm, mouse gastrulation, transcriptional control}, + language = {English}, + month = {August}, + note = {Publisher: Elsevier}, + number = {0}, + pmid = {37633271}, + title = {Eomes restricts {Brachyury} functions at the onset of mouse gastrulation}, + url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(23)00396-9}, + urldate = {2023-08-28}, + volume = {0}, + year = {2023} +} + +@article{schwabenland_neonatal_2023, + abstract = {While the precise processes underlying a sex bias in the development of central nervous system (CNS) disorders are unknown, there is growing evidence that an early life immune activation can contribute to the disease pathogenesis. When we mimicked an early systemic viral infection or applied murine cytomegalovirus (MCMV) systemically in neonatal female and male mice, only male adolescent mice presented behavioral deficits, including reduced social behavior and cognition. This was paralleled by an increased amount of infiltrating T cells in the brain parenchyma, enhanced interferon-γ (IFNγ) signaling, and epigenetic reprogramming of microglial cells. These microglial cells showed increased phagocytic activity, which resulted in abnormal loss of excitatory synapses within the hippocampal brain region. None of these alterations were seen in female adolescent mice. Our findings underscore the early postnatal period’s susceptibility to cause sex-dependent long-term CNS deficiencies following infections.}, + author = {Schwabenland, Marius and Mossad, Omar and Sievert, Annika and Peres, Adam G. and Ringel, Elena and Baasch, Sebastian and Kolter, Julia and Cascone, Giulia and Dokalis, Nikolaos and Vlachos, Andreas and Ruzsics, Zsolt and Henneke, Philipp and Prinz, Marco and Blank, Thomas}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-38373-0}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Development of the nervous system, Neuroimmunology}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {2721}, + title = {Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment}, + url = {https://www.nature.com/articles/s41467-023-38373-0}, + urldate = {2023-05-16}, + volume = {14}, + year = {2023} +} + +@article{seckin_dinler_regulation_2023, + abstract = {Plant hormones and antioxidant system changes occur during plants' exposure to stress conditions. Although the interactions of some plant hormones (abscisic acid, salicylic acid, jasmonic acid, nitric oxide, and ethylene) with the glutathione s-transferase (GST) enzyme, which is one of the antioxidant enzymes, have already been reported, the influence of gibberellic acid (GA3) on this enzyme under saline conditions has not yet been reported. Plant material for the experiments was obtained from M14G144 cultivar of maize (Zea mays L.) plants grown as a soil culture in growth chambers at 22 °C, 65–70\% moisture, 16-h light/8-h dark conditions, and with full strength Hoagland solution for 8 days under controlled growth conditions. Then, the plants were exposed to salt stress (350 mM NaCl and 100, 300, and 500 ppm GA3) simultaneously. In maize leaves, GA3 treatment alleviated the physiological parameters under salt stress. Specifically, the treatments with 100 and 500 ppm of GA3 were able to trigger GST enzyme and isoenzyme activities as well as hydrogen sulfide accumulation and anthocyanin content, although the lowest malondialdehyde, hydrogen peroxide, and superoxide radical content were under the treatment of 300 ppm of GA3. Besides this, GST gene expression levels were found to be upregulated between 1.5 and fourfold higher in all the plants treated with GA3 at different concentrations in proportion to salt stress. These results first indicated that the reason for the changes in GA3-treated plants was the stimulating role of this hormone to maintain GST regulation in maize plants.}, + author = {Seckin Dinler, Burcu and Cetinkaya, Hatice and Secgin, Zafer}, + doi = {10.1007/s12298-022-01269-2}, + issn = {0974-0430}, + journal = {Physiology and Molecular Biology of Plants}, + keywords = {{\textgreater}UseGalaxy.eu, Anthocyanin, Phytohormone, Reactive oxygen species, Salinity, Zea mays}, + language = {en}, + month = {January}, + number = {1}, + pages = {69--85}, + title = {The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves}, + url = {https://doi.org/10.1007/s12298-022-01269-2}, + urldate = {2023-03-15}, + volume = {29}, + year = {2023} +} + +@article{semenzato_genomic_2022, + abstract = {Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.}, + author = {Semenzato, Giulia and Alonso-Vásquez, Tania and Del Duca, Sara and Vassallo, Alberto and Riccardi, Christopher and Zaccaroni, Marco and Mucci, Nadia and Padula, Anna and Emiliani, Giovanni and Palumbo Piccionello, Antonio and Puglia, Anna Maria and Fani, Renato}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms10050919}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, antimicrobial resistance, bacterial endophytes, essential oil, microbiome, plant growth-promoting bacteria}, + language = {en}, + month = {May}, + number = {5}, + pages = {919}, + title = {Genomic {Analysis} of {Endophytic} {Bacillus}-{Related} {Strains} {Isolated} from the {Medicinal} {Plant} {Origanum} vulgare {L}. {Revealed} the {Presence} of {Metabolic} {Pathways} {Involved} in the {Biosynthesis} of {Bioactive} {Compounds}}, + url = {https://www.mdpi.com/2076-2607/10/5/919}, + urldate = {2022-09-24}, + volume = {10}, + year = {2022} +} + +@article{semenzato_genomic_2023, + abstract = {Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant’s microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.}, + author = {Semenzato, Giulia and Del Duca, Sara and Vassallo, Alberto and Bechini, Angela and Calonico, Carmela and Delfino, Vania and Berti, Fabiola and Vitali, Francesco and Mocali, Stefano and Frascella, Angela and Emiliani, Giovanni and Fani, Renato}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms24054845}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, endophytes, essential oil, genome, plant microbiota, volatile organic compounds}, + language = {en}, + month = {January}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {4845}, + title = {Genomic, {Molecular}, and {Phenotypic} {Characterization} of {Arthrobacter} sp. {OVS8}, an {Endophytic} {Bacterium} {Isolated} from and {Contributing} to the {Bioactive} {Compound} {Content} of the {Essential} {Oil} of the {Medicinal} {Plant} {Origanum} vulgare {L}.}, + url = {https://www.mdpi.com/1422-0067/24/5/4845}, + urldate = {2023-03-15}, + volume = {24}, + year = {2023} +} + @article{senapathi_biomolecular_2019, abstract = {Motivation. The pathway from genomics through proteomics and onto a molecular description of biochemical processes make the discovery of drugs and biom}, author = {Senapathi, Tharindu and Bray, Simon and Barnett, Christopher B. and Grüning, Björn and Naidoo, Kevin J.}, @@ -3758,6 +9380,61 @@ @article{senapathi_bridge_2020 year = {2020} } +@article{senft_biologists_2023, + abstract = {Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.}, + author = {Senft, Rebecca A. and Diaz-Rohrer, Barbara and Colarusso, Pina and Swift, Lucy and Jamali, Nasim and Jambor, Helena and Pengo, Thomas and Brideau, Craig and Llopis, Paula Montero and Uhlmann, Virginie and Kirk, Jason and Gonzales, Kevin Andrew and Bankhead, Peter and Iii, Edward L. Evans and Eliceiri, Kevin W. and Cimini, Beth A.}, + doi = {10.1371/journal.pbio.3002167}, + issn = {1545-7885}, + journal = {PLOS Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Artificial light, Fluorescence, Fluorescence imaging, Fluorescence microscopy, Image analysis, Light, Light microscopy, Open source software}, + language = {en}, + month = {June}, + note = {Publisher: Public Library of Science}, + number = {6}, + pages = {e3002167}, + title = {A biologist’s guide to planning and performing quantitative bioimaging experiments}, + url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167}, + urldate = {2023-07-02}, + volume = {21}, + year = {2023} +} + +@article{shankar_structure_2023, + abstract = {Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.}, + author = {Shankar, Manwi and Rani, Majji Sai Sudha and Gopi, Priyanka and P, Arsha and Pandya, Prateek}, + doi = {10.1016/j.compbiolchem.2023.107976}, + issn = {1476-9271}, + journal = {Computational Biology and Chemistry}, + keywords = {{\textgreater}ChemicalToolbox, Bismarck Brown Y, C.I. 21000, Circular Dichroism Spectroscopy, Fluorescence Spectroscopy, Molecular Docking, Molecular Dynamics, chemicaltoolbox}, + month = {October}, + pages = {107976}, + title = {Structure and {Energetics} of {Serum} {Protein} {Complex} of {Tea} {Adulterant} {Dye} {Bismarck} {Brown} {Y} using {Experimental} and {Computational} {Methods}}, + url = {https://www.sciencedirect.com/science/article/pii/S1476927123001676}, + urldate = {2023-11-04}, + year = {2023} +} + +@article{sharaf_bridging_2023, + abstract = {The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientific knowledge and innovation and drive economic growth.}, + author = {Sharaf, Abdoallah and Ndiribe, Charlotte C. and Omotoriogun, Taiwo Crossby and Abueg, Linelle and Badaoui, Bouabid and Badiane Markey, Fatu J. and Beedessee, Girish and Diouf, Diaga and Duru, Vincent C. and Ebuzome, Chukwuike and Eziuzor, Samuel C. and Jaufeerally Fakim, Yasmina and Formenti, Giulio and Ghanmi, Nidhal and Guerfali, Fatma Zahra and Houaga, Isidore and Ideozu, Justin Eze and Katee, Sally Mueni and Khayi, Slimane and Kuja, Josiah O. and Kwon-Ndung, Emmanuel Hala and Marks, Rose A. and Moila, Acclaim M. and Mungloo-Dilmohamud, Zahra and Muzemil, Sadik and Nigussie, Helen and Osuji, Julian O. and Ras, Verena and Tchiechoua, Yves H. and Zoclanclounon, Yedomon Ange Bovys and Tolley, Krystal A. and Ziyomo, Cathrine and Mapholi, Ntanganedzeni and Muigai, Anne W. T. and Djikeng, Appolinaire and Ebenezer, ThankGod Echezona}, + copyright = {2023 Springer Nature America, Inc.}, + doi = {10.1038/s41587-023-01933-2}, + issn = {1546-1696}, + journal = {Nature Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Agricultural genetics, Communication and replication, Developing world, Education, Plant genetics}, + language = {en}, + month = {September}, + note = {Number: 9 +Publisher: Nature Publishing Group}, + number = {9}, + pages = {1348--1354}, + title = {Bridging the gap in {African} biodiversity genomics and bioinformatics}, + url = {https://www.nature.com/articles/s41587-023-01933-2}, + urldate = {2023-09-17}, + volume = {41}, + year = {2023} +} + @article{sharma_pan-cancer_2019, abstract = {Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, RNA folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous mutations found in human cancer and characterize their properties. We provide the user-friendly, comprehensive resource for synonymous mutations in cancer, SynMICdb (http://SynMICdb.dkfz.de), which also contains orthogonal information about gene annotation, recurrence, mutation loads, cancer association, conservation, alternative events, impact on mRNA structure and a SynMICdb score. Notably, synonymous and missense mutations are depleted at the 5'-end of the coding sequence as well as at the ends of internal exons independent of mutational signatures. For patient-derived synonymous mutations in the oncogene KRAS, we indicate that single point mutations can have a relevant impact on expression as well as on mRNA secondary structure., Synonymous mutations do not alter amino acid sequence but may exert oncogenic effects in other ways. Here, the authors present a catalogue of synonymous mutations in cancer and characterise their properties.}, author = {Sharma, Yogita and Miladi, Milad and Dukare, Sandeep and Boulay, Karine and Caudron-Herger, Maiwen and Groß, Matthias and Backofen, Rolf and Diederichs, Sven}, @@ -3775,19 +9452,51 @@ @article{sharma_pan-cancer_2019 year = {2019} } -@article{shi_recapitulating_2022, - author = {Shi, Shaojun and Verstegen, Monique MA and Roest, Henk P and Ardisasmita, Arif I and Cao, Wanlu and Roos, Floris JM and de Ruiter, Petra E and Niemeijer, Marije and Pan, Qiuwei and IJzermans, Jan NM and {others}}, - journal = {Cellular and Molecular Gastroenterology and Hepatology}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - note = {Publisher: Elsevier}, - number = {2}, - pages = {541--564}, - title = {Recapitulating {Cholangiopathy}-{Associated} {Necroptotic} {Cell} {Death} {In} {Vitro} {Using} {Human} {Cholangiocyte} {Organoids}}, - volume = {13}, - year = {2022} -} +@article{sheikh_volatile_2023, + abstract = {The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycete-caused diseases, such as Pythium myriotylum-caused rhizome rot in ginger, leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using Nicotiana benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass contents. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stresses, and the mechanisms of action of P. oligandrum as a biocontrol agent. +IMPORTANCE Plant growth promotion plays a vital role in enhancing production of agricultural crops, and Pythium oligandrum is known for its plant growth-promoting potential through production of auxins and induction of resistance by elicitors. This study highlights the significance of P. oligandrum-produced VOCs in plant growth promotion and disease resistance. Transcriptomic analyses of leaves of ginger plants exposed to P. oligandrum VOCs revealed the upregulation of genes involved in plant growth hormone signaling and stress responses. Moreover, the concentration of growth hormones significantly increased in P. oligandrum VOC-exposed ginger plants. Additionally, the disease severity was reduced in P. myriotylum-infected ginger plants exposed to P. oligandrum VOCs. In ginger, P. myriotylum-caused rhizome rot disease results in severe losses, and biocontrol has a role as part of an integrated pest management strategy for rhizome rot disease. Overall, growth enhancement and disease reduction in plants exposed to P. oligandrum-produced VOCs contribute to its role as a biocontrol agent.}, + author = {Sheikh, Taha Majid Mahmood and Zhou, Dongmei and Ali, Haider and Hussain, Sarfraz and Wang, Nan and Chen, Siqiao and Zhao, Yishen and Wen, Xian and Wang, Xiaoyu and Zhang, Jinfeng and Wang, Lunji and Deng, Sheng and Feng, Hui and Raza, Waseem and Fu, Pengxiao and Peng, Hao and Wei, Lihui and Daly, Paul}, + doi = {10.1128/spectrum.01510-23}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01510--23}, + title = {Volatile {Organic} {Compounds} {Emitted} by the {Biocontrol} {Agent} {Pythium} oligandrum {Contribute} to {Ginger} {Plant} {Growth} and {Disease} {Resistance}}, + url = {https://journals.asm.org/doi/10.1128/spectrum.01510-23}, + urldate = {2023-08-09}, + volume = {0}, + year = {2023} +} + +@article{shi_modeling_2023, + abstract = {Background +Ischemia of the bile duct is a common feature in liver disease and transplantation, which represents a major cause of morbidity and mortality, especially after liver transplantation. Detailed knowledge of its pathogenesis remains incomplete due to the lack of appropriate in vitro models. +Methods +To recapitulate biliary damage induced by ischemia and reperfusion in vitro, human intrahepatic cholangiocyte organoids (ICOs) were grown at low oxygen levels of 1\% up to 72 h, followed by re-oxygenation at normal levels. +Findings +ICOs stressed by ischemia and subsequent re-oxygenation represented the dynamic change in biliary cell proliferation, upregulation of epithelial–mesenchymal transition (EMT)-associated markers, and the evocation of phase-dependent cell death programs similar to what is described in patients. Clinical-grade alpha-1 antitrypsin was identified as a potent inhibitor of both ischemia-induced apoptosis and necroptosis. +Interpretation +These findings demonstrate that ICOs recapitulate ischemic cholangiopathy in vitro and enable drug assessment studies for the discovery of new therapeutics for ischemic cholangiopathies. +Funding +Dutch Digestive Foundation MLDS D16-26; TKI-LSH (Topconsortium Kennis en Innovatie-Life Sciences \& Health) grant RELOAD, EMC-LSH19002; Medical Delta program “Regenerative Medicine 4D”; China Scholarship Council No. 201706230252.}, + author = {Shi, Shaojun and Roest, Henk P. and van den Bosch, Thierry P. P. and Bijvelds, Marcel J. C. and Boehnert, Markus U. and de Jonge, Jeroen and Dekker, Sven O. and de Vries, Antoine A. F. and de Jonge, Hugo R. and Verstegen, Monique M. A. and van der Laan, Luc J. W.}, + doi = {10.1016/j.ebiom.2022.104431}, + issn = {2352-3964}, + journal = {eBioMedicine}, + keywords = {{\textgreater}UseGalaxy.eu, Biliary injury, Drug screening, Ischemia-reperfusion injury, Liver transplantation, Organoid}, + language = {en}, + month = {February}, + pages = {104431}, + title = {Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents}, + url = {https://www.sciencedirect.com/science/article/pii/S2352396422006132}, + urldate = {2023-03-15}, + volume = {88}, + year = {2023} +} -@article{shi_recapitulating_2022-1, +@article{shi_recapitulating_2022, author = {Shi, Shaojun and Verstegen, Monique M. A. and Roest, Henk P. and Ardisasmita, Arif I. and Cao, Wanlu and Roos, Floris J. M. and Ruiter, Petra E. de and Niemeijer, Marije and Pan, Qiuwei and IJzermans, Jan N. M. and Laan, Luc J. W. van der}, doi = {10.1016/j.jcmgh.2021.10.009}, journal = {Cellular and Molecular Gastroenterology and Hepatology}, @@ -3801,6 +9510,48 @@ @article{shi_recapitulating_2022-1 year = {2022} } +@article{siatra_return_2023, + abstract = {The single curative measure for heart failure patients is a heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have identified a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes, in vivo, in vitro and ex vivo. Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the center of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues. The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.}, + author = {Siatra, Panagiota and Vatsellas, Giannis and Chatzianastasiou, Athanasia and Balafas, Evangelos and Manolakou, Theodora and Papapetropoulos, Andreas and Agapaki, Anna and Mouchtouri, Eleni-Taxiarchia and Ruchaya, Prashant J. and Korovesi, Artemis G. and Mavroidis, Manolis and Thanos, Dimitrios and Beis, Dimitris and Kokkinopoulos, Ioannis}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41536-023-00280-9}, + issn = {2057-3995}, + journal = {npj Regenerative Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Stem cells}, + language = {en}, + month = {March}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--15}, + title = {Return of the {Tbx5}; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart}, + url = {https://www.nature.com/articles/s41536-023-00280-9}, + urldate = {2023-03-15}, + volume = {8}, + year = {2023} +} + +@article{silva_comparative_2024, + abstract = {We explored the metabolic integration of Blattella germanica and its obligate endosymbiont Blattabacterium cuenoti by the transcriptomic analysis of the fat body of quasi-aposymbiotic cockroaches, where the endosymbionts were almost entirely removed with rifampicin. Fat bodies from quasi-aposymbiotic insects displayed large differences in gene expression compared to controls. In quasi-aposymbionts, the metabolism of phenylalanine and tyrosine involved in cuticle sclerotization and pigmentation increased drastically to compensate for the deficiency in the biosynthesis of these amino acids by the endosymbionts. On the other hand, the uricolytic pathway and the biosynthesis of uric acid were severely decreased, probably because the reduced population of endosymbionts was unable to metabolize urea to ammonia. Metabolite transporters that could be involved in the endosymbiosis process were identified. Immune system and antimicrobial peptide (AMP) gene expression was also reduced in quasi-aposymbionts, genes encoding peptidoglycan-recognition proteins, which may provide clues for the maintenance of the symbiotic relationship, as well as three AMP genes whose involvement in the symbiotic relationship will require additional analysis. Finally, a search for AMP-like factors that could be involved in controlling the endosymbiont identified two orphan genes encoding proteins smaller than 200 amino acids underexpressed in quasi-aposymbionts, suggesting a role in the host–endosymbiont relationship.}, + author = {Silva, Francisco J. and Domínguez-Santos, Rebeca and Latorre, Amparo and García-Ferris, Carlos}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25084228}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Blattabacterium}, \textit{Blattella germanica}, {\textgreater}UseGalaxy.eu, antimicrobial peptides, cuticle, fat body, metabolite transporters, peptidoglycan-recognition proteins, transcriptome, tyrosine metabolism, uricolytic pathway}, + language = {en}, + month = {January}, + note = {Number: 8 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {8}, + pages = {4228}, + title = {Comparative {Transcriptomics} of {Fat} {Bodies} between {Symbiotic} and {Quasi}-{Aposymbiotic} {Adult} {Females} of {Blattella} germanica with {Emphasis} on the {Metabolic} {Integration} with {Its} {Endosymbiont} {Blattabacterium} and {Its} {Immune} {System}}, + url = {https://www.mdpi.com/1422-0067/25/8/4228}, + urldate = {2024-05-17}, + volume = {25}, + year = {2024} +} + @article{simon-chica_novel_2021, abstract = {Macrophages (MΦ), known for immunological roles such as phagocytosis and antigen presentation, have been found to electrotonically couple to cardiomyocytes (CM) of the atrio-ventricular node via Cx43, affecting cardiac conduction in isolated mouse hearts. Here, we characterise passive and active electrophysiological properties of murine cardiac resident MΦ, and model their potential electrophysiological relevance for CM.We combined classic electrophysiological approaches with 3 D florescence imaging, RNA-sequencing, pharmacological interventions and computer simulations. We used Cx3cr1eYFP/+ mice wherein cardiac MΦ were fluorescently labelled. FACS-purified fluorescent MΦ from mouse hearts were studied by whole-cell patch-clamp. MΦ electrophysiological properties include: membrane resistance 2.2 ± 0.1 GΩ (all data mean±SEM), capacitance 18.3 ± 0.1 pF, resting membrane potential -39.6 ± 0.3 mV, and several voltage-activated, outward or inwardly-rectifying potassium currents. Using ion channel blockers (barium, TEA, 4-AP, margatoxin, XEN-D0103, DIDS), flow cytometry, immuno-staining and RNA-sequencing, we identified Kv1.3, Kv1.5 and Kir2.1 as channels contributing to observed ion currents. MΦ displayed four patterns for outward and two for inward-rectifier potassium currents. Additionally, MΦ showed surface expression of Cx43, a prerequisite for homo- and/or heterotypic electrotonic coupling. Experimental results fed into development of an original computational model to describe cardiac MΦ electrophysiology. Computer simulations to quantitatively assess plausible effects of MΦ on electrotonically coupled CM showed that MΦ can depolarise resting CM, shorten early and prolong late action potential duration, with effects depending on coupling strength and individual MΦ electrophysiological properties, in particular resting membrane potential and presence/absence of Kir2.1.Our results provide a first electrophysiological characterisation of cardiac resident MΦ, and a computational model to quantitatively explore their relevance in the heterocellular heart. Future work will be focussed at distinguishing electrophysiological effects of MΦ–CM coupling on both cell types during steady-state and in patho-physiological remodelling, when immune cells change their phenotype, proliferate, and/or invade from external sources.Cardiac tissue contains resident macrophages (MΦ) which, beyond immunological and housekeeping roles, have been found to electrotonically couple via connexins to cardiomyocytes (CM), stabilising atrio-ventricular conduction at high excitation rates. Here, we characterise structure and electrophysiological function of murine cardiac MΦ and provide a computational model to quantitatively probe the potential relevance of MΦ-CM coupling for cardiac electrophysiology. We find that MΦ are unlikely to have major electrophysiological effects in normal tissue, where they would hasten early and slow late CM-repolarisation. Further work will address potential arrhythmogenicity of MΦ in patho-physiologically remodelled tissue containing elevated MΦ-numbers, incl. non-resident recruited cells.