ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes

Insertion sequences (ISs) are among the smallest and simplest autonomous transposable elements. ISfinder (http://www-is.biotoul.fr/) is a dedicated IS database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. Online tools are gradually being added. At present, it is difficult to visualize the global distribution of ISs in a given bacterial genome. Such information would facilitate understanding of the impact of these small transposable elements on shaping their host genome. Here we describe ISbrowser (http://www-genome.biotoul.fr/ISbrowser.php), an extension to the ISfinder platform and a tool which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes

Arcing on Solar Generators by Collection of Ionospheric Plasma Currents

International audienceThere are several well-known possibilities to trigger a secondary arc on solar arrays by creation of conductive plasma produced in the gap between two solar cell strings. It could be by electrostatic discharges due to an inverse potential gradient condition, micrometeoroid impacts or laser impacts. The development of electrical propulsion for satellites requires higher voltages on solar arrays. These voltages strongly modify the plasma-satellite interactions, especially by increasing the collection of plasma currents. By studying this plasma collection current on solar cell samples, we have detected secondary arcs between two strings without any triggering event as previously described. Focusing on this event, we found that a series of physical phenomena may lead to secondary arcing situation: heating by plasma current collection, outgassing, Paschen discharge conditions and then secondary arcing. We have reproduced on solar cell like samples what occurs when an arc starts and the conditions for its occurrence. Thereby, we have defined when this phenomenon is able to happen on real solar arrays

IS4 family goes genomic

<p>Abstract</p> <p>Background</p> <p>Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS<it>4 </it>family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS<it>4 </it>elements. In this study, this genomic database was used to update the structural and functional definition of the IS<it>4 </it>family.</p> <p>Results</p> <p>A total of 227 IS<it>4</it>-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS<it>4 </it>family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS<it>4 </it>elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS<it>4 </it>subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus.</p> <p>Conclusion</p> <p>The present taxonomic update of IS<it>4 </it>and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.</p

La lecture comme jeu : pratiques ludiques de la littérature en régime audiovisuel

Cet article examine la manière dont certaines cultures médiatiques instituent des mises en scène ludiques de la littérature, de la télévision à YouTube. À la télévision, le format de l’émission littéraire s’est peu à peu cristallisé comme un programme d’information, se démarquant du « monde ludique » (Jost, 1997). À l’inverse, la plateforme de partage de vidéos YouTube, mobilisant une forte culture de la « trivialité » (Jeanneret, 2008), de la participation et de la collectivité, a rapidement constitué un espace privilégié pour « jouer » avec le littéraire. S’y développent alors de nouveaux gestes ritua-lisés qui donnent lieu à des réappropriations du livre et de sa matérialité, en périphérie des enjeux textuels traditionnellement mobilisés.&nbsp;Cet article examine la manière dont certaines cultures médiatiques instituent des mises en scène ludiques de la littérature, de la télévision à YouTube. À la télévision, le format de l’émission littéraire s’est peu à peu cristallisé comme un programme d’information, se démarquant du « monde ludique » (Jost, 1997). À l’inverse, la plateforme de partage de vidéos YouTube, mobilisant une forte culture de la « trivialité » (Jeanneret, 2008), de la participation et de la collectivité, a rapidement constitué un espace privilégié pour « jouer » avec le littéraire. S’y développent alors de nouveaux gestes ritua-lisés qui donnent lieu à des réappropriations du livre et de sa matérialité, en périphérie des enjeux textuels traditionnellement mobilisés.&nbsp

Littérature populaire et sociabilités numériques : le best-seller sur YouTube

Depuis 2009, les contributions d’internautes partageant leur passion pour la littérature via la publication de vidéos se multiplient au sein de la plateforme audiovisuelle Youtube. Appelés “Booktubeurs”, ces lecteurs 2.0 forment une communauté structurée par des normes spécifiques, qui renouvellent les modes d’expression du jugement littéraire. Cet article analyse la manière dont ces nouvelles sociabilités contribuent à la mise en circulation d'une vision particulière du best-seller, influencée par le contexte médiatique dans lequel elle s’inscrit. Entre professionnalisme et amateurisme, l’hybridité du Booktubeur brouille les frontières entre littérature “légitime” et littérature “de consommation”. Au sein de ce microcosme numérique, le best-seller est associé à un imaginaire protéiforme, à la fois propre au lieu où il est évoqué, et tributaire d'une mémoire sociale indépassable.

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

Insertion sequences (ISs) play a key role in prokaryotic genome evolution but are seldom well annotated. We describe a web application pipeline, ISsaga (http://issaga.biotoul.fr/ISsaga/issaga_index.php), that provides computational tools and methods for high-quality IS annotation. It uses established ISfinder annotation standards and permits rapid processing of single or multiple prokaryote genomes. ISsaga provides general prediction and annotation tools, information on genome context of individual ISs and a graphical overview of IS distribution around the genome of interest

Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy

Background: Improving the hydrolytic performance of hemicellulases on lignocellulosic biomass is of considerable importance for second-generation biorefining. To address this problem, and also to gain greater understanding of structure-function relationships, especially related to xylanase action on complex biomass, we have implemented a combinatorial strategy to engineer the GH11 xylanase from Thermobacillus xylanilyticus (Tx-Xyn). Results: Following in vitro enzyme evolution and screening on wheat straw, nine best-performing clones were identified, which display mutations at positions 3, 6, 27 and 111. All of these mutants showed increased hydrolytic activity on wheat straw, and solubilized arabinoxylans that were not modified by the parental enzyme. The most active mutants, S27T and Y111T, increased the solubilization of arabinoxylans from depleted wheat straw 2.3-fold and 2.1-fold, respectively, in comparison to the wild-type enzyme. In addition, five mutants, S27T, Y111H, Y111S, Y111T and S27T-Y111H increased total hemicellulose conversion of intact wheat straw from 16.7%(tot. xyl) (wild-type Tx-Xyn) to 18.6% to 20.4%(tot. xyl). Also, all five mutant enzymes exhibited a better ability to act in synergy with a cellulase cocktail (Accellerase 1500), thus procuring increases in overall wheat straw hydrolysis. Conclusions: Analysis of the results allows us to hypothesize that the increased hydrolytic ability of the mutants is linked to (i) improved ligand binding in a putative secondary binding site, (ii) the diminution of surface hydrophobicity, and/or (iii) the modification of thumb flexibility, induced by mutations at position 111. Nevertheless, the relatively modest improvements that were observed also underline the fact that enzyme engineering alone cannot overcome the limits imposed by the complex organization of the plant cell wall and the lignin barrier

Drifting plasma collection by a positive biased tether wire in LEO-like plasma conditions: current measurement and plasma diagnostic

BETs is a three-year project financed by the Space Program of the European Commission, aimed at developing an efficient deorbit system that could be carried on board any future satellite launched into Low Earth Orbit (LEO). The operational system involves a conductive tape-tether left bare to establish anodic contact with the ambient plasma as a giant Langmuir probe. As a part of this project, we are carrying out both numerical and experimental approaches to estimate the collected current by the positive part of the tether. This paper deals with experimental measurements performed in the IONospheric Atmosphere Simulator (JONAS) plasma chamber of the Onera-Space Environment Department. The JONAS facility is a 9- m3 vacuum chamber equipped with a plasma source providing drifting plasma simulating LEO conditions in terms of density and temperature. A thin metallic cylinder, simulating the tether, is set inside the chamber and polarized up to 1000 V. The Earth's magnetic field is neutralized inside the chamber. In a first time, tether collected current versus tether polarization is measured for different plasma source energies and densities. In complement, several types of Langmuir probes are used at the same location to allow the extraction of both ion densities and electron parameters by computer modeling (classical Langmuir probe characteristics are not accurate enough in the present situation). These two measurements permit estimation of the discrepancies between the theoretical collection laws, orbital motion limited law in particular, and the experimental data in LEO-like conditions without magnetic fields. In a second time, the spatial variations and the time evolutions of the plasma properties around the tether are investigated. Spherical and emissive Langmuir probes are also used for a more extensive characterization of the plasma in space and time dependent analysis. Results show the ion depletion because of the wake effect and the accumulation of- ions upstream of the tether. In some regimes (at large positive potential), oscillations are observed on the tether collected current and on Langmuir probe collected current in specific sites

The Arthrobacter arilaitensis Re117 Genome Sequence Reveals Its Genetic Adaptation to the Surface of Cheese

Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe3+/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids