Orientador: Fernando Sebastián Baldi Rey / Coorientador: Angélica Simone Cravo Pereira / Coorientador: Gregório Miguel Ferreira de Camargo / Banca: Ana Fabrícia Braga Magahães / Banca: Rodrigo Pelicioni Savegnago / Banca: Raysildo Barbosa Lobo / Banca: Aline Silva Mello Cesar / Resumo: Objetivou-se identificar regiões no genôma de bovinos da raça Nelore que apresentam variações no número de cópias (CNV) e, associar estes CNV com o perfil de ácidos graxos da carne. Além disso, objetivou-se realizar associação genica ampla utilizando os método de single step (GWASss) a fim de detectar regiões genômicas associadas aos ácidos graxos dos grupos saturados, mono e poliinsaturados, assim como os omegas 3, 6 e sua relação. O estudo de caracterização e distribuição dos CNVs ao longo do genoma de bovinos Nelore, foi realizado através do software PennCNV utizando dados genotípicos de 3.794 aniamais, resultando em 399.361 CNVs identificados. Após controle de qualidade, 2.902 foram mantidos nas analises, resultando em 195.873 CNVs, com tamanho medio de 54,744 pb, maximo de 8.7 Mb e minimo 3 kb. As regiões de CNV foram geradas pela sobreposição dos CNVs através do software CNVRuler. Os cromossomos que mostraram maior incidencia de CNVR foram BTA19 (24,26%), BTA23 (18,68%) e BTA25 (18,05%). Ja os que mostraram menor incidencia foram BTA29 (1,63%), BTA13 (9,72%) and BTA8 (9,72%). As 9.805 regiões da CNV estimadas no presente estudo cobrem aproximadamente 13.05% do genoma bovino e sobrepõem-se a 5.495 genes conhecidos que envolvem processos biológicos que poderiam estar envolvidos na adaptação ambiental da subespécie a áreas tropicais. O estudo de GWASss identificou 115 janelas que explicaram mais de 1% da variação genética aditiva para os 22 ácidos graxos estudados. A ident... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The objective of this study was to identify genomic regions of Nellore cattle that present variations in the number of copies (CNV) and to associate these CNV with the fatty acid profile of the meat. In addition, the objective of this study was to carry out a genome-wid association using the single step method (GWASss) to detect genomic regions associated with saturated, mono and polyunsaturated fatty acids, as well as omega 3, 6 and their relationship. The study of the characterization and distribution of CNVs along the Nellore genome was performed by PennCNV software using genotypic data of 3,794 animals, resulting in 399,361 CNVs identified. After quality control, 2,902 were maintained in the analyzes, resulting in 195,873 CNVs, with an average size of 54,744 pb, maximum of 8.7 Mb and minimum 3 kb. The CNV regions were generated by the overlap of the CNVs by CNVRuler software. The chromosomes that showed the highest incidence of CNVR were BTA19 (24.26%), BTA23 (18.68%) and BTA25 (18.05%). Those with the lowest incidence were BTA29 (1.63%), BTA13 (9.72%) and BTA8 (9.72%). The 9,805 CNV regions estimated in the present study covered approximately 13.05% of the bovine genome and overlaped 5,495 genes known to envolve in biological processes that could be involved in the environmental adaptation of the subspecies to tropical areas. The GWASss study showed 115 windows that explained more than 1% of the additive genetic variation for the 22 fatty acids studied. The identification of these regions and their genes, such as ELOVL5, ESRRG, PCYT1A and the ABC group genes (ABCA5, ABCA6 and ABCA10) are genes directly and indirectly related to lipid metabolism. The GWAS between AG phenotypes and CNVs resulted in a total of 186 CNVRs that were significant for the saturated (43), monosaturated (42), poly... (Complete abstract click electronic access below) / Doutor

Orientador: Roberto Carvalheiro / Coorientador: Marina Rufino Salinas Fortes / Coorientador: Lucia Galvão de Albuquerque / Banca: Ricardo Vieira Ventura / Banca: Yuri Tani Utsunomiya / Banca: Henrique Nunes de Oliveira / Banca: Gerardo Alves Fernandes Júnior / Resumo: O poder estatístico de um único estudo de associação genômica ampla (GWAS) para detectar loci de características quantitativas (QTL) é esperado ser menor do que combinando resultados de GWAS independentes de múltiplas raças, isto é, de diferentes raças, especialmente para características complexas, como as de puberdade. Utilizar populações independentes e métodos para detectar novas regiões genômicas e validar regiões previamente conhecidas como associadas com a característica de interesse em populações independentes é uma estratégia viável para identificar QTLs mais acuradamente. O objetivo deste estudo foi detectar regiões genômicas controlando características de precocidade sexual em três raças de gado de corte tropical (Nelore, Brahman e Composto Tropical - CT), utilizando duas estratégias, meta-analise utilizando diferentes raças e validação cruzada de QTL entre raças. No estudo de meta-análise as características incluídas foram idade ao primeiro parto (IPP), prenhez precoce (PP), e circunferência escrotal (CEN) medida aos 18 meses de idade no Nelore, e a idade ao surgimento do primeiro corpo lúteo (IPCL), intervalo do primeiro anestro pós-parto (IPAPP) e circunferência escrotal medida aos 18 meses de idade (CE18B) para o Brahman. A meta-análise foi realizada utilizando um método multi-característica. Um total de 108 polimorfismos de nucleotídeo único (SNP) significativos a um P-valor empírico de 1.39 × 10−5 (FDR < 0.05), foram encontrados neste estudo. Tais SNP signific... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The statistical power of an individual genome-wide association study (GWAS) to detect quantitative trait loci (QTL) is expected to be lower than combining independent GWAS results from multi-breed, i.e., from different breeds, especially for complex traits, as puberty traits. Using independent populations and methods to detect new genomic regions and validate in independent populations known regions associated with the trait of interest is a feasible strategy to identify QTLs more accurately. The aim with this study was to detect genomic regions controlling sexual precocity traits across three tropical beef cattle breeds (Nellore, Brahman and Tropical Composite - TC) by using two approaches, meta-analysis using different breeds and QTL validation across different breeds. In the meta-analysis study the traits included were age at first calving (AFC), early pregnancy (EP), and scrotal circumference (SCN) measured at 18 months of age for Nellore, and age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference measured at 18 months of age (SC18B) for Brahman cattle. The meta-analysis was performed using a multi-trait method. A total of 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10−5 (FDR < 0.05), were found in this study. Those significant SNP were distributed over 19 out of 29 autosomes, and the major of them were located on BTA14. In the meta-analysis study we identified five association regions harbouring the majority of the significant SNP (76%), namely: BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. In the acr... (Complete abstract click electronic access below) / Doutor

Orientador: Humberto Tonhati / Coorientador: Gregório Miguel Ferreira de Camargo / Coorientador: Naudin Alejandro Hurtado Lugo / Banca: Lenira El Faro Zadra / Banca: Henrique Nunes de Oliveira / Resumo: Considerando a importância das doenças que afetam o desempenho produtivo dos animais na indústria leiteira em todo o mundo é necessário implementar ferramentas moleculares que auxiliem na identificação e controle destas doenças. Quando ocorre alguma infecção em um organismo superior, existe aumento do número de células de defesa e o sistema imune inato proporciona uma linha de defesa contra os patógenos. Os "Toll Like Receptors" (TLR) são proteínas da membrana que desempenham um papel chave na imunidade, reconhecendo patógenos e, posteriormente, ativando as respostas. O presente estudo foi realizado para identificar SNPs no gene TLR4 bubalino e analisar suas associações com características de importância produtiva, incluindo a contagem de células somáticas (CCS). Foram utilizadas amostras de DNA de 130 búfalas da raça Murrah. A região codificante do gene TLR4 foi amplificada através de reações de PCR e posteriormente sequenciada. Os polimorfismos encontrados tiveram suas frequências alélicas e genotípicas calculadas e verificadas quanto ao equilíbrio de Hardy-Weinberg, além de serem utilizados para os estudos de associação. Foram identificados 13 polimorfismos do tipo SNP para as regiões sequenciadas do gene TLR4, sendo que a maioria encontra-se em região codificante. Encontrou-se associação significativa, com porcentagem de gordura dos Snps g514>C/T (P=0,0040) e g536>A/T (P=0,0035). As associações para CCS demostrou-se altamente significantes (p=<0,001) para todos os Snps (g... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Molecular markers might be developed to investigate genetic variants associated to the disease and assist selection process in order to identify resistant animals. When the mammary gland is infected, there is an increase in the defense cells, also called somatic cells. It is a defense line of the immune system against pathogens. The "tool like receptors" TLR are membrane proteins that have an important role in the immunity, recognizing pathogens and activating adequate responses. The present study aimed to investigate the association of TLR4 gene SNPs with productive characteristics and SCC in buffaloes. The DNA was extracted from hair follicules of 130 Murrah buffaloes. The fragments were amplified by Polymerase Chain Reaction (PCR) and sequenced. Thirteen SNPs were found. Allelic and genotypic frequencies were calculated as well as the adhesion to Hardy-Weinberg equilibrium and the linkage disequilibrium (r2) and the association to the characteristic. For SCC was tested methodology linear generalized mixed model, assuming Poisson distribution. Bonferroni correction was applied for the number of SNPs. Thirteen SNP polymorphisms were identified in coding region of the TLR4 (g322>G/A, g514>C/T, g536>A/T, g8338>A/C, g8341>A/G, g8342>T/G, g8343>G/A, g8345>A/G, g8413>A/G, g8428>G/A, g8438>A/C, g8578>G/T, g8582>A/C). The SNPs g514>C/T and g536>A/T had significant association whit %G. All the SNPs were associated (p=0.001) whit the CCS. Other authors also reported the association of TRL4 SNPs to the trait. The results show that the SNPs of TLR4 gene can be used as molecular markers in buffaloes / Mestre

Orientador: José Fernando Garcia / Banca: Flávia Lombardi Lopes / Banca: Maricy Apparício Ferreira / Banca: Wagner Luis Ferreira / Banca: Silvana de Cássia Paulan / Resumo: Variante funcional (functional variant - FV) é um polimorfismo da sequência de DNA que possui efeitos sobre a função ou mesmo sobre o nível de expressão de um ou mais genes. Por apresentarem alta probabilidade de interferência em fenótipos celulares, teciduais ou mesmo sistêmicos, as FVs são alvos frequentes de pressão de seleção negativa ou positiva em uma população. Algumas FVs podem, inclusive, causar perda parcial ou total da função gênica, caso no qual estas recebem a denominação de loss-of-function variant (LoFV). Os cães domésticos (Canis lupus familiaris) possuem baixa variabilidade genética decorrente da intensa seleção artificial feita pelo homem para fenótipos extremos de características morfológicas e comportamentais. Os altos níveis de endogamia nas populações caninas favorecem a intensificação da ação da deriva genética e, por consequência, o aumento da prevalência de FVs e LoFVs que seriam mantidas em baixa frequência se estas populações apresentassem maior variabilidade genética. Assim, o cão doméstico é um modelo valioso para estudos de processos fisiológicos e de doenças genéticas humanas. O recente surgimento de ferramentas para análise genômica têm auxiliado na identificação de FVs e LoFVs de interesse zootécnico e biomédico em cães. Estas variantes podem ser mapeadas através de duas estratégias distintas, porém complementares, de varredura genômica. A primeira, denominada de estudo de associação genômica ampla (Genome-Wide Association Study - GWAS), consi... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Functional variant (FV) is a DNA sequence polymorphism that has effects on the function or even the level of expression of one or more genes. FVs are frequent targets of negative or positive selection in a population due to its high probability of interfering in cell, tissue or system phenotypes. Some FVs may even cause partial or total loss of gene function, in which case they are called loss-of-function variants (LoFVs). Domestic dogs (Canis lupus familiaris) have low genetic variability resulting from intense human-driven artificial selection for extreme phenotypes of morphological and behavioral traits. High levels of inbreeding in canine populations favor the intensification of genetic drift and, consequently, an increase in the prevalence of FVs and LoFVs that would be maintained at low frequencies if these populations presented higher genetic variability. Thus, the domestic dog is a valuable model for studying physiological processes and human genetic diseases. The recent emergence of tools for genomic analysis has assisted in the identification of FVs and LoFVs of zootechnical and biomedical interest in dogs. These variants can be mapped through two distinct but complementary genomic scanning strategies. The first, known as Genome-Wide Association Study (GWAS), involves testing of phenotype-genotype associations. The second consists in the search for allelic combinations, called haplotypes, that occur in high frequency, but that present deficiency of homozygosity. In ... (Complete abstract click electronic access below) / Doutor

Adiponectina é um hormônio produzido e secretado em abundância pelo tecido adiposo, que regula o metabolismo melhorando a sensibilidade à insulina pela sua ação hepática e muscular. Diferentemente dos outros hormônios do tecido adiposo, seus níveis séricos diminuem à medida que aumenta a adiposidade e são inversamente correlacionados com a obesidade, resistência à insulina e síndrome metabólica. Variações no gene da adiponectina foram associadas a níveis de adiponectina, resistência à insulina e risco de diabetes. O objetivo deste estudo foi avaliar os níveis de adiponectina e as variantes no gene da adiponectina em crianças e adolescentes obesos e sem obesidade e correlacionar os achados às características antropométricas e metabólicas. Níveis de adiponectina sérica foram mais baixos em obesos e em indivíduos púberes. Em não obesos, os níveis de adiponectina a correlacionaram-se negativamente com a adiposidade, entretanto nos obesos, a resistência à insulina e o desenvolvimento puberal foram os fatores de diminuição dos níveis de adiponectina. Independentemente da adiposidade, da resistência à insulina e da puberdade, menores níveis de adiponectina (abaixo de 10g/mL) correlacionaram-se com maior risco de hipertrigliceridemia, baixo HDLC e síndrome metabólica. Na análise do gene da adiponectina foram identificados os SNPs -11391G>A (rs17300539), -11377C>G (rs822387) na região promotora, +45T>G (rs22411766) no exon 2, +349A>G (rs6773957) no intron 2, Y111H (rs17366743) e a mutação G90S no exon 3. O SNP-11391G>A estava em desequilíbrio de ligação de Hardy-Weinberg. As variantes Y111H e G90S estavam em forte desequilíbrio de ligação com SNP-11377C>G e G90S com SNP+45T>G. Foi observada associação do alelo G do SNP-11377 a maior adiposidade central e menores níveis séricos de glicose. Após construção dos haplótipos com os SNPs -11377C>G, +45T>G e +349A>G observou-se que a presença do alelo G do SNP-11377T>G associou-se a maior obesidade (GTA vs CTA) , enquanto que a presença dos alelos recessivos dos outros SNPs diminuiu essa associação (GTA vs GGG). Na presença do alelo G do SNP+349A>G (CTG vs CTA), foi observada maior freqüência de indivíduos hipertensos, entretanto a associação dos alelos recessivos dos SNPs -11377C>G e +45T>G (CTG vs GGG) diminuiu a freqüência de hipertensão. Os resultados do presente estudo demonstram que níveis de adiponectina diferem em crianças e adolescentes dependendo do grau de adiposidade e puberdade e que níveis mais baixos estão associados às alterações metabólicas de maior risco cardiovascular na obesidade. Variantes no gene da adiponectina podem estar em desequilíbrio de ligação com um SNP funcional ou um pool gênico responsável por maior risco de obesidade e desenvolvimento de alterações metabólicas relacionadas ao aumento da adiposidade / Adiponectin, present in high concentrations in blood circulation is produced in adipocytes. Adiponectin regulates insulin sensibility acting in liver and muscle. Plasma