Catálogo Taxonômico da Fauna do Brasil: setting the baseline knowledge on the animal diversity in Brazil

The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classifications. In this context, the Brazilian megadiverse fauna is no exception, and the Catálogo Taxonômico da Fauna do Brasil (CTFB) (http://fauna.jbrj.gov.br/), made public in 2015, represents a database on biodiversity anchored on a list of valid and expertly recognized scientific names of animals in Brazil. The CTFB is updated in near real time by a team of more than 800 specialists. By January 1, 2024, the CTFB compiled 133,691 nominal species, with 125,138 that were considered valid. Most of the valid species were arthropods (82.3%, with more than 102,000 species) and chordates (7.69%, with over 11,000 species). These taxa were followed by a cluster composed of Mollusca (3,567 species), Platyhelminthes (2,292 species), Annelida (1,833 species), and Nematoda (1,447 species). All remaining groups had less than 1,000 species reported in Brazil, with Cnidaria (831 species), Porifera (628 species), Rotifera (606 species), and Bryozoa (520 species) representing those with more than 500 species. Analysis of the CTFB database can facilitate and direct efforts towards the discovery of new species in Brazil, but it is also fundamental in providing the best available list of valid nominal species to users, including those in science, health, conservation efforts, and any initiative involving animals. The importance of the CTFB is evidenced by the elevated number of citations in the scientific literature in diverse areas of biology, law, anthropology, education, forensic science, and veterinary science, among others

Caracterização de variantes virais de HIV-1 em indivíduos soropositivos com perfil de controle da progressão para a AIDS e da replicação viralavaliação da ocorrência de variantes de escape da resposta imune

Submitted by Angelo Silva ([email protected]) on 2016-07-20T13:42:38Z No. of bitstreams: 2 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) 71854.pdf: 3870328 bytes, checksum: e6d51ee1222bd1369079ed339e270c1b (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2016-08-24T19:10:02Z (GMT) No. of bitstreams: 2 71854.pdf: 3870328 bytes, checksum: e6d51ee1222bd1369079ed339e270c1b (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5)Made available in DSpace on 2016-08-24T19:10:02Z (GMT). No. of bitstreams: 2 71854.pdf: 3870328 bytes, checksum: e6d51ee1222bd1369079ed339e270c1b (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2016Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilA infecção pelo HIV se caracteriza pela existência de um período de latência clínica (ou período assintomático) entre a infecção aguda e a fase de AIDS, cuja duração é extremamente variável, gerando distintos perfis de progressão entre os indivíduos infectados pelo HIV. Uma pequena fração de indivíduos infectados (5-10%), denominados não progressores de longo termo (LTNP), permanece clinicamente assintomática e com altos valores de TCD4+ (>500 cells/\F06Dl) durante mais de 8 anos de infecção na ausência de tratamento. Alguns desses indivíduos conseguem ainda bloquear quase totalmente a replicação e a evolução viral, gerando uma verdadeira latência evolutiva. O objetivo do presente estudo foi analisar o perfil mutacional do HIV-1 e a dinâmica de emergência e manutenção de mutantes virais de escape da resposta imune em pacientes HIV-1 positivos classificados como LTNPs com diferentes níveis de controle da replicação viral. Para tal, utilizou-se uma casuística de 12 indivíduos LTNPs, classificados como controladores virêmicos (VC) e controladores de elite com (ECB) e sem Blips (EC) de acordo com os seus níveis de controle da infecção. Para cada indivíduo, foram extraídas amostras de DNA a partir de PBMCs obtidos durante a visita mais antiga (V1) e mais recente (VX) disponíveis. O DNA extraído foi utilizado para amplificação e sequenciamento, através de uma metodologia de NGS, dos genes Gag e Nef. As sequências obtidas permitiram o mapeamento do gene nef inteiro (cobertura média de 212.674 seqs/pb) e dos primeiros 1000pbs de Gag (cobertura média de 286.463 seqs/pb) Os consensos de cada mapeamento foram utilizados para as análises de divergência entre V1 e VX e variantes com frequências maior que 0,5% em cada pb mapeado foram consideradas verdadeiras. As análises de evolução evidenciaram o baixo nível de diversidade e divergência dos genes Gag e Nef entre os indivíduos controladores. Indivíduos ECs apresentaram menor perfil mutacional em ambos os genes analisados quando comparados com indivíduos ECB e VC. Enquanto Gag apresentou maior conservação que Nef em VCs, ambos os genes apresentaram semelhante variabilidade in ECs, indicando que o maior controle da viremia limita a evolução em nas duas regiões. Em alguns indivíduos ECBs, evidências de superinfecção e hipermutação mediada por APOBEC3G foi observada. As análises das mutações em regiões de epítopos restritos por CTL demonstraram a presença de mutações indicativas de escape da resposta imune surgidas entre V1 e VX na maioria dos indivíduos. Mutações não sinônimas foram encontradas em baixas frequências para todos os indivíduos, incluindo ECs, indicando que tais variantes surgem, mas a grande maioria não obtém sucesso evolutivoThe HIV infection is characterized by the existence of a clinical latency period (os asymptomatic period) between the acute infection and the AIDS phase, whose duration is extremely variable, generating distinct progression profiles between Hiv infected individuals. A small fraction of infected individuals (5-10%), named long term non progressors (LTNP), remains clinically asymptomatic and with high TCD4+ levels (>500cells/ul) during more than 8 years of infection in absence of treatment. Some of these individuals can even block almost all the viral replication and evolution, generating an evolutionary latency. The objective of this study was to analyze the mutational profile of HIV-1 and the emergency and maintenance dynamic of immune response escape mutants in HIV-1 positive patients classified as LTNPs and with different levels of viral replication control. For this end, a group of 12 LTNP patients, classified as viremic controllers (VC) and Elite Controllers with (ECB) and without Blips (EC) according to their level of viremia control, was used. For each individual, DNA samples were extracted from PBMCs obtained during the earliest (V1) and most recent visits (VX) available. The extracted DNA was used to amplification and sequencing, through a NGS methodology, of the Gag and Nef genes. The sequences obtained allowed to map the whole Nef gene (medium coverage of 286.463 reads/pb) and the first 1000bps of Gag (medium coverage of 212.674 reads/pb) The consensus sequences of each mapping were used to divergence analyses between V1 and VX and variants with frequencies higher than 0,5% in each mapped bp were considered real. The evolution analyses showed a lower degree of diversity and divergence of Gag and Nef genes between controllers. EC individuals presented lower mutational profile in both genes when compared with ECB and VC patients. While Gag presented higher conservation than Nef in VCs, both genes had showed similar variability in ECs, indicating that a higher viremia control limit the evolution in both regions. In some ECB individuals, evidence of superinfection and APOBEC3g mediated Hypermutation was observed. The analyses of mutation along regions of CTL-restricted epitopes had showed the presence of mutations arised between V1 and VX, which were indicative of imune response escape, in most individuals. Non synonymous mutations had been found in lower frequencies in all individuals, including ECs, indicating that those escape variantes arise, but most don\2019t manage to obtain evolutionary succes

Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control

Abstract Background Despite the low level of viral replication in HIV controllers (HICs), studies have reported viral mutations related to escape from cytotoxic T-lymphocyte (CTL) response in HIV-1 plasma sequences. Thus, evaluating the dynamics of the emergence of CTL-escape mutants in HICs reservoirs is important for understanding viremia control. To analyze the HIV-1 mutational profile and dynamics of CTL-escape mutants in HICs, we selected 11 long-term non-progressor individuals and divided them into the following groups: (1) viremic controllers (VCs; n = 5) and (2) elite controllers (ECs; n = 6). For each individual, we used HIV-1 proviral DNA from PBMCs related to earliest (VE) and latest (VL) visits to obtain gag and nef sequences using the Illumina HiSeq system. The consensus of each mapped gene was used to assess viral divergence, and next-generation sequencing data were employed to identify SNPs and variations within and flanking CTL epitopes. Results Divergence analysis showed higher values for nef compared to gag among the HICs. EC and VC groups showed similar divergence rates for both genes. Analysis of the number of SNPs showed that VCs present more variability in both genes. Synonymous/non-synonymous mutation ratios were < 1 for gag among ECs and for nef among ECs and VCs, exhibiting a predominance of non-synonymous mutations. Such mutations were observed in regions encoding CTL-restricted epitopes in all individuals. All ECs presented non-synonymous mutations in CTL epitopes but generally at low frequency (< 1%); all VCs showed a high number of mutations, with significant frequency changes between VE and VL visits. A higher frequency of internal mutations was observed for gag epitopes, with significant changes across visits compared to Nef epitopes, indicating a pattern associated with differential genetic pressure. Conclusions The high genetic conservation of HIV-1 gag and nef among ECs indicates that the higher level of viremia control restricts the evolution of both genes. Although viral replication levels in HICs are low or undetectable, all individuals exhibited CTL epitope mutations in proviral gag and nef variants, indicating that potential CTL escape mutants are present in HIC reservoirs and that situations leading to a disequilibrium of the host-virus relationship can result in the spread of CTL-escape variants

