Description of microsporidia in simulids: molecular and morphological characterization of microsporidia in the larvae of Simulium pertinax Kollar (Diptera: Simuliidae)

Introduction Microsporidia constitute the most common black fly pathogens, although the species' diversity, seasonal occurrence and transmission mechanisms remain poorly understood. Infections by this agent are often chronic and non-lethal, but they can cause reduced fecundity and decreased longevity. The objective of this study was to identify microsporidia infecting Simulium (Chirostilbia) pertinax (Kollar, 1832) larvae from Caraguatatuba, State of São Paulo, Brazil, by molecular and morphological characterization. Methods Larvae were collected at a single point in a stream in a rural area of the city and were kept under artificial aeration until analysis. Polydispyrenia spp. infection was characterized by the presence of at least 32 mononuclear spores measuring 6.9 ± 1.0 × 5.0 ± 0.7µm in persistent sporophorous vesicles. Similarly, Amblyospora spp. were characterized by the presence of eight uninucleate spores measuring 4.5 × 3.5µm in sporophorous vesicles. Results The molecular analysis confirmed the presence of microsporidian DNA in the 8 samples (prevalence of 0.51%). Six samples (Brazilian larvae) were related to Polydispyrenia simulii and Caudospora palustris reference sequences but in separate clusters. One sample was clustered with Amblyospora spp. Edhazardia aedis was the positive control taxon. Conclusions Samples identified as Polydispyrenia spp. and Amblyospora spp. were grouped with P. simulii and Amblyospora spp., respectively, corroborating previous results. However, the 16S gene tree showed a considerable distance between the black fly-infecting Amblyospora spp. and the mosquito-infecting spp. This distance suggests that these two groups are not congeneric. Additional genomic region evaluation is necessary to obtain a coherent phylogeny for this group.Instituto Butantan Laboratório de ParasitologiaFundação Oswaldo Cruz Centro de Pesquisa Gonçalo Moniz Laboratório de ImunoparasitologiaUniversidade Federal de São Paulo (UNIFESP) Disciplina de InfectologiaSuperintendência de Controle de Endemias Laboratório de Entomologia MédicaUniversidade Federal de São Paulo (UNIFESP) Disciplina de Gastroenterologia Departamento de MedicinaSuperintendência de Controle de Endemias Laboratório de SimulídeosMosquito and Fly Research Unit United States Department of AgricultureUNIFESP, Disciplina de InfectologiaUNIFESP, Disciplina de Gastroenterologia Depto. de MedicinaSciEL

Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence

The mosquito Aedes aegypti (L.) is vector of several arboviruses including dengue, yellow fever, chikungunya, and more recently zika. Previous transcriptomic studies have been performed to elucidate altered pathways in response to viral infection. However, the intrinsic coupling between alimentation and infection were unappreciated in these studies. Feeding is required for the initial mosquito contact with the virus and these events are highly dependent. Addressing this relationship, we reinterrogated datasets of virus-infected mosquitoes with two different diet schemes (fed and unfed mosquitoes), evaluating the metabolic cross-talk during both processes. We constructed coexpression networks with the differentially expressed genes of these comparison: virus-infected versus blood-fed mosquitoes and virus-infected versus unfed mosquitoes. Our analysis identified one module with 110 genes that correlated with infection status (representing ~0.7% of the A. aegypti genome). Furthermore, we performed a machine-learning approach and summarized the infection status using only four genes (AAEL012128, AAEL014210, AAEL002477, and AAEL005350). While three of the four genes were annotated as hypothetical proteins, AAEL012128 gene is a membrane amino acid transporter correlated with viral envelope binding. This gene alone is able to discriminate all infected samples and thus should have a key role to discriminate viral infection in the A. aegypti mosquito. Moreover, validation using external datasets found this gene as differentially expressed in four transcriptomic experiments. Therefore, these genes may serve as a proxy of viral infection in the mosquito and the others 106 identified genes provides a framework to future studies

HIV-1 Nucleotide Sequence Comprehensive Analysis: A Computational Approach

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-03-07T17:15:55Z No. of bitstreams: 1 Kasprzykowski JI HIV-1 Nucleotide Sequence ....pdf: 4566421 bytes, checksum: 19a37e850b2f602decac14374926dad0 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-03-07T17:31:03Z (GMT) No. of bitstreams: 1 Kasprzykowski JI HIV-1 Nucleotide Sequence ....pdf: 4566421 bytes, checksum: 19a37e850b2f602decac14374926dad0 (MD5)Made available in DSpace on 2018-03-07T17:31:03Z (GMT). No. of bitstreams: 1 Kasprzykowski JI HIV-1 Nucleotide Sequence ....pdf: 4566421 bytes, checksum: 19a37e850b2f602decac14374926dad0 (MD5) Previous issue date: 2017Oswaldo Cruz Foundation and Feira de Santana State University.Feira de Santana State University. Applied Computing Post Graduate Program. Feira de Santana, BA, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Imunoparasitologia. Salvador, BA, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Pós-graduação em Biotecnologia, Saúde e Investigação. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Imunoparasitologia. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Imunoparasitologia. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Imunoparasitologia. Salvador, BA, BrasilFeira de Santana State University. Applied Computing Post Graduate Program. Feira de Santana, BA, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Imunoparasitologia. Salvador, BA, BrasilAbstract: Background: Acquired Immunodeficiency Syndrome (AIDS) is a large-scale pandemic caused by the infection of Human Immunodeficiency Virus (HIV). This virus infects over 40 million people worldwide. In the search for pandemic control, many drug resistance tests have been performed, resulting in the generation of large genomic data amount. These data are stored in biological databases, increasing on a daily basis. However, the majority of genomic data lacks important information, regarding virus subtype distribution, in the primary databases, e.g. GenBank. Objective: A novel software tool to obtain, index and analyze highly mutational virus data, such as all HIV-1 sequence data from GenBank. Method: The software aligns all sequences containing a complete genome (HXB2) for mapping purposes. In addition, all sequences with subtype references are locally aligned to classify all data into genotypic niches. Results: Our results detail the prevalence of every subtype from a global HIV-1 sequence perspective, highlighting increases in the number of sequences related to recombinant subtypes. We were also able to identify country-based distribution of sequences according to geographical data distribution. All data were analyzed on a reasonable timescale, particularly in comparison to classic methods. Conclusion: Our software represents an important contribution to HIV molecular epidemiology and offers a technique to rapidly classify new sequences, in addition to providing insight about sequence coverage density, subtype and country distribution. This data, together with cross-referencing, will aid in the generation of a novel, comprehensive and updated HIV-1 database

Networking the host immune response in Plasmodium vivax malaria

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2013-11-25T17:21:54Z No. of bitstreams: 1 Mendonça Vitor RR Networking the host....pdf: 537180 bytes, checksum: f779ebf4192be14c04b483489e271c97 (MD5)Made available in DSpace on 2013-11-25T17:21:54Z (GMT). No. of bitstreams: 1 Mendonça Vitor RR Networking the host....pdf: 537180 bytes, checksum: f779ebf4192be14c04b483489e271c97 (MD5) Previous issue date: 2013Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Faculdade de Medicina. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, BrasilUniversidade de São Paulo. Instituto de Matemática e Estatística. São Paulo, SP, Brasil / Universidade Tecnológica Federal do Paraná. Coordenação de Informática. Cornélio Procópio, BrasilNational Institute of Allergy and Infectious Diseases. National Institutes of Health. Laboratory of Parasitic Diseases. Bethesda, MD, USAFundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Faculdade de Medicina. Salvador, BA, Brasil / Instituto Nacional de Ciência e Tecnologia. Instituto de Investigação em Imunologia. São Paulo, SP, BrasilBackground: Plasmodium vivax malaria clinical outcomes are a consequence of the interaction of multiple parasite, environmental and host factors. The host molecular and genetic determinants driving susceptibility to disease severity in this infection are largely unknown. Here, a network analysis of large-scale data from a significant number of individuals with different clinical presentations of P. vivax malaria was performed in an attempt to identify patterns of association between various candidate biomarkers and the clinical outcomes. Methods: A retrospective analysis of 530 individuals from the Brazilian Amazon, including P. vivax-infected individuals who developed different clinical outcomes (148 asymptomatic malaria, 187 symptomatic malaria, 13 severe non-lethal malaria, and six severe lethal malaria) as well as 176 non-infected controls, was performed. Plasma levels of liver transaminases, bilirubins, creatinine, fibrinogen, C-reactive protein, superoxide dismutase (SOD)-1, haem oxygenase (HO)-1 and a panel composed by multiple cytokines and chemokines were measured and compared between the different clinical groups using network analysis. Results: Non-infected individuals displayed several statistically significant interactions in the networks, including associations between the levels of IL-10 and IL-4 with the chemokine CXCL9. Individuals with asymptomatic malaria displayed multiple significant interactions involving IL-4. Subjects with mild or severe non-lethal malaria displayed substantial loss of interactions in the networks and TNF had significant associations more frequently with other parameters. Cases of lethal P. vivax malaria infection were associated with significant interactions between TNF ALT, HO-1 and SOD-1. Conclusions: The findings imply that clinical immunity to P. vivax malaria is associated with multiple significant interactions in the network, mostly involving IL-4, while lethality is linked to a systematic reduction of complexity of these interactions and to an increase in connections between markers linked to haemolysis-induced damage

Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2019-12-16T11:53:58Z No. of bitstreams: 1 Ramos Pablo I . Leveraging...pdf: 3323461 bytes, checksum: 578b227bea15bb4a3114f428396fddb2 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2019-12-16T12:16:34Z (GMT) No. of bitstreams: 1 Ramos Pablo I . Leveraging...pdf: 3323461 bytes, checksum: 578b227bea15bb4a3114f428396fddb2 (MD5)Made available in DSpace on 2019-12-16T12:16:34Z (GMT). No. of bitstreams: 1 Ramos Pablo I . Leveraging...pdf: 3323461 bytes, checksum: 578b227bea15bb4a3114f428396fddb2 (MD5) Previous issue date: 2019Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil [Universal 28/2018; grant protocol 427183/2018-9]. LA received a postdoctoral fellowship from the Coordenação de Aperfeiçoamento de Pessoal de 725 Nível Superior (CAPES). AQ acknowledges funding from Fundação Oswaldo Cruz (INOVA - Process VPPIS-001-FIO-18-45). Publication fees were defrayed by Fundação Oswaldo Cruz. The funders had no role in study design, analysis, decision to publish, or preparation of the manuscriptFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Centro de Integração de Dados e Conhecimentos para Saúde. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Federal University of Rio de Janeiro. Centro de Ciências da Saúde. Laboratório de Genética Molecular e Biotecnologia Vegetal. Rio de Janeiro, RJ, Brasil.Universidade Federal do Ceará. Departamento de Bioquímica e Biologia Molecular. Fortaleza, CE, Brasil.Fundação José Silveira. Multinational Organization Network Sponsoring Translational and Epidemiological Research. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Centro de Integração de Dados e Conhecimentos para Saúde. Salvador, BA, Brasil.Recent technological advances for the acquisition of multi-omics data have allowed an unprecedented understanding of the complex intricacies of biological systems. In parallel, a myriad of computational analysis techniques and bioinformatics tools have been developed, with many efforts directed towards the creation and interpretation of networks from this data. In this review, we begin by examining key network concepts and terminology. Then, computational tools that allow for their construction and analysis from high-throughput omics datasets are presented. We focus on the study of functional relationships such as co-expression, protein-protein interactions, and regulatory interactions that are particularly amenable to modeling using the framework of networks. We envisage that many potential users of these analytical strategies may not be completely literate in programming languages and code adaptation, and for this reason, emphasis is given to tools' user-friendliness, including plugins for the widely adopted Cytoscape software, an open-source, cross-platform tool for network analysis, visualization, and data integration

LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-04-09T12:23:03Z No. of bitstreams: 1 Torres F LeishDB a database....pdf: 1129886 bytes, checksum: 99df57f8962e39c88562071df67546d4 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-04-09T12:43:22Z (GMT) No. of bitstreams: 1 Torres F LeishDB a database....pdf: 1129886 bytes, checksum: 99df57f8962e39c88562071df67546d4 (MD5)Made available in DSpace on 2018-04-09T12:43:22Z (GMT). No. of bitstreams: 1 Torres F LeishDB a database....pdf: 1129886 bytes, checksum: 99df57f8962e39c88562071df67546d4 (MD5) Previous issue date: 2017Fundação de Amparo a Pesquisa do Estado da Bahia (FAPESB) [BOL3832/2014 and BOL591/2016, respectively, to F.T.], Brazil; Fondecyt Iniciaci on, Comisi on Nacional de Investigaci on Cient ıfica y Tecnol ogica (CONICYT) [11161020 toV.M.C.], Chile; Fondo de Investigaci on y Desarrollo Universidad Mayor (FIDUM) [OI 100913 to V.M.C.], Chile.Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Estadual de Feira de Santana. P os-Graduação em Computação Aplicada. Feira de Santana, BA, BrasilUniversidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, ChileUniversidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, ChileFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, BrasilUniversidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile / Beagle Bioinformatics. Santiago, Chile / Instituto Vandique. João Pessoa, PB, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Estadual de Feira de Santana. P os-Graduação em Computação Aplicada. Feira de Santana, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, BrasilLeishmania braziliensis is the etiological agent of cutaneous leishmaniasis, a disease with high public health importance, affecting 12 million people worldwide. Although its genome sequence was originally published in 2007, the two reference public annotations still presents at least 80% of the genes simply classified as hypothetical or putative proteins. Furthermore, it is notable the absence of non-coding RNA (ncRNA) sequences from Leishmania species in public databases. These poorly annotated coding genes and ncRNAs could be important players for the understanding of this protozoan biology, the mechanisms behind host-parasite interactions and disease control. Herein, we performed a new prediction and annotation of L. braziliensis protein-coding genes and noncoding RNAs, using recently developed predictive algorithms and updated databases. In summary, we identified 11 491 ORFs, with 5263 (45.80%) of them associated with proteins available in public databases. Moreover, we identified for the first time the repertoire of 11 243 ncRNAs belonging to different classes distributed along the genome. The accuracy of our predictions was verified by transcriptional evidence using RNA-seq, confirming that they are actually generating real transcripts. These data were organized in a public repository named LeishDB (www.leishdb.com), which represents an improvement on the publicly available data related to genomic annotation for L. braziliensis. This updated information can be useful for future genomics, transcriptomics and metabolomics studies; being an additional tool for genome annotation pipelines and novel studies associated with the understanding of this protozoan genome complexity, organization biology, and development of innovative methodologies for disease control and diagnostics

High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2016-04-11T17:49:07Z No. of bitstreams: 1 SantAnna BMM High-quality....pdf: 174607 bytes, checksum: a87bda6da64e45bda4a5d8375638373d (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2016-04-11T18:05:58Z (GMT) No. of bitstreams: 1 SantAnna BMM High-quality....pdf: 174607 bytes, checksum: a87bda6da64e45bda4a5d8375638373d (MD5)Made available in DSpace on 2016-04-11T18:05:58Z (GMT). No. of bitstreams: 1 SantAnna BMM High-quality....pdf: 174607 bytes, checksum: a87bda6da64e45bda4a5d8375638373d (MD5) Previous issue date: 2015Universidade Federal da Bahia. Salvador, BA, BrasilUniversidade Federal do Recôncavo da Bahia. UFRB. Cruz das Almas, BA, BrasilUniversidade Mayor. Centro de Genómica y Bioinformática. Santiago, ChileUniversidade Federal de Lavras. UFLA. Lavras, BrasilUniversidade Federal da Bahia. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilBacillus amyloliquefaciens strain 629 is an endophyte isolated from Theobroma cacao L. Here, we report the draft genome sequence (3.9 Mb) of B. amyloliquefaciens strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding sequences, and an average 46.5% G+C conten

Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil

Agradecimentos a ATLQ e LAS que contribuíram igualmente para este trabalho, além de Elisabeth Deliège por sua assistência técnica.Submitted by Éder Freyre ([email protected]) on 2011-08-08T19:15:22Z No. of bitstreams: 1 Queiroz_Santos_Moreau_etal.pdf: 396458 bytes, checksum: 62c07b8e130826e538d5865d6211b15d (MD5)Made available in DSpace on 2011-08-08T19:15:22Z (GMT). No. of bitstreams: 1 Queiroz_Santos_Moreau_etal.pdf: 396458 bytes, checksum: 62c07b8e130826e538d5865d6211b15d (MD5) Previous issue date: 2007Pesquisa parcialmente financiada pela Fundação de Amparo a Pesquisa do Estado da Bahia (FAPESB) e PN-DST/AIDS, Ministério da Saúde, Brasil.Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Laboratório Avançado de Saúde Pública. Salvador, BA, BrasilEscola Bahiana de Medicina e Saúde Pública / Fundação para o Desenvolvimento da Ciência. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Laboratório Avançado de Saúde Pública. Salvador, BA, BrasilUniversity of Oxford. Department of Zoology. Oxford, United KingdomUniversity of Wisconsin Medical School. Department of Pathology. Madison, USAFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Laboratório Avançado de Saúde Pública. Salvador, BA, Brasil / Escola Bahiana de Medicina e Saúde Pública / Fundação para o Desenvolvimento da Ciência. Salvador, BA, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Laboratório Avançado de Saúde Pública. Salvador, BA, Brasil / Escola Bahiana de Medicina e Saúde Pública / Fundação para o Desenvolvimento da Ciência. Salvador, BA, BrasilGenetic analysis of HIV-1 is essential to improve treatment strategies and select epitopes for vaccine programs. The objective of this study was to determine whether known CD4+ and CD8+ epitopes were present in Brazilian HIV-1 strains. We used previously described CD8+ and CD4+ epitopes from the Los Alamos laboratory to search for these epitopes in the Brazilian sequences using the HIVbase program and we compared the frequency results with the analyses using physical-chemical profile tools from Network Protein Sequence Analysis (NPSA), and the SYFPEITHI program. Furthermore, this analysis was carried out with the Prosite tool using the GeneDoc program and ds/dn analyses using the Synonymous Nonsynonymous Analysis Program (SNAP). The HIVbase epitope mapping demonstrated that 30 CD8+ and 6 CD4+ epitopes were present in the Brazilian sequences at a high frequency. Only two of these epitopes were heavily glycosylated. Interestingly, ds/dn analyses showed evidence of purifying selective pressure. These types of analyses could be useful for the assessment of possible vaccine efficiency in populations

Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil

Genetic analysis of HIV-1 is essential to improve treatment strategies and select epitopes for vaccine programs. The objective of this study was to determine whether known CD4+ and CD8+ epitopes were present in Brazilian HIV-1 strains. We used previously described CD8+ and CD4+ epitopes from the Los Alamos laboratory to search for these epitopes in the Brazilian sequences using the HIVbase program and we compared the frequency results with the analyses using physical-chemical profile tools from Network Protein Sequence Analysis (NPSA), and the SYFPEITHI program. Furthermore, this analysis was carried out with the Prosite tool using the GeneDoc program and ds/dn analyses using the Synonymous Nonsynonymous Analysis Program (SNAP). The HIVbase epitope mapping demonstrated that 30 CD8+ and 6 CD4+ epitopes were present in the Brazilian sequences at a high frequency. Only two of these epitopes were heavily glycosylated. Interestingly, ds/dn analyses showed evidence of purifying selective pressure. These types of analyses could be useful for the assessment of possible vaccine efficiency in populations