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Search Results: 1 - 10 of 19225 matches for " Cordaux Richard "
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Insertion Sequence Inversions Mediated by Ectopic Recombination between Terminal Inverted Repeats
Alison Ling,Richard Cordaux
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015654
Abstract: Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.
Selection-Driven Extinction Dynamics for Group II Introns in Enterobacteriales
Sébastien Leclercq, Richard Cordaux
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052268
Abstract: Transposable elements (TEs) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model) or by saturation of host genomes (Sat-DE model). Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.
Modeling the amplification dynamics of human alu retrotransposons.
Hedges Dale J,Cordaux Richard,Xing Jinchuan,Witherspoon David J
PLOS Computational Biology , 2005,
Abstract: Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.
International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories
Ainouche Abdelkader,Bétermier Mireille,Chandler Mick,Cordaux Richard
Mobile DNA , 2012, DOI: 10.1186/1759-8753-3-17
Abstract: An international conference on Transposable Elements (TEs) was held 21–24 April 2012 in Saint Malo, France. Organized by the French Transposition Community (GDR Elements Génétiques Mobiles et Génomes, CNRS) and the French Society of Genetics (SFG), the conference’s goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew more than 217 attendees and most contributed through poster presentations (117), invited talks and short talks selected from poster abstracts (48 in total). The talks were organized into four scientific sessions, focused on: impact of TEs on genomes, control of transposition, evolution of TEs and mechanisms of transposition. Here, we present highlights from the talks given during the platform sessions. The conference was sponsored by Alliance pour les sciences de la vie et de la santé (Aviesan), Centre national de la recherche scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Institut de recherche pour le développement (IRD), Institut national de la recherche agronomique (INRA), Université de Perpignan, Université de Rennes 1, Région Bretagne and Mobile DNA. Chair of the organization committee Jean-Marc Deragon Organizers Abdelkader Ainouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Ga l Cristofari, Jean-Marc Deragon, Pascale Lesage, Didier Mazel, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira and Clémentine Vitte
Widespread Wolbachia infection in terrestrial isopods and other crustaceans
Richard Cordaux,Samuel Pichon,Houda Ben Afia Hatira,Vincent Doublet
ZooKeys , 2012, DOI: 10.3897/zookeys.176.2284
Abstract: Wolbachia bacteria are obligate intracellular alpha-Proteobacteria of arthropods and nematodes. Although widespread among isopod crustaceans, they have seldom been found in non-isopod crustacean species. Here, we report Wolbachia infection in fourteen new crustacean species. Our results extend the range of Wolbachia infections in terrestrial isopods and amphipods (class Malacostraca). We report the occurrence of two different Wolbachia strains in two host species (a terrestrial isopod and an amphipod). Moreover, the discovery of Wolbachia in the goose barnacle Lepas anatifera (subclass Thecostraca) establishes Wolbachia infection in class Maxillopoda. The new bacterial strains are closely related to B-supergroup Wolbachia strains previously reported from crustacean hosts. Our results suggest that Wolbachia infection may be much more widespread in crustaceans than previously thought. The presence of related Wolbachia strains in highly divergent crustacean hosts suggests that Wolbachia endosymbionts can naturally adapt to a wide range of crustacean hosts. Given the ability of isopod Wolbachia strains to induce feminization of genetic males or cytoplasmic incompatibility, we speculate that manipulation of crustacean-borne Wolbachia bacteria might represent potential tools for controlling crustacean species of commercial interest and crustacean or insect disease vectors.
A Thirty Million Year-Old Inherited Heteroplasmy
Vincent Doublet, Catherine Souty-Grosset, Didier Bouchon, Richard Cordaux, Isabelle Marcadé
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002938
Abstract: Due to essentially maternal inheritance and a bottleneck effect during early oogenesis, newly arising mitochondrial DNA (mtDNA) mutations segregate rapidly in metazoan female germlines. Consequently, heteroplasmy (i.e. the mixture of mtDNA genotypes within an organism) is generally resolved to homoplasmy within a few generations. Here, we report an exceptional transpecific heteroplasmy (predicting an alanine/valine alloacceptor tRNA change) that has been stably inherited in oniscid crustaceans for at least thirty million years. Our results suggest that this heteroplasmy is stably transmitted across generations because it occurs within mitochondria and therefore escapes the mtDNA bottleneck that usually erases heteroplasmy. Consistently, at least two oniscid species possess an atypical trimeric mitochondrial genome, which provides an adequate substrate for the emergence of a constitutive intra-mitochondrial heteroplasmy. Persistence of a mitochondrial polymorphism on such a deep evolutionary timescale suggests that balancing selection may be shaping mitochondrial sequence evolution in oniscid crustaceans.
