Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions

Subtype C human immunodeficiency vírus type 1 (HIV-1) is rapidly diversifying among populations, which display extensiva polymorphism of genes encoding class I human leukocyte antigen (HLA) proteins, as detected in different regions of the world. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes considering 128 subtype C externai glycoprotein gp120 sequences selected from GenBank were identified to A*0201, A*0301, A*1101 and 8*07 HLA alleles using Epijen software. NetChop allowed to predict proteasome cleavage followed by prediction of binding to transport associated with antigen processing on TapPred. Glycosylation and positively selected sites within epitope sequences were also observed. Furthermore, three-dimensional structures of subtype C gp120 were predicted from consensus sequences in PHYRE and the PYMOL software was used to verify positions occupied by conserved epitopes. Finally, we predicted discontinuous B cell epitopes in DiscoTope 1.2. There is a recognized evolutionary force of HIV-1 to escape from B cells and CTL responses mutating sites that can negatively select the viral population. ' These types of analyses could be useful to understand HIV-1 epidemiology associated with polymorphisms in HLA alleles frequent in a determined region. 1t is expected that such knowledge may provide additional support for vaccine development

Mãe, obrigada pelos microRNAs

Os microRNAs (miRNAs) são pequenas moléculas de RNA não codificante que têm grande importância nos mais diversos processos celulares, pois atuam na regulação da expressão gênica pós-transcricional. Estima-se que estes RNAs tenham controle de, em média, 30% da regulação de genes codificantes de proteínas em mamíferos. Da mesma forma, na fase zigótica do desenvolvimento embrionário, os miRNAs maternos desempenham funções notáveis e são fundamentais para a degradação dos próprios transcritos maternos. Este evento é determinante para a transição materno-zigótica, momento onde o zigoto passa a expressar completamente e de maneira independente seus próprios mRNAs, e; portanto, são vitais para o desenvolvimento inicial do embrião. O presente estudo, através de uma revisão narrativa de literatura, busca descrever os mecanismos de ação de miRNAs maternos presentes em zigotos de diversas espécies durante o desenvolvimento embrionário. Foram selecionados estudos disponíveis na base de dados PubMed através da busca utilizando palavras-chave descritas pelos Descritores em Ciências da Saúde (DeCS). Palavras-Chave: MicroRNA; oócito; zigoto; embrião; revisã

Mãe, obrigada pelos microRNAs

Os microRNAs (miRNAs) são pequenas moléculas de RNA não codificante que têm grande importância nos mais diversos processos celulares, pois atuam na regulação da expressão gênica pós-transcricional. Estima-se que estes RNAs tenham controle de, em média, 30% da regulação de genes codificantes de proteínas em mamíferos. Da mesma forma, na fase zigótica do desenvolvimento embrionário, os miRNAs maternos desempenham funções notáveis e são fundamentais para a degradação dos próprios transcritos maternos. Este evento é determinante para a transição materno-zigótica, momento onde o zigoto passa a expressar completamente e de maneira independente seus próprios mRNAs, e; portanto, são vitais para o desenvolvimento inicial do embrião. O presente estudo, através de uma revisão narrativa de literatura, busca descrever os mecanismos de ação de miRNAs maternos presentes em zigotos de diversas espécies durante o desenvolvimento embrionário. Foram selecionados estudos disponíveis na base de dados PubMed através da busca utilizando palavras-chave descritas pelos Descritores em Ciências da Saúde (DeCS).   Palavras-Chave: MicroRNA; oócito; zigoto; embrião; revisã

Could phylogenetic analysis be used for feline Leukemia Virus (FeLV) classification?

