Thermogravimetry and neutron thermodiffractometry studies of the H-YBa2Cu3O7 system.

The high Tc superconducting oxide YBa2Cu3O7¿x reacts with hydrogen gas. Thermogravimetric, X-ray and neutron scattering experiments allow us to propose a two-step type of hydrogen bonding. Firstly, a few hydrogen atoms fill some oxygen vacancies and may favourably modify the electron state, giving rise to a slight increase in the critical temperature. Secondly, after a prolonged heating period, the collapse of the YBa2Cu3O7¿x type framework and of superconductivity were observed, and a new, highly hydrogenated material appeared

Intérêt de l’amendement et du paillage pour les plantations forestières en région méditerranéenne : le projet FP7 Sustaffor

En région méditerranéenne, il est nécessaire de faire l’entretien des jeunes plantations d’arbres pour faire face à la sécheresse et à la végétation concurrente. Ces interventions ont un grand impact économique, en plus d’avoir, lors de l’utilisation de plusieurs techniques (arrosage d’urgence, dégagement chimique ou mécanique), un effet négatif sur l’environnement. Dans le cadre du projet Sustaffor, de nouveaux produits innovants sont développés : un amendement de sol et trois prototypes de paillis, dont deux sont biodégradables (un nouveau biopolymère et une toile de jute) et un réutilisable (en caoutchouc recyclé). Ces produits sont étudiés dans le nord-est de l’Espagne dans quatre bioclimats méditerranéens représentatifs : semi-aride, méditerranéen continental, méditerranéen humide et étage montagnard. Durant les deux premières saisons de végétation, le nouvel amendement de sol a eu un effet très positif pour les sols légers ayant une faible capacité de rétention d’eau. Le paillage a été très efficace dans les conditions les plus productives et, dans une moindre mesure, en conditions limitantes. Les nouveaux produits permettent de réduire entre autres les entretiens nécessaires dans les plantations d’arbres, tout en présentant un avantage environnemental

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

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

Crustal structure of active deformation zones in Africa: Implications for global crustal processes

The Cenozoic East African rift (EAR), Cameroon Volcanic Line (CVL), and Atlas Mountains formed on the slow-moving African continent, which last experienced orogeny during the Pan-African. We synthesize primarily geophysical data to evaluate the role of magmatism in shaping Africa's crust. In young magmatic rift zones, melt and volatiles migrate from the asthenosphere to gas-rich magma reservoirs at the Moho, altering crustal composition and reducing strength. Within the southernmost Eastern rift, the crust comprises ~20% new magmatic material ponded in the lower crust sills, and intruded as sills and dikes at shallower depths. In the Main Ethiopian rift, intrusions comprise 30% of the crust below axial zones of dike-dominated extension. In the incipient rupture zones of the Afar rift, magma intrusions fed from crustal magma chambers beneath segment centers create new columns of mafic crust, as along slow-spreading ridges. Our comparisons suggest that transitional crust, including seaward-dipping sequences, is created as progressively smaller screens of continental crust are heated and weakened by magma intrusion into 15-20 km-thick crust. In the 30Ma-Recent CVL, which lacks a hotspot age-progression, extensional forces are small, inhibiting the creation and rise of magma into the crust. In the Atlas orogen, localized magmatism follows the strike of the Atlas Mountains from the Canary Islands hotspot towards the Alboran Sea. CVL and Atlas magmatism has had minimal impact on crustal structure. Our syntheses show that magma and volatiles are migrating from the asthenosphere through the plates, modifying rheology and contributing significantly to global carbon and water fluxes

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing, and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing, and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease

A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples

<p>Abstract</p> <p>Background</p> <p>Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor sample CN to normal reference sample CN. While advances in microarray technology have improved detection of copy number alterations, the increase in the number of measured signals, noise from array probes, variations in signal-to-noise ratio across batches and disparity across laboratories leads to significant limitations for the accurate identification of CNA regions when comparing tumor and normal samples.</p> <p>Methods</p> <p>To address these limitations, we designed a novel "Virtual Normal" algorithm (VN), which allowed for construction of an unbiased reference signal directly from test samples within an experiment using any publicly available normal reference set as a baseline thus eliminating the need for an in-lab normal reference set.</p> <p>Results</p> <p>The algorithm was tested using an optimal, paired tumor/normal data set as well as previously uncharacterized pediatric malignant gliomas for which a normal reference set was not available. Using Affymetrix 250K Sty microarrays, we demonstrated improved signal-to-noise ratio and detected significant copy number alterations using the VN algorithm that were validated by independent PCR analysis of the target CNA regions.</p> <p>Conclusions</p> <p>We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation.</p