I’ll describe our recent efforts to model protein evolution and amino-acid substitutions by (1) designing an easy to use pipeline to estimate amino-acid replacement matrices for specific protein groups, (2) using the knowledge of the protein structure, when available, (3) simplifying mixture models that have been proposed so far.

Originally it was thought that, at least in eukaryotes, gene order is random. However, in all well studied genomes genes of similar expression sit in close proximity to each other. Why is this? In this talk I'll present evidence that gene order is in part selected as it affects the noise level of genes. This explains operons organization in bacteria, clustering of essential genes and gene orientation in yeast

Is protein evolution just about protein function? In this talk I'll show that the processes involved in protein manufacture, rather than end-function, have a major role in determining rates of evolution and choice of both codons and amino acids. I'll examine in detail two issues, splicing and nucleosome occupancy

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Aging is an intrinsic feature of living organisms, which is partly genetically determined. In budding yeast, a mother cell can produce a limited number of daughter cells before it enters senescence. Over the last fifteen years, budding yeast has emerged as a compelling organism in which to investigate the genetic mechanisms that regulate longevity. Yet a precise and quantitative understanding of the transition to replicative senescence is still missing, in part because of the lack of techniques to monitor age-induced cellular processes over a long enough period of time. We have developed a new microfluidics technique to track the successive divisions of single yeast cells from birth to death under the microscope. Using this methodology, we have started to characterize the transition to replicative senescence in a quantitative manner using custom data analysis. Our data reveal that aging cells experience a large variability in cell cycle durations and undergo stochastic and partially…

DNA methyltransferases are best known as components of restriction-modification (R-M) systems. These serve as a form of immune response for bacteria against incoming DNA. However, these are also selfish elements acting akin to toxin-antitoxin systems. In addition, there are also solitary methyltransferases, which are not associated with restriction enzymes. These may have core regulatory functions, as best studied for the Dam methylase in E. coli; and / or they may confer protection against parasitism by R-M systems, as demonstrated for the Dcm methylase in E. coli. Here I will talk about a comparative genomics survey investigating the balance between the occurrences of DNA methyltransferases as solitary or R-M systems. I will finally present a discussion on the role of the DNA cytosine methyltransferase in regulating gene expression in E. coli.

L’accumulation de données de séquences chez les procaryotes pose de nombreux défis aux évolutionnistes. Tout d’abord, la prise de conscience, relativement récente, de l’importance fondamentale des transferts horizontaux dans l’évolution des procaryotes fait que l’approche phylogénétique classique, sous la forme d’un arbre des espèces unique, est sans doute un mauvais descripteur de la diversité. Les génomes procaryotes étant mieux décrits comme des mosaïques génétiques, il paraît prometteur de complémenter cette approche classique par l’exploration de méthodes alternatives, comme les forêts d’arbres ou encore les réseaux évolutionnaires. Par ailleurs, ces transferts se font souvent par l’intermédiaire d’éléments génétiques mobiles, comme les plasmides ou les virus, et il est donc essentiel d’inclure ces objets dans l’analyse pour avoir une vision plus complète de l’évolution. Enfin, la quantité considérable de séquences disponibles impose le développement de méthodes d’analyses pragmatiques, aussi rapides que possible. Cette conférence présentera quelques pistes de réponses à ces questions, en particulier…