miRkwood: a tool for the reliable identification of microRNAs in plant genomes

International audienceBackground: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions. Conclusion: miRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool

GaAs photonic crystal cavity with ultra-high Q: microwatt nonlinearity at 1.55 μ\mu m

We have realized and measured a GaAs nanocavity in a slab photonic crystal based on the design by Kuramochi et al. [Appl. Phys.Lett., \textbf{88}, 041112, (2006)]. We measure a quality factor Q=700,000, which proves that ultra-high Q nanocavities are also feasible in GaAs. We show that, due to larger two-photon absorption (TPA) in GaAs, nonlinearities appear at the microwatt-level and will be more functional in gallium arsenide than in silicon nanocavities.Comment: 3 pages, 2 figures, accepted for publication in Optics Letter

El rechazo entre iguales: una visión general

III Jornadas Internacionales del Grupo GREIHablar de aceptación y rechazo entre iguales es un tema de gran relevancia en nuestro contexto social actual. Este hecho es consecuencia de la importancia que tiene la atracción interpersonal como índice de adaptación socioemocional, ya que la realidad evidencia que una buena aceptación en el grupo de compañeros y compañeras favorece una buena adaptación y bienestar socioemocional, mientras que niveles bajos de aceptación social son factores de riesgo y de problemática en el tema de interacción socialAcceptance and rejection between peers have become a relevant issue in our current social context. This is a consequence of the importance that interpersonal attraction is bestowed as a socio-emotional adaptation system. Indeed, as reality evidences, strong acceptance levels among peers foster not only better adaptation within the group but also better levels of socio-emotional well-being. However, low social acceptance levels stand as problematic risk factors regarding social interaction

Impact of Say on Pay on Executive Compensation of Firms Listed on the Toronto Stock Exchange

International audienceUnlike in a number of other countries, the United Kingdom and the United States being two examples, SoP is not prescribed by regulation in Canada. To contribute to the debate on the relevance of a regulation adapted to the Canadian context, this article measures the impact of Say on Pay in firms listed on the Toronto Stock Exchange that voluntarily adopted this practice. Based on a sample of 45 firms, the study results show that the adoption of SoP does not improve the pay-performance relationship or lead to lower executive total compensation. These findings therefore raise questions about the effectiveness of Say on Pay as a governance tool

The floristic biodiversity of poplar plantations of Champagne-Ardenne

This article essentially presents findings in the area of floristic biodiversity associated with poplar plantations in the large valleys of the Champagne area as compared to those in meadows and sub-natural forests. In addition to the current use of the soil, this study considers various factors of variation for poplar stands such as age, the presence of an understory and cropping history. The strongest effects relate to the age of the poplar stand and the presence or absence of an understory. The poplar stands of Champagne-Ardenne show significant floristic biodiversity due to their rapid dynamics (‘nested’ succession) and the divergences of plant communities depending on whether or not an understory is present. Poplar stands that have an understory are more favourable to forest communities, while poplars stands with no understory are more favourable to the flora typical of magnophorba.Cet article présente essentiellement les résultats obtenus en matière de biodiversité floristique associée aux peupleraies cultivées dans les grandes vallées de Champagne, en comparaison avec celle des prairies et des forêts subnaturelles. En dehors de l’usage actuel du sol, l’étude prend en compte divers facteurs de variation de la peupleraie tels que l’âge, la présence d’un sous-étage et l’antécédent cultural. Les effets les plus forts concernent l’âge de la peupleraie et la présence ou l’absence d’un sous-étage. Les peupleraies de Champagne-Ardenne présentent une biodiversité floristique conséquente en raison de leur dynamique rapide (succession emboîtée) et de la divergence des communautés végétales suivant la présence ou non d’un sousétage. Ainsi les peupleraies à sous-étage favorisent les communautés forestières, tandis que les peupleraies sans sous-étage favorisent la flore typique de mégaphorbiaie

Finding and analysing microRNAs in plant genomes with miRkwood

National audienceMicroRNAs (miRNAs) play a crucial role in the post-transcriptional regulation of eukaryotic gene expression, in plants and animals. Many aspects of the biogenesis and evolution of miRNAs in animals and plants differ. For example, unlike miRNAs of animals, which are mainly found in introns or exons from coding genes, most plant miRNAs are encoded by discrete genes. Moreover, miRNAs are released from their precursors using distinct pathways in the two kingdoms. Also, miRNA precursors are more heterogeneous in plants than in animals, varying greatly in size and structure. These differences have justified dedicated approaches for miRNA gene finding. However although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Considering this gap, we have developed miRkwood, a user-friendly web server specifically designed for plant miRNAs. miRkwood is able to face the diversity of plant pre-miRNAs and allows the prediction of precursors of both conserved and non-conserved miRNAs. Moreover, it offers an intuitive and comprehensive user interface to navigate in the data, as well as many export options (GFF, CSV, FASTA, ODT) to allow the user to conduct further analyses on a local computer. miRkwood can deal with both short genomic sequences (up to 100 000 nt) and full small RNA sequencing reads (provided that a BAM file is available). It is accessible at http://bioinfo.lifl.fr/mirkwoo

Energy Harvesting Using Composite Silicon/Lithium Niobate Vibrating Structures

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Stochastic foraging paths primarily drives within-species variations of prey consumption rates

The speed at which individuals interact, in particular prey and predators, affects ecological processes at all scales, including how fast matter and energy flow through ecosystems, and how stable communities are. Environmental heterogeneity and individual variabilities are generally believed to be the main factors underlying the variation of consumption rates of prey by predators. We challenge this view by comparing predicted variability from a stochastic model to experimental data. We first analyze a stochastic model of a simple random walk with elementary ecological processes involved in prey consumption, including prey depletion, predator movements and prey handling. We provide sharp approximations of the distribution of the consumption rate and a quantitative prediction of the coefficient of variation when stochastic foraging is the only source of variability. Predictions are then compared to the coefficients of variation estimated from data from dozens of various species and experimental contexts. We show that the predictions only accounting for intrinsic stochasticity in foraging are compatible with the range of observed values, in particular in 1 or 2 dimensional space. After evaluating the robustness of our model’s predictions through stochastic computer simulations, we conclude that the main driver of the variation of the consumption rate is the foraging process itself rather than environmental or between-individual variabilities. Our approach lays the foundations for unifying foraging theory and population ecology, and as such has many empirical and theoretical implications for both fields

Lightning ground flash patterns over Paris aera between 192 and 2003: influence of pollution

International audience12 summers of cloud-to-ground (CG) lightning flashes data over a 200 km × 200 km domain centered on Paris (France) have been analyzed to infer the possible influence of pollution on lightning activity. Lightning flashes densities are calculated on a 5 km × 5 km grid, filtered for discarding extremely high events, and differentiated from weekdays to week-end days, with a specific insight upwind, over, and downwind Paris. Lightning flashes are more numerous in the North-East part of the domain and increasingly large events progressively concentrate over Paris and over some hills around. The former result indicates a possible influence of pollution on lightning activity downwind of Paris; the latter probably illustrates the influence of the urban heat island and of the relief on the convection strengthening. Furthermore, the number of positive CG flashes is rather uniformly distributed on the whole domain, except in the North-East where it appears somewhat relatively lower meanwhile negative CG are relatively more numerous in that region. This corresponds to a reduction in the percentage of positive CG downwind of Paris. Additionally, lightning activity appears weaker downwind of Paris during weekend days. A specific daily analysis of the lightning density in circles distributed along the direction of prevailing wind through Paris shows that the lightning activity appears higher downwind during the days most worked as Tuesday, Wednesday and Thursday. This higher electric activity persists up to about 40 km on Wednesday, and up to about 80 km on Tuesday and Thursday (most days worked). The electrification seems therefore more important downwind of Paris during the more polluted days