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1.
Braz. j. biol ; 84: e248656, 2024. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1345542

ABSTRACT

Abstract Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.


Resumo Muitas espécies de Cichla colonizaram com sucesso lagos e reservatórios do Brasil desde os anos 1960, causando graves prejuízos à vida selvagem nesses locais. Neste estudo, 135 tucunarés foram coletados em um complexo de reservatórios a fim de identificar se representavam uma espécie dominante ou múltiplas espécies, uma vez que diversas espécies de Cichla foram registradas na bacia. Os espécimes foram identificados com base na coloração, dados morfométricos e merísticos, e por marcadores mitocondriais COI, 16S rDNA e Região Controle (RC). A sobreposição dos dados morfométricos e o padrão similar de coloração impediram a identificação utilizando as chaves de identificação disponíveis na literatura. Entretanto, as análises bayesiana e de máxima verossimilhança de dados moleculares demonstraram a ocorrência de uma única espécie, Cichla kelberi. Um único haplótipo foi observado para o 16S e RC, enquanto três foram detectados para o COI, com um haplótipo dominante presente em 98,5% das amostras. A baixa diversidade nos exemplares introduzidos de C. kelberi evidenciou um número limitado de linhagens maternas fundadoras. O sucesso da invasão parece depender de fatores abióticos, como a maior transparência da água de ambientes lênticos que favorece predadores visuais que, atrelado à ausência de predadores, fez do C. kelberi um invasor bem-sucedido nesses reservatórios.


Subject(s)
Animals , Cichlids/genetics , Phylogeny , Genetic Variation/genetics , Haplotypes/genetics , Lakes , Bayes Theorem
2.
Braz. j. biol ; 81(4): 917-927, Oct.-Dec. 2021. tab, graf
Article in English | LILACS | ID: biblio-1153455

ABSTRACT

Abstract The trahira or wolf fish - Hoplias malabaricus- is a valid species, although recent cytogenetic and molecular studies have indicated the existence of a species complex. In this context, the present study analyzed the mitochondrial COI marker to determine the levels of genetic diversity of specimens from the Brazilian state of Maranhão, and verify the occurrence of distinct lineages within the study area. Samples were collected from the basins of the Turiaçu, Pindaré, Mearim, Itapecuru, and Parnaíba rivers. A 630-bp fragment was obtained from 211 specimens, with 484 conserved and 108 variable sites, and 60 haplotypes (Hd = 0,947; π = 0,033). The phylogenetic analyses indicated the existence of three distinct lineages of H. malabaricus from Maranhão. Genetic distances of 1.5-8.2% were found between all the populations analyzed, while the variation between haplogroups ranged from 2.1% to 7.7%. The AMOVA indicated that most of the molecular variation was found among groups, with high FST values. The high levels of genetic variability found in the present study are supported by the available cytogenetic data. These findings reinforce the need for the development of effective programs of conservation and management independently for each river basin, in order to preserve the genetic variability found in this taxon.


Resumo A traíra - Hoplias malabaricus- é uma espécie válida, embora recentes estudos citogenéticos e moleculares tenham indicado a existência de um complexo de espécies. Neste contexto, o presente estudo analisou o marcador mitocondrial COI para determinar os níveis de diversidade genética dos espécimes do estado do Maranhão e verificar a ocorrência de linhagens distintas dentro da área de estudo. As amostras foram coletadas nas bacias dos rios Turiaçu, Pindaré, Mearim, Itapecuru e Parnaíba. As análises filogenéticas indicaram a existência de três linhagens distintas nas populações do Maranhão. Obteve-se um fragmento de 630 pb de 211 espécimes, com 484 sítios conservados, 108 variáveis e 60 haplótipos (Hd = 0,947; π = 0,033). As análises filogenéticas indicaram a ocorrência de três linhagens distintas de H. malabaricus do Maranhão. Distâncias genéticas de 1.5 a 8.2% foram encontradas entre todas as populações analisadas, enquanto a variação entre os haplogrupos variou de 2.1% a 7.7%. A AMOVA indicou que a maior variação molecular foi entre os grupos, com altos valores de FST. Os altos níveis de variabilidade genética encontrados no presente estudo são suportados pelos dados citogenéticos disponíveis. Essas descobertas reforçam a necessidade de desenvolver programas de conservação e manejo independentemente para cada bacia hidrográfica, a fim de preservar a variabilidade genética encontrada neste táxon.


Subject(s)
Animals , DNA Barcoding, Taxonomic , Characiformes/genetics , Phylogeny , Genetic Variation/genetics , Haplotypes/genetics , Brazil , Rivers
3.
Braz. j. biol ; 81(3): 584-591, July-Sept. 2021. tab, graf
Article in English | LILACS | ID: biblio-1153386

ABSTRACT

Abstract The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.


Resumo A raposa-voadora (Pteropus giganteus), também conhecida como morcego indiano, pertence à ordem dos Chiroptera e à família Pteropodidae. A presente pesquisa dá ênfase ao código de barras de DNA de P. giganteus em Azad Jammu e Caxemira. Sequências genéticas dos morcegos foram amplificadas, e os produtos de PCR foram sequenciados e examinados por software de bioinformática. De espécies congenérica e coespecífica, foram estimados composição nucleotídica e desvio de nucleotídeos K2P, diversidade de haplótipos e número de haplótipos. A análise mostrou que todas as cinco amostras estudadas de P. giganteus apresentaram baixos teores de G (19,8%) em comparação com C (27,8%), A (25,1%) e T (27,3%). A diversidade de haplótipos calculada foi de 0,60%, e a distância média intraespecífica de K2P foi de 0,001%, com um elevado número de substituições transicionais. O estudo sugeriu que P. giganteus (R = 0,00) não se desviou da evolução neutra. É possível concluir que o gene mtDNA é um marcador favorável para identificação de espécies de morcegos do que genes nucleares por causa de suas características distintivas e pode servir como um marco para a identificação de espécies interconectadas em nível molecular e para a determinação genética de populações.


Subject(s)
Animals , Chiroptera/genetics , Pakistan , Haplotypes/genetics , DNA, Mitochondrial , DNA Barcoding, Taxonomic
4.
Braz. j. med. biol. res ; 54(6): e10317, 2021. graf
Article in English | LILACS | ID: biblio-1249305

ABSTRACT

Physical performance is a multifactorial and complex trait influenced by environmental and hereditary factors. Environmental factors alone have been insufficient to characterize all outstanding phenotypes. Recent advances in genomic technologies have enabled the investigation of whole nuclear and mitochondrial genome sequences, increasing our ability to understand interindividual variability in physical performance. Our objective was to evaluate the association of mitochondrial polymorphic loci with physical performance in Brazilian elite military personnel. Eighty-eight male military personnel who participated in the Command Actions Course of the Army were selected. Total DNA was obtained from blood samples and a complete mitochondrial genome (mtDNA) was sequenced using Illumina MiSeq platform. Twenty-nine subjects completed the training program (FINISHED, 'F'), and fifty-nine failed to complete (NOT_FINISHED, 'NF'). The mtDNA from NF was slightly more similar to genomes from African countries frequently related to endurance level. Twenty-two distinct mtDNA haplogroups were identified corroborating the intense genetic admixture of the Brazilian population, but their distribution was similar between the two groups (FST=0.0009). Of 745 polymorphisms detected in the mtDNA, the position G11914A within the NADPH gene component of the electron transport chain, was statistically different between F and NF groups (P=0.011; OR: 4.286; 95%CI: 1.198-16.719), with a higher frequency of the G allele in group F individuals). The high performance of military personnel may be mediated by performance-related genomic traits. Thus, mitochondrial genetic markers such as the ND4 gene may play an important role on physical performance variability.


Subject(s)
Humans , Male , DNA, Mitochondrial/genetics , Military Personnel , Haplotypes/genetics , Brazil , Physical Functional Performance , NADP
5.
Einstein (Säo Paulo) ; 17(1): eAO4477, 2019. tab, graf
Article in English | LILACS | ID: biblio-984373

ABSTRACT

ABSTRACT Objective To described the allele and haplotype frequencies of human leukocyte antigen genes at the -A, -B loci and human platelet antigen genes for human platelet antigen systems 1 to 9, 11 and 15 in blood. Methods We included 867 healthy unrelated volunteer donors who donated platelets between January 2011 and December 2014. Microarray genotyping was performed using a BeadChip microarray. Medium resolution typing of the human leukocyte antigen at loci A and B was carried out using sequence-specific oligonucleotide probe hybridization. We used multivariate analysis and our human leukocyte antigen population was compared to data from the United States national bone marrow donor program. Human platelet antigen results were compared to a literature review and data from around the world. Results Our human leukocyte antigen haplotype results were more similar to those of hispanics, followed by caucasians. Likewise, our human platelet antigen sample is more similar to those of Argentina, Rio Grande do Sul and Italy. Conclusion This was the first article that discusses human platelet antigen and human leukocyte antigen data together. Rare genotypes or antibody associations can make patient management difficult. A blood bank with genotyped donors allows for optimal transfusion and can contribute to better results. Our information can serve as basis for a database of platelet antigen polymorphisms.


RESUMO Objetivo Descrever as frequências alélicas e haplotípicas de genes dos antígenos leucocitários humanos nos loci -A,- B e dos antígenos plaquetários humanos para os sistemas HPA-1 a 9, 11 e 15. Métodos Foram incluídos 867 doadores voluntários, saudáveis, não relacionados, que doaram plaquetas por aférese entre janeiro de 2011 e dezembro de 2014. A genotipagem foi realizada usando microarray BeadChip. A tipificação de resolução intermediária dos antígenos leucocitários humanos loci A e B foi realizada por meio de hibridização com sonda para oligonucleotídeos por sequência específica. Utilizamos análises multivariadas e o antígeno leucocitário humano de nossa população foi comparado com a do programa nacional de doadores de medula óssea norte-americano. Já os resultados dos antígenos plaquetários humanos foram comparados à revisão da literatura e a dados de populações de outros países. Resultados Os resultados do haplótipo de antígenos leucocitários humanos são mais parecidos com os dos hispânicos, seguidos dos caucasianos. Igualmente, a amostra de antígenos plaquetários humanos foi mais semelhante às da Argentina, do Rio Grande do Sul e da Itália. Conclusão Este foi o primeiro artigo a discutir antígenos plaquetários e leucocitários humanos simultaneamente. Genótipos raros ou associações de anticorpos podem dificultar o manejo clínico do paciente. Um banco de sangue com doadores genotipados permite um melhor resultado e transfusão possíveis. Estas informações podem servir de base para um banco de dados sobre polimorfismos de antígenos plaquetários.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Aged , Polymorphism, Genetic/genetics , Haplotypes/genetics , Antigens, Human Platelet/genetics , Alleles , Genotyping Techniques/methods , HLA Antigens/genetics , Tissue Donors , Platelet Transfusion , Gene Frequency/genetics , Genotype
6.
J. pediatr. (Rio J.) ; 92(6): 602-608, Nov.-Dec. 2016. tab
Article in English | LILACS | ID: biblio-829120

ABSTRACT

Abstract Objective: To verify genetic determinants associated with stroke in children with sickle cell disease (SCD). Methods: Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal), haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA), using the chi-squared test in the program SPSS® version 14.0. Results: Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR) was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p = 0.001) and males (24.1% vs. 9.6%; p = 0.044). The presence of α-thal (p = 0.196), the CAR haplotype (p = 0.543), and socioeconomic factors were not statistically significant in association with the occurrence of stroke. Conclusion: There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD.


Resumo Objetivo: Verificar fatores genéticos associados ao acidente vascular encefálico (AVE) em crianças com doença falciforme (DF). Métodos: Coorte prospectiva de 110 crianças submetidas à triagem neonatal pelo Programa de Triagem Neonatal, entre 1998-2007, com o diagnóstico de DF, atendidas em serviço público regional de referência em hemoglobinopatias. As variáveis analisadas foram: tipo de hemoglobinopatia, sexo, coexistência da alfa-Talassemia (α-Tal), haplótipos do cluster da cadeia beta globina e AVE. A análise estatística final foi feita com 66 crianças com anemia falciforme, por meio do teste do qui-quadrado no programa SPSS® 14.0. Resultados: Entre as crianças com DF, 60% eram portadoras de anemia falciforme. A prevalência da coexistência com a α-Tal foi de 30,3% e o haplótipo Bantu (CAR) foi identificado em 89,2%. A incidência de AVE foi significativamente maior nas crianças com AF (27,3% versus 2,3%; p = 0,001) e no sexo masculino (24,1% versus 9,6%; p = 0,044. A presença da α-Tal (p = 0,196), do haplótipo CAR (p = 0,543) e de fatores socioeconômicos não foi significantemente associada à ocorrência de AVE. Conclusão: O AVE apresenta alta incidência em crianças com AF e em crianças do sexo masculino. Coexistência de α-Tal ou de haplótipos do cluster da betaglobina não apresentaram associação significante com AVE. A heterogeneticidade entre as populações previamente avaliadas e a não reprodutibilidade entre estudos indicam a necessidade de novas pesquisas para verificar o papel desses fatores genéticos no AVE em crianças com DF.


Subject(s)
Humans , Male , Female , Child , Adolescent , Stroke/genetics , Anemia, Sickle Cell/genetics , Haplotypes/genetics , Chi-Square Distribution , Sex Factors , Incidence , Prospective Studies , Risk Factors , alpha-Thalassemia/genetics , Ultrasonography, Doppler, Transcranial , Stroke/etiology , Stroke/epidemiology , Anemia, Sickle Cell/complications
7.
Rev. Soc. Bras. Med. Trop ; 48(supl.1): 70-78, 2015. graf
Article in English | LILACS | ID: lil-748365

ABSTRACT

A scoping review was conducted to describe the epidemiological characteristics of the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic in the State of Amazonas, Brazil, from 2001 to 2012, and temporary patterns were estimated from surveillance data. The results suggest that in its third decade, the Amazon HIV/AIDS epidemic is far from being stabilized and displays rising AIDS incidence and mortality rates and late diagnoses. The data suggest that AIDS cases are hitting mostly young adults and have recently shifted toward men, both homosexual and heterosexual. AIDS cases among the indigenous people have remained stable and low. However, the epidemic has disseminated to the interior of the state, which adds difficulties to its control, given the geographical isolation, logistical barriers, and culturally and ethnically diverse population. Antiretroviral (ARV) therapy has been decentralized, but peripheral ARV services are still insufficient and too distant from people who need them. Recently, the expansion of point-of-care (POC) rapid HIV testing has been contributing to overcoming logistical barriers. Other new POC devices, such as the PIMA CD4 analyzer, will bring the laboratory to the patient. AIDS uniquely coexists with other tropical infections, sharing their epidemiological profiles. The increased demand for HIV/AIDS care services can only be satisfied through increased decentralization to peripheral health units, which can also naturally integrate care with other tropical infections and can promote a shift from vertical to integrated programming. Future challenges involve building surveillance data on HIV case notification and covering the spectrum of engagement in care, including adherence to treatment and follow-up loss.


Subject(s)
Animals , DNA, Mitochondrial/genetics , Dogs/genetics , Gene Flow/genetics , Wolves/genetics , Base Sequence , Genetic Variation , Genetics, Population , Georgia (Republic) , Hybridization, Genetic , Haplotypes/genetics , Microsatellite Repeats/genetics , Pedigree , Phylogeny , Phylogeography , Sequence Analysis, DNA
8.
Article in English | WPRIM | ID: wpr-223791

ABSTRACT

The role of genetic polymorphisms of NAD(P)H:quinone oxidoreductase 1 (NQO1), which is known to be related to carcinogen metabolism and oxidative status, was evaluated for lung cancer development. The genotypes of two NQO1 polymorphisms, namely, IVS1-27C>G and Ex6+40C>T, were determined in 616 lung cancer cases and 616 lung cancer-free controls and haplotypes composed of the two polymorphisms were estimated. In the evaluation of the effect of the NQO1 genotypes or diplotypes, we did not find any significant association with lung cancer risk after adjusting for body mass index and smoking status. However, when we evaluated the effect of the NQO1 diplotypes for lung cancer risk in combination with smoking, smokers without the C-T/C-T diplotype showed a significantly increased risk of lung cancer compared with nonsmokers without the C-T/C-T diplotype (adjusted OR, 2.2; 95% CI, 1.67-3.02), and smokers with the C-T/C-T diplotype showed the highest OR of lung cancer (adjusted OR, 2.7; 95% CI, 1.78-4.21). Moreover, a trend test showed an additive interaction between smoking and the NQO1 C-T/C-T diplotype (P(trend) < 0.01). The additive effect of smoking and the NQO1 C-T/C-T diplotype was more apparent in squamous cell carcinoma, although this effect was statistically significant in all lung cancer cell types (all cell types, P(trend) < 0.05). This result suggests that haplotypes of the NQO1 gene play an important role in the development of lung cancer by interaction with smoking.


Subject(s)
Aged , Carcinoma, Non-Small-Cell Lung/epidemiology , Female , Genetic Predisposition to Disease , Haplotypes/genetics , Humans , Lung Neoplasms/epidemiology , Male , Middle Aged , NAD(P)H Dehydrogenase (Quinone)/genetics , Polymorphism, Single Nucleotide/genetics , Risk , Small Cell Lung Carcinoma/epidemiology , Smoking/adverse effects
9.
Biomédica (Bogotá) ; 34(4): 598-604, oct.-dic. 2014. graf, tab
Article in Spanish | LILACS | ID: lil-730944

ABSTRACT

Institución donde se ejecutó el trabajo: Programa de Estudio y Control de Enfermedades Tropicales, PECET, Unidad de Malacología Médica y Trematodos (UMMT), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia Introducción. La fasciolosis es la enfermedad transmitida por vectores con mayor distribución latitudinal, longitudinal y altitudinal, debido a la capacidad colonizadora del parásito Fasciola hepatica y de sus huéspedes intermediarios, los moluscos limneidos. Estos caracoles se investigan por su importancia epidemiológica, pero su identificación taxonómica es difícil por la similitud fenotípica entre especies. En este sentido, con respecto a Lymnaea cousini , un huésped de F. hepatica en Colombia, existe incertidumbre en razón de su similitud morfológica con L. meridensis , descrita recientemente en Venezuela. Objetivo. Confirmar con el marcador del gen de la citocromo oxidasa I en el ADN mitocondrial COI (ADNmt), el estatus taxonómico de ejemplares morfológicamente caracterizados como L. cousini provenientes de Nariño, Norte de Santander y Santander (Colombia), depositados en la Colección de Moluscos Vectores de la Universidad de Antioquia, VHET N° 37. Materiales y métodos. Para la amplificación del COI mitocondrial, se extrajo ADN total del pie de cada ejemplar con el estuche DNeasy Blood and Tissue (Qiagen ® ). Los productos amplificados se enviaron a secuenciar a Macrogen Inc., Corea. Las 27 secuencias generadas en esta investigación se compararon con secuencias publicadas en el GenBank, incluidas las secuencias de la localidad tipo de L. cousini. Resultados. Se encontraron dos nuevos haplotipos de L. cousini para Colombia. Los especímenes de Nariño correspondían al haplotipo A, referenciado en Ecuador, y los especímenes de Santander y Norte de Santander, a un nuevo haplotipo al que se denominó D. Conclusión. Mediante el marcador mitocondrial del COI , se confirmó que los especímenes pertenecían a la especie L. cousini . Con el hallazgo se duplicó el número de haplotipos conocidos de la especie en Colombia y se amplió su distribución geográfica al suroeste y nordeste de la región altoandina colombiana.


Introduction: Fasciolosis is the disease transmitted by vectors with the highest latitudinal, longitudinal, and altitudinal distribution due to the colonizing capacity of the parasite Fasciola hepatica and its intermediate hosts, Lymnaeidae mollusks. These snails are under research due to their epidemiological importance, but their taxonomic identification is difficult given their interspecific phenotypical similarity. For this reason, there is uncertainty regarding Lymnaea cousini -a host of F. hepatica in Colombia- due to the morphological similarity it has with Lymnaea meridensis , recently described for Venezuela. Objective: To confirm with the COI marker (ADNmt) the taxonomic status of individuals morphologically identified as L. cousini from Nariño, Norte de Santander, and Santander (Colombia), deposited in the Vector Mollusks Collection VHET No. 37 of Universidad de Antioquia. Materials and methods: The amplification of the mitochondrial COI required total DNA extraction of each individual´s foot using the DNeasy Blood and Tissue Kit (Qiagen®). Products amplified were sent for sequencing to Macrogen Inc., Korea. Twenty seven sequences generated in this research were compared to sequences published in the GenBank, including sequences of the type locality of L. cousini . Results: Two new haplotypes of L. cousini were obtained for Colombia. Specimens from Nariño correspond to haplotype A, referenced for Ecuador, and specimens from Santander and Norte de Santander belong to a new haplotype we called haplotype D. Conclusion : By using the mitochondrial COI marker, we confirmed that the species under study did correspond to L. cousini . The number of known haplotypes of the species for Colombia has been duplicated and its geographical distribution has been extended to the southwest and northeast of the Colombian high Andean region.


Subject(s)
Animals , Disease Vectors/classification , Electron Transport Complex IV/analysis , Fasciola hepatica , Lymnaea/classification , Base Sequence , Biomarkers , Colombia , DNA , DNA, Mitochondrial/genetics , Electron Transport Complex IV/genetics , Haplotypes/genetics , Lymnaea/enzymology , Lymnaea/genetics , Molecular Sequence Data , Phylogeny , Protein Subunits , Sequence Alignment , Sequence Homology, Nucleic Acid
10.
Mem. Inst. Oswaldo Cruz ; 109(7): 918-922, 11/2014. tab, graf
Article in English | LILACS | ID: lil-728814

ABSTRACT

The human beta defensin 1 (hBD-1) antimicrobial peptide is a member of the innate immune system known to act in the first line of defence against microorganisms, including viruses such as human papillomavirus (HPV). In this study, five functional polymorphisms (namely g-52G>A, g-44C>G and g-20G>A in the 5’UTR and c.*5G>A and c.*87A>G in the 3’UTR) in the DEFB1 gene encoding for hBD-1 were analysed to investigate the possible involvement of these genetic variants in susceptibility to HPV infection and in the development of HPV-associated lesions in a population of Brazilian women. The DEFB1 g-52G>A and c.*5G>A single-nucleotide polymorphisms (SNPs) and the GCAAA haplotype showed associations with HPV-negative status; in particular, the c.*5G>A SNP was significantly associated after multiple test corrections. These findings suggest a possible role for the constitutively expressed beta defensin-1 peptide as a natural defence against HPV in the genital tract mucosa.


Subject(s)
Adolescent , Adult , Aged , Female , Humans , Middle Aged , Young Adult , Papillomavirus Infections/genetics , Polymorphism, Single Nucleotide/genetics , Reproductive Tract Infections/virology , beta-Defensins/genetics , Brazil/epidemiology , Case-Control Studies , Genetic Predisposition to Disease , Haplotypes/genetics , Papillomavirus Infections/epidemiology
12.
J. bras. patol. med. lab ; 50(2): 98-99, Mar-Apr/2014.
Article in English | LILACS | ID: lil-712711

ABSTRACT

Introduction:Sickle cell disease (SCD) is a hereditary, hematologic, multifactorial disease, with high prevalence worldwide; its cause is a mutation in the sixth codon of the beta globin gene (βs).Objective: To identify the haplotypes present in people with SCD in Amapá, and relate them to African descent. Methods: We analyzed, by molecular techniques, 46 blood samples from people with SCD in Macapá, the capital of Amapá, with the purpose of obtaining information about haplotype frequency distribution, which helps understand the ethnic background of Amapá's population. Results: Our study revealed that the most frequent haplotype is Bantu (61.2%), followed by Benin (26.6%) and Senegal (12.2%). Results showed statistical differences from studies conducted in other regions. A high frequency of the Senegal haplotype stands out, in comparison with some Brazilian studies. Conclusion: Amapá's results exhibit unique characteristics when compared to haplotypes in other regions, with high frequency of Senegal and Benin haplotypes, absence of atypical, Cameroon and Saudi, confirming that Brazil shows ethnic background diversity, as well as different haplotype frequencies...


Introdução: A doença falciforme é uma doença hereditária, hematológica, de caráter multifatorial, com alta prevalência mundial; sua causa é a mutação no sexto códon do gene da globina beta (βs). Objetivo:Identificar os haplótipos presentes em indivíduos com doença falciforme no Amapá e relacioná-los com a origem afrodescendente. Método: Foram analisadas por meio de técnicas moleculares 46 amostras de sangue de indivíduos com doença falciforme de Macapá, capital do Amapá, com a finalidade de fornecer informações sobre a distribuição das frequências dos haplótipos, contribuindo para o entendimento da formação étnica da população amapaense. Resultados: Nosso estudo revelou que o mais frequente é o haplótipo Bantu (61,2%), seguido de Benin (26,6%) e Senegal (12,2%). Nossos resultados apresentaram diferenças estatísticas em relação a estudos realizados em outras regiões, destacando-se que o presente estudo mostra uma frequência elevada do haplótipo Senegal quando comparado com alguns estudos brasileiros. Conclusão: Os resultados amapaenses apresentam características únicas quando relacionados com os haplótipos de outras regiões, com alta frequência de Senegal e Benin, ausência de atípicos, Camarões e Saudi, confirmando que o Brasil apresenta diversidade de origens étnicas, bem como diferentes frequências de haplótipos...


Subject(s)
Humans , Anemia, Sickle Cell/ethnology , Blacks/ethnology , Haplotypes/genetics , Anemia, Sickle Cell/blood , Blacks/genetics
13.
Journal of Veterinary Research. 2014; 69 (1): 49-55
in Persian | IMEMR | ID: emr-157610

ABSTRACT

Lactoferrin [Lf], an iron binding glycoprotein, has a variety of physiological roles and its foremost is antimicrobial properties. Therefore, the lactoferrin gene can be considered as a potential candidate gene for resistance to mastitis. This study was carried out to determine the haplotype frequency of the 5'-flanking region of bovine lactoferrin gene in local and Holstein cattle breeds of Iran using PCR-SSCPand DNA sequencing. Genomic DNA was isolated from 100 blood samples of two cattle breeds [50 Local, 50 Holstein]. Two new primer pairs were designed from Lf sequence to amplify a part of 5'-flanking region of the gene. The amplified fragment was screened by single strand conformation polymorphism [SSCP] and DNA sequencing. The multiple alignments were carried out for the nucleotide sequences of different SSCPpatterns. In silico analysis of identified single nucleotide polymorphisms [SNPs] within the 5'-flanking region of bovine Lf gene was screened, to identify any association on transcription factor binding affinity. Analysis of the whole samples revealed three SSCP patterns [A, B and C] for amplified fragment that C haplotype was the only variant identified in local breed samples. The bioinformatics analysis revealed that the Tto G trans version at position -602 created an AML-1 transcription binding site in combined genotype A. In -586 position, Tto C transition abolished binding site of AML-1 transcription factor. Therefore, to apply Lf gene for marker-assisted selection, additional studies are required to evaluate the functional role of these identified polymorphic sites on gene expression and somatic cell counts in cattle


Subject(s)
Animals , Mastitis, Bovine/genetics , Polymorphism, Single-Stranded Conformational , Haplotypes/genetics , Polymorphism, Single Nucleotide , Gene Expression , Transcription Factors , Cattle/genetics , Computational Biology , Genotype
14.
Article in English | WPRIM | ID: wpr-121885

ABSTRACT

Echinococcus granulosus is the causative agent of cystic echinococcosis with medical and veterinary importance in China. Our main objective was to discuss the genotypes and genetic diversity of E. granulosus present in domestic animals and humans in western China. A total of 45 hydatid cyst samples were collected from sheep, humans, and a yak and subjected to an analysis of the sequences of mitochondrial cytochrome b (cytb) gene. The amplified PCR product for all samples was a 1,068 bp band. The phylogenetic analysis showed that all 45 samples were identified as E. granulosus (genotype G1). Ten haplotypes were detected among the samples, with the main haplotype being H1. The haplotype diversity was 0.626, while the nucleotide diversity was 0.001. These results suggested that genetic diversity was low among our samples collected from the west of China based on cytb gene analysis. These findings may provide more information on molecular characteristics of E. granulosus from this Chinese region.


Subject(s)
Animals , Animals, Domestic/parasitology , Base Composition , Base Sequence , Cattle/parasitology , China , Cytochromes b/genetics , DNA, Helminth/genetics , Echinococcosis , Echinococcus granulosus/classification , Genetic Variation , Haplotypes/genetics , Humans , Mitochondria/genetics , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction/veterinary , Sequence Alignment , Sequence Analysis, DNA , Sheep/parasitology , Tibet
15.
Yonsei Medical Journal ; : 232-239, 2014.
Article in English | WPRIM | ID: wpr-50977

ABSTRACT

PURPOSE: UGT1A1, UGT2B7, and UGT2B15 are well-known pharmacogenes that belong to the uridine diphosphate glucuronyltransferase gene family. For personalized drug treatment, it is important to study differences in the frequency of core markers across various ethnic groups. Accordingly, we screened single nucleotide polymorphisms (SNPs) of these three genes and analyzed differences in their frequency among five ethnic groups, as well as attempted to predict the function of novel SNPs. MATERIALS AND METHODS: We directly sequenced 288 subjects consisting of 96 Korean, 48 Japanese, 48 Han Chinese, 48 African American, and 48 European American subjects. Subsequently, we analyzed genetic variability, linkage disequilibrium (LD) structures and ethnic differences for each gene. We also conducted in silico analysis to predict the function of novel SNPs. RESULTS: A total of 87 SNPs were detected, with seven pharmacogenetic core SNPs and 31 novel SNPs. We observed that the frequencies of UGT1A1 *6 (rs4148323), UGT1A1 *60 (rs4124874), UGT1A1 *93 (rs10929302), UGT2B7 *2 (rs7439366), a part of UGT2B7 *3 (rs12233719), and UGT2B15 *2 (rs1902023) were different between Asian and other ethnic groups. Additional in silico analysis results showed that two novel promoter SNPs of UGT1A1 -690G>A and -689A>C were found to potentially change transcription factor binding sites. Moreover, 673G>A (UGT2B7), 2552T>C, and 23269C>T (both SNPs from UGT2B15) changed amino acid properties, which could cause structural deformation. CONCLUSION: Findings from the present study would be valuable for further studies on pharmacogenetic studies of personalized medicine and drug response.


Subject(s)
Asians/genetics , Whites/genetics , Female , Gene Frequency/genetics , Glucuronosyltransferase/genetics , Haplotypes/genetics , Humans , Linkage Disequilibrium/genetics , Male , Polymorphism, Single Nucleotide/genetics
16.
Rev. bras. ter. intensiva ; 25(4): 284-289, Oct-Dec/2013. tab
Article in Portuguese | LILACS | ID: lil-701399

ABSTRACT

Objetivo: Haplótipos do HLA têm sido associados a muitas doenças autoimunes, mas não foi descrita qualquer associação na sepse. O objetivo desse estudo é investigar o sistema HLA como um possível marcador de suscetibilidade genética à sepse. Métodos: Estudo prospectivo de coorte, incluindo pacientes admitidos em unidade de terapia intensiva e controles-saudáveis obtidos em lista de doadores de transplante renal. Foram excluídos pacientes abaixo dos 18 anos de idade, gestantes ou HIV positivos, pacientes com doença maligna metastática ou sob quimioterapia, pacientes com hepatopatia avançada, com condições de fim de vida. O DNA foi extraído de sangue total, e a haplotipagem de HLA foi realizada com a tecnologia MiliPlex®. Resultados: Foram incluídos 1.121 pacientes (1.078 doadores de rim, 20 pacientes com sepse grave e 23 pacientes admitidos por choque séptico) entre outubro de 2010 e outubro de 2012. Os participantes positivos para HLA-A*31 tiveram risco aumentado de desenvolver sepse (OR: 2,36 IC95%: 1,26-5,35). Não foi identificada outra associação significativa, quando considerado como nível de significância o valor de p<0,01. Conclusão: A expressão de HLA-A*31 está associada ao risco de desenvolvimento de sepse. .


Objective: The HLA haplotype has been associated with many autoimmune diseases, but no associations have been described in sepsis. This study aims to investigate the HLA system as a possible marker of genetic sepsis susceptibility. Methods: This is a prospective cohort study including patients admitted to an intensive care unit and healthy controls from a list of renal transplant donors. Patients with less 18 years of age; pregnant or HIV positive patients; those with metastatic malignancies or receiving chemotherapy; or with advanced liver disease; or with end-of-life conditions were excluded. The DNA was extracted from the whole blood and HLA haplotypes determined using MiliPlex® technology. Results: From October 2010 to October 2012, 1,121 patients were included (1,078 kidney donors, 20 patients admitted with severe sepsis and 23 with septic shock). HLA-A*31 positive subjects had increased risk of developing sepsis (OR 2.36, 95%CI 1.26-5.35). Considering a p value <0.01, no other significant association was identified. Conclusion: HLA-A*31 expression is associated to risk of developing sepsis. .


Subject(s)
Humans , Genetic Predisposition to Disease , HLA-A Antigens/genetics , Sepsis/genetics , Shock, Septic/genetics , Biomarkers , Cohort Studies , Haplotypes/genetics , Intensive Care Units , Prospective Studies
17.
Mem. Inst. Oswaldo Cruz ; 108(8): 947-961, 6/dez. 2013. tab, graf
Article in English | LILACS | ID: lil-697142

ABSTRACT

The development and rapid spread of chloroquine resistance (CQR) in Plasmodium falciparum have triggered the identification of several genetic target(s) in the P. falciparum genome. In particular, mutations in the Pfcrt gene, specifically, K76T and mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75 and 76), are considered to be highly related to CQR. These various mutations form several different haplotypes and Pfcrt gene polymorphisms and the global distribution of the different CQR- Pfcrt haplotypes in endemic and non-endemic regions of P. falciparum malaria have been the subject of extensive study. Despite the fact that the Pfcrt gene is considered to be the primary CQR gene in P. falciparum , several studies have suggested that this may not be the case. Furthermore, there is a poor correlation between the evolutionary implications of the Pfcrt haplotypes and the inferred migration of CQR P. falciparum based on CQR epidemiological surveillance data. The present paper aims to clarify the existing knowledge on the genetic basis of the different CQR- Pfcrt haplotypes that are prevalent in worldwide populations based on the published literature and to analyse the data to generate hypotheses on the genetics and evolution of CQR malaria.


Subject(s)
Humans , Antimalarials/pharmacology , Chloroquine/pharmacology , Drug Resistance/genetics , Haplotypes/genetics , Malaria, Falciparum/parasitology , Membrane Transport Proteins/genetics , Plasmodium falciparum/genetics , Protozoan Proteins/genetics , DNA, Protozoan/genetics , Malaria, Falciparum/drug therapy , Polymorphism, Genetic , Plasmodium falciparum/drug effects
18.
Clinics ; 68(1): 5-9, Jan. 2013. ilus, tab
Article in English | LILACS | ID: lil-665911

ABSTRACT

OBJECTIVE: The JAK2 46/1 haplotype has recently been described as a major contributing factor to the development of myeloproliferative neoplasm, whether positive or negative forthe JAK2 V617F mutation. The G allele, identified by a single-nucleotide polymorphism known as JAK2 rs10974944, is part of the JAK2 46/1 haplotype. The aim of this study was to verify the association between the presence of the G allele and the development of BCR-ABL-negative chronic myeloproliferative neoplasms in our population. METHODS: Blood and oral mucosa swab samples were obtained from 56 patients of two local Brazilian hospitals who had previously been diagnosed with BCR-ABL-negative chronic myeloproliferative neoplasms. Blood samples from 90 local blood donors were used as controls. The presence of the G allele was assessed using a PCR-RFLP assay after extracting DNA from the samples. RESULTS: The presence of the G allele was strongly associated with the presence of BCR-ABL-negative chronic myeloproliferative neoplasms (p = 0.0001; OR = 2.674; 95% CI = 1.630-4.385) in the studied population. CONCLUSION: In agreement with previous reports, the JAK2 46/1 haplotype, represented in this study by the presence of the G allele, is an important predisposing factor in the oncogenetic development of these neoplasms in our population.


Subject(s)
Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Young Adult , Haplotypes/genetics , /genetics , Myeloproliferative Disorders/genetics , Brazil , Chi-Square Distribution , Chronic Disease , Fusion Proteins, bcr-abl/genetics , Gene Frequency , Mutation/genetics , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length/genetics , Sex Distribution
19.
Rio de Janeiro; s.n; 2013. 114 p. ilus, tab.
Thesis in Portuguese | LILACS | ID: lil-711959

ABSTRACT

A leishmaniose visceral (LV) ou calazar é uma doença endêmica, crônica, grave e de alta letalidade se não tratada. Os estudos apontam a proteína Lectina Ligante de Manose (MBL), codificada pelo gene MBL2, como uma peça-chave na imunidade inata, dada a sua função no reconhecimento microbiano, na eliminação, inflamação e morte celular. Neste trabalho realizamos um estudo do tipo caso-controle que teve como objetivo investigar a associação entre variantes no gene MBL2 e a suscetibilidade à LV em indivíduos residentes em áreas endêmicas da Ilha de São Luís-MA. A amostra foi constituída por 322 indivíduos, sendo 161 casos com LV, não aparentados, de ambos os sexos, residentes em áreas endêmicas da doença na Ilha de São Luís e 161 controles saudáveis, não infectados e não aparentados da mesma região. A identificação dos casos de LV se deu por meio do contato constante com os principais hospitais e ambulatórios de referência para a doença na cidade. Também foram feitas buscas de pacientes com LV em ambiente domiciliar, a partir de registros da FUNASA-MA. A análise molecular consistiu na genotipagem de 6 variantes localizadas na região promotora [posições -550 (C>G), -221(G>C), +4(C>T)] e codificadora [códons 52 (C>T), 54 (G>A) e 57 (G>A)] do gene MBL2, através da reação em cadeia da polimerase e sequenciamento automático. A dosagem da proteína MBL no soro foi realizada pelo teste de ELISA. Verificamos que os fenótipos MBL dependem do conjunto de alelos presentes no gene MBL2, sendo nítido o efeito que as variantes defectivas causam nos níveis da proteína. Não encontramos diferença significativa entre casos e controles em relação à distribuição dos genótipos MBL2 e dos níveis séricos de MBL. As frequências alélicas das variantes exônicas na amostra total mostram que o alelo A é o mais comum (74,8%) e que os alelos defectivos (B, C e D) se encontram principalmente em heterozigose (36,6%), o que reforça a ideia de que alelos MBL2 defectivos são mantidos na população ...


Visceral leishmaniasis (VL), also known as kalazar, is an endemic, chronic, severe and highly lethal disease when not treated. Studies have shown that the protein Mannose-biding lectin (MBL), encoded by the gene MBL2, is the major player in innate immune system due its role in microbial recognition, elimination and inflammation as well as in the cell death. In the current work, we conducted a case-control study which aimed to investigate the association between variants in the gene MBL2 and the susceptibility to VL in individuals living in endemic areas of the São Luís - MA. 322 individuals participated in this study. Of these, 161 were VL cases being unrelated individuals of both sexes, and inhabitants from endemic areas of the disease in São Luís. The other 161 individuals were uninfected healthy controls, being unrelated and from the same region. The identification of VL cases occurred by visiting reference hospitals and clinics in the city. VL patients were identified in the household environment through the records of FUNASA-MA. Molecular analysis consisted in genotyping six variants located in the promoter region [positions -550 (C> G), -221 (G> C), +4 (C> T)] and coding region [codons 52 (C> T), 54 (G> A) and 57 (G> A)] of the MBL2 gene by polymerase chain reaction and automated DNA sequencing. The concentrations of MBL protein in the serum was performed by ELISA. We found that MBL phenotypes depend on the number of alleles present in the gene MBL2, being clear the consequence of the defective variants in the protein levels. There was no significant difference between cases and controls regarding the distribution of MBL2 genotypes and MBL serum levels. The allele frequencies of exon variants in the overall sample showed that the A allele is the most common (74.8%) and that the defective alleles (B, C and D) are mainly heterozygous (36.6%). This highlights the idea that defective MBL2 alleles are maintained in the population to confer selective ...


Subject(s)
Humans , Male , Female , Genetic Variation , Mannose-Binding Lectin/genetics , Leishmaniasis, Visceral/genetics , Case-Control Studies , Enzyme-Linked Immunosorbent Assay/methods , Gene Frequency , Genetic Association Studies , Haplotypes/genetics , Immunity, Innate , Polymerase Chain Reaction/methods
20.
Mem. Inst. Oswaldo Cruz ; 108(supl.1): 3-10, 2013. tab, graf
Article in English | LILACS | ID: lil-697827

ABSTRACT

The increasing population of Aedes aegypti mosquitoes on Madeira Island (Portugal) resulted in the first autochthonous dengue outbreak, which occurred in October 2012. Our study establishes the first genetic evaluation based on the mitochondrial DNA (mtDNA) genes [cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4)] and knockdown resistance ( kdr ) mutations exploring the colonisation history and the genetic diversity of this insular vector population. We included mosquito populations from Brazil and Venezuela in the analysis as putative geographic sources. The Ae. aegypti population from Madeira showed extremely low mtDNA genetic variability, with a single haplotype for COI and ND4. We also detected the presence of two important kdr mutations and the quasi-fixation of one of these mutations (F1534C). These results are consistent with a unique recent founder event that occurred on the island of Ae. aegypti mosquitoes that carry kdr mutations associated with insecticide resistance. Finally, we also report the presence of the F1534C kdr mutation in the Brazil and Venezuela populations. To our knowledge, this is the first time this mutation has been found in South American Ae. aegypti mosquitoes. Given the present risk of Ae. aegypti re-invading continental Europe from Madeira and the recent dengue outbreaks on the island, this information is important to plan surveillance and control measures.


Subject(s)
Animals , Aedes/genetics , Electron Transport Complex IV/genetics , Insect Vectors/genetics , Mutation/genetics , NADH Dehydrogenase/genetics , Animal Distribution , Brazil , Disease Outbreaks , DNA, Mitochondrial/genetics , Dengue/epidemiology , Haplotypes/genetics , Insecticide Resistance/genetics , Portugal/epidemiology , Venezuela
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