published_or_final_version / abstract / Pathology / Master / Master of Philosophy

published_or_final_version / Biochemistry / Master / Master of Philosophy

published_or_final_version / Biochemistry / Master / Master of Philosophy

M.Sc. / Tuberculosis, of which the causative agent is Mycobacterium tuberculosis, presents itself as a serious health problem globally, especially in Africa. Susceptibility to this infectious disease is influenced by the virulence of the strain of mycobacteria, environmental factors, and genetic variation within the host. The Vitamin D Receptor gene or VDR has been identified as a candidate gene for TB susceptibility. This gene codes for the VDR protein that mediates the biological actions of the active form of vitamin D. Vitamin D has been shown to impair growth of Mycobacterium tuberculosis in human monocytes and macrophages. Vitamin D also provides a link between Toll-like receptor activation and the antibacterial responses of innate immunity in its production of cathelicidin. The VDR protein is a transcription factor that mediates the effects of the active form of vitamin D. Vitamin D has an immunomodulatory role and variations in the VDR gene may result in variations in the functioning of the VDR protein, and hence variations in response to infection. The VDR gene includes the largely non-coding 5’ regulatory region exons 1a-1f and the coding exons 2-9. As a result of increased awareness of the heritability of gene expression and reports of disease associations with VDR promoter region variants, the focus of the research described in this dissertation was the regulatory region of the VDR gene. Polymorphisms that occur within the regulatory region were viii investigated, as were the effects these polymorphisms may have on gene expression, influencing host susceptibility to tuberculosis, with an emphasis on African populations. VDR polymorphisms have been shown to be involved in susceptibility to tuberculosis, particularly the FokI SNP in exon 2, BsmI and ApaI in intron 8 and the synonomous TaqI in exon 9. However, results have been inconsistent. SNPs shown to be associated with TB may serve as markers of truly functional SNP with which they are in linkage disequilibrium (LD). The majority of these association studies involve single nucleotide polymorphisms (SNPs) found in the introns or are silent mutations in the coding exons. Variations in the 5’ regulatory region have been shown to affect gene expression, in particular if they influence the binding sites of transcription factors.

Orientador: Humberto Tonhati / Coorientador: Robson Carlos Antunes / Banca: João Ademir de Oliveira / Banca: Nedênia Bonvinos Staluzza / Banca: Leonardo Augusto Fonseca Pascoal / Banca: Ana Carolina Portella Silveira / Resumo: Os genes MC4R, FABP3, DGAT1 e LEPR são de grande importância no estudo das características reprodutivas de suínos, uma vez que, estão relacionados com ingestão alimentar, taxa de crescimento, redução da gordura subcutânea e lactação. Neste sentido, objetivou-se identificar geneticamente polimorfismos do tipo SNP nos genes MC4R (SNPg.1578C>T), FABP3 (SNPg.-240T>C), DGAT1 (SNPg.9422C>T) e LEPR (SNPg.5396A>G; SNPg.5395T>A) em suínos da raça Piau e em duas linhagens maternas comerciais industriais de suínos europeus e chineses. Para isso, foi extraído DNA a partir de sangue periférico de um grupo de 304 suínos. Mediante ARMS-PCR Multiplex, foram amplificados fragmentos específicos que, posteriormente, foram genotipados em sequenciador automático para a realização da eletroforese com corantes fluorescentes. Foram encontrados SNP no gene MC4R (SNPg.1578C>T) e FABP3 (SNPg.-240T>C) para os três grupos genéticos analisados com as três variações genotípicas (CC, TT, CT e TT, TC, CC, respectivamente). O SNP (SNPg.9422C>T) do gene DGAT1 apresentou as três variações genotípicas no grupo genético de suínos europeus (CC, CT e TT). Entretanto, para os grupos genéticos Piau e europeus com raças chinesas apresentaram apenas as duas variações genotípicas de homozigotos (CC e TT). Para o gene LEPR (SNPg.5396A>G; SNPg.5395T>A) os grupos genéticos europeus com raças chinesas e Piau apresentaram os genótipos GG, AA e o grupo genético com raças europeias apresentou as duas variações genotípicas de homozigoto (GG e AA) e apenas um animal apresentou o genótipo heterozigoto (AG e TA). Os polimorfismos dos genes FABP3 (SNPg.-240T>C), DGAT1 (SNPg.9422C>T) apresentaram frequências genotípicas altas para os alelos C em relação aos alelos T e no gene MC4R (SNPg.1578C>T) apresentou menor frequência. Para os polimorfismos do gene LEPR (SNPg.5396A>G e SNPg.5395T>A) apresentou-se fixado nas populações estudadas... / Abstract: The MC4R, FABP3, DGAT1 and LEPR genes are great importance in the study of traits of swine breeding, since they are related to feed intake, growth rate, reduction of subcutaneous fat and lactation. The aim of this study was to identify SNP in MC4R(SNPg.1578C> T), FABP3 (SNPg.-240T> C), DGAT1 (SNPg.9422C> T) and LEPR (SNPg.5396A> G; SNPg.5395T> A) genes in pigs of Piau breed and two commercial industrial maternal lineages of European and Chinese pigs. For this, DNA was extracted from peripheral blood of 304 pigs. By ARMS-PCR Multiplex, specific fragments were amplified and genotyped in automated sequencer to perform electrophoresis marked with fluorescent dyes. SNP were identified in the MC4R (SNPg.1578C>T) and FABP3 (SNPg.-240T> C) genes the three genotypic variations (CC, TT, CT and TT, TC, CC, respectively) were identified in all genetic groups analyzed. The SNP (SNPg.9422C> T) of DGAT1 gene presented the three genotypic variations (CC, CT and TT) in the European genetic group. However, for the Piau and Europeans with Chinese genetic groups showed only the two homozygous genotypic variations (CC and TT). For LEPR gene (SNPg.5396A>G; SNPg.5395T>A), the European genetic group with Chinese and Piau breeds showed the GG, AA genotypes and the European breeds genetic group showed two genotyps, homozygous variations (GG, AA) and only one heterozygous animal (AG, TA). Polymorphisms of FABP3 (SNPg.-240T>C) and DGAT1 (SNPg.9422C>T) genes showed high genotypic frequency for the C allele when compared to T allele and the MC4R gene (SNPg.1578C>T) showed less frequently. For polymorphisms in the LEPR gene (SNPg.5396A>G; SNPg.5395T>A) had set up in the populations studied, showing low variability within the population. All polymorphisms evaluated by analysis of variance were associated (P <0.05) with the reproductive traits and only the DGAT1 gene was associated (P <0.05) with the production for average weight at weaning and the total litter ... / Doutor

Orientador: Rogério Abdallah Curi / Coorientador: Luciana Correia de Almeida Regitano / Banca: Julio Cesar de Carvalho Balieiro / Banca: Guilherme Costa Venturini / Banca: Fernando Sebastian Baldi Rey / Banca: Guilherme de Camargo Ferraz / Resumo: Dentre os equinos selecionados para velocidade, a linhagem de corrida da raça Quarto de Milha se destaca pelo alto desempenho em provas de curtas distâncias, sendo considerados os mais velozes do mundo. Apesar de, no Brasil, o efetivo de animais ser relativamente menor na linhagem de corrida do que nas demais, sua importância econômica é substancial. Tendo em vista o interesse econômico e científico relacionado a esta característica atlética, poucos esforços têm sido realizados para a maior compreensão de seus mecanismos genéticos e fisiológicos. Este trabalho teve como objetivos: 1) realizar a imputação de genótipos em duas vias entre indivíduos de uma amostra populacional relativamente pequena de cavalos de corrida da raça Quarto de Milha genotipados com painéis de 54k ou de 65k, bem como avaliar a acurácia de imputação por meio de simulações; 2) realizar estudo de associação ampla do genoma (GWAS) em cavalos da linhagem de corrida da raça Quarto de Milha por meio da utilização de chips equinos de genotipagem de SNPs, visando a prospecção de regiões cromossômicas, genes e polimorfismos relacionados ao desempenho; 3) analisar exomas de equinos de corrida da raça Quarto de Milha contrastantes para Índice de Velocidade máximo (IV max) em regiões previamente associadas à característica por meio de GWAS, visando a prospecção de polimorfismos gênicos causais, ligados ou em forte desequilíbrio de ligação com o desempenho em corridas. A imputação foi realizada ut... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. Although in Brazil the effective number of animals in the racing line is relatively smaller compared to the other lines, its economic importance is substantial. Despite economic and scientific interest in this athletic trait, few efforts have been made to better understand the genetic and physiological mechanisms underlying this trait. The objectives of this study were: 1) to perform two-step genotype imputation between individuals in a relatively small population sample of racing Quarter Horses genotyped with the 54k or 65k panel, and to evaluate the accuracy of imputation through simulations; 2) to perform genome-wide association studies (GWAS) in Quarter Horses of the racing line using equine SNP genotyping chips for prospecting chromosome regions, genes and polymorphisms related to performance; 3) analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypes were imputed using 116 horses genotyped with the 54k SNP array and 233 animals genotyped with the 65k array. For the simulations, random samples were chosen to compose the imputed and reference populations in ... (Complete abstract click electronic access below) / Doutor

Briefly, some findings in my research are as follows: (1) The genetic variants of the CA repeats in IGF1 promoter 1 can affect the activity of promoter 1, and the CA repeat showed a suppressive effect on the activity of the promoter 1 of IGF1 gene. EMSA results have shown that the CA repeats could bind to certain nuclear protein. (2) The SNPs T/C (rs5742612) and T/A (rs2288377) can also affect the activity of the promoter 1 in IGF1 gene, and the activity of C-A haplotype is significantly higher than that of T-T haplotype. EMSA results have shown that the SNP T/A (rs2288377) could bind to certain nuclear protein. (3) I developed the new dual reporter assay method to investigate the transactivation interaction between the SNP T/G (rs2071430) and C/A (rs17000900) in the MxA promorer. This new method can not only improve the detection limit for small difference between haplotypes, but also calculate the model of transactivation effect between these two SNPs. The results were better than those of traditional method, and it gave a clear-cut demonstration of the effect of interaction between these two SNPs on the activity of MxA promoter. / In addition, in the IGF1 study, the core promoter region of promoter 2 was identified through 5' deletion mutagenesis methods. Moreover, a cell-type specific mechanism of bidirectional activation of promoter was found. / Recently, more and more studies focus on gene function with the completion of the Human Genome Project. It is well known that polymorphism of human genome sequence is a common phenomenon in the human population. Specially, a lot of genetic polymorphisms, including single nucleotide polymorphisms (SNPs) and microsatellites, have been reported in the regulatory region of many genes. However, the effects of most of these genetic polymorphisms on gene expression are still unknown. The polymorphisms in the promoter can play an important role in the gene regulation. For example, some SNPs located in the transcription factor binding site (TFBS) can affect gene transcription. So, it is very necessary to directly study the effect of genetic variants on promoter transactivation activities. In this study, we studied the effect of genetic polymorphisms on gene expression through reporter gene assay, electrophoretic mobility shift assay (EMSA), and so on. And the candidate genes include insulin-like growth factor 1 (IGF1) and myxovirus resistence 1 (MxA). Some SNPs and microsatellites have been reported in the promoters of these genes. In our previous researches, we focused on the study of the association between these polymorphisms and some diseases, and it was found that a few SNPs significantly associated with relevant diseases. Based on the previous results, in my project, I developed new functional assays and also improved existing methods to analyse the functional effect of these genetic variants of promoters on transactivation activities. / by Huang, Wei. / "March 2008." / Adviser: Nelson Leung Sang Tang. / Source: Dissertation Abstracts International, Volume: 70-03, Section: B, page: 1483. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (p. 139-145). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Much of modern population genetics revolves around neutral genetic differences among individuals, populations, and species. In this dissertation, I study how sex-specific life history traits affects neutral diversity levels within populations (polymorphism) and between species (divergence) on autosomes and sex chromosomes. In chapter 1, I consider the effects of sex specific life histories, and particularly generation times, on substitution rates along the great ape phylogeny. Using a model that approximates features of the mutational process in most mammals, and fitting the model on data from pedigree-studies in humans, I predict the effects of life history traits on specific great ape lineages. As I show, my model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among great ape lineages. The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant apes, given sex-specific life histories. In so doing, it largely bridges the gap reported traditional fossil-based estimates of mutation rates, and recent pedigree-based estimates. In chapter 2, I consider the effects of sex- and age- dependent mortalities, fecundities, reproductive variances and mutation rates on polymorphism levels in humans. Using a coalescence framework, I provide closed formulas for the expected polymorphism rate, accounting for life history effects. These formulas generalize and simplify previous models. Applying the model to humans, my results suggest that the effects of life history – and of sex differences in generation times in particular – attenuate how changes in historical population sizes affect X to autosome polymorphism ratios. Applying these results to observations across human populations, I find that life history effects and demographic histories can largely explain the reduction in X to autosome polymorphism ratios outside Africa. More generally, my work elucidates the major role of sex-specific life history traits – and male and female generation times in particular – in shaping patterns of neutral genetic diversity within and between species.

