Article
Multidisciplinary Sciences
Nathalie Feiner, Illiam S. C. Jackson, Edward L. Stanley, Tobias Uller
Summary: Anolis lizards originated in continental America, colonized the Greater Antillean islands, and recolonized the mainland, resulting in different evolutionary trajectories. The evolutionary modularity in Anolis differs between the Greater Antillean islands and the Primary Mainland group. The macroevolutionary trends of the locomotor skeleton in Anolis illustrate lasting effects of ecological opportunities on morphological diversification.
NATURE COMMUNICATIONS
(2021)
Review
Medicine, General & Internal
Rosario Vasta, Ruth Chia, Bryan J. Traynor, Adriano Chio
Summary: This review discusses the role of genetic and environmental factors in motor neuron degeneration and suggests that gene-environment interactions may contribute to the unknown etiology of ALS. Climate is the underlying basis for multiple environmental factors, and the impact of global temperature increase on gene-environment interactions should be monitored.
Article
Psychology, Multidisciplinary
Mabliny Thuany, Paulo Felipe Ribeiro Bandeira, Douglas Vieira, Katja Weiss, Beat Knechtle, Thayse Natacha Gomes
Summary: This study investigated the interplay between runners and their environment using a network approach. Public illumination in the North and Mid-West regions and sidewalks in the Northeast and Southeast regions were found to be the most important variables for runners. It is important for large countries to consider cultural, historical, and environmental backgrounds in order to improve physical activity levels and health outcomes.
FRONTIERS IN PSYCHOLOGY
(2023)
Article
Fisheries
Liang-Chun Wang, Li-Hsuan Chen, Yu-Che Chiu, Chung-Yi Liou, Han -Chung Chen, Chia-Yun Lu, Jian-Lin Chen
Summary: The mucosal microbiome has an important role in regulating host health. Research in humans and mice has provided detailed information on microbiome-host immunity interactions. Teleost fish, living in aquatic environments, have a growing body of research on the role of the mucosal microbiome, but studies on the skin microbiome have just started. This review examines the colonization of the skin microbiome, its response to environmental change, the regulation with the host immune system, and the potential study models to address current challenges.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Vipul Batra, Emily Norman, Hannah L. Morgan, Adam J. Watkins
Summary: The health of adults can be influenced by various lifestyle and environmental factors, which can increase the risk of non-communicable diseases in the future. The Developmental Origins of Health and Disease (DOHaD) concept suggests that events before birth can shape adult health, and both parents play a role in the development and well-being of their offspring. However, few studies have explored the combined influences of both parents on offspring well-being.
Article
Microbiology
Cristina Lasarte-Monterrubio, Paula Guijarro-Sanchez, Alba Belles, Juan Carlos Vazquez-Ucha, Jorge Arca-Suarez, Carlos Fernandez-Lozano, German Bou, Alejandro Beceiro
Summary: This study characterized the development of carbapenem resistance in clinical isolates of Acinetobacter junii and Acinetobacter nosocomialis due to the acquisition of a plasmid-borne bla(OXA-24/40) gene, as well as the dissemination of this gene between species of Acinetobacter for the first time. The presence of a new plasmid carrying the carbapenem-resistance gene bla(OXA-24/40) was identified in both strains, facilitating the horizontal transfer of carbapenem resistance. The identification of plasmids similar to the GR12 group carrying bla(OXA-24/40) in multiple Acinetobacter species suggests a concerning dissemination and spread of carbapenem resistance in this bacterial genus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Psychiatry
Renato Polimanti, Daniel F. Levey, Gita A. Pathak, Frank R. Wendt, Yaira Z. Nunez, Robert J. Ursano, Ronald C. Kessler, Henry R. Kranzler, Murray B. Stein, Joel Gelernter
Summary: The study revealed significant associations between multiple substance dependence diagnoses and suicidality, with genetic background moderating these associations.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Astronomy & Astrophysics
Chiara Bartolini, Alessandro Ignesti, Myriam Gitti, Fabrizio Brighenti, Anna Wolter, Alessia Moretti, Benedetta Vulcani, Bianca M. Poggianti, Marco Gullieuszik, Jacopo Fritz, Neven Tomicic
Summary: X-ray studies of jellyfish galaxies provide insights into the physics of the interaction between the interstellar medium (ISM) and intracluster medium (ICM). This study of the GASP jellyfish galaxy JO194 reveals extended X-ray emission originating from the ICM radiative cooling in the spiral arms, rather than from star formation. The observations suggest that conditions for extended X-ray emission are established at the beginning of the stripping process and can persist in galaxies in different clusters and evolutionary stages.
