diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 5c45aa9d..5e066f12 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -872,6 +872,7 @@ @article{arshad_comparative_2024 abstract = {Abstract. Arshad A, Aditama R, Rahayu MS, Natawijaya A, Matra DD, Sudarsono S. 2024. Comparative study of chloroplast genomes across seven Salacca species. Biodiversitas 25: 4043-4058. Chloroplast (Cp) genomes play a vital role in comprehending plant evolution, biodiversity, and phylogenetics. Snake fruit is a tropical fruit in the Indo-Malayan region. This work compares seven Salacca species Cp genomes to clarify their genetics and evolutionary connections. Cp genomes were constructed using sequencing data from the BGISeq-500 platform and the GetOrganelle assemblers. The assembled Cp genomes have a standard four-part structure and vary in length from 157,047 to 158,182 kilobase pairs (kbp). Comparative genomics analysis found the ycf1 gene to have the highest number of single nucleotide polymorphisms (SNPs), revealing missing amino acids in Salacca affinis. The Cp genomes showed a high prevalence of mononucleotide SSR motifs. With a few exceptions, especially Salacca wallichiana, most Cp genomes showed stable borders between the large single copy (LSC), inverted repeat (IR), and short single copy (SSC) sections. This research underscores the importance of Cp genome information for identifying species, a crucial tool for evolutionary studies and breeding purposes. Furthermore, it emphasizes the intimate genetic connection between Salacca and Cocos nucifera, which contrasts with Phoenix dactylifera. This thorough research provides vital insights into the genetics of Salacca species and highlights the usefulness of Cp genome data in subsequent analyses.}, author = {Arshad, Arslan and Aditama, Redi and Rahayu, Megayani Sri and Natawijaya, Azis and Matra, Deden Deradjat and Sudarsono, Sudarsono}, copyright = {Copyright (c) 2024 Biodiversitas Journal of Biological Diversity}, + doi = {10.13057/biodiv/d251104}, issn = {2085-4722}, journal = {Biodiversitas Journal of Biological Diversity}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -964,6 +965,25 @@ @article{atxaerandio-landa_practical_2022 year = {2022} } +@article{baei_pharmacophore_2025, + abstract = {Due to its global burden, Targeting Hepatitis B virus (HBV) infection in humans is crucial. Herbal medicine has long been significant, with flavonoids demonstrating promising results. Hence, the present study aimed to establish a way of identifying flavonoids with anti-HBV activities. Flavonoid structures with anti-HBV activities were retrieved. A flavonol-based pharmacophore model was established using LigandScout v4.4. Screening was performed using the PharmIt server. A QSAR equation was developed and validated with independent sets of compounds. The applicability domain (AD) was defined using Euclidean distance calculations for model validation. The best model, consisting of 57 features, was generated. High-throughput screening (HTS) using the flavonol-based model resulted in 509 unique hits. The model’s accuracy was further validated using a set of FDA-approved chemicals, demonstrating a sensitivity of 71\% and a specificity of 100\%. Additionally, the QSAR model with two predictors, x4a and qed, exhibited predictive solid performance with an adjusted-R2 value of 0.85 and 0.90 of Q2. PCA showed essential patterns and relationships within the dataset, with the first two components explaining nearly 98\% of the total variance. Current HBV therapies tend to fail to provide a complete cure, emphasizing the need for new therapies. This study’s importance was to highlight flavonols as potential anti-HBV medicines, presenting a supplementary option for existing therapy. The QSAR model has been validated with two separate chemical sets, guaranteeing its reproducibility and usefulness for other flavonols by utilizing the predictive characteristics of X4A and qed. These results provide new possibilities for discovering future anti-HBV drugs by integrating modeling and experimental research.}, + author = {Baei, Basireh and Askari, Parnia and Askari, Fatemeh Sana and Kiani, Seyed Jalal and Mohebbi, Alireza}, + doi = {10.1371/journal.pone.0316765}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Antiviral therapy, Drug discovery, Drug research and development, Drug screening, Hepatitis B virus, High throughput screening, Library screening, Principal component analysis}, + language = {en}, + month = {January}, + note = {Publisher: Public Library of Science}, + number = {1}, + pages = {e0316765}, + title = {Pharmacophore modeling and {QSAR} analysis of anti-{HBV} flavonols}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0316765}, + urldate = {2025-01-19}, + volume = {20}, + year = {2025} +} + @article{bafna_dynamic_2023, abstract = {The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer–gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35\% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.