Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 966
Filter
1.
Braz. j. biol ; 84: e248656, 2024. tab, graf
Article in English | MEDLINE, 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.
Article in English | WPRIM | ID: wpr-922401

ABSTRACT

OBJECTIVES@#To study the association of β2-drenergic receptor (@*METHODS@#A total of 143 children with asthma who attended the hospital from October 2016 to October 2020 were enrolled as the asthma group, among whom 61 children had mild symptoms (mild group) and 82 children had moderate-to-severe symptoms (moderate-to-severe group). A total of 137 healthy children were enrolled as the control group. Peripheral venous blood samples were collected from the two groups. The SNaPshot SNP technique was used to analyze the SNP and haplotypes of the @*RESULTS@#Polymorphisms were observed in the @*CONCLUSIONS@#SNP/haplotype of the


Subject(s)
Asthma/genetics , Case-Control Studies , Child , Genetic Predisposition to Disease , Genotype , Haplotypes , Humans , Polymorphism, Single Nucleotide , Receptors, Adrenergic, beta-2/genetics , Regulatory Sequences, Nucleic Acid
6.
Braz. dent. j ; 31(1): 19-24, Jan.-Feb. 2020. tab
Article in English | LILACS | ID: biblio-1089269

ABSTRACT

Abstract This study evaluated the association between polymorphisms in genes encoding estrogen receptors 1 (ESR1) and 2 (ESR2), vitamin D receptor (VDR) and in microRNA17 (which binds to ESR1 and VDR) with persistent apical periodontitis (PAP) after the endodontic treatment. We included 162 patients who completed endodontic treatment at least one year ago and presented apical periodontitis at the beginning of the root canal therapy. Clinical and radiographic exams were performed to evaluate the presence of PAP or healthy periradicular tissues (healed). Saliva samples were collected as a genomic DNA. The genotyping of ESR1 (rs2234693 and rs9340799), ESR2 (rs1256049 and rs4986938), VDR (rs739837 and rs2228570) and miRNA17 (rs4284505) were performed by real-time PCR. Chi-square test was used to the distribution of genotype and allele frequencies. Haplotype analysis was also performed. Eighty-nine patients were included in the "healed" group and 73 in the "PAP" group. No association was found between the allelic and genotypic polymorphisms studied and PAP (p>0.05). Haplotype analysis also did not demonstrated an association (p>0.05). In conclusion, the genetic polymorphisms in ESR1, ESR2, VDR and miRNA17 are not associated with PAP.


Resumo Este estudo avaliou a associação entre polimorfismos em genes que codificam os receptores de estrogênio 1 (ESR1) e 2 (ESR2), receptor de vitamina D (VDR) e no microRNA17 (que se liga à ESR1 e VDR) e a periodontite apical persistente (PAP) após o tratamento endodôntico. Foram incluídos 162 pacientes com tratamento endodôntico concluído há pelo menos um ano e que apresentavam periodontite apical no início da terapia endodôntica. Exames clínicos e radiográficos foram realizados para avaliar a presença de PAP ou tecidos perirradiculares saudáveis (cicatrizados). As amostras de saliva foram coletadas como fonte de DNA genômico. A genotipagem de ESR1 (rs2234693 e rs9340799), ESR2 (rs1256049 e rs4986938), VDR (rs739837 e rs2228570) e miRNA17 (rs4284505) foram realizadas por PCR em tempo real. O teste do qui-quadrado foi utilizado para a distribuição das frequências genotípicas e alélicas. A análise de haplótipos também foi realizada. Oitenta e nove pacientes foram incluídos no grupo "curado" e 73 no grupo "PAP". Não foi encontrada associação entre os polimorfismos alélicos e genotípicos estudados e a PAP (p>0,05). Concluí-se que os polimorfismos genéticos em ESR1, ESR2, VDR e miRNA17 não estão associados à PAP.


Subject(s)
Humans , Polymorphism, Genetic , Vitamin D , Receptors, Calcitriol/genetics , MicroRNAs/genetics , Estrogen Receptor alpha/genetics , Estrogen Receptor beta/genetics , Haplotypes , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Estrogens , Gene Frequency
7.
Rev. Soc. Bras. Med. Trop ; 53: e20190566, 2020. tab
Article in English | ColecionaSUS, LILACS, ColecionaSUS, SES-SP | ID: biblio-1136804

ABSTRACT

Abstract INTRODUCTION: Among patients with Chagas disease, men have a higher risk of worse pathological symptoms than women. We aimed to explore the role of the Y chromosome in men diagnosed with Chagas disease and assess the relationship between their ancestry and disease status. METHODS In this comparative study, we analyzed 150 men with unrelated non-chagasic disease (nCD) and 150 men with unrelated chagasic disease (CD). We assessed the serological diagnosis of Chagas disease, biochemical parameters, thoracic X-rays, electrocardiogram, and transthoracic echocardiography and determined the haplogroup by analyzing a set of 17 microsatellites from the Y chromosome. We examined the associations between common Y chromosome haplogroups and the clinical parameters of risk by logistic regression. RESULTS For all patients, the most common haplogroups were R1b (43%), G2a (9%), and E1b1b (9%). The R1b and G2a haplogroup was more frequent in men with nCD and CD, respectively. As expected, we observed a high proportion of symptomatic patients in the CD group independent of the haplogroups. Men from both groups classified as having the R1b haplogroup showed less clinical evidence of disease. Multivariate analysis showed that CD patients without R1b were about five times more likely to have a cardio-thorax index >0.5% (OR [odds ratio] = 5.1, 95% CI [confidence interval] = 3.31-8.17). Men without the R1b haplogroup were 2.5 times more likely to show EcoCG alterations (OR = 2.50, 95% CI = 0.16-3.94). CONCLUSIONS: Our results provided evidence that the R1b haplogroup may have a potential protective cardiovascular effect for its carriers.


Subject(s)
Humans , Male , Female , Chagas Disease/complications , Chagas Disease/genetics , Cardiomyopathies , Haplotypes , Odds Ratio , Chromosomes, Human, Y/genetics
8.
Journal of Experimental Hematology ; (6): 1397-1405, 2020.
Article in Chinese | WPRIM | ID: wpr-827105

ABSTRACT

OBJECTIVE@#To analyze the characteristics of allelic and haplotypic polymorphisms of human leukocyte antigens at HLA-A, -B, -C, DRB1 and DQB1 loci in Guangxi Zhuang population.@*METHODS@#Polymerase chain reaction-sequence based typing (PCR-SBT) was used to detect. The five loci (HLA-A, -B, -C, -DRB1, -DQB1) in 350 unrelated Zhuang ethnic individual from Guangxi region. Allelic and haplotypic frequencies were calculated by using Arlequin software 3.5.2.2. Phylogeny tree were constructed by using MEGA software 6.0, and SPSS software was used for principal component analysis.@*RESULTS@#Among the five loci in the population, only HLA-A and DRB1 loci were observed as departures from Hardy-Weinberg expectations. A total of 19 HLA-A, 42 HLA-B, 22 HLA-C, 25 HLA-DRB1 and 15 HLA-DQB1 alleles were found in 350 samples. The most highest frequent alleles were A*11: 01(28.57%), B*46: 01(14.00%), C*01: 02(18.43%), DRB1*16: 02 (15.71%)and DQB1*05: 02 (35.00%) . The most common five loci haplotype was A*33: 03-C*03: 02-B*58: 01-DRB1*03: 01-DQB1*02: 01(6.86%). The phylogenetic tree analysis showed that Guangxi Zhuang population had a relative close genetic relationship with southern Han Chinese populations.@*CONCLUSION@#This reaserch found that the HLA-A, B, C, DRB1 and DQB1 loci are highly polymorphic in Guangxi Zhuang population.


Subject(s)
Alleles , China , Gene Frequency , HLA-A Antigens , Genetics , HLA-B Antigens , Genetics , HLA-DRB1 Chains , Genetics , Haplotypes , Humans , Phylogeny
9.
Article in Chinese | WPRIM | ID: wpr-880775

ABSTRACT

OBJECTIVE@#Haplotype amplification on germline variants is suggested to imply potential selective advantages and clonal expansion susceptibility and has become an important signature for seeking cancer susceptibility gene.Here we propose an improved association method that fully considers the haplotype amplification status.@*METHODS@#The haplotype amplification status was estimated by the variant allelic frequencies.We adopted a permutation test on variant allelic frequencies to divide the candidate variants into multiple groups.A likelihood clustering method was then applied to establish the neighborhood system of the hidden Markov random field framework.A filtering pipeline was introduced into the proposed method to further refine the candidate variants, including a Wilson's interval filter and a false discovery rate controller.The final candidate set along with the haplotype amplification status was collapsed into the weighted virtual sites for association tests.@*RESULTS@#Through simulated tests on a series of datasets, we compared the type Ⅰ error rates of different minor allele frequencies, which stably fell within 2%, suggesting good robustness of the algorithm.In addition, we compared another 5 published association approaches for Type-Ⅰ and Type-Ⅱ error rates with the proposed method, which resulted in the error rates all within 2%, demonstrating significant advantages and a good statistical ability of the proposed method.@*CONCLUSIONS@#The proposed method can accurately identify tumor susceptibility variants in haplotype amplification area with good robustness and stability.


Subject(s)
Algorithms , Cluster Analysis , Gene Amplification , Gene Frequency , Haplotypes , Humans , Neoplasms/genetics , Polymorphism, Single Nucleotide
10.
Electron. j. biotechnol ; 40: 17-21, July. 2019. tab, ilus
Article in English | LILACS | ID: biblio-1053211

ABSTRACT

Background: Mastitis is one of the most serious diseases of dairy cattle, causing substantial financial losses. While predisposition to reduced somatic cell count in milk has been considered for in cattle breeding programs as the key indicator of udder health status, scientists are seeking genetic markers of innate immune response, which could be helpful in selecting cows with improved immunity to mastitis. Lipocalin-2 (LCN2) is a protein involved in the response of the immune system by eliminating iron ions which are necessary for the growth of pathogenic bacteria, so LCN2 may be considered as a natural bacteriostatic agent and could become a marker of infection. Results: A total of five SNPs were identified in LCN2 gene (one in the promoter, three in exon 1, and one in intron 1). A single haplotype block was identified. The locus g.98793763GNC was found to have a significant impact on protein levels in milk, and alleles of this locus were identified to have a significant positive dominance effect on this trait. None of the four analysed loci had a statistically significant impact on the milk yield, fat levels in milk or the somatic cell score. LCN-2 gene had no significant impact on the incidence of mastitis in the cows. Conclusions: Although the identified SNPs were not found to have any impact on the somatic cell count or the incidence of mastitis in cows, it seems that further research is necessary, covering a larger population of cattle, to confirm the association between lipocalin-2 and milk production traits and mastitis.


Subject(s)
Animals , Cattle , Polymorphism, Genetic , Milk/immunology , Lipocalin-2/genetics , Mastitis, Bovine/genetics , Haplotypes , Breeding , Polymorphism, Single Nucleotide , Alleles , Lipocalin-2/chemistry , Mammary Glands, Animal , Mastitis, Bovine/immunology
11.
Arch. endocrinol. metab. (Online) ; 63(3): 280-287, May-June 2019. tab, graf
Article in English | LILACS | ID: biblio-1011172

ABSTRACT

ABSTRACT Objective Methylenetetrahydrofolate reductase (MTHFR) is involved in DNA methylation that is associated with autoimmune pathology. We investigated the association between MTHFR genetic polymorphisms at g.677C>T and g.1298A>C and their haplotypes, and the risk of thyroid dysfunction among Jordanian females. Subjects and methods A case-control study involving 98 hypothyroidism cases, 66 hyperthyroidism cases and 100 controls was conducted. Polymerase chain reaction/restriction fragment length polymorphism technique was performed to determine genotypes. Statistical analysis using SPSS software was performed. Results Genetic analysis showed a significant difference in genotype frequency of g.1298A>C between cases, and controls [hypothyroidism: AA (45.9%), AC (37.8%), CC (16.3%); hyperthyroidism: AA (9.1%), AC (69.7%), CC (21.2%); controls: AA (37.8%), AC (29.6%), CC (32.7%); CChypo vs. AAhypo: 2.55, 95% CI: (1.18-5.52); OR at least on Chypo: 1.79, 95% CI: (1.07-2.99)]; CChyper vs. AAhyper: 4.01, 95% CI: (1.79-9.01); OR at least on Chyper: 0.18, 95% CI: (0.07-0.48)]. There was no significant difference in genotype frequency of g.677C>T between cases and controls [hypothyroidism: CC (50.0%), CT (32.7%), TT (17.3%); hyperthyroidism: CC (77.3%), CT (15.2%), TT (7.6%); controls: CC (55.6%), CT (32.3%), TT (12.1%)]. There was a significant difference of MTHFR haplotypes among hypothyroidism cases and controls. TA and CC had a lower hypothyroidism risk whereas; TC showed a higher risk. Conclusions g.1298A>C genetic polymorphism of MTHFR may modulate the risk of thyroid disease. CC, TA, and TC haplotypes affect the risk of hypothyroidism. Larger samples should be included in the future to verify the role of MTHFR polymorphisms in thyroid diseases.


Subject(s)
Humans , Female , Adult , Middle Aged , Young Adult , Polymorphism, Restriction Fragment Length/genetics , Polymorphism, Single Nucleotide/genetics , Methylenetetrahydrofolate Reductase (NADPH2)/genetics , Hyperthyroidism/genetics , Hypothyroidism/genetics , Haplotypes , Case-Control Studies , Polymerase Chain Reaction , Risk Factors , DNA Methylation , Genetic Predisposition to Disease , Alleles , Genotype , Jordan
12.
Mem. Inst. Oswaldo Cruz ; 114: e190149, 2019. tab, graf
Article in English | LILACS | ID: biblio-1040610

ABSTRACT

Human polycystic echinococcosis is a parasitic infection caused by the larval stage of Echinococcus vogeli, which occurs in rural areas of Central and South America. Until now, little information on the genetic variability of E. vogeli is available. Here, 32 samples from human-excised E. vogeli cysts had a 396-bp sequence of the mitochondrial cytochrome oxidase I (COI) gene sequenced and compared to another 17 COI sequences representing nine Echinococcus species. A Bayesian COI tree revealed that all E. vogeli sequences formed a monophyletic and well-supported clade with an E. vogeli reference sequence. The occurrence of geographically restricted E. vogeli COI haplotypes suggests retention of ancestral polymorphisms with little migration in Acre, Brazil.


Subject(s)
Humans , Animals , Genetic Variation/genetics , Echinococcus/genetics , Haplotypes , Brazil , Bayes Theorem , Echinococcosis/parasitology , Echinococcus/isolation & purification
13.
Mem. Inst. Oswaldo Cruz ; 114: e190184, 2019. graf
Article in English | LILACS | ID: biblio-1040604

ABSTRACT

American visceral leishmaniasis (AVL) has two main scenarios of transmission as follows: scattered cases in rural areas and urban outbreaks. Urban AVL is in active dispersion from the northeastern border of Argentina-Paraguay-Brazil to the South. The presence of Lutzomyia longipalpis was initially reported in urban environments in the northwestern border of the country. The presence of Lu. longipalpis, environmental variables associated with its distribution, and its genetic diversity were assessed in Salvador Mazza, Argentina, on the border with Bolivia. The genetic analysis showed high haplotype diversity, low nucleotide diversity, and low nucleotide polymorphism index. We discuss the hypothesis of an expanding urban population with introgressive hybridisation of older haplogroups found in their path in natural forest or rural environments, acquiring a new adaptability to urban environments, and the possibility of changes in vector capacity.


Subject(s)
Animals , Male , Psychodidae/genetics , Genetic Variation/genetics , Animal Distribution , Insect Vectors/genetics , Argentina , Psychodidae/classification , Bolivia , Haplotypes , Brazil , DNA, Mitochondrial/genetics , Leishmaniasis, Cutaneous/transmission , Genes, Insect/genetics , Phylogeography , Insect Vectors/classification
14.
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
15.
Journal of Liver Cancer ; : 46-54, 2019.
Article in English | WPRIM | ID: wpr-765705

ABSTRACT

BACKGROUND/AIMS: Phosphatase and tensin homolog (PTEN) is a known tumor suppressor gene that is downregulated in hepatocellular carcinoma (HCC). Here, we investigated the association between single nucleotide polymorphisms (SNPs) of PTEN and HCC development in patients with hepatitis B virus (HBV) infection. METHODS: Six SNPs of PTEN at positions rs1234221, rs1903860, rs1234220, rs1903858, rs2299941, and rs17431184 were analyzed in a development population (417 chronic HBV carriers without HCC and 281 chronic HBV carriers with HCC). PTEN rs1903858, rs1903860, and rs2299941 SNPs were further assessed for the development of HCC in a validation population of 200 patients with HBV-related liver cirrhosis. RESULTS: In the development population, PTEN rs1903860 C allele, rs1903858 G allele, and rs2299941 G allele were associated with a low risk of HCC. The haplotype A-T-A-A-A was associated with an increased risk of HCC (recessive model; odds ratio=2.277, 95% confidence interval [CI] =1.144-4.532, P=0.019). In the validation population, PTEN rs2299941 G allele was the only significant protective genetic polymorphism related to HCC development after adjustment for age and sex (hazard ratio=0.582, 95% CI =0.353–0.962, P=0.035). CONCLUSIONS: These findings suggest that genetic polymorphisms in PTEN may affect HCC development in patients with chronic HBV infection.


Subject(s)
Alleles , Carcinoma, Hepatocellular , Genes, Tumor Suppressor , Haplotypes , Hepatitis B virus , Hepatitis B , Hepatitis , Humans , Liver Cirrhosis , Polymorphism, Genetic , Polymorphism, Single Nucleotide
16.
Article in English | WPRIM | ID: wpr-761778

ABSTRACT

Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.


Subject(s)
Asian Continental Ancestry Group , Base Sequence , China , Databases, Nucleic Acid , DNA, Mitochondrial , Haplotypes , Humans , Japan , Korea , Mitochondria , Spirometra , Trees
17.
Article in English | WPRIM | ID: wpr-761751

ABSTRACT

Human infections due to the monkey malaria parasite Plasmodium knowlesi is increasingly being reported from most Southeast Asian countries specifically Malaysia. The parasite causes severe and fatal malaria thus there is a need for urgent measures for its control. In this study, the level of polymorphisms, haplotypes and natural selection of full-length pkmsp8 in 37 clinical samples from Malaysian Borneo along with 6 lab-adapted strains were investigated. Low levels of polymorphism were observed across the full-length gene, the double epidermal growth factor (EGF) domains were mostly conserved, and non-synonymous substitutions were absent. Evidence of strong negative selection pressure in the non-EGF regions were found indicating functional constrains acting at different domains. Phylogenetic haplotype network analysis identified shared haplotypes and indicated geographical clustering of samples originating from Peninsular Malaysia and Malaysian Borneo. This is the first study to genetically characterize the full-length msp8 gene from clinical isolates of P. knowlesi from Malaysia; however, further functional characterization would be useful for future rational vaccine design.


Subject(s)
Asian Continental Ancestry Group , Borneo , Epidermal Growth Factor , Genetic Variation , Haplorhini , Haplotypes , Humans , Malaria , Malaysia , Merozoites , Parasites , Plasmodium knowlesi , Selection, Genetic
18.
Article in English | WPRIM | ID: wpr-761726

ABSTRACT

Echinococcus granulosus is an important zoonotic parasite globally causing cystic echinococcosis (CE) in humans and animals. In this study, prevalence of CE and variation of cox1 gene sequence were analyzed with isolates E. granulosus collected from different areas in northern Xinjiang, China. The survey showed that 3.5% of sheep and 4.1% of cattle were infected with CE. Fragment of cox1 was amplified from all the positive sheep and cattle samples by PCR. In addition, 26 positive samples across the 4 areas were included. The isolates were all E. granulosus sensu stricto (s.s.) containing 15 haplotypes (Hap1-15), and clustered into 2 genotypes, G1 (90.1%, 91/101) and G3 (9.9%, 10/101). Hap1 was the most common haplotype (48.5%, 49/101). Hap9 were found in humans samples, indicating that sheep and cattle reservoir human CE. It is indicate that E. granulosus may impact on control of CE in livestock and humans in the region.


Subject(s)
Animals , Cattle , China , Cross-Sectional Studies , Echinococcosis , Echinococcus granulosus , Echinococcus , Genotype , Haplotypes , Humans , Livestock , Parasites , Polymerase Chain Reaction , Prevalence , Sheep
19.
Article | WPRIM | ID: wpr-763557

ABSTRACT

OBJECTIVE: Genetics factors are likely to play a role in the risk, clinical presentation and treatment outcome in major depressive disorder (MDD). In this study, we investigated the role of three candidate genes for MDD; calcium voltage-gated channel subunit alpha1 C (CACNA1C), cholinergic receptor nicotinic alpha 7 subunit (CHRNA7), and mitogen-activated protein kinase 1 (MAPK1). METHODS: Two-hundred forty-two MDD patients and 326 healthy controls of Korean ancestry served as samples for the analyses. Thirty-nine single nucleotide polymorphisms (SNPs) within CACNA1C, CHRNA7, and MAPK1 genes were genotyped and subsequently tested for association with MDD (primary analysis) and other clinical features (symptoms’ severity, age of onset, history of suicide attempt, treatment outcome) (secondary analyses). Single SNPs, haplotypes and epistatic analyses were performed. RESULTS: Single SNPs were not associated with disease risk and clinical features. However, a combination of alleles (haplotype) within MAPK1 was found associated with MDD-status. Secondary analyses detected a possible involvement of CACNA1C haplotype in resistance to antidepressant treatment. CONCLUSION: These data suggest a role for MAPK1 and CACNA1C in MDD risk and treatment resistance, respectively. However, since many limitations characterize the analysis, the results must be considered with great caution and verified.


Subject(s)
Age of Onset , Alleles , Calcium , Depression , Depressive Disorder, Major , Genetics , Haplotypes , Humans , Mitogen-Activated Protein Kinase 1 , Neuronal Plasticity , Polymorphism, Single Nucleotide , Suicide , Treatment Outcome
20.
Yonsei Medical Journal ; : 659-666, 2019.
Article in English | WPRIM | ID: wpr-762094

ABSTRACT

PURPOSE: To investigate associations for polymorphisms in β-carotene 9′,10′-oxygenase (BCO2, rs10431036 and rs11214109), proprotein convertase subtilisin kexin type 9 (PCSK9, rs11583680), and tribbles pseudokinase 1 (TRIB1, rs17321515 and rs2954029), as well as lifestyle factors, with ischemic stroke (IS). MATERIALS AND METHODS: This nested case-control study included 161 patients with IS and 483 matched control individuals. We collected medical reports, lifestyle details, and blood samples from individuals and used the PCR-ligase detection reaction method to genotype single nucleotide polymorphisms (SNPs). RESULTS: The GA+AA genotype of rs10431036 (p<0.001) and rs17321515 (p=0.003), the CT+TT genotype of rs11214109 (p=0.005), and the TA+AA genotype of rs2954029 (p=0.006) in dominant models increased the risk of IS. In additive models, the GG genotype of rs17321515 (p=0.005) and the TT genotype of rs2954029 (p=0.008) increased the risk of IS. Adequate intake of fruits/vegetables reduced the risk of IS (p=0.005). Although there was no interaction between genes and fruits/vegetables, people with inadequate intake of fruits/vegetables who carried a risk genotype had a higher risk of IS than those only having inadequate fruits/vegetables intake or those only carrying a risk genotype. Also, the haplotypes AC, AT, and GT (comprising rs10431036 and rs11214109) and GT (comprising rs2954029 and rs17321515) were found to be associated with an increased risk of IS (p<0.05). CONCLUSION: Polymorphisms in BCO2 and TRIB1 and fruits/vegetables intake were associated with IS. These results provide the theoretical basis for gene screening to prevent chronic cerebrovascular diseases.


Subject(s)
Case-Control Studies , Cerebrovascular Disorders , Genotype , Haplotypes , Humans , Life Style , Mass Screening , Methods , Polymorphism, Single Nucleotide , Proprotein Convertases , Stroke , Subtilisin
SELECTION OF CITATIONS
SEARCH DETAIL