A case report of HIV-1 superinfection in an HIV controller leading to loss of viremia control: a retrospective of 10 years of follow-up

Submitted by Janaína Nascimento ([email protected]) on 2019-08-09T12:58:59Z No. of bitstreams: 1 ve_Caetano_Diogo_etal_INI_2019.pdf: 1669871 bytes, checksum: 8910aa4c77e7bd848da5db4f5a62c43d (MD5)Approved for entry into archive by Janaína Nascimento ([email protected]) on 2019-08-09T13:34:01Z (GMT) No. of bitstreams: 1 ve_Caetano_Diogo_etal_INI_2019.pdf: 1669871 bytes, checksum: 8910aa4c77e7bd848da5db4f5a62c43d (MD5)Made available in DSpace on 2019-08-09T13:34:02Z (GMT). No. of bitstreams: 1 ve_Caetano_Diogo_etal_INI_2019.pdf: 1669871 bytes, checksum: 8910aa4c77e7bd848da5db4f5a62c43d (MD5) Previous issue date: 2019Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Background: HIV controllers (HICs) are a rare group of HIV-1-infected individuals able to naturally control viral replication. Several studies have identified the occurrence of HIV dual infections in seropositive individuals leading to disease progression. In HICs, however, dual infections with divergent outcomes in pathogenesis have been described. Case presentation: Here, we present a case report of a HIC diagnosed in late 1999 who displayed stable CD4+ T cell levels and low plasmatic viral load across 12 years of follow-up. In early 2013, the patient started to present an increase in viral load, reaching a peak of 10,000 copies/ml in early 2014, followed by an oscillation of viremia at moderate levels in the following years. The genetic diversity of env proviral quasispecies from peripheral blood mononuclear cells (PBMCs) was studied by single genome amplification (SGA) at six timepoints across 2009–2017. Phylogenetic analyses of env sequences from 2009 and 2010 samples showed the presence of a single subtype B variant (called B1). Analyses of sequences from 2011 and after revealed an additional subtype B variant (called B2) and a subsequent dominance shift in the proviral quasispecies frequencies, with the B2 variant becoming the most frequent from 2014 onwards. Latent syphilis related to unprotected sexual intercourse was diagnosed a year before the first detection of B2, evidencing risk behavior and supporting the superinfection hypothesis. Immunologic analyses revealed an increase in CD8+ and CD4+ T cell immune activation following viremia increase and minor T cell subset alterations during follow-up. HIV-specific T cell responses remained low throughout the follow-up period. Conclusions: Altogether, these results show that loss of viremia control in the HIC was associated with superinfection. These data alert to the negative consequences of reinfection on HIV pathogenesis, even in patients with a long history of viremia control and an absence of disease progression, reinforcing the need for continued use of adequate prevention strategies

Patterns of Diversity and Humoral Immunogenicity for HIV-1 Antisense Protein (ASP)

HIV-1 has an antisense gene overlapping env that encodes the ASP protein. ASP functions are still unknown, but it has been associated with gp120 in the viral envelope and membrane of infected cells, making it a potential target for immune response. Despite this, immune response patterns against ASP are poorly described and can be influenced by the high genetic variability of the env gene. To explore this, we analyzed 100k HIV-1 ASP sequences from the Los Alamos HIV sequence database using phylogenetic, Shannon entropy (Hs), and logo tools to study ASP variability in worldwide and Brazilian sequences from the most prevalent HIV-1 subtypes in Brazil (B, C, and F1). Data obtained in silico guided the design and synthesis of 15-mer overlapping peptides through spot synthesis on cellulose membranes. Peptide arrays were screened to assess IgG and IgM responses in pooled plasma samples from HIV controllers and individuals with acute or recent HIV infection. Excluding regions with low alignment accuracy, several sites with higher variability (Hs > 1.5) were identified among the datasets (25 for worldwide sequences, 20 for Brazilian sequences). Among sites with Hs 20% in the 48 variable sites identified were included in 92 peptides, divided into 15 sets, representing near full-length ASP. During the immune screening, the strongest responses were observed in three sets, one in the middle and one at the C-terminus of the protein. While some sets presented variations potentially associated with epitope displacement between IgG and IgM targets and subtype-specific signatures appeared to impact the level of response for some peptides, signals of cross-reactivity were observed for some sets despite the presence of B/C/F1 signatures. Our data provides a map of ASP regions preferentially targeted by IgG and IgM responses. Despite B/C/F1 subtype signatures in ASP, the amino acid variation in some areas preferentially targeted by IgM and IgG did not negatively impact the response against regions with higher immunogenicity

