Afro-Derived Amazonian Populations: Inferring Continental Ancestry and Population Substructure

A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations

Origin of the hemoglobin S gene in a northern Brazilian population: the combined effects of slave trade and internal migrations

ABSTRACT We analyzed DNA polymorphisms in the -globin gene cluster of 30 sickle cell anemia patients from Belém, the capital city of the State of Pará, in order to investigate the origin of the S mutation. Sixty-seven percent of the S chromosomes were Bantu type, 30% were Benin type, and 3% were Senegal type. The origin of the S mutation in this population, estimated on the basis of bS-linked haplotypes, contradicts the historical records of direct slave trade from Africa to the northern region of Brazil. Historical records indicate a lower percentage of people from Benin. These discrepancies are probably due to domestic slave trade and later internal migrations, mainly from northeastern to northern regions. Haplotype distribution in Belém did not differ significantly from that observed in other Brazilian regions, although historical records indicate that most slaves from Atlantic West Africa, where the Senegal haplotype is prevalent, were destined for the northern region, whereas the northeast (Bahia, Pernambuco and Maranhão) was heavily supplied with slaves from Central West Africa, where the Benin haplotype predominates

Hanseníase em menores de 15 anos: expressão da magnitude e da força da transmissão recente, no estado do Pará, 2006 a 2015 / Leprosy in children under 15 years of age: expression of the magnitude and strength of recent transmission, in Pará state, 2006 to 2015

A hanseníase é uma doença infectocontagiosa, curável, contudo, com grande potencial para gerar incapacidade física. Conhecer o impacto da hanseníase em menores de 15 anos permite estimar o nível de transmissão, a intensidade da endemia e avaliar a efetividade dos serviços de saúde em combater essa enfermidade, que é mais prevalente em populações pobres e representa um crescente problema de saúde no estado do Pará. O objetivo deste estudo foi estudar a distribuição geográfica da hanseníase em menores de 15 anos, na Região Metropolitana de Belém, estado do Pará. Estudo quantitativo, com desenho de estudo ecológico, dos casos notificados de hanseníase, em menores de 15 anos de idade, abrangendo o período de 2006 a 2015. Foram calculados indicadores epidemiológicos e utilizou-se o software livre com código-fonte aberto QGis 2.18 para a construção dos mapas. Dos 675 casos, havia predomínio das formas paucibacilares e maior frequência da forma clínica dimorfa. A evolução da taxa média, padronizada, de detecção da hanseníase em menores de 15 anos, apontou muito hiperendemicidade nos municípios de Castanhal, que tinha cobertura populacional da Estratégia Saúde da Família consolidada, e de Marituba, com cobertura intermediária. A magnitude da endemia, a força da morbidade e a tendência da doença, apontadas pelos indicadores de acompanhamento epidemiológico, permaneceram elevadas e a cobertura da Estratégia Saúde da Família, embora consolidada na maioria dos municípios, não se distribuiu de forma homogênea a garantir cobertura universal aos territórios. Esses resultados contribuem para a análise da distribuição geográfica da hanseníase, importante para a identificação de áreas para alocação de recursos, visando controle e redução da doença. 

Avaliação da frequência alélica e haplotípica do sistema HLA para os loci HLA-A, HLA-B e HLA-DRB1 de receptores renais e doadores intervivo do estado do Pará, Brasil/ Evaluation of the allelic and haplotypic frequency of the HLA system for HLA-A, HLA-B e HLA-DRB1 loci of renal receptors and living donors from the state of Pará, Brazil

Introdução: A descoberta dos antígenos leucocitários humano (HLA) trouxe o reconhecimento de que a compatibilidade do sistema HLA entre doador e receptor é um fator importante em transplantes de órgãos, tecidos e células. No transplante renal, a compatibilidade desse sistema está associada a sobrevida do enxerto em longo prazo e a incompatibilidade está envolvida diretamente na reatividade imunológica do receptor contra células do doador, o que pode levar a processos de rejeição celular e humoral. Objetivo: Esse trabalho teve como objetivo avaliar a frequência alélica e haplotípica de doadores e pacientes renais paraenses e possível associação com doenças. Método: As frequências alélicas e haplotípicas do HLA-A, -B e -DRB1 foram avaliadas em 475 doadores e receptores renais registrados na Fundação HEMOPA. Os programas Arlequin v.3.11 e PyPop v.0.7 foram utilizados para calcular as frequências alélicas e haplotípicas, equilíbrio de Hardy-Weinberg, teste de neutralidade e cálculo de desequilíbrio de ligação. As patologias que apresentaram prevalência maior que cinco dentre os pacientes estudados foram escolhidas para realizar a associação com os alelos HLA. A verificação da frequência dos alelos e haplótipos foi realizada com comparativos entre artigos publicados e utilização de ferramentas de pesquisa em sistemas de informação e sites sobre estudos em populações. Resultados: As doenças de base mais encontradas nos pacientes foram hipertensão arterial sistêmica, doença renal crônica e glomerulonefrite crônica. Os alelos mais comuns encontrados nos indivíduos paraenses foram HLA-A*02, HLA-A*24, HLA-A*31, HLA-B*35, HLA-B*15, HLA-B*51, HLA-DRB1*04, HLA-DRB1*13 e HLA-DRB1*01. Os loci do estudo apresentaram-se em equilíbrio de Hardy-Weinberg e o maior desequilíbrio de ligação foi entre os lócus B e DRB1. O haplótipo mais frequente nos indivíduos paraenses foi A*02 B*44 DRB1*07. Enquanto nos pacientes e doadores, os haplótipos mais observados foram A*02 B*51 DRB1*11 e A*02 B*44 DRB1*04, respectivamente. Conclusões: Esse é o primeiro estudo sobre a diversidade HLA com doadores e pacientes candidatos a transplante renal na região Norte do país. Nossos resultados de frequência alélica e haplotípica foram semelhantes aos encontrados em outros estudos na população brasileira. Esses dados reforçam o conceito de que os genes HLA são uma ferramenta confiável para investigar a composição étnica de uma população.

