diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 53adf4901..6ca67acfc 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}, @@ -106,6 +141,40 @@ @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{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}, @@ -147,6 +216,22 @@ @article{arcari_interplay_2022 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 +379,6 @@ @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}, @@ -466,6 +539,20 @@ @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 +608,26 @@ @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 +698,23 @@ @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 +735,23 @@ @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}, @@ -917,13 +1045,15 @@ @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} } @@ -1122,6 +1252,25 @@ @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 +1285,24 @@ @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 +1463,23 @@ @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{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}, @@ -1404,6 +1588,24 @@ @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 +1667,27 @@ @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 +1707,22 @@ @article{gaafar_novel_2020 year = {2020} } +@article{gallus_fructobacillus_nodate, + 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}, + 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} +} + @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 +2013,23 @@ @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}, @@ -2000,6 +2256,25 @@ @article{jalili_galaxy_2020 year = {2020} } +@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{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.}, @@ -2089,6 +2364,55 @@ @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{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 +2426,24 @@ @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}, @@ -2272,6 +2614,23 @@ @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 +2735,28 @@ @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 +2822,25 @@ @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_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}, @@ -2720,6 +3120,23 @@ @article{mauer_genomics_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_2022-1, author = {McDonald, Marisa S. and Palecanda, Sitara and Cohen, Jonathan H. and Porter, Megan L.}, doi = {10.1242/jeb.243256}, journal = {Journal of Experimental Biology}, @@ -2801,6 +3218,25 @@ @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 +3272,45 @@ @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{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 +3338,24 @@ @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{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.}, @@ -2949,6 +3442,23 @@ @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 +3513,21 @@ @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 +3565,39 @@ @article{naimi_direct_2021 year = {2021} } +@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 +3613,33 @@ @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{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}, @@ -3255,6 +3829,21 @@ @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}, @@ -3355,6 +3944,21 @@ @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}, @@ -3627,6 +4231,25 @@ @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 +4300,25 @@ @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 +4369,25 @@ @article{schlecht_transcriptomic_2020 year = {2020} } +@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{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.}, @@ -3776,18 +4437,6 @@ @article{sharma_pan-cancer_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_recapitulating_2022-1, 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}, @@ -3817,6 +4466,22 @@ @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 +4496,27 @@ @article{soares_hierarchical_2021 year = {2021} } +@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 +4571,24 @@ @article{stephen_jr_comparative_2022 year = {2022} } +@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}, @@ -3932,6 +4636,28 @@ @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 +4783,22 @@ @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 +4846,21 @@ @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{verma_identification_2022, author = {Verma, Divya and Bagchi, Preenon and IA, Shylesh Murthy}, doi = {10.21203/rs.3.rs-1253773/v1}, @@ -4132,6 +4889,23 @@ @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}, @@ -4365,6 +5139,50 @@ @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 +5240,23 @@ @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}, @@ -4640,6 +5475,25 @@ @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{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 +5506,21 @@ @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} +}