The Major Histocompatibility Complex class II B (MHC II B) gene encodes a protein that is part of the adaptive immune system and critical for the non-self recognition ability of immune cells. This gene has been characterized in the Bald Eagle, ten unique alleles were found in two subpopulations at the geographic extremes of the range margins. Geographic genetic variation is suggested by the presence of population specific alleles. The results showed considerable divergence of groups of Bald Eagle alleles when compared to alleles from other birds of prey. Particular codons within the exon II show signs of balancing selection driving the evolution of the MHC II B. Transcription data showed statistically significant differential expression of alleles. This can be interpreted as meaning a particular locus is being preferentially expressed in blood. The analysis of the polymorphism of this adaptive marker may aid managers of wildlife during this age of global climate change and the biodiversity crisis. / by Andrew Smith. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Made available in DSpace on 2014-06-11T19:31:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-06-15Bitstream added on 2014-06-13T19:40:53Z : No. of bitstreams: 1 balthazar_ea_dr_arafcf.pdf: 644870 bytes, checksum: ec0e6d8394bc755610e1c99cbf4f1415 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Universidade Estadual Paulista (UNESP) / A interação entre gene e meio ambiente tem sido apontada como responsável pelo aumento das doenças crônicas metabólicas, cujos fatores de risco vêm se manifestando nas populações humanas, em idades cada vez mais precoces. Objetivo: Analisar os efeitos dos polimorfismos -514C/T no gene da LIPC e CT84 no gene da ApoA1, bem como da mutação missense no gene da ApoE sobre os fatores de risco para doenças crônicas, numa amostra de adolescentes, de um município do interior do Estado de São Paulo, Brasil. Metodologia: Foi realizado um estudo transversal com 214 adolescentes de ambos os sexos com idade mínima de 10 anos. Na coleta de dados foram incluídos: questionário de freqüência alimentar e de atividades físicas especifico para adolescentes, antropometria, aferição da pressão arterial, dosagens bioquímicas (insulina, glicose, colesterol total e frações, triglicerídeos e Apoa1) e genotipagem por PCR-real time dos genes selecionados. Resultados: Os adolescentes portadores do alelo raro para o polimorfismo -514CT do gene LIPC apresentaram maior prevalência de síndrome metabólica. Em relação ao polimorfismo TC84 da ApoA1, os adolescentes com o genótipo TT apresentaram maior prevalência de hipertrigliceridemia e se encontraram mal adaptados à prática de atividade física e consumo de carboidrato. Analisando a mutação missense do gene da ApoE foi verificado que os adolescentes portadores do alelo ApoE4 apresentaram maior prevalência de fatores de risco para doenças crônicas e eram beneficiados pelo consumo de gordura em substituições aos carboidratos. Conclusão: Recomendações dietéticas e prática de atividades físicas direcionadas ao perfil genético do adolescente poderão prevenir o desenvolvimento de fatores de risco metabólico e o aparecimento de doenças crônicas na vida adulta / The interactions between genes and environment has been identified as responsible for the increase of chronic metabolic diseases, in which risk factors are positioning themselves in human populations at earlier years of age. Objective: To analyze the effects of the polymorphisms -514CT LIPC gene and CT84 ApoA1 gene, as well as, missense mutation ApoE gene on the outcome of risk factors for chronic diseases in a sample of adolescents from a city in the state of Sao Paulo, Brazil. Methods: It was conducted a cross-sectional study in 214 adolescents of both sexes with a minimum of 10 years of age. The data collection included: food frequency and physical activity questionnaire, anthropometry, blood pressure, biochemical measurements (insulin, glucose, Total cholesterol and fractions, triglycerides e Apoa1) and genotyping of the selected genes by PCR-real time. Results: The adolescents with the rare allele for the -514CT LIPC polymorphism had higher prevalence of metabolic syndrome. Regarding TC84 ApoA1 polymorphism, the adolescent’s carriers of the TT genotype had higher prevalence of hypertriglyceridemia and found themselves ill-suited to the practice of physical activity and carbohydrate consumption. Analyzing the missense mutation of the ApoE gene it was found that adolescents with the ApoE4 allele had a higher prevalence of risk factors for chronic diseases and were benefited by the consumption of fat to carbohydrate substitutions. Conclusion: A dietary and physical activity treatment targeted to the genetic profile of the adolescent may prevent the development of metabolic risk factors and the onset of chronic diseases in adulthood