Dental Occlusion in a Split Amazon Indigenous Population: Genetics Prevails over Environment

Background: Studies examining human and nonhuman primates have supported the hypothesis that the recent increase in the occurrence of misalignment of teeth and/or incorrect relation of dental arches, named dental malocclusion, is mainly attributed to the availability of a more processed diet and the reduced need for powerful masticatory action. For the first time on live human populations, genetic and tooth wear influences on occlusal variation were examined in a split indigenous population. The Arara-Iriri people are descendants of a single couple expelled from a larger village. In the resultant village, expansion occurred through the mating of close relatives, resulting in marked genetic cohesion with substantial genetic differences. Methodology/Principal Findings: Dental malocclusion, tooth wear and inbreeding coefficient were evaluated. The sample examined was composed of 176 individuals from both villages. Prevalence Ratio and descriptive differences in the outcomes frequency for each developmental stage of the dentition were considered. Statistical differences between the villages were examined using the chi-square test or Fisher’s exact statistic. Tooth wear and the inbreeding coefficient (F) between the villages was tested with Mann-Whitney statistics. All the statistics were performed using two-tailed distribution at p#0.05. The coefficient inbreeding (F) confirmed the frequent incestuous unions among the Arara-Iriri indigenous group. Despite the tooth wear similarities, we found a striking difference in occlusal patterns between the two Arara villages. In the original village, dental malocclusion was present in about one third of the population; whilst in the resultant village, the occurrence was almost doubled. Furthermore, the morphological characteristics of malocclusion were strongly different between the groups. Conclusions/Significance: Our findings downplay the widespread influence of tooth wear, a direct evidence of what an individual ate in the past, on occlusal variation of living human populations. They also suggest that genetics plays the most important role on dental malocclusion etiology

Inherited hemoglobin disorders in an Afro-Amazonian community: Saracura

The most common hemoglobinopathies, viz, hemoglobins S and C, and α-and β-thalassemias, were investigated through the molecular screening of 116 subjects from the community of Saracura, comprising fugitive African slaves from farms of the municipality of Santarém, in the west of Pará State, Brazilian Amazon. The observed frequency of the HBB*S gene (0.9%) was significantly lower than that encountered in other Afro-derived communities in the region. Concomitantly, the absence of the HBB*C allele has been reported for most of the Afro-Amazonian communities thus far studied. As remnant populations of quilombos are generally small, the heterogeneous distribution of HBB*S and HBB*C alleles among them is probably due to genetic drift and/or founder effect. The observed frequency of 3.7 kb deletion in Saracura (8.5%) was consistent with the African origin of the population, with a certain degree of local differentiation and admixture with individuals of Caucasian ancestry, placed in evidence by the occurrence of - -(MED) deletion (1.2%), a common mutation in Mediterranean regions. As regards f-thalassemia, among the seven different mutations found in Saracura, three βºand two β+ mutations were of Mediterranean origin, and two β+ of African. Thus, only 28% of the local β-thalassemia mutations found in Saracura were of African origin

Comparative Genomic Analysis of Lactobacillus plantarum: An Overview

Background. Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics. Results. The finding of the current study indicates that the core genome of L. plantarum presents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes of L. pentosus KCA1 and L. plantarum WCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat. Conclusions. Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains

Prevalence of hereditary risk factors for thrombophilia in Belém, Brazilian Amazon

Different risk factors for venous thromboembolism (VTE) have been identified, including hereditary abnormalities in the mechanisms of coagulation and fibrinolysis. We investigated five genetic polymorphisms (FVL G1691A, FII G20210A, MTHFR C677T, TAFI A152G and TAFI T1053C) associated with VTE in individuals from the city of Belém in the Brazilian Amazon who had no history of VTE. No significant difference was found between the observed and expected genotype frequencies for the loci analyzed. We found high frequencies of MTHFR C677T (33.9%) and TAFI T1053C (74%) and low frequencies of FVL (1.6%), FII G20210A (0.8%) and TAFI A152G (0.8%). The FVL G1691A, FII G20210A and MTHFR C677T frequencies were similar to those for European populations and populations of European descent living in the city of Ribeirão Preto in the Brazilian state of São Paulo. The frequency of the two TAFI mutations in the Belém individuals was not significantly different from that described for individuals from Ribeirão Preto. We suggest that the risks for VTE in the population of Belém are of the same magnitude as that observed in European populations and in populations with an expressive European contribution

Distribution of CCR5- 32, CCR2-64I, and SDF1-3 A Mutations in Populations from the Brazilian Amazon Region

The frequency distribution of the CCR5- 32, CCR2-64I, and SDF1-3 A alleles was studied in the urban population of Bele´m and in Afro- Brazilians, Amerindians, and Japanese immigrants in the state of Para´, Brazil. The results suggest that Amerindians may be genetically more susceptible to HIV-1 infection and disease progression than the other human groups studied