How bioinformatics enables livestock applied sciences in the genomic era

This review paper presents the three main approaches currently used in livestock genomic sciences where the bioinfomatics plays a critical role. They are named as Genomic Selection (GS), Genome Wide Association Study (GWAS) and Signatures of Selection (SS). The subsides for the construction of this article were generated in a current project (started in 2011), so called Zebu Genome Consortium (ZGC), which joins researchers from different institutions and countries, aiming to scientifically explore genomic information of Bos taurus indicus cattle breeds and deliver useful information to breeders and academic community, specially from the tropical regions of the world. © 2012 Springer-Verlag.

Search for heavy bottom-like quarks in 4.9 fb-1 of pp collisions at √s = 7 TeV

Results are presented from a search for heavy bottom-like quarks, pair-produced in pp collisions at √s = 7TeV, undertaken with the CMS experiment at the LHC. The b′ quarks are assumed to decay exclusively to tW. The b′b̄′ → tW-t̄W+ process can be identified by its distinctive signatures of three leptons or two leptons of same charge, and at least one b-quark jet. Using a data sample corresponding to an integrated luminosity of 4.9 fb-1, observed events are compared to the standard model background predictions, and the existence of b′ quarks having masses below 611 GeV/c2 is excluded at 95% confidence level.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. © 2013 Petersen et al.

The Mode of Action of Recombinant Mycobacterium tuberculosis Shikimate Kinase: Kinetics and Thermodynamics Analyses

Tuberculosis remains as one of the main cause of mortality worldwide due to a single infectious agent, Mycobacterium tuberculosis. The aroK-encoded M. tuberculosis Shikimate Kinase (MtSK), shown to be essential for survival of bacilli, catalyzes the phosphoryl transfer from ATP to the carbon-3 hydroxyl group of shikimate (SKH), yielding shikimate-3-phosphate and ADP. Here we present purification to homogeneity, and oligomeric state determination of recombinant MtSK. Biochemical and biophysical data suggest that the chemical reaction catalyzed by monomeric MtSK follows a rapid-equilibrium random order of substrate binding, and ordered product release. Isothermal titration calorimetry (ITC) for binding of ligands to MtSK provided thermodynamic signatures of non-covalent interactions to each process. A comparison of steady-state kinetics parameters and equilibrium dissociation constant value determined by ITC showed that ATP binding does not increase the affinity of MtSK for SKH. We suggest that MtSK would more appropriately be described as an aroL-encoded type II shikimate kinase. Our manuscript also gives thermodynamic description of SKH binding to MtSK and data for the number of protons exchanged during this bimolecular interaction. The negative value for the change in constant pressure heat capacity (ΔCp) and molecular homology model building suggest a pronounced contribution of desolvation of non-polar groups upon binary complex formation. Thermodynamic parameters were deconvoluted into hydrophobic and vibrational contributions upon MtSK:SKH binary complex formation. Data for the number of protons exchanged during this bimolecular interaction are interpreted in light of a structural model to try to propose the likely amino acid side chains that are the proton donors to bulk solvent following MtSK:SKH complex formation. © 2013 Rosado et al.

Searches for long-lived charged particles in pp collisions at □ =7 and 8 TeV

Abstract: Results of searches for heavy stable charged particles produced in pp collisions at □ = 7 and 8 TeV are presented corresponding to an integrated luminosity of 5.0 fb-1 and 18.8 fb-1, respectively. Data collected with the CMS detector are used to study the momentum, energy deposition, and time-of-flight of signal candidates. Leptons with an electric charge between e/3 and 8e, as well as bound states that can undergo charge exchange with the detector material, are studied. Analysis results are presented for various combinations of signatures in the inner tracker only, inner tracker and muon detector, and muon detector only. Detector signatures utilized are long time-of-flight to the outer muon system and anomalously high (or low) energy deposition in the inner tracker. The data are consistent with the expected background, and upper limits are set on the production cross section of long-lived gluinos, scalar top quarks, and scalar τ leptons, as well as pair produced long-lived leptons. Corresponding lower mass limits, ranging up to 1322 GeV/c 2 for gluinos, are the most stringent to date. [Figure not available: see fulltext.] © 2013 Cern for the benefit of the CMS collaboration.

Sistema de coleta, análise e detecção de código malicioso baseado no sistema imunológico humano

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identificação de assinaturas de seleção e anotação do genoma em bovinos da raça Nelore

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Assinaturas geoelétricas em área contaminada por hidrocarboneto no pólo industrial de Cubatão - SP

Pós-graduação em Geociências e Meio Ambiente - IGCE

Evolução metamórfica (P-T-t) de granulitos e migmatitos do Complexo Guaxupé na região de São João da Boa Vista, SP

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação da qualidade e quantidade do carbono e do nitrogênio no solo em Iperó-SP

Pós-graduação em Engenharia Civil e Ambiental - FEB

Valor prognóstico e preditivo de genes candidatos selecionados após análise de oligoarrays em carcinomas mamários

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genome-wide scans to uncover loci underlying bovine reproductive biology

Pós-graduação em Medicina Veterinária - FCAV

Um modelo de detecção de eventos em redes baseado no rastreamento de fluxos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Proposta de uma ferramenta de visualização e realidade virtual para o monitoramento de tráfego de redes de computadores

Pós-graduação em Ciência da Computação - IBILCE

Estudos de imagens provenientes de membranas de borracha natural com aditivos metálicos utilizando técnicas de Fourier, Gabor e Wavelets

Pós-graduação em Ciência e Tecnologia de Materiais - FC