diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 53adf4901..abd52c2d3 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}, @@ -39,6 +92,28 @@ @article{aggarwal_role_2021 year = {2021} } +@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 +152,23 @@ @article{ahmed_high_2020 year = {2020} } +@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{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 +198,55 @@ @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{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 +261,53 @@ @article{amaral_tcti_2022 year = {2022} } +@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{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_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 +320,24 @@ @article{apostolakos_occurrence_2021 year = {2021} } +@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_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 +353,114 @@ @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{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} +} + +@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 +480,25 @@ @incollection{bagnacani_tools_2019 year = {2019} } +@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 +626,29 @@ @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{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}, @@ -388,6 +731,27 @@ @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}, @@ -406,6 +770,55 @@ @article{bazzucchi_near-complete_2020 year = {2020} } +@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} +} + +@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{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{blacklock_examination_2022, author = {Blacklock, Emily}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, @@ -466,6 +879,20 @@ @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 +948,44 @@ @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 = {2023-07-31}, + 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 +1023,23 @@ @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 +1055,19 @@ @article{bovio_differential_2018 year = {2018} } +@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{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 +1086,23 @@ @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 +1123,34 @@ @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 +1168,49 @@ @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}, @@ -723,6 +1293,48 @@ @article{buttimer_isolation_2020 year = {2020} } +@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}, @@ -774,19 +1386,58 @@ @phdthesis{cantarella_insights_2020 year = {2020} } -@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}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, - month = {September}, - note = {Publisher: American Society for Microbiology}, - number = {10}, - title = {Evolutionary {Trajectories} toward {Ceftazidime}-{Avibactam} {Resistance} in {Klebsiella} pneumoniae {Clinical} {Isolates}}, - url = {https://doi.org/10.1128/aac.00574-21}, - volume = {65}, - year = {2021} -} - +@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}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + month = {September}, + note = {Publisher: American Society for Microbiology}, + number = {10}, + title = {Evolutionary {Trajectories} toward {Ceftazidime}-{Avibactam} {Resistance} in {Klebsiella} pneumoniae {Clinical} {Isolates}}, + url = {https://doi.org/10.1128/aac.00574-21}, + volume = {65}, + year = {2021} +} + @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 +1456,27 @@ @article{cermak_unexpected_2020 year = {2020} } +@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 +1503,25 @@ @article{chen_versatile_2018 year = {2018} } +@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{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 +1552,20 @@ @article{chiara_next_2021 year = {2021} } +@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}, @@ -886,6 +1591,15 @@ @article{cordellier_next-generation_2021 year = {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{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}, @@ -917,13 +1631,15 @@ @article{dad_molecular_2020 } @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} } @@ -945,6 +1661,44 @@ @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_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{delroisse_photophore_2021, author = {Delroisse, Jérôme and Duchatelet, Laurent and Flammang, Patrick and Mallefet, Jérôme}, doi = {10.3389/fmars.2021.627045}, @@ -1046,6 +1800,23 @@ @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{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}, @@ -1108,6 +1879,27 @@ @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{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 +1914,25 @@ @informatik.uni-freiburg.de year = {2018} } +@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 +1947,37 @@ @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{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 +2121,27 @@ @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_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 +2159,43 @@ @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 +2239,27 @@ @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 +2270,70 @@ @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{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 +2348,42 @@ @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_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{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 +2425,24 @@ @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}, @@ -1465,6 +2504,27 @@ @article{friedrich_tryptophan_2021 year = {2021} } +@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}, @@ -1484,6 +2544,69 @@ @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{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}, @@ -1774,6 +2897,55 @@ @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}, @@ -1825,6 +2997,51 @@ @article{hamprecht_candida_2019 year = {2019} } +@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{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}, @@ -1980,6 +3197,129 @@ @phdthesis{holthausen_bermejo_workflow-based_2019 year = {2019} } +@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{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{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{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} +} + +@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{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}, @@ -2000,9 +3340,92 @@ @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.}, +@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 = {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{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{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}, @@ -2048,6 +3471,65 @@ @article{kalmbach_genome-wide_2019 year = {2019} } +@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{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 +3571,133 @@ @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 +3711,24 @@ @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 +3741,39 @@ @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 +3789,25 @@ @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 +3839,42 @@ @phdthesis{konovalovas_molecular_2018 year = {2018} } +@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{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 +3987,23 @@ @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{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}, @@ -2344,6 +4076,24 @@ @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{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.}, @@ -2376,6 +4126,71 @@ @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{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{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 +4206,45 @@ @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}, @@ -2441,6 +4295,40 @@ @article{liang_reciprocal_2020 year = {2020} } +@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}, @@ -2457,6 +4345,24 @@ @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 +4392,23 @@ @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{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}, @@ -2631,6 +4554,40 @@ @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 +4663,21 @@ @article{marzoli_next_2020 year = {2020} } +@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 +4691,23 @@ @article{mauer_genomics_2021 year = {2021} } +@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}, @@ -2801,6 +4790,25 @@ @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_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.}, @@ -2836,9 +4844,67 @@ @article{mehta_updates_2021 year = {2021} } -@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.}, +@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{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.}, journal = {arXiv}, keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods}, month = {April}, @@ -2863,6 +4929,45 @@ @article{migur_temperature-regulated_2021 year = {2021} } +@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{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 +5034,27 @@ @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{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 +5075,23 @@ @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{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}, @@ -3003,17 +5146,21 @@ @article{musmeci_draft_2021 year = {2021} } -@article{nagy_draft_2021, - 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{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, @@ -3051,6 +5198,60 @@ @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 +5267,51 @@ @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{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 +5339,22 @@ @article{niemoller_bisulfite-free_2021 year = {2021} } +@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} +} + +@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{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}, @@ -3147,6 +5409,59 @@ @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} +} + @article{oselusi_cheminformatic_2021, author = {Oselusi, Samson Olaitan and Christoffels, Alan and Egieyeh, Samuel Ayodele}, doi = {10.3390/molecules26133970}, @@ -3213,6 +5528,25 @@ @article{page-karjian_fibropapillomatosis_2021 year = {2021} } +@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, 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{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 +5559,27 @@ @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 +5610,40 @@ @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{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 +5656,27 @@ @article{pelletier_standardized_2021 year = {2021} } +@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}, @@ -3311,6 +5721,47 @@ @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}, @@ -3338,6 +5789,28 @@ @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{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}, @@ -3355,6 +5828,58 @@ @article{pinter_functional_2021 year = {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{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}, @@ -3381,6 +5906,25 @@ @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{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}, @@ -3440,6 +5984,23 @@ @article{ranchou-peyruse_microbial_2021 year = {2021} } +@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 +6087,26 @@ @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 +6123,19 @@ @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}, @@ -3611,6 +6205,37 @@ @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{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 +6252,25 @@ @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{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.}, @@ -3659,6 +6303,27 @@ @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 +6342,25 @@ @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 +6396,24 @@ @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 +6429,103 @@ @article{schlecht_transcriptomic_2020 year = {2020} } +@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 +6557,46 @@ @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{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 +6614,51 @@ @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 +6672,27 @@ @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{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 +6709,22 @@ @article{simon-chica_novel_2021 year = {2021} } +@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 +6739,66 @@ @article{soares_hierarchical_2021 year = {2021} } +@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{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 +6853,83 @@ @article{stephen_jr_comparative_2022 year = {2022} } +@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_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 +6960,40 @@ @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 +7011,46 @@ @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}, @@ -4057,6 +7176,42 @@ @article{tosar_ri-sec-seq_2021 year = {2021} } +@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{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 +7247,24 @@ @article{uellendahl-werth_benchmark_2020 year = {2020} } +@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{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 +7277,38 @@ @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 +7337,23 @@ @article{videm_chira_2021 year = {2021} } +@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{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}, @@ -4167,6 +7389,27 @@ @article{villa_degradation_2020 year = {2020} } +@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}, @@ -4180,6 +7423,24 @@ @article{voelker_high-quality_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_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}, @@ -4206,6 +7467,109 @@ @incollection{von_suchodoletz_lessons_2020 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{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_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: 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{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, author = {Weigang, Sebastian and Fuchs, Jonas and Zimmer, Gert and Schnepf, Daniel and Kern, Lisa and Beer, Julius and Luxenburger, Hendrik and Ankerhold, Jakob and Falcone, Valeria and Kemming, Janine and Hofmann, Maike and Thimme, Robert and Neumann-Haefelin, Christoph and Ulferts, Svenja and Grosse, Robert and Hornuss, Daniel and Tanriver, Yakup and Rieg, Siegbert and Wagner, Dirk and Huzly, Daniela and Schwemmle, Martin and Panning, Marcus and Kochs, Georg}, doi = {10.1101/2021.04.30.21256244}, @@ -4217,6 +7581,25 @@ @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}, @@ -4241,6 +7624,23 @@ @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}, @@ -4257,6 +7657,24 @@ @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 +7704,25 @@ @article{wichers_common_2021 year = {2021} } +@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{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 +7802,67 @@ @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 +7920,23 @@ @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 +7971,27 @@ @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 +8042,19 @@ @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}, @@ -4538,6 +8087,27 @@ @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{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.}, @@ -4621,6 +8191,27 @@ @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{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 +8231,68 @@ @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{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{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 +8305,79 @@ @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} +}