From 8d2c677abdc8daca9f312b511afc360377c5e1e6 Mon Sep 17 00:00:00 2001 From: annefou Date: Sun, 30 Apr 2023 23:16:27 +0000 Subject: [PATCH] Update citations --- _bibliography/citations-eu.bib | 1982 +++++++++++++++++++++++++++++++- 1 file changed, 1926 insertions(+), 56 deletions(-) diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 53adf4901..4a1110822 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -7,6 +7,41 @@ @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}, @@ -77,6 +112,23 @@ @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 +158,55 @@ @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 +221,38 @@ @article{amaral_tcti_2022 year = {2022} } +@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 +265,24 @@ @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 +298,43 @@ @article{arcari_interplay_2022 year = {2022} } +@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{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} +} + @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}, @@ -294,18 +482,6 @@ @article{bartas_changes_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{batut_asaim_2018-1, 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}, @@ -406,6 +582,23 @@ @article{bazzucchi_near-complete_2020 year = {2020} } +@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 +659,20 @@ @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 +728,26 @@ @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{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.}, @@ -591,19 +818,23 @@ @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 +855,23 @@ @article{bray_intuitive_2020 year = {2020} } +@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 +889,27 @@ @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{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}, @@ -831,6 +1100,25 @@ @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}, @@ -917,13 +1205,15 @@ @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 +1235,27 @@ @article{davey_intrinsically_2019 year = {2019} } +@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 +1357,23 @@ @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}, @@ -1122,6 +1450,25 @@ @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 +1483,24 @@ @article{emperle_mutations_2019 year = {2019} } +@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}, @@ -1296,6 +1661,43 @@ @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}, @@ -1349,6 +1751,23 @@ @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{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 +1782,24 @@ @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{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 +1841,24 @@ @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 +1920,27 @@ @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 +1960,69 @@ @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 +2313,23 @@ @article{guendel_group_2020 year = {2020} } +@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{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 +2381,27 @@ @article{hamprecht_candida_2019 year = {2019} } +@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 +2557,23 @@ @phdthesis{holthausen_bermejo_workflow-based_2019 year = {2019} } +@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{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}, @@ -2000,14 +2594,75 @@ @article{jalili_galaxy_2020 year = {2020} } -@article{jude_draft_2019, - abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.}, - author = {Jude, Brooke A.}, - doi = {10.1128/MRA.00683-19}, - editor = {Dunning Hotopp, Julie C.}, - issn = {2576-098X}, - journal = {Microbiology Resource Announcements}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, +@article{jarvis_semi-automated_2022, + abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.}, + author = {Jarvis, Erich D. and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R. and Porubsky, David and Cheng, Haoyu and Asri, Mobin and Logsdon, Glennis A. and Carnevali, Paolo and Chaisson, Mark J. P. and Chin, Chen-Shan and Cody, Sarah and Collins, Joanna and Ebert, Peter and Escalona, Merly and Fedrigo, Olivier and Fulton, Robert S. and Fulton, Lucinda L. and Garg, Shilpa and Gerton, Jennifer L. and Ghurye, Jay and Granat, Anastasiya and Green, Richard E. and Harvey, William and Hasenfeld, Patrick and Hastie, Alex and Haukness, Marina and Jaeger, Erich B. and Jain, Miten and Kirsche, Melanie and Kolmogorov, Mikhail and Korbel, Jan O. and Koren, Sergey and Korlach, Jonas and Lee, Joyce and Li, Daofeng and Lindsay, Tina and Lucas, Julian and Luo, Feng and Marschall, Tobias and Mitchell, Matthew W. and McDaniel, Jennifer and Nie, Fan and Olsen, Hugh E. and Olson, Nathan D. and Pesout, Trevor and Potapova, Tamara and Puiu, Daniela and Regier, Allison and Ruan, Jue and Salzberg, Steven L. and Sanders, Ashley D. and Schatz, Michael C. and Schmitt, Anthony and Schneider, Valerie A. and Selvaraj, Siddarth and Shafin, Kishwar and Shumate, Alaina and Stitziel, Nathan O. and Stober, Catherine and Torrance, James and Wagner, Justin and Wang, Jianxin and Wenger, Aaron and Xiao, Chuanle and Zimin, Aleksey V. and Zhang, Guojie and Wang, Ting and Li, Heng and Garrison, Erik and Haussler, David and Hall, Ira and Zook, Justin M. and Eichler, Evan E. and Phillippy, Adam M. and Paten, Benedict and Howe, Kerstin and Miga, Karen H.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41586-022-05325-5}, + issn = {1476-4687}, + journal = {Nature}, + keywords = {{\textgreater}UseGalaxy.eu, Centromeres, Genetic variation, Genome assembly algorithms, Genomics}, + language = {en}, + month = {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{jude_draft_2019, + abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.}, + author = {Jude, Brooke A.}, + doi = {10.1128/MRA.00683-19}, + editor = {Dunning Hotopp, Julie C.