Gestion des chênaies méditerranéennes pour l’adaptation aux changements globaux

Cet article expose les principales mesures de gestion forestière qui, à la lumière des connaissances actuelles, semblent être les plus efficaces pour l’adaptation au changement global des formations de chênes (Quercus ilex sous-espèce. ilex, Quercus ilex subsp. ballota, Quercus suber, Quercus faginea, Quercus pyrenaica, Quercus pubescens et Quercus canariensis) dans le milieu méditerranéen occidental. Les mesures proposées se basent sur les axes suivants : amélioration de la vitalité des forêts, adaptations des actions de régénération, réduction de la vulnérabilité face aux grands incendies forestiers, développement de l’hétérogénéité, facilitation de l’adaptation génétique et, pour finir, amélioration de la qualité de l’habitat et de la fonction de conservation de la biodiversité. Deux niveaux de mise en œuvre de ces mesures sont considérés : (i) le peuplement et (ii) la forêt ou le paysage. Les mesures sont de divers type, bien que toutes soient applicables aux divers domaines de la gestion forestière, que ce soit au niveau de l’exécution ou de la planification

Polychromatic Laser Guide Star. Progress report and modeless laser

International audienceWe report the current status of the polychromatic laser guide star pro-gramme ELP-OA, and the new developments: the modeless laser allowinga continuous match of the laser FWHM with that of the Na D2 line in themesosphere, and ATTILA the ¯rst bench of the ELP-OA demonstrator

R-Gada: a fast and flexible pipeline for copy number analysis in association studies

<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies (GWAS) using Copy Number Variation (CNV) are becoming a central focus of genetic research. CNVs have successfully provided target genome regions for some disease conditions where simple genetic variation (i.e., SNPs) has previously failed to provide a clear association.</p> <p>Results</p> <p>Here we present a new R package, that integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. Using a large dataset containing 270 HapMap individuals (Affymetrix Human SNP Array 6.0 Sample Dataset) we demonstrate a flexible pipeline implemented with the package. It requires less than one minute per sample (3 million probe arrays) on a single core computer, and provides a flexible parallelization for very large datasets. Case-control data were generated from the HapMap dataset to demonstrate a GWAS analysis.</p> <p>Conclusions</p> <p>The package provides the tools for creating a complete integrated pipeline from data normalization to statistical association. It can effciently handle a massive volume of data consisting of millions of genetic markers and hundreds or thousands of samples with very accurate results.</p

Optimization of cw sodium laser guide star efficiency

Context: Sodium laser guide stars (LGS) are about to enter a new range of laser powers. Previous theoretical and numerical methods are inadequate for accurate computations of the return flux and hence for the design of the next-generation LGS systems. Aims: We numerically optimize the cw (continuous wave) laser format, in particular the light polarization and spectrum. Methods: Using Bloch equations, we simulate the mesospheric sodium atoms, including Doppler broadening, saturation, collisional relaxation, Larmor precession, and recoil, taking into account all 24 sodium hyperfine states and on the order of 100 velocity groups. Results: LGS return flux is limited by "three evils": Larmor precession due to the geomagnetic field, atomic recoil due to radiation pressure, and transition saturation. We study their impacts and show that the return flux can be boosted by repumping (simultaneous excitation of the sodium D2a and D2b lines with 10-20% of the laser power in the latter). Conclusions: We strongly recommend the use of circularly polarized lasers and repumping. As a rule of thumb, the bandwidth of laser radiation in MHz (at each line) should approximately equal the launched laser power in Watts divided by six, assuming a diffraction-limited spot size.Comment: 15 pages, 12 figures, to be published in Astronomy & Astrophysics, AA/2009/1310

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

<p>Abstract</p> <p>Background</p> <p>Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal <it>ad-hoc </it>SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells.</p> <p>Results</p> <p>The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.</p> <p>Conclusions</p> <p>The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.</p

VASAO: visible all sky adaptive optics: a new adaptive optics concept for CFHT

International audienceVASAO is an ambitious project that explores new conceptual direction in the field of astronomical adaptive optics. In the era of 8 meter and larger telescopes, and their instrument costs and telescope time pressure, there is a natural niche for such ground-breaking conceptual development in the 4 meter class telescope. The aim of VASAO is to provide diffraction limited imaging in the visible with 100% sky coverage; the challenge (but potential rewards) arises from the simultaneity of these requirements. To this end, CFHT is conducting a feasibility study based on the polychromatic guide star concept (Foy et al., 1995 [4]) coupled with a high order curvature AO system, presented in this paper. A number of experiments have been started (or carried out) to study the challenges and limits of the techniques involved in an operational setting; these include the FlyEyes detector, and a polychromatic tip-tilt test on natural stars. Because such a project straddles such a fine line between facility instrument and experimental facility, careful thought has to be given to the balance between modes of operations and potential astrophysical targets

Algebraic Comparison of Partial Lists in Bioinformatics

The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or just within a meta-analysis comparison, instead of one list it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained. Here we introduce a method, based on the algebraic theory of symmetric groups, for studying the variability between lists ("list stability") in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated first on synthetic data in a gene filtering task and then for finding gene profiles on a recent prostate cancer dataset

Cellular Prion Protein Mediates alpha-Synuclein Uptake, Localization, and Toxicity In Vitro and In Vivo

Background The cellular prion protein (PrPC) is a membrane-bound, multifunctional protein mainly expressed in neuronal tissues. Recent studies indicate that the native trafficking of PrPC can be misused to internalize misfolded amyloid beta and α-synuclein (aSyn) oligomers. Objectives We define PrPC's role in internalizing misfolded aSyn in α-synucleinopathies and identify further involved proteins. Methods We performed comprehensive behavioral studies on four transgenic mouse models (ThySyn and ThySynPrP00, TgM83 and TgMPrP00) at different ages. We developed PrPC-(over)-expressing cell models (cell line and primary cortical neurons), used confocal laser microscopy to perform colocalization studies, applied mass spectrometry to identify interactomes, and determined disassociation constants using surface plasmon resonance (SPR) spectroscopy. Results Behavioral deficits (memory, anxiety, locomotion, etc.), reduced lifespans, and higher oligomeric aSyn levels were observed in PrPC-expressing mice (ThySyn and TgM83), but not in homologous Prnp ablated mice (ThySynPrP00 and TgMPrP00). PrPC colocalized with and facilitated aSyn (oligomeric and monomeric) internalization in our cell-based models. Glimepiride treatment of PrPC-overexpressing cells reduced aSyn internalization in a dose-dependent manner. SPR analysis showed that the binding affinity of PrPC to monomeric aSyn was lower than to oligomeric aSyn. Mass spectrometry-based proteomic studies identified clathrin in the immunoprecipitates of PrPC and aSyn. SPR was used to show that clathrin binds to recombinant PrP, but not aSyn. Experimental disruption of clathrin-coated vesicles significantly decreased aSyn internalization. Conclusion PrPC's native trafficking can be misused to internalize misfolded aSyn through a clathrin-based mechanism, which may facilitate the spreading of pathological aSyn. Disruption of aSyn-PrPC binding is, therefore, an appealing therapeutic target in α-synucleinopathies. <br