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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.

Meta-analysis of QTL for Fusarium head blight resistance in Chinese wheat landraces using genotyping by sequencing

Cai, Jin 2016 (has links)
Doctor of Philosophy Department of Agronomy Guihua Bai Guorong Zhang Fusarium head blight (FHB) is a devastating fungal disease in wheat, reducing not only grain yield but also quality. The pathogen produces the mycotoxin deoxynivalenol (DON) that induces severe toxicological problems in human and animals. Using host resistance has been the most efficient way to control the disease. To identify quantitative trait loci (QTLs) for FHB resistance in Chinese landrace Haiyanzhong (HYZ), a recombinant inbred lines (RILs) population derived from a cross between HYZ and Wheaton was developed. The RILs were evaluated for percentage of symptomatic spikelets (PSS) in three greenhouse experiments, and genotyped using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) developed from genotyping-by-sequencing (GBS). Eight QTLs were identified for type II (PSS) resistance on chromosomes 5A, 6B, 7D, 2B (2), 3B, 4B, and 4D, with 5A as the major QTL. Ten SNPs closely linked to 5A, 6B, and 2B QTLs were successfully converted to Kompetitave allelic specific PCR (KASP) assays. To identify common QTLs across different populations, we constructed high-density GBS-SNP maps in an additional four RIL populations derived from the Chinese landraces, Wangshuibai (WSB), Baishanyuehuang (BSYH), Huangfangzhu (HFZ), and Huangchandou (HCD) and conducted meta-analysis of the QTLs for FHB resistance using a consensus map developed from the five populations. We identified six MQTLs on chromosomes 3BS (2), 3A, 3D, 2D, and 4D and 23 tightly linked GBS-SNPs to the MQTLs. These GBS-SNPs were successfully converted to KASPs. The KASPs linked to MQTLs can be used for pyramiding these QTL in breeding programs. To quickly reduce FHB damage in U.S. hard winter wheat (HWW), we transferred Fhb1, a major QTL with stable effects on FHB resistance, from Ning7840 into three adapted HWW cultivars Overland, Jagger, and Overley, by marker-assisted backcross (MAB), and assessed the effect of Fhb1 on FHB resistance in these different backgrounds. The results showed that Fhb1 can significantly lower FHB severity, Fusarium-damaged kernel (FDK), and DON accumulation in the all the three HWW backgrounds. Some of the selected lines showed high levels of FHB resistance, but agronomically similar traits as recurrent parents, can be used as resistant parents to improve HWW FHB resistance.

Agronomic, genetic and genomic approaches for predicting heterosis in sorghum [Sorghum bicolor (L.) Moench]

Maulana, Frank 2016 (has links)
Doctor of Philosophy Department of Agronomy Tesfaye Tesso The approach used to identify inbred lines that can produce superior hybrids is costly and time-consuming. It requires creation of all possible crosses and evaluation of the crosses to estimate combining abilities for the desired traits. Predicting heterosis or hybrid performance in any way possible may help to reduce the number of crosses to be made and evaluated. In this study, four sets of experiments were conducted to determine whether heterosis can be predicted based on inbred line performance, genetic distance between parents and genomic prediction model. The first experiment was aimed at assessing the levels of genetic diversity, population structure and linkage disequilibrium (LD) in 279 public sorghum inbred lines, based on 66,265 SNPs generated using the genotyping-by-sequencing (GBS) platform. The inbred lines were developed at different times over the last two decades and harbor robust diversity in pedigree and agronomic characteristics. Some of the inbreds are resistant to Acetolactate synthase (ALS) and Acetyl co-enzyme-A carboxylase (ACC) inhibitor herbicides. The mean polymorphic information content (PIC) and gene diversity across the entire inbreds were 0.35 and 0.46, respectively with non-herbicide resistant inbreds harboring more diversity than the herbicide resistant ones. The population structure analysis clustered the inbred lines into three major subgroups according to pedigree and fertility-reaction with the maintainer lines (B-lines) distinctly forming a separate cluster. Analysis of molecular variance (AMOVA) revealed more variation within subgroups than among subgroups. Substantial linkage disequilibrium (LD) was detected between the markers in the population with marked variation between chromosomes. This information may facilitate the use of the inbreds in sorghum breeding programs and provide perspectives for optimizing marker density for gene mapping and marker-assisted breeding. The second experiment, based on 102 F1 hybrids developed by intercrossing closely and distantly related inbreds, was conducted to investigate the relationship of genetic distance between parents with hybrid vigor or heterosis. The F1 hybrids alongside their parents were evaluated at two environments in a randomized complete block design with three replications. The results show that correlations of genetic distance between parents with hybrid performance and heterosis were variable and dependent on the trait. Though most were statistically non-significant and not strong to be used as predictor for heterosis, the results tend to show that certain level of genetic distance between parents is needed to capture maximum heterosis and hybrid performance. The objective of the third research study was to determine whether traits measured on parents can be used to predict hybrid performance in sorghum and to assess the combining ability of selected inbreds. Forty-six parental inbred lines and 75 F1 hybrids generated from intercrossing the inbreds were evaluated in four environments in a randomized complete block design with three replications. The average performance of the parents (mid-parent) was significantly correlated with hybrid performance for thousand kernel weight, days to flowering and plant height. Significant general (GCA) and specific (SCA) combining abilities were observed for most traits, with highly significant GCA effects observed for most traits as compared to SCA indicating that additive genetic effects are more important in affecting the inheritance of the traits measured. Results show that studying parental inbred line performance could generate important information for predicting hybrid performance in sorghum. The fourth experiment was aimed at assessing the efficacy of genomic prediction of hybrid performance in sorghum. Genomic prediction was performed with five-fold cross-validation procedure on 204 F1 hybrids developed using 102 inbred lines. A total of 66,265 SNP markers generated using genotyping-by-sequencing were used in this study. Results showed that increasing training population size increased prediction accuracies for all traits with the effect being different for different traits. Also, considering additive effects alone versus additive and dominance effects in the model showed similar trend of prediction accuracy but the full model (considering both additive and dominance effects of the markers) provided better prediction at least for some of the traits. The results suggest that genomic prediction could become an effective tool for predicting the performance of untested sorghum hybrids thus adding efficiency to hybrid selection.