ASTROPHYSICAL JOURNAL
(2022)
Review
Agriculture, Dairy & Animal Science
Rodolfo Martin-del-Campo, Maria Fernanda Calderon-Campuzano, Isaias Rojas-Lleonart, Raquel Briseno-Duenas, Alejandra Garcia-Gasca
Summary: Congenital malformations can lead to embryonic mortality in sea turtles, and are caused by both genetic and environmental factors. Monitoring and controlling certain environmental factors in nesting beaches may reduce the transfer of toxic compounds to the embryos. Changes in early developmental pathways can result in congenital malformations, particularly in the craniofacial region and body regions such as the carapace.
Article
Clinical Neurology
Isabella Badini, Kaushalya Jayaweera, Gayani Pannala, Anushka Adikari, Sisira Siribaddana, Athula Sumathipala, Tom A. Mcadams, Lisa Harber-Aschan, Matthew Hotopf, Fruhling V. Rijsdijk, Helena M. S. Zavos
Summary: This study investigated the relationship between socioeconomic status and depression symptoms in a Sri Lankan population. It found that low socioeconomic status is associated with depression symptoms and that there are gender differences in the genetic influences on socioeconomic indicators. These findings have important implications for cross-cultural investigations of the role of socioeconomic factors in depression and for identifying targets for social interventions.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Article
Business, Finance
Libo Yin, Ruxue Bai
Summary: Based on information uncertainty, this paper explains the diversification discount in the Chinese A-shares market as a result of mispricing. Empirical evidence shows an overestimation of a diversified company's value due to uncertain information, with high sentiment exacerbating this overestimation. Additionally, new evidence is provided on the year breakpoint in the diversification discount, indicating a change in ex post mispricing related to the macroeconomic environment.
INTERNATIONAL REVIEW OF FINANCIAL ANALYSIS
(2023)
Article
Biology
Ella Katz, Jia-Jie Li, Benjamin Jaegle, Haim Ashkenazy, Shawn R. Abrahams, Clement Bagaza, Samuel Holden, Chris J. Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Summary: This study measured the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions and found that geography, environmental parameters, demography, and different genetic processes all influence specific chemotypes and their distribution. It revealed that causal loci in specialized metabolism contain frequent independently generated alleles, suggesting potential within-species convergence and providing a new perspective on the complexity of selective forces and mechanisms shaping allelic variation.
Article
Environmental Sciences
Xingjie Wu, Shuikuan Bei, Xi Zhou, Yu Luo, Zhibin He, Chunxu Song, Huimin Yuan, Barbara Pivato, Werner Liesack, Jingjing Peng
Summary: Cellular motility is crucial for effective colonization of the rhizosphere, and it is linked to other genetic traits. This study used metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between genetic makeup of motile bacteria and rhizosphere colonization. The results showed that genes encoding cellular motility were important predictors of bacterial niche differentiation, and highly motile genomes were more abundant in rhizosphere soil compared to bulk soil. These highly motile genomes were also enriched in beneficial traits related to carbohydrate utilization and nutrient cycling.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Neurosciences
Patricia Maidana Miguel, Michael J. Meaney, Patricia Pelufo Silveira
Summary: Executive functions (EFs) are responsible for cognitive control of emotions and behaviors, as well as information processing for learning and memory. Impairments in EFs, including attention, working memory, flexibility, and self-regulation, are associated with various psychopathologies throughout life. EF development starts in early childhood and continues into early adulthood, with vulnerability to environmental influences. Genetic factors also contribute to interindividual variation in EFs, and recent studies have explored the relationship between early-life adversity, genetics, and EF development.
