Showing results 501 to 520 on 7974 in total
No abstract
Evo-devo has generated great excitement in recent years, but of late the excitement seems to be waning. In part this is due to exaggerated expectations, but I think the problem has been exacerbated by poorly chosen projects. Unlike molecular taxonomy or genetics, that almost always generate publishable results from the usual experiments, poorly chosen evo-devo projects can take a great deal of work but generate no useful results. A good project tests a hypothesis, rather than simply gathering data. Projects of gradate students and post docs must safe, that is, virtually certain to generate publishable results. Systems with known genes at several levels of genetic control are safest. There are, in fact, many excellent projects, and some will be mentioned. Developmental homeostasis should be considered in evaluating genetic results. New technology is greatly enhancing the power of evo-devo. I illustrate recommendations for evo-devo with work by Kate Warner that has generated a theory for the origin of distinct sepals and petals.
.
Léo Coutellec est étudiant en thèse sous la direction d'Anne Françoise Schmidt en épistémologie et éthique. Il a reçu le prix 2008 de la société française d'histoire des sciences et des techniques pour son mémoire de Master 2 "Histoire des fondements du concept de commensalisme en biologie au XIXème siècle. Contribution à l'histoire des découvertes sur les associations chez les êtres vivants", fait à l'Université Claude Bernard Lyon 1 sous la direction d'Olivier Perru.Ce séminaire sera en français - Seminar in French
.
Microorganisms rely largely on changes of the transcriptional activity to adapt to the variations of the environment. However, it has not be possible until recently to obtain a knowledge of the transcriptional activity that could compare with the completeness of the genome sequences. Ideally the data should be unbiased with respect to the set of conditions, as well as with respect to the segments of chromosome whose transcription is assessed. The oligonucleotide tiling array technology provides this opportunity and was used in this work to quantify the transcriptional activity of B. subtilis. A set of 97 conditions (240 hybridizations) were explored to provide the broadest coverage of the biology of the bacterium. As a validation of our experimental design, we observed that most known genes belonged to the highly expressed ones in at least one condition. The data allowed the precise and systematic mapping of the transcribed regions and of the changes in transcriptional activity of B. subtilis.Here we will present our main findings concerning the architecture of transcriptional control in this versatile bacterium. We will also present two distinct statistical models motivated by the analysis of this data. The purpose of the first model is to improve the processing of the hybridization signal with a hidden-Markov model. The second model intends to relate the expression data to the presence of sequence motifs in the genome with a transdimensional MCMC algorithm.http://genome.jouy.inra.fr/~pnicolas/ A Basysbio/Bacell SysMO collaborative work.
.
Courant 2005, le constat de contamination des poissons du Rhône par les PCB près de Lyon a entraîné une série d'investigations conduisant à l'interdiction de consommation sur un secteur allant de l'amont de Lyon jusqu'à la mer Méditerranée. Alors qu'un lien a pu être mis en évidence entre la contamination des poissons et celle des sédiments, un projet de recherche a été élaboré dans le but de développer un modèle trophique décrivant le transfert des PCB du sédiment à des espèces « clés » de poissons. Des analyses PCB ont alors été réalisées sur 3 espèces de poissons (le barbeau, le chevaine et la brème, espèces longévives suffisamment communes pour être retrouver facilement dans le Rhône et susceptibles d'accumuler des PCB) et sur différentes espèces d'invertébrés faisant partie du régime alimentaire de ces poissons. Trois sites ont été échantillonnés : (1) un site de « référence », en amont de Lyon et de le première zone contaminée ; (2) un site proche de Lyon et (3) un site en aval de Lyon. A partir de l'analyse des contenus stomacaux des poissons et des données en isotopes stables (Carbone et Azote) mesurées sur les poissons et leurs potentielles sources de nourriture (invertébrés et plantes aquatiques), le réseau trophique de ces espèces a pu être décrit. Par ailleurs, les données de contamination observées ont montré un gradient de contamination des poissons entre l'amont et l'aval de Lyon, avec peu (ou pas) d'individus au dessus du seuil sanitaire (fixé à 8pg TEQ/g poids frais) en amont, et une majorité (voire une totalité) d'individus au dessus du seuil en aval. La description de cette contamination en fonction de différents facteurs explicatifs sera présentée, ainsi que les principes du modèle trophique en cours de développement. Séminaire en Français - Seminar in French
