Showing results 581 to 600 on 7987 in total
Transposable elements (TEs) are now known to occupy a huge proportion of most multicellular eukaryotic genomes, yet the factors influencing their proliferation are only beginning to be investigated. In addition to giving a brief overview of their role in genome evolution, I will discuss recent work on a few important factors (sex, horizontal transfer, and transposition rates) that influence the coevolutionary dynamics between TEs and the host genomes they inhabit.
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L'exploration numérique de modèles, basée sur la simulation, s'est beaucoup développée depuis une quinzaine d'années. L'analyse de sensibilité globale, en particulier, permet d'étudier et comparer l'influence de paramètres ou variables d'entrée incertains sur les sorties d'un modèle, en considérant des plages de variation de ces facteurs plutôt que des dérivées autour de valeurs ponctuelles. Les principes de l'analyse de sensibilité globale seront présentés, ainsi que quelques méthodes telles que Sobol' et FAST. L'approche sera illustrée sur un modèle théorique développé pour étudier la propagation d'un champignon sur un paysage agricole.
Modularity is a characteristic of molecular evolution as it helps reuse autonomous module in different context and thus expedite evolutionary innovation. Protein domains are the evolutionary units of proteins and their rearrangements generate a rich molecular variety on which selection can act. These rearrangement processes can be well studied using HMM-based methods -- which are readily implemented in many custom databases such as PFAM or SUPERFAMILY -- because HMMs have a high accuracy and domain rearrangements occur relatively rarely compared to site based mutations. Accordingly, rearrangement events become amenable to study using the ever growing wealth of available genomes. So far, we used insect and plant genomes for comparative studies as they are well resolved and diverse taxonomic groups. We find high diversity in domain arrangements in even very closely related organisms and provide -- to the best of our knowledge for the first time -- branch specific rates for domain gain and loss and fusion and fission. We find a dramatic loss of domains along every lineage which is offset by a large number of fusion, fission and rearrangements. The majority of all new domain arrangements can be explained by just one step of modular rearrangement events but frequency of fission and terminal deletions increase over time. We find a particularly high rate of rearrangements in signaling molecules. Furthermore, newly emerging domains are predominantly single domain and have a high degree of disorder probability. They thus most likely result from neighbouring genomic regions. Most strikingly, and remniscent of the tenet that paralogs evolve fastest shortly ofter creation, we also find that novel domains establish higher copy numbers within their genomes than older domains did and are predominantly associated with environmental adaptation such as biotic defence, abiotic stress response, reproduction and development. These results also demonstrate how easily domain based analyses can analyse adaptive changes and complement other, more established methods such as site based methods or gene family growth. Current research compares signals of domain rearrangements across clades and explores methods to resolve phylogenies using domain based events instead of site based analyses.
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A good understanding of mammalian societies requires measuring patterns and comprehending processes of dispersal in each sex. We investigated dispersal behaviour in arvicoline rodents, a subfamily of mammals widespread in northern temperate environments and characterized by a multivoltine life cycle. We compared dispersal across and within species focusing on the effects of external (condition-dependent) and internal (phenotype-dependent) factors. Consequences for population genetic structures are discussed.Jean-Francois se propose aussi de donner dans l'après midi une intervention rapide de 30 mins sur le thème suivant où tous les personnels des sciences de l'environnement - écologie - évolution seraient conviésOuverture de la plateforme PLANAQUA et Ecotron IleDeFrance à la communauté nationale Jean-François Le Galliard, CNRS, Laboratoire Ecologie-Evolution, CEREEP-Ecotron IleDeFrance, Paris Le CEREEP-Ecotron IleDeFrance coordonne pour l'Institut Ecologie-Environnement et l'Ecole normale supérieure la construction d'une série de plateformes expérimentales dédiées à la recherche en écologie. En 2013, le centre procédera à l'ouverture nationale de deux équipements récemments installés sur site à savoir une plateforme complète de mésocosmes aquatiques et un premier ensemble d'Ecolabs, simulateurs climatiques dédiés à l'étude des écosystèmes confinés et inscrits dans la TGIR Ecotrons du CNRS. Au cours de ce bref exposé, les caractéristiques techniques de ces équipements ainsi que les procédures de dépôt des projets pour l'année 2013 seront décrites.
(travail en collaboration avec A. Arribas-Gil, Univ. Carlos III, Madrid) Dans cet exposé, je parlerai tout d'abord de l'alignement statistique de 2 séquences, qui permet d'aligner ces séquences sans choisir a priori les paramètres de l'alignement. Ces paramètres sont en fait déterminés par maximum de vraisemblance, dans un modèle d'évolution de ces deux séquences. Dans un second temps, je montrerai commen on peut modifier l'algorithme d'alignement statistique pour prendre en compte la non indépendance dans l'évolution des sites de la séquence. J'illustre ces résultats sur une paire de séquences "jouet" (alpha-globine humaine HBA1 et pseudo-gène HBPA1).