Utilizing a historical wheat collection to develop new tools for modern plant breeding

Rife, Trevor W. 2016 (has links)
Doctor of Philosophy Genetics Interdepartmental Program Jesse Poland The Green Revolution is credited with saving billions of lives by effectively harnessing new genetic resources and breeding strategies to create high-yielding varieties for countries lacking adequate food security. To keep the next billion people in a state of food security, plant breeders will need to rapidly incorporate novel approaches and technologies into their breeding programs. The work presented here describes new genomic and phenomic strategies and tools aimed at accelerating genetic gain in plant breeding. Plant breeders have long relied on regional testing networks to evaluate new breeding lines across many locations. These are an attractive resource for both retrospective and contemporary analysis due to the vast amount of data available. To characterize genetic progress of plant breeding programs in the Central Plains, entries from the Southern Regional Performance Nursery dating back to 1992 were evaluated in field trials. The trend for annual improvement was 1.1% yr⁻¹, matching similar reports for genetic gain. During the same time period, growth of on-farm yields stagnated. Genomic selection, a promising method to increase genetic gain, was tested using historical data from the SRPN. A temporal-based model showed that, on average, yield predictions outperformed a year-to-year phenotypic correlation. A program-based model found that the predictability of a breeding program was similar when using either data from a single program or from the entire regional collection. Modern DNA marker platforms either characterize a small number of loci or profile an entire genome. Spiked genotyping-by-sequencing (sGBS) was developed to address the need in breeding programs for both targeted loci and whole-genome selection. sGBS uses a low-cost, integrated approach that combines targeted amplicons with reduced representation genotyping-by-sequencing. This approach was validated using converted and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34. Plant breeding programs generate vast quantities of data during evaluation and selection of superior genotypes. Many programs still rely on manual, error-prone methods to collect data. To make this process more robust, we have developed several open-source phenotyping apps with simple, intuitive interfaces. A contemporary Green Revolution will rely on integrating many of these innovative technologies into modern breeding programs.

Caracterização do polimorfismo e associação dos genes da kappa-caseína e da beta-lactoglobulina com a produção de leite em bovinos da raça Girolando.

Ítala Iara Medeiros de Araújo 6 February 2013 (has links)
Os genes candidatos da kappa-caseína (CSN3) e da beta-lactoglobulina (LGB) estão envolvidos na composição, processamento e qualidade do leite e estão ligados às características de produção. Objetivou-se avaliar as frequências alélicas e genotípicas do gene da kappa-caseína (CSN3) e da beta-lactoglobulina (LGB) e associá-las à produção de leite de bovinos participantes do Teste de Progênie da Raça Girolando, por meio de análise das variáveis de produção de leite em até 305 dias (P305) e de capacidade prevista de transmissão (PTA) de leite. Para o estudo do polimorfismo, foram genotipados 138 touros e 729 vacas (n = 867) para o CSN3 e 131 touros e 737 vacas (n = 868) para LGB. Para a análise de associação foram avaliados 127 touros e 536 vacas (n = 663) para CSN3 e 127 touros e 536 vacas (n = 663), para LGB. A diferenciação dos alelos A/B dos genes estudados foi obtida por meio da técnica de PCR-RFLP. As frequências alélicas, genotípicas e o cálculo da probabilidade de equilíbrio de Hardy-Weinberg (EHW) foram estabelecidos por meio do programa Popgen versão1.32 e testado pelo teste χ ao nível de significância de 1%. O estudo de associação foi realizado por meio de análise de regressão utilizando o procedimento GLM do SAS 9.1. As frequências genotípicas e alélicas para o gene CSN3 foram, respectivamente, 0,7324 (AA); 0,2468 (AB); 0,0208 (BB) e 0,8558 (A); 0,1442 (B) e para o LGB foram, respectivamente, 0,2604 (AA); 0,4827 (AB); 0,2569 (BB) e 0,5017 (A); 0,4983 (B). A população encontra-se em EHW para ambos os genes. Não foi detectada associação entre os genes avaliados e as variáveis analisadas. Candidate genes of the kappa-casein (CSN3) and beta-lactoglobulin (LGB) are involved in the composition, processing and quality of milk and are linked to production characteristics. This study aimed to evaluate the allele and genotype frequencies of kappa-casein gene (CSN3) and beta-lactoglobulin (LGB) and associate them with milk production of cattle participants Progeny Test Breed Girolando through analysis of variables milk yield in 305 days (P305) and predicted transmitting ability (PTA) for milk. For the study of polymorphisms were genotyped sires 138 and 729 cows (n = 867) for CSN3 and 737 and 131 bulls and cows (n = 868) to LGB. For the association analysis were evaluated 127 bulls and 536 cows (n = 663) and 127 for CSN3 bulls and 536 cows (n = 663) for LGB. The differentiation of allele A / B genes studied was obtained by PCR-RFLP. Allele frequencies, genotype and calculating the probability of Hardy-Weinberg equilibrium (HWE) were established through the program Popgen versão1.32 and tested by χ test at a significance level of 1%. The association study was performed by regression analysis using the GLM procedure of SAS 9.1. The allele and genotype frequencies for the gene CSN3 were, respectively, 0.7324 (AA), 0.2468 (AB) 0.0208 (BB) and 0.8558 (A) 0.1442 (B) and the LGB were, respectively, 0.2604 (AA), 0.4827 (AB) 0.2569 (BB) and 0.5017 (A) 0.4983 (B). The population is in HWE for both genes. No association was found between genes evaluated and analyzed variables.

Comparação genotípica e fenotípica de diferentes isolados clínicos de colonização e candidemia por Candida rugosa Genotypic and phenotypic comparisons among different clinical isolates of colonization and candidemia by Candida rugosa

Terçarioli, Gisela Ramos [UNIFESP] 29 July 2009 (has links)
Introduction: Candida rugosa is an emergent pathogen recognized by its higher occurrence in Latin American countries. This yeast has the ability to colonize and cause human bloodstream infections as well as to show resistance to several antifungal drugs, specifically to azoles. Objectives: To compare phenotypic properties such as virulence attributes and antifungal susceptibility, as well as to perform molecular identification and typing of C. rugosa clinical isolates obtained from patients who were either colonized or developed candidemia due to this species during the hospitalization period. We were also interested in evaluating such differences among strains isolated across two different periods: 1995/96 and 2001/02. Material and Methods: The strains were phenotypically characterized according to virulence factors, including the production of extra cellular enzymes (protease, phospholipase and lipase) and biofilm formation. We performed susceptibility testing to 5 antifungal drugs by using broth microdilution: amphotericin B, fluconazole, voriconazole, caspofungin and anidulafungin. To confirm identification to the species level and evaluate genetic variability, we have employed RAPD, microsatelite and rDNA ITS region sequencing. Results: Phenotypic properties varied considerably among the isolates, specifically regarding to hydrolytic enzymes production. Most of the isolates were low proteinase producers. The strains were phospholipase negative and showed a not very expressive biofilm formation in general. Nevertheless, lipase production was the only virulence factor considerably expressed by the clinical isolates, specifically by blood strains, suggesting the importance of this attribute in C. rugosa infection. The strains were sensitive to all the antifungal drugs tested, except fluconazole. The clinical isolates were highly related as determined by 3 different methods. However the control strain ATCC10571 was considered genotipically very different Our isolates were 90.5% similar among them and 87% similar to C. rugosa control strain as determined by RAPD, and 92% similar among them and 86,5% similar to ATCC10571, as determined by microsatelite. All the isolates were identified as C. rugosa by ITS region sequencing. The percentage of similarity ranged from 89% to 93% for the clinical isolates, and 99% to C. rugosa ATCC10571. Conclusions: It was not possible to establish a direct relationship between the expression of all virulence properties and patients clinical outcomes. However there is mounting evidence that lipase activity influences candidemia due to C. rugosa. It is possible that clonal dissemination in the hospital environment have occurred throughout several years. In addition, the genetic differences found between our isolates C. rugosa control strain ATCC10571, together with the phenotypic differences observed, such as higher biofilm formation and rough colony morphology, as well as low lipase activity for this control strain, suggest the genetic heterogeneity among the taxon C. rugosa. Introdução: Candida rugosa é um patógeno emergente que merece destaque pela sua maior ocorrência em países da América Latina. Esta levedura tem o potencial de colonizar e causar infecções de corrente sanguínea no homem, bem como de apresentar resistência a diversos antifúngicos, principalmente aos azólicos. Objetivos: comparar caracteres fenotípicos, como atributos de virulência e sensibilidade antifúngica, além de realizar identificação e tipagem molecular de isolados clínicos de C. rugosa obtidos de pacientes que desenvolveram candidemia, com cepas isoladas de pacientes que foram somente colonizados por esta espécie, sem desfecho de candidemia na internação. Também foi de nosso interesse avaliar tais diferenças entre as cepas provenientes de pacientes internados ao longo de dois períodos avaliados: 1995/96 e 2001/02. Material e Métodos: As cepas foram caracterizadas fenotipicamente quanto a fatores de virulência, incluindo a produção de enzimas extracelulares (proteinase, fosfolipase e lipase) e a formação de biofilme. Foram realizados teste de susceptibilidade a cinco antifúngicos pelo método de microdiluição em caldo, sendo eles: anfotericina B, fluconazol, voriconazol, caspofungina e anidulafungina. Para confirmação de espécie e avaliação de variabilidade genotípica, foram utilizadas as técnicas moleculares de RAPD, microssatélite e sequenciamento da região ITS (rRNA). Resultados: Observou-se grande variabilidade nos resultados referentes à produção de enzimas hidrolíticas. A população foi classificada, no geral, como baixa produtora de proteinase, não produtora de fosfolipase e baixa e média produtora de biofilme. A produção de lipase foi o único fator de virulência expresso de maneira considerável pelos isolados clínicos, destacando-se a alta produção desta enzima por cepas isoladas de sangue, sugerindo a importância da mesma no estabelecimento de infecção por C. rugosa. Com relação à sensibilidade aos antifúngicos, os isolados mostraram-se sensíveis a todas as drogas, exceto ao fluconazol. A avaliação dos resultados obtidos por 3 diferentes métodos moleculares demonstrou alto relacionamento filogenético entre os isolados clínicos, exceto pela cepa de referência a qual foi sempre posicionada em diferente cluster. A análise genotípica revelou similaridade de 90,5% entre todos os isolados, e de 87% para a cepa de referência ATCC1051 pela técnica de RAPD, e uma similaridade de 92% entre os isolados clínicos e de 86,5% para a cepa controle pelo método de microssatélite. O seqüenciamento da região ITS identificou todos os isolados como sendo C. rugosa, apresentando uma identidade que variou de 89% a 93% para os isolados clínicos, e 99% para a cepa de referência ATCC10571. Conclusões: Não foi possível estabelecer uma correlação direta entre a expressão de todos os fatores fenotípicos avaliados e o desfecho clínico dos pacientes, embora haja evidências importantes da atividade de lipase influenciando candidemia por C. rugosa. Sugere-se que houve uma disseminação clonal dos isolados de C. rugosa no ambiente hospitalar avaliado ao longo de vários anos. Adicionalmente, as diferenças genéticas encontradas entre os isolados clínicos e a cepa de referência ATCC10571, juntamente com algumas diferenças fenotípicas observadas exclusivamente nesta cepa, tais como alta produção de biofilme, macromorfologia acentuadamente rugosa e baixa atividade de lipase, indicam a possibilidade de heterogeneidade do táxon C. rugosa.

ß-2 microglobulina e citocinas séricas como indicadores de falha terapêutica aos anti-retrovirais