adiponectin decreases as adiposity increases and are inversely related to insulin resistance and metabolic syndrome. Variants in the adiponectin encoding gene have been associated with adiponectin levels, insulin resistance and type 2 diabetes. The aim of this study was to evaluate adiponectin levels, identify variants in the adiponectin gene and determine the relationship between adiponectin levels, genetic variances and anthropometric and metabolic features in obese and non-obese children and adolescents. We found lower adiponectin levels in obese and pubertal individuals. Adiponectin was inversely correlated to adiposity in non-obese. Instead, in obese youngsters, adiponectin levels were negatively associated to insulin resistance and pubertal state. Independent of adiposity, insulin resistance and pubertal stage, lower adiponectin levels (under 10g/mL) were related to lower HDLC, higher triglycerides and higher risk of having metabolic syndrome. We have identified 6 variants in adiponectin gene: SNPs -11391G>A (rs17300539), -11377C>G (rs822387) in promoter region, SNP+45T>G (rs22411766) in exon 2, SNP+349A>G (rs6773957) in intron 2 and SNP Y111H (rs17366743) and G90S mutation in exon 3. We found strong linkage disequilibrium between variant Y111H and -11377C>G SNP and between G90S mutation and -11377C>G and +45T>G SNPs. We detected an association between -11377C>G G allele and higher central adiposity and lower glucose levels. Haplotypes were constructed using the SNPs -11377C>G, +45T>G and +349A>G, and the results showed an association between -11377SNP G allele presence and higher adiposity (GTA vs CTA), whereas the presence of the recessive alleles of SNPs +45T>G and +349A>G was associated to a lower adiposity (GTA vs GGG). Hypertension was more frequent in the presence of +349A>G G allele (CTG vs CTA), whereas the presence of the recessive alleles of SNPs -11377 and +45T>G (CTG vs GGG) was not associated to hypertension. This study suggests that adiponectin levels, in Brazilian children and adolescents, depends on degree of adiposity and pubertal stage and that lower adiponectin concentrations are associated to altered metabolic features and higher cardiovascular risk. Variants in the adiponectin encoding gene can be in linkage disequilibrium with susceptibility regions responsible to higher risk of obesity and metabolic related features

Os sais de lítio são utilizados no tratamento dos transtornos do humor há mais de 50 anos. É a principal medicação prescrita para pacientes com diagnóstico de transtorno bipolar (TB), No entanto, aproximadamente 70% dos pacientes não respondem satisfatoriamente, ou seja, são refratários ao tratamento com lítio. Tendo em vista a importância do uso do lítio no tratamento de TB e a influência de fatores genéticos na variabilidade da biodisponibilidade do medicamento e em seus efeitos (95%), é de extrema importância esclarecer o papel da farmacogenética envolvida na resposta ao lítio. O objetivo deste trabalho foi detectar possíveis marcadores genéticos em pacientes com TB para melhor predição da resposta à terapia medicamentosa Para tanto, estudamos os polimorfismos dos genes relacionados ao mecanismo de ação do lítio: glicogênio- sintase quinase 3 - beta (GSK3-Beta), fator neurotrófico derivado do cérebro (BDNF), Receptor neurotrófico de tirosina quinase tipo 2 (NTRK2) e proteína ligada ao elemento de resposta cAMP (CREB) em pacientes bipolares respondedores e refratários ao tratamento com lítio com fenótipo determinado por escalas HDRS e YMRS, e análise dos prontuários, e escala ALDA. Na nossa amostra, os polimorfismos CREB1-1H (G > A), CREB1-7H (C > T), BDNF (rs6265 - G > A) e NTRK2 (rs1387923 - T > C) não apresentaram associação significativa dos genótipos com a resposta à terapia com lítio. Para os resultados obtidos na análise genotípica correspondente ao polimorfismo rs334558 (C > T) do gene GSK3-Beta, verificamos maior incidência do genótipo heterozigoto CT em pacientes respondedores e maior incidência do genótipo polimórfico homozigoto TT em pacientes refratários. Para a metodologia ALDA, não obtivemos diferenças que relacionassem os polimorfismos selecionados a refratariedade ao