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http://www.beldade.nl/
Mammals show a broad array of different life history strategies. Theory suggests that this diversity has evolved because organisms are constrained in their ability to invest in two or more life history traits, and so must trade-off investment in different components. The proximate underlying causes for these trade-offs are largely unknown. I will first present results from experiments that test whether oxidative stress, a pathological process involved in ageing, is a physiological cost of reproduction in house mice (Mus musculus domesticus). I explore whether oxidative stress increases during energetically demanding reproductive periods, such as lactation in females, or accumulates after a long period of reproductive investment. I will then discuss a recent comparative study across mammals. Here I explore how the placenta, an organ that exhibits great morphological diversity, has evolved in relation to different life history strategies.
Le Cancer Survival Group (London School of Hygiene and Tropical Medicine) concentre ses efforts de recherche des 10 dernières années sur les inégalités de survie du cancer et les mécanismes sous-jacents. Nous nous sommes particulièrement intéressés aux inégalités géographiques et socio-économiques au Royaume-Uni. Cette présentation décrira les méthodes utilisées, les principaux résultats et leurs présentations dans un format utilisable en santé publique et par les responsables des soins de santé.
http://compgen.bscb.cornell.edu/~acs/Quelques références représentatives:• Guertin MJ*, Martins AL*, Siepel A, Lis JT. Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genetics, 2012;8(3):e1002610.• Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et. al. (63 co-authors). A high-resolution map of evolutionary constraint in the human genome based on 29 eutherian mammals. Nature 478(7370):476-482, 2011.• Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43(10):1031-1034, 2011.• Lowe CB, Kellis M, Siepel A, Raney B, Clamp M, Salama SR, Kingsley D, Lindblad-Toh K, Haussler D. Three different periods of regulatory innovation during vertebrate evolution. Science 333(6045):1019-1024, 2011.• Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: Phylogenetic analysis with space/time models. Briefings in Bioinformatics 12(1):41-51, 2011.• Vinar T, Brejova B, Song G, Siepel A. Reconstructing histories of complex gene clusters on a phylogeny. J Comput Biol 17(9):1267-1279, 2010.• Pollard KS, Hubisz MJ, Rosenboom K, Siepel A. Detection of non-neutral substitution rates on Mammalian phylogenies. Genome Res, 20:110-121, 2010.• Siepel A. Phylogenomics of primates and their ancestral populations. Genome Res, 19:1929-1941, 2009.• Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes. PLoS Genet, 4(8):e1000144, 2008..
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Background. Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular.Result. We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, which models possibly duplicated ancestral genes. We also prove that for matrices with rows of degrees 2 and 3, without multiplicity and without weights on the rows, the problem is NP-complete, thus tracing sharp tractability boundaries. I also give a preliminary result on a method for generating these binary matrices of degree 2, i.e., a method for inferring ancestral adjacencies, and how the Linearization Problem fits into this larger context.Conclusion. As it happened for the breakpoint median problem, also used in ancestral genome reconstruction, relaxing the definition of a genome turns an intractable problem into a tractable one. The relaxation is adapted to some biological contexts, such as bacterial genomes with several replicons, possibly partially assembled. Algorithms can also be used as heuristics for hard variants. More generally, this work opens a way to better understand linearization results for ancestral genome structure inference.
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Apres une introduction aux modeles de Hawkes multivaries, j'expliquerai en detail en quoi ces processus peuvent etre pertinents pour modeliser les distances evitees ou favorisees entre motifs (ou elements regulateurs de la transcription) le long de la chaine d'ADN, mais aussi pour modeliser les interactions entre trains de potentiels d'action en neurosciences. Apres avoir explique quels sont les principaux moyens pour estimer de maniere parametrique dans ces modeles les fonctions d'interaction, je detaillerai comment s'affranchir d'hypotheses parametriques sur ces fonctions et obtenir une methode statistique qui s'adapte aux donnees sans que l'on ait aucune hypothese majeure a faire. Je finirai en expliquant que l'on peut tester que ces modeles sont valides sur les donnees en question.
Francisella tularensis is a Gram-negative bacterium causing tularemia in humans. This zoonotic agent can infect a wide range of hosts including amoebae, arthropods and mammals. The ability of Francisella to cause disease is linked to its ability to replicate within host cells. Upon phagocytosis by macrophages, Francisella escapes from the phagosome to reach the host cytosol where it can replicate to very high numbers. I will present both the virulence factors controlling the intracellular life cycle and the host factors that detect Francisella in the host cytosol leading to the mounting of an efficient immune response.