Almeida, Ricardo Augusto Monteiro de Barros [UNESP] 26 February 2009 (has links)
Iniciativas como a “WHO/UNAIDS ‘3 by 5’ permitiram que se atingisse, no ano de 2007, a marca de 3 milhões de pessoas com acesso à terapia antiretroviral (TARV) em países de baixa e média renda. O aumento da cobertura nestes países demanda custos importantes com anti-retrovirais, porém também levanta outro problema, que é o monitoramento da terapia em localidades de poucos recursos. Há consenso no fato de que devem ser pesquisados marcadores de eficácia da TARV mais acessíveis. Considerando o comportamento da β-2 microglobulina sérica e das citocinas séricas TNF-α, IFN-γ, IL-2, IL-4 e IL-10 com relação à atividade inflamatória induzida pela replicação do HIV-1, o objetivo deste estudo foi o de verificar o comportamento destas substâncias como indicadores da presença, ou não, de falha terapêutica à HAART. Entre agosto de 2004 e novembro de 2005, 89 indivíduos infectados pelo HIV-1, atendidos pela Área de Doenças Tropicais da Faculdade de Medicina de Botucatu-UNESP, e 20 indivíduos normais, doadores de sangue do Hemocentro de Botucatu [43 mulheres e 66 homens; idade média = 39,7 anos (22 - 66 anos)] foram divididos em 4 grupos: G1- 15 indivíduos infectados pelo HIV-1, virgens de tratamento ou sem HAART há pelo menos seis meses e com contagens de linfócitos T CD4 + menores que 350 células/mm3; G2- 31 indivíduos infectados pelo HIV-1, em uso de HAART e sem falha terapêutica virológica (FT); G3- formado por 43 indivíduos infectados pelo HIV-1, em uso de HAART e com FT, e GC- formado por 20 indivíduos normais, não infectados pelo HIV-1, que serviram de controles para as citocinas séricas. Foram revisados os dados demográficos, clínicos e de HAART e realizados os exames β-2 microglobulina sérica, citocinas séricas (TNF-α, IFN-γ, IL-2, IL-4 e IL-10), genotipagem do HIV-1, carga viral plasmática (CV) e linfócitos T CD4 + e T CD8 +. Para... Initiatives such as WHO/UNAIDS ‘3 by 5’ made it possible to achieve the figure of 3 million people with access to antiretroviral therapy (ART) in middle- and low-income countries in 2007. The increase in these countries’ coverage leads to important expenditure on antiretroviral drugs; however, it also raises another problem, which is therapy monitoring in low-income locations. There is agreement on the fact that more accessible ART efficacy markers must be studied. By considering the behavior of serum β-2 microglobulin and serum cytokines TNF-α, IFN-γ, IL-2, IL-4 and IL-10 in relation to inflammatory activity induced by HIV-1 replication, the objective of this study was to assess the behavior of such substances as indicators of the presence, or not, of antiretroviral therapeutic failure (TF). From August 2004 to November 2005, 89 HIV-1-infected individuals assisted by the Tropical Diseases Sector of the Botucatu School of Medicine – UNESP and 20 normal blood donors at the Blood Transfusion Center of Botucatu [43 female and 66 male; mean age = 39.7 years (22 - 66 years)] were divided into 4 groups: G1- 15 HIV-1-infected individuals, previously untreated or without HAART for at least six months and CD4 + < 350 cells/mm3; G2- 31 HIV-1-infected individuals undergoing HAART without virological therapeutic failure (TF), G3- 43 HIV-1-infected individuals undergoing HAART with TF, and CG- 20 normal individuals who served as controls for serum cytokines. Demographic, clinical and HAART data were reviewed, and serum β-2 microglobulin, serum cytokines (TNFα, IFN-γ, IL-2, IL-4 and IL-10), HIV-1 genotyping, plasma viral load (VL) and T CD4 + and T CD8 + lymphocytes tests were performed. The Mann-Whitney test for independent samples was used for between-group comparison in the case of numeric variables, and Fisher’s exact test was applied for category variables. Statistical difference... (Complete abstract click electronic access below)

Prospecção de assinaturas de seleção em regiões de QTL associadas com características reprodutivas em novilhas Nelore Prospection of selection signatures in QTL regions associated to reproductive features in Nelore heifers

Montes Vergara, Donicer Eduardo [UNESP] 24 March 2016 (has links)
Características reprodutivas, como a ocorrência de prenhez precoce, são mais importantes economicamente ao comparar-se com as características de crescimento. Desta forma, o aumento da taxa de fertilidade e emprego de animais geneticamente superiores é determinante no progresso da produtividade nas fazendas comerciais de produção de carne bovina. A seleção modifica as frequências alélicas de uma população ao transmitir as variantes gênicas mais interessantes. Considerando o desequilíbrio de ligação, alguns locos adjacentes às mutações favoráveis são transmitidos ao longo das gerações. Estes são conhecidos como assinaturas de seleção e podem ser identificados com o uso de “chips” de SNP e metodologias estatísticas adequadas. Com o objetivo de identificar assinaturas de seleção recentes em QTL previamente mapeados para características reprodutivas de fêmeas bovinas ligadas à precocidade sexual, foram genotipadas 2.035 fêmeas da raça Nelore (Bos taurus indicus) com o chip “Illumina BovineHD BeadChip”. Posteriormente foi inferida a fase de ligação dos SNPs e a reconstrução dos haplótipos. A detecção de assinaturas de seleção foi realizada por meio da aplicação da metodologia “Relative Extended Haplotype Homozygosity” (REHH). A identificação de genes que contribuem para a importância da característica nestas regiões foi feita com a ferramenta Map Viewer do “National Center for Biotechnology Information”- NCBI e GBrowse carregada com o genoma bovino versão UMD 3.1. Foram detectadas 2.756 regiões núcleo, com tamanho médio 27,6 ± 29,1 Kb, abrangendo 70,1 Mb dos 25 cromossomos estudados. Dos SNPs utilizados, 17.312 participaram da formação das regiões núcleo, com o mínimo de 10 no BTA27 e o máximo de 20 SNPs nos cromossomos 1, 3-7, 9-15,18-21, e 23-24. Foram identificadas 40 assinaturas de seleção recentes com diferentes níveis de significância e 56 genes A maioria dos genes localizados nas regiões de assinaturas de seleção tem relação com os processos biológicos de metabolismo mitocondrial, desenvolvimento pós-embrionário, regulação da taxa de ovulação e fertilidade, resposta imune, metabolismo de triglicerídeo, proliferação celular e neurônios receptores olfativos. A investigação de mecanismos regulatórios da expressão dos genes associados aos processos biológicos descritos pode oferecer conhecimentos sobre os mecanismos moleculares que afetam a característica ocorrências de prenhez precoce, na raça Nelore. Some reproductive traits such as early pregnancy are more profitable than those related to growth. Increasing fertility rate and using genetically superior animals are crucial in productivity of meat commercial farms. Artificial selection modifies allele frequencies of a cattle population by transmitting the most significant gene variants. Considering linkage disequilibrium, some loci adjacent to favorable mutations are transmitted across generations. Known as signatures of selection, such locations can be identified by the SNP chips, and appropriate statistical methods. To determine recent selection signature in quantitative trait loci (QTL) previously mapped for reproductive cow features linked to sexual precocity, 2,035 Nelore (Bos taurus indicus) females were genotyped by Illumina Bovine chip. After, inferring the connection phase of SNPs allowed haplotype reconstruction. Selection signatures were detected by Relative Extended Haplotype Homozygosity (REHH) method. Genes supposedly important were recognized by Map Viewer from the National Center for Biotechnology Information (NCBI), and also through a loaded GBrowse with bovine genome UMD, version 3.1. A total of 2,756 core regions were detected, with an average size of 27.6 ± 29.1 Kb, covering 70.1 Mb of 25 chromosomes. 17,312 SNPs are involved in the formation of core regions with at least 10 on BTA27, and a maximum of 20 SNPs on 1, 3-7, 9-15, 18-21, and 23-24 chromosomes. We identify 40 possible recent selection signatures, with different levels of significance, and 56 positional candidate genes. Most of genes located in selection signature regions are related to biological processes of mitochondrial metabolism, post-embryonic development, ovulation rate regulation and fertility, immune response, triglyceride metabolism, cell proliferation, and olfactory receptor neurons. The investigation of regulatory mechanisms of gene expression associated with biological processes described can provide knowledge on the molecular mechanisms affecting characteristic of early pregnancy occurrences in Nellore.

Detecção e genotipagem do papilomavirus humano (HPV) em mulheres com neoplasia intra-epitelial cervical de alto grau Detection and genotyping of the human papilomavirus (HPV) in women with high grade cervical intraepithelial neoplasia

Denise da Rocha Pitta Lima de Moraes 2008 (has links)
Resumo: Introdução: Este estudo faz parte de uma linha de pesquisa cuja finalidade é avaliar testes de detecção de papilomavírus humano (HPV) envolvidos na carcinogênese e rastreamento de câncer cervical. Até recentemente, a captura híbrida 2 (HC2) para detecção de um pool de HPV de alto risco oncogênico foi o método clínico mais estudado por este grupo. Entretanto, frente à evidente diferença no risco de evolução das lesões cervicais, a genotipagem do HPV através de análise do ácido nucléico passou a ser relevante. Objetivo: Avaliar a distribuição de infecções simples e múltiplas de diferentes tipos de HPV em mulheres com neoplasia intra-epitelial cervical de alto grau (NIC2 e NIC3). Sujeitos e Métodos: Foram avaliados os genótipos específicos de HPV da amostra cervical de 106 mulheres utilizando Roche Linear Array® human papillomavirus (LA-HPV) genotyping assay (Roche Diagnostics,USA). O material foi coletado antes da conização cervical. Foram comparadas as proporções de NIC2 e NIC3 em grupos de mulheres infectadas com tipos de HPV dos grupos filogenéticos Alfa7 (A7) e Alfa9 (A9). Três situações foram consideradas: mulheres com 1) infeccão simples; 2) infecção múltipla; 3) infecção simples e múltipla. Foram comparadas as proporções de diferentes combinações de tipos de HPV em grupos de mulheres com NIC2 e NIC3. Resultados: Pelo menos um tipo de HPV foi detectado em 99% das amostras. Infecções múltiplas foram detectadas em 68 (64,7%) das amostras. Os genótipos de alto risco mais freqüentemente detectados em infecção simples ou múltipla foram HPV16 (57,1%), HPV58 (24,7%), HPV33 (15,2%), HPV52 (13,3%), HPV31 (10,4%) e HPV51 (7,6%) e HPV18 (6,6%). A probabilidade de mulheres com NIC3 serem infectadas com HPV da espécie A9 foi maior. Os HPV 16 e ou 18, associados ou não com outros tipos virais foram mais frequentemente encontrados nas mulheres com NIC3 do que naquelas com NIC2. Conclusão: A severidade da NIC esteve associada com a presença de tipos de HPV incluídos na classificação filogenética A9 e por infecções que incluem HPV16 e 18 combinados ou não com outros genótipos de HPV ;;Abstract:Objective: To evaluate the distribution of single and multiple infections of different human papillomavirus (HPV) types in women with high grade cervical intraepithelial neoplasia (CIN2 and CIN3) and to assess the relation of the various combinations of virus with the severity of CIN. Subject and methods: Cervical samples from 106 women treated due to CIN2 (18) or CIN3 (88) were examined for specific HPV genotypes using Roche Linear Array® Human Papillomavirus (LA-HPV)(Roche Diagnostics, USA). The material was collected immediately before cervical conization. The proportion of CIN2 and CIN3 in groups of women infected with varying HPV phylogenetic groups Alpha7 (A7) and Alpha9 (A9) was compared. Three situations were considered: women with 1) single infection; 2) multiple infections; 3) the whole sample. The proportions of CIN2 and CIN3 in groups of women with different combinations of HPV types were compared. Results: At least one HPV type was detected in 99% of the whole series. Multiple infections were detected in 68 (64.7%) samples. The most frequent high-risk genotypes detected (single/multiple) were HPV16 (57.1%), HPV58 (24.7%), HPV33 (15.2%), HPV52 (13.3%), HPV31 (10.4%), HPV51 (7.6%) and HPV18 (6.6%). Women with CIN3 were more infected with HPV of species A9. HPV16 and/or HPV18, associated or not with other viral types, were more frequently found in specimens of women with CIN3 than in those of women with CIN2. Conclusions: the severity of high-grade CIN may be associated by the presence of HPV types included in the A9 phylogenetic classification and by infections including HPV16 and 18 combined or not with other HPV genotypes

Analise molecular dos genotipos do virus da hepatite B em pacientes do estado de São Paulo, sudeste do Brasil Molecular analysis of the genotypes of hepatitis B virus (HBV) in patients in state of São Paulo, Southeast of Brazil