BIOLOGICAL PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Miriam Merenciano, Josefa Gonzalez
Summary: Establishing causal links between adaptive mutations and ecologically relevant phenotypes is crucial but challenging. This study focuses on a natural transposable element insertion in Drosophila melanogaster and demonstrates its impact on the cold and immune stress response. The results highlight the complexity of gene-environment interactions and the importance of considering multiple developmental stages and environmental conditions when studying the effects of genetic variants.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Noemie Lefrancq, Valerie Bouchez, Nadia Fernandes, Alex-Mikael Barkoff, Thijs Bosch, Tine Dalby, Thomas Akerlund, Jessica Darenberg, Katerina Fabianova, Didrik F. Vestrheim, Norman K. Fry, Juan Jose Gonzalez-Lopez, Karolina Gullsby, Adele Habington, Qiushui He, David Litt, Helena Martini, Denis Pierard, Paola Stefanelli, Marc Stegger, Jana Zavadilova, Nathalie Armatys, Annie Landier, Sophie Guillot, Samuel L. Hong, Philippe Lemey, Julian Parkhill, Julie Toubiana, Simon Cauchemez, Henrik Salje, Sylvain Brisse
Summary: This study used 3344 sequences from 23 countries to demonstrate the presence of numerous transmission chains of Bordetella pertussis within a subnational region, and the number of chains was strongly associated with host population size. Vaccine policy has an impact on the genotype dynamics of B. pertussis, which is responsible for 160,000 deaths annually.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Virology
Fanny Laforet, Celine Antoine, Bob Blasdel Reuter, Johann Detilleux, Jean-Paul Pirnay, Sylvain Brisse, Abdoulaye Fall, Jean-Noel Duprez, Veronique Delcenserie, Damien Thiry
Summary: This study isolated and characterized two new bacteriophages against a K. pneumoniae strain from urinary tract infections. The bacteriophages showed high efficacy in vitro and in vivo, reducing bacterial titers and improving the survival of infected larvae in a G. mellonella model.
Article
Microbiology
Bertrand Neron, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, Eduardo P. C. Rocha
Summary: Integrons are flexible gene-exchanging platforms that play a crucial role in spreading antibiotic resistance genes among nosocomial pathogens. IntegronFinder, a widely used software, lacks functionality to handle large datasets. This study introduces IntegronFinder version 2, which improves efficiency and usability, allows for analysis of incomplete genome data, and includes new functions. The relevance of IntegronFinder is demonstrated by analyzing integron distribution across 20,000 genomes and identifying integrons and antibiotic resistance genes in 4,000 Klebsiella pneumoniae genomes.
Article
Biochemistry & Molecular Biology
Manuel Ares-Arroyo, Charles Coluzzi, Eduardo P.C. Rocha
Summary: Plasmids can be transferred between cells by conjugation, driving bacterial evolution. By studying plasmids in Escherichia coli and Staphylococcus aureus, we have solved the mystery of plasmid transfer mechanisms and revealed the functional dependencies between plasmids. These findings are important for understanding the evolutionary relationships of plasmids and the spread of antibiotic resistance genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Francesca D'Angelo, Eduardo P. C. Rocha, Olaya Rendueles
Summary: The extracellular capsule, a virulence factor found in many pathogens, has a controversial role in antimicrobial resistance. Our study found that noncapsulated strains of Klebsiella pneumoniae exhibited increased resistance to polymyxins, but not to other antibiotics. These findings caution against the use of therapeutic agents targeting the capsule, as it may lead to its inactivation.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Liam P. Shaw, Eduardo P. C. Rocha, R. Craig MacLean
Summary: Restriction-modification systems (R-M systems) are important defense systems in bacteria, and their distribution and impact on plasmid evolution and host range have been studied. It was found that plasmid genes are more likely to avoid R-M targets than core genes, and this avoidance is stronger in smaller plasmids with broader host ranges. Two evolutionary strategies for plasmids were identified: small plasmids adapt through sequence composition, while large plasmids adapt through carrying additional genes for protection. These findings provide evidence of the importance of R-M systems as barriers to plasmid transfer.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jorge A. Moura de Sousa, Alfred Fillol-Salom, Jose R. Penades, Eduardo P. C. Rocha
Summary: We developed SatelliteFinder to identify satellites in bacterial genomes, detecting a vast number of them, with some found in novel taxa. The gene repertoires and genomic organizations of satellites are variable but relatively conserved. The independent evolution of hijacking modules suggests that phage satellites have ancient, diverse origins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Garance Sarton-Loheac, Carlos Gustavo Nunes da Silva, Florent Mazel, Gilles Baud, Vincent de Bakker, Sudip Das, Yassine El Chazli, Kirsten Ellegaard, Marc Garcia-Garcera, Natasha Glover, Joanito Liberti, Lorena Nacif Marcal, Aiswarya Prasad, Vincent Somerville, German Bonilla-Rosso, Philipp Engel
Summary: Genomic data from six neotropical stingless bee species from Brazil revealed that most stingless bee gut bacteria are distantly related to those found in honey bees and bumblebees but have similar functional capabilities. The evolution of the social bee gut microbiota involved host switches and independent symbiont gain and losses, rather than strict codiversification. There was also substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches.
