Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance

Indexación: Web of Science; Scopus.The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.http://journal.frontiersin.org/article/10.3389/fmicb.2017.00456/ful

Genomic analysis of 48 paenibacillus larvae bacteriophages

Indexación: Scopus.Funding: Research at UNLV was funded by National Institute of General Medical Sciences grant GM103440 (NV INBRE), the UNLV School of Life Sciences, and the UNLV College of Sciences. E.C.-N. was funded by CONICYT-FONDECYT de iniciación en la investigación 11160905. Research at BYU was funded by the BYU Microbiology & Molecular Biology Department, and private donations through LDS Philanthropies.The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvae phage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes in the 50–55 kbp range that use the direct terminal repeat (DTR) DNA-packaging strategy. The DTR phages form a distinct cluster, while the cos phages form three clusters and a singleton. Putative functions were identified for about half of all phage proteins. Structural and assembly proteins are located at the front of the genome and tend to be conserved within clusters, whereas regulatory and replication proteins are located in the middle and rear of the genome and are not conserved, even within clusters. All P. larvae phage genomes contain a conserved N-acetylmuramoyl-L-alanine amidase that serves as an endolysin. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/1999-4915/10/7/37

An approach to phenotypic analysis and environmental variability. The examples of the genera Dianthus L. and Lotus L. in the north of Portugal

The analysis of the correlation between phenotypic plasticity and environmental variability has been very useful to describe the morphologic responses of individuals to environmental factors affecting them (in the present contribution the altitudinal variation), from a genecological perpective. However, the literature shows that the studies in this area have had a monospecific or monogeneric use. As a consequence, intergeneric comparative descriptions have not been possible. In the present work we propose an analytical method to compare the morphological expressivity of individuals included in the genera Dianthus and Lotus from the north of Portugal by means of a contingency matrix. This matrix was elaborated on the basis of amplitude parameters, in order to describe the variability present in the basic matrix of each genus studied. The results pointed out the existence of opposite phenotypic behaviours dependent on the altitudinal variation, thus indicating the importance of the analysis between different groups of taxa as a reference for the comparison of their morphological expressivities

Bosonization in Higher Dimensions

Using the recently discovered connection between bosonization and duality transformations (hep-th/9401105 and hep-th/9403173), we give an explicit path-integral representation for the bosonization of a massive fermion coupled to a U(1) gauge potential (such as electromagnetism) in d space (D=d+1 spacetime) dimensions. The bosonic theory is described by a rank d-1 antisymmetric Kalb-Ramond-type gauge potential. We construct the bosonized lagrangian explicitly in the limit of large fermion mass. We find that the resulting action is local for d=2 (and given by a Chern-Simons action), but nonlocal for d larger than 3. By coupling to a statistical Chern-Simons field for d=2, we obtain a bosonized formulation of anyons. The bosonic theory may be further dualized to a theory involving purely scalars, for any d, and we show this to be governed by a higher-derivative lagrangian for which the scalar decouples from the U(1) gauge potential.Comment: (We had omitted some references and had misspelled `aficionados') plain TeX, 11 pages, McGill-94/33, NEIP-94-006, OSLO-TP 10-9

Noncommutative Electromagnetism As A Large N Gauge Theory

We map noncommutative (NC) U(1) gauge theory on R^d_C X R^{2n}_{NC} to U(N -> \infty) Yang-Mills theory on R^d_C, where R^d_C is a d-dimensional commutative spacetime while R^{2n}_{NC} is a 2n-dimensional NC space. The resulting U(N) Yang-Mills theory on R^d_C is equivalent to that obtained by the dimensional reduction of (d+2n)-dimensional U(N) Yang-Mills theory onto R^d_C. We show that the gauge-Higgs system (A_\mu,\Phi^a) in the U(N -> \infty) Yang-Mills theory on R^d_C leads to an emergent geometry in the (d+2n)-dimensional spacetime whose metric was determined by Ward a long time ago. In particular, the 10-dimensional gravity for d=4 and n=3 corresponds to the emergent geometry arising from the 4-dimensional N=4 vector multiplet in the AdS/CFT duality. We further elucidate the emergent gravity by showing that the gauge-Higgs system (A_\mu,\Phi^a) in half-BPS configurations describes self-dual Einstein gravity.Comment: 25 pages; More clarifications, to appear in Eur. Phys. J.

Condensed matter and AdS/CFT

I review two classes of strong coupling problems in condensed matter physics, and describe insights gained by application of the AdS/CFT correspondence. The first class concerns non-zero temperature dynamics and transport in the vicinity of quantum critical points described by relativistic field theories. I describe how relativistic structures arise in models of physical interest, present results for their quantum critical crossover functions and magneto-thermoelectric hydrodynamics. The second class concerns symmetry breaking transitions of two-dimensional systems in the presence of gapless electronic excitations at isolated points or along lines (i.e. Fermi surfaces) in the Brillouin zone. I describe the scaling structure of a recent theory of the Ising-nematic transition in metals, and discuss its possible connection to theories of Fermi surfaces obtained from simple AdS duals.Comment: 39 pages, 12 figures; Lectures at the 5th Aegean summer school, "From gravity to thermal gauge theories: the AdS/CFT correspondence", and the De Sitter Lecture Series in Theoretical Physics 2009, University of Groninge

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Homocysteine, S-adenosylmethionine and S-adenosylhomocysteine are associated with retinal microvascular abnormalities: the Hoorn Study

The aim of the present study was to investigate the relationship between homocysteine and homocysteine metabolism components and retinal microvascular disorders in subjects with and without Type 2 diabetes. In this population-based study of 256 participants, aged 60-85 years, we determined total plasma homocysteine, SAM (S-adenosylmethionine) and SAH (S-adenosylhomocysteine) in plasma and erythrocytes, total folate in serum and erythrocytes, 5-MTHF (5-methyltetrahydrofolate), and vitamins B12 and B6. Participants were examined ophthalmologically by means of indirect funduscopy and two-field 45° fundus photography, and were graded for retinopathy and retinal sclerotic vessel abnormalities. A computer-assisted method was used to measure retinal vessel diameters. Total plasma homocysteine was inversely associated with retinal arteriolar diameters {standardized β, -0.20 [95% CI (confidence interval), -0.33 to - 0.07]} or a decrease of 3.78 μm CRAEs (central retinal arteriolar equivalents) per 1 S.D. increase in homocysteine level (= 4.6 μmol/l). In addition, the SAM/SAH ratio in plasma was inversely associated with retinal sclerotic vessel abnormalities and retinopathy [odds ratios, 0.61 (95% CI, 0.39-0.96) and 0.50 (95% CI, 0.30-0.83) per 1 S.D. respectively]. The associations were independent of age, sex, glucose tolerance status, other homocysteine metabolism components and cardiovascular risk factors. In conclusion, the results of the present study support the concept that total plasma homocysteine and a low SAM/SAH ratio in plasma, which may reflect reduced transmethylation reactions, may contribute to the pathogenesis of (retinal) microangiopathy. © The Authors