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Genome rearrangement: what is possible to analyze and what is not yet?
In the first part of this talk we present a recent analysis of Yersinia genomes. The Yersinia family accumulated many rearrangement mutations in the last few tenthousands years, which offers an unprecedented opportunity to study evolution of genome structure and arrangement. During the analysis, we realized that the current MCMC methods that provide samples from the posterior distribution of genome rearrangement scenarios converge slowly. The second part of the talk is about the theoretical convergence of MCMC methods for inferring genome rearrangements.
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"La morphométrie appliquée aux rongeurs: un marqueur des processus de l'évolution".
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Life history evolution in insects: resource allocation, utilization and acquisition.
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How fallow deer (Dama dama) achieve their distribution in the Preserve of Castelporziano (Italy)? Fully-explicit spatial models reveal that environmental factors prevail on optimal behaviour.
The Istituto Nazionale per la Fauna Selvatica performs consulting and research activities to promote the knowledge and the conservation of wildlife with special reference to mammals and birds. I'm working in the mammal section of the Institute and I carry on researches on the use of space, habitat and population dynamics of wild ungulates (red, roe and fallow deer, wild boars). In the last years I was interested in the problem of population estimate of wildlife population using distance sampling. At Castelporziano I developed a long-term research on ungulates of Mediterranean using capture-mark-recapture to investigate population dynamics of fallow deer and wild boar. Recently we started a project to use GPS-GSM collar to investigate habitat selection of red deer. Together with field work I'm very much interested in developing statistical and mathematical models. A recent approach was to use distance sampling data to investigate local density to be correlated with short term variation in habitat quality.
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Dynamique évolutive des associations symbiotiques: le projet SymBiocode.
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Titre.
La caractérisation de l'influence des facteurs environnementaux sur la fertilité des couples est un enjeu important de santé publique. Dans une approche épidémiologique, cette caractérisation peut reposer sur différents modes d'échantillonnage des sujets. L'approche la plus couramment utilisée est rétrospective et repose sur le recrutement de femmes ayant déjà eu une grossesse. Cette approche a l'avantage d'être simple du point de vue logistique mais exclut les couples involontairement inféconds. Nous illustrerons les conséquences de cette exclusion en termes de biais et de perte de puissance statistique à partir de simulations et de données réelles, et discuterons les intérêts et limites de trois approches alternatives : 1) l'approche de cohorte incidente (dans laquelle les couples sont recrutés avant le début d'une tentative de grossesse et suivis), 2) l'approche de cohorte prévalente (dans laquelle on recrute les couples au cours de la tentative de grossesse, avec un suivi) et 3) l'approche des durées en cours, qui repose elle aussi sur un échantillon de couples recrutés en cours de tentative de grossesse, mais sans suivi. Dans chaque cas, les modèles de survie adaptés au mode d'échantillonnage seront brièvement présentés et illustrés, notamment à partir de l'Observatoire épidémiologique de la fertilité en France. Références : Keiding, N. (1992) Independent delayed entry (with discussion). In Klein, J. P. and Goel, P. K. (eds) Survival analysis: State of the Art. Kluwer, Dordrecht, pp. 309-326. Keiding, N., Kvist, K., Hartvig, H., Tvede, M. and Juul, S. (2002) Estimating time to pregnancy from current durations in a cross-sectional sample. Biostatistics 3, 565-578. Scheike, T. H. and Keiding, N. (2006) Design and analysis of time-to-pregnancy. Stat Methods Med Res 15, 127-140. Slama, R., Kold-Jensen, T., Scheike, T., Ducot, B., Spira, A. and Keiding, N. (2004) How would a decline in sperm concentration over time influence the probability of pregnancy? Epidemiology 15, 458-465. Slama, R., Ducot, B., Carstensen, L., Lorente, C., de La Rochebrochard, E., Leridon, H., Keiding, N. and Bouyer, J. (2006) Feasibility of the Current-Duration Approach to Studying Human Fecundity. Epidemiology 17, 440-449.
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Détermination du rôle de la peptidase bactérienne PepF par inférence statistique et validation expérimentale des rôles prédits.
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Les effets des changements climatiques sur la biodiversité au Canada.
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A la recherche des sites de recombinaison méiotique: des régions cachées et mobiles dans le génome?
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Phenotypic Transitions in a multi-trait landscape
A central question in molecular evolution concerns the nature of phenotypic transitions, in particular if neutral mutations hamper or somehow facilitate adaptability of proteins or RNAs to new requirements.Proteins and RNA have been found to accomplish different task by fluctuate between different phenotypes (structures), with frequencies and thus intensity of the associated trait being proportional to their stability. Therefore, functional promiscuity may correspond to different structures with energies close to the ground state which then represent multiple selectable traits. We here postulate that these near-ground state structures facilitate smooth transitions between phenotypes. Using biophysical model systems with exhaustive mappings of genotypes (sequences) onto phenotypes (structures), we demonstrate that this is indeed possible because of a smooth gradient of stability along which any phenotype can be optimised and also because of mutational proximity of similar phenotypes in genotype space.Our model provides a rationalisation of the intriguing, and otherwise puzzling experimental observation that adaptation to new requirements, e.g. latent function of a promiscuous enzyme, can proceed while the "old", phenotypically dominant function is maintained along a series of seemingly neutral mutations.Thus pleiotropy may facilitate adaptation of latent traits BEFORE gene duplications and increase the effective adaptability of proteins
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Shape Abstraction in RNA Folding and Family Modelling
When humans reason about functional structures of RNA, they speak of long hairpins with miRNA precursors, of clover leaf structures with tRNA, of neighouring hairpins with attenuators, and so on. Most of the time, we do not care about individual base pairs or helix sizes, while the overall arrangment of helices and loops really matters.RNA folding programs, however, used to be ignorant of abstraction in RNA, deceiving us with a single, minimum free energy structure, or overwhelming us with a plethora of near-optimal structures, most of which are quite similar and therefore redundant.RNA shape abstraction alleviates this situation. RNA shapes are abstract structure images, retaining adjacency and nesting of structural features, but disregarding size information. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion in the near-optimal folding space, and provides a non-heuristic and complete account of an RNA molecule's structural inclinations. Quite magically, some long-studied problems become easy.In the presentation, I will shortly review the notion of abstract shapes. I will then discuss several applications of this concept, including a highly effective filtering method when working with structural classes of RNA described by covariance models, such as provided by the Rfam data base.
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Titre à venir
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Pour en savoir plus cliquez sur le[ lien suivant->http://biomserv.univ-lyon1.fr/~dray/sedar/ ]
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"Le Kama Sutra des nucléosomes aux promoteurs: positions, variantes et contraintes physiques".
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Approche comparative de l'optimisme dans les modèles intégrant des variables clinico-biologiques classiques et des gènes.
Avec l'introduction des biopuces dans le domaine clinique, certains auteurs ont affrmé que les biomarqueurs issus de l'étude du transcriptome avaient de meilleures capacités prédictives que les biomarqueurs clinico-biologiques connus jusqu'à maintenant. Cependant, les deux types de variables sont dans des situations très différentes ; si la plupart des biomarqueurs cliniques ont été validés, la phase de sélection est encore pleinement d'actualité pour les biomarqueurs transcriptomiques. L'objectif de ce travail a été de quantifier l'optimisme relatif aux variables transcriptomiques d'une part, et aux clinico-biologiques classiques d'autre part, quand les deux types de variables sont introduits dans un même modèle de survie. Le R_ de Kent et O'Quigley a été utilisé à cet effet. Basé sur des simulations, ce travail a permis de montrer comment le processus de sélection introduisait un fort optimisme dans le cas des gènes.Contact : Mme Mariethé CHAUMEIL Inscription gratuite mais obligatoire avant le mardi 24 juin 2008
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Titre à venir
Cyanobacteria are photossintetic procariotes that produce secundary metabolites named cyanotoxins. Cyanotoxins are classified in three main groups: the hepatotoxins, dermatotoxins and the neurotoxins. Many studies have shown that cynobacteria and their toxins exert deleterious effects in several aquatic organisms, such as acute (i.e. reduction in survivorship, feeding inhibition, paralysis) and chronic effects (i.e. reduction in growth and fecundity), besides biochemical and behavioral effects. As the main target of these toxins seem to be herbivorous zooplâncton, many research have foccused this link as the main route of cyanotoxins, showing indeed its potential for bioaccumulation in the food chain. However, the large variability found in results of many studies has lead to equivocal conclusions. Although the unequivocal evidence of deleterious effects of cyanobacteria and their toxins, the resistance of some zooplâncton species and the absence of effect of microcystins on Daphnia in some studies have lead to question the role of this toxin as a chemical defense mechanism against the zooplâncton grazing. Therefore, more studies are needed to clarify the role of cyanotoxins on aquatic organisms.
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Titre à venir
"Projet ANR "AVC - in silico" : modélisation multi-échelle des mécanismes physiopathologiques mis en jeu dans l'accident vasculaire cérébral ischémique".
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Titre à venir
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Son séminaire portera sur : "Splicing and the evolution of protein coding genes."
Pour en savoir plus sur ces activités vous pouvez consulter le lien suivant : http://www.bath.ac.uk/bio-sci/research/profiles/hurst-l.html.
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Ajustement de l'efficacité mitochondriale en réponse aux contraintes énergétiques et/ou oxydatives chez le manchot royal (Aptenodytes patagonicus) et le caneton de barbarie (Cairina moschata).
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