Reduction of inflammation and T cell activation after 6 months of cART initiation during acute, but not in early chronic HIV-1 infection

Abstract Objectives To investigate the impact of early combined antiretroviral therapy (cART) on inflammation biomarkers and immune activation during acute and early chronic HIV-1 infection. Methods We included 12 acute (AHI), 11 early chronic (EcHI), and 18 late chronic HIV-1-infected (LcHI) individuals who were treated with cART and 18 HIV-1-uninfected (HIV-neg) individuals. Plasmatic levels of inflammation biomarkers, CD8+CD38+HLA-DR+ T cell frequencies, CD4 T cell counts, CD4/CD8 ratio, total HIV-1 DNA and plasmatic viral load were evaluated. Mann–Whitney test, Pearson and Spearman correlation, and linear regression models were used for statistical analyses. Results IP-10, IL-18, and sCD163 were significantly elevated at pre-ART in the AHI and EcHI groups, showing a significant reduction after 6 months of cART in the AHI group, achieving similar levels to the HIV-neg group. For the EcHI group, the IP-10 and sCD163 levels were also significantly reduced on M6-ART; however, IP-10 levels remained higher than in the HIV-neg group, and no significant reduction of IL-18 levels was observed. The CD8+ T cell activation levels were elevated in the AHI and EcHI groups at pre-ART and showed a significant reduction on M6-ART, but they were similar to levels seen for HIV-neg only after 12 months of cART. At pre-ART, IP-10 levels but not IL-18 levels were positively correlated with HIV-1 viral load in the AHI group. Conclusions Early initiation of cART in HIV infection can reduce systemic inflammation, but the earlier normalization of the inflammation markers was only observed when cART was initiated in the acute phase of infection. A slower dynamic of reduction was observed for CD8+ T cell activation

Association between <i>PSIP1</i> haplotypes and AIDS progression.

<p>Results are shown as OR (95% confidence interval; p-value). LTNP  =  long-term nonprogressors, TP  =  typical progressors and RP  =  rapid progressors. n.d.  =  not done.</p

LEDGF/p75 genomic organization and structure.

<p>A) <i>PSIP1</i> gene organization: Exons are represented as grey blocks and numbered according to their position in the chromossome. 5′ UTR and 3′UTR are indicated by black blocks. Introns are represented by black lines. The SNPs analyzed in the present study are indicated by arrows according to their genomic position. *rs2277191 is located in a non coding region between the two <i>PSIP1</i> 5′UTR regions. B) Protein structure: LEDGF/p75 protein domains are represented: PWWP (proline-tryptophan-tryptophan-proline domain); NLS (nuclear localization signal); AT hook (adenine-thymine rich DNA binding region) and IBD (integrase binding domain). The positions associated to the interaction with HIV-1 integrase (K364, I365, D366, F406, V408) and the positions I436 and I473 previously described to present rare missense mutations in LTNPs (Ballana et al., 2012) were investigated in this study.</p

Association between <i>PSIP1</i> SNPs and AIDS progression.

<p>Results are shown as OR (95% confidence interval; p-value) estimated under a codominant model. LTNP  =  long-term nonprogressors, TP  =  typical progressors and RP  =  rapid progressors. n.d  =  not determined.</p

General characteristics of the subjects according to the study group and clinical classification.

<p>*Age at sample collection for population controls (HIV−) and at first positive test for HIV+ patients.</p><p>**Results are shown as N (frequency).</p><p>***p<0.05 for ethnicity comparisons according to χ² test. LTNP  =  long-term nonprogressors, TP  =  typical progressors and RP  =  rapid progressors.</p