Priscilla Aparecida Tonetto 2006 (has links)
Resumo: O vírus da hepatite B (VHB) pode ser classificado em oito principais genótipos (A-H), e essa classificação tem uma distribuição geográfica determinada. Os genótipos do VHB podem influenciar na progressão de doença. O objetivo foi determinar os genótipos e os subtipos do VHB e correlacioná-los com as variáveis clínicas epidemiológicas, laboratoriais e histológicas. Foram determinados os genótipos de 139 amostras de soro de pacientes infectados pelo VHB, coletadas em Campinas, no estado de São Paulo, Brasil. O método para genotipagem utilizado foi o seqüenciamento parcial do gene S do VHB. Os primers utilizados foram desenhados a partir de seqüências do gene S, com genótipo determinado, depositadas no GenBank. Todas as seqüências obtidas foram comparadas com as seqüências depositadas no GenBank para determinação dos genótipos. O genótipo A (55%) do VHB foi o mais predominante na população, seguido pelos genótipos C (3%), D (38%) e F (4%). Entre os pacientes infectados pelos genótipos A e D, observou-se uma provável descendência africana de 18% (14/76) e 11% (6/53), respectivamente. Entre os quatro pacientes infectados pelo genótipo C, dois possuíam descendência asiática e dois eram caucasianos. Todos os pacientes infectados pelo genótipo F eram caucasianos sem ascendência indígena relatada. Aproximadamente 30% dos pacientes eram HBeAg positivo e 70% eram HBeAg negativo. A carga viral do DNA-VHB foi aproximadamente cinco vezes mais alta entre os HBeAg positivo quando comparada aos HBeAg negativo. Os genótipos A e D são os mais prevalentes entre os pacientes, aparentemente em virtude da imigração européia em nossa região ;;Abstract:Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression. Our objective was to determine the genotypes and the subtypes of HBV and to correlate them with the with variables clinical epidemiologies, laboratories and histological. Hepatitis B virus genotypes were determined in 139 plasma samples collected in Campinas, in the state of São Paulo, Brazil from HBV-infected patients. A method for genotyping hepatitis B virus by partial HBsAg gene sequencing with primers common to all known genotypes was developed. The results of sequencing corresponded to those found in HBV isolates obtained from GenBank, including all of the known HBV genotypes. HBV genotype A was predominant in our sample, appearing in 76 patients (55%), while genotypes C, D and F was found in 4 (3%), 53 (38%) and 6 (4%) of the patients, respectively. Among the patients infected by genotypes A and D, were observed a probably African descendents of the 18.3% (14/76) and 11.3% (6/53), respectively. Among the genotype C infected patients, 2 (50%) were of Asian descendents and 2 were Caucasians. The genotype F infected patients were all Caucasians without told indigenous origin. About 30% of the patients were HBeAg positive and 70% were HBeAg negative. The viral load of HBV-DNA was about 5 times higher among HBeAg positive than in HBeAg-negative patients. Genotypes A and D were the most prevalent among our HBV-infected patients, apparently a consequence of the types of immigration to our region

Évaluation de marqueurs génétiques du complexe Mycobacterium tuberculosis combinée à l'utilisation d'outils bioinformatiques : apport en épidémiologie et phylogénie de la tuberculose Evaluation of genetic of Mycobacterium tuberculosis combined with the use of bioinformatics tools : input for epidemiology and phylogeny of tuberculosis

Millet, Julie 7 June 2011 (has links)
Ce travail de thèse intitulé «Evaluation de marqueurs génétiques du complexe Mycobacterium tuberculosis combinée à l'utilisation d'outils bioinformatiques: apport en épidémiologie et phylogénie de la tuberculose» a consisté en la sélection et l'évaluation de marqueurs minisatellites dans le cadre d'études épidémiologiques et phylogénétiques du bacille tuberculeux, Une première partie a ainsi porté sur l'épidémie de tuberculose en Guadeloupe, Martinique, et Guyane française ainsi que dans un pays continental à faible incidence de tuberculose, la Suède, Les résultats montrent les disparités existant entre les populations de patients tuberculeux des 3 départements français d'Amérique (DFA) ainsi que les similitudes génotypiques existant entre les bacilles tuberculeux. Par ailleurs le rôle majeur joué par les cas d'importation dans l'épidémie de tuberculose a été montré aussi bien dans les DFA qu'en Suède. Nous nous sommes ensuite intéressés à une utilisation optimale des minisatellites pour une meilleure discrimination de la famille génotypique émergeante « Beijing» circulant au Japon (Osaka, Kobe et Okinawa), ainsi qu'en Russie. Nous avons constaté le faible pouvoir discriminant du format classique 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) et proposons plusieurs nouvelles stratégies de typage basées plusieurs marqueurs minisatellites incluant certains locus hypervariables. Enfin, dans un troisième volet, nous avons étudié la diversité génétique des bacilles tuberculeux circulant actuellement dans la Caraïbe. laquelle semble refléter le passé historique très particulier de cette zone géographique au croisement d'une multitude de peuplements. This thesis entitled "Evaluation of genetic markers of Mycobacterium tuberculosis combined with the use of bioinformatics tools: input for epidemiology and phylogeny of tuberculosis" deals with the selection and evaluation of minisatellite markers in the context of epidemiological and phylogenetic studies of the tubercle bacillus M. tuberculosis. The first part of the present work has focused on the epidemic of tuberculosis in Guadeloupe, Martinique and French Guiana as well as in a low incidence continental country, i.e Sweden. The results show differences between populations of TB patients in the three French Departments of America and similarities between the genotypes of the circulating tubercle bacilli Moreover, results highlight the important role played by imported cases for TB epidemic the three French departments of America and Sweden. ln a second part, minisatellite markers have been evaluated for a better discrimination of strains of the emerging genotype "Beijing" circulating in Japan (Osaka, Kobe and Okinawa), and Russia. A low discriminatory power of classical format 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) was observed and new combinations of minisatellites have also been proposed including hypervariable locus. Finally, the genetic diversity of tubercle bacilli circulating in the Caribbean was investigated which currently seem to reflect historical past of this very special region at the intersection of a multitude of cultures and peoples.

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