Isolation and Characterization of Microsatellite Loci for the Isopod Crustacean Armadillidium vulgare and Transferability in Terrestrial Isopods
Isabelle Giraud, Victorien Valette, Nicolas Bech, Frédéric Grandjean, Richard Cordaux
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076639
Abstract: Armadillidium vulgare is a terrestrial isopod (Crustacea, Oniscidea) which harbors Wolbachia bacterial endosymbionts. A. vulgare is the major model for the study of Wolbachia-mediated feminization of genetic males in crustaceans. As a consequence of their impact on host sex determination mechanisms, Wolbachia endosymbionts are thought to significantly influence A. vulgare evolution on various grounds, including population genetic structure, diversity and reproduction strategies. To provide molecular tools for examining these questions, we isolated microsatellite loci through 454 pyrosequencing of a repeat-enriched A. vulgare genomic library. We selected 14 markers and developed three polymorphic microsatellite multiplex kits. We tested the kits on two A. vulgare natural populations and found high genetic variation, thereby making it possible to investigate the impact of Wolbachia endosymbionts on A. vulgare nuclear variation at unprecedented resolution. In addition, we tested the transferability of these kits by cross-species amplification in five other terrestrial isopod species harboring Wolbachia endosymbionts. The microsatellite loci showed good transferability in particular in Armadillidium nasatum and Chaetophiloscia elongata, for which these markers represent promising tools for future genetic studies.
Modeling the Amplification Dynamics of Human Alu Retrotransposons
Dale J Hedges ,Richard Cordaux ,Jinchuan Xing,David J Witherspoon,Alan R Rogers,Lynn B Jorde,Mark A Batzer
PLOS Computational Biology , 2005, DOI: 10.1371/journal.pcbi.0010044
Abstract: Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.
On the Prevention of Obesity and a Philosophy for Healthy Living  [PDF]
Richard Visser
Food and Nutrition Sciences (FNS) , 2012, DOI: 10.4236/fns.2012.37128
Abstract: Overweight and obesity have now reached historical, maximal peak values, with nearly one-third of world population suffering from these conditions. We are now witnessing the impact of this epidemic upon the global health status, with non-communicable diseases on the rise. We have also witnessed the shortcomings and failures of past actions taken when obesity is already present. In this essay the author reviews efforts made in the past regarding identification and treatment of obesity, and propose that actions should be taken before the onset of this disease, by motivating people to make intelligent, healthy choices when it comes to food and physical activity. A philosophy for healthy living should become central to the intervention actions, for them to be successful and sustained. Prevention of obesity should involve all those concerned irregardless of their position in society and curricular training, in order to create a multi-lateral, multi-national effort that will protect our families and our children from the consequences of this epidemic.
A Supportive Approach to Supervising Students Reading for a Phd in Systems and Software Engineering  [PDF]
Richard Lai
Creative Education (CE) , 2012, DOI: 10.4236/ce.2012.326138
Abstract: Supervising a PhD student is a complex teaching task as it involves a very unstructured environment and many intellectual challenges and stimuli, and it often requires a compatible student/supervisor relationship for successful outcomes. It is therefore not surprising that it has been reported that an aspect of teaching and learning that has been overlooked in higher education is research student supervision. Typical problems of poor supervision include: high rates of dissatisfaction with supervisors and high attrition rates and slow rates of completion for students. It has also been reported that there is no set prescription on appropriate and successful supervision; rather, the interactions between quality and style of supervision, and the field of study have all to be considered. It is not easy to know what a student and his/her supervisor should be doing in order to succeed. We are thus motivated to present in this paper our approach to supervising students reading for a PhD in systems and software engineering. This approach is centered on motivating students to learn and to do research by having supervisory activities that support their development throughout their candidature.
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