Abstract Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.

Resumo Introdução: A rinossinusite crônica é uma doença multifatorial cuja patogênese, influenciada por fatores genéticos e ambientais, ainda é incerta. Estudos genéticos anteriores mostraram que pacientes com rinossinusite crônica têm expressão reduzida do gene da Interleucina-22 (IL-22). Objetivo: Identificar e comparar a frequência de polimorfismos no gene IL22RA1 (receptor subunidade alfa 1 da interleucina 22) entre os pacientes com rinossinusite crônica com ou sem pólipos nasais. Método: Amostras de sangue periférico foram coletadas de 70 pacientes com rinossinusite crônica com pólipos nasais, 14 pacientes com rinossinusite crônica sem pólipos nasais e 68 indivíduos sem rinossinusite crônica, seguido por extração de DNA e análise da sequência do gene IL22RA1. Resultados: Dos dez polimorfismos identificados no gene IL22RA1, três não foram encontrados em alguma banco de dados genético analisado. Pacientes com rinossinusite crônica apresentaram maior frequência da inserção frameshift c.113_114insA, possivelmente patogênica. Por outro lado, no grupo controle, o polimorfismo c.435A>C mostrou predominância significativa do alelo mutado, talvez relacionado a uma proteção potencial contra o fenótipo da rinossinusite crônica. O polimorfismo c.770C> T, caracterizado como uma variante não sinônima, foi encontrado exclusivamente em pacientes negros com rinossinusite crônica com pólipos nasais. Conclusões: Embora nenhuma relação causal direta possa ser estabelecida entre os polimorfismos do gene IL22RA1 e a fisiopatologia da rinossinusite crônica, variações genéticas como c.113_114insA e c.435A>C podem estar envolvidas na suscetibilidade ou proteção contra o fenótipo da rinossinusite crônica, respectivamente. Testar essa hipótese exigirá estudos com coortes maiores.

Abstract Introduction: Chronic rhinosinusitis is a multifactorial disease whose pathogenesis, influenced rhinosinusitis; by both genetic and environmental factors, is still unclear. Previous genetic studies have shown that patients with chronic rhinosinusitis have reduced expression of the Interleukin-22 (IL-22) gene. Objective: Identify and compare the frequency of polymorphisms in the IL22RA1 gene (IL22 alpha-1 subunit receptor) among chronic rhinosinusitis patients – either with or without nasal polyps. Methods: Peripheral blood samples were collected from 70 chronic rhinosinusitis with polyps patients, 14 chronic rhinosinusitis without polyps patients and 68 subjects without chronic rhinosinusitis, followed by DNA extraction and IL22RA1 gene sequence analysis. Results: Among ten polymorphisms identified in the IL22RA1 gene, three were not found in any of the genetic databases analyzed. Chronic rhinosinusitis patients displayed higher frequency of the c.113_114insA frameshift insertion, possibly pathogenic. Conversely, in the control group, polymorphism c.435A > C had a significant predominance of the mutated allele, perhaps related to a potential protection against the chronic rhinosinusitis phenotype. Polymorphism c.770C > T, characterized as a non-synonymous variant, was exclusively found in Black chronic rhinosinusitis with polyps patients. Conclusions: Although no direct causal relationship could be established between IL22RA1 gene polymorphisms and the pathophysiology of chronic rhinosinusitis, genetic variations such as c.113_114insA and c.435A > C may be involved in the susceptibility to or protection against the chronic rhinosinusitis phenotype, respectively. Testing this hypothesis will require studies with larger cohorts.

A maior proporção de fumantes entre negros no Brasil tem sido atribuída a desigualdades socioeconômicas, mas fatores genéticos também poderiam contribuir para esse achado. Este estudo visou investigar associações entre status tabágico com ancestralidade definida geneticamente e características socioeconômicas em brasileiros. Amostras de sangue foram colhidas de 448 voluntários (66,7% homens; idade: 37,1±11,4 anos) classificados como fumantes atuais (FA: 60,9%), ex-fumantes (EF:8,9%) e não fumantes (NF:30,1%).Misturas éticas individuais foram determinadas empregando-se um painel informativo de ancestralidade composto por 48 polimorfismos de deleções e inserções. FA mostraram menor proporção de ancestralidade europeia do que NF (0,837±0,243 X 0,883±0,194; p≤0,05) e EF (0,837±0,243 X 0,864±0,230; p≤0,05), e maior proporção de ancestralidade africana sub-saárica do que EF (0,128±0,222 X 0,07±0,174, p≤0,05) e NF (0,128±0,222 X 0,085±0,178, p≤0,05). NF informaram maior número de anos de escola do que FA (11,2±3,7 X 8,9±3,8; p≤0,001). FA foram menos comuns na Classe econômica A (30%) e mais comuns na Classe B (56,8%). Em análise multivariada, apenas menor número de anos escolares e menor classe econômica estiveram associados com chances maiores para FA. O uso de marcadores de genética molecular para caracterizar o background étnico confirmou que diferenças socioeconômicas são os principais determinantes de maiores taxas de tabagismo entre negros no Brasil.

The higher proportion of smokers among Black people in Brazil has been attributed to socioeconomic disparities, but genetic factors could also contribute for this finding. This study aimed at investigating associations between smoking status with genetically defined ethnic ancestry and socioeconomic features in Brazilians. Blood samples were collected from 448 volunteers (66.7% male; age: 37.1±11.4 years) classified as current smokers (CS: 60.9%), former smokers (FS: 8.9%) and never smokers (NS: 30.1%). Individual interethnic admixtures were determined using a 48 insertion-deletion polymorphisms ancestry-informative-marker panel. CS showed a lower amount of European ancestry than NS (0.837±0.243 X 0.883±0.194, p≤0.05) and FS (0.837±0.243 X 0.864±0.230, p≤0.05), and a higher proportion of African Sub-Saharan ancestry than FS (0.128±0.222 X 0.07±0.174, p≤0.05) and NS (0.128±0.222 X 0.085±0.178, p≤0.05). NS reported a higher number of years in school than CS (11.2±3.7 X 8.9±3.8, p≤0.001). CS were less common in economic Class A (30%) and more common in Class B (56.8%). In multivariate analysis, only lower number of school years and lower economic class were associated with higher chances for CS. The use of genetic molecular markers for characterizing ethnic background confirmed that socioeconomic disparities are the main determinants of higher smoking rates among Blacks in Brazil.

INTRODUCTION: American tegumentary leishmaniasis (ATL) represents one of the most important public health issues in the world. An increased number of autochthonous cases of ATL in the Northeastern region of São Paulo State has been documented in the last few years, leading to a desire to determine the Leishmania species implicated. METHODS: PCR followed by DNA sequencing was carried out to identify a 120bp fragment from the universal kDNA minicircle of the genus Leishmania in 61 skin or mucosal biopsies from patients with ATL. RESULTS: DNA sequencing permitted the identification of a particular 15bp fragment (5' …GTC TTT GGG GCA AGT... 3') in all samples. Analysis by the neighbor-joining method showed the occurrence of two distinct groups related to the genus Viannia (V) and Leishmania (L), each with two subgroups. Autochthonous cases with identity to a special Leishmania sequence not referenced in Genbank predominated in subgroup V.1, suggesting the possible existence of a subtype or mutation of Leishmania Viannia in this region. In the subgroup L.2, which showed identity with a known sequence of L. (L.) amazonensis, there was a balanced distribution of autochthonous and non-autochthonous cases, including the mucosal and mucocutaneus forms in four patients. The last observation may direct us to new concepts, since the mucosal compromising has commonly been attributed to L. (V.) braziliensis, even though L. (L.) amazonensis is more frequent in the Amazonian region. CONCLUSIONS: These results confirm the pattern of distribution and possible mutations of these species, as well as the change in the clinical form presentation of ATL in the São Paulo State.

Nesse estudo nós usamos a técnica de Differential Display Reverse Transcriptase - Polymerase Chain Reaction (DDRT-PCR) para comparamos o perfil de mRNA em Melipona scutellaris durante o desenvolvimento ontogenético pós-embrionário e em operárias adultas, rainha natural e induzida pelo Hormônio Juvenil III. Fragmentos diferencialmente expressos foram detectados usando as seguintes combinações de primers: HT11G-AP05; HT11C-AP05; HT11G-OPF12; HT11G-OPA16. Dos 9 ESTs descrito nesse trabalho, 6 tiveram expressão diferencial nas fases de larva L1 e L2, sugerindo serem mecanismos chave no regulação do desenvolvimento larval em Melipona. A combinação HT11G-AP05 revelou em L1 e L2 um produto com similaridade à proteína tioredoxina redutase de Clostridium sporogenes, uma proteína importante durante os processos de oxidoredução. Esse estudo representa as primeiras evidências moleculares do perfil de expressão durante o desenvolvimento ontogenético em abelhas do gênero Melipona.

We have compared gene expression, using the Differential Display Reverse Transcriptase - Polymerase Chain Reaction (DDRT-PCR) technique, by means of mRNA profile in Melipona scutellaris during ontogenetic postembryonic development, in adult worker, and in both Natural and Juvenile Hormone III-induced adult queen. Six, out of the nine ESTs described here, presented differentially expressed in the phases L1 or L2, or even in both of them, suggesting that key mechanisms to the development of Melipona scutellaris are regulated in these stages. The combination HT11G-AP05 revealed in L1 and L2 a product which matches to thioredoxin reductase protein domain in the Clostridium sporogenes, an important protein during cellular oxidoreduction processes. This study represents the first molecular evidence of differential gene expression profiles toward a description of the genetic developmental traits in the genus Melipona.

Gene expression profiles contain the expression level of thousands of genes. Depending on the issue under investigation, this large amount of data makes analysis impractical. Thus, it is important to select subsets of relevant genes to work with. This paper investigates different metrics for gene selection. The metrics are evaluated based on their ability in selecting genes whose expression profile provides information to distinguish between tumor and normal tissues. This evaluation is made by constructing classifiers using the genes selected by each metric and then comparing the performance of these classifiers. The performance of the classifiers is evaluated using the error rate in the classification of new tissues. As the dataset has few tissue samples, the leave-one-out methodology was employed to guarantee more reliable results. The classifiers are generated using different machine learning algorithms. Support Vector Machines (SVMs) and the C4.5 algorithm are employed. The experiments are conduced employing SAGE data obtained from the NCBI web site. There are few analysis involving SAGE data in the literature. It was found that the best metric for the data and algorithms employed is the metric logistic.

PURPOSE: To investigate the prevalence of prostate carcinoma in a sample of volunteers known to have a large proportion of Bantu African ancestors, and the performance of total PSA (tPSA), PSA density (PSAD) and free-to-total PSA ratio (f/tPSA) on the diagnosis. MATERIALS AND METHODS: A total of 473 volunteers (range: 40 - 79 years) were screened for prostate carcinoma. Those with tPSA >2 ng/ml and/or abnormal digital rectal examination were submitted to a transrectal ultrasound-directed biopsy (10 cores). The volunteers were classified as White, Mulatto or Black according to physical characteristics and to ancestors race reference. The following variable number of tandem repeats (VNTR) were analyzed in the blood of 120 volunteers without cancer and in 27 patients with prostate cancer: D4S43, PAH, F13A1, APOB and vW-1. RESULTS: The biopsies performed in 121 volunteers revealed cancer in 27 (5.7% of 473). The proportions of cancer in White, Mulatto and Black were respectively: 0.6% (1/148), 6.7% (6/90) and 8.5% (20/235) (p = 0.006). The VNTRs analysis revealed heterogeneity in White, Mulatto and Black anthropologic phenotypes with the following admixture of Caucasian, African and Amerindian gene lineages: 67.5 ± 8%, 20.8 ± 8%, 11.7 ± 7%; 54.8 ± 9%, 36.3 ± 5%, 8.9 ± 7%; and, 45.3 ± 3%, 45.9 ± 4%, 8.8 ± 7%. Such a mixture was 50.5 ± 9%, 49 ± 8% and 0.5 ± 4% in volunteers bearing cancer, and 59.1 ± 7%, 31.7 ± 8% and 9.2 ± 5% in those without cancer. The sensitivity and specificity of tPSA at cut-off levels of 2, 2.5 and 4 ng/ml for volunteers with tPSA <= 10 ng/ml were respectively: 100% and 6,6%, 100% and 36,6%, 69,2% and 62,2%. PSAD at a cut-off level of 0.08 or 0.10, and f/tPSA at a cut-off level of 20% were able to increase significantly tPSA specificity without loss on sensitivity. CONCLUSIONS: The tumor prevalence was higher in Non-White than in White phenotype. The association of tPSA at a cut-off level of 2.5 ng/ml with a PSAD of 0.08 or a f/tPSA of 20% for biopsy indication deserves further investigations as an alternative to tPSA cut-off level of 4 ng/ml.

As doenças hereditária da hemoglobina são as mais comuns doenças monogênicas e atualmente bem conhecidas do ponto de vista molecular, fato este que propiciou um avanço no seu controle e manuseio. A população brasileira caracteriza-se pela multiplicidade étnica e a caracterização da Hb D torna-se importante por este dado, associado ao fato de que os métodos de detecção das hemoglobinopatias comumente não identificam esta fração anormal que apresenta a peculiaridade de migração eletroforéticia em pH alcalino na mesma zona observada nas Hb S e G. Neste relato é apresentado um estudo familiar no qual é empregada metodologia adequada, o HLPC, que permite a identificação da Hb D.

Inherited disorders of hemoglobin, the most common monogenic disease, are now well understood at the molecular level, knowledge, which has led to considerable improvements in their control and management. The Brazilian population is multiethnic, and the correct characterization of the Hb D is important, mainly because the method available for detection of abnormal hemoglobins, present a migration in the same zone at alkaline pH, for Hb S, D, and G for example. In this paper we studied a family with an abnormal hemoglobin like S in alkaline electrophoresis, by appropriated methods including HPLC and molecular analysis, characterized as hemoglobin D Los Angeles.