Web Resources on Tuberculosis: Information, Research, and Data Analysis

Since the first edition of this book in 2013, many new tools and databases have become publicly available, as well as several have been discontinued. Here, we present an updated version of web resources on tuberculosis, providing more detailed information on some key concepts. However, the purpose of this chapter is by no means to offer an exhaustive list of all the resources available on the Internet about TB, the topic of this book. This would be a massive and perhaps futile work since the evolution of the Internet occurs at a very fast pace. Rather, this chapter concentrates on a selection of the most important, relevant and stable websites with relevance to several aspects of TB, such as research, treatment, main institutions, funding, and specialized platforms. We think this should complement all the other information already presented in this book, offering the reader a more integrated view of the disease, as well as access to new platforms and systems specialized in the analysis of data generated by a series of new technologies such as DNA sequencing

Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ Genomes

Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and me chanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages

Genetic Data Showing Evolutionary Links between Leishmania and Endotrypanum

Striking similarities at the morphological, molecular and biological levels exist between many trypanosomatids isolated from sylvatic insects and/or vertebrate reservoir hosts that make the identification of medically important parasites demanding. Some molecular data have pointed to the relationship between some Leishmania species and Endotrypanum, which has an important epidemiological significance and can be helpful to understand the evolution of those parasites. In this study, we have demonstrated a close genetic relationship between Endotrypanum and two new leishmanial species, L. (V.) colombiensis and L. (V.) equatorensis. We have used (a) numerical zymotaxonomy and (b) the variability of the internal transcribed spacers of the rRNA genes to examine relationships in this group. The evolutionary trees obtained revealed high genetic similarity between L. (V.) colombiensis, L. (V.) equatorensis and Endotrypanum, forming a tight cluster of parasites. Based on further results of (c) minicircle kDNA heterogeneity analysis and (d) measurement of the sialidase activity these parasites were also grouped together

A plataforma PDTIS de bioinformática: da seqüência à função

Desde os anos 1980, a Bioinformática tem adquirido uma importância crescente nas ciências biológicas. Devido à complexidade de ferramentas tanto de hardware quanto de software, e a necessidade de ter-se um gerenciamento especializado de infra-estruturas de rede, processamento e armazenamento de dados, muitas instituições de pesquisa organizaram um núcleo de bioinformática (core facility, CPD, Centro de (Bio)informática etc.). Neste artigo, descrevemos uma evolução típica de atividades na área de bioinformática e a organização de um núcleo mínimo com suporte institucional. Desde o final da década de 1980, a Fiocruz tem contribuído para o estabelecimento e desenvolvimento da Bioinformática no Rio de Janeiro, através de diferentes iniciativas. Iniciando com cursos de análise de seqüências ministrados na Fiocruz, hoje a instituição conta com um serviço permanente de Bioinformática, integrado a outras atividades estratégicas desenvolvidas, através de uma rede temática de plataformas com suporte de um Programa de Desenvolvimento Tecnológico em Insumos para a Saúde (PDTIS), cujas principais atribuições concentram-se no suporte, no estabelecimento de novas metodologias e na participação ativa em projetos de desenvolvimento tecnológico. Neste artigo, descrevemos a Plataforma PDTIS de Bioinformática, o seu escopo, os seus recursos e as suas atividades de suporte, ensino e pesquisa, considerando que muitos outros centros de pesquisa encontram-se em situação similar O surgimento da Bioinformática como uma nova área do conhecimento e um histórico de seu desenvolvimento na Fiocruz também são apresentados, de forma resumida

Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria

β-lactamases, which are found in several bacterial species and environments, are the main cause of resistance to β-lactams in Gram-negative bacteria. In 2009, a protein (LRA-13) with two β-lactamase domains (one class C domain and one class D domain) was experimentally characterised, and an extended action spectrum against β-lactams consistent with two functional domains was found. Here, we present the results of searches in the non-redundant NCBI protein database that revealed the existence of a group of homologous bifunctional β-lactamases in the genomes of environmental bacteria. These findings suggest that bifunctional β-lactamases are widespread in nature; these findings also raise concern that bifunctional β-lactamases may be transferred to bacteria of clinical importance through lateral gene transfer mechanisms

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes

Submitted by Sandra Infurna ([email protected]) on 2020-01-02T18:43:53Z No. of bitstreams: 1 MarcosCatanho_WinDegrave_etal_IOC_2006.pdf: 936007 bytes, checksum: b5adc17d98653706e246fefb9c19cf90 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2020-01-02T18:51:22Z (GMT) No. of bitstreams: 1 MarcosCatanho_WinDegrave_etal_IOC_2006.pdf: 936007 bytes, checksum: b5adc17d98653706e246fefb9c19cf90 (MD5)Made available in DSpace on 2020-01-02T18:51:22Z (GMT). No. of bitstreams: 1 MarcosCatanho_WinDegrave_etal_IOC_2006.pdf: 936007 bytes, checksum: b5adc17d98653706e246fefb9c19cf90 (MD5) Previous issue date: 2006Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Fernandes Figueira. Departamento de Genética. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Rio de Janeiro, RJ, Brasil.Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/ or dynamic comparison of these data. GenoMycDB (http://www. dbbm.fiocruz.br/GenoMycDB) is a relational database built for largescale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution

Comparando genomas: bancos de dados e ferramentas computacionais para a análise comparativa de genomas procarióticos

Since the 1990's, the complete genetic code of more than 600 living organisms has been deciphered, such as bacteria, yeasts, protozoan parasites, invertebrates and vertebrates, including Homo sapiens, and plants. More than 2,000 other genome projects representing medical, commercial, environmental and industrial interests, or comprising model organisms, important for the development of the scientific research, are currently in progress. The achievement of complete genome sequences of numerous species combined with the tremendous progress in computation that occurred in the last few decades allowed the use of new holistic approaches in the study of genome structure, organization and evolution, as well as in the field of gene prediction and functional classification. Numerous public or proprietary databases and computational tools have been created attempting to optimize the access to this information through the web. In this review, we present the main resources available through the web for comparative analysis of prokaryotic genomes. We concentrated on the group of mycobacteria that contains important human and animal pathogens. The birth of Bioinformatics and Computational Biology and the contributions of these disciplines to the scientific development of this field are also discussed.Desde a década de 1990, os esforços internacionais no sentido de obter seqüências genômicas completas levaram à determinação de todo o código genético de mais de 600 organismos, entre estes, procariotos, leveduras, protozoários, plantas, invertebrados e vertebrados, incluindo o próprio Homo sapiens. Atualmente, mais de 2.000 outros projetos genoma estão em andamento, representando interesses médicos, comerciais, ambientais e industriais, ou contemplando organismos-modelos importantes para o desenvolvimento de pesquisas científicas. Aliada ao vertiginoso avanço da computação nas últimas décadas, a obtenção de seqüências genômicas completas de inúmeros organismos têm permitido o uso de abordagens holísticas e ao mesmo tempo inovadoras no estudo da estrutura, organização e evolução dos genomas e na predição e classificação funcional de genes, entre outros. Inúmeros bancos de dados e ferramentas computacionais de acesso público ou privado têm sido criados na tentativa de organizar e permitir acesso eficiente e rápido a estas informações através da internet. Nesta revisão apresentamos os principais recursos disponíveis publicamente na internet para a análise comparativa de genomas procarióticos, especialmente de genomas micobacterianos, grupo que contém importantes patógenos humanos e de animais. A Bioinformática e a Biologia Computacional, áreas do conhecimento responsáveis pelo desenvolvimento e aplicação de tais instrumentos computacionais, são também abordadas, enfatizando-se suas origens e contribuições para o desenvolvimento da ciência

Comparing genomes: databases and computational tools for comparative analysis of prokaryotic genomes

Made available in DSpace on 2017-01-30T12:01:03Z (GMT). No. of bitstreams: 2 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) 25.pdf: 1877787 bytes, checksum: abfb93d2012dd9cb5aaac01461d1dbe0 (MD5) Previous issue date: 2007Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática.Rio de Janeiro, RJ, Brasil.Desde a década de 1990, os esforços internacionais no sentido de obter seqüências genômicas completas levaram à determinação de todo o código genético de mais de 600 organismos, entre estes, procariotos, leveduras, protozoários, plantas, invertebrados e vertebrados, incluindo o próprio Homo sapiens. Atualmente, mais de 2.000 outros projetos genoma estão em andamento, representando interesses médicos, comerciais, ambientais e industriais, ou contemplando organismos-modelos importantes para o desenvolvimento de pesquisas científicas. Aliada ao vertiginoso avanço da computação nas últimas décadas, a obtenção de seqüências genômicas completas de inúmeros organismos têm permitido o uso de abordagens holísticas e ao mesmo tempo inovadoras no estudo da estrutura, organização e evolução dos genomas e na predição e classificação funcional de genes, entre outros. Inúmeros bancos de dados e ferramentas computacionais de acesso público ou privado têm sido criados na tentativa de organizar e permitir acesso eficiente e rápido a estas informações através da internet. Nesta revisão apresentamos os principais recursos disponíveis publicamente na internet para a análise comparativa de genomas procarióticos, especialmente de genomas micobacterianos, grupo que contém importantes patógenos humanos e de animais. A Bioinformática e a Biologia Computacional, áreas do conhecimento responsáveis pelo desenvolvimento e aplicação de tais instrumentos computacionais, são também abordadas, enfatizando-se suas origens e contribuições para o desenvolvimento da ciência.Since the 1990’s, the complete genetic code of more than 600 living organisms has been deciphered, such as bacteria, yeasts, protozoan parasites, invertebrates and vertebrates, including Homo sapiens, and plants. More than 2,000 other genome projects representing medical, commercial, environmental and industrial interests, or comprising model organisms, important for the development of the scientific research, are currently in progress. The achievement of complete genome sequences of numerous species combined with the tremendous progress in computation that occurred in the last few decades allowed the use of new holistic approaches in the study of genome structure, organization and evolution, as well as in the field of gene prediction and functional classification. Numerous public or proprietary databases and computational tools have been created attempting to optimize the access to this information through the web. In this review, we present the main resources available through the web for comparative analysis of prokaryotic genomes. We concentrated on the group of mycobacteria that contains important human and animal pathogens. The birth of Bioinformatics and Computational Biology and the contributions of these disciplines to the scientific development of this field are also discussed