Recherche avancée
Affichage des résultats 161 à 180 sur 1266 au total
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Effective normalization for copy number variation in Hi-C data
Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data. Chromosome conformation data, such as Hi-C, is not different. The most widely used type of normalization of Hi-C data casts estimations of unwanted effects as a matrix balancing problem, relying on the assumption that all genomic regions interact as much as any other. Here, we show that these approaches, while very effective on fully haploid or diploid genome, fail to correct for unwanted effects in the presence of copy number variations. We propose a simple extension to matrix balancing methods that properly models the copy-number variation effects. Our approach can either retain the copy-number variation effects or remove it. We show that this leads to better downstream analysis of the three-dimensional organization of rearranged genome.
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Mechanisms of lineage-specific genome evolution in Mammals
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ECOLOGICAL-GENETIC FACTORS DETERMINING THE STRUCTURE AND FUNCTIONS OF THE MARMOT ALARM CALL
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Adult sex ratios and primate sex roles
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The rise of phenomics: photogrammetry technique applied to a study of allometry in deer antler size
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Le projet AURAGEN : présentation du projet et retombées attendues
Dans le cadre du projet France Médecine Génomique annoncé par le Premier ministre en juin 2016, deux projets pilotes de plateformes de séquençage très haut débit ont été retenues : les projets SeqOIA (Paris-Île-de-France) et AURAGEN (région Auvergne Rhône Alpes). Après quelques rappels sur le contexte du plan France Médecine génomique, le projet AURAGEN sera détaillé avec ses 5 axes : pré analytique, analytique, post analytique, médico-économique et formation. Il s'agit d'un projet de génomique qui sera inclus dans le parcours de soins des patients présentant une maladie rare ou un cancer. Nous présenterons également les projets pilotes en lien avec le plan France médecine génomique et les retombées attendues tant au niveau diagnostique que de la recherche.
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Alternative splicing in human parasites
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Male violence and sexual intimidation in wild chacma baboons
Sexual intimidation is frequent in humans, but its evolutionary origin remain speculative because few animal studies have investigated comparable, long-term forms of sexual violence. In our study, we focused on a population of wild chacma baboons and showed that males intimidate females to mate with them, and that sexual violence is the main source of injuries for females. Aggression and matings were found to be decoupled temporally, which may explain why some forms of sexual violence have been largely overlooked in well-studied animal populations. This study suggests that long-term sexual coercion may be widespread across mammalian societies, with important implications for understanding the evolution of mate choice and sexual conflict in mammals, as well as the origins of human sexual violence.
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Costs of compensatory and accelerated growth in a hibernating mammal
Yellow-bellied marmots (Marmota flaviventer) live in highly seasonal environments and have limited time for development and fat accumulation. An increase in body mass is a strong determinant of overwinter survival, thus immature marmots (juveniles and yearlings) starting the active season with low body mass may exhibit compensatory growth. Additionally, adults may exhibit accelerated fat accumulation to compensate for mass loss during hibernation. We investigated the potential costs of accelerated growth in a wild population of yellow-bellied marmots, using individual survival and longevity as proxies for fitness. Mass measurements from 2002-2015 were used to calculate individual seasonal growth rates. We estimated annual survival from 130 adults, 239 yearlings and 643 juveniles and longevity from 76 females. Individuals were distributed in two areas that differ in elevation, down- and up-valley, where the latter is an overall harsher environment. As results, juvenile survival increased with growth rate, with location and initial body mass changing the shape of this association. For yearlings, both location and initial body mass influenced the relationship between growth rate and survival. Yearlings exhibiting compensatory growth had had lower survival up-valley, and higher survival down-valley. No significant effect was found for longevity or adult annual survival. Thus, yearlings appear to represent the development stage in which the costs of rapid growth are the highest, and compensatory growth may be beneficial depending on the environmental conditions. Juveniles benefit from accelerated growth, which suggests that the conflicting demands of structural growth and fat accumulation vs. body maintenance may be less drastic at this developmental stage. Overall, the benefits and costs of rapid growth are age- and site- dependent and the costs of compensatory growth be seen in the short-term in this species, instead of paid later in life.
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Penser les origines de la vie et sa définition : deux objectifs distincts, mais indissociables. Aspects épistémologiques et historiques.
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The nature of individual and collective reactions to danger in humans: evidence from interviews with survivors of the Bataclan attacks
Individual and collective reactions to threat are largely conceived as individualistic and anti-social: when exposed to threat, humans would revert to self-preservative motives, trying to flee as fast as possible, sometimes at the expense of others. This conception, which can be traced back to the non-empirical conclusions of sociologist and social psychologist Gustave Le Bon, has met immediate intellectual success and is widespread both in academic and lay audiences. However, more recent work based on interviews with survivors from a diversity of disasters has consistently shown a very different pattern: humans do not display self-preservative behaviour when exposed to threat. In fact, they show a high degree of pro-sociality in such contexts, even when their life is directly at risk. Those results remain questionable. In particular, it is not clear how the type of danger people are exposed to can modulate their individual and collective responses to it. Another important issue is the methodology being used in those studies, which does not allow comparing between different moments of the event. Indeed, it is possible that immediate reactions to threat are self-preservative, with prosocial responses overcoming individualistic ones later on. Finally, previous work does not distinguish between genuine altruistic acts (where the action is immediately costly to the agent - eg exposing oneself to danger to help another person) and apparent altruistic behaviour (clearing an access, which directly benefits the agent). We have conducted interviews with survivors from the attacks at the Bataclan (13-11-2015 in Paris) asking them to describe with precision their own actions and others' at different moments of the attacks. In this talk, I will try to clarify the interplay between individualistic and prosocial motives and their temporality during collective exposure to deadly threat, drawing from our work with survivors from the Bataclan attacks. I will also suggest future directions to better understand the evolution of prosocial traits in such circumstances, in humans and other social species.
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Titre à venir
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New insights into the genome dynamics of the bdelloid rotifer Adineta vaga and its DNA repair mechanisms
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The behavioral ecology of predators and dangerous prey
The study of predator-prey behavior is of primary importance to the field of ecology. However, few studies measure interactions between predators and their most dangerous prey. Our team used long-term datasets from Yellowstone National Park and Scandinavia to evaluate 1) the role of cooperative hunting in the ability of predators to hunt dangerous prey, 2) how predator preference for differentially dangerous prey species changes in relation to their relative abundance, and 3) how the kill rate of a top predator was affected by the presence of another. We found that 1) wolves (Canis lupus) were more cooperative when hunting bison (Bison bison), their most dangerous North American prey, than when hunting elk (Cervus elaphus). 2) Contrary to the prey switching hypothesis, wolves in northern Yellowstone attacked and killed disproportionately more of the rarer, but safer species; wolves maintained a strong preference against bison, even when this species was more than twice as abundant as elk. Analyses of wolf-bison behavioral interactions indicate that wolf preference against bison reflected an inability to consistently overcome bison antipredator defenses. 3) Finally, although brown bears (Ursus arctos) can monopolize wolf kills, we found no support in either Yellowstone or Scandinavia for the common assumption that brown bears cause wolves to kill more often. On the contrary, our results showed the opposite effect, suggesting that brown bear presence actually reduces wolf kill rate. One potential explanation for decreased wolf kill rate is the energetic costs associated with prematurely abandoning a kill to hunt dangerous prey. This research contributes to the current body of work addressing the effects of wolf reintroduction in Yellowstone, and sheds light on the behavioral relationships at play in a special type of predator-prey interaction: predators that hunt dangerous prey.
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Transcriptomic rewiring induced by domestication : a case study in tomato
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Adaptation of A-to-I RNA editing and the impact on genome evolution
Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. We detected strong signatures of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission in Drosophila. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. If time permitting, I will also talk about other work related to adaptive evolution at the post-transcriptional level.
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Prebiotic dynamics of compartmentalized replicators
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Développement pubertaire normal et pathologique chez l'enfant
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Découverte du fonctionnement et de l'évolution d'un virus multipartite, le Faba bean necrotic stunt virus
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Sequencing and applications using Oxford Nanopore long reads at Genoscope
Sequencing by nanopore is a promising technology that makes it possible to determine the sequence of a DNA fragment without amplification and without synthesizing a DNA strand. Available since 2014 the Oxford Nanopore sequencer, named MinION, is a portable device that enables the sequencing of complex genomes at low cost. Nowadays, the MinION can deliver several gigabases of data and is able to sequence DNA fragments up to 1Mb. The presentation will provide an overview of how the device has evolved over the last two years and what are the main applications today. Next we'll end up with the presentation of the PromethION, the high-throughput platform that promise to lower the cost of sequencing a human genome to <1000$.