Article
Biology
Leila Fattel, Dennis Psaroudakis, Colleen F. Yanarella, Kevin O. Chiteri, Haley A. Dostalik, Parnal Joshi, Dollye C. Starr, Ha Vu, Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill
Summary: Genome-wide functional annotations are crucial for studying gene function and traits in plants. By comparing functional annotation data from different species, similarities and differences can be identified, leading to the generation of novel hypotheses about gene function and evolutionary relationships.
Article
Orthopedics
Xiaochen Su, Anfa Chen, Menghao Teng, Wenchen Ji, Yingang Zhang
Summary: This study identified multiple candidate genes associated with spondyloarthritis (SpA) using a tissue-specific transcriptome-wide association study (TWAS) approach. These findings may provide novel insights into the genetic mechanism, diagnosis, and treatment of SpA.
JOURNAL OF ORTHOPAEDIC SURGERY AND RESEARCH
(2023)
Article
Immunology
Jiawen Xu, Jun Ma, Yi Zeng, Haibo Si, Yuangang Wu, Shaoyun Zhang, Bin Shen
Summary: In this study, a cross-tissue transcriptome-wide association study was conducted to identify a group of genes and pathways associated with JIA, providing novel clues to uncover the pathogenesis of JIA.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Tiphaine Mace, Eliel Gonzalez-Garcia, Didier Foulquie, Fabien Carriere, Julien Pradel, Christian Durand, Sebastien Douls, Charlotte Allain, Sara Parisot, Dominique Hazard
Summary: This study conducted a genome-wide study in sheep and identified genetic variants associated with the regulation of BR. The leptin receptor gene (LEPR) was highlighted as a major candidate gene for improving adaptive capacities through genetic selection.
Article
Biochemistry & Molecular Biology
Michael Wainberg, Daniele Merico, Matthew C. Keller, Eric B. Fauman, Shreejoy J. Tripathy
Summary: This study introduces a causal gene prioritization method, PsyOPS, specifically designed for psychiatric GWAS loci. Despite its simple form, PsyOPS achieves state-of-the-art performance compared to prior methods. Genes prioritized by PsyOPS have a higher likelihood of direct regulation by GWAS variants, supported by experimental evidence.
MOLECULAR PSYCHIATRY
(2022)
Article
Cell & Tissue Engineering
J. Xu, H. Si, Y. Zeng, Y. Wu, S. Zhang, B. Shen
Summary: Through transcriptome-wide association study (TWAS), we identified 295 genes and 79 genes associated with lumbar spinal stenosis (LSS) in skeletal muscle and whole blood, respectively. Comparing with the mRNA expression profiles of LSS, 18 overlapped genes were found. This study revealed the genetic mechanism behind the pathological changes in LSS and provided new insights for early diagnosis and intervention.
BONE & JOINT RESEARCH
(2023)
Article
Cell & Tissue Engineering
J. Xu, H. Si, Y. Zeng, Y. Wu, S. Zhang, Y. Liu, M. Li, B. Shen
Summary: This study integrated gene expression and genome-wide association study data to identify potential susceptibility genes and functional pathways associated with degenerative cervical spondylosis (DCS). The findings provide new insights into the genetic mechanism of DCS development and potential targets for intervention and treatment.
BONE & JOINT RESEARCH
(2023)
Article
Critical Care Medicine
Tamara Hernandez-Beeftink, Beatriz Guillen-Guio, Jose M. Lorenzo-Salazar, Almudena Corrales, Eva Suarez-Pajes, Rui Feng, Luis A. Rubio-Rodriguez, Megan L. Paynton, Raquel Cruz, M. Isabel Garcia-Laorden, Miryam Prieto-Gonzalez, Aurelio Rodriguez-Perez, Demetrio Carriedo, Jesus Blanco, Alfonso Ambros, Elena Gonzalez-Higueras, Elena Espinosa, Arturo Muriel, Eduardo Tamayo, Maria M. Martin, Leonardo Lorente, David Dominguez, Abelardo Garcia de Lorenzo, Heather M. Giannini, John P. Reilly, Tiffanie K. Jones, Jose M. Anon, Marina Soro, Angel Carracedo, Louise Wain, Nuala J. Meyer, Jesus Villar, Carlos Flores
Summary: Sepsis is a severe systemic inflammatory response to infections with high mortality rate. First GWAS of 28-day sepsis survival identified novel variants associated with reduced survival, including a missense variant in SAMD9. Further studies with larger sample sizes are needed to validate the findings.
Article
Agriculture, Dairy & Animal Science
Y. Chen, H. Atashi, C. Grelet, R. R. Mota, S. Vanderick, H. Hu, N. Gengler
Summary: This study aimed to identify genomic regions associated with NEI and its composition traits, and analyze their functional annotation. Three genomic regions were found to explain the largest proportion of genetic variation in NEI and its composition traits, and 16 candidate genes were identified. The study provides insights into the genetic mechanisms underlying N use efficiency-related traits.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Microbiology
David S. Milner, Luis Javier Galindo, Nicholas A. T. Irwin, Thomas A. Richards
Summary: This article discusses two related topics in evolutionary microbiology: the variation of gene repertoire within species groups and the role of metabolite transporters as accessory proteins. It emphasizes the importance of improved sampling and understanding of eukaryotic microbial pangenome variation and outlines the key factors in gene duplication and transporter gene family evolution. The article also highlights the significance of functional characterization of transporter-encoding genes and analysis of their gain and loss from accessory genomes in revealing information about the ecology and virulence evolution of microbes. It advocates for the systematic study of eukaryotic pangenomes through genome sequencing and functional analysis of genes within the accessory gene repertoire.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Microbiology
Yuan Yuan, Yara Seif, Kevin Rychel, Reo Yoo, Siddharth Chauhan, Saugat Poudel, Tahani Al-bulushi, Bernhard O. Palsson, Anand Sastry
Summary: By combining pan-genome and transcriptomic analytics, variations in transcriptional regulatory networks across six strains of Salmonella enterica serovar Typhimurium were revealed.
Article
Endocrinology & Metabolism
Xiaojian Mao, Liangliang Tang, Hongyi Li, Wen Zhang, Li Liu, Heyong Wang, Abdalbari Headar
Summary: This study aims to explore the functions and gene sets of mutated genes related to hyperthyroidism in children. Through gene ontology and biological signaling pathway analysis, it was found that hormone activity and response to peptide hormone are the most significant gene ontology functions and thyroid hormone signaling pathway is the most significant biological signaling pathway. The identified mutated genes provide insights into the expected effects of multiple mutated genes on hyperthyroidism in children.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Julie Colpitts, Philip Dunstan McLoughlin, Jocelyn Poissant
Summary: This study reveals that Sable Island horses are more inbred than domestic breeds, and most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift, highlighting the value of this population as a reservoir of equine genetic variation.
Article
Biochemistry & Molecular Biology
Sean K. McKenzie, Max E. Winston, Felix Grewe, Gabriel Vargas Asensio, Natalia Rodriguez-Hernandez, Benjamin E. R. Rubin, Catalina Murillo-Cruz, Christoph von Beeren, Corrie S. Moreau, Garret Suen, Adrian A. Pinto-Tomas, Daniel J. C. Kronauer
Summary: Mass raiding evolution has made army ants dominant predators in the tropics. The genome of New World army ant Eciton burchellii is compact with a reduced gene complement, but has an expanded gene subfamily related to hydrocarbon recognition. This modification in the chemosensory system may aid in behavioral coordination and prey selection during social predation for army ants and their relatives.
Article
Genetics & Heredity
Nana Liu, Longjiang Zhang, Tian Tian, Jingliang Cheng, Bing Zhang, Shijun Qiu, Zuojun Geng, Guangbin Cui, Quan Zhang, Weihua Liao, Yongqiang Yu, Hui Zhang, Bo Gao, Xiaojun Xu, Tong Han, Zhenwei Yao, Wen Qin, Feng Liu, Meng Liang, Qiang Xu, Jilian Fu, Jiayuan Xu, Wenzhen Zhu, Peng Zhang, Wei Li, Dapeng Shi, Caihong Wang, Su Lui, Zhihan Yan, Feng Chen, Jiance Li, Jing Zhang, Dawei Wang, Wen Shen, Yanwei Miao, Junfang Xian, Jia-Hong Gao, Xiaochu Zhang, Mulin Jun Li, Kai Xu, Xi-Nian Zuo, Meiyun Wang, Zhaoxiang Ye, Chunshui Yu, CHIMGEN Consortium
Summary: Genome-wide association meta-analyses in populations of East Asian and European ancestries identify variant-trait associations for 44 hippocampal traits and provide insight into the genetic architectures of hippocampal and subfield volumes.
Article
Microbiology
Pierre-Emmanuel Douarre, Ludovic Mallet, Nicolas Radomski, Arnaud Felten, Michel-Yves Mistou
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
L. Schwendimann, D. Merda, T. Berger, S. Denayer, C. Feraudet Tarisse, A. J. Klaui, S. Messio, M. Y. Mistou, Y. Nia, J. A. Hennekinne, H. U. Graber
Summary: This study investigated the relationship between the vSa beta type, clonal complex (CC), and the production of enterotoxins SEG and SEI by Staphylococcus aureus strains. It was found that the amount of SEG and SEI produced correlated with the vSa beta type and CC of a strain, and the whole-genome sequencing data could be used to predict enterotoxin production and source of an outbreak strain. These results show promising indications for better understanding the role SEG and SEI play in foodborne outbreaks caused by S. aureus.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Federica Palma, Nicolas Radomski, Alizee Guerin, Yann Sevellec, Benjamin Felix, Arnaud Bridier, Christophe Soumet, Sophie Roussel, Laurent Guillier
Summary: The study found that mobile elements were associated with biocide tolerance in Lm strains. These elements, including prophage-related loci, the Tn6188_qacH transposon, and pLMST6_emrC plasmid, were widespread in food strains and linked to tolerance to benzalkonium-chloride and didecyldimethylammonium-chloride. Additionally, genes encoding for cell-surface proteins were associated with tolerance to benzalkonium-chloride and polymeric biguanide.
Article
Multidisciplinary Sciences
Mathilde Bonis, Arnaud Felten, Sylvie Pairaud, Angelie Dijoux, Veronique Maladen, Ludovic Mallet, Nicolas Radomski, Arnaud Duboisset, Chantal Arar, Xavier Sarda, Gaelle Vial, Michel-Yves Mistou, Olivier Firmesse, Jacques-Antoine Hennekinne, Sabine Herbin
Summary: This study revealed that Bacillus thuringiensis (Bt) could be a major causative agent of foodborne outbreaks (FBOs), with most FBO-associated Bt isolates showing a genetic relationship. More than 51% of Bt isolates were found in dishes containing raw vegetables, particularly tomatoes.
Article
Microbiology
Sabrina Cadel-Six, Emeline Cherchame, Pierre-Emmanuel Douarre, Yue Tang, Arnaud Felten, Pauline Barbet, Eva Litrup, Sangeeta Banerji, Sandra Simon, Federique Pasquali, Michele Gourmelon, Nana Mensah, Maria Borowiak, Michel-Yves Mistou, Liljana Petrovska
Summary: The study highlights the evolution of the epidemic European monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) ST34, which occurred in two steps in the 1980s and 1990s, involving the acquisition of multiple heavy metal resistances to adapt to the environment and enhance antimicrobial resistance. This evolution was facilitated by the integration of different genetic elements and phages, contributing to the spread and success of this serovar.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Adriano Di Pasquale, Nicolas Radomski, Iolanda Mangone, Paolo Calistri, Alessio Lorusso, Cesare Camma
Summary: In the face of the ongoing global pandemic, an Italian research center has established a workflow for accurately identifying PANGO lineages of SARS-CoV-2 samples and building discriminant MST to aid in fast assessment of epidemiological clusters. This method showed higher discriminatory power and speed compared to traditional phylogenomic inference methods.
Article
Microbiology
Michael Koczerka, Pierre-Emmanuel Douarre, Florent Kempf, Sebastien Holbert, Michel-Yves Mistou, Olivier Grepinet, Isabelle Virlogeux-Payant
Summary: The study revealed the widespread presence of the rck gene in various subspecies of Salmonella, raising questions about its evolution. The results emphasize the important role of rck in virulence and contribute to understanding the role of Rck in the pathogenesis of Salmonella.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biotechnology & Applied Microbiology
Federica Palma, Iolanda Mangone, Anna Janowicz, Alexandra Moura, Alexandra Chiaverini, Marina Torresi, Giuliano Garofolo, Alexis Criscuolo, Sylvain Brisse, Adriano Di Pasquale, Cesare Camma, Nicolas Radomski
Summary: This study identified parameters influencing the precision of cgMLST profiles in Listeria monocytogenes, highlighting the impact of genetic background, cgMLST workflows, completeness, depth, and breadth of coverage on precision. All tested workflows performed well at >= 40X depth of coverage, showing consistent cluster definitions using a reference cut-off of <= 7 allele differences. The research suggests that bioinformatics workflows dedicated to cgMLST allele calling are robust when paired-end reads are of high quality and sequencing depth is sufficient.