}, author = {Bafna, Akanksha and Banks, Gareth and Hastings, Michael H. and Nolan, Patrick M.}, @@ -1968,6 +1988,26 @@ @article{bossche_critical_2021 year = {2021} } +@article{boulogne_meta-analysis_2025, + abstract = {The marine diatom Phaeodactylum tricornutum is currently used for various industrial applications, including the pharmaceutical industry as a cost-effective cell biofactory to produce Biologics. Recent studies demonstrated that P. tricornutum can produce functional monoclonal antibodies, such application is currently limited by the production yield that hinders industrialization. Therefore, it is necessary to understand and control the cell biology of P. tricornutum to improve the Biologics production yield. Transcriptomic analyses have recently been used by the pharmaceutical industry to improve the production of Biologics in mammalian cells, especially Biologics titer and cell productivity. Hence, in the present work, we performed a meta-analysis of seven publicly available RNA-Seq datasets from different strains of P. tricornutum, for which the culture conditions were chosen as similar as possible. We analyzed the differential expression of genes that are involved in biological processes that are well known to potentially impact the bioproduction and critical quality attributes of Biologics. Therefore, the expression of genes involved in the N-glycan biosynthesis, protein export and secretion, protein quality control and proteasome, as well as those encoding proteases were analyzed and compared. The results pave the way towards optimizing Biologics production in P. tricornutum and highlight that the Pt4, Pt3 Ov and Pt8 strains seem to be the most promising P. tricornutum strains.}, + author = {Boulogne, Isabelle and Toustou, Charlotte and Bardor, Muriel}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-87620-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}Plant Galaxy, {\textgreater}UseGalaxy.eu, Bioinformatics, Glycobiology, Marine biology, RNA}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {3603}, + title = {Meta-analysis of {RNA}-{Seq} datasets allows a better understanding of {P}. tricornutum cellular biology, a requirement to improve the production of {Biologics}}, + url = {https://www.nature.com/articles/s41598-025-87620-5}, + urldate = {2025-02-01}, + volume = {15}, + year = {2025} +} + @article{boutigny_direct_2023, abstract = {A targeted enrichment method was developed to sequence Xylella fastidiosa genomic DNA directly from plant samples. The method was evaluated on various plant species infected with different strains at different levels of contamination. After enrichment, X. fastidiosa genome coverage was above 99.9\% for all tested samples.}, author = {Boutigny, Anne-Laure and Remenant, Benoit and Legendre, Bruno and Beven, Véronique and Rolland, Mathieu and Blanchard, Yannick and Cunty, Amandine}, @@ -4222,7 +4262,7 @@ @article{feng_transcription_2022 @article{fernandes_alise_2023, abstract = {Alternative Splicing (AS) is a co-transcriptional mechanism that enables the eukaryote to extend its proteome even with a limited number of genes. The cellular machinery performs AS by combining alternative regions of the isoforms in both productive and non-productive transcripts. AS events can be predicted using RNASeq data. In plants, the most frequent event is the retention of introns (IR) that can have a regulatory effect, for example, inserting a premature stop codon (PTC) that leads to degradation of the transcript through the nonsense-mediated decay (NMD) pathway. To study potential AS events in the biological process of coffee bean and tomato ripening, we conducted a DAS study using RNASeq data obtained for differential expression experiment and the referential coffee genome to identify differential AS (DAS). For this, we developed pipelines in Python to perform an automated curation of the 202 target genes that were identified with 241 DAS events by rMATS in the comparisons of early green fruits, intermediate yellow and final red ripening stage. We then carried out a manual curation of the 241 events enriched with the Interproscan5 annotation with further experimentally validating of Potassium channel AKT1 and Apyrase 7 genes under differential alternative expression during coffee grain ripening using conventional PCR and qPCR. Due to challenges identified during this analysis associated with the relationship of AS events and RNASeq data processing, we built an application of user- friendly APP to predict AS in RNASeq data. The application development is composed of three modules named GeneAPPScript, GeneAPPServer, GeneAPPExplorer. The GeneAPPScript module is a powerful wrapper that enables to perform a complete DAS analysis from obtaining network data to functional annotation of genes under DAS. This module can run on Debian distros, such as the Google Collaboratory (Colab) environment where it was developed. The GeneAPPServer module is a Flask backend that allows you to integrate outputs from different DAS analysis software that generate data in tabular outputs. Using GeneAPPExplorer, the user can generate dozens of graphs to graphically visualize important results implicit in technical tables exported by DAS analysis software. In addition, through the webapp, the researcher has access to tables enriched with functional and structural annotation data and event attributes. GeneAPP will contribute to the analysis of AS in several other works deposited in public databases where only differential expression at the gene level was analyzed, allowing further explanation when exploring the transcriptome at the isoform level.}, author = {Fernandes, Miquéias}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {en}, month = {August}, note = {Accepted: 2024-04-17T00:37:44Z @@ -5744,6 +5784,26 @@ @article{hering_eikenella_2021 year = {2021} } +@article{hermawaty_novo_2025, + abstract = {Agarwood is a highly prized resinous wood produced by select members of the Thymelaeaceae plant family. Its formation in Aquilaria species has been expedited using various induction techniques, revealing insights into factors affecting the chemical constituents of artificially induced agarwood. Building on this, our research delved into the potential of another Thymelaeaceae member, Gyrinops versteegii, as an alternate agarwood source. Inoculation of juvenile G. versteegii stems with local strain of Fusarium solani successfully induced the production of sesquiterpenes and chromone compounds. On a molecular level, a de novo transcriptome reconstruction and analysis highlighted biological processes related to the plant-type hypersensitive response and DNA damage 2 days post-fungal inoculation. Notably, terpenoid biosynthesis was observed only in the group exposed to the fungus for an extended duration (28 days), where DNA damage response also played a pivotal role. Despite the inherent limitations of de novo transcriptome reconstruction, capturing only a few of sesquiterpenes biosynthesis-related genes, our findings underscore the potential of G. verteegii in producing high-quality agarwood. Future high-resolution transcriptome data could further elucidate this promising avenue.}, + author = {Hermawaty, Dina and Setyobudi, Titis and Nugrahapraja, Husna and Turjaman, Maman and Faizal, Ahmad}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-87486-7}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Metabolomics, Plant biotechnology, Plant genetics, Plant physiology, Plant stress responses, Plant symbiosis, Sequencing}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {2977}, + title = {De novo transcriptome assembly and analysis during agarwood induction in {Gyrinops} versteegii {Gilg}. seedling}, + url = {https://www.nature.com/articles/s41598-025-87486-7}, + urldate = {2025-01-27}, + volume = {15}, + year = {2025} +} + @article{hernandez_design_2020, abstract = {Biological control is emerging as a feasible alternative to chemical pesticides in agriculture. Measuring the microbial biocontrol agent (mBCA) populations in the environment is essential for an accurate risk assessment and to optimize the usage of an mBCA-based plant protection product. In this manuscript, a workflow to obtain a large number of qPCR markers suitable for robust strain-specific detection and quantification is presented. The workflow starts from whole genome sequencing data and consists on (i) identifying the strain-specific sequences, (ii) designing specific primer/probe sets for qPCR assays, and (iii) empirically verifying the performance of the assays. The first two stages involve exclusively computer work, but they are intended for researchers with little or no bioinformatic background: only knowledge of the BLAST suite tools and working with spreadsheets are required, and familiarity with the Galaxy environment and next-generation sequencing concepts are strongly advised. All bioinformatic work can be implemented using publically available resources and a regular desktop computer, no matter the operating system, connected to the Internet. The workflow was tested with 5 bacterial strains from different species under development as mBCAs, and yielded thousands of candidate markers and a triplex qPCR assay for each candidate mBCA. The qPCR assays were successfully tested in soils of different nature, water from different sources, and samples from different plant tissues. The mBCA detection limits and population dynamics in the different matrices are similar to those in qPCR assasys designed by other means. In summary a new accessible, amenable, cost-effective and robust, workflow to obtain a large number of strain-specific qPCR markers, is presented.}, author = {Hernández, Iker and Sant, Clara and Martínez, Raquel and Fernández, Carolina}, @@ -6067,6 +6127,7 @@ @article{hosseini_astrocytes_2024 @article{hosseinzadeh_gene_2023, abstract = {Heat stress in poultry houses, especially in warm areas, is one of the main environmental factors that restrict the growth of broilers or laying performance of layers, suppresses the immune system, and deteriorates egg quality and feed conversion ratio. The molecular mechanisms underlying the response of chicken to acute heat stress (AHS) have not been comprehensively elucidated. Therefore, the main object of the current work was to investigate the liver gene expression profile of chickens under AHS in comparison with their corresponding control groups, using four RNA-seq datasets. The meta-analysis, GO and KEGG pathway enrichment, WGCNA, machine-learning, and eGWAS analyses were performed. The results revealed 77 meta-genes that were mainly related to protein biosynthesis, protein folding, and protein transport between cellular organelles. In other words, under AHS, the expression of genes involving in the structure of rough reticulum membrane and in the process of protein folding was adversely influenced. In addition, genes related to biological processes such as “response to unfolded proteins,” “response to reticulum stress” and “ERAD pathway” were differentially regulated. We introduce here a couple of genes such as HSPA5, SSR1, SDF2L1, and SEC23B, as the most significantly differentiated under AHS, which could be used as bio-signatures of AHS. Besides the mentioned genes, the main findings of the current work may shed light to the identification of the effects of AHS on gene expression profiling of domestic chicken as well as the adaptive response of chicken to environmental stresses.}, author = {Hosseinzadeh, Sevda and Hasanpur, Karim}, + doi = {10.3389/fgene.2023.1102136}, issn = {1664-8021}, journal = {Frontiers in Genetics}, keywords = {{\textgreater}UseGalaxy.eu, EGWAS, Heat stress, WGCNA, chicken, machine learning}, @@ -8877,7 +8938,7 @@ @article{marzoli_next_2020 abstract = {The predator Asian hornet (Vespa velutina) represents one of the major threats to honeybee survival. Viral spillover from bee to wasp has been supposed in several studies, and this work aims to identify and study the virome of both insect species living simultaneously in the same foraging area. Transcriptomic analysis was performed on V. velutina and Apis mellifera samples, and replicative form of detected viruses was carried out by strand-specific RT-PCR. Overall, 6 and 9 different viral types were reported in V. velutina and A. mellifera, respectively, and five of these viruses were recorded in both hosts. Varroa destructor virus-1 and Cripavirus NB-1/2011/HUN (now classified as Triato-like virus) were the most represented viruses detected in both hosts, also in replicative form. In this investigation, Triato-like virus, as well as Aphis gossypii virus and Nora virus, was detected for the first time in honeybees. Concerning V. velutina, we report for the first time the recently detected honeybee La Jolla virus. A general high homology rate between genomes of shared viruses between V. velutina and A. mellifera suggests the efficient transmission of the virus from bee to wasp. In conclusion, our findings highlight the presence of several known and newly reported RNA viruses infecting A. mellifera and V. velutina. This confirms the environment role as an important source of infection and indicates the possibility of spillover from prey to predator.}, author = {Marzoli, Filippo and Forzan, Mario and Bortolotti, Laura and Pacini, Maria Irene and Rodríguez‐Flores, María Shantal and Felicioli, Antonio and Mazzei, Maurizio}, copyright = {© 2020 Wiley‐VCH GmbH}, - doi = {https://doi.org/10.1111/tbed.13878}, + doi = {10.1111/tbed.13878}, issn = {1865-1682}, journal = {Transboundary and Emerging Diseases}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Vespidae, honey bee viruses, next-generation sequencing, virology}, @@ -9324,7 +9385,7 @@ @article{miao_putative_2020 abstract = {We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The feature genes, which are differentially expressed in the particular cell group, jointly discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterised by the feature genes as markers. To benchmark this approach, we use expert-annotated scRNA-seq datasets from a range of experiments, as well as comparing to existing cell annotation methods, which are all based on a pre-existing reference. We show that our method automatically identifies the 'ground truth' cell assignments with high accuracy. Moreover, our method, Single Cell Clustering Assessment Framework (SCCAF) predicts new putative biologically meaningful cell-states in published data on haematopoiesis and the human cortex. SCCAF is available as an open-source software package on GitHub (https://github.com/SCCAF/sccaf) and as a Python package index and has also been implemented as a Galaxy tool in the Human Cell Atlas.