Odds ratio (OR) is a statistic commonly encountered in professional or scientific medical literature. Most readers perceive it as relative risk (RR), although most of them do not know why that would be true. But since such perception is mostly correct, there is nothing (or almost nothing) wrong with that. It is nevertheless useful to be reminded now and then what is the relation between the relative risk and the odds ratio, and when by equating the two statistics we are sometimes forcing OR to be something it is not. Another statistic which is often also perceived as a relative risk is the hazard ratio (HR). We encounter it, for example, when we fit the Cox model to survival data. Under proportional hazards it is probably "natural" to think in the following way: if the probability of death in one group is at every time point k-times as high as the probability of death in another group, then the relative risk must be k, regardless of where in time we are. Well, we shall see if this is true
The discussion on the specific roles of heredity and environment in these aggregations has been restricted by the limited amount of available empiric data combined with an incomplete understanding of the tumorigenic process. Several major advances have recently provided the potential to explore a large fraction of the human genome diversity, making effective the search for association while requiring minimal functional hypotheses. Since 2006, the genotyping of sets of DNAs on hundreds of thousand of loci has become routine practice, thus opening the Genome Wide Association Studies era. More than three hundred publications describing results of GWAS studies have now been published providing a better view on the mechanism by which genetic diversity may modulate human phenotype and disease risk. GWAS for susceptibility to over twenty different cancer types have been performed unraveling for each of type one to dozens of susceptibility loci. Observations of multiple independent hits in the same region are not infrequent with the most striking example being a 500 kb region, in the vicinity of the MYC oncogene, which harbors multiple susceptibility loci for at least 4 different cancer types. Occasionally the same susceptibility locus may be shared with other trait/disease suggesting etiological relationships. Allele specific odd ratios for common cancer are usually small (i.e. less than 1.5). There is mounting evidence that common polymorphism will only explain a small fraction of the heritability of common diseases. A complementary hypothesis posits that a substantial part of this heritability is due to many, genetically independent, rare mutations, a proposition that has recently gained experimental support. Although some of the cancer-associated markers are located within or in proximity of genes with conspicuous functional relevance to cancer, other loci are distant from any characterized gene and the altered functions remain elusive. Taking advantage of the new generation sequencing technology, search for very rare variants in candidate functional regions may provide an effective identification strategy. In contrast, definite identification of the actual genetic variation which is directly responsible for the observed association in the initial GWAS oppose major difficulties due to the presence of strong local linkage disequilibrium. GWAS and their follow-up studies still lack power to conclusively evaluate the role of gene/gene and gene/environment interaction in defining individual cancer risk. This lack of information obscures the delineation of the place that DNA typing will occupy in cancer prevention or early detection programs. .
One of the principal questions in the study of animal-bacterial interactions is: What are the cellular and molecular differences between beneficial and pathogenic associations? The study of several invertebrate symbioses has demonstrated that, although the outcomes are different, beneficial and pathogenic assocations share much of the same molecular language. This presentation will focus upon contributions to the field made by the study of the relationship between the Hawaiian bobtail squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri. In this symbiosis, the bacteria are acquired anew each generation and form persistent interactions along the apical surfaces of host epithelia, a pattern of symbiosis that is perhaps the most widespread among animals. The mechanisms underlying the processes of host-symbiont recognition, induction of partner development, and the maintenance of a balanced relationship will be highlighted.