}, author = {Simon-Chica, Ana and Fernández, Marbely C and Wülfers, Eike M and Lother, Achim and Hilgendorf, Ingo and Seemann, Gunnar and Ravens, Ursula and Kohl, Peter and Schneider-Warme, Franziska}, @@ -3817,6 +9568,42 @@ @article{simon-chica_novel_2021 year = {2021} } +@article{singh_biophysical_2024, + abstract = {Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics–Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.}, + author = {Singh, Pratik and Gopi, Priyanka and Rani, Majji Sai Sudha and Singh, Shweta and Pandya, Prateek}, + copyright = {© 2024 John Wiley \& Sons Ltd.}, + doi = {10.1002/jmr.3076}, + issn = {1099-1352}, + journal = {Journal of Molecular Recognition}, + keywords = {{\textgreater}ChemicalToolbox, binding, circular dichorism spectroscopy, conformational analysis, fluorescence spectroscopy, human serum albumin, molecular simulations, quantum mechanical calculations, tetramethrin, thermodynamics, toxicity prediction}, + language = {en}, + month = {February}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmr.3076}, + number = {n/a}, + pages = {e3076}, + title = {Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmr.3076}, + urldate = {2024-02-20}, + volume = {n/a}, + year = {2024} +} + +@techreport{singh_identification_2022, + abstract = {Abstract +Approximately, 10\% of the world population is facing the challenge of food allergy in direct or indirect way. In this study, a genome-wide identification and annotation of the novel putative allergen from Almond is performed. Initially, the whole proteome of Almond (31,000 proteins) was scanned by Allergenonline, a publically available database of already reported allergens from different sources. The detailed analysis suggests that there are 430 putative allergens which reduced to 45 on motif-based screening using AllFam database. These predicted allergens are annotated for their function by using PFAM, GO databases and orthology analysis. To validate our prediction, we have used structural insights of allergen and antibody interactions for one of the predicted putative allergen protein, homologous to Pru ar 3.0101allergen from Apricot. The structure of putative allergen was modeled and molecular docking studies were performed against the antibody. The best docked conformation was subjected to molecular simulation studies to confirm the stable binding of these two molecules. This detailed analysis suggests that the identified allergen will show cross reactivity similar to Pru ar 3.0101 allergen from Apricot. This is one of the first report of identifying and annotating the homologous of Pru ar 3.0101 allergen in Almond.}, + author = {Singh, Arshwinder and Upadhyay, Atul Kumar}, + doi = {10.21203/rs.3.rs-1507943/v1}, + institution = {In Review}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + title = {Identification and annotation of peptide allergens in {Prunus} dulcis}, + type = {preprint}, + url = {https://www.researchsquare.com/article/rs-1507943/v1}, + urldate = {2022-09-24}, + year = {2022} +} + @article{soares_hierarchical_2021, author = {Soares, Mário A. F. and Soares, Diogo S. and Teixeira, Vera and Heskol, Abeer and Bressan, Raul Bardini and Pollard, Steven M. and Oliveira, Raquel A. and Castro, Diogo S.}, doi = {10.1101/gad.348174.120}, @@ -3831,6 +9618,133 @@ @article{soares_hierarchical_2021 year = {2021} } +@article{soggia_bioelectrochemical_2024, + abstract = {Microbial electrosynthesis (MES) cell use is an innovative approach for single-cell proteins (SCP) production. Coupling MES with the valorization of CO2 from anaerobic digestion and nitrogen from livestock effluents has beneficial environmental effects, reducing greenhouse gas emissions and nitrogen overloading. In addition, the reducing power needed can come from surplus renewable energy. In this study, MES with a biochar-functionalized cathode was tested at varying polarizations, i.e. non polarized, -0.6 V and -1.0 V vs Ag/AgCl, and biogas-derived CO2 and recovered ammonia from pig slurry was supplied. Negative polarization switched the microbial community from heterotrophic, typical of unpolarized MES, to a mix of both heterotrophic and autotrophic/electrotrophic communities at -0.6 V and to mainly autotrophic/electrotrophic at -1.0 V. The more negative polarization allowed the highest CO2 and N capture, i.e. 39 ± 2 \% of the supplied CO2, and 6.7 ± 0.8 \% supplied N. Microbial biomass characterization indicated a protein content on dry matter basis of 33.1 ± 1.3 \% (unpolarized), 43.2 ± 0.6 \% (-0.6 V) and 69.1 ± 1.0 \% (-1.0 V). The amino acids profiles investigated showed a high nutritional value of the produced biomass, not far from those of conventional protein sources used for producing feed/food.}, + author = {Soggia, Gabriele and Goglio, Andrea and Cristiani, Pierangela and Luciani, Ivan and Clagnan, Elisa and Adani, Fabrizio}, + doi = {10.1016/j.renene.2024.120761}, + issn = {0960-1481}, + journal = {Renewable Energy}, + keywords = {{\textgreater}UseGalaxy.eu, Ammonia, Biocathode, Carbon dioxide, Microbial electrosynthesis, Power-to-protein, Single-cell protein}, + month = {June}, + pages = {120761}, + title = {Bioelectrochemical protein production valorizing {NH3}-rich pig manure-derived wastewater and {CO2} from anaerobic digestion}, + url = {https://www.sciencedirect.com/science/article/pii/S0960148124008292}, + urldate = {2024-06-07}, + year = {2024} +} + +@article{soleau_first_2024, + abstract = {The emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype’s reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444\_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype.}, + author = {Soleau, Nathan and Ganet, Sarah and Werlen, Stéphanie and Collignon, Lia and Cointe, Aurélie and Bonacorsi, Stéphane and Sergentet, Delphine}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25105428}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Shiga-toxin-producing \textit{Escherichia coli} (STEC), characterization, emerging pathogen, first isolation, serotype O80:H2, whole-genome sequencing}, + language = {en}, + month = {January}, + note = {Number: 10 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {10}, + pages = {5428}, + shorttitle = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}}, + title = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}:{H2} in {French} {Healthy} {Cattle}: {Genomic} {Characterization} and {Phylogenetic} {Position}}, + url = {https://www.mdpi.com/1422-0067/25/10/5428}, + urldate = {2024-06-07}, + volume = {25}, + year = {2024} +} + +@book{somashekhar_proceedings_2023, + abstract = {This is an open access book. We are pleased to announce our 3rd International Conference on Bioinformatics and Data Science (ICBDS – 2022) and 9th International Conference on Public Mental Health and Neurosciences (ICPMN – 2022) which was a unique conference where we connectted Biological Function through Computational Genomics to the world of integrated medicine and therapeutics. Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. This science aims to understand the complex relationship between genotype and phenotype on a global (genome-wide) scale of different biological processes. Most researchers now study genes or regions on a “genome-wide” scale (i.e. all or multiple genes/regions at the same time), with the hope of narrowing them down to a list of candidate genes or regions to analyze in more detail. There are several specific functional genomics approaches depending on what we are focused on DNA level (genomics and epigenomics), RNA level (transcriptomics), protein level (proteomics), metabolite level (metabolomics) and phenotype level (phenomics). The recent trends in gene and genome editing technologies, promising genomic information can be modulated in the areas of medicine, agriculture and environment. Big data is a promising in many research areas, but still it is computationally challenging and non-availability of experts to handle big-data with reduced speed and cost. With the increasing use of advanced technology and the exploding amount of big-data in, it is imperative to introduce effective and efficient methods to handle big data using computing technologies. The big data analytics technique is required to solve the problems in bioinformatics such as the storage of vast information generated by analyzing the big-data. Big data analytics can examine large data sets, analyze and correlate genomic and proteomic information. Big data research finds a huge application in Neuroscience and Brain research. Our unique conference connects genomics to the world of genomics to integrated medicine including yogic sciences.}, + author = {Somashekhar, R. and Bagchi, Preenon and Rajesh, T. S. and Hill, Richard and Rossi, Kathryn}, + isbn = {978-94-6463-164-7}, + keywords = {{\textgreater}UseGalaxy.eu, Science / Life Sciences / Anatomy \& Physiology, Science / Life Sciences / Biology, Science / Life Sciences / Molecular Biology}, + language = {en}, + month = {June}, + note = {Google-Books-ID: GsPDEAAAQBAJ}, + publisher = {Springer Nature}, + title = {Proceedings of the {Joint} 3rd {International} {Conference} on {Bioinformatics} and {Data} {Science} ({ICBDS} 2022)}, + year = {2023} +} + +@article{soorni_genome-wide_2023, + abstract = {Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase.}, + author = {Soorni, Aboozar and Karimi, Marzieh and Al Sharif, Batoul and Habibi, Khashayar}, + doi = {10.1186/s12870-022-04031-8}, + issn = {1471-2229}, + journal = {BMC Plant Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Bolting, Lettuce, Long non-coding RNA, Regulation}, + language = {en}, + month = {January}, + number = {1}, + pages = {3}, + title = {Genome-wide screening and characterization of long noncoding {RNAs} involved in flowering/bolting of {Lactuca} sativa}, + url = {https://doi.org/10.1186/s12870-022-04031-8}, + urldate = {2023-03-15}, + volume = {23}, + year = {2023} +} + +@article{soriano-sexto_identification_2022, + abstract = {Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100\%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.}, + author = {Soriano-Sexto, Alejandro and Gallego, Diana and Leal, Fátima and Castejón-Fernández, Natalia and Navarrete, Rosa and Alcaide, Patricia and Couce, María L. and Martín-Hernández, Elena and Quijada-Fraile, Pilar and Peña-Quintana, Luis and Yahyaoui, Raquel and Correcher, Patricia and Ugarte, Magdalena and Rodríguez-Pombo, Pilar and Pérez, Belén}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms232112850}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, allelic expression imbalance, differential gene expression, inherited metabolic disorders, multi-omics, targeted transcriptomics}, + language = {en}, + month = {January}, + note = {Number: 21 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {21}, + pages = {12850}, + title = {Identification of {Clinical} {Variants} beyond the {Exome} in {Inborn} {Errors} of {Metabolism}}, + url = {https://www.mdpi.com/1422-0067/23/21/12850}, + urldate = {2022-11-06}, + volume = {23}, + year = {2022} +} + +@article{sozzoni_chromosome-level_2023, + abstract = {Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic, and temperate zones, suffered a steep population decline following an abrupt warming of sea surface temperature across its distribution range and is currently listed as Vulnerable by the International Union for the Conservation of Nature. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level reference genome and annotation for the black-legged kittiwake using a combination of Pacific Biosciences HiFi sequencing, Bionano optical maps, Hi-C reads, and RNA-Seq data. The final assembly spans 1.35 Gb across 32 chromosomes, with a scaffold N50 of 88.21 Mb and a BUSCO completeness of 97.4\%. This genome assembly substantially improves the quality of a previous draft genome, showing an approximately 5× increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the diversification of Charadriiformes. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype–genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems.}, + author = {Sozzoni, Marcella and Ferrer Obiol, Joan and Formenti, Giulio and Tigano, Anna and Paris, Josephine R and Balacco, Jennifer R and Jain, Nivesh and Tilley, Tatiana and Collins, Joanna and Sims, Ying and Wood, Jonathan and Benowitz-Fredericks, Z Morgan and Field, Kenneth A and Seyoum, Eyuel and Gatt, Marie Claire and Léandri-Breton, Don-Jean and Nakajima, Chinatsu and Whelan, Shannon and Gianfranceschi, Luca and Hatch, Scott A and Elliott, Kyle H and Shoji, Akiko and Cecere, Jacopo G and Jarvis, Erich D and Pilastro, Andrea and Rubolini, Diego}, + doi = {10.1093/gbe/evad153}, + issn = {1759-6653}, + journal = {Genome Biology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + number = {8}, + pages = {evad153}, + title = {A {Chromosome}-{Level} {Reference} {Genome} for the {Black}-{Legged} {Kittiwake} ({Rissa} tridactyla), a {Declining} {Circumpolar} {Seabird}}, + url = {https://doi.org/10.1093/gbe/evad153}, + urldate = {2023-10-28}, + volume = {15}, + year = {2023} +} + +@article{spano_comparative_2023, + abstract = {Globe artichoke ecotypes sanitized from plant pathogen infections are characterized by high vegetative vigor, productivity, and quality of capitula. The recent availability on the market of these plants has renewed the interest of farmers and pharmaceutical industries in the crop. Globe artichoke exhibits interesting nutraceutical properties due to the high content of health-promoting bioactive compounds (BACs), such as polyphenols, that could be extracted from waste biomass. The production of BACs depends on several factors including the plant portion considered, the globe artichoke variety/ecotype, and the physiological status of the plants, linked to biotic and abiotic stresses. We investigated the influence of viral infections on polyphenol accumulation in two Apulian late-flowering ecotypes “Locale di Mola tardivo” and “Troianella”, comparing sanitized virus-free material (S) vs. naturally virus-infected (non-sanitized, NS) plants. Transcriptome analysis of the two ecotypes highlighted that differentially expressed genes (DEGs), in the two tested conditions, were mainly involved in primary metabolism and processing of genetic/environmental information. The up-regulation of the genes related to the biosynthesis of secondary metabolites and the analysis of peroxidase activity suggested that their modulation is influenced by the phytosanitary status of the plant and is ecotype-dependent. Conversely, the phytochemical analysis showed a remarkable decrease in polyphenols and lignin accumulation in S artichokes compared to NS plants. This unique study analyzes the potential of growing vigorous, sanitized plants, in order to have high amounts of ‘soft and clean’ biomass, finalized for BAC extraction for nutraceutical purposes. This, in turn, opens new perspectives for a circular economy of sanitized artichokes, in line with the current phytosanitary standards and sustainable development goals.}, + author = {Spanò, Roberta and Fortunato, Stefania and Linsalata, Vito and D’Antuono, Isabella and Cardinali, Angela and de Pinto, Maria Concetta and Mascia, Tiziana}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/plants12081600}, + issn = {2223-7747}, + journal = {Plants}, + keywords = {{\textgreater}UseGalaxy.eu, artichoke ecotype, artichoke transcriptome, bioactive compounds, lignin, peroxidase, virus sanitation}, + language = {en}, + month = {January}, + note = {Number: 8 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {8}, + pages = {1600}, + title = {Comparative {Analysis} of {Bioactive} {Compounds} in {Two} {Globe} {Artichoke} {Ecotypes} {Sanitized} and {Non}-{Sanitized} from {Viral} {Infections}}, + url = {https://www.mdpi.com/2223-7747/12/8/1600}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + @article{spradling_mitochondrial_2021, author = {Spradling, Theresa A. and Place, Alexandra C. and Campbell, Ashley L. and Demastes, James W.}, doi = {10.1371/journal.pone.0254138}, @@ -3885,6 +9799,142 @@ @article{stephen_jr_comparative_2022 year = {2022} } +@article{stillger_neoadjuvant_2024, + abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.}, + author = {Stillger, Maren N. and Kurowski, Konrad and Bronsert, Peter and Brombacher, Eva and Kreutz, Clemens and Werner, Martin and Tang, Laura and Timme-Bronsert, Sylvia and Schilling, Oliver}, + copyright = {© 2024 The Authors. International Journal of Cancer published by John Wiley \& Sons Ltd on behalf of UICC.}, + doi = {10.1002/ijc.34867}, + issn = {1097-0215}, + journal = {International Journal of Cancer}, + keywords = {{\textgreater}UseGalaxy.eu, data-independent acquisition, mass spectrometry, neoadjuvant therapy, pancreatic ductal adenocarcinoma, proteogenomics}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ijc.34867}, + number = {12}, + pages = {2162--2175}, + title = {Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift {ECM} composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ijc.34867}, + urldate = {2024-05-17}, + volume = {154}, + year = {2024} +} + +@article{stojkovic_targeted_2024, + abstract = {Detrimental molecular processes in multiple sclerosis (MS) lead to the cellular accumulation of lipid peroxidation products and iron in the CNS, which represents the main driving force for ferroptosis. Ferroptosis is an iron-dependent form of regulated cell death, with proposed roles in neurodegeneration, oligodendrocyte loss and neuroinflammation in the pathogenesis of MS. Ferroptosis-related gene expression signature and molecular markers, which could reflect MS severity and progression, are currently understudied in humans. To tackle these challenges, we have applied a curated approach to create and experimentally analyze a comprehensive panel of ferroptosis-related genes covering a wide range of biological processes associated with ferroptosis. We performed the first ferroptosis-related targeted RNAseq on PBMCs from highly distinctive MS phenotype groups: mild relapsing–remitting (RR) (n = 24) and severe secondary progressive (SP) (n = 24), along with protein detection of GPX4 and products of lipid peroxidation (MDA and 4-HNE). Out of 138 genes, 26 were differentially expressed genes (DEGs), indicating changes in both pro- and anti-ferroptotic genes, representing a molecular signature associated with MS severity. The top three DEGs, as non-core ferroptosis genes, CDKN1A, MAP1B and EGLN2, were replicated by qPCR to validate findings in independent patient groups (16 RR and 16 SP MS). Co-expression and interactions of DEGs were presented as additional valuable assets for deeper understanding of molecular mechanisms and key targets related to MS severity. Our study integrates a wide genetic signature and biochemical markers related to ferroptosis in easily obtainable PBMCs of MS patients with clinical data and disease severity, thus providing novel molecular markers which can complement disease-related changes in the brain and undergo further research as potential therapeutic targets.}, + author = {Stojkovic, Ljiljana and Jovanovic, Ivan and Dincic, Evica and Djordjevic, Ana and Kuveljic, Jovana and Djuric, Tamara and Stankovic, Aleksandra and Vojinovic, Slobodan and Zivkovic, Maja}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25053016}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, PBMCs, ferroptosis, gene expression, multiple sclerosis, severity, targeted RNAseq}, + language = {en}, + month = {January}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {3016}, + title = {Targeted {RNAseq} {Revealed} the {Gene} {Expression} {Signature} of {Ferroptosis}-{Related} {Processes} {Associated} with {Disease} {Severity} in {Patients} with {Multiple} {Sclerosis}}, + url = {https://www.mdpi.com/1422-0067/25/5/3016}, + urldate = {2024-05-17}, + volume = {25}, + year = {2024} +} + +@article{strateva_analysis_2023, + abstract = {Abstract The present study aimed to explore the genotypic and phenotypic characteristics of biofilm formation in Bulgarian nosocomial Stenotrophomonas maltophilia isolates (n = 221) during the period 2011–2022, by screening for the presence of biofilm-associated genes (BAG) (spgM, rmlA and rpfF), their mutational variability, and assessment of the adherent growth on a polystyrene surface. The methodology included: PCR amplification, whole-genome sequencing (WGS) and crystal violet microtiter plate assay for biofilm quantification. The overall incidence of BAG was: spgM 98.6\%, rmlA 86\%, and rpfF 66.5\%. The most prevalent genotype was spgM+/rmlA+/rpfF+ (56.1\%), followed by spgM+/rmlA+/rpfF- (28.5\%), and spgM+/rmlA-/rpfF+ (9.5\%), with their significant predominance in lower respiratory tract isolates compared to those with other origin (P {\textless} 0.001). All strains examined were characterized as strong biofilm producers (OD550 from 0.224 ± 0.049 to 2.065 ± 0.023) with a single exception that showed a weak biofilm-forming ability (0.177 ± 0.024). No significant differences were observed in the biofilm formation according to the isolation source, as well as among COVID-19 and non-COVID-19 isolates (1.256 ± 0.028 vs. 1.348 ± 0.128, respectively). Also, no correlation was found between the biofilm amounts and the corresponding genotypes. WGS showed that the rmlA accumulated a larger number of variants (0.0086 per base) compared to the other BAG, suggesting no critical role of its product to the biofilm formation. Additionally, two of the isolates were found to harbour class 1 integrons (7-kb and 2.6-kb sized, respectively) containing sul1 in their 3′ conservative ends, which confers sulfonamide resistance. To the best of our knowledge, this is the first study on S. maltophilia biofilm formation in Bulgaria, which also identifies novel sequence types (ST819, ST820 and ST826). It demonstrates the complex nature of this adaptive mechanism in the multifactorial pathogenesis of biofilm-associated infections.