Article
Biology
Olaya Rendueles, Jorge A. M. de Sousa, Eduardo P. C. Rocha
Summary: Many bacterial genomes carry prophages that can eliminate competitors, and bacteria can develop resistance through various mechanisms, such as surface receptor modification or lysogenization. The adaptation process of phage resistance involves both genetic and non-genetic changes. Our study showed that the frequency of capsulated cells in phage-sensitive populations increased over time, indicating the fine-tuning of capsule production as an adaptation to reduce phage absorption.
Article
Genetics & Heredity
Ebenezer Foster-Nyarko, Hugh Cottingham, Ryan R. Wick, Louise M. Judd, Margaret M. C. Lam, Kelly L. Wyres, Thomas D. Stanton, Kara K. Tsang, Sophia David, David M. Aanensen, Sylvain Brisse, Kathryn E. Holt
Summary: Oxford Nanopore Technologies (ONT) sequencing has potential for genomic epidemiology and public health investigations of bacterial pathogens, but low base-call accuracy limits its reliability for critical tasks. In this study, we tested the accuracy of ONT-only assemblies for genotyping and cluster detection. We found that the SUP basecalling method performed the best, accurately identifying capsule type, multi-locus sequence type, and acquired antimicrobial resistance genes. However, cluster detection was challenging with ONT data.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Marta Lourenco, Lisa Osbelt, Virginie Passet, Francois Gravey, Daniela Megrian, Till Strowig, Carla Rodrigues, Sylvain Brisse
Summary: Klebsiella pneumoniae (Kp) is a major contributor to global antimicrobial resistance. This study presents a new strategy for isolating anti-Kp phages using capsule-deficient Kp mutants as hosts. This strategy offers promise for therapeutic development by circumventing the Kp capsule host restriction barrier.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Eve Tessier, Melanie Hennart, Edgar Badell, Virginie Passet, Julie Toubiana, Antoine Biron, Ann-Claire Gourinat, Audrey Merlet, Julien Colot, Sylvain Brisse
Summary: The study analyzed the clinical and microbiological features of Corynebacterium diphtheriae isolates in New Caledonia. The majority of isolates were from cutaneous sources and were associated with Staphylococcus aureus and/or Streptococcus pyogenes. Toxigenic isolates were observed in patients returning from Vanuatu. The isolates showed susceptibility to commonly used antibiotics. The study highlights the importance of diphtheria surveillance and improving immunization in neighboring islands.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Kristina Museux, Gabriele Arcari, Guido Rodrigo, Melanie Hennart, Edgar Badell, Julie Toubiana, Sylvain Brisse
Summary: We report on the occurrence and clinical and microbiological characteristics of infections caused by members of the CdSC in companion animals. This is the first study based on a systematic analysis of a very large animal cohort (18,308 samples) and provides data on the frequency of CdSC isolates in various types of clinical samples from animals. The findings suggest that CdSC members can cause infections in animals such as rhinitis, dermatitis, non-healing wounds, and otitis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Charles Coluzzi, Martin Guillemet, Fanny Mazzamurro, Marie Touchon, Maxime Godfroid, Guillaume Achaz, Philippe Glaser, Eduardo P. C. Rocha
Summary: Horizontal gene transfer has a significant impact on the evolution of core genes, with mutations providing resistance to antibiotics and shaping the emergence of adaptive mutations. The rapid accumulation of these mutations increases the acquisition rate of other antibiotic resistances, leading to multidrug resistance.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