Article
Multidisciplinary Sciences
Benjamin Felix, Yann Sevellec, Federica Palma, Pierre Emmanuel Douarre, Arnaud Felten, Nicolas Radomski, Ludovic Mallet, Yannick Blanchard, Aurelie Leroux, Christophe Soumet, Arnaud Bridier, Pascal Piveteau, Eliette Ascensio, Michel Hebraud, Renata Karpiskova, Tereza Gelbicova, Marina Torresi, Francesco Pomilio, Cesare Camma, Adriano Di Pasquale, Taran Skjerdal, Ariane Pietzka, Werner Ruppitsch, Monica Ricao Canelhas, Bojan Papic, Ana Hurtado, Bart Wullings, Hana Bulawova, Hanna Castro, Miia Lindstrom, Hannu Korkeala, Zanete Steingolde, Toomas Kramarenko, Lenka Cabanova, Barbara Szymczak, Manfred Gareis, Verena Oswaldi, Elisabet Marti, Anne-Mette Seyfarth, Jean-Charles Leblanc, Laurent Guillier, Sophie Roussel
Summary: Listeria monocytogenes is a common bacterium that causes serious foodborne illness. Understanding its adaptation mechanisms in food is important for improving food safety. A dataset of genomes from Lm strains collected in 19 European countries was constructed, providing insights into Lm ecology and aiding in surveillance efforts. This dataset serves as a basis for discovering genetic traits underlying Lm adaptation to different ecological niches.
Article
Microbiology
Madeleine De Sousa Violante, Valerie Michel, Karol Romero, Laetitia Bonifait, Louise Bauge, Agnes Perrin-Guyomard, Carole Feurer, Nicolas Radomski, Ludovic Mallet, Michel-Yves Mistou, Sabrina Cadel-Six
Summary: In this study, the genomic diversity of 304 S. Mbandaka strains isolated from bovine and poultry sectors in north-western France was analyzed. The phylogenomic analysis revealed main clustering by host and emphasized the circulation of 12 different major clones, potentially related to the adaptation of the serovar in the food production chain. The identified mutations characteristic of each major cluster could be used to design useful probes for food safety surveillance.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Alessio Di Lorenzo, Iolanda Mangone, Patrizia Colangeli, Daniela Cioci, Valentina Curini, Giacomo Vincifori, Maria Teresa Mercante, Adriano Di Pasquale, Simona Iannetti
Summary: The Istituti Zooprofilattici Sperimentali (IZSs) were appointed by the Italian Ministry of Health to carry out diagnostic tests for COVID-19. The IZS-Teramo conducted tests using Real Time RT-PCR on nasopharyngeal swabs, and developed bioinformatics workflows to monitor virus variants.
Article
Biotechnology & Applied Microbiology
Pierluigi Castelli, Andrea De Ruvo, Andrea Bucciacchio, Nicola D'Alterio, Cesare Camma, Adriano Di Pasquale, Nicolas Radomski
Summary: This study investigates the impact of different machine learning methods on the source prediction performance of L. monocytogenes genomic data. The results show that accessory genes and pan kmers had higher accuracy compared to core alleles and SNPs. The accuracy was higher with 80% training dataset splitting compared to other proportions. Near-zero variance removal did not significantly affect the accuracy of core alleles, accessory genes, and pan kmers, but significantly decreased the accuracy of core SNPs. SVM and XGB models performed better than other models in terms of accuracy.
Article
Genetics & Heredity
Madeleine De Sousa Violante, Gaetan Podeur, Valerie Michel, Laurent Guillier, Nicolas Radomski, Renaud Lailler, Simon Le Hello, Francois-Xavier Weill, Michel-Yves Mistou, Ludovic Mallet
Summary: This study presents a retrospective genomic analysis of Salmonella enterica subsp. enterica Dublin outbreaks in France between 2015 and 2017. The analysis reveals the importance of geographical distance, transformation steps, and genomic diversity in the evolution of S. Dublin populations. The study also highlights the effectiveness of bacterial surveillance in representing diversity.
NAR GENOMICS AND BIOINFORMATICS
(2022)