}, + issn = {2576-098X}, + journal = {Microbiology Resource Announcements}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, language = {en}, month = {August}, number = {35}, @@ -2048,6 +2703,27 @@ @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{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 +2765,76 @@ @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} +} + +@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{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{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 +2848,24 @@ @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 +2878,21 @@ @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{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 +2908,25 @@ @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.}, @@ -2272,6 +3070,23 @@ @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}, @@ -2376,6 +3191,28 @@ @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{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}, @@ -2441,6 +3278,40 @@ @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}, @@ -2486,6 +3357,23 @@ @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 +3519,23 @@ @article{maier_ready--use_2021 year = {2021} } +@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}, @@ -2719,6 +3624,23 @@ @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 +3723,25 @@ @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.}, @@ -2836,6 +3777,64 @@ @article{mehta_updates_2021 year = {2021} } +@article{meier_antileukemic_2022, + abstract = {The prognosis of AML patients with adverse genetics, such as a complex, monosomal karyotype and TP53 lesions, is still dismal even with standard chemotherapy. DNA-hypomethylating agent monotherapy induces an encouraging response rate in these patients. When combined with decitabine (DAC), all-trans retinoic acid (ATRA) resulted in an improved response rate and longer overall survival in a randomized phase II trial (DECIDER; NCT00867672). The molecular mechanisms governing this in vivo synergism are unclear. We now demonstrate cooperative antileukemic effects of DAC and ATRA on AML cell lines U937 and MOLM-13. By RNA-sequencing, derepression of {\textgreater}1200 commonly regulated transcripts following the dual treatment was observed. Overall chromatin accessibility (interrogated by ATAC-seq) and, in particular, at motifs of retinoic acid response elements were affected by both single-agent DAC and ATRA, and enhanced by the dual treatment. Cooperativity regarding transcriptional induction and chromatin remodeling was demonstrated by interrogating the HIC1, CYP26A1, GBP4, and LYZ genes, in vivo gene derepression by expression studies on peripheral blood blasts from AML patients receiving DAC + ATRA. The two drugs also cooperated in derepression of transposable elements, more effectively in U937 (mutated TP53) than MOLM-13 (intact TP53), resulting in a “viral mimicry” response. In conclusion, we demonstrate that in vitro and in vivo, the antileukemic and gene-derepressive epigenetic activity of DAC is enhanced by ATRA.}, + author = {Meier, Ruth and Greve, Gabriele and Zimmer, Dennis and Bresser, Helena and Berberich, Bettina and Langova, Ralitsa and Stomper, Julia and Rubarth, Anne and Feuerbach, Lars and Lipka, Daniel B. and Hey, Joschka and Grüning, Björn and Brors, Benedikt and Duyster, Justus and Plass, Christoph and Becker, Heiko and Lübbert, Michael}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41408-022-00715-4}, + issn = {2044-5385}, + journal = {Blood Cancer Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Acute myeloid leukaemia, Cancer models, Preclinical research}, + language = {en}, + month = {August}, + number = {8}, + pages = {1--13}, + shorttitle = {The antileukemic activity of decitabine upon {PML}/{RARA}-negative {AML} blasts is supported by all-trans retinoic acid}, + title = {The antileukemic activity of decitabine upon {PML}/{RARA}-negative {AML} blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation}, + url = {https://www.nature.com/articles/s41408-022-00715-4}, + urldate = {2022-08-29}, + volume = {12}, + year = {2022} +} + +@article{metris_aircraft_2023, + abstract = {Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.}, + author = {Métris, Kimberly L. and Métris, Jérémy}, + doi = {10.7717/peerj.15171}, + issn = {2167-8359}, + journal = {PeerJ}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Publisher: PeerJ Inc.}, + pages = {e15171}, + shorttitle = {Aircraft surveys for air {eDNA}}, + title = {Aircraft surveys for air {eDNA}: probing biodiversity in the sky}, + url = {https://peerj.com/articles/15171}, + urldate = {2023-04-18}, + volume = {11}, + year = {2023} +} + +@article{mevada_variant_2022, + abstract = {SARS-CoV-2 is an RNA coronavirus responsible for Acute Respiratory Syndrome (COVID-19). In January 2021, the re-occurrence of COVID-19 infection was at its peak, considered the second wave of epidemics. In the initial stage, it was considered a double mutant strain due to two significant mutations observed in their Spike protein (E484Q and L452R). Although it was first detected in India later on, it was spread to several countries worldwide, causing high fatality due to this strain. In the present study, we investigated the spreading of B.1.617 strain worldwide through 822 genome sequences submitted in GISAID on 21 April 2021. All genome sequences were analyzed for variations in genome sequences based on their effects due to changes in nucleotides. At Allele frequency 0.05, there were a total of 47 variations in ORF1ab, 22 in Spike protein gene, 6 variations in N gene, 5 in ORF8 and M gene, four mutations in Orf7a, and one nucleotide substitution observed for ORF3a, ORF6 and ORF7b gene. The clustering for similar mutations mentioned B.1.617 sub-lineages. The outcome of this study established relative occurrence and spread worldwide. The study’s finding represented that “double mutant” strain is not only spread through traveling but it is also observed to evolve naturally with different mutations observed in B.1.617 lineage. The information extracted from the study helps to understand viral evolution and genome variations of B.1.617 lineage. The results support the need of separating B.1.617 into sub-lineages.}, + author = {Mevada, Vishal and Patel, Rajesh and Dudhagara, Pravin and Gandhi, Himani and Beladiya, Urvisha and Vaghamshi, Nilam and Godhaniya, Manoj and Ghelani, Anjana}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/covid2050038}, + issn = {2673-8112}, + journal = {COVID}, + keywords = {{\textgreater}UseGalaxy.eu, B.1.617, double mutant strain of SARS-CoV-2, variant analysis}, + language = {en}, + month = {May}, + number = {5}, + pages = {513--531}, + title = {Variant {Analysis} and {Strategic} {Clustering} to {Sub}-{Lineage} of {Double} {Mutant} {Strain} {B}.1.617 of {SARS}-{CoV}-2}, + url = {https://www.mdpi.com/2673-8112/2/5/38}, + urldate = {2022-09-24}, + volume = {2}, + year = {2022} +} + @article{miao_putative_2020, abstract = {We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The feature genes, which are differentially expressed in the particular cell group, jointly discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterised by the feature genes as markers. To benchmark this approach, we use expert-annotated scRNA-seq datasets from a range of experiments, as well as comparing to existing cell annotation methods, which are all based on a pre-existing reference. We show that our method automatically identifies the 'ground truth' cell assignments with high accuracy. Moreover, our method, Single Cell Clustering Assessment Framework (SCCAF) predicts new putative biologically meaningful cell-states in published data on haematopoiesis and the human cortex. SCCAF is available as an open-source software package on GitHub (https://github.com/SCCAF/sccaf) and as a Python package index and has also been implemented as a Galaxy tool in the Human Cell Atlas.}, author = {Miao, Zhichao and Moreno, Pablo and Huang, Ni and Papatheodorou, Irene and Brazma, Alvis and Teichmann, Sarah A.}, @@ -2863,6 +3862,45 @@ @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 +3967,27 @@ @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 +4008,23 @@ @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 +4079,21 @@ @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 +4131,60 @@ @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 +4200,51 @@ @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}, @@ -3147,6 +4326,42 @@ @article{oeyen_sawfly_2020 year = {2020} } +@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}, @@ -3255,6 +4470,21 @@ @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{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}, @@ -3338,6 +4568,28 @@ @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 +4607,21 @@ @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{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}, @@ -3440,6 +4707,23 @@ @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}, @@ -3627,6 +4911,25 @@ @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.}, @@ -3677,6 +4980,25 @@ @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}, @@ -3727,6 +5049,64 @@ @article{schlecht_transcriptomic_2020 year = {2020} } +@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.}, @@ -3775,19 +5155,33 @@ @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{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 +5195,27 @@ @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 +5232,22 @@ @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 +5262,45 @@ @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{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 +5355,45 @@ @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{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{sun_complete_2021, author = {Sun, Shu-Wei and Huang, Jing-Chao and Liu, Yan-Qun}, doi = {10.1080/23802359.2021.1945975}, @@ -3915,6 +5424,25 @@ @article{sun_stencil_2022 year = {2022} } +@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, 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 +5460,28 @@ @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{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 +5607,22 @@ @article{tosar_ri-sec-seq_2021 year = {2021} } +@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}, @@ -4104,6 +5670,38 @@ @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{vaquero-sedas_epigenetic_2023, + 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 = {January}, + number = {1}, + pages = {47--55}, + title = {Epigenetic nature of {Arabidopsis} thaliana telomeres}, + url = {https://doi.org/10.1093/plphys/kiac471}, + urldate = {2023-03-15}, + volume = {191}, + 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 +5730,23 @@ @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}, @@ -4206,6 +5821,23 @@ @incollection{von_suchodoletz_lessons_2020 year = {2020} } +@article{weber_histone_2023, + abstract = {The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.}, + author = {Weber, Lisa Marie and Jia, Yulin and Stielow, Bastian and Gisselbrecht, Stephen S and Cao, Yinghua and Ren, Yanpeng and Rohner, Iris and King, Jessica and Rothman, Elisabeth and Fischer, Sabrina and Simon, Clara and Forné, Ignasi and Nist, Andrea and Stiewe, Thorsten and Bulyk, Martha L and Wang, Zhanxin and Liefke, Robert}, + doi = {10.1093/nar/gkac1188}, + issn = {0305-1048}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {2}, + pages = {574--594}, + title = {The histone acetyltransferase {KAT6A} is recruited to unmethylated {CpG} islands via a {DNA} binding winged helix domain}, + url = {https://doi.org/10.1093/nar/gkac1188}, + urldate = {2023-03-15}, + volume = {51}, + year = {2023} +} + @article{weigang_within-host_2021, 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 +5849,25 @@ @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 +5892,23 @@ @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}, @@ -4365,6 +6033,50 @@ @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{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 +6134,23 @@ @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 +6185,27 @@ @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.}, @@ -4621,6 +6371,27 @@ @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 +6411,68 @@ @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 +6485,40 @@ @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{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} +}