The surface envelope (SU) protein determines the cell tropism and consequently the pathogenesis of the feline leukemia virus (FeLV) in felids. Recombination of exogenous FeLV (exFeLV) with endogenous retroviruses (enFeLV) allows the emergence of more pathogenic variants. Currently, phenotypic testing through interference assays is the only method to distinguish among subgroups—namely, FeLV-A, -B, -C, -E, and -T. This study proposes a new method for FeLV classification based on molecular analysis of the SU gene. A total of 404 publicly available SU sequences were used to reconstruct a maximum likelihood tree. However, only 63 of these sequences had available information about phenotypic tests or subgroup assignments. Two major clusters were observed: (a) clade FeLV-A, which includes FeLV-A, FeLV-C, FeLV-E, and FeLV-T sequences, and (b) clade enFeLV, which includes FeLV-B and enFeLV strains. We found that FeLV-B, FeLV-C, FeLV-E, and FeLV-T SU sequences share similarities to FeLV-A viruses and most likely arose independently through mutation or recombination from this strain. FeLV-B and FeLV-C arose from recombination between FeLV-A and enFeLV viruses, whereas FeLV-T is a monophyletic subgroup that has probably originated from FeLV-A through combined events of deletions and insertions. Unfortunately, this study could not identify polymorphisms that are specifically linked to the FeLV-E subgroup. We propose that phylogenetic and recombination analysis together can explain the current phenotypic classification of FeLV viruses

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California

The HIV epidemic in San Mateo County is sustained by multiple overlapping risk groups and is an important hub for HIV transmission in northern California. Limited access to care has led historically to delayed clinical presentation, higher rates of opportunistic infections, and an increased prevalence of antiretroviral drug resistance. The virologic and clinical consequences of treatment within these multiple ethnic and behavioral groups are poorly understood, highlighting the need for efficient surveillance strategies that are able to elucidate transmission networks and drug resistance patterns. We obtained sequence data from a group of 316 HIV-positive individuals in the San Mateo AIDS Program over a 14-year period and integrated epidemiologic, phylogenetic, and network approaches to characterize transmission clusters, risk factors and drug resistance. Drug resistance mutations were identified using the Stanford HIV Drug Resistance Database. A maximum likelihood tree was inferred in RAxML and subjected to clustering analysis in Cluster Picker. Network analysis using pairwise genetic distances was performed in HIV-TRACE. Participants were primarily male (60%), white Hispanics and non-Hispanics (32%) and African American (20.6%). The most frequent behavior risk factor was male-male sex (33.5%), followed by heterosexual (23.4%) and injection drug use (9.5%). Nearly all sequences were subtype B (96%) with subtypes A, C, and CRF01_AE also observed. Sequences from 65% of participants had at least one drug resistance mutation. Clustered transmissions included a higher number of women when compared to non-clustered individuals and were more likely to include heterosexual or people who inject drugs (PWID). Detailed analysis of the largest network (N = 47) suggested that PWID played a central role in overall transmission of HIV-1 as well as bridging men who have sex with men (MSM) transmission with heterosexual/PWID among primarily African American men. Combined phylogenetic and network analysis of HIV sequence data identified several overlapping risk factors in the epidemic, including MSM, heterosexual and PWID transmission with a disproportionate impact on African Americans and a high prevalence of drug resistance

Absence of A3Z3-related hypermutations in the env and vif proviral genes in FIV naturally infected cats

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) proteins comprise an important family of restriction factors that produce hypermutations on proviral DNA and are able to limit virus replication. Vif, an accessory protein present in almost all lentiviruses, counteracts the antiviral A3 activity. Seven haplotypes of APOBEC3Z3 (A3Z3) were described in domestic cats (hap I–VII), and in-vitro studies have demonstrated that these proteins reduce infectivity of vif-defective feline immunodeficiency virus (FIV). Moreover, hap V is resistant to vif-mediated degradation. However, studies on the effect of A3Z3 in FIV-infected cats have not been developed. Here, the correlation between APOBEC A3Z3 haplotypes in domestic cats and the frequency of hypermutations in the FIV vif and env genes were assessed in a retrospective cohort study with 30 blood samples collected between 2012 and 2016 from naturally FIV-infected cats in Brazil. The vif and env sequences were analyzed and displayed low or undetectable levels of hypermutations, and could not be associated with any specific A3Z3 haplotype

Reviewing the History of HIV-1: Spread of Subtype B in the Americas

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and Bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950–1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion

Complete genome sequences of two bovine alphaherpesvirus 5 subtype C strains from southeast Brazil

Bovine alphaherpesvirus 5 causes meningoencephalitis in cattle, belongs to the Herpesviridae family, and can be divided into subtypes a, b, and c. Limited information is available about subtype c. Here, we report the complete genome sequences of two strains, P160/96, and ISO97/45, isolated from cattle in southeast Brazil

Anticorpos contra a raiva em soros de morcegos hematófagos

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Caracterização antigênica e molecular de amostras de herpesvírus bovino

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