Asthma and rhinitis have different genetic profiles for IL13, IL17A and GSTP1 polymorphisms

BACKGROUND: Asthma and rhinitis have a complex etiology, depending on multiple genetic and environmental risk factors. An increasing number of susceptibility genes are currently being identified, but the majority of reported associations have not been consistently replicated across populations of different genetic backgrounds. PURPOSE: To evaluate whether polymorphisms of IL4R (rs1805015), IL13 (rs20541), IL17A (rs2275913) and GSTP1 (rs1695) genes are associated with rhinitis and/or asthma in adults of Portuguese ancestry. METHODS: 192 unrelated healthy individuals and 232 patients, 83 with rhinitis and 149 with asthma, were studied. All polymorphisms were detected by real time polymerase chain reaction (PCR) using TaqMan assays. RESULTS: Comparing to controls, significant association with asthma was observed for GSTP1 rs1695 AA genotype (odds ratio (OR) - 1.96; 95% CI - 1.18 to 3.25; p=0.010). The association sustains for allergic asthma (OR - 2.17; 95% CI - 1.23 to 3.80; p=0.007). IL13 rs20541 GG genotype was associated with less susceptibility to asthma (OR - 0.55, 95% CI - 0.33 to 0.94, p=0.028). Among patients, IL17A rs2275913 AA genotype was less associated with asthma than with rhinitis (OR - 0.20; 95% CI of 0.07 to 0.56; p=0.002). A similar association was found for IL13 rs20541 GG genotype (OR - 0.48; 95% CI of 0.25 to 0.93; p=0.031). There were no significant differences in the distribution of allelic and genotypic frequencies between patients and controls for the IL4R polymorphism' analyzed. CONCLUSION: These results support the existence of a significant association between GSTP1 rs1695 and IL13 rs20541 SNPs, with susceptibility to asthma, in the population studied. Different genotype profiles of IL17A and IL13 genes seem to influence the clinical pattern of disease expression mainly confined to the upper airways, as rhinitis, or including the lower airways, as asthma.

Caracterização fisio-molecular de cultivares de feijão (Phaseolus vulgaris L.) em resposta à deficiência hídrica

The identification of genotypes for drought tolerance has a great importance in breeding programs. The aim of this study was to characterize genotypes of beans in response to drought tolerance in different reproductive stages through physiologic, agronomic and molecular analysis. The experiment was conducted in greenhouse, using a randomized block design with four replicates; 10 cultivars: ANFC 9, ANFP 110, BRS Esplendor, BRSMG Realce, IPR Siriri, IPR Tangará, IPR Tuiuiu, IPR Uirapuru, IAC Imperador and IAC Milênio under two conditions of irrigation: plants irrigated during their entire life cycle, and plants under irrigation suppression in the reproductive stage (R7) until 16% of field capacity, when the irrigation was restored. In the last four days of stress, the gas exchanges were analyzed, and in the last day of stress was analyzed the percentage of closed stomata in the abaxial surface of the leaves, collected in different times of the day (9h, 12h, 15h and 18h). Additionally, plant samples were collected for the following analysis: fresh and dry mass of leaves, stems and legumes, and proline content in leaves and roots. The plants were harvested at the physiological maturity and the yield components and grain yield were determined. In addition, in order to identify polymorphisms in the sequences of promoters and genes related to drought, seven pairs of primers were tested on the group of genotypes. The drought susceptibility indexes (ISS) ranged from 0.65 to 1.10 in the group of genotypes, which the lowest values observed were for IAC Imperador (0.65) and BRS Esplendor (0.87), indicating the ability of these two genotypes to maintain grain yield under water stress condition. All genotypes showed reduction in yield components under water stress. IAC Imperador (43.4%) and BRS Esplendor (60.6%) had the lowest reductions in productivity and kept about 50% of the stomata closed during all the different times evaluated at last day of irrigation suppression. IAC Imperador showed greater water use efficiency and CO2 assimilation rate under drought stress. IPR Tuiuiú, IPR Tangará and IAC Imperador had the highest proline concentrations in the roots. Under water stress condition, there was a strong positive correlation (0.696) between the percentage of stomata closed with the number of grains per plant (0.696) and the fresh mass of leaves (0.731), the maximum percentage of stomata closed 73.71% in water stress. The accumulation of proline in the root was the character that most contributed to the divergence between the genotypes under water deficit, but not always the genotypes that have accumulated more proline were the most tolerant. The polymorphisms in DNA of coding and promoting sequences of transcription factors studied in this experiment did not discriminate tolerant genotypes from the sensitive ones to water stress.

Análise do efeito de polimorfismos não-sinônimos em genes de reparo de DNA da via BER na resposta inflamatória da meningite

In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis and also developed a system to enable the functional analysis of polymorphic proteins. Patients with bacterial meningitis (BM), aseptic meningitis (AM) and controls (non-infected) genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. The levels of NF-κB and c-Jun were measured in CSF by dot blot assays. A significant (P<0.05) increase in the frequency of APE1 148Glu allele in BM and AM patients was observed. A significant increase in the genotypes Asn/Asn in control group and Asn/Glu in BM group was also found. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs increased significantly in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 148Glu allele or OGG1 326Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1Asn148Glu, OGG1Ser326Cys or PARP-1Val762Ala. Reductions in the levels ofIL-6, IL-1Ra, MCP-1/CCL2and IL-8/CXCL8 were observed in the presence of APE1148Glu allele in BM patients, however no differences were observed in the levels of NF-κB and c-Jun considering genotypes and analyzed groups. Using APE1 as model, a system to enable the analysis of cellular effects and functional characterization of polymorphic proteins was developed using strategies of cloning APE1 cDNA in pIRES2-EGFP vector, cellular transfection of the construction obtained, siRNA for endogenous APE1 and cellular cultures genotyping. In conclusion, we obtained evidences of an effect of SNPs in DNA repair genes on the regulation of immune response. This is a pioneering work in the field that shows association of BER variant enzymes with an infectious disease in human patients, suggesting that the SNPs analyzed may affect immune response and damage by oxidative stress level during brain infection. Considering these data, new approaches of functional characterization must be developed to better analysis and interactions of polymorphic proteins in response to this context

Enfoque genómico en la enfermedad cardiovascular

Introducción: las enfermedades cardiovasculares (EC) constituyen la principal causa de muerte a nivel mundial. La etiología es multifactorial, pueden influir diversos factores como la dieta, los hábitos de vida, el nivel de ejercicio físico o la carga genética. El gran número de genes implicados, así como sus diversas variantes, pueden influir sobre el riesgo de padecer enfermedades cardiovasculares por medio de distintas vías. Objetivo: determinar la relación existente entre diferentes polimorfismos genéticos y el riesgo individual de EC en población infantil y adulta. Métodos: se llevó a cabo una búsqueda bibliográfica utilizando la base de datos PubMed. La búsqueda se limitó a un periodo de diez años y a metaanálisis realizados en humanos. Resultados: se establece relación entre el riesgo de enfermedad cardiovascular y los siguientes polimorfismos genéticos: cromosoma 9p21, apolipoproteína A5, apolipoproteínas E2, E3 y E4, gen PPARG o PPARΥ, genes implicados en el metabolismo lipídico, gen MTHFR, citocromo P450, factor V de coagulación o factor de Leiden (FVL) y gen VKORC. Conclusiones: Se han identificado un gran número de genes relacionados con la enfermedad cardiovascular. La carga genética puede influir de manera directa o indirecta sobre el riesgo cardiovascular, modificando factores de riesgo para enfermedad cardiovascular o actuando sobre la medicación empleada para tratarla.

Estudo de polimorfismos genéticos e da sua associaçäo com capacidades de produçäo leiteira em caprinos de raça Algarvia e ovinos de raça Serra da Estrela

Dissertação de mest. em Química Celular, Unidade de Ciências Exactas e Humanas, Univ. do Algarve, 1996

Periodontite e expressão génica

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas Moniz

Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.

Background: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.

Muscle-related polymorphisms (MSTN rs1805086 and ACTN3 rs1815739) are not associated with exceptional longevity in Japanese centenarians

Myostatin (MSTN) and α-actinin-3 (ACTN3) genes are potentially associated with preservation of muscle mass and oxidative capacity, respectively. To explore the possible role of these genes in exceptional longevity (EL), the allele/genotype frequency distribution of two polymorphisms in MSTN (rs1805086, K153R) and ACTN3 (rs1815739, R577X) was studied in Japanese centenarians of both sexes (n = 742) and healthy controls (n = 814). The rs1805086 R-allele (theoretically associated with muscle mass preservation at the expense of oxidative capacity) was virtually absent in the two groups, where genotype distributions were virtually identical. Likewise, no differences in allele (p = 0.838 (women); p = 0.193 (men); p = 0.587 (both sexes)) or genotype distribution were found between groups for ACTN3 rs1815739 (p = 0.975 (women), p = 0.136 (men), p = 0.752 (both sexes)). Of note, however, the frequency of the rs1805086 R-allele observed here is the lowest been reported to date whereas that of the 'highly oxidative/efficient' rs1815739 XX genotype in Japanese male centenarians (33.3%) or supercentenarians of both sexes (≥110 years) are the highest (32.6%), for a non-American population. No definite conclusions can be inferred in relation to EL owing to its lack of association with both rs1815739 and rs1805086. However, it cannot be excluded that these gene variants could eventually be related to a "healthy" metabolic phenotype in the Japanese population. Further research might determine if such metabolic profile is among the factors that can potentially predispose these individuals to live longer than Caucasians and what genetic variants might be actually involved.

Genotypic profile of Pantanal creole sheep regarding susceptibility or resistance to scrapie.

The objective of this work was to determine the genotypic profile specific to scrapie in codons 136, 154, and 171 of the PRNP gene of the Pantanal creole sheep. Genomic DNA was extracted from blood samples collected from 66 sheep, and the regions of interest on the DNA strand were amplified by PCR. Five haplotypes were identified: ARR, alanine, arginine, arginine; ARQ, alanine, arginine, glutamine; AHQ, alanine, histidine, glutamine; ARH, alanine, arginine, histidine; and VRQ, valine, arginine, glutamine. The most common genotypes were ARQ/ARQ (27%) and ARR/ARQ (24%). The genotypic profile of the Pantanal creole sheep shows low to moderate susceptibility.

Transferibilidade de locos microssatélites desenvolvidos em outras espécies de palmeiras para Astrocaryum vulgare Mart.

Astrocaryum vulgare Mart., conhecida por tucumã-do-Pará, possui uso popular na região amazônica e grandes potencialidades de aproveitamento em indústrias farmacêutica, cosmética e de biodiesel. A exploração ainda é extrativista, tornando fundamentais informações sobre a variabilidade genética existente em áreas de ocorrência natural. A variabilidade genética pode ser acessada por marcadores microssatélites ou SSR, considerados ideais para estudo em populações naturais. Entretanto, não há relatos de desenvolvimento de microssatélites para A. vulgare. O objetivo foi avaliar a transferibilidade de locos SSR desenvolvidos para outras espécies de palmeiras em A. vulgare. Realizou-se a extração de DNA a partir de amostras de folíolos de tucumanzeiros de sete povoamentos e após a quantificação os DNA?s foram submetidos à PCR, com os locos desenvolvidos para Bactris gasipaes, Phoenix dactylifera e Astrocaryum aculeatum. As condições de amplificação seguiram o protocolo desenvolvido para A. aculeatum, com pequenas adaptações. Os produtos amplificados foram aplicados em gel de agarose a 3,5%, corado com brometo de etídio e submetidos à eletroforese horizontal. Os perfis dos géis foram fotodocumentados e as imagens armazenadas digitalmente. A transferibilidade dos locos foi avaliada com base na amplificação dos produtos, sua nitidez e ausência de bandas inespecíficas. Todos os locos de A. aculeatum e a maioria dos de B. gasipaes amplificaram, com 75% deles transferíveis para o genoma de A. vulgare, enquanto que apenas dois dos locos de P. dactylifera amplificaram, com muitas bandas inespecíficas, mostrando-se inviáveis para estudos do genoma da espécie.

Caracterização genética da pimenta-do-reino e do cupuaçu através de isoenzimas.

O objetivo da pesquisa foi analisar a variação isoenzimática presente em híbridos e cultivares de pimenta-do-reino (Piper nigrum) e acessos de cupuaçu (Theobroma grandiflorum). O material utilizado foi proveniente dos bancos de germoplasma da Embrapa Amazônia Oriental. As metodologias para a extração das enzimas, formulação de tampões do gel e da cuba e para os procedimentos de coloração foram os descritos por Tsumura, 1990, modificado. Foram testados dezoito sistemas enzimáticos: FUM, ACP; PGI; SKDH; ACO; GOT; G6PD ; 6PGD; DIA; MNR; ME; MDH; GDH; PGM; TZO; ADH; LAP e SoDH. As interpretações genéticas foram feitas de acordo com o método descrito por Alfenas et al., 1991. Concluiu-se, através dos padrões eletroforéticos encontrados, que seis sistemas empregados apresentaram polimorfismo enzimático para a pimenta-do-reino e quatro para o cupuaçu. A presença de heterozigosidade nos materiais estudados significa variabilidade a ser explorada no programa de melhoramento genetic° destas espécies. A resolução obtida nestes sistemas com bandas bem nítidas indica a presença de atividade enzimática em folhas jovens de pimenta-do-reino e cupuaçu.

Diversidade genética estimada através de marcadores ISSR de Colletotrichum graminicola no Brasil.

A antracnose do milho causada pelo fungo Colletotrichum graminicola é uma das principais doenças da cultura no Brasil e no mundo, atacando praticamente todas as partes da planta. Neste trabalho, foi avaliada a variabilidade genética de 95 isolados monospóricos de C. graminicola provenientes dos estados de Goiás, Minas Gerais, Santa Catarina, São Paulo, Paraná e Rio Grande do Sul. Foram avaliados 15 primers ISSR, sendo selecionados nove que resultaram em um maior polimorfismo. Os fragmentos de DNA gerados pelas análises de ISSR foram avaliados mediante inspeção visual dos géis. Bandas de mesmo peso molecular, em indivíduos diferentes, foram consideradas idênticas e designadas em função da ausência (0) e presença (1) no gel. Baseado na matriz, foi gerado um dendrograma pelo método UPGMA, utilizando as 66 bandas amplificadas pelos nove primers ISSR. Ao analisar o dendrograma, foi traçada uma linha divisória no valor da distância de dissimilaridade de 0,3, dividindo os isolados em sete grupos. Baseado nos resultados, foi possível concluir que a variabilidade genética entre os isolados de C. graminicola é alta, sendo os marcadores ISSR eficazes na determinação de sua variabilidade. Os isolados utilizados no presente trabalho não apresentam estruturação geográfica.

Caracterização genética de uma população natural de bacurizeiro (Platonia insignis Mart.) por meio de marcadores ISSR.

Nativa da Região Amazônica, o bacuri (Platonia insignis Mart) é uma espécie frutífera comumente utilizada na cultura alimentar da região Norte do Brasil. Apresenta grande importância para as populações rurais como fonte de renda, devido à sua comercialização. Devido à alta capacidade de reprodução, por meio da reprodução assexuada, pode ocorrer adensamento de indivíduos com alta similaridade, ocasionando diminuição na variabilidade genética populacional. O presente trabalho teve como objetivo caracterizar a diversidade genética presente em uma população natural de Platonia insignis localizada no município de Bragança, no Estado do Pará, por meio de marcadores ISSR (inter simple sequence repeats). Dessa forma, foram genotipadas 78 plantas adultas de uma população de floresta secundária com seis primers ISSR. Os primers amplificaram 42 locos, dos quais 34 foram polimórficos, representando uma taxa de 81% polimorfismo com média de 5,66 de locos polimórficos por primer. Dentro das áreas de coleta, foram encontrados 53 indivíduos considerados clones, representando 68 % do total, considerando similaridade mínima de 0,95. Desta forma, foi possível visualizar a alta incidência de clones na população.

Comparison of sequence variants in the PDK4 and COX4I2 genes between racing and cutting lines of quarter horses and associations with the speed index.

Different selection objectives within the Quarter Horse breed led to the formation of groups with distinct skills, including the racing and cutting lines. With a smaller population size in Brazil, but of great economic representativeness, the racing line is characterized by animals that can reach high speeds over short distances and within a short period of time. The cutting line is destined for functional tests, exploring skills such as agility and obedience. Although the athletic performance of horses is likely to be influenced by a large number of genes, few genetic variants have so far been related to this trait and this was done exclusively in Thoroughbreds, including the g.38973231G>A singlenucleotide polymorphism in the PDK4 gene and the g.22684390C>T single-nucleotide polymorphism in the COX4I2 gene. The results of the present study demonstrate the presence of polymorphic PDK4 and COX4I2 genes in Quarter Horses. The analysis of 296 racing animals and 68 cutting animals revealed significant differences in allele and genotype frequencies between the two lines. The same was not observed when these frequencies were compared between extreme racing performance phenotypes. There were also no significant associations between alleles of the two polymorphisms and the speed index. These results suggest that the alleles of the PDK4 and COX4I2 genes, which are related to better racecourse performance in Thoroughbreds, are probably associated with beneficial adaptations in aerobic metabolism and therefore play secondary roles in sprint racing performance in Quarter Horses, which is mainly anaerobic.

Marcador alelo-específico associado com níveis de expressão do gene ZmMATE1 em milho.

2016