Search Results - "Eduardo Rocha"

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? by Rocha, Eduardo P C, Bikard, David

“…Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly,…”
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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility by Denise, Rémi, Abby, Sophie S, Rocha, Eduardo P C

“…Processes of molecular innovation require tinkering and shifting in the function of existing genes. How this occurs in terms of molecular evolution at long…”
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Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes by Treangen, Todd J, Rocha, Eduardo P C

“…Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive…”
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Genetic and life-history traits associated with the distribution of prophages in bacteria by Touchon, Marie, Bernheim, Aude, Rocha, Eduardo PC

“…Nearly half of the sequenced bacteria are lysogens and many of their prophages encode adaptive traits. Yet, the variables driving prophage distribution remain…”
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The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems by Abby, Sophie S, Rocha, Eduardo P C

“…Type 3 secretion systems (T3SSs) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the…”
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Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids by Redondo-Salvo, Santiago, Fernández-López, Raúl, Ruiz, Raúl, Vielva, Luis, de Toro, María, Rocha, Eduardo P. C., Garcillán-Barcia, M. Pilar, de la Cruz, Fernando

“…Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we…”
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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity by Maury, Mylène M, Tsai, Yu-Huan, Charlier, Caroline, Touchon, Marie, Chenal-Francisque, Viviane, Leclercq, Alexandre, Criscuolo, Alexis, Gaultier, Charlotte, Roussel, Sophie, Brisabois, Anne, Disson, Olivier, Rocha, Eduardo P C, Brisse, Sylvain, Lecuit, Marc

“…Marc Lecuit, Sylvain Brisse and colleagues combine Listeria monocytogenes population genomic data with human epidemiological and clinical data to study human…”
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The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella by Touchon, Marie, Rocha, Eduardo P C

“…Prokaryotes thrive in spite of the vast number and diversity of their viruses. This partly results from the evolution of mechanisms to inactivate or silence…”
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MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems by Abby, Sophie S, Néron, Bertrand, Ménager, Hervé, Touchon, Marie, Rocha, Eduardo P C

“…Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a…”
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Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae by Haudiquet, Matthieu, Buffet, Amandine, Rendueles, Olaya, Rocha, Eduardo P. C

“…Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the…”
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Integrative and conjugative elements and their hosts: composition, distribution and organization by Cury, Jean, Touchon, Marie, Rocha, Eduardo P C

“…Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and…”
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph by Gautreau, Guillaume, Bazin, Adelme, Gachet, Mathieu, Planel, Rémi, Burlot, Laura, Dubois, Mathieu, Perrin, Amandine, Médigue, Claudine, Calteau, Alexandra, Cruveiller, Stéphane, Matias, Catherine, Ambroise, Christophe, Rocha, Eduardo P C, Vallenet, David

“…The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in…”
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The chromosomal organization of horizontal gene transfer in bacteria by Oliveira, Pedro H., Touchon, Marie, Cury, Jean, Rocha, Eduardo P. C.

“…Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome…”
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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries by Denise, Rémi, Abby, Sophie S., Rocha, Eduardo P.C.

“…Protein secretion is important for many biotic and abiotic interactions. The evolution of protein secretion systems of bacteria, and related nanomachines,…”
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Pervasive domestication of defective prophages by bacteria by Bobay, Louis-Marie, Touchon, Marie, Rocha, Eduardo P. C.

“…Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have…”
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The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation by Guglielmini, Julien, Quintais, Leonor, Garcillán-Barcia, Maria Pilar, de la Cruz, Fernando, Rocha, Eduardo P C

“…Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and…”
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The systemic imprint of growth and its uses in ecological (meta)genomics by Vieira-Silva, Sara, Rocha, Eduardo P C

“…Microbial minimal generation times range from a few minutes to several weeks. They are evolutionarily determined by variables such as environment stability,…”
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CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins by Couvin, David, Bernheim, Aude, Toffano-Nioche, Claire, Touchon, Marie, Michalik, Juraj, Néron, Bertrand, Rocha, Eduardo P C, Vergnaud, Gilles, Gautheret, Daniel, Pourcel, Christine

“…Abstract CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive…”
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Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids by Coluzzi, Charles, Garcillán-Barcia, Maria Pilar, de la Cruz, Fernando, Rocha, Eduardo P.C.

“…Abstract Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to…”
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Phage-plasmids promote recombination and emergence of phages and plasmids by Pfeifer, Eugen, Rocha, Eduardo P. C.

“…Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the…”
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