lítio. Acreditamos que o pequeno número amostral incluídos em nosso estudo pode ter prejudicado a determinação desses polimorfismos na resposta ao lítio / Lithium salts have been used in the treatment of mood disorders for more than 50 years. It is the main medication prescribed for patients diagnosed with bipolar disorder (BD). However, approximately 70% of the patients do not respond satisfactorily, that is, they are refractory to treatment with lithium. Given the importance of using lithium in the treatment of BD and the influence of genetic factors on the variability of the bioavailability of the drug and its effects (95%), it is extremely important to clarify the role of pharmacogenetics involved in the lithium response. The goal of this study was to detect possible genetic markers in BD patients to better predict the response to drug therapy. In order to do so, we studied the polymorphisms of genes related to the mechanism of action of lithium: glycogen synthase kinase 3 - beta (GSK3-Beta), brain-derived neutrophic factor (BDNF) tyrosine kinase type 2 neurotrophic receptor (NTRK2) and cAMP response element-binding protein (CREB) in responders and refractory bipolar patients that used lithium in the treatment. The phenotype was determined by HDRS and YMRS scales, and analysis of charts, and ALDA scale. In our sample, the polymorphisms CREB1-1H (G > A), CREB1-7H (C > T), BDNF (rs6265 - G > A) and NTRK2 (rs1387923 - T > C) had no significant association of genotypes with the response to lithium therapy. For the results obtained in the genotype analysis corresponding to the polymorphism rs334558 (C > T) of the GSK3-Beta gene, we verified a higher incidence of the heterozygous CT genotype in responding patients and a higher incidence of the polymorphic homozygous TT genotype in refractory patients. For the ALDA methodology, we did not obtain differences that related the selected polymorphisms to refractoriness to lithium. We believe that the small sample size included in our study may have impaired the determination of these polymorphisms in lithium response

Orientador: Rogério Abdallah Curi / Coorientador: Guilherme Luis Pereira / Coorientador: Julio Cesar de Carvalho Balieiro / Banca: Laura Leandro da Rocha / Banca: Luis Artur Loyola Chardulo / Resumo: O Mangalarga Marchador é o cavalo de sela brasileiro, possui dois tipos de andamentos característicos, a marcha batida e a marcha picada, que proporcionam maior comodidade ao cavaleiro durante a cavalgada e o trabalho. É principalmente utilizado para trabalho em fazendas de gado de corte e vem se destacando em diferentes modalidades de esportes hípicos. Este estudo teve como objetivo caracterizar, por meio da genotipagem de SNP em larga escala, o desequilíbrio de ligação (LD), calculado por r², de equinos da raça brasileira Mangalarga Marchador criados no Brasil. Também foi investigado o tamanho efetivo (Ne) da população, bem como as suas estruturas e relações. Foram utilizados 240 equinos Mangalarga Marchador, de ambos os sexos, e registrados na associação brasileira de criadores da raça (ABCCMM). O número de SNP informativos foi de 377.308. Análises de componentes principais mostraram que cavalos Mangalarga Marchador de marcha batida e de marcha picada pertencem a uma mesma população, ou seja, estes grupos não segregaram de forma significativa dentro da raça, o que deve ser levado em consideração nos estudos genético-populacionais. O r² genômico calculado foi de 0,096±0,166. O LD decaiu consideravelmente a partir de distâncias superiores a 15 e 20 Kb, apresentando valores inferiores a 0,3 e 0,2, respectivamente. O Ne atual foi de 99 animais. Houve acentuada redução neste parâmetro ao se tomar as estimativas de 16 gerações passadas, em que o Ne estimado foi de 650 animais. E... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The Mangalarga Marchador is the Brazilian saddle horse, has two types of characteristic movements, the batida and the picada gait, that provide greater comfort to the rider during the cavalcade and the work. It is mainly used for work on beef cattle farms and has been emphasizing different modalities of equestrian sports. The objective of this study was to characterize, by means of large scale SNP genotyping, the linkage disequilibrium (LD), calculated by r², of Brazilian Mangalarga Marchador breed horses raised in Brazil. We also investigated the effective size (Ne) of the population, as well as their structures and relationships. A total of 240 Mangalarga Marchador horses, of both sexes, and registered in the Brazilian association of breeders (ABCCMM) were used. The number of informative SNPs was 377,308. Principal component analyzes showed that Mangalarga marchador of the two diferente gaits belong to the same population, that is, these groups did not segregate significantly within the breed, which should be taken into account in the genetic-population studies. The calculated r² genomic was 0.096 ± 0.166. The LD declined considerably from distances greater than 15 and 20 Kb, presenting values lower than 0.3 and 0.2, respectively. The current Ne was 99 animals. There was a marked reduction in this parameter when taking the estimates of 16 generations passed, in which the estimated Ne was 650 animals. These results may be linked to a broad and partially open genetic basis an... (Complete abstract click electronic access below) / Mestre

Ko Kin Ming Jeffery. / Thesis submitted in: July 2005. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 99-111). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / Table of Contents --- p.ix / List of Tables --- p.xiii / List of Figures --- p.xv / List of Abbreviations --- p.xvi / Chapter Chapter 1: --- Introduction --- p.1 / Chapter 1.1 --- Malignant Lymphoma --- p.1 / Chapter 1.2 --- Non-Hodgkin's Lymphoma --- p.1 / Chapter 1.3 --- Diffuse Large B-cell Lymphoma --- p.2 / Chapter 1.3.1 --- General Features of Diffuse Large B-cell Lymphoma --- p.2 / Chapter 1.3.2 --- Morphologic variants of Diffuse Large B-cell Lymphoma --- p.4 / Chapter 1.3.2.1 --- Centroblastic vairant --- p.5 / Chapter 1.3.2.2 --- Immunoblastic variant --- p.5 / Chapter 1.3.2.3 --- Anaplastic variant --- p.6 / Chapter 1.3.3 --- Immunophenotype of Diffuse Large B-cell Lymphoma --- p.6 / Chapter 1.3.3.1 --- Lineage-associated antigens --- p.6 / Chapter 1.3.3.1.1 --- B-cell lineage antigens --- p.6 / Chapter 1.3.3.1.2 --- T-cell lineage antigens --- p.7 / Chapter 1.3.3.2 --- Antigen involved in regulation of cell proliferation and apoptosis --- p.8 / Chapter 1.3.3.2.1 --- Proliferation markers --- p.8 / Chapter 1.3.3.2.2 --- Cell cycle regulators --- p.8 / Chapter 1.3.3.2.3 --- Protein controlling apoptosis --- p.10 / Chapter 1.3.4 --- Subtypes of Diffuse Large B-cell Lymphoma --- p.10 / Chapter 1.3.4.1 --- Classification method of DLBCL subtypes --- p.11 / Chapter 1.3.4.1.1 --- DNA microarray --- p.11 / Chapter 1.3.4.1.2 --- Immunohistochemistry pattern --- p.14 / Chapter 1.3.4.1.2.1 --- CD10 --- p.16 / Chapter 1.3.4.1.2.2 --- Bcl-6 --- p.16 / Chapter 1.3.4.1.2.3 --- CD138 --- p.17 / Chapter 1.3.4.1.2.4 --- MUM1/IRF4 --- p.17 / Chapter 1.3.4.2 --- Prognosis of 、DLBCL subtypes --- p.19 / Chapter 1.4 --- Interleukin 10 --- p.22 / Chapter 1.4.1 --- The IL-10 gene --- p.23 / Chapter 1.4.2 --- IL-10 promoter --- p.23 / Chapter 1.5 --- IL-10 receptor --- p.24 / Chapter 1.6 --- Cellular Signaling Pathways Regulated by IL-10 --- p.25 / Chapter 1.6.1 --- Jak/Stat Pathway --- p.25 / Chapter 1.6.2 --- Inhibition of NF B pathway --- p.26 / Chapter 1.7 --- Function of IL-10 --- p.27 / Chapter 1.7.1 --- Effects of IL-10 on immune cells in vitro --- p.27 / Chapter 1.7.2 --- Effects of IL-10 on B-cells --- p.28 / Chapter 1.8 --- IL-10 and IL-10 receptor in malignant diseases --- p.29 / Chapter 1.8.1 --- Melanoma --- p.29 / Chapter 1.8.2 --- Carcinoma --- p.30 / Chapter 1.8.3 --- Lymphoma --- p.30 / Chapter 1.9 --- Single Nucleotide Polymorphism (SNP) --- p.33 / Chapter 1.9.1 --- SNPs in cancer research --- p.34 / Chapter 1.9.1.1 --- Susceptibility to cancer and SNPs --- p.35 / Chapter 1.9.1.2 --- Outcome and SNPs --- p.35 / Chapter 1.10 --- SNP in the IL-10 promoter --- p.36 / Chapter 1.11 --- IL-10 promoter SNP in DLBCL --- p.37 / Chapter Chapter 2: --- Aims of Study --- p.39 / Chapter Chapter 3: --- Materials and Methods --- p.41 / Chapter 3.1 --- Sample Recruitment --- p.41 / Chapter 3.2 --- DNA preