The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance. Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species. This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments. The all-intracellular bacterial order of Legionellales is much more diverse, prevalent and globally distributed than previously thought

Security enhancements for FPGA-based MPSoCs: a boot-to-runtime protection flow for an embedded Linux-based system

International audienceNowadays, embedded systems become more and more complex: the hardware/software codesign approach is a method to create such systems in a single chip which can be based on reconfigurable technologies such as FPGAs (Field-Programmable Gate Arrays). In such systems, data exchanges are a key point as they convey critical and confidential information and data are transmitted between several hardware modules and software layers. In case of an FPGA development life cycle, OS (Operating System) / data updates as runtime communications can be done through an insecure link: attackers can use this medium to make the system misbehave (malicious injection) or retrieve bitstream-related information (eavesdropping). Recent works propose solutions to securely boot a bitstream and the associated OS while runtime transactions are not protected. This work proposes a full boot-to-runtime protection flow of an embedded Linux kernel during boot and confidentiality/integrity protection of the external memory containing the kernel and the main application code/data. This work shows that such a solution with hardware components induces an area occupancy of 10% of a xc6vlx240t Virtex-6 FPGA while having an improved throughput for Linux booting and lowlatency security for runtime protection

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly

Remark on an example by R.Schoen concerning the scalar curvature

soumis à Differential Geometry and its ApplicationsGeneralization of an example by R.Schoen of multiple solutions for the Yamabe Problem on Manifolds with positive scalar curvature

Internal structure and fragmentation kinetics of silica granules

International audienceTo improve the mechanical properties of tires, silica granules can be incorporated into the elastomer as well as carbon black. Ideally, the fragmentation of the granules in the elastomer must be obtained with low mechanical stresses and lead to very small fragments distributed homogeneously in the material. On the other hand, granules must present a sufficient cohesion, in order to avoid the generation of fine particles during handling operations. Thus it appears necessary to control the mechanical strength of granules and the mechanism of their fragmentation. In this experimental study, we investigated the fragmentation of silica granules of 250 microns produced by spray drying. For this, we characterized by granulometry the evolution of the Particle Size Distribution of silica powder in water. The granules were suspended in water and submitted to ultrasounds. This treatment is used to create the fragmentation that occurs by viscous shearing in industrial rubber processing. A core-shell structure, characteristic of granules obtained by atomization process, was observed by SEM. Furthermore, by varying the intensity of mechanical stress, the multi-scale structure of granules was evidenced as well as the existence of different regimes of fragmentation. The kinetics of fragmentation was experimentally followed on two grades of silica that showed significant differences in their behavior during the fragmentation process

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Communication orale, résuméLa diversité microbienne d’un sol est difficile à caractériser. Ceci s’explique par une accessibilité plus ou moins importante des populations au sein d’une matrice hétérogène et structurée, mais aussi par l’incapacité à résoudre une information constituée de 100 000 à 1 000 000 d’espèces différentes par gramme de sol. Toutefois, récemment, d’importantes avancées en biologie moléculaire ont permis de mieux caractériser la diversité des communautés microbiennes du sol in situ et ce sans a priori. Ainsi, la puissance des nouvelles générations de séquençage comme le pyroséquençage permettent de travailler en haut-débit afin d’obtenir plusieurs dizaines, voire plusieurs centaines de milliers de séquences à partir d’un ADN méta-génomique. De premières études ont déjà été réalisées avec cette technique afin d’aborder la diversité bactérienne des sols. Ces études ont, pour la première fois, permis de quantifier de façon exhaustive la diversité microbienne de sols en termes de richesse spécifique et de démontrer la pertinence, la faisabilité et la robustesse de cette approche. Cette approche est maintenant unanimement reconnue pour sa pertinence et ses potentialités très importantes, et ce afin de déterminer la diversité des microorganismes telluriques. Notre approche consiste en la caractérisation de la diversité taxonomique (bactérienne et fongique) de sols sur des échantillonnages de grande ampleur dans le temps et dans l’espace, avec comme objectifs : (i) de faire un inventaire exhaustif de la diversité microbienne tellurique, (ii) d’évaluer sa distribution spatiale, (iii) de mieux comprendre sa régulation et, (iv) in fine, de pouvoir relier cette diversité en fonctionnement biologique du sol et en services écosystémiques [1-3]. Cependant, l’étude d’un aussi grand nombre d’échantillons va entraîner la production massive de séquences. Ce caractère massif, ainsi que les caractéristiques inhérentes aux séquences obtenues par cette technique requièrent le développement d’outils bioinformatiques adaptés, optimisés et évalués, afin d’analyser rapidement et efficacement ce type de données. Ce nouveau pipeline d’analyse doit tout d’abord être facile d’utilisation et répondre aux attentes des différents utilisateurs, qu’ils soient compétents en bio-informatique, ou novices dans l’analyse de tels jeux de données. Il doit également permettre de gérer un grand nombre de séquences et d’automatiser les grandes étapes d’analyse (prétraitement, filtration, clustérisation, assignation taxonomique, calculs d’indices d’abondance et de diversité, taux de couverture,…). L’ensemble du système devra enfin être transféré sur un serveur de calcul et accessible au travers d’un serveur Web pour être accessible à la collectivité des écologistes microbiens. L’objectif étant de coupler, sur un grand nombre d’échantillons, cette approche avec des mesures d’activités et de faire le lien entre la diversité microbienne et l’aptitude des sols à rendre des services