}, + author = {Strateva, Tanya and Trifonova, Angelina and Sirakov, Ivo and Borisova, Dayana and Stancheva, Mikaela and Keuleyan, Emma and Setchanova, Lena and Peykov, Slavil}, + doi = {10.1556/030.2023.01920}, + issn = {1217-8950, 1588-2640}, + journal = {Acta Microbiologica et Immunologica Hungarica}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + note = {Publisher: Akadémiai Kiadó +Section: Acta Microbiologica et Immunologica Hungarica}, + number = {1}, + pages = {11--21}, + shorttitle = {Analysis of biofilm formation in nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria}}, + title = {Analysis of biofilm formation in nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria}: {An} 11-year study (2011–2022)}, + url = {https://akjournals.com/view/journals/030/70/1/article-p11.xml}, + urldate = {2023-03-15}, + volume = {70}, + year = {2023} +} + +@article{strateva_first_2024, + abstract = {Abstract Cefiderocol (CFDC) is a first-in-class siderophore cephalosporin with potent activity against multidrug-resistant Gram-negative bacteria including carbapenem-resistant Acinetobacter baumannii. The present study aimed to explore the CFDC resistance mechanisms of an extensively drug-resistant A. baumannii isolate from Bulgaria. The A. baumannii Aba52 strain (designated Aba52) was obtained in 2018 from a blood sample of a critically ill patient. The methodology included antimicrobial susceptibility testing, whole-genome sequencing (WGS), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), multilocus sequence typing, and phylogenomic analysis. The isolate demonstrated high-level resistance to CFDC (MIC = 64 mg L−1), resistance to carbapenems, aminoglycosides, fluoroquinolones, sulfamethoxazole-trimethoprim, and tigecycline, as well as susceptibility only to colistin. WGS-based resistome analysis revealed the existence of blaOXA-23, blaOXA-66 and blaADC-73. Seven non-conservative missense mutations affecting iron transport-related genes were detected: exbD4 (p.Ser61Pro), tonB2 (p.Ala268Val), bauA (p.Thr61Ala), ftsI (p.Ala515Val), piuA (p.Gly216Val), and feoB (p.Ser429Pro and p.Thr595Ala). A variety of virulence factors associated with adherence, biofilm formation, enzyme production, immune invasion, iron uptake, quorum sensing, and two-component regulatory systems were identified, suggesting a significant pathogenic potential of Aba52. The performed RT-qPCR analysis showed diminished (0.17) and absent expression of the pirA and piuA genes, respectively, encoding TonB-dependent siderophore receptors. Aba52 belonged to the widespread high-risk sequence type ST2 (Pasteur scheme). To the best of our knowledge, this is the first documented case of CFDC-resistant A. baumannii in Bulgaria even though, CFDC has never been applied in our country. The emerging resistance highlights the crucial need for nationwide surveillance targeting the implementation of novel antibiotics.}, + author = {Strateva, Tanya and Peykov, Slavil}, + doi = {10.1556/030.2024.02201}, + issn = {1217-8950, 1588-2640}, + journal = {Acta Microbiologica et Immunologica Hungarica}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + note = {Publisher: Akadémiai Kiadó +Section: Acta Microbiologica et Immunologica Hungarica}, + number = {aop}, + title = {First detection of a cefiderocol-resistant and extensively drug-resistant {Acinetobacter} baumannii clinical isolate in {Bulgaria}}, + url = {https://akjournals.com/view/journals/030/aop/article-10.1556-030.2024.02201/article-10.1556-030.2024.02201.xml}, + urldate = {2024-01-27}, + volume = {-1}, + year = {2024} +} + +@article{strateva_genotypic_2023, + abstract = {Abstract The present study aimed to explore the virulence characteristics in 221 Bulgarian nosocomial Stenotrophomonas maltophilia isolates (2011–2022) via screening for the presence of virulence genes, their mutational variability, and the corresponding enzyme activity. PCR amplification, enzymatic assays, whole-genome sequencing (WGS), and biofilm quantification on a polystyrene plate were performed. The incidence of virulence determinants was as follows: stmPr1 (encoding for the major extracellular protease StmPr1) 87.3\%, stmPr2 (minor extracellular protease StmPr2) 99.1\%, Smlt3773 locus (outer membrane esterase) 98.2\%, plcN1 (non-hemolytic phospholipase C) 99.1\%, and smf-1 (type-1 fimbriae, biofilm-related gene) 96.4\%. The 1621-bp allele of stmPr1 was most frequently found (61.1\%), followed by the combined allelic variant (17.6\%), stmPr1-negative genotype (12.7\%), and 868-bp allele (8.6\%). Protease, esterase, and lecithinase activity was observed in 95\%, 98.2\%, and 17.2\% of the isolates, respectively. The WGS-subjected isolates (n = 9) formed two groups. Five isolates possessed only the 1621-bp variant of stmPr1, higher biofilm formation ability (Optical Density at λ = 550 nm (OD550): 1.253–1.789), as well as a low number of mutations in the protease genes and smf-1. Three other isolates had only the 868-bp variant, weaker biofilm production (OD550: 0.788–1.108), and higher number of mutations within these genes. The only weak biofilm producer (OD550 = 0.177) had no stmPr1 alleles. In conclusion, the similar PCR detection rates did not allow differentiation of the isolates. In contrast, WGS permitted stmPr1 alleles-based differentiation. To the best of our knowledge, this is the first Bulgarian study presenting genotypic and phenotypic insights into virulence factors of S. maltophilia isolates.}, + author = {Strateva, Tanya and Trifonova, Angelina and Stratev, Alexander and Peykov, Slavil}, + doi = {10.1556/030.2023.02059}, + issn = {1217-8950, 1588-2640}, + journal = {Acta Microbiologica et Immunologica Hungarica}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Publisher: Akadémiai Kiadó +Section: Acta Microbiologica et Immunologica Hungarica}, + number = {aop}, + title = {Genotypic and phenotypic insights into virulence factors of nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria} (2011–2022)}, + url = {https://akjournals.com/view/journals/030/aop/article-10.1556-030.2023.02059/article-10.1556-030.2023.02059.xml}, + urldate = {2023-07-31}, + volume = {-1}, + year = {2023} +} + +@article{subramoney_identification_2022, + abstract = {The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS-CoV-2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID-19 real-time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS-CoV-2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole-genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0\% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9\% (173/175) of samples, of which 88.0\% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7\%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5\%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS-CoV-2 will be beneficial in limited-resource settings.}, + author = {Subramoney, Kathleen and Mtileni, Nkhensani and Bharuthram, Avani and Davis, Ashlyn and Kalenga, Beauty and Rikhotso, Mikateko and Maphahlele, Mpho and Giandhari, Jennifer and Naidoo, Yeshnee and Pillay, Sureshnee and Ramphal, Upasana and Ramphal, Yajna and Tegally, Houriiyah and Wilkinson, Eduan and Mohale, Thabo and Ismail, Arshad and Mashishi, Bonolo and Mbenenge, Nonhlanhla and de Oliveira, Tulio and Makatini, Zinhle and Fielding, Burtram C. and Treurnicht, Florette K. and Africa, Network for Genomics Surveillance in South}, + doi = {10.1002/jmv.27797}, + issn = {1096-9071}, + journal = {Journal of Medical Virology}, + keywords = {{\textgreater}UseGalaxy.eu, Omicron BA.1, SARS-CoV-2, genotyping, variants of concern}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.27797}, + number = {8}, + pages = {3676--3684}, + title = {Identification of {SARS}-{CoV}-2 {Omicron} variant using spike gene target failure and genotyping assays, {Gauteng}, {South} {Africa}, 2021}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27797}, + urldate = {2022-09-24}, + volume = {94}, + year = {2022} +} + +@article{subramoney_sars-cov-2_2023, + abstract = {Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respiratory samples, from individuals of all ages, received at the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic hospital, Gauteng, South Africa, from June 2020 to May 2022. Single nucleotide polymorphism (SNP) assays and whole genome sequencing were performed on a random selection of SARS-CoV-2 positive samples. The allele frequency (AF) was determined using TaqMan Genotyper software for SNP PCR analysis and galaxy.eu for analysis of FASTQ reads from sequencing. The SNP assays identified 5.3\% (50/948) of Delta cases with heterogeneity at delY144 (4\%; 2/50), E484Q (6\%; 3/50), N501Y (2\%; 1/50) and P681H (88\%; 44/50), however only heterogeneity for E484Q and delY144 were confirmed by sequencing. From sequencing we identified 9\% (210/2381) of cases with Beta, Delta, Omicron BA.1, BA.2.15, and BA.4 lineages that had heterogeneity in the S protein. Heterogeneity was primarily identified at positions 19 (1.4\%) with T19IR (AF 0.2–0.7), 371 (92.3\%) with S371FP (AF 0.1–1.0), and 484 (1.9\%) with E484AK (0.2–0.7), E484AQ (AF 0.4–0.5) and E484KQ (AF 0.1–0.4). Mutations at heterozygous amino acid positions 19, 371 and 484 are known antibody escape mutations, however the impact of the combination of multiple substitutions identified at the same position is unknown. Therefore, we hypothesise that intra-host SARS-CoV-2 quasispecies with heterogeneity in the S protein facilitate competitive advantage of variants that can completely/partially evade host’s natural and vaccine-induced immune responses.}, + author = {Subramoney, Kathleen and Mtileni, Nkhensani and Davis, Ashlyn and Giandhari, Jennifer and Tegally, Houriiyah and Wilkinson, Eduan and Naidoo, Yeshnee and Ramphal, Yajna and Pillay, Sureshnee and Ramphal, Upasana and Simane, Andiswa and Reddy, Bhaveshan and Mashishi, Bonolo and Mbenenge, Nonhlanhla and Oliveira, Tulio de and Fielding, Burtram C. and Treurnicht, Florette K.}, + doi = {10.1371/journal.pone.0286373}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Antibodies, Microbial mutation, Mutation, Mutation detection, Respiratory infections, SARS CoV 2, Single nucleotide polymorphisms, Substitution mutation}, + language = {en}, + month = {May}, + note = {Publisher: Public Library of Science}, + number = {5}, + pages = {e0286373}, + title = {{SARS}-{CoV}-2 spike protein diversity at an intra-host level, among {SARS}-{CoV}-2 infected individuals in {South} {Africa}, 2020 to 2022}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286373}, + urldate = {2023-06-03}, + volume = {18}, + year = {2023} +} + @article{sun_complete_2021, author = {Sun, Shu-Wei and Huang, Jing-Chao and Liu, Yan-Qun}, doi = {10.1080/23802359.2021.1945975}, @@ -3915,6 +9965,40 @@ @article{sun_stencil_2022 year = {2022} } +@article{sundar_-silico_2023, + abstract = {The emergence of drug resistant Mycobacterium tuberculosis strains increases the burden on the treatment of tuberculosis. In this study, through in-silico transcriptome analysis of drug-treated M. tuberculosis samples, novel drug targets for the treatment of drug resistance in tuberculosis were identified. Gene expression datasets of tuberculosis patients samples treated with different antibiotics (Isoniazid, Rifampicin, Pyrazinamide, Bedaquiline and Linezolid) were considered in this study. DESeq2 was used to identify the differentially regulated genes. Novel genes which were up-regulated during antibiotic treatment were identified which could be antibiotic resistance factors. Further, to understand the resistance mechanism of the novel genes, we performed gene ontology and gene network analysis for the differentially up-regulated genes. Thus, the in-silico transcriptome analysis paves way for a deeper understanding of the antibiotic resistance in M. tuberculosis.}, + author = {Sundar, Shobana}, + doi = {10.1016/j.ijtb.2023.06.010}, + issn = {0019-5707}, + journal = {Indian Journal of Tuberculosis}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic resistance, Transcriptome}, + language = {en}, + month = {June}, + title = {In-silico transcriptome analysis of antibiotic-treated {Mycobacterium} tuberculosis identifies novel antibiotic resistance factors}, + url = {https://www.sciencedirect.com/science/article/pii/S0019570723001166}, + urldate = {2023-07-31}, + year = {2023} +} + +@incollection{suzuki_genomic_2023, + abstract = {Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.}, + address = {New York, NY}, + author = {Suzuki, Masato and Hashimoto, Yusuke and Hirabayashi, Aki and Yahara, Koji and Yoshida, Mitsunori and Fukano, Hanako and Hoshino, Yoshihiko and Shibayama, Keigo and Tomita, Haruyoshi}, + booktitle = {Nanopore {Sequencing}: {Methods} and {Protocols}}, + doi = {10.1007/978-1-0716-2996-3_16}, + editor = {Arakawa, Kazuharu}, + isbn = {978-1-07-162996-3}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Antimicrobial resistance, Chromosome, ESKAPE pathogens, Mobile genetic element, Mycobacteria, Phage, Plasmid, Virulence}, + language = {en}, + pages = {227--246}, + publisher = {Springer US}, + series = {Methods in {Molecular} {Biology}}, + title = {Genomic {Epidemiological} {Analysis} of {Antimicrobial}-{Resistant} {Bacteria} with {Nanopore} {Sequencing}}, + url = {https://doi.org/10.1007/978-1-0716-2996-3_16}, + urldate = {2023-03-15}, + year = {2023} +} + @article{szachniuk_rnapolis:_2019, author = {Szachniuk, Marta}, doi = {10.2478/fcds-2019-0012}, @@ -3932,6 +10016,46 @@ @article{szachniuk_rnapolis:_2019 year = {2019} } +@article{tabarelli_chasing_2022, + abstract = {The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome assembly for apple was released and is now considered to be the reference genome. Moreover, as in several other species, the identified TCP genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the TCP gene family based on the latest genome assembly of M. × domestica. Compared to the previous classification, the number of TCP genes decreased from 52 to 40 as a result of the addition of three sequences and the deduction of 15. An analysis of the intragenic identity led to the identification of 15 pairs of orthologs, shedding light on the forces that shaped the evolution of this gene family. Furthermore, a revised nomenclature system is proposed that is based both on the intragenic identity and the homology with Arabidopsis thaliana (A. thaliana) TCPs in an effort to set a common standard for the TCP classification that will facilitate any future interspecific analysis.}, + author = {Tabarelli, Mattia and Malnoy, Mickael and Janik, Katrin}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/genes13101696}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {\textit{Malus} × \textit{domestica}, \textit{TCP} gene family, {\textgreater}UseGalaxy.eu, GDDH13v1.1 genome assembly}, + language = {en}, + month = {October}, + note = {Number: 10 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {10}, + pages = {1696}, + shorttitle = {Chasing {Consistency}}, + title = {Chasing {Consistency}: {An} {Update} of the {TCP} {Gene} {Family} of {Malus} × {Domestica}}, + url = {https://www.mdpi.com/2073-4425/13/10/1696}, + urldate = {2022-11-06}, + volume = {13}, + year = {2022} +} + +@article{tajuddin_genomic_2023, + abstract = {Vibrio alginolyticus is a Gram-negative bacterium commonly associated with mackerel poisoning. A bacteriophage that specifically targets and lyses this bacterium could be employed as a biocontrol agent for treating the bacterial infection or improving the shelf-life of mackerel products. However, only a few well-characterized V. alginolyticus phages have been reported in the literature. In this study, a novel lytic phage, named ΦImVa-1, specifically infecting V. alginolyticus strain ATCC 17749, was isolated from Indian mackerel. The phage has a short latent period of 15 min and a burst size of approximately 66 particles per infected bacterium. ΦImVa-1 remained stable for 2 h at a wide temperature (27–75 °C) and within a pH range of 5 to 10. Transmission electron microscopy revealed that ΦImVa-1 has an icosahedral head of approximately 60 nm in diameter with a short tail, resembling those in the Schitoviridae family. High throughput sequencing and bioinformatics analysis elucidated that ΦImVa-1 has a linear dsDNA genome of 77,479 base pairs (bp), with a G + C content of {\textasciitilde} 38.72\% and 110 predicted gene coding regions (106 open reading frames and four tRNAs). The genome contains an extremely large virion-associated RNA polymerase gene and two smaller non-virion-associated RNA polymerase genes, which are hallmarks of schitoviruses. No antibiotic genes were found in the ΦImVa-1 genome. This is the first paper describing the biological properties, morphology, and the complete genome of a V. alginolyticus-infecting schitovirus. When raw mackerel fish flesh slices were treated with ΦImVa-1, the pathogen loads reduced significantly, demonstrating the potential of the phage as a biocontrol agent for V. alginolyticus strain ATCC 17749 in the food.}, + author = {Tajuddin, Sofiah and Khan, Asif M. and Chong, Li Chuin and Wong, Chuan Loo and Tan, Jia Sen and Ina-Salwany, Md Yasin and Lau, Han Yih and Ho, Kok Lian and Mariatulqabtiah, Abdul Razak and Tan, Wen Siang}, + doi = {10.1007/s00253-022-12312-3}, + issn = {1432-0614}, + journal = {Applied Microbiology and Biotechnology}, + keywords = {{\textgreater}Pasteur, {\textgreater}UseGalaxy.eu, Bacteriophage, Biocontrol, Bioinformatics, Food poisoning, Genome, Schitoviridae, Vibrio alginolyticus, Vibriosis}, + language = {en}, + month = {February}, + number = {2}, + pages = {749--768}, + title = {Genomic analysis and biological characterization of a novel {Schitoviridae} phage infecting {Vibrio} alginolyticus}, + url = {https://doi.org/10.1007/s00253-022-12312-3}, + urldate = {2023-07-31}, + volume = {107}, + year = {2023} +} + @article{tangaro_laniakea_2020, abstract = {AbstractBackground. While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios wher}, author = {Tangaro, Marco Antonio and Donvito, Giacinto and Antonacci, Marica and Chiara, Matteo and Mandreoli, Pietro and Pesole, Graziano and Zambelli, Federico}, @@ -4013,6 +10137,24 @@ @article{tekman_single-cell_2020 year = {2020} } +@article{tetzlaff_small_2024, + abstract = {The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii’s block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.}, + author = {Tetzlaff, Sabrina and Hillebrand, Arne and Drakoulis, Nikiforos and Gluhic, Zala and Maschmann, Sascha and Lyko, Peter and Wicke, Susann and Schmitz-Linneweber, Christian}, + doi = {10.7554/eLife.95407}, + editor = {Nicolás, Marisa and Sussel, Lori}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu, Toxoplasma gondii, mitochondria, mitogenome, polysomes, rRNA, rribosome}, + month = {February}, + note = {Publisher: eLife Sciences Publications, Ltd}, + pages = {e95407}, + title = {Small {RNAs} from mitochondrial genome recombination sites are incorporated into {T}. gondii mitoribosomes}, + url = {https://doi.org/10.7554/eLife.95407}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + @article{thanki_aequatus:_2018, abstract = {Background. Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, inclu}, author = {Thanki, Anil S. and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert P.}, @@ -4028,6 +10170,54 @@ @article{thanki_aequatus:_2018 year = {2018} } +@article{thompson_draft_2023, + author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, + doi = {10.1128/mra.00470-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + note = {Publisher: American Society for Microbiology}, + number = {1}, + pages = {e00470--23}, + title = {Draft genome sequence of {Amycolatopsis} camponoti {RTGN1}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00470-23}, + urldate = {2024-05-17}, + volume = {13}, + year = {2023} +} + +@article{thompson_draft_2023-1, + author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, + doi = {10.1128/mra.00486-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + note = {Publisher: American Society for Microbiology}, + number = {2}, + pages = {e00486--23}, + title = {Draft genome sequence of {Streptomyces} poriferorum {RTGN2}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00486-23}, + urldate = {2024-05-17}, + volume = {13}, + year = {2023} +} + +@article{thompson_draft_2024, + author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, + doi = {10.1128/mra.01132-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: American Society for Microbiology}, + number = {2}, + pages = {e01132--23}, + title = {Draft genome sequences of five {Mycobacterium} strains, isolated from {Alnus} glutinosa root nodules}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01132-23}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + @article{torres-paz_maternally_2019, abstract = {Sequential developmental events, starting from the moment of fertilization, are crucial for the acquisition of animal body plan. Subtle modifications in such early events are likely to have major impacts in later morphogenesis, bringing along morphological diversification. Here, comparing the blind cave and the surface morphotypes of Astyanax mexicanus fish, we found heterochronies during gastrulation that produce organizer and axial mesoderm tissues with different properties (including differences in the expression of dkk1b) that may have contributed to cavefish brain evolution. These variations observed during gastrulation depend fully on maternal factors. The developmental evolution of retinal morphogenesis and hypothalamic patterning are among those traits that retained significant maternal influence at larval stages. Transcriptomic analysis of fertilized eggs from both morphotypes and reciprocal F1 hybrids showed a strong and specific maternal signature. Our work strongly suggests that maternal effect genes and developmental heterochronies that occur during gastrulation have impacted morphological brain change during cavefish evolution.}, author = {Torres-Paz, Jorge and Leclercq, Julien and Rétaux, Sylvie}, @@ -4057,6 +10247,99 @@ @article{tosar_ri-sec-seq_2021 year = {2021} } +@article{toth_divergence_2024, + abstract = {Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon ‘Candidatus Phytoplasma asteris’ were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of ‘Ca. P. asteris’ and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.}, + author = {Toth, Rafael and Ilic, Anna-Marie and Huettel, Bruno and Duduk, Bojan and Kube, Michael}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms12051016}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, carrot, hybrid assembly, phylogeny, virulence factors}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {1016}, + title = {Divergence within the {Taxon} ‘{Candidatus} {Phytoplasma} asteris’ {Confirmed} by {Comparative} {Genome} {Analysis} of {Carrot} {Strains}}, + url = {https://www.mdpi.com/2076-2607/12/5/1016}, + urldate = {2024-06-07}, + volume = {12}, + year = {2024} +} + +@article{toth_genomic_2024, + abstract = {Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9\% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.}, + author = {Tóth, Kinga and Damjanova, Ivelina and Laczkó, Levente and Buzgó, Lilla and Lesinszki, Virág and Ungvári, Erika and Jánvári, Laura and Hanczvikkel, Adrienn and Tóth, Ákos and Szabó, Dóra}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13040363}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Escherichia coli}, \textit{bla}$_{\textrm{CTX-M-15}}$, \textit{bla}$_{\textrm{CTX-M-27}}$, {\textgreater}UseGalaxy.eu, C1-M27, C2/H30RX, ST131, long-read sequencing, whole genome sequencing (WGS)}, + language = {en}, + month = {April}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {363}, + title = {Genomic {Epidemiology} of {C2}/{H30Rx} and {C1}-{M27} {Subclades} of {Escherichia} coli {ST131} {Isolates} from {Clinical} {Blood} {Samples} in {Hungary}}, + url = {https://www.mdpi.com/2079-6382/13/4/363}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + +@article{trifonova_combination_2023, + abstract = {Background The SARS-CoV-2 virus significantly changed our knowledge about coronaviruses. The interplay between SARS-CoV-2 and the human host, the infection ranges from asymptomatic to lethal, and differences in the degree of disease severity are important examples.Methods In this retrospective study, 24 nasopharyngeal swabs from 21 out of 457 patients with SARS-CoV-2 infection were analysed by whole-genome sequencing. The principal selection criteria were the duration of infection and disease severity.Results Two co-occurring rare mutations in the SARS-CoV-2 M gene were detected in six samples. Three of these samples were collected from an immunocompromised patient with fatal outcome, two from an immunocompetent patient, and one from a patient with severe disease and fatal outcome, all with a prolonged course of infection.Conclusions Although this interesting finding was demonstrated in a small number of patients, the results increase the knowledge regarding the significance of mutations in the M gene of SARS-CoV-2 in the context of persistent infection and viral escape mechanisms.}, + author = {Trifonova, Angelina and Syarov, Atanas and Takov, Svetlomir and Angelov, Krassimir and Vazharova, Radoslava and Terzieva, Velislava}, + doi = {10.1080/23744235.2023.2238077}, + issn = {2374-4235}, + journal = {Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, M gene, SARS-CoV-2, mutation, prolonged infection}, + month = {July}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/23744235.2023.2238077}, + number = {0}, + pages = {1--5}, + pmid = {37493404}, + title = {Combination of two rare mutations in the {SARS}-{CoV}-2 {M} gene in patients with severe and prolonged {COVID}-19}, + url = {https://doi.org/10.1080/23744235.2023.2238077}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + +@article{trinh-minh_effect_2024, + abstract = {Objective.S100A4 is a DAMP protein. S100A4 is overexpressed in patients with systemic sclerosis (SSc), andlevels correlate with organ involvement and disease activity. S100A4−/−mice are protected fromfibrosis. The aim ofthis study was to assess the antifibrotic effects of anti-S100A4 monoclonal antibody (mAb) in murine models of SScand in precision cut skin slices of patients with SSc.Methods.The effects of anti-S100A4 mAbs were evaluated in a bleomycin-induced skinfibrosis model and inTsk-1 mice with a therapeutic dosing regimen. In addition, the effects of anti-S100A4 mAbs on precision cut SSc skinslices were analyzed by RNA sequencing.Results.Inhibition of S100A4 was effective in the treatment of pre-established bleomycin-induced skinfibrosis andin regression of pre-establishedfibrosis with reduced dermal thickening, myofibroblast counts, and collagen accumu-lation. Transcriptional profiling demonstrated targeting of multiple profibrotic and proinflammatory processes relevantto the pathogenesis of SSc on targeted S100A4 inhibition in a bleomycin-induced skinfibrosis model. Moreover, tar-geted S100A4 inhibition also modulated inflammation- andfibrosis-relevant gene sets in precision cut SSc skin slicesin an ex vivo trial approach. Selected downstream targets of S100A4, such as AMP-activated protein kinase,calsequestrin-1, and phosphorylated STAT3, were validated on the protein level, and STAT3 inhibition was shown toprevent the profibrotic effects of S100A4 onfibroblasts in human skin.Conclusion.Inhibition of S100A4 confers dual targeting of inflammatory andfibrotic pathways in complementarymouse models offibrosis and in SSc skin. These effects support the further development of anti-S100A4 mAbs asdisease-modifying targeted therapies for SSc.}, + author = {Trinh-Minh, Thuong and Györfi, Andrea Hermina and Tomcik, Michal and Tran-Manh, Cuong and Zhou, Xiang and Dickel, Nicholas and Tümerdem, Bilgesu Safak and Kreuter, Alexander and Burmann, Sven Niklas and Borchert, Signe Vedel and Hussain, Rizwan Iqbal and Hallén, Jonas and Klingelhöfer, Jörg and Kunz, Meik and Distler, Jörg H.W.}, + doi = {10.1002/art.42781}, + issn = {2326-5191}, + journal = {Arthritis and Rheumatology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + number = {5}, + pages = {783--795}, + title = {Effect of {Anti}-{S100A4} {Monoclonal} {Antibody} {Treatment} on {Experimental} {Skin} {Fibrosis} and {Systemic} {Sclerosis}–{Specific} {Transcriptional} {Signatures} in {Human} {Skin}}, + volume = {76}, + year = {2024} +} + +@article{tsai_biogenesis_2022, + author = {Tsai, Hsin-Yue and Cheng, Hsian-Tang and Tsai, Yi-Ting}, + doi = {10.1126/sciadv.abm0699}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Association for the Advancement of Science}, + number = {32}, + pages = {eabm0699}, + title = {Biogenesis of {C}. elegans spermatogenesis small {RNAs} is initiated by a zc3h12a-like ribonuclease}, + url = {https://www.science.org/doi/full/10.1126/sciadv.abm0699}, + urldate = {2022-09-24}, + volume = {8}, + year = {2022} +} + @article{tu_molecular_2021, author = {Tu, Zhiwei and Setlow, Peter and Brul, Stanley and Kramer, Gertjan}, doi = {10.3390/microorganisms9030667}, @@ -4092,6 +10375,68 @@ @article{uellendahl-werth_benchmark_2020 year = {2020} } +@phdthesis{ummethum_proximity_2024, + author = {Ummethum, Henning}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {February}, + school = {Ludwig-Maximilians-Universität München}, + title = {Proximity labeling as a tool to study transcription-replication interference}, + type = {Text.{PhDThesis}}, + url = {https://edoc.ub.uni-muenchen.de/33323/}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{umpeleva_identification_2024, + author = {Umpeleva, Tatiana and Chetverikova, Elena and Belyaev, Danila and Eremeeva, Natalya and Boteva, Tatiana and Golubeva, Ludmila and Vakhrusheva, Diana and Vasilieva, Irina}, + doi = {10.1128/spectrum.03749-23}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {3}, + pages = {e03749--23}, + title = {Identification of genetic determinants of bedaquiline resistance in {Mycobacterium} tuberculosis in {Ural} region, {Russia}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.03749-23}, + urldate = {2024-05-17}, + volume = {12}, + year = {2024} +} + +@article{valadez-moctezuma_first_2023, + abstract = {Although Opuntia is one of the most emblematic and promising crops in Mexico, no extensive genomic resources are available. Herein, we present the first transcriptomic datasets of three species of Opuntia. Comparative transcriptome profiling provides insights into the molecular and physiological functions between species and tissues. Total RNA from young cladodes and developing fruits of O. ficus-indica, O. robusta and O. joconostle was purified and sequenced by Massive Analysis of cDNA Ends technology, an RNA-seq variant. A total of 8383, 7890, and 5300 transcripts and GC content of 40.1, 39.9 and 40.1\% were obtained for the de novo assembly of O. ficus-indica, O. robusta and O. joconostle, respectively. For annotations, about 22.2–23.7\% of transcripts had matches in the UniProtKB/Swiss-Prot database. Moreover, the enriched 21 COG categories, 282 KEGG pathways and 2793 GO terms revealed that the transcriptomes obtained included functionally diverse genes in Opuntia. Differentially expressed transcripts (DETs) between fruit and cladode resulted in the enrichment of 13 significant KEGG pathways and 80 GO terms, where some genes viz. FULL, CYP75B1, and CMB1 were upregulated in the fruits of the three species. Between species, the most enriched GOs fell into the category of “Cellular Components”, which would explain the morphological and physiological differences between the three species. Moreover, DETs comparisons between fruit types and between cladodes were also reported. Overall, the transcriptomic data generated in this study provide the initial resources to understand the biology of Opuntia, offering new insight to understand its morphology, systematic and adaptation.}, + author = {Valadez-Moctezuma, Ernestina and Samah, Samir and Mascorro-Gallardo, J. Oscar and Marbán-Mendoza, Nahum and Aranda-Osorio, Gilberto and Flores-Girón, Emmanuel and Brito-Nájera, Guadalupe and Rodríguez de la O, José Luis}, + doi = {10.1007/s10722-022-01480-w}, + issn = {1573-5109}, + journal = {Genetic Resources and Crop Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, MACE, O. ficus-indica, O. joconostle, O. robusta, RNA-seq}, + language = {en}, + month = {March}, + number = {3}, + pages = {951--970}, + title = {The first transcriptomic analyses of fruits and cladodes for comparison between three species of {Opuntia}}, + url = {https://doi.org/10.1007/s10722-022-01480-w}, + urldate = {2023-07-31}, + volume = {70}, + year = {2023} +} + +@article{valadez-moctezuma_novo_2023, + abstract = {Although Agave angustifolia Haw is one of the most cultural and industrial promising species in Mexico, no extensive genomic resources were available. Herein, we explore the transcriptome data set of this species. Total RNA from stem, roots, young and mature leaves was purified and sequenced by NovaSeq6000 system. From the de novo assembly of A. angustifolia, a total of 358,170 transcripts with average length of 1117 bp, N50 of 858 bp, and GC mean content of 43.5\% were obtained. About 48.7\% of the transcripts had open reading frame (ORF). Hence, 63.4\% and 42.7\% of the ORFs were annotated using Blastp and Blastx against UniProtKB database, respectively, uncovering the presence of at least 29,273 genes in the A. angustifolia transcriptome. The six pairwise comparisons between plant tissues resulted in the identification of 123,181 differentially expressed transcripts (23,978 were upregulated and 79,203 were downregulated). Several carbohydrate metabolism pathways were significantly enriched from the comparisons between leaves and stems. Thus, genes regulated for the fructan, starch and sucrose biosynthesis were discussed. Furthermore, genes involved in cellulose synthesis were explored being the members of the cellulose synthase genes subfamily were highly expressed in young leaf, while the members of the cellulose synthase-like subfamily were preferentially expressed in mature leaf. Moreover, A. angustifolia transcriptome served for the identification of 30,766 SSR and 21,686 VNTR potential markers. Overall, the transcriptomic data generated in this study provide an invaluable resource to understand the biology of A. angustifolia, offering new insight to understand their physiology and adaptation.}, + author = {Valadez-Moctezuma, Ernestina and Samah, Samir and Mascorro-Gallardo, J. Oscar and Reynoso, José J. López and Marbán-Mendoza, Nahum and Aranda-Osorio, Gilberto and Brito-Nájera, Guadalupe}, + doi = {10.1007/s11816-023-00861-6}, + issn = {1863-5474}, + journal = {Plant Biotechnology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Agave, Cellulose, Fructan, Gene expression, RNA-seq, SSRs}, + language = {en}, + month = {September}, + title = {The de novo transcriptome assembly of {Agave} angustifolia {Haw}, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development}, + url = {https://doi.org/10.1007/s11816-023-00861-6}, + urldate = {2023-09-21}, + year = {2023} +} + @article{valsecchi_rna_2020, author = {Valsecchi, Claudia Isabelle Keller and Basilicata, M. Felicia and Georgiev, Plamen and Gaub, Aline and Seyfferth, Janine and Kulkarni, Tanvi and Panhale, Amol and Semplicio, Giuseppe and Manjunath, Vinitha and Holz, Herbert and Dasmeh, Pouria and Akhtar, Asifa}, doi = {10.1038/s41586-020-2935-z}, @@ -4104,6 +10449,38 @@ @article{valsecchi_rna_2020 year = {2020} } +@article{vaquero-sedas_epigenetic_2022, + abstract = {The epigenetic features of defined chromosomal domains condition their biochemical and functional properties. Therefore, there is considerable interest in studying the epigenetic marks present at relevant chromosomal loci. Telomeric regions, which include telomeres and subtelomeres, have been traditionally considered heterochromatic. However, whereas the heterochromatic nature of subtelomeres has been widely accepted, the epigenetic status of telomeres remains controversial. Here, we studied the epigenetic features of Arabidopsis (Arabidopsis thaliana) telomeres by analyzing multiple genome-wide ChIP-seq experiments. Our analyses revealed that Arabidopsis telomeres are not significantly enriched either in euchromatic marks like H3K4me2, H3K9ac, and H3K27me3 or in heterochromatic marks such as H3K27me1 and H3K9me2. Thus, telomeric regions in Arabidopsis have a bimodal chromatin organization with telomeres lacking significant levels of canonical euchromatic and heterochromatic marks followed by heterochromatic subtelomeres. Since heterochromatin is known to influence telomere function, the heterochromatic modifications present at Arabidopsis subtelomeres could play a relevant role in telomere biology.}, + author = {Vaquero-Sedas, María I and Vega-Palas, Miguel A}, + doi = {10.1093/plphys/kiac471}, + issn = {0032-0889}, + journal = {Plant Physiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + pages = {kiac471}, + title = {Epigenetic nature of {Arabidopsis} thaliana telomeres}, + url = {https://doi.org/10.1093/plphys/kiac471}, + urldate = {2022-11-06}, + year = {2022} +} + +@article{vergata_how_2023, + abstract = {Phylloremediation for the reduction of air particulate matter (PM) is an interesting opportunity to significantly contribute to improve the air quality of urban environment. The aim of this study was to: 1) gain insight into the gene regulatory networks modulating leaf responses to polluted air, 2) identify possible changes in the leaf microbiome due to particulate matter in the real urban environment. The leaf transcriptome and microbiome were analyzed for Photinia x fraseri L. plants cultivated for three months in pots in two close-by areas under different levels of air PMs (low and high). PCA and heat map analysis showed that 28 differentially expressed genes in common between the three pairwise comparisons were able to clearly discriminate plants under higher PM levels. The pollutants were mainly sensed by plants through a restructuring modification of cell wall and membrane due to the main repression of lipid desaturases. In addition, high PMs showed a clear repression of genes belonging to primary metabolism pathways involved in C assimilation. Microbiome analysis showed no significant changes in taxonomic diversity indexes for the bacterial communities, whereas fungi belonging to the genera Epicoccum and Dioszegia were differently affected by the different exposure to PM levels. A model of transcriptional regulation to air PMs in plants has been proposed.}, + author = {Vergata, Chiara and Contaldi, Felice and Baccelli, Ivan and Basso, Marcos Fernando and Santini, Alberto and Pecori, Francesco and Buti, Matteo and Mengoni, Alessio and Vaccaro, Francesca and Moura, Barbara Basso and Ferrini, Francesco and Martinelli, Federico}, + doi = {10.1016/j.envexpbot.2023.105313}, + issn = {0098-8472}, + journal = {Environmental and Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu, Co-expression analysis, Particulate matter, Photinia x fraseri, RNA-seq}, + language = {en}, + month = {May}, + pages = {105313}, + title = {How does particulate matter affect plant transcriptome and microbiome?}, + url = {https://www.sciencedirect.com/science/article/pii/S0098847223001089}, + urldate = {2023-06-05}, + volume = {209}, + year = {2023} +} + @article{verma_identification_2022, author = {Verma, Divya and Bagchi, Preenon and IA, Shylesh Murthy}, doi = {10.21203/rs.3.rs-1253773/v1}, @@ -4132,6 +10509,80 @@ @article{videm_chira_2021 year = {2021} } +@article{vieira_da_cruz_pyridylpiperazine_2024, + abstract = {Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump is the dominant constitutive system by which Enterobacterales like Escherichia coli and Klebsiella pneumoniae extrude antibiotics. Here, we describe the medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor. In vitro evaluation of BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression. Using cryo-EM, BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor. Finally, proof of concept studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection.}, + author = {Vieira Da Cruz, Anais and Jiménez-Castellanos, Juan-Carlos and Börnsen, Clara and Van Maele, Laurye and Compagne, Nina and Pradel, Elizabeth and Müller, Reinke T and Meurillon, Virginie and Soulard, Daphnée and Piveteau, Catherine and Biela, Alexandre and Dumont, Julie and Leroux, Florence and Deprez, Benoit and Willand, Nicolas and Pos, Klaas M and Frangakis, Achilleas S and Hartkoorn, Ruben C and Flipo, Marion}, + doi = {10.1038/s44321-023-00007-9}, + issn = {1757-4676}, + journal = {EMBO Molecular Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, AcrAB-TolC, Antibiotic Efflux Pump, Antimicrobial Resistance, Cryo-EM, Efflux Pump Inhibitor}, + month = {January}, + note = {Num Pages: 111 +Publisher: Springer Nature}, + number = {1}, + pages = {93--111}, + title = {Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against {K}. pneumoniae}, + url = {https://www.embopress.org/doi/full/10.1038/s44321-023-00007-9}, + urldate = {2024-05-17}, + volume = {16}, + year = {2024} +} + +@article{vieira_polymyxin_2024, + abstract = {Until 2015, polymyxin resistance was primarily attributed to chromosomal mutations. However, with the first report of mobile colistin resistance (mcr-1) in commensal Escherichia coli from food animals in China, the landscape has changed. To evaluate the presence of polymyxin resistance in Salmonella spp., a drop screening test for colistin and polymyxin B was carried out on 1156 isolates of non-human origin (animals, food, and the environment), received in Brazil, between 2016 and 2021. Subsequently, 210 isolates with resistant results in the drop test were subjected to the gold-standard test (broth microdilution) for both colistin and polymyxin B. Whole-genome sequencing (WGS) of 102 resistant isolates was performed for a comprehensive analysis of associated genes. Surprisingly, none of the isolates resistant to colistin in the drop test harbored any of the mcr variants (mcr-1 to mcr-10). WGS identified that the most common mutations were found in pmrA (n= 22; T89S) and pmrB (n = 24; M15T, G73S, V74I, I83A, A111V). Other resistance determinants were also detected, such as the aac(6′)-Iaa gene in 72 isolates, while others carried beta-lactamase genes (blaTEM-1 blaCTX-M-2, blaCMY-2). Additionally, genes associated with fluoroquinolone resistance (qnrB19, qnrS1, oqxA/B) were detected in 11 isolates. Colistin and polymyxin B resistance were identified among Salmonella from non-human sources, but not associated with the mcr genes. Furthermore, the already-described mutations associated with polymyxin resistance were detected in only a small number of isolates, underscoring the need to explore and characterize unknown genes that contribute to resistance.}, + author = {Vieira, Thais and Dos Santos, Carla Adriana and de Jesus Bertani, Amanda Maria and Costa, Gisele Lozano and Campos, Karoline Rodrigues and Sacchi, Cláudio Tavares and Cunha, Marcos Paulo Vieira and Carvalho, Eneas and da Costa, Alef Janguas and de Paiva, Jacqueline Boldrin and Rubio, Marcela da Silva and Camargo, Carlos Henrique and Tiba-Casas, Monique Ribeiro}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13020110}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Salmonella} spp., {\textgreater}UseGalaxy.eu, antimicrobial resistance, colistin, polymyxin}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {110}, + shorttitle = {Polymyxin {Resistance} in {Salmonella}}, + title = {Polymyxin {Resistance} in {Salmonella}: {Exploring} {Mutations} and {Genetic} {Determinants} of {Non}-{Human} {Isolates}}, + url = {https://www.mdpi.com/2079-6382/13/2/110}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + +@article{vijaykrishna_expanding_2022, + abstract = {Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie’s remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data\_managers/data\_manager\_refgenie\_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.}, + author = {VijayKrishna, Nagampalli and Joshi, Jayadev and Coraor, Nate and Hillman-Jackson, Jennifer and Bouvier, Dave and van den Beek, Marius and Eguinoa, Ignacio and Coppens, Frederik and Davis, John and Stolarczyk, Michał and Sheffield, Nathan C and Gladman, Simon and Cuccuru, Gianmauro and Grüning, Björn and Soranzo, Nicola and Rasche, Helena and Langhorst, Bradley W and Bernt, Matthias and Fornika, Dan and de Lima Morais, David Anderson and Barrette, Michel and van Heusden, Peter and Petrillo, Mauro and Puertas-Gallardo, Antonio and Patak, Alex and Hotz, Hans-Rudolf and Blankenberg, Daniel}, + doi = {10.1093/bioadv/vbac030}, + issn = {2635-0041}, + journal = {Bioinformatics Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {vbac030}, + title = {Expanding the {Galaxy}’s reference data}, + url = {https://doi.org/10.1093/bioadv/vbac030}, + urldate = {2022-09-24}, + volume = {2}, + year = {2022} +} + +@article{viljoen_rabies-related_2023, + author = {Viljoen, Natalie and Ismail, Arshad and Weyer, Jacqueline and Markotter, Wanda}, + doi = {10.1128/MRA.00621-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + note = {Publisher: American Society for Microbiology}, + number = {11}, + pages = {e00621--23}, + title = {A rabies-related lyssavirus from a {Nycticeinops} schlieffeni bat with neurological signs, {South} {Africa}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00621-23}, + urldate = {2023-12-28}, + volume = {12}, + year = {2023} +} + @article{villa_data_2021, abstract = {Pervasive transcription originating from the ubiquitous activity of RNA Polymerase II (RNAPII) generates a vast mass of non-coding RNAs (ncRNAs) that represent a potential harm to gene expression. In the compact genome of the yeast Saccharomyces cerevisiae, the main genomewide safeguard against pervasive ncRNAs is the Nrd1-Nab3-Sen1 (NNS) complex, composed of two RNA-binding proteins (Nrd1 and Nab3) and the helicase Sen1. The NNS complex directs transcription termination of ncRNA genes and promotes the rapid degradation of pervasive transcripts from yeast nuclei through its physical and functional coupling to the nuclear RNA exosome. We have recently shown that inhibition of the exosome in yeast cells leads to the accumulation of ncRNAs complexed with Nab3 and Nrd1, decreasing recycling of these termination factors to sites of transcription and inducing global termination defects at NNS targets. Consistent with the notion that ncRNAs out-titrate Nab3 and Nrd1 termination factors, we have shown that a similar genomewide termination impairment could be achieved by expressing a circular RNA decoy containing a Nab3 binding target [1]. In relation to this previous research article, here we expand our observations on the effect of the circular RNA decoy on NNS termination. We aimed at verifying that the Nab3 binding sequence present on the decoy is indeed efficiently sequestering Nab3 as intended by design, leading to the expected decrease of Nab3 binding on NNS targets. We employed the crosslinking and cDNA analysis protocol (CRAC) on yeast cells expressing the circular ncRNA decoy or a control construct. We present data from high-resolution genomewide RNA binding of Nab3 in three independent biological replicates of these S.cerevisiae cells, normalized by spiked-in S.pombe lysates. These data allow the useful assessment of the extent of co-transcriptional binding decrease of Nab3 by decoy ncRNA titration and will be valuable for further analyses of NNS targeting mechanisms.}, author = {Villa, Tommaso and Jaszczyszyn, Yan and Libri, Domenico}, @@ -4167,43 +10618,282 @@ @article{villa_degradation_2020 year = {2020} } -@article{voelker_high-quality_2021, - author = {Voelker, Julia and Shepherd, Mervyn and Mauleon, Ramil}, - doi = {10.46471/gigabyte.28}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, +@article{vitali_employing_2023, + abstract = {Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.}, + author = {Vitali, Francesco and Frascella, Arcangela and Semenzato, Giulia and Del Duca, Sara and Palumbo Piccionello, Antonio and Mocali, Stefano and Fani, Renato and Emiliani, Giovanni}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12071179}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {{\textgreater}UseGalaxy.eu, VOCs, biosynthesis pathways, endophyte, medicinal plants}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {1179}, + title = {Employing {Genome} {Mining} to {Unveil} a {Potential} {Contribution} of {Endophytic} {Bacteria} to {Antimicrobial} {Compounds} in the {Origanum} vulgare {L}. {Essential} {Oil}}, + url = {https://www.mdpi.com/2079-6382/12/7/1179}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + +@article{voelker_high-quality_2021, + author = {Voelker, Julia and Shepherd, Mervyn and Mauleon, Ramil}, + doi = {10.46471/gigabyte.28}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: GigaScience Press}, + pages = {1--15}, + title = {A high-quality draft genome for {Melaleuca} alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species}, + url = {https://doi.org/10.46471/gigabyte.28}, + volume = {2021}, + year = {2021} +} + +@article{voelker_terpene_2023, + abstract = {Terpene synthases (TPS) are responsible for the terminal biosynthetic step of terpenoid production. They are encoded by a highly diverse gene family believed to evolve by tandem duplication in response to adaptive pressures. Taxa in the Myrtaceae family are renowned for their diversity of terpenoid-rich essential oils, and among them, the tribe Eucalypteae has the largest TPS gene family found in any plant ({\textgreater} 100 TPS). In this study, comparative analysis of Melaleuca alternifolia (tea tree), from the related tribe Melaleuceae, revealed some Myrtaceae have smaller TPS families, as a total of 58 putatively functional full-length TPS genes, and 21 pseudogenes were identified by manual annotation of a newly released long-read assembly of the genome. The TPS-a and TPS-b2 subfamilies that synthesise secondary compounds often mediating plant-environment interactions were more diminutive than those in eucalypts, probably reflecting key differences in the evolutionary histories of the two lineages. Of the putatively functional TPS-b1, 13 clustered into a region of around 400 kb on one scaffold. The organisation of these TPS suggested that tandem duplication was instrumental in the evolution and diversity of terpene chemistry in Melaleuca. Four TPS-b1 likely to catalyse the synthesis of the three monoterpenoid components that are used to classify tea tree chemotypes were encoded within a single small region of 87 kb in the larger cluster of TPS-b1, raising the possibility that coregulation and linkage may lead to their behaviour as a single locus, providing an explanation for the categorical inheritance of complex multiple-component chemotypes in the taxon.}, + author = {Voelker, Julia and Mauleon, Ramil and Shepherd, Mervyn}, + doi = {10.1007/s00606-023-01847-1}, + issn = {1615-6110}, + journal = {Plant Systematics and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, Eucalypts, Genetics, Monoterpenes, Myrtaceae, TPS manual annotation, Tea tree}, + language = {en}, + month = {April}, + number = {3}, + pages = {13}, + title = {The terpene synthase genes of {Melaleuca} alternifolia (tea tree) and comparative gene family analysis among {Myrtaceae} essential oil crops}, + url = {https://doi.org/10.1007/s00606-023-01847-1}, + urldate = {2023-07-31}, + volume = {309}, + year = {2023} +} + +@article{volkova_multi-omics_2024, + abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, + author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, + doi = {10.1016/j.envexpbot.2023.105600}, + issn = {0098-8472}, + journal = {Environmental and Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu, Barley, Ionising radiation, Metabolomics, Multi-omics, Phytoremediation, Proteomics, Radioresistance, Secondary metabolites, Transcriptomics, Translation}, + month = {February}, + pages = {105600}, + title = {Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation}, + url = {https://www.sciencedirect.com/science/article/pii/S0098847223003957}, + urldate = {2024-04-28}, + volume = {218}, + year = {2024} +} + +@article{volkova_radiosensitivity_2021, + author = {Volkova, Polina Yu and Duarte, Gustavo T. and Kazakova, Elizaveta A. and Makarenko, Ekaterina S. and Bitarishvili, Sofia V. and Bondarenko, Vladimir S. and Perevolotskii, Alexander N. and Geras'kin, Stanislav A. and Garbaruk, Dmitrii K. and Turchin, Larisa M.}, + doi = {10.1016/j.scitotenv.2021.146206}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + month = {July}, + note = {Publisher: Elsevier BV}, + pages = {146206}, + title = {Radiosensitivity of herbaceous plants to chronic radiation exposure: {Field} study in the {Chernobyl} exclusion zone}, + url = {https://doi.org/10.1016/j.scitotenv.2021.146206}, + volume = {777}, + year = {2021} +} + +@incollection{von_suchodoletz_lessons_2020, + author = {Von Suchodoletz, Dirk and Bauer, Jonathan and Zharkov, Oleg}, + booktitle = {E-{Science}-{Tage} 2019}, + keywords = {+RefPublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, + note = {Version Number: 1}, + publisher = {University Library Heidelberg}, + title = {Lessons learned from {Virtualized} {Research} {Environments} in today’s scientific compute infrastructures}, + url = {https://books.ub.uni-heidelberg.de/index.php/heibooks/catalog/book/598/c8418}, + urldate = {2020-05-27}, + year = {2020} +} + +@techreport{vorobyeva_suhw_2023, + abstract = {Abstract + +Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in +Drosophila +has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) IBP to genome topology remains unclear. In this study, we provide evidence for the existence of long-range interactions (LRIs) between Su(Hw) and Combgap ChIP-Seq peaks, reflected in the indirect binding of these proteins to chromatin in ChIP experiments. Loss of Su(Hw) binding results in the disappearance of Su(Hw)-Combgap LRIs and a decrease in spatial self-interactions among a subset of Su(Hw) sites. Our findings suggest that Su(Hw)-Combgap LRIs are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding.}, + author = {Vorobyeva, Nadezhda E. and Krasnov, Alexey N. and Erokhin, Maksim and Chetverina, Darya and Mazina, Marina}, + doi = {10.21203/rs.3.rs-3014225/v1}, + institution = {In Review}, + keywords = {{\textgreater}HiCExplorer, {\textgreater}UseGalaxy.eu, Hi-C}, + language = {en}, + month = {June}, + title = {Su({Hw}) interacts with {Combgap} to establish long-range chromatin contacts}, + type = {preprint}, + url = {https://www.researchsquare.com/article/rs-3014225/v1}, + urldate = {2023-06-13}, + year = {2023} +} + +@article{voronezhskaya_multi-omics_2023, + abstract = {Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl exclusion zone and areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns and conducted coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Plants growing under chronic radiation exposure showed complex and multidirectional biological effects, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants showed signs of DNA damage, redox imbalance, and stress responses. The upregulation of histones, chaperones, peroxidases, and secondary metabolism was noted.}, + author = {Voronezhskaya, Viktoria and Volkova, Polina and Bitarishvili, Sofia and Shesterikova, Ekaterina and Podlutskii, Mikhail and Clement, Gilles and Meyer, Christian and Duarte, Gustavo Turqueto and Kudin, Maksim and Garbaruk, Dmitrii and Turchin, Larisa and Kazakova, Elizaveta}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/plants12122318}, + issn = {2223-7747}, + journal = {Plants}, + keywords = {\textit{Fabaceae}, {\textgreater}UseGalaxy.eu, abiotic stress, low doses, metabolomics, proteomics, transcriptomics}, + language = {en}, + month = {January}, + note = {Number: 12 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {12}, + pages = {2318}, + title = {Multi-{Omics} {Analysis} of {Vicia} cracca {Responses} to {Chronic} {Radiation} {Exposure} in the {Chernobyl} {Exclusion} {Zone}}, + url = {https://www.mdpi.com/2223-7747/12/12/2318}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + +@article{vozenin_more_2024, + abstract = {The pervasiveness of deep space radiation remains a confounding factor for the transit of humans through our solar system. Spacecraft shielding both protects astronauts but also contributes to absorbed dose through galactic cosmic ray interactions that produce secondary particles. The resultant biological effects drop to a minimum for aluminum shielding around 20 g/cm2 but increase with additional shielding. The present work evaluates for the first time, the impact of secondary pions on central nervous system functionality. The fractional pion dose emanating from thicker shielded spacecraft regions could contribute up to 10\% of the total absorbed radiation dose. New results from the Paul Scherrer Institute have revealed that low dose exposures to 150 MeV positive and negative pions, akin to a Mars mission, result in significant, long-lasting cognitive impairments. These surprising findings emphasize the need to carefully evaluate shielding configurations to optimize safe exposure limits for astronauts during deep space travel.}, + author = {Vozenin, Marie-Catherine and Alaghband, Yasaman and Drayson, Olivia G. G. and Piaget, Filippo and Leavitt, Ron and Allen, Barrett D. and Doan, Ngoc-Lien and Rostomyan, Tigran and Stabilini, Alberto and Reggiani, Davide and Hajdas, Wojciech and Yukihara, Eduardo G. and Norbury, John W. and Bailat, Claude and Desorgher, Laurent and Baulch, Janet E. and Limoli, Charles L.}, + doi = {10.1667/RADE-23-00241.1.S1}, + issn = {0033-7587}, + journal = {Radiation Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {2}, + pages = {93--103}, + shorttitle = {More {May} {Not} be {Better}}, + title = {More {May} {Not} be {Better}: {Enhanced} {Spacecraft} {Shielding} {May} {Exacerbate} {Cognitive} {Decrements} by {Increasing} {Pion} {Exposures} during {Deep} {Space} {Exploration}}, + url = {https://doi.org/10.1667/RADE-23-00241.1.S1}, + urldate = {2024-04-28}, + volume = {201}, + year = {2024} +} + +@article{vukovikj_-depth_2023, + abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51\%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C\_1 haplotype (p=0.0013), where 10.5\% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.}, + author = {Vukovikj, Maja and Boshevska, Golubinka and Janchevska, Elizabeta and Buzharova, Teodora and Preshova, Ardian and Simova, Milica and Peshnacka, Aneta and Kocinski, Dragan and Kuzmanovska, Gordana and Memeti, Shaban and Gjorgoski, Icko}, + issn = {2673-818X}, + journal = {Frontiers in Virology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {In-depth genetic characterization of the {SARS}-{CoV}-2 pandemic in a two-year frame in {North} {Macedonia} using second and third generation sequencing technologies}, + url = {https://www.frontiersin.org/articles/10.3389/fviro.2022.1064882}, + urldate = {2023-06-05}, + volume = {2}, + year = {2023} +} + +@phdthesis{wadhawan_investigating_2022, + abstract = {Enterococcus faecalis is a Gram-positive bacterium found in the normal gut microbiota of diverse species, including vertebrates and invertebrates, as well as being common in the environment. It is also an opportunistic pathogen with a broad host range. One of the hosts E. faecalis can infect is the fruit fly, Drosophila melanogaster. The Drosophila immune response is distinct from that of humans and interacts with E. faecalis differently. To study this interaction we carried out experimental evolution via serial passage of E. faecalis in Drosophila. We generated E. faecalis strains with much-enhanced ability to survive and proliferate within this host. Strains selected in this way are specifically resistant to the Toll-induced Bomanin family of effector peptides, resulting not only in higher E. faecalis numbers but also in a significant increase in pathogenicity. Many of these Drosophila-selected strains also exhibit marked increases or decreases in antimicrobial resistance. Whole genome sequencing showed that most selected strains carried single mutations and that many of these mutations were in genes encoding proteins known to be involved in bacterial surface characteristics and antimicrobial resistance (mprF\_2, liaF, yxdM, croS, bgsA). To test if Drosophila antimicrobial peptides kill E. faecalis using mechanisms similar to antibiotics we generated E. faecalis strains that were resistant to daptomycin. Some of these daptomycin-adapted strains also acquired resistance to the Drosophila immune response. Daptomycin-adapted E. faecalis strains have mutations in the same genes or the same regulatory systems as were observed in Drosophila-adapted strains. As common genetic mechanisms underlie the resistance of E. faecalis to daptomycin and the Drosophila immune response, these results indicate these two systems target the same conserved bacterial properties in E. faecalis. They also demonstrate that the selection and emergence of antibiotic resistance in vivo does not require antibiotic exposure.}, + author = {Wadhawan, Ashima Deepak}, + copyright = {Creative Commons Attribution NonCommercial Licence}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en-US-GB}, + month = {December}, + note = {Accepted: 2023-06-12T16:00:04Z +Publisher: Imperial College London}, + title = {Investigating the determinants of {Enterococcus} faecalis virulence in {Drosophila} melanogaster}, + url = {http://spiral.imperial.ac.uk/handle/10044/1/104869}, + urldate = {2023-07-31}, + year = {2022} +} + +@article{wang_genome_2024, + abstract = {The co-evolution between symbionts and their insect hosts has led to intricate functional interdependencies. Advances in DNA-sequencing technologies have not only reduced the cost of sequencing but, with the advent of highly accurate long-read methods, have also enabled facile genome assembly even using mixed genomic input, thereby allowing us to more easily assess the contribution of symbionts to their insect hosts. In this study, genomic data recently generated from Peregrinus maidis was used to assemble the genome of a bacterial symbiont, Pm Arsenophonus sp. This {\textasciitilde}4.9-Mb assembly is one of the largest Arsenophonus genomes reported to date. The Benchmarking Universal Single-Copy Orthologs (BUSCO) result indicates that this Pm Arsenophonus assembly has a high degree of completeness, with 96\% of the single-copy Enterobacterales orthologs found. The identity of the Pm Arsenophonus sp. was further confirmed by phylogenetic analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates a major contribution by Pm Arsenophonus sp. to the biosynthesis of B vitamins and essential amino acids in P. maidis, where threonine and lysine production is carried out solely by Pm Arsenophonus sp. This study not only provides deeper insights into the evolutionary relationships between symbionts and their insect hosts, but also adds to our understanding of insect biology, potentially guiding the development of novel pest control methods.}, + author = {Wang, Yu-Hui and Mikaelyan, Aram and Coates, Brad S. and Lorenzen, Marcé}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects15020113}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{Arsenophonus} sp., \textit{Peregrinus maidis}, {\textgreater}UseGalaxy.eu, genome assembly, hemiptera}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {113}, + title = {The {Genome} of {Arsenophonus} sp. and {Its} {Potential} {Contribution} in the {Corn} {Planthopper}, {Peregrinus} maidis}, + url = {https://www.mdpi.com/2075-4450/15/2/113}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + +@article{wang_growth_2024, + abstract = {The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had {\textasciitilde}90\% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.}, + author = {Wang, Lunji and Zhao, Yishen and Chen, Siqiao and Wen, Xian and Anjago, Wilfred Mabeche and Tian, Tianchi and Chen, Yajuan and Zhang, Jinfeng and Deng, Sheng and Jiu, Min and Fu, Pengxiao and Zhou, Dongmei and Druzhinina, Irina S. and Wei, Lihui and Daly, Paul}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/biom14020148}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu, CAZymes, XYR1/XlnR/XLR-1, cellulose, transcriptional regulation}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {148}, + title = {Growth, {Enzymatic}, and {Transcriptomic} {Analysis} of xyr1 {Deletion} {Reveals} a {Major} {Regulator} of {Plant} {Biomass}-{Degrading} {Enzymes} in {Trichoderma} harzianum}, + url = {https://www.mdpi.com/2218-273X/14/2/148}, + urldate = {2024-05-17}, + volume = {14}, + year = {2024} +} + +@article{wang_systems-level_2023, + abstract = {Chemical modifications of transcripts with a 5′ cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.}, + author = {Wang, Jin and Chew, Bing Liang Alvin and Lai, Yong and Dong, Hongping and Xu, Luang and Liu, Yu and Fu, Xin-Yuan and Lin, Zhenguo and Shi, Pei-Yong and Lu, Timothy K. and Luo, Dahai and Jaffrey, Samie R. and Dedon, Peter C.}, + copyright = {2023 Springer Nature Limited}, + doi = {10.1038/s41596-023-00857-0}, + issn = {1750-2799}, + journal = {Nature Protocols}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, RNA modification}, + language = {en}, month = {August}, - note = {Publisher: GigaScience Press}, - pages = {1--15}, - title = {A high-quality draft genome for {Melaleuca} alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species}, - url = {https://doi.org/10.46471/gigabyte.28}, - volume = {2021}, - year = {2021} + note = {Publisher: Nature Publishing Group}, + pages = {1--28}, + title = {A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the {RNA} cap epitranscriptome}, + url = {https://www.nature.com/articles/s41596-023-00857-0}, + urldate = {2023-08-15}, + year = {2023} } -@article{volkova_radiosensitivity_2021, - author = {Volkova, Polina Yu and Duarte, Gustavo T. and Kazakova, Elizaveta A. and Makarenko, Ekaterina S. and Bitarishvili, Sofia V. and Bondarenko, Vladimir S. and Perevolotskii, Alexander N. and Geras'kin, Stanislav A. and Garbaruk, Dmitrii K. and Turchin, Larisa M.}, - doi = {10.1016/j.scitotenv.2021.146206}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - month = {July}, - note = {Publisher: Elsevier BV}, - pages = {146206}, - title = {Radiosensitivity of herbaceous plants to chronic radiation exposure: {Field} study in the {Chernobyl} exclusion zone}, - url = {https://doi.org/10.1016/j.scitotenv.2021.146206}, - volume = {777}, - year = {2021} +@article{watson_modification_2024, + abstract = {Single-cell RNA sequencing (scRNAseq) is a rapidly advancing field enabling the characterisation of heterogeneous gene expression profiles within a population. The cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phases to cells within scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as only G1, S or G2/M. Existing discrete cell phase assignment tools are unable to differentiate between G2 and M and continuous-phase-assignment tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. In this study, bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence-activated cell sorting. These gene lists were used to develop a methodology which can distinguish G2 and M phase cells in scRNAseq datasets. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle to identify a mitotic-specific cell population.}, + author = {Watson, Steven and Porter, Harry and Sudbery, Ian and Thompson, Ruth}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms25094589}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, RNA sequencing, bioinformatics, cell cycle, mitosis, phase assignment}, + language = {en}, + month = {January}, + note = {Number: 9 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {9}, + pages = {4589}, + title = {Modification of {Seurat} v4 for the {Development} of a {Phase} {Assignment} {Tool} {Able} to {Distinguish} between {G2} and {Mitotic} {Cells}}, + url = {https://www.mdpi.com/1422-0067/25/9/4589}, + urldate = {2024-05-17}, + volume = {25}, + year = {2024} } -@incollection{von_suchodoletz_lessons_2020, - author = {Von Suchodoletz, Dirk and Bauer, Jonathan and Zharkov, Oleg}, - booktitle = {E-{Science}-{Tage} 2019}, - keywords = {+RefPublic, {\textgreater}UseGalaxy.eu}, - language = {eng}, - note = {Version Number: 1}, - publisher = {University Library Heidelberg}, - title = {Lessons learned from {Virtualized} {Research} {Environments} in today’s scientific compute infrastructures}, - url = {https://books.ub.uni-heidelberg.de/index.php/heibooks/catalog/book/598/c8418}, - urldate = {2020-05-27}, - year = {2020} +@article{weber_histone_2023, + abstract = {The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.}, + author = {Weber, Lisa Marie and Jia, Yulin and Stielow, Bastian and Gisselbrecht, Stephen S and Cao, Yinghua and Ren, Yanpeng and Rohner, Iris and King, Jessica and Rothman, Elisabeth and Fischer, Sabrina and Simon, Clara and Forné, Ignasi and Nist, Andrea and Stiewe, Thorsten and Bulyk, Martha L and Wang, Zhanxin and Liefke, Robert}, + doi = {10.1093/nar/gkac1188}, + issn = {0305-1048}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {2}, + pages = {574--594}, + title = {The histone acetyltransferase {KAT6A} is recruited to unmethylated {CpG} islands via a {DNA} binding winged helix domain}, + url = {https://doi.org/10.1093/nar/gkac1188}, + urldate = {2023-03-15}, + volume = {51}, + year = {2023} } @article{weigang_within-host_2021, @@ -4217,6 +10907,25 @@ @article{weigang_within-host_2021 year = {2021} } +@incollection{wein_analysis_2023, + abstract = {Mass spectrometry is an ideal method for the discovery and characterization of modified RNAs. Unlike other traditional sequencing methods, mass spectrometry can identify and localize multiple types of modifications in tandem. One of the traditional hurdles to using this powerful technique has been a paucity of software to interpret the complicated data produced by these experiments. Here I describe how to use the NucleicAcidSearchEngine (NASE), a component of OpenMS as well as best practices for acquiring RNA data, and potential pitfalls in the analysis process.}, + address = {New York, NY}, + author = {Wein, Samuel}, + booktitle = {Computational {Epigenomics} and {Epitranscriptomics}}, + doi = {10.1007/978-1-0716-2962-8_15}, + editor = {Oliveira, Pedro H.}, + isbn = {978-1-07-162962-8}, + keywords = {{\textgreater}UseGalaxy.eu, Mass spectrometry, OpenMS, RNA, Transcriptomics}, + language = {en}, + pages = {225--239}, + publisher = {Springer US}, + series = {Methods in {Molecular} {Biology}}, + title = {Analysis of {RNA} {Sequences} and {Modifications} {Using} {NASE}}, + url = {https://doi.org/10.1007/978-1-0716-2962-8_15}, + urldate = {2023-03-15}, + year = {2023} +} + @article{weise_foxg1_2018, abstract = {Rett syndrome is a complex neurodevelopmental disorder that is mainly caused by mutations in MECP2. However, mutations in FOXG1 cause a less frequent form of atypical Rett syndrome, called FOXG1 syndrome. FOXG1 is a key transcription factor crucial for forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Using genome-wide small RNA sequencing and quantitative proteomics, we identified that FOXG1 affects the biogenesis of miR200b/a/429 and interacts with the ATP-dependent RNA helicase, DDX5/p68. Both FOXG1 and DDX5 associate with the microprocessor complex, whereby DDX5 recruits FOXG1 to DROSHA. RNA-Seq analyses of Foxg1cre/+ hippocampi and N2a cells overexpressing miR200 family members identified cAMP-dependent protein kinase type II-beta regulatory subunit (PRKAR2B) as a target of miR200 in neural cells. PRKAR2B inhibits postsynaptic functions by attenuating protein kinase A (PKA) activity; thus, increased PRKAR2B levels may contribute to neuronal dysfunctions in FOXG1 syndrome. Our data suggest that FOXG1 regulates PRKAR2B expression both on transcriptional and posttranscriptional levels.}, author = {Weise, Stefan C. and Arumugam, Ganeshkumar and Villarreal, Alejandro and Videm, Pavankumar and Heidrich, Stefanie and Nebel, Nils and Dumit, Verónica I. and Sananbenesi, Farahnaz and Reimann, Viktoria and Craske, Madeline and Schilling, Oliver and Hess, Wolfgang R. and Fischer, Andre and Backofen, Rolf and Vogel, Tanja}, @@ -4241,15 +10950,31 @@ @article{werner_mitochondrial_2022 year = {2022} } +@article{werner_targeted_2023, + abstract = {Pancreatic ductal adenocarcinoma (PDAC) represents one of the most aggressive and lethal malignancies worldwide with an urgent need for new diagnostic and therapeutic strategies. One major risk factor for PDAC is the pre-indication of chronic pancreatitis (CP), which represents highly inflammatory pancreatic tissue. Kallikreins (KLKs) are secreted serine proteases that play an important role in various cancers as components of the tumor microenvironment. Previous studies of KLKs in solid tumors largely relied on either transcriptomics or immunodetection. We present one of the first targeted mass spectrometry profiling of kallikrein proteases in PDAC, CP, and normal pancreas. We show that KLK6 and KLK10 are significantly upregulated in PDAC (n=14) but not in CP (n=7) when compared to normal pancreas (n=16), highlighting their specific intertwining with malignancy. Additional explorative proteome profiling identified 5936 proteins in our pancreatic cohort and observed disease-specific proteome rearrangements in PDAC and CP. As such, PDAC features an enriched proteome motif for extracellular matrix (ECM) and cell adhesion while there is depletion of mitochondrial energy metabolism proteins, reminiscent of the Warburg effect. Although often regarded as a PDAC hallmark, the ECM fingerprint was also observed in CP, alongside with a prototypical inflammatory proteome motif as well as with an increased wound healing process and proteolytic activity, thereby possibly illustrating tissue autolysis. Proteogenomic analysis based on publicly accessible data sources identified 112 PDAC-specific and 32 CP-specific single amino acid variants, which among others affect KRAS and ANKHD1. Our study emphasizes the diagnostic potential of kallikreins and provides novel insights into proteomic characteristics of PDAC and CP.}, + author = {Werner, Janina and Bernhard, Patrick and Cosenza-Contreras, Miguel and Pinter, Niko and Fahrner, Matthias and Pallavi, Prama and Eberhard, Johannes and Bronsert, Peter and Rückert, Felix and Schilling, Oliver}, + doi = {10.1016/j.neo.2022.100871}, + issn = {1476-5586}, + journal = {Neoplasia}, + keywords = {{\textgreater}UseGalaxy.eu, FFPE, KLK, Mass Spectrometry, PDAC}, + language = {en}, + month = {February}, + pages = {100871}, + title = {Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling}, + url = {https://www.sciencedirect.com/science/article/pii/S1476558622000963}, + urldate = {2023-03-15}, + volume = {36}, + year = {2023} +} + @article{weterings_duration_2021, abstract = {Background Escherichia coli sequence type ST131 is a recently emerged worldwide pandemic clonal group. Antibiotic resistance, virulence factors or colonisation fitness are mentioned among other as possible factors contributing to the worldwide success. In this study, we assessed the duration of rectal ESBL- producing E. coli colonisation in the residents, and compare duration of colonisation for ESBL-ST131 versus ESBL-non-ST131.MethodsRectal or faecal samples were obtained from residents of nursing home A between 2013 and 2019 and nursing home B between 2017 and 2019, with repeated point prevalence surveys at intervals of three to six months. Extended-spectrum β-lactamase (ESBL)-producing strains of E. coli were identified on selective culture and selective\&nbsp;enrichment\&nbsp;broth, and examined by antimicrobial susceptibility testing. In nursing home A multilocus sequence typing (MLST) and cluster analyse was performed by respectively O25:ST131-specific PCR and amplified fragment length polymorphism (AFLP). In nursing home B whole genome sequencing data were used to determine MLST and to perform a cluster analyse. Kaplan Meier survival analysis was performed to calculate the median time of rectal colonisation of ESBL-EC with a Log-Rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131.ResultsA total of 144 residents were included: 84 residents (58\%) with ESBL-ST131 rectal colonisation and 60 residents (42\%) with ESBL-non-ST131 rectal colonisation. Survival analysis showed a median colonisation length of 13 months for ESBL-ST131 (95\%CI: 7,2 – 18,7) versus 8,3 months (95\%CI: 2,8 – 13,8) for ESBL-non-ST131 (p = 0,028). Remarkably, in the subgroup ST131 the median colonisation length was significantly longer in female than in males: 25,7 months versus 8,1 months (p = 0,013).ConclusionHere we found a prolonged colonisation duration of ESBL-ST131 compared to ESBL-non-ST131 in residents of Dutch nursing homes. Prolonged colonisation duration complicates the controlling and ending an ESBL-ST131 outbreak, especially in long stay settings such as nursing homes.\&nbsp;}, author = {Weterings, Veronica and Goede, Tineke de and Hendriks, Yvonne and Kilsdonk, Linda and Mulders, Ans and Wier, Bregje van de and Kluytmans, Jan}, doi = {10.21203/rs.3.rs-136458/v1}, + issn = {2693-5015}, journal = {Research Square}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, month = {August}, - note = {ISSN: 2693-5015 -Type: article}, shorttitle = {Duration of {Colonisation} {With} {Extended}-spectrum {Beta}-lactamase-producing {Escherichia} {Coli}}, title = {Duration of {Colonisation} {With} {Extended}-spectrum {Beta}-lactamase-producing {Escherichia} {Coli}: {Results} of an {Open} {Cohort} {Study} {With} {Dutch} {Nursing} {Home} {Residents} (2013 – 2019)}, url = {https://www.researchsquare.com/article/rs-136458/v1}, @@ -4257,6 +10982,24 @@ @article{weterings_duration_2021 year = {2021} } +@article{whitmore_inadvertent_2023, + abstract = {The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from ‘wildlife’ environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.}, + author = {Whitmore, Liam and McCauley, Mark and Farrell, Jessica A. and Stammnitz, Maximilian R. and Koda, Samantha A. and Mashkour, Narges and Summers, Victoria and Osborne, Todd and Whilde, Jenny and Duffy, David J.}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41559-023-02056-2}, + issn = {2397-334X}, + journal = {Nature Ecology \& Evolution}, + keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Ecological genetics, Science, Sequencing, Zoology, technology and society}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + pages = {1--16}, + title = {Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental {DNA}}, + url = {https://www.nature.com/articles/s41559-023-02056-2}, + urldate = {2023-05-18}, + year = {2023} +} + @article{wibberg_nbi_2019, abstract = {The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR network. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training \& Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 250 training courses were carried out with more than 5,200 participants and these courses received recommendation rates of almost 90\% (status as of October 2019). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.}, author = {Wibberg, Daniel and Batut, Bérénice and Belmann, Peter and Blom, Jochen and Glöckner, Frank Oliver and Grüning, Björn and Hoffmann, Nils and Kleinbölting, Nils and Rahn, René and Rey, Maja and Scholz, Uwe and Sharan, Malvika and Tauch, Andreas and Trojahn, Ulrike and Usadel, Björn and Kohlbacher, Oliver}, @@ -4286,6 +11029,75 @@ @article{wichers_common_2021 year = {2021} } +@article{wight_anthropogenic_2024, + author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.}, + doi = {10.1128/aem.01809-23}, + journal = {Applied and Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {3}, + pages = {e01809--23}, + title = {Anthropogenic contamination sources drive differences in antimicrobial-resistant {Escherichia} coli in three urban lakes}, + url = {https://journals.asm.org/doi/full/10.1128/aem.01809-23}, + urldate = {2024-06-07}, + volume = {90}, + year = {2024} +} + +@article{wight_anthropogenic_2024, + author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.}, + doi = {10.1128/aem.01809-23}, + journal = {Applied and Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01809--23}, + title = {Anthropogenic contamination sources drive differences in antimicrobial-resistant {Escherichia} coli in three urban lakes}, + url = {https://journals.asm.org/doi/abs/10.1128/aem.01809-23}, + urldate = {2024-02-17}, + volume = {0}, + year = {2024} +} + +@article{williams_discovery_2023, + abstract = {The deep sea is known to host novel bacteria with the potential to produce a diverse array of undiscovered natural products. Thus, understanding these bacteria is of broad interest in ecology and could also underpin applied drug discovery, specifically in the area of antimicrobials....}, + author = {Williams, Sam E. and Back, Catherine R. and Best, Eleanor and Mantell, Judith and Stach, James E. M. and Williams, Tom A. and Race, Paul R. and Curnow, Paul}, + doi = {10.1099/mgen.0.000996}, + issn = {2057-5858}, + journal = {Microbial Genomics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + number = {5}, + pages = {mgen000996}, + pmcid = {PMC10272871}, + pmid = {37166955}, + title = {Discovery and biosynthetic assessment of '{Streptomyces} ortus' sp. nov. isolated from a deep-sea sponge}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10272871/}, + urldate = {2023-07-31}, + volume = {9}, + year = {2023} +} + +@article{willnow_nuclear_2024, + abstract = {Histone acetylation regulates gene expression, cell function and cell fate1. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila wing disc. H3K18ac, H4K8ac and total lysine acetylation are increased in the outer rim of the disc. This acetylation pattern is controlled by nuclear position, whereby nuclei continuously move from apical to basal locations within the epithelium and exhibit high levels of H3K18ac when they are in proximity to the tissue surface. These surface nuclei have increased levels of acetyl-CoA synthase, which generates the acetyl-CoA for histone acetylation. The carbon source for histone acetylation in the rim is fatty acid β-oxidation, which is also increased in the rim. Inhibition of fatty acid β-oxidation causes H3K18ac levels to decrease in the genomic proximity of genes involved in disc development. In summary, there is a physical mark of the outer rim of the wing and other imaginal epithelia in Drosophila that affects gene expression.}, + author = {Willnow, Philipp and Teleman, Aurelio A.}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41586-024-07471-4}, + issn = {1476-4687}, + journal = {Nature}, + keywords = {{\textgreater}UseGalaxy.eu, Cell proliferation, Differentiation}, + language = {en}, + month = {June}, + note = {Publisher: Nature Publishing Group}, + pages = {1--9}, + title = {Nuclear position and local acetyl-{CoA} production regulate chromatin state}, + url = {https://www.nature.com/articles/s41586-024-07471-4}, + urldate = {2024-06-08}, + year = {2024} +} + @article{winkler_contrast_2020, abstract = {Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differentialmass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficientdiscovery of ‘regions of interest’ (ROI) is of utmost importance in MSI. However, often the discovery of ROIs is hampered by high background noise and artifact signals. Especially in ambient ionization MSI, unmasking biologically relevant information from crude data sets is challenging. Therefore, we implemented a Threshold Intensity Quantization (TrIQ) algorithm for augmenting the contrast in MSI data visualizations. The simple algorithm reduces the impact of extreme values (‘outliers’) and rescales the dynamic range of mass signals. We provide an R script for post-processing MSI data in the imzML community format (https://bitbucket.org/lababi/msi.r) and implemented the TrIQ in our open-source imaging software RmsiGUI (https://bitbucket.org/lababi/rmsigui/). Applying these programs to different biological MSI data sets demonstrated the universal applicability of TrIQ for improving the contrast in the MSI data visualization. We show that TrIQ improves a subsequent detection of ROIs by sectioning. In addition, the adjustment of the dynamic signal intensity range makes MSI data sets comparable.}, author = {Winkler, Robert and Rosas-Román, Ignacio}, @@ -4365,6 +11177,67 @@ @article{witmer_epigenetic_2020 year = {2020} } +@article{wittenburg_canonical_2022, + abstract = {The FAIR principles have been accepted globally as guidelines for improving +data-driven science and data management practices, yet the incentives for +researchers to change their practices are presently weak. In addition, +data-driven science has been slow to embrace workflow technology despite clear +evidence of recurring practices. To overcome these challenges, the Canonical +Workflow Frameworks for Research (CWFR) initiative suggests a large-scale +introduction of self-documenting workflow scripts to automate recurring +processes or fragments thereof. This standardised approach, with FAIR Digital +Objects as anchors, will be a significant milestone in the transition to FAIR +data without adding additional load onto the researchers who stand to benefit +most from it. This paper describes the CWFR approach and the activities of the +CWFR initiative over the course of the last year or so, highlights several +projects that hold promise for the CWFR approaches, including Galaxy, Jupyter +Notebook, and RO Crate, and concludes with an assessment of the state of the +field and the challenges ahead.}, + author = {Wittenburg, Peter and Hardisty, Alex and Le Franc, Yann and Mozaffari, Amirpasha and Peer, Limor and Skvortsov, Nikolay A. and Zhao, Zhiming and Spinuso, Alessandro}, + doi = {10.1162/dint_a_00132}, + issn = {2641-435X}, + journal = {Data Intelligence}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + number = {2}, + pages = {286--305}, + title = {Canonical {Workflows} to {Make} {Data} {FAIR}}, + url = {https://doi.org/10.1162/dint_a_00132}, + urldate = {2022-09-07}, + volume = {4}, + year = {2022} +} + +@article{wittke_eodie_2023, + abstract = {Remote sensing satellites provide a vast amount of data to monitor and observe Earth’s surface and events on it. To use these data efficiently in subsequent analysis and decision-making, highly automated easy-to-use tools are needed. Here, we present Earth Observation Data Information Extractor (EODIE). EODIE is a toolkit to extract object-level time-series information from several multispectral satellite remote sensing platforms and to produce analysis-ready products for subsequent data analysis. EODIE has a modular design that makes it adjustable for end-user requirements. Users have a possibility to exchange and add modules in EODIE for flexible processing in different computing environments. With EODIE, remote sensing data can be processed to object level array, geotiff or statistics information of different (vegetation) indices or plain wavelength intervals.}, + author = {Wittke, Samantha and Fouilloux, Anne and Lehti, Petteri and Varho, Juuso and Kivimäki, Arttu and Karhu, Maiju and Karjalainen, Mika and Vaaja, Matti and Puttonen, Eetu}, + doi = {10.1016/j.softx.2023.101421}, + issn = {2352-7110}, + journal = {SoftwareX}, + keywords = {{\textgreater}UseGalaxy.eu, Big data processing, Earth observation, Open-source software, Remote sensing}, + language = {en}, + month = {July}, + pages = {101421}, + title = {{EODIE} — {Earth} {Observation} {Data} {Information} {Extractor}}, + url = {https://www.sciencedirect.com/science/article/pii/S2352711023001176}, + urldate = {2023-07-31}, + volume = {23}, + year = {2023} +} + +@article{wolf_-depth_2022, + abstract = {Microglia are the tissue-resident macrophages of the retina and brain, being critically involved in organ development, tissue homeostasis, and response to cellular damage. Until now, little is known about the molecular signature of human retinal microglia and how it differs from the one of brain microglia and peripheral monocytes. In addition, it is not yet clear to what extent murine retinal microglia resemble those of humans, which represents an important prerequisite for translational research. The present study applies fluorescence-activated cell sorting to isolate human retinal microglia from enucleated eyes and compares their transcriptional profile with the one of whole retinal tissue, human brain microglia as well as classical, intermediate and non-classical monocytes. Finally, human retinal microglia are compared to murine retinal microglia, isolated from Cx3cr1GFP/+ mice. Whereas human retinal microglia exhibited a high grade of similarity in comparison to their counterparts in the brain, several enriched genes were identified in retinal microglia when compared to whole retinal tissue, as well as classical, intermediate, and non-classical monocytes. In relation to whole retina sequencing, several risk genes associated with age-related macular degeneration (AMD) and diabetic retinopathy (DR) were preferentially expressed in retinal microglia, indicating their potential pathophysiological involvement. Although a high degree of similarity was observed between human and murine retinal microglia, several species-specific genes were identified, which should be kept in mind when employing mouse models to investigate retinal microglia biology. In summary, this study provides detailed insights into the molecular profile of human retinal microglia, identifies a plethora of tissue-specific and species-specific genes in comparison to human brain microglia and murine retinal microglia, and thus highlights the significance of retinal microglia in human retinal diseases and for translational research approaches.}, + author = {Wolf, Julian and Boneva, Stefaniya and Rosmus, Dennis-Dominik and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Schlecht, Anja and Lange, Clemens}, + issn = {1664-3224}, + journal = {Frontiers in Immunology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {In-{Depth} {Molecular} {Profiling} {Specifies} {Human} {Retinal} {Microglia} {Identity}}, + url = {https://www.frontiersin.org/articles/10.3389/fimmu.2022.863158}, + urldate = {2022-09-24}, + volume = {13}, + year = {2022} +} + @article{wolf_comparative_2021, abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods{\textless}/h3{\textgreater} {\textless}p{\textgreater}The present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Transcriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size \textit{in vivo}.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Funding{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study was funded by the Helmut-Ecker-Stiftung and the Volker-Homann-Stiftung.{\textless}/p{\textgreater}}, author = {Wolf, Julian and Schlecht, Anja and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Lange, Clemens}, @@ -4422,6 +11295,23 @@ @article{wolf_corneal_2020 year = {2020} } +@article{wolf_deciphering_2022, + abstract = {Hyalocytes are the tissue-resident innate immune cell population of the vitreous body with important functions in health and vitreoretinal disease. The purpose of this study is to gain new insights into the biology and function of human hyalocytes in comparison to other innate immune cells. The present study applies fluorescence-activated cell sorting and RNA sequencing to compare the transcriptional profiles of human hyalocytes, retinal microglia (rMG) and classical, intermediate, and non-classical monocytes isolated from the same patients. Immunohistochemistry was applied for morphological characterization of human hyalocytes. Pairwise analysis indicates distinct differences between hyalocytes and monocytes, whereas a high degree of similarity to rMG is apparent, with comparable expression levels of established microglia markers, such as TREM2, P2RY12, and TMEM119. Among the top expressed genes in hyalocytes, SPP1, CD74, and C3, were significantly upregulated when compared with monocytes. Despite the high level of similarity of hyalocytes and rMG, ten highly expressed genes in hyalocytes compared to microglia were identified, among them FOS, DUSP1, and EGR2. This study reveals a high degree of similarity between hyalocytes and retinal microglia. Nevertheless, hyalocytes exhibit some expression differences that may adapt them to the specific needs of the vitreous and provide the basis for deciphering the multiple roles of this fascinating cell population in health and vitreoretinal diseases.}, + author = {Wolf, Julian and Boneva, Stefaniya and Rosmus, Dennis-Dominik and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Schlecht, Anja and Lange, Clemens}, + doi = {10.1167/iovs.63.3.9}, + issn = {1552-5783}, + journal = {Investigative Ophthalmology \& Visual Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {3}, + pages = {9}, + title = {Deciphering the {Molecular} {Signature} of {Human} {Hyalocytes} in {Relation} to {Other} {Innate} {Immune} {Cell} {Populations}}, + url = {https://doi.org/10.1167/iovs.63.3.9}, + urldate = {2022-09-24}, + volume = {63}, + year = {2022} +} + @article{wolf_human_2022, author = {Wolf, Julian and Boneva, Stefaniya and Schlecht, Anja and Lapp, Thabo and Auw-Haedrich, Claudia and Lagrèze, Wolf and Agostini, Hansjürgen and Reinhard, Thomas and Schlunck, Günther and Lange, Clemens}, doi = {10.1016/j.ygeno.2022.110286}, @@ -4456,6 +11346,27 @@ @article{wolf_transcriptional_2020 year = {2020} } +@article{wolf_transcriptional_2023, + abstract = {This study characterizes the transcriptional profile and the cellular tumor microenvironment of conjunctival extranodal marginal zone lymphoma (EMZL) and identifies prognostically relevant biomarkers. Ten formalin-fixed and paraffin-embedded conjunctival EMZL and eight healthy conjunctival specimens were analyzed by Massive Analysis of cDNA Ends (MACE) RNA sequencing. The 3417 upregulated genes in conjunctival EMZL were involved in processes such as B cell proliferation and Rac protein signaling, whereas the 1188 downregulated genes contributed most significantly to oxidative phosphorylation and UV protection. The tumor microenvironment, as determined by deconvolution analysis, was mainly composed of multiple B cell subtypes which reflects the tumor’s B cell lineage. However, several T cell types, including T helper 2 cells and regulatory T cells, as well as innate immune cell types, such as anti-inflammatory macrophages and plasmacytoid dendritic cells, were also strongly enriched in conjunctival EMZL. A 13-biomarker prognostic panel, including S100A8 and S100A9, classified ocular and extraocular tumor recurrence, exceeded prognostic accuracy of Ann Arbor and American Joint Committee on Cancer (AJCC) staging, and demonstrated prognostic value for patient survival in 21 different cancer types in a database of 12,332 tumor patients. These findings may lead to new options of targeted therapy and may improve prognostic prediction for conjunctival EMZL.}, + author = {Wolf, Julian and Reinhard, Thomas and Hajdu, Rozina Ida and Schlunck, Günther and Auw-Haedrich, Claudia and Lange, Clemens}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/biom13010115}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu, EMZL, RNA sequencing, cellular tumor microenvironment, conjunctival lymphoma, formalin-fixation and paraffin-embedding (FFPE), prognosis, recurrence}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {115}, + title = {Transcriptional {Profiling} {Identifies} {Prognostic} {Gene} {Signatures} for {Conjunctival} {Extranodal} {Marginal} {Zone} {Lymphoma}}, + url = {https://www.mdpi.com/2218-273X/13/1/115}, + urldate = {2023-03-15}, + volume = {13}, + year = {2023} +} + @article{wolff_galaxy_2018, abstract = {Abstract. Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visu}, author = {Wolff, Joachim and Bhardwaj, Vivek and Nothjunge, Stephan and Richard, Gautier and Renschler, Gina and Gilsbach, Ralf and Manke, Thomas and Backofen, Rolf and Ramírez, Fidel and Grüning, Björn A.}, @@ -4506,6 +11417,19 @@ @incollection{wolfien_workflow_2019 year = {2019} } +@article{wolkowicz_utility_2017, + abstract = {Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e.g. library preparation). Nowadays there is a possibility to implement pocket size MinION - real time whole genome sequencer into BSL-3 and 4 laboratory for rapid and precise diagnostic purposes.}, + author = {Wołkowicz, Tomasz}, + doi = {10.1093/bfgp/elx033}, + journal = {Briefings in Functional Genomics}, + keywords = {+Workbench, {\textgreater}UseGalaxy.eu}, + month = {November}, + title = {The utility and perspectives of {NGS}-based methods in {BSL}-3 and {BSL}-4 laboratory – sequencing and analysis strategies}, + url = {https://academic.oup.com/bfg/advance-article/doi/10.1093/bfgp/elx033/4616141}, + urldate = {2017-12-01}, + year = {2017} +} + @article{wright*_structure_2018, abstract = {Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in “wet” laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also briefly mention recent advances in whole-genome interactomics and how this may influence the field of predictive RNA research.}, author = {Wright*, Patrick R. and Mann*, Martin and Backofen*, Rolf}, @@ -4523,6 +11447,26 @@ @article{wright*_structure_2018 year = {2018} } +@article{wurzbacher_planctoellipticum_2024, + abstract = {In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6\% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6\%. Optimal growth of strain SH412T occurs at pH 7.0–7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division (“budding”) and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.}, + author = {Wurzbacher, Carmen E. and Haufschild, Tom and Hammer, Jonathan and van Teeseling, Muriel C. F. and Kallscheuer, Nicolai and Jogler, Christian}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-56373-y}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial genomics, Bacterial physiology}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {5741}, + title = {Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family {Planctomycetaceae} isolated from wastewater of the aeration lagoon of a sugar processing plant in {Northern} {Germany}}, + url = {https://www.nature.com/articles/s41598-024-56373-y}, + urldate = {2024-04-28}, + volume = {14}, + year = {2024} +} + @article{wylie_whole-genome_2019, abstract = {Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100\% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.}, author = {Wylie, Kristine M. and Wylie, Todd N. and Minx, Patrick J. and Rosen, David A.}, @@ -4538,6 +11482,43 @@ @article{wylie_whole-genome_2019 year = {2019} } +@article{xu_reprogramming_2023, + abstract = {Xu and colleagues report that the poly-U-specific endoribonuclease ENDU-2/ENDOU activates a transcriptional reprogramming after a brief heat shock and this has a long-term beneficial effect in the model organism C. elegans.}, + author = {Xu, Fan and Li, Ruoyao and von Gromoff, Erika D. and Drepper, Friedel and Knapp, Bettina and Warscheid, Bettina and Baumeister, Ralf and Qi, Wenjing}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41467-023-39882-8}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--16}, + title = {Reprogramming of the transcriptome after heat stress mediates heat hormesis in {Caenorhabditis} elegans}, + url = {https://www.nature.com/articles/s41467-023-39882-8}, + urldate = {2023-07-18}, + volume = {14}, + year = {2023} +} + +@article{yan_diet-like_2023, + abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at −0.2 V where an abundance of Geobacter (49\%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.}, + author = {Yan, Yuqing and Zhang, Jiayao and Tian, Lili and Yan, Xuejun and Du, Lin and Leininger, Aaron and Zhang, Mou and Li, Nan and Ren, Zhiyong Jason and Wang, Xin}, + doi = {10.1016/j.watres.2023.119911}, + issn = {0043-1354}, + journal = {Water Research}, + keywords = {{\textgreater}UseGalaxy.eu, Anaerobic digestion, Direct interspecies electron transfer, Methanogenesis, Mutualism}, + month = {May}, + pages = {119911}, + title = {{DIET}-like mutualism of {Geobacter} and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate}, + url = {https://www.sciencedirect.com/science/article/pii/S0043135423003470}, + urldate = {2023-10-28}, + volume = {235}, + year = {2023} +} + @article{yanta_cryptogenotyper_2021, abstract = {Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3\% (428/431) and 95.1\% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6\% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.}, author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.}, @@ -4585,6 +11566,27 @@ @article{yoshida_dataset_2020 year = {2020} } +@article{yousif_sars-cov-2_2023, + abstract = {As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.}, + author = {Yousif, Mukhlid and Rachida, Said and Taukobong, Setshaba and Ndlovu, Nkosenhle and Iwu-Jaja, Chinwe and Howard, Wayne and Moonsamy, Shelina and Mhlambi, Nompilo and Gwala, Sipho and Levy, Joshua I. and Andersen, Kristian G. and Scheepers, Cathrine and von Gottberg, Anne and Wolter, Nicole and Bhiman, Jinal N. and Amoako, Daniel Gyamfi and Ismail, Arshad and Suchard, Melinda and McCarthy, Kerrigan}, + copyright = {2023 Springer Nature Limited}, + doi = {10.1038/s41467-023-41369-5}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Epidemiology, Genomics, SARS-CoV-2}, + language = {en}, + month = {October}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {6325}, + title = {{SARS}-{CoV}-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses}, + url = {https://www.nature.com/articles/s41467-023-41369-5}, + urldate = {2023-10-12}, + volume = {14}, + year = {2023} +} + @article{youssar_intercellular_2019, abstract = {Nematode-trapping fungi (NTF) are a large and diverse group of fungi, which may switch from a saprotrophic to a predatory livestyle if nematodes are present. Different fungi have developed different trapping devices, ranging from adhesive cells to constricting rings. After trapping, fungal hyphae penetrate the worm, secrete lytic enzymes and form a hyphal network inside the body. We sequenced the genome of Duddingtonia flagrans, a biotechnologically important NTF used to control nematode populations in fields. The 36.64 Mb genome encodes 9,927 putative proteins, among which are more than 638 predicted secreted proteins. Most secreted proteins are lytic enzymes, but more than 200 were classified as small secreted proteins ({\textless} 300 amino acids). 117 putative effector proteins were predicted, suggesting interkingdom communication during the colonization. As a first step to analyze the function of such proteins or other phenomena at the molecular level, we developed a transformation system, established the fluorescent proteins GFP and mCherry, adapted an assay to monitor protein secretion, and established gene-deletion protocols using homologous recombination or CRISPR/Cas9. One putative effector protein, PefB, was transcriptionally induced during the interaction. We show that the mature protein is able to be imported into nuclei in C. elegans cells. In addition, we studied trap formation and show that cell-to-cell communication is required for ring closure. The availability of the genome sequence and the establishment of many molecular tools will open new avenues to studying this biotechnologically relevant nematode-trapping fungus.}, author = {Youssar, Loubna and Wernet, Valentin and Hensel, Nicole and Yu, Xi and Hildebrand, Heinz-Georg and Schreckenberger, Birgit and Kriegler, Marius and Hetzer, Birgit and Frankino, Phillip and Dillin, Andrew and Fischer, Reinhard}, @@ -4621,6 +11623,63 @@ @article{yu_bromodomain-containing_2021 year = {2021} } +@article{yuan_ezh2_2022, + abstract = {Inflammasome contributes to the pathogenesis of various inflammatory diseases, but the epigenetic mechanism controlling its activation remains elusive. Here, we found that the histone methyltransferase Ezh2 mediates the activation of multiple types of inflammasomes in macrophages/microglia independent of its methyltransferase activity and thus promotes inflammasome-related pathologies. Mechanistically, Ezh2 functions through its SANT2 domain to maintain the enrichment of H3K27 acetylation in the promoter region of the long noncoding RNA (lncRNA) Neat1, thereby promoting chromatin accessibility and facilitating p65-mediated transcription of Neat1, which is a critical mediator of inflammasome assembly and activation. In addition, the tumour suppressor protein p53 competes with Ezh2 for the same binding region in the Neat1 promoter and thus antagonises Ezh2-induced Neat1 transcription and inflammasome activation. Therefore, loss of Ezh2 strongly promotes the binding of p53, which recruits the deacetylase SIRT1 for H3K27 deacetylation of the Neat1 promoter and thus suppresses Neat1 transcription and inflammasome activation. Overall, our study demonstrates an epigenetic mechanism involved in modulating inflammasome activation through an Ezh2/p53 competition model and highlights a novel function of Ezh2 in maintaining H3K27 acetylation to support lncRNA Neat1 transcription.}, + author = {Yuan, Jia and Zhu, Qingchen and Zhang, Xingli and Wen, Zhenzhen and Zhang, Guiheng and Li, Ni and Pei, Yifei and Wang, Yan and Pei, Siyu and Xu, Jing and Jia, Pan and Peng, Chao and Lu, Wei and Qin, Jun and Cao, Qian and Xiao, Yichuan}, + copyright = {2022 The Author(s), under exclusive licence to ADMC Associazione Differenziamento e Morte Cellulare}, + doi = {10.1038/s41418-022-00992-3}, + issn = {1476-5403}, + journal = {Cell Death \& Differentiation}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Inflammasome}, + language = {en}, + month = {October}, + note = {Number: 10 +Publisher: Nature Publishing Group}, + number = {10}, + pages = {2009--2023}, + title = {Ezh2 competes with p53 to license {lncRNA} {Neat1} transcription for inflammasome activation}, + url = {https://www.nature.com/articles/s41418-022-00992-3}, + urldate = {2022-12-03}, + volume = {29}, + year = {2022} +} + +@article{yusuf_exploring_2023, + abstract = {The Epidermal Growth Factor Receptor (EGFR) pathway plays a pivotal role in cancer progression, making it a prime target for anticancer drug development. Scutellaria baicalensis, a traditional Chinese medicinal herb, harbors bioactive compounds with promising pharmacological properties, including potential EGFR tyrosine kinase inhibition. In this study, we employed a comprehensive approach merging cheminformatics and molecular docking techniques to investigate the glioblastoma multiforme inhibitory potentials of the bioactive compounds from the plant, with a focus against EGFR. Our findings revealed significant binding affinities ranging from −9.010 to −6.427 kcal/mol and intricate molecular interactions between compounds from S. baicalensis and the EGFR. Notably, Ganhuangenin, 5,7,2′,5′-tetrahydroxyflavone, (2R)-2-(2,6-dihydroxyphenyl)-3,4-dihydro-2H-chromene-5,7-diol, and tenaxin I showed particularly high binding affinities, with scores ranging from −9.010 to −8.649 kcal/mol. These compounds even outperformed erlotinib, a standard ligand with a score of −8.539 kcal/mol. Importantly, they interacted with key amino acid residues (Met769, Glu738, and Thr766) through hydrogen bonding. These interactions were driven by specific structural features, including aromatic rings, hydrogen bond donors and acceptors, and hydrophobic interactions and the reliability of these results was further confirmed through induced-fit docking, reinforcing the potential inhibitory effects of these compounds on the flexible protein. Additionally, all of the top-scoring compounds from S. baicalensis adhered to established drug-likeness rules, including Lipinski's criteria, Ghose's rules, Veber's guidelines, and Egan's rules. However, it's worth noting that scutellarin had some violations in these rules. Remarkably, none of the identified compounds were likely to cause hepatotoxicity, mutagenicity, or cytotoxicity, suggesting that they could be considered as safe candidates for anti-cancer agents. This multidisciplinary investigation bridges traditional herbal knowledge and modern drug discovery, offering insights into the potential of S. baicalensis bioactive compounds as novel EGFR-targeting agents. The results underscore the value of chemoinformatics and molecular docking studies in exploring natural compounds for cancer therapy, paving the way for further research in the field.}, + author = {Yusuf, Amina J. and Adegboyega, Abayomi E. and Yakubu, Abdulbasit H. and Johnson, Grace I. and Asomadu, Rita O. and Adeduro, Mary N. and Chukwuma, Ifeoma F. and Ugwah-Oguejiofor, Chinenye J. and Okoh, Olayinka S. and Johnson, Titilayo O.}, + doi = {10.1016/j.imu.2023.101406}, + issn = {2352-9148}, + journal = {Informatics in Medicine Unlocked}, + keywords = {{\textgreater}ChemicalToolbox, Bioactive compounds, Cancer therapy, Computational drug discovery, EGFR tyrosine kinase, Natural products}, + month = {January}, + pages = {101406}, + shorttitle = {Exploring {Scutellaria} baicalensis bioactives as {EGFR} tyrosine kinase inhibitors}, + title = {Exploring {Scutellaria} baicalensis bioactives as {EGFR} tyrosine kinase inhibitors: {Cheminformatics} and molecular docking studies}, + url = {https://www.sciencedirect.com/science/article/pii/S2352914823002526}, + urldate = {2023-11-22}, + volume = {43}, + year = {2023} +} + +@article{zafar_identification_2024, + abstract = {Olfactory systems are indispensable for insects as they, including Western Flower Thrips (Frankliniella occidentalis), use olfactory cues for ovipositing and feeding. F. occidentalis use odorant binding proteins (OBPs) to transport semiochemicals to odorant receptors to induce a behavioural response from the sensillum lymph of the insect’s antennae. This study identifies four OBPs of F. occidentalis and analyses their expression at three stages of growth: larvae, adult males and adult females. Further, it investigates the presence of conserved motifs and their phylogenetic relationship to other insect species. Moreover, FoccOBP3 was in silico characterized to analyse its structure along with molecular docking and molecular dynamics simulations to understand its binding with semiochemicals of F. occidentalis. Molecular docking revealed the interactions of methyl isonicotinate, p-anisaldehyde and (S)-(-)-verbenone with FoccOBP3. Moreover, molecular dynamics simulations showed bonding stability of these ligands with FoccOBP3, and field trials validated that Lurem TR (commercial product) and p-anisaldehyde had greater attraction as compared to (S)-(-)-verbenone, given the compound’s binding with FoccOBP3. The current study helps in understanding the tertiary structure and interaction of FoccOBP3 with lures using computational and field data and will help in the identification of novel lures of insects in the future, given the importance of binding with OBPs. Communicated by Ramaswamy H. Sarma}, + author = {Zafar, Zeeshan and Wood, Martyn J. and Fatima, Sidra and Bhatti, Muhammad Faraz and Shah, Farooq A. and Saud, Zack and Loveridge, E. Joel and Karaca, Ismail and Butt, Tariq M.}, + doi = {10.1080/07391102.2024.2317990}, + issn = {0739-1102}, + journal = {Journal of Biomolecular Structure and Dynamics}, + keywords = {{\textgreater}UseGalaxy.eu, Frankliniella occidentalis, odorant-binding proteins, p-anisaldehyde, semiochemicals, verbenone}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/07391102.2024.2317990}, + number = {0}, + pages = {1--16}, + pmid = {38415377}, + title = {Identification of the odorant binding proteins of {Western} {Flower} {Thrips} ({Frankliniella} occidentalis), characterization and binding analysis of {FoccOBP3} with molecular modelling, molecular dynamics simulations and a confirmatory field trial}, + url = {https://doi.org/10.1080/07391102.2024.2317990}, + urldate = {2024-05-17}, + volume = {0}, + year = {2024} +} + @article{zavala-alvarado_transcriptional_2020, abstract = {Pathogenic Leptospira spp. are the causative agents of the waterborne zoonotic disease leptospirosis. Leptospira are challenged by numerous adverse conditions, including deadly reactive oxygen species (ROS), when infecting their hosts. Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. In L. interrogans, genes encoding defenses against ROS are repressed by the peroxide stress regulator, PerR. In this study, RNA sequencing was performed to characterize both the L. interrogans response to low and high concentrations of hydrogen peroxide and the PerR regulon. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to detoxify oxidants produced during peroxide stress. In addition, canonical molecular chaperones of the heat shock response and DNA repair proteins from the SOS response were required for Leptospira recovering from oxidative damage. Identification of the PerR regulon upon exposure to H2O2 allowed to define the contribution of this regulator in the oxidative stress response. This study has revealed a PerR-independent regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, the oxidative stress response. We have shown that PerR-regulated genes encoding a TonB-dependent transporter and a two-component system (VicKR) are involved in Leptospira tolerance to superoxide. This could represent the first defense mechanism against superoxide in L. interrogans, a bacterium lacking canonical superoxide dismutase. Our findings provide an insight into the mechanisms required by pathogenic Leptospira to overcome oxidative damage during infection-related conditions. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms in this life-threatening pathogen.}, author = {Zavala-Alvarado, Crispin and Sismeiro, Odile and Legendre, Rachel and Varet, Hugo and Bussotti, Giovanni and Bayram, Jan and Huete, Samuel G. and Rey, Guillaume and Coppée, Jean-Yves and Picardeau, Mathieu and Benaroudj, Nadia}, @@ -4640,6 +11699,165 @@ @article{zavala-alvarado_transcriptional_2020 year = {2020} } +@article{zebua_bacterial_2022, + abstract = {Peatland fires affect the diversity of bacteria, particularly key species bacteria (BKS). BKS has an important role in the structure of ecological community as key taxa to forming the composition and function. This study determined unique BKS candidates of the secondary forest which may not be found in burned areas. These candidates were detected in silico from the 16S rRNA gene sequence. The 16S rRNA gene sequence was determined by next-generation sequencing (NGS) method from peat soil DNA sampled from secondary forest and burned areas in the Giam Siak Kecil Biosphere Reserve, Bukit Batu (GSK-BB). BKS candidates were selected from a phylogenetic tree constructed by using MEGA version 6.06. Selected BKS was in the same cluster as secondary forest and were re-selected using BLASTn: AlignTwo or More Sequence analysis to ensure the uniqueness of the sequences. Based on the selected candidates, specific primers were designed to amplify the 16S rRNA BKS gene. Sensitivity was tested in silico using FastPCR application to ensure that candidates were only in secondary forest. There were 19 BKS candidates found in the secondary forest and not in burnt land (BKS\_SFB) that were classified into three groups. Based on the in silico PCR amplification of the 16S rRNA gene using the designed primer, we obtained two high specificity BKS candidates, i.e. BKS SFB2 (455 bp) and BKS SFB3 (473 bp). The two candidates are potential as DNA barcodes for peatland quality monitoring after burning.}, + author = {Zebua, P. K. and {Nelvia} and Pratiwi, N. W. and Zul, D.}, + doi = {10.1088/1755-1315/1025/1/012023}, + issn = {1755-1315}, + journal = {IOP Conference Series: Earth and Environmental Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {May}, + note = {Publisher: IOP Publishing}, + number = {1}, + pages = {012023}, + title = {Bacterial key species candidates for biomonitoring peatland burnt in the {Giam} {Siak} {Kecil}-{Bukit} {Batu} biosphere reserve, {Riau}}, + url = {https://doi.org/10.1088/1755-1315/1025/1/012023}, + urldate = {2022-09-24}, + volume = {1025}, + year = {2022} +} + +@article{zerouki_whole-genome_2023, + abstract = {Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine–Cytosine content of 46.4\%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at − 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications.}, + author = {Zerouki, C. and Chakraborty, K. and Kuittinen, S. and Pappinen, A. and Turunen, O.}, + doi = {10.1007/s00438-023-02073-7}, + issn = {1617-4623}, + journal = {Molecular Genetics and Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Cold adaptation, Gremmenia infestans, Mass spectrometry, Metabolomic enzymes, Phacidium infestans, Whole-genome sequence}, + language = {en}, + month = {October}, + title = {Whole-genome sequence and mass spectrometry study of the snow blight fungus {Phacidium} infestans ({Karsten}) {DSM} 5139 growing at freezing temperatures}, + url = {https://doi.org/10.1007/s00438-023-02073-7}, + urldate = {2023-10-14}, + year = {2023} +} + +@article{zhang_complete_2024, + abstract = {There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.}, + author = {Zhang, Gaoji and Xu, Tangjun and Chen, Yukun and Xu, Wei and Wang, Yinuo and Li, Yuanyuan and Zhu, Fuyuan and Liu, Hongyi and Ruan, Honghua}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cimb46030159}, + issn = {1467-3045}, + journal = {Current Issues in Molecular Biology}, + keywords = {\textit{Nedyopus patrioticus}, {\textgreater}UseGalaxy.eu, color polymorphism, mitochondrial genomes, phylogenetic analysis}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {3}, + pages = {2514--2527}, + shorttitle = {Complete {Mitochondrial} {Genomes} of {Nedyopus} patrioticus}, + title = {Complete {Mitochondrial} {Genomes} of {Nedyopus} patrioticus: {New} {Insights} into the {Color} {Polymorphism} of {Millipedes}}, + url = {https://www.mdpi.com/1467-3045/46/3/159}, + urldate = {2024-05-17}, + volume = {46}, + year = {2024} +} + +@article{zhang_first_2024, + abstract = {This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25\%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.}, + author = {Zhang, Gaoji and Gao, Ming and Chen, Yukun and Wang, Yinuo and Gan, Tianyi and Zhu, Fuyuan and Liu, Hongyi}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/genes15020254}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {\textit{L. scaber}, {\textgreater}UseGalaxy.eu, Diplopoda, genomic features, mitochondrial genome, phylogenetic analysis}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {254}, + shorttitle = {The {First} {Complete} {Mitochondrial} {Genome} of the {Genus} {Litostrophus}}, + title = {The {First} {Complete} {Mitochondrial} {Genome} of the {Genus} {Litostrophus}: {Insights} into the {Rearrangement} and {Evolution} of {Mitochondrial} {Genomes} in {Diplopoda}}, + url = {https://www.mdpi.com/2073-4425/15/2/254}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + +@article{zhang_nfatc1_2023, + abstract = {Background \& Aims +Loss of AT-rich interactive domain-containing protein 1A (ARID1A) fosters acinar-to-ductal metaplasia (ADM) and pancreatic carcinogenesis by down-regulating transcription programs controlling acinar cell identity. However, how ARID1A reacts to metaplasia-triggering environmental cues remains elusive. Here, we aimed to elucidate the role of ARID1A in controlling ductal pancreatic gene signatures and deciphering hierarchical signaling cues determining ARID1A-dependent chromatin regulation during acinar cell reprogramming. +Methods +Acinar cell explants with differential ARID1A status were subjected to genome-wide expression analyses. The impact of epidermal growth factor receptor (EGFR) signaling, NFATc1 activity, and ARID1A status on acinar reprogramming processes were characterized by ex vivo ADM assays and transgenic mouse models. EGFR-dependent ARID1A chromatin binding was studied by chromatin immunoprecipitation sequencing analysis and cellular fractionation. +Results +EGFR signaling interferes with ARID1A-dependent transcription by inducing genome-wide ARID1A displacement, thereby phenocopying ARID1A loss-of-function mutations and inducing a shift toward ADM permissive ductal transcription programs. Moreover, we show that EGFR signaling is required to push ARID1A-deficient acinar cells toward a metaplastic phenotype. Mechanistically, we identified the transcription factor nuclear factor of activated T cells 1 as the central regulatory hub mediating both EGFR signaling-induced genomic ARID1A displacement and the induction of ADM-promoting gene signatures in the absence of ARID1A. Consequently, pharmacologic inhibition of NFATc1 or its depletion in transgenic mice not only preserves genome-wide ARID1A occupancy, but also attenuates acinar metaplasia led by ARID1A loss. +Conclusions +Our data describe an intimate relationship between environmental signaling and chromatin remodeling in orchestrating cell fate decisions in the pancreas, and illustrate how ARID1A loss influences transcriptional regulation in acinar cell reprogramming.}, + author = {Zhang, Zhe and Wang, Xin and Hamdan, Feda H. and Likhobabina, Anna and Patil, Shilpa and Aperdannier, Lena and Sen, Madhobi and Traub, Jacobe and Neesse, Albrecht and Fischer, André and Papantonis, Argyris and Singh, Shiv K. and Ellenrieder, Volker and Johnsen, Steven A. and Hessmann, Elisabeth}, + doi = {10.1016/j.jcmgh.2023.01.015}, + issn = {2352-345X}, + journal = {Cellular and Molecular Gastroenterology and Hepatology}, + keywords = {{\textgreater}UseGalaxy.eu, ARID1A, Acinar-to-Ductal Metaplasia, EGFR, NFATc1, Pancreas, Transcription}, + language = {en}, + month = {February}, + title = {{NFATc1} {Is} a {Central} {Mediator} of {EGFR}-{Induced} {ARID1A} {Chromatin} {Dissociation} {During} {Acinar} {Cell} {Reprogramming}}, + url = {https://www.sciencedirect.com/science/article/pii/S2352345X23000188}, + urldate = {2023-03-15}, + year = {2023} +} + +@article{zhang_replication_2022, + abstract = {Transcription replication collisions (TRCs) constitute a major intrinsic source of genome instability but conclusive evidence for a causal role of TRCs in tumor initiation is missing. We discover that lack of the H4K20-dimethyltransferase KMT5B (also known as SUV4-20H1) in muscle stem cells de-represses S-phase transcription by increasing H4K20me1 levels, which induces TRCs and aberrant R-loops in oncogenic genes. The resulting replication stress and aberrant mitosis activate ATR-RPA32-P53 signaling, promoting cellular senescence, which turns into rapid rhabdomyosarcoma formation when p53 is absent. Inhibition of S-phase transcription ameliorates TRCs and formation of R-loops in Kmt5b-deficient MuSCs, validating the crucial role of H4K20me1-dependent, tightly controlled S-phase transcription for preventing collision errors. Low KMT5B expression is prevalent in human sarcomas and associated with tumor recurrence, suggesting a common function of KMT5B in sarcoma formation. The study uncovers decisive functions of KMT5B for maintaining genome stability by repressing S-phase transcription via control of H4K20me1 levels.}, + author = {Zhang, Ting and Künne, Carsten and Ding, Dong and Günther, Stefan and Guo, Xinyue and Zhou, Yonggang and Yuan, Xuejun and Braun, Thomas}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41467-022-34577-y}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer epigenetics, Cancer stem cells, Mechanisms of disease}, + language = {en}, + month = {November}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {6907}, + title = {Replication collisions induced by de-repressed {S}-phase transcription are connected with malignant transformation of adult stem cells}, + url = {https://www.nature.com/articles/s41467-022-34577-y}, + urldate = {2022-12-03}, + volume = {13}, + year = {2022} +} + +@article{zhao_rrm_2024, + abstract = {Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.}, + author = {Zhao, Rui and Wu, Wen-Ai and Huang, Yi-Hua and Li, Xin-Kai and Han, Jia-Qi and Jiao, Wu and Su, Yin-Na and Zhao, He and Zhou, Yang and Cao, Wu-Qiang and Zhang, Xun and Wei, Wei and Zhang, Wan-Ke and Song, Qing-Xin and He, Xin-Jian and Ma, Biao and Chen, Shou-Yi and Tao, Jian-Jun and Yin, Cui-Cui and Zhang, Jin-Song}, + copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation}, + doi = {10.1111/nph.19686}, + issn = {1469-8137}, + journal = {New Phytologist}, + keywords = {{\textgreater}UseGalaxy.eu, RNA-binding protein, alternative splicing, grain size, methylation, rice}, + language = {en}, + month = {April}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19686}, + number = {n/a}, + title = {An {RRM} domain protein {SOE} suppresses transgene silencing in rice}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19686}, + urldate = {2024-05-17}, + volume = {n/a}, + year = {2024} +} + +@article{zhu_bas_2024, + author = {Zhu, Tao and Wei, Chuangqi and Yu, Yaoguang and Zhang, Zhenzhen and Zhu, Jiameng and Liang, Zhenwei and Song, Xin and Fu, Wei and Cui, Yuhai and Wang, Zhi-Yong and Li, Chenlong}, + doi = {10.1016/j.devcel.2024.01.021}, + issn = {1534-5807}, + journal = {Developmental Cell}, + keywords = {{\textgreater}UseGalaxy.eu, BAS-chromatin-remodeling complexes, BZR1, Brassinosteroid, SWI/SNF, chromatin accessibility, growth and development, phytohormone}, + language = {English}, + month = {April}, + note = {Publisher: Elsevier}, + number = {7}, + pages = {924--939.e6}, + pmid = {38359831}, + title = {The {BAS} chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in {Arabidopsis}}, + url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00041-8}, + urldate = {2024-05-17}, + volume = {59}, + year = {2024} +} + @article{zhuang_time-_2021, author = {Zhuang, Xinyu and Schlunck, Günther and Wolf, Julian and Rosmus, Dennis-Dominik and Bleul, Tim and Luo, Ren and Böhringer, Daniel and Wieghofer, Peter and Lange, Clemens and Reinhard, Thomas and Lapp, Thabo}, doi = {10.1159/000516669}, @@ -4652,3 +11870,79 @@ @article{zhuang_time-_2021 year = {2021} } +@article{zhuang_time-_2022, + abstract = {\textbf{\textit{Purpose:}} The pattern of immune cells infiltrating the corneal stroma has been extensively studied in mice, but data on human tissue have been far less elaborate. To further characterize the number and differentiation state of resident immune cells in organ-cultured human corneal tissue, we employed a comprehensive bioinformatic deconvolution (xCell) of bulk RNA-sequencing (RNA-seq) data, immunohistochemistry (IHC), and flow cytometry (FC). \textbf{\textit{Methods:}} A transcriptome-based analysis of immune cell types in human corneal samples was performed. The results were validated by IHC, focusing on the identification of pro-inflammatory (M1) and regulatory (M2) macrophages. A protocol was established to identify these 2 different macrophage populations in human corneal tissue by means of FC. Subsequently, corneal samples in organ culture were differentially stimulated by IL-10, IL-4 \& IL-13, or LPS and macrophage populations were evaluated regarding their response to these stimuli. Furthermore, cell survival was analyzed in correlation with time in organ culture. \textbf{\textit{Results:}} xCell-based mathematical deconvolution of bulk RNA-seq data revealed the presence of CD8 T cells, Th17 cells, dendritic cells, and macrophages as the predominant immune cell types in organ-cultured human corneal tissue. Furthermore, RNA-seq allowed the detection of different macrophage marker genes in corneal samples, including \textit{PTPRC} (CD45), \textit{ITGAM} (CD11b), \textit{CD14}, and \textit{CD74}. Our RNA-seq data showed no evidence of a relevant presence of monocytes in human corneal tissue. The presence of different macrophage subtypes was confirmed by IHC. The disintegration and subsequent FC analysis of human corneal samples showed the presence of both M1 (HLA-DR$^{\textrm{+}}$, CD282$^{\textrm{+}}$, CD86$^{\textrm{+}}$, and CD284$^{\textrm{+}}$) and M2 (CD163$^{\textrm{+}}$ and CD206$^{\textrm{+}}$) macrophage subtypes. Furthermore, we found that the total number of macrophages in corneal samples decreased more than the total cell count with increasing tissue culture time. Treatment with IL-10 led to higher total cell counts per cornea and to an increased expression of the M2 marker CD163 (\textit{p} \&\#x3c; 0.05) while expression levels of various M1 macrophage markers were not significantly reduced by interleukin treatment. \textbf{\textit{Conclusions:}} Regarding different macrophage populations, untreated human corneas showed more M1 than M2 macrophages. With increasing organ culture time, these macrophages decreased. In terms of cell dynamics, adding interleukins to the organ culture medium influenced the phenotype of macrophages within the cornea as detected by FC. Modifying the immunomodulatory properties of human grafts appears a promising approach to further reduce the risk of graft rejection in patients. In this context, treatment with interleukins was more effective in upregulating M2 macrophages than in suppressing M1 macrophages in corneal tissue.}, + author = {Zhuang, Xinyu and Schlunck, Günther and Wolf, Julian and Rosmus, Dennis-Dominik and Bleul, Tim and Luo, Ren and Böhringer, Daniel and Wieghofer, Peter and Lange, Clemens and Reinhard, Thomas and Lapp, Thabo}, + doi = {10.1159/000516669}, + issn = {1662-811X, 1662-8128}, + journal = {Journal of Innate Immunity}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {english}, + note = {Publisher: Karger Publishers}, + number = {2}, + pages = {98--111}, + pmid = {34182556}, + title = {Time- and {Stimulus}-{Dependent} {Characteristics} of {Innate} {Immune} {Cells} in {Organ}-{Cultured} {Human} {Corneal} {Tissue}}, + url = {https://www.karger.com/Article/FullText/516669}, + urldate = {2022-09-24}, + volume = {14}, + year = {2022} +} + +@article{zilbauer_roadmap_2023, + abstract = {The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.}, + author = {Zilbauer, Matthias and James, Kylie R. and Kaur, Mandeep and Pott, Sebastian and Li, Zhixin and Burger, Albert and Thiagarajah, Jay R. and Burclaff, Joseph and Jahnsen, Frode L. and Perrone, Francesca and Ross, Alexander D. and Matteoli, Gianluca and Stakenborg, Nathalie and Sujino, Tomohisa and Moor, Andreas and Bartolome-Casado, Raquel and Bækkevold, Espen S. and Zhou, Ran and Xie, Bingqing and Lau, Ken S. and Din, Shahida and Magness, Scott T. and Yao, Qiuming and Beyaz, Semir and Arends, Mark and Denadai-Souza, Alexandre and Coburn, Lori A. and Gaublomme, Jellert T. and Baldock, Richard and Papatheodorou, Irene and Ordovas-Montanes, Jose and Boeckxstaens, Guy and Hupalowska, Anna and Teichmann, Sarah A. and Regev, Aviv and Xavier, Ramnik J. and Simmons, Alison and Snyder, Michael P. and Wilson, Keith T.}, + copyright = {2023 Springer Nature Limited}, + doi = {10.1038/s41575-023-00784-1}, + issn = {1759-5053}, + journal = {Nature Reviews Gastroenterology \& Hepatology}, + keywords = {{\textgreater}UseGalaxy.eu, Biotechnology, Gastrointestinal system}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + pages = {1--18}, + title = {A {Roadmap} for the {Human} {Gut} {Cell} {Atlas}}, + url = {https://www.nature.com/articles/s41575-023-00784-1}, + urldate = {2023-06-03}, + year = {2023} +} + +@article{zinati_deciphering_2023, + abstract = {Abiotic stress in cucumber (Cucumis sativus L.) may trigger distinct transcriptome responses, resulting in significant yield loss. More insight into the molecular underpinnings of the stress response can be gained by combining RNA-Seq meta-analysis with systems biology and machine learning. This can help pinpoint possible targets for engineering abiotic tolerance by revealing functional modules and key genes essential for the stress response. Therefore, to investigate the regulatory mechanism and key genes, a combination of these approaches was utilized in cucumber subjected to various abiotic stresses. Three significant abiotic stress-related modules were identified by gene co-expression network analysis (WGCNA). Three hub genes (RPL18, δ-COP, and EXLA2), ten transcription factors (TFs), one transcription regulator, and 12 protein kinases (PKs) were introduced as key genes. The results suggest that the identified PKs probably govern the coordination of cellular responses to abiotic stress in cucumber. Moreover, the C2H2 TF family may play a significant role in cucumber response to abiotic stress. Several C2H2 TF target stress-related genes were identified through co-expression and promoter analyses. Evaluation of the key identified genes using Random Forest, with an area under the curve of ROC (AUC) of 0.974 and an accuracy rate of 88.5\%, demonstrates their prominent contributions in the cucumber response to abiotic stresses. These findings provide novel insights into the regulatory mechanism underlying abiotic stress response in cucumber and pave the way for cucumber genetic engineering toward improving tolerance ability under abiotic stress.}, + author = {Zinati, Zahra and Nazari, Leyla}, + copyright = {2023 Springer Nature Limited}, + doi = {10.1038/s41598-023-40189-3}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Molecular biology}, + language = {en}, + month = {August}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {12942}, + title = {Deciphering the molecular basis of abiotic stress response in cucumber ({Cucumis} sativus {L}.) using {RNA}-{Seq} meta-analysis, systems biology, and machine learning approaches}, + url = {https://www.nature.com/articles/s41598-023-40189-3}, + urldate = {2023-08-13}, + volume = {13}, + year = {2023} +} + +@article{zirngibl_triose_2023, + abstract = {Plants have evolved multiple strategies to cope with rapid changes in the environment. During high light (HL) acclimation, the biosynthesis of photoprotective flavonoids, such as anthocyanins, is induced. However, the exact nature of the signal and downstream factors for HL induction of flavonoid biosynthesis (FB) is still under debate. Here, we show that carbon fixation in chloroplasts, subsequent export of photosynthates by triose phosphate/phosphate translocator (TPT), and rapid increase in cellular sugar content permit the transcriptional and metabolic activation of anthocyanin biosynthesis during HL acclimation. In combination with genetic and physiological analysis, targeted and whole-transcriptome gene expression studies suggest that reactive oxygen species and phytohormones play only a minor role in rapid HL induction of the anthocyanin branch of FB. In addition to transcripts of FB, sugar-responsive genes showed delayed repression or induction in tpt-2 during HL treatment, and a significant overlap with transcripts regulated by SNF1-related protein kinase 1 (SnRK1) was observed, including a central transcription factor of FB. Analysis of mutants with increased and repressed SnRK1 activity suggests that sugar-induced inactivation of SnRK1 is required for HL-mediated activation of anthocyanin biosynthesis. Our study emphasizes the central role of chloroplasts as sensors for environmental changes as well as the vital function of sugar signaling in plant acclimation.}, + author = {Zirngibl, Max-Emanuel and Araguirang, Galileo Estopare and Kitashova, Anastasia and Jahnke, Kathrin and Rolka, Tobias and Kühn, Christine and Nägele, Thomas and Richter, Andreas S.}, + doi = {10.1016/j.xplc.2022.100423}, + issn = {2590-3462}, + journal = {Plant Communications}, + keywords = {{\textgreater}UseGalaxy.eu, SnRK1, acclimation, anthocyanin, flavonoid biosynthesis, high light, sugar signaling}, + language = {en}, + month = {January}, + number = {1}, + pages = {100423}, + series = {Focus {Issue} on {Chloroplast} {Biology}}, + title = {Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation}, + url = {https://www.sciencedirect.com/science/article/pii/S2590346222002553}, + urldate = {2023-03-15}, + volume = {4}, + year = {2023} +}