}, author = {Miao, Zhichao and Moreno, Pablo and Huang, Ni and Papatheodorou, Irene and Brazma, Alvis and Teichmann, Sarah A.}, journal = {arXiv}, - keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods}, + keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods, ⛔ No DOI found}, month = {April}, note = {arXiv: 2004.09847 version: 1}, @@ -10549,7 +10610,7 @@ @article{omer_acemannan_2023 @article{ortega_ramirez_molecular_2024, abstract = {open}, author = {ORTEGA RAMÍREZ, JAZMÍN ALEJANDRA}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {it}, month = {December}, note = {Accepted: 2024-12-09T11:07:53Z}, @@ -10594,7 +10655,7 @@ @article{ostrovsky_using_2021 abstract = {Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density Basic Protocol 2: Calling peaks for ChIP-seq data Basic Protocol 3: Compare datasets using genomic coordinates Basic Protocol 4: Working with multiple alignments Basic Protocol 5: Single cell RNA-seq}, author = {Ostrovsky, Alexander and Hillman‐Jackson, Jennifer and Bouvier, Dave and Clements, Dave and Afgan, Enis and Blankenberg, Daniel and Schatz, Michael C. and Nekrutenko, Anton and Taylor, James and Team, the Galaxy and Lariviere, Delphine}, copyright = {© 2021 Wiley Periodicals LLC}, - doi = {https://doi.org/10.1002/cpz1.31}, + doi = {10.1002/cpz1.31}, issn = {2691-1299}, journal = {Current Protocols}, keywords = {+Education, +Galactic, +HowTo, +IsGalaxy, +Project, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Galaxy, computational biology, web application}, @@ -12024,6 +12085,50 @@ @article{rodrigues_alves_barbosa_phenotypic_2024 year = {2024} } +@misc{rodriguez-alarcon_microbial_2024, + abstract = {This study aimed to investigate the microbial diversity of bacteria in the +composite microbial community associated with Culicoides reevesi biting +midges from Buenaventura municipality in the state of Chihuahua, Mexico, +using a Sanger sequencing 16s rRNA metagenomics approach. Adult +females of Culicoides reevesi were collected by human landing catches +in the rainy season of 2023 and morphologically identified. They were +grouped into pools of 25 individuals from which genomic DNA (gDNA) was +extracted. Sanger sequencing of 16S rRNA was performed for a total of +4 pools, and the amplicon sequencing of the V3-V4 hypervariable region +was done on Illumina Mseq platform to detect bacterial communities. The +bioinformatic analysis included quality assessment, taxonomic classification, +and visualization. The evaluation of the microbial community involved +assessing taxa abundance and diversity using Mothur and QIIME2 software +included in Galaxy Tool Shed (https://usegalaxy.eu/). Our study presents, +for the first time in México and worldwide, an in-depth analysis of the +bacteriome composition in C. reevesi, utilizing a 16S rRNA metagenomic +approach. We emphasize the prevalence of dominant bacterial phyla, +particularly Proteobacteria, alongside varying abundances of Actinobacteria, +Firmicutes, Acidobacteria, and Bacteroidota, with a notable occurrence +of Tenericutes. We identified intriguing species of both human and animal +pathogenic bacteria. Moreover, we observed the absence of unidentified +bacterial sequences, alongside the presence of other bacterial groups +associated with the environment or plants. This has implications for both +healthcare and ecological management, potentially simplifying control +measures but also posing risks if the dominant species are harmful. This +research enhances our understanding of the microbiome associated with +Culicoides species, such as Culicoides reevesi, underscoring the need for +further investigation to fully grasp their ecological importance and impact on +public health.}, + author = {Rodríguez-Alarcón, Carlos Arturo and Garza Hernandez, Javier Alfonso and Gonzalez Peña, Rodolfo and Hidalgo Martínez, David Orlando and Huerta, Herón and Adame Gallegos, Jaime R. and De Luna Santillana, Erick J. and Laredo-Tiscareño, Stephanie Viridiana and García Rejón, Julian E. and Hernández-Triana, Luis M.}, + copyright = {CC0 1.0 Universal}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en\_US}, + month = {November}, + note = {Accepted: 2025-01-20T21:38:58Z}, + shorttitle = {{MICROBIAL} {DIVERSITY} {OF} {CULICOIDES} {REEVESI} {FROM} {CHIHUAHUA}, {MEXICO}}, + title = {{MICROBIAL} {DIVERSITY} {OF} {CULICOIDES} {REEVESI} {FROM} {CHIHUAHUA}, {MEXICO}: {A} {METAGENOMIC} {ANALYSIS} {OF} {RRNA} {16S}}, + type = {Memoria en abstract}, + url = {https://cathi.uacj.mx/handle/20.500.11961/30964}, + urldate = {2025-01-28}, + year = {2024} +} + @article{rogg_srgap1_2021, author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph}, doi = {10.1681/asn.2020081126}, @@ -14007,7 +14112,7 @@ @article{tetzlaff_small_2024 @article{teznerova_ago-hook_2023, abstract = {Metylace DNA řízená malými RNA (RdDM) je důležitá dráha, jež prostřednictvím navození metylace DNA reguluje genovou expresi a podílí se na obraně proti invazivním DNA elementům (zejména transposonům). Klíčovou roli v RdDM dráze hrají proteiny Argonaut (AGO) s malými RNA (sRNA), které jsou k cílové DNA sekvenčně komplementární. S proteiny Argonaut jsou schopné interagovat domény zvané AGO-hooky. U rostlin se v RdDM dráze uplatňují dva proteiny s AGO-hook doménami: NRPE1 a SPT5L. Na řešitelském pracovišti bylo nedávno objeveno, že součástí komplexu Pol V (stejně jako zmíněné dva proteiny) je ještě třetí protein SPT6L. Role SPT6L role dosud nebyla popsána, ale předpokládáme, že rovněž hraje roli v RdDM dráze. Tato práce se zabývá studiem všech tří AGO-hook domén přítomných v Pol V komplexu a jejich rolí v RdDM dráze u rostliny Arabidopsis thaliana, od přípravy mutantů postrádajících různé kombinace uvedených AGO-hook domén po studium jejich role a zastupitelnosti při metylaci DNA v různých lokusech. Klíčová slova AGO-hook, Arabidopsis thaliana, NRPE1, SPT5L, SPT6L, siRNA, epigenetické značení chromatinu, protein Argonaut}, author = {Teznerová, Kateřina}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {cs\_CZ}, month = {September}, note = {Accepted: 2024-09-12T06:33:52Z @@ -14102,7 +14207,7 @@ @article{thompson_draft_2024 year = {2024} } -@article{thompson_draft_2024-1, +@article{thompson_draft_2024, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, doi = {10.1128/mra.01132-23}, journal = {Microbiology Resource Announcements}, @@ -15974,7 +16079,7 @@ @article{zehr_patterns_2023 abstract = {Viruses may acquire mutations that result in a tropism shift. RNA viruses, such as Coronaviruses (CoVs), are susceptible to tropism shifts. A tropism shift occurs when a virus alters the tissue or cell type it infects, which can have important implications for disease pathogenesis, virulence, transmission, and treatment control. Tropism shifts can occur after cross-species jumps, as well as result from within-host evolution. Beyond the human host, CoVs can be highly pathogenic to a wide variety of wildlife and companion animals. A spillover event from animals to humans, resulting in a tropism shift, has occurred at some point in the evolutionary history of all three highly pathogenic human CoVs: severe acute respiratory syndrome coronavirus (SARS-CoV), middle eastern respiratory syndrome coronavirus (MERS), and severe acute respiratory syndrome 2 (SARS-CoV-2). Therefore, studying the evolution of CoVs in non-human animals may be of critical importance for pandemic prevention. This was the focus of my dissertation, to apply state-of-the-art codon models of evolution to a variety of CoV viral sequences to identify how natural selection may alter viral proteins priming them for tropism shifts. Statistical codon models can infer both which codon sites and genes have been subject to positive or negative selection, effectively differentiating signal between random mutations and those that may impact fitness. These models may also compare selection at homologous sites between different phenotypes (i.e., Spike protein sequences isolated from the gastrointestinal tract and those from macrophages) to identify where selection is acting differently between the phenotypes. In chapter 2 I examined a CoV sequence isolated from hospitalized humans in Malaysia that resembled a Canine Coronavirus (CCoV) to investigate how natural selection had shaped the Spike protein sequence in related animal CoV sequences priming it to jump into humans. In chapter 3 I compared the natural selection signals at specific codon positions in the Spike protein from sequences isolated from two separate feline tropisms (gastrointestinal and macrophage) to identity which adaptive mutations may be associated with the tropism shift and subsequent shift in virulence. This was performed on Feline Coronavirus (FCoVs), where almost 90\% of all wild and domestic cats are gastrointestinally infected with FCoVs, and infection becomes highly pathogenic as a result of the shift in tropism to the macrophages. Since intra-host evolution can impact tropism shifts, in Chapter 4 I performed a detailed high-throughout analysis of intra-host evolution of RNAseq data of Equine Coronavirus (ECoV), as well as natural selection analyses of related embecoviruses that have colonized the human host. Taken together, I report on novel signals of natural selection across viral proteins, with an emphasis on Spike, on a diverse set of CoV clades that shed light on the complexities of coronavirus evolution as it relates to tropism shifts.}, author = {Zehr, Jordan}, copyright = {http://rightsstatements.org/vocab/InC/1.0/}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {eng}, month = {May}, note = {Accepted: 2023-09-03T14:54:54Z