MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level

BACKGROUND: The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. DESCRIPTION: Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. CONCLUSION: The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic

Expression and function of G-protein-coupled receptorsin the male reproductive tract

This review focuses on the expression and function of muscarinic acetylcholine receptors (mAChRs), α1-adrenoceptors and relaxin receptors in the male reproductive tract. The localization and differential expression of mAChR and α1-adrenoceptor subtypes in specific compartments of the efferent ductules, epididymis, vas deferens, seminal vesicle and prostate of various species indicate a role for these receptors in the modulation of luminal fluid composition and smooth muscle contraction, including effects on male fertility. Furthermore, the activation of mAChRs induces transactivation of the epidermal growth factor receptor (EGFR) and the Sertoli cell proliferation. The relaxin receptors are present in the testis, RXFP1 in elongated spermatids and Sertoli cells from rat, and RXFP2 in Leydig and germ cells from rat and human, suggesting a role for these receptors in the spermatogenic process. The localization of both receptors in the apical portion of epithelial cells and smooth muscle layers of the vas deferens suggests an involvement of these receptors in the contraction and regulation of secretion.Esta revisão enfatiza a expressão e a função dos receptores muscarínicos, adrenoceptores α1 e receptores para relaxina no sistema reprodutor masculino. A expressão dos receptores muscarínicos e adrenoceptores α1 em compartimentos específicos de dúctulos eferentes, epidídimo, ductos deferentes, vesícula seminal e próstata de várias espécies indica o envolvimento destes receptores na modulação da composição do fluido luminal e na contração do músculo liso, incluindo efeitos na fertilidade masculina. Além disso, a ativação dos receptores muscarínicos leva à transativação do receptor para o fator crescimento epidermal e proliferação das células de Sertoli. Os receptores para relaxina estão presentes no testículo, RXFP1 nas espermátides alongadas e células de Sertoli de rato e RXFP2 nas células de Leydig e germinativas de ratos e humano, sugerindo o envolvimento destes receptores no processo espermatogênico. A localização de ambos os receptores na porção apical das células epiteliais e no músculo liso dos ductos deferentes de rato sugere um papel na contração e na regulação da secreção.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de FarmacologiaUNIFESP, EPM, Depto. de FarmacologiaSciEL

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

A HISTOLOGICAL STUDY OF THE EFFECT OF DIAMETER ENLARGEMENT OF THE APICAL PORTION OF THE ROOT-CANAL

111042843

ANTI-MICROBIAL EFFECTS OF ENDODONTIC FILLING CEMENTS ON MICROORGANISMS FROM ROOT-CANAL

55662262

Application of a brazilian test of expressive vocabulary in european portuguese children

Objetivo: investigar o desempenho de crianças falantes do Português Europeu em prova brasileira de vocabulário expressivo, buscando apontar se existem diferenças entre as faixas etárias e o gênero, além de verificar sua aplicabilidade nesta população. Método: a amostra foi constituída de 150 crianças em desenvolvimento típico, de ambos os gêneros, com idade entre 5 e 6 anos. Todas frequentavam escolas de ensino públicas na região norte de Portugal. Para avaliação do desempenho semântico, foi utilizada a prova do vocabulário expressivo do teste de linguagem infantil – ABFW, considerando a porcentagem de designações verbais usuais e a classificação (adequado / inadequado) de acordo com os valores de referência brasileiros. Resultados: o desempenho das crianças portuguesas indicou que aos 6 anos elas têm maior porcentagem de acertos no vocabulário expressivo. Quanto ao gênero, houve apenas diferenças pontuais: as meninas demonstraram maior domínio nos campos semânticos vestuário (em ambas as idades) e móveis e utensílios (aos 5 anos), já os meninos demonstraram maior domínio no campo semântico meios de transporte (6 anos). Com relação à classificação, não houve diferença entre as faixas etárias no desempenho geral, apenas o campo semântico formas e cores teve mais indivíduos de 6 anos com desempenho inadequado. Conclusão: os valores de referência adotados na população brasileira para classificação do desempenho indicaram que mais de 80% das crianças de cada faixa etária poderiam ser classificadas com desempenho adequado, o que sugere que tal prova possua potencial como instrumento de avaliação quantitativa do vocabulário em Português Europeu nesta faixa etária.Objective: to investigate the performance of European Portuguese children in a Brazilian test of expressive vocabulary, seeking to identify differences between age groups and gender, and to verify its applicability in this population. Methods: the sample consisted of 150 typical developed children, of both genders, between the ages of 5 and 6. All children attended public schools in the north area of Portugal. To assess the semantic performance, the expressive vocabulary sub-test of the language test (ABFW) was used, considering the percentage of usual verbal assignments and the classification (adequate/inadequate) according to the Brazilian reference values. Results: the performance of the European Portuguese children indicated that at age 6 they have a higher percentage of correct answers in expressive vocabulary. As for the gender, there were only occasional differences: the girls showed a greater dominance in the semantic fields of clothing (both ages) and furniture and utensils (at age 5), whereas the boys showed more dominance in the semantic field means of transportation (6 years). Regarding classification, there was no difference between age groups in overall performance. Only the semantic field shapes and colors had more individuals of 6 years with inadequate performance. Conclusion: the reference values adopted in the Brazilian population for semantic performance indicated that more than 80% of the children of each age group could have their performance classified as adequate. Such evidence suggests that this tool shows potential as an instrument of quantitative vocabulary’s assessment of 5 and 6-years old children in European Portuguese.(undefined)info:eu-repo/semantics/publishedVersio