Armenian national grapevine collection: Conservation, characterization and prospects

The general strategy for grapevine genetic resources conservation in Armenia encompasses the collection of the still existing diversity and the use of protection techniques to minimize the losses over time. Being studied mainly by ampelography, the genetic diversity of Armenian grapevine needs to be re-investigated in accordance with modern requirements and international scales. The purpose of the presented research was the first large-scale molecular characterization of Armenian grape varieties by molecular methods using a set of 24 simple sequence repeat (SSR) markers encompassing the nine SSR markers recommended by the European project GrapeGen06. The obtained results indicate the uniqueness of the major part of the investigated varieties and reveal a substantial level of genetic variation within the Armenian grapevine. Based on the realized large-scale investigation a true-to-type inventory of Armenian grape germplasm will be realized and documented in theVitis International Variety Catalogue and in the European Vitisdatabase. The next step having strategic importance in terms of conservation of grape genetic resources in Armenia will be establishment of the first ArmenianVitis database with multi-crop passport description of all varieties preserved in grape collection

On the Easy Use of Scientific Computing Services for Large Scale Linear Algebra and Parallel Decision Making with the P-Grade Portal

International audienceScientific research is becoming increasingly dependent on the large-scale analysis of data using distributed computing infrastructures (Grid, cloud, GPU, etc.). Scientific computing (Petitet et al. 1999) aims at constructing mathematical models and numerical solution techniques for solving problems arising in science and engineering. In this paper, we describe the services of an integrated portal based on the P-Grade (Parallel Grid Run-time and Application Development Environment) portal (http://www.p-grade.hu) that enables the solution of large-scale linear systems of equations using direct solvers, makes easier the use of parallel block iterative algorithm and provides an interface for parallel decision making algorithms. The ultimate goal is to develop a single sign on integrated multi-service environment providing an easy access to different kind of mathematical calculations and algorithms to be performed on hybrid distributed computing infrastructures combining the benefits of large clusters, Grid or cloud, when needed

New Physics in b -> s mu+ mu-: CP-Conserving Observables

We perform a comprehensive study of the impact of new-physics operators with different Lorentz structures on decays involving the b -> s mu+ mu- transition. We examine the effects of new vector-axial vector (VA), scalar-pseudoscalar (SP) and tensor (T) interactions on the differential branching ratios and forward-backward asymmetries (A_{FB}'s) of Bsbar -> mu+ mu-, Bdbar -> Xs mu+ mu-, Bsbar -> mu+ mu- gamma, Bdbar -> Kbar mu+ mu-, and Bdbar -> K* mu+ mu-, taking the new-physics couplings to be real. In Bdbar -> K* mu+ mu-, we further explore the polarization fraction f_L, the angular asymmetry A_T^{(2)}, and the longitudinal-transverse asymmetry A_{LT}. We identify the Lorentz structures that would significantly impact these observables, providing analytical arguments in terms of the contributions from the individual operators and their interference terms. In particular, we show that while the new VA operators can significantly enhance most of the asymmetries beyond the Standard Model predictions, the SP and T operators can do this only for A_{FB} in Bdbar -> Kbar mu+ mu-.Comment: 54 pages, JHEP format, 45 figures (included). 5/6/2013: typos in K* mu mu angular coefficients corrected, typos in Eq. (D.12) corrected, added a missing term in I3LT in Eq. (D.16). Numerical analysis unchange

Butyrophilin-like 2 regulates site-specific adaptations of intestinal γδ intraepithelial lymphocytes

Tissue-resident γδ intraepithelial lymphocytes (IELs) orchestrate innate and adaptive immune responses to maintain intestinal epithelial barrier integrity. Epithelia-specific butyrophilin-like (Btnl) molecules induce perinatal development of distinct Vγ TCR+ IELs, however, the mechanisms that control γδ IEL maintenance within discrete intestinal segments are unclear. Here, we show that Btnl2 suppressed homeostatic proliferation of γδ IELs preferentially in the ileum. High throughput transcriptomic characterization of site-specific Btnl2-KO γδ IELs reveals that Btnl2 regulated the antimicrobial response module of ileal γδ IELs. Btnl2 deficiency shapes the TCR specificities and TCRγ/δ repertoire diversity of ileal γδ IELs. During DSS-induced colitis, Btnl2-KO mice exhibit increased inflammation and delayed mucosal repair in the colon. Collectively, these data suggest that Btnl2 fine-tunes γδ IEL frequencies and TCR specificities in response to site-specific homeostatic and inflammatory cues. Hence, Btnl-mediated targeting of γδ IEL development and maintenance may help dissect their immunological functions in intestinal diseases with segment-specific manifestations

Search for Doubly-Charged Higgs Boson Production at HERA

A search for the single production of doubly-charged Higgs bosons H^{\pm \pm} in ep collisions is presented. The signal is searched for via the Higgs decays into a high mass pair of same charge leptons, one of them being an electron. The analysis uses up to 118 pb^{-1} of ep data collected by the H1 experiment at HERA. No evidence for doubly-charged Higgs production is observed and mass dependent upper limits are derived on the Yukawa couplings h_{el} of the Higgs boson to an electron-lepton pair. Assuming that the doubly-charged Higgs only decays into an electron and a muon via a coupling of electromagnetic strength h_{e \mu} = \sqrt{4 \pi \alpha_{em}} = 0.3, a lower limit of 141 GeV on the H^{\pm\pm} mass is obtained at the 95% confidence level. For a doubly-charged Higgs decaying only into an electron and a tau and a coupling h_{e\tau} = 0.3, masses below 112 GeV are ruled out.Comment: 15 pages, 3 figures, 1 tabl

Forward pi^0 Production and Associated Transverse Energy Flow in Deep-Inelastic Scattering at HERA

Deep-inelastic positron-proton interactions at low values of Bjorken-x down to x \approx 4.10^-5 which give rise to high transverse momentum pi^0 mesons are studied with the H1 experiment at HERA. The inclusive cross section for pi^0 mesons produced at small angles with respect to the proton remnant (the forward region) is presented as a function of the transverse momentum and energy of the pi^0 and of the four-momentum transfer Q^2 and Bjorken-x. Measurements are also presented of the transverse energy flow in events containing a forward pi^0 meson. Hadronic final state calculations based on QCD models implementing different parton evolution schemes are confronted with the data.Comment: 27 pages, 8 figures and 3 table

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

<p>Abstract</p> <p>Background</p> <p>As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (<it>Cucumis sativus </it>var. <it>sativus</it>), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set.</p> <p>Results</p> <p>The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at <url>http://cmb.bnu.edu.cn/Cucumis_sativus_v20/</url>.</p> <p>Conclusions</p> <p>We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes.</p

Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing

<p>Abstract</p> <p>Background</p> <p>Despite tremendous progress in understanding the mechanisms of constitutive and alternative splicing, an important and widespread step along the gene expression pathway, our ability to deliberately regulate gene expression at this step remains rudimentary. The present study was performed to investigate whether a theophylline-dependent "splice switch" that sequesters the branchpoint sequence (BPS) within RNA-theophylline complex can regulate alternative splicing.</p> <p>Results</p> <p>We constructed a series of pre-mRNAs in which the BPS was inserted within theophylline aptamer. We show that theophylline-induced sequestering of BPS inhibits pre-mRNA splicing both in vitro and in vivo in a dose-dependent manner. Several lines of evidence suggest that theophylline-dependent inhibition of splicing is highly specific, and thermodynamic stability of RNA-theophylline complex as well as the location of BPS within this complex affects the efficiency of splicing inhibition. Finally, we have constructed an alternative splicing model pre-mRNA substrate in which theophylline caused exon skipping both in vitro and in vivo, suggesting that a small molecule-RNA interaction can modulate alternative splicing.</p> <p>Conclusion</p> <p>These findings provide the ability to control splicing pattern at will and should have important implications for basic, biotechnological, and biomedical research.</p