Single Nucleotide Variants And Indels Identified From Whole-genome Re-sequencing Of Guzerat, Gyr, Girolando And Holstein Cattle Breeds

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. © 2017 Stafuzza et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.123Conselho Nacional de Desenvolvimento Científico e TecnológicoCAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorFAPEMIG, Fundação de Amparo à Pesquisa do Estado de Minas GeraisConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

The swinholide biosynthesis gene cluster from a terrestrial cyanobacterium, Nostoc sp. strain UHCC 0450

Swinholides are 42-carbon ring polyketides with a 2-fold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of a symbiotic heterotrophic proteobacterium. Here, we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp. strain UHCC 0450. We located the 85-kb trans-AT polyketide synthase (PKS) swinholide biosynthesis gene cluster from a draft genome of Nostoc sp. UHCC 0450. The swinholide and misakinolide biosynthesis gene clusters share an almost identical order of catalytic domains, with 85% nucleotide sequence identity, and they group together in phylogenetic analysis. Our results resolve speculation around the true producer of swinholides and demonstrate that bacteria belonging to two distantly related phyla both produce structural variants of the same natural product. In addition, we described a biosynthesis cluster from Anabaena sp. strain UHCC 0451 for the synthesis of the cytotoxic and antifungal scytophycin. All of these biosynthesis gene clusters were closely related to each other and created a group of cytotoxic macrolide compounds produced by trans-AT PKSs of cyanobacteria and proteobacteria. © 2018 American Society for Microbiology.We thank Lyudmila Saari for purifying the cyanobacterial strains into axenic cultures. This work was supported by the Academy of Finland grants 258827 and 273798 to K.S. and 288235 to P.P. A.H. is a student at the Doctoral Programme in Microbiology and Biotechnology. A.A. was funded in part by the Strategic Funding grant UID/Multi/ 04423/2013 through national funds provided by the Portuguese National Science Foundation (FCT) and the European Regional Development Fund (ERDF) in the framework of the program PT2020, by the European Structural and Investment Funds (ESIF) through the Competitiveness and Internationalization Operational Program-COMPETE 2020, and by the Structured Programs of R&D&I INNOVMAR (NORTE-01-0145-FEDER-000035-NOVELMAR), CORAL NORTE (NORTE-01-0145-FEDER-000036), and MarInfo (NORTE-01-0145-FEDER-000031), funded by the Northern Regional Operational Pro-gram (NORTE2020) through the ERDF. The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publicatio

Qualidade sanitária e fisiológica de sementes de abóbora variedade menina Brasileira.

O trabalho teve como objetivos avaliar e correlacionar a qualidade sanitária e fisiológica de sementes de abóbora, variedade Menina Brasileira (Cucurbita moschata.). Foram avaliados dois lotes de sementes de abóbora produzidas no sistema agroecológico e quatro no sistema convencional, com e sem tratamento químico. Os lotes foram submetidos aos testes de sanidade, seguindo a metodologia do “Blotter test”, com congelamento, germinação e vigor (primeira contagem, índice de velocidade de germinação, envelhecimento acelerado e emergência de plântulas). Os resultados indicaram a separação dos lotes de diferentes origens a partir da qualidade sanitária e fisiológica, onde as maiores incidências de fungos foram observadas nos lotes agroecológicos e o maior potencial fisiológico foi observado nos lotes de origem convencional não tratados. Foram encontrados os fungos Fusarium oxysporum, Alternaria alternata, Cladosporium cucumerinum, Aspergillus niger, Penicillium digitatum, Rhizopus stolonifer e Phoma terrestris. A qualidade sanitária não interferiu na qualidade fisiológica das sementes de abóbora, variedade Menina Brasileira

The first 62 AGNs observed with SDSS-IV MaNGA : I. Their characterization and definition of a control sample

We report the characterization of the first 62 Mapping Nearby Galaxies at the Apache Point Observatory active galactic nuclei (AGNs) hosts and the definition of a control sample of non-active galaxies. This control sample was selected in order to match the AGN hosts in terms of stellar mass, redshift, visual morphology and inclination. The stellar masses are in the range 9.4 < log M/M < 11.5, and most objects have redshifts ≤0.08. The AGN sample is mostly comprised low-luminosity AGN, with only 17 ‘strong AGN’ with L([O III]λ5007 Å) ≥ 3.8 × 1040 erg s−1. The inner 1–3 kpc of the control sample galaxies are dominated by the oldest (≥ 4Gyr) component, with a small contribution of intermediate age and young stars (<940 Myr). Examining the relationship between the stellar population properties and L([O III]), we find that with increasing L([O III]), the AGN exhibit a decreasing contribution from the oldest stellar population relative to control galaxies and an increasing contribution from the younger components (∼40 Myr).We also find a correlation of the mean age differences (AGN–control) with L([O III]), in the sense that more luminous AGNs are younger than the control objects, while the low-luminosity AGNs are older. These results support a connection between the growth of the galaxy bulge via formation of new stars and the growth of the Supermassive Black Hole via accretion in the AGN phase

Photosynthesis, stomatal conductance and leaf water potential in crabwood (Carapa guianensis)

Leaf water potential is one of the most important factors affecting stomatal functioning. The aim of this study was to assess the effect of variation in diurnal irradiance and vapour pressure deficit on photosynthesis (A), stomatal conductance (g s) and leaf water potential (psi) in Carapa guianensis (Aubl.). Data were collected from 07:00 to 17:00 h. Photosynthetic rates reached a maximum (2.5 µmol m-2 s-1) at 10:00 h, thereafter declined to a minimum of 1 µmol m-2 s-1 at 16:00 h. Stomatal conductance oscillated during the day, from 0.04 mol m-2 s-1 (at midday) to 0.02.mol.m-2.s-1 at the end of the afternoon. Leaf water potential was higher early in the morning (-0.3 MPa) and lower (-0.75 MPa) at mid-afternoon (14:30 -15:00 h). After reaching a minimum, psi increased up to -0.64 MPa at sunset. Photosynthetic rates increased linearly as a function of g s (P < 0.01). Also there was a positive relationship between psi and g s (P< 0.01). Photosynthetic rates declined during the day after reaching a peak early in the morning, which makes clear that environmental factors that influence psi greatly affect carbon assimilation of C. guianensis.O potencial hídrico da folha é um dos fatores mais importantes que afetam o funcionamento dos estômatos. O objetivo deste trabalho foi avaliar o efeito da variação diurna na irradiância e déficit de pressão de vapor (DPV) na fotossíntese (A), condutância estomática (g s) e potencial hídrico da folha (psi) em Carapa guianensis (Aubl.). Os dados foram coletados de 07:00 às 17:00 h. A taxa fotossintética atingiu um valor máximo (2,5 µmol m-2 s-1) às 10:00 h, depois declinou até atingir um mínimo de 1 µmolm-2 s-1 às 16:00 h. A condutância estomática oscilou durante o dia, de 0,04 molm-2s-1 (ao meio dia) para 0,02 molm-2s- 1 no final da tarde. O potencial hídrico da folha foi máximo nas primeiras horas do dia (-0,3 MPa) e mínimo (-0,75 MPa) no meio da tarde (14:30 a 15:00 h). Após ter alcançado um mínimo, o psi aumentou até -0,64 MPa no fim da tarde. A taxa fotossintética aumentou linearmente em função do g s (P < 0,01). Também houve uma relação positiva entre psi e g s (P < 0,01). A taxa fotossintética declinou durante o dia após ter alcançado um pico no início da manhã, demonstrando que os fatores ambientais que afetam o psi têm efeito significativo na assimilação do carbono de C. guianensis

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

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio