E-Biothon : Une plate-forme pour accélérer les recherches en biologie, santé et environnement

National audienceE-Biothon : Une plate-forme pour accélérer les recherches en biologie, santé et environnemen

High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

International audienceIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed

Molecular and elemental characterization of heavy petroleum products

Les pétroles utilisés en raffinage étant de plus en plus lourds et chargés en métaux et hétéroélements, il est d’une grande importance pour les activités de raffinage de connaître la spéciation de ces espèces au sein des produits pétroliers et leurs comportements durant les procédés de raffinage. Afin d’apporter des réponses à cette problématique des techniques de caractérisation élémentaire et moléculaire ont été utilisées notamment par ICP MS Haute Résolution et FT ICR MS respectivement. Ces techniques analytiques sont appliquées à différents échantillons pétroliers provenant parfois de procédés de raffinage et les informations obtenues au niveau élémentaire et moléculaire sont utilisées de manières complémentaires pour améliorer notre compréhension des mécanismes se produisant au sein de nos échantillons durant les activités de raffinage.The crude oils available for the refining industry are heavier and heavier and more concentrated in metals and heteroelements. It is thus of great importance to study the speciation of these species within the petroleum products and their behavior during the refining processes. To answer that problematic, elemental and molecular characterization techniques have been used, mainly High Resolution ICP MS and FT ICR MS for the elemental and molecular characterization respectively. The analytical techniques quoted are used for the analysis of several petroleum products sometimes originating from refining processes and the information obtained at the elemental and molecular level are combined to improve our understanding of the mechanisms occurring within our samples during refining activities

TransTOOL: A restructuring tool for the parallelization of applications using High Performance Fortran

International audienceno abstrac

Catalytic subunit stoichiometry within the cellulose synthase complex

Cellulose synthesis is driven by large plasma membrane-inserted protein complexes, which in plants have 6-fold symmetry. In Arabidopsis (Arabidopsis thaliana), functional cellulose synthesis complexes (CSCs) are composed of at least three different cellulose synthase catalytic subunits (CESAs), but the actual ratio of the CESA isoforms within the CSCs remains unresolved. In this work, the stoichiometry of the CESAs in the primary cell wall CSC was determined, after elimination of CESA redundancy in a mutant background, by coimmunoprecipitation and mass spectrometry using label-free quantitative methods. Based on spectral counting, we show that CESA1, CESA3, and CESA6 are present in a 1:1:1 molecular ratio

Parallel Computing: From Multicores and GPU's to Petascale. Proceedings of ParCO 2009

This book series publishes research and development results on all aspects of parallel computing. Topics may include one or more of the following: high-speed computing architectures (Grids, clusters, Service Oriented Architectures, etc.), network technology, performance measurement, system software, middleware, algorithm design, development tools, software engineering, services and applications