Genome Analysis of Minibacterium massiliensis Highlights the Convergent Evolution of Water-Living Bacteria

Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a β-proteobacteria that was recovered from 0.22-μm filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors

Une approche sémantique pour représenter l'indice de végétation d'images Sentinel-2 et son évolution

Cet article propose une représentation sémantique (en RDF) d'indices de végétation calculés sur des images Sentinel-2. Cette représentation s'appuie sur une ontologie qui intègre la notion de tuile définie par l'ESA, i.e. une zone fixe de la surface terrestre. A chaque tuile, nous associons des indices de végétation calculés à partir des images dont l'emprise au sol correspond. Nous présentons cette ontologie et montrons comment ces représentations permettent d'étudier l'évolution de ces indices à partir de requêtes sur les données RDF

Marqueurs moléculaires utilisables en sélection chez la canne à sucre : cas de la résistance à la rouille brune

Les cultivars modernes de canne à sucre (Saccharum spp., 2n=100 à 130) sont hautement polyploïdes, aneuploïdes et d'origine interspécifique. Un gène majeur (Bru1) conférant la résistance à la rouille brune, causée par le champignon Puccinia melanocephala, a été identifié chez le cultivar R570. Nous avons analysé 380 cultivars modernes et clones en cours de sélection, représentatifs de la diversité mondiale, à l'aide de 22 marqueurs moléculaires regroupés dans un segment de 8,2cM génétiquement lié à Bru1 chez R570. Nos résultats révèlent un fort déséquilibre de liaison dans la région autour de Bru1 et de fortes associations entre la plupart des marqueurs et la résistance à la rouille. Deux marqueurs PCR flanquant le segment portant Bru1 sont complètement associés et sont présents uniquement chez les clones résistants. Ces marqueurs constituent des marqueurs moléculaires diagnostics de Bru1. 86% des 194 clones de canne à sucre résistants possèdent les marqueurs diagnostics de Bru1, révélant que ce gène constitue la principale source de résistance à la rouille brune chez les cultivars modernes. Les marqueurs PCR diagnostics de Bru1 devraient être particulièrement utiles pour identifier des cultivars possédant des sources de résistance alternatives à Bru1 afin de diversifier la base génétique de la résistance à la rouille brune dans les programmes de sélection. (Résumé d'auteur

Identification d'un profil de composés organiques volatils pour la détection de l'odeur de verra dans les échantillons de graisse par GC×GC-TOFMS de l'espace de tête.

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French Roadmap for complex Systems 2008-2009

This second issue of the French Complex Systems Roadmap is the outcome of the Entretiens de Cargese 2008, an interdisciplinary brainstorming session organized over one week in 2008, jointly by RNSC, ISC-PIF and IXXI. It capitalizes on the first roadmap and gathers contributions of more than 70 scientists from major French institutions. The aim of this roadmap is to foster the coordination of the complex systems community on focused topics and questions, as well as to present contributions and challenges in the complex systems sciences and complexity science to the public, political and industrial spheres

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations