Improvement of three nucleic acid isolation protocols for an overall diagnosis of viruses on six vegetative propagated plants

Biological Resources Center (BRCs) must be able to guarantee the sanitary status of the resources they distribute, in order to prevent the spread or emergence of diseases. However, BRCs' vegetatively propagated crops do not benefit from the partial sanitation occurring through a seed cycle. This is particularly a problem for viral diseases, which have an overall high prevalence in vegetatively propagated crops. Variously effective sanitation methods exist for recovering virus-free plants but their successful implementation depends on on the availability of sensitive, polyvalent and reliable diagnosis tests for all relevant virus species. The main objective of the SafePGR project is to improve the knowledge of the diversity of viruses infecting the vegetatively propagated crops addressed by the partners' BRCs (Universidad do Açores, Universidad da Madeira, INRA-CIRAD Guadeloupe and CIRAD La Réunion). Among the various issues addressed in achieving the goals of the SafePGR project, we need to develop new tools for an overall diagnosis of viruses. Thus, recent metagenomics methods associated with high-throughput sequencing will be tested. For this purpose, we started to develop and adapt three different nucleic acids extractions on six plants species: banana, garlic, sugarcane, sweet potato, vanilla and yam. First, we succeeded to extract small RNAs using Trizol or phenol:chloroform methods on these six species. Then, we have developed a protocol to semi-purify viral particles. The third protocol consisted in an enrichment of double-stranded RNAs. The quality and quantity of extracted nucleic acid varied among plant species. Overall, the extracted RNAs from garlic, sugarcane, sweet potato and vanilla were fulfilling criteria of quality and quantity for being used for metagenomic approaches whereas the ones from banana and yam were not adequate. These preliminary results tend to indicate that it would be probably difficult to develop a universal nucleic acid isolation method that could be routinely used by our partners' BRCs. (Texte intégral

Oxalate formation under the hyperarid conditions of the Atacama desert as a mineral marker to provide clues to the source of organic carbon on Mars

In this study, we report the detection and characterization of the organic minerals weddellite (CaC2O4 · 2H2O) and whewellite (CaC2O4 · H2O) in the hyperarid, Mars-like conditions of the Salar Grande, Atacama desert, Chile. Weddellite and whewellite are commonly of biological origin on Earth and have great potential for preserving records of carbon geochemistry and possible biological activity on Mars if they are present there. Weddellite and whewellite have been found as secondary minerals occurring inside the lower detrital unit that fills the Salar Grande basin. The extremely low solubility of most oxalate minerals inhibits detection of oxalate by ion chromatography (IC). Crystalline oxalates, including weddellite and whewellite, were detected by X-ray diffraction (XRD). The association of weddellite with surface biota and its presence among subsurface detrital materials suggest the potential of a biological origin for Salar Grande weddellite and whewellite. In this regard, biological activity is uniquely capable of concentrating oxalates at levels detectable by XRD. The complementary detection of oxalate-bearing phases through IC in the upper halite-rich unit suggests the presence of a soluble oxalate phase in the basin that is not detected by XRD. The formation, transport, and concentration of oxalate in the Salar Grande may provide a geochemical analogue for oxalate-bearing minerals recently suggested to exist on Mars

Multilevel Contracts for Trusted Components

This article contributes to the design and the verification of trusted components and services. The contracts are declined at several levels to cover then different facets, such as component consistency, compatibility or correctness. The article introduces multilevel contracts and a design+verification process for handling and analysing these contracts in component models. The approach is implemented with the COSTO platform that supports the Kmelia component model. A case study illustrates the overall approach.Comment: In Proceedings WCSI 2010, arXiv:1010.233

Quark exchange model for charmonium dissociation in hot hadronic matter

A diagrammatic approach to quark exchange processes in meson-meson scattering is applied to the case of inelastic reactions of the type (Q\barQ)+(q\barq)\rightarrow (Q\barq) + (q\barQ), where $Q$ and $q$ refer to heavy and light quarks, respectively. This string-flip process is discussed as a microscopic mechanism for charmonium dissociation (absorption) in hadronic matter. The cross section for the reaction $J/\psi + \pi \to D+ \bar D$ is calculated using a potential model, which is fitted to the meson mass spectrum. The temperature dependence of the relaxation time for the \J/Psi distribution in a homogeneous thermal pion gas is obtained. The use of charmonium for the diagnostics of the state of hot hadronic matter produced in ultrarelativistic nucleus-nucleus collisions is discussed.Comment: 24 pages, 3 tables, 7 figure

BB flavour tagging using charm decays at the LHCb experiment

An algorithm is described for tagging the flavour content at production of neutral $B$ mesons in the LHCb experiment. The algorithm exploits the correlation of the flavour of a $B$ meson with the charge of a reconstructed secondary charm hadron from the decay of the other $b$ hadron produced in the proton-proton collision. Charm hadron candidates are identified in a number of fully or partially reconstructed Cabibbo-favoured decay modes. The algorithm is calibrated on the self-tagged decay modes $B^+ \to J/\psi \, K^+$ and $B^0 \to J/\psi \, K^{*0}$ using $3.0\mathrm{\,fb}^{-1}$ of data collected by the LHCb experiment at $pp$ centre-of-mass energies of $7\mathrm{\,TeV}$ and $8\mathrm{\,TeV}$. Its tagging power on these samples of $B \to J/\psi \, X$ decays is $(0.30 \pm 0.01 \pm 0.01) \%$.Comment: All figures and tables, along with any supplementary material and additional information, are available at http://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-027.htm

Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for <i>Elovl2</i> in glucose-induced insulin secretion.

In type 2 diabetes (T2D), pancreatic β cells become progressively dysfunctional, leading to a decline in insulin secretion over time. In this study, we aimed to identify key genes involved in pancreatic beta cell dysfunction by analyzing multiple mouse strains in parallel under metabolic stress. Male mice from six commonly used non-diabetic mouse strains were fed a high fat or regular chow diet for three months. Pancreatic islets were extracted and phenotypic measurements were recorded at 2 days, 10 days, 30 days, and 90 days to assess diabetes progression. RNA-Seq was performed on islet tissue at each time-point and integrated with the phenotypic data in a network-based analysis. A module of co-expressed genes was selected for further investigation as it showed the strongest correlation to insulin secretion and oral glucose tolerance phenotypes. One of the predicted network hub genes was &lt;i&gt;Elovl2&lt;/i&gt; , encoding Elongase of very long chain fatty acids 2. &lt;i&gt;Elovl2&lt;/i&gt; silencing decreased glucose-stimulated insulin secretion in mouse and human β cell lines. Our results suggest a role for &lt;i&gt;Elovl2&lt;/i&gt; in ensuring normal insulin secretory responses to glucose. Moreover, the large comprehensive dataset and integrative network-based approach provides a new resource to dissect the molecular etiology of β cell failure under metabolic stress

Further tests on liquid-nitrogen-cooled, thin silicon-crystal monochcromators using a focused wiggler synchrotron beam

A newly designed, cryogenically cooled, thin Si crystal monochromator was tested at the European Synchrotron Radiation Facility (ESRF) beamline BL3. It exhibited less than 1 arcsec of thermal strain up to a maximum incident power of 186 W and average power density of 521 W/mm{sup 2}. Data were collected for the thin (0.7 mm) portion of the crystal and for the thick (>25 mm) part. Rocking curves were measured as a function of incident power. With a low power beam, the Si(333) rocking curve at 30 keV for the thin and thick sections was < 1 arcsec FWHM at room temperature. The rocking curve of the thin section increased to 2.0 arcsec when cooled to 78 K, while the thick part was unaffected by the reduction in temperature. The rocking curve of the thin section broadened to 2.5 arcsec FWHM and that of the thick section broadened to 1.7 arcsec at the highest incident power. The proven range of performance for this monochromator has been extended to the power density, but not the absorbed power, expected for the Advanced Photon Source (APS) undulator A in closed-gap operation (first harmonic at 3.27 keV) at a storage-ring current of 300 mA

Search for supersymmetry with a dominant R-parity violating LQDbar couplings in e+e- collisions at centre-of-mass energies of 130GeV to 172 GeV

A search for pair-production of supersymmetric particles under the assumption that R-parity is violated via a dominant LQDbar coupling has been performed using the data collected by ALEPH at centre-of-mass energies of 130-172 GeV. The observed candidate events in the data are in agreement with the Standard Model expectation. This result is translated into lower limits on the masses of charginos, neutralinos, sleptons, sneutrinos and squarks. For instance, for m_0=500 GeV/c^2 and tan(beta)=sqrt(2) charginos with masses smaller than 81 GeV/c^2 and neutralinos with masses smaller than 29 GeV/c^2 are excluded at the 95% confidence level for any generation structure of the LQDbar coupling.Comment: 32 pages, 30 figure

A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

Background: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the imputation approach may be limited by the low accuracy of the imputed rare variants. To improve imputation accuracy of rare variants, various approaches have been suggested, including increasing the sample size of the reference panel, using sequencing data from study-specific samples (i.e., specific populations), and using local reference panels by genotyping or sequencing a subset of study samples. While these approaches mainly utilize reference panels, imputation accuracy of rare variants can also be increased by using exome chips containing rare variants. The exome chip contains 250 K rare variants selected from the discovered variants of about 12,000 sequenced samples. If exome chip data are available for previously genotyped samples, the combined approach using a genotype panel of merged data, including exome chips and SNP chips, should increase the imputation accuracy of rare variants. Results: In this study, we describe a combined imputation which uses both exome chip and SNP chip data simultaneously as a genotype panel. The effectiveness and performance of the combined approach was demonstrated using a reference panel of 848 samples constructed using exome sequencing data from the T2D-GENES consortium and 5,349 sample genotype panels consisting of an exome chip and SNP chip. As a result, the combined approach increased imputation quality up to 11 %, and genomic coverage for rare variants up to 117.7 % (MAF < 1 %), compared to imputation using the SNP chip alone. Also, we investigated the systematic effect of reference panels on imputation quality using five reference panels and three genotype panels. The best performing approach was the combination of the study specific reference panel and the genotype panel of combined data. Conclusions: Our study demonstrates that combined datasets, including SNP chips and exome chips, enhances both the imputation quality and genomic coverage of rare variants