La contamination à l'uranium appauvri et l'américium-241 représente respectivement une exposition à un métal lourd, dont la toxicité chimique domine largement le stress radiologique, et une irradiation alpha interne. Les effets de ces radionucléides ont été récemment étudiés sur plusieurs générations successives chez le microcrustacé Daphnia magna, afin d'évaluer le risque écologique lié à la présence de ces radionucléides dans les écosystèmes aquatiques. De nombreuses perturbations de l'histoire de vie (survie, fécondité, âge de maturité) et de la physiologie (nutrition, respiration, croissance en taille et masse) des daphnies, variables en fonction du contaminant considéré, de la concentration ou de la dose radiologique subie et de la durée d'exposition, ont ainsi été mises en évidence en conditions controlées au laboratoire. L'approche est pertinente sur un plan toxicologique et à l'échelle de l'organisme, tandis que les conséquences au niveau d'une population dans un contexte écologique réaliste sont plus difficiles à appréhender. Cette difficulté tient en autre au fait que les populations en milieu naturel sont constamment soumises aux variations des conditions environnementales - notamment de la ressource - qui altèrent leur capacité à survivre, croître et faire face à la toxicité des polluants. Différents modèles énergétiques (DEBtox, Production Nette) sont considérés pour simuler la dynamique de population de D. magna exposé aux différents radionucléides. Ces modèles individu-centrés décrivent l'acquisition de l'énergie via la nutrition et son allocation à la survie, la croissance et la reproduction. L'approche repose sur l'hypothèse que toute perturbation de l'acquisition d'énergie ou du coût métabolique de la survie induite par les contaminants, intervient au dépens des processus importants pour la croissance de population. On examine en particulier l'importance de prendre en compte une dynamique individuelle réaliste (la croissance lors de cycles de mues successifs dans le cas de Daphnia) pour modéliser les processus physiologiques. A terme, les modèles doivent permettre de tester à quel degré les contraintes naturelles du milieu peuvent influencer la réponse des organismes et des populations aux polluants chimiques et radiologiques.Séminaire en Français - Seminar in French
Le Biostatisticien dispose de données observées qui agissent sur son objet d'étude mais il doit prendre en compte l'existence d'autres facteurs, non observés, agissant eux aussi. En production industrielle, la quantification semble appropriée et suffisante pour évaluer le processus de fabrication. Ce n'est pas le cas en biologie à cause d'une part de la diversité qui règne dans le vivant et d'autre part sur les effets d'amplification diverses chez le vivant plus que la matière inerte.Contact: Mme Mariethé CHAUMEIL Inscription gratuite mais obligatoire avant le lundi 07 juin 2010 Courriel: mariethe.chaumeil@chu-lyon.fr
In the absence of a clear understanding of its genetic basis, Cytoplasmic Incompatibility (CI) has so far been conceptualized using a simple toxin-antitoxin model. Under this model, a symbiont's ³compatibility type² is determined by the specific interaction between two components: a modification factor (mod, expressed in sperm) and a rescue factor (resc, expressed in the eggs). Here we confront this model to a well studied, complex and puzzling CI study system: the mosquito Culex pipiens. We show that a more elaborate model is required to account for the observed pattern, including multiple mod and resc genes, and possibly quantitative variation in gene products. We develop such a model and fit its parameters to the data using a parsimony approach. We thereby produce explicit predictions with regards to the genetic architecture of CI; namely, we infer that at least five mod / resc pairs are required to explain the data. These predictions provide a starting point for future genetic and genomic analyses of CI and will hopefully contribute to the decryption of its molecular basis.
Susana Coelho will present a paper recently published in Nature by an international consortium coordinated by Roscoff on the Ectocarpus genome and the independent evolution of multicellularity in brown algae. Denis Roze will present his theoretical work on deleterious mutations and selection for sex and recombination.
Population-level effects of chemicals, for example pesticides, depend not only on exposure and toxicity but also on ecological factors. It is impossible to fully address these factors empirically. Mechanistic effect models, for example ecological models, can solve this problem. They can be used to extrapolate results from single species tests and higher tier tests to the population level and larger scales. Currently, however, there is no common framework that would allow developing such models and assessing their quality in a coherent way. The EU-funded project CREAM ("Mechanistic Effect Models for Ecological Risk Assessments of Chemicals") aims at developing and establishing such a framework. CREAM will not only focus on what Good Modelling Practice is but also on how it can be developed and established. CREAM's central approach will be to use a common framework for documenting the modelling process, dubbed TRACE (Transparent Comprehensive Modelling) documentation. TRACE provides a common structure for organizing and, at the same time, documenting the modelling process on a day-to-day basis. I will demonstrate the use of TRACE using example models. Finally, I will discuss a main further challeng of ecological modelling for chemical risk assessment: the agreement on practical but meaningful population-level endpoints.See the two regional speakers on the SEMOVI web page : http://www.cgmc.univ-lyon1.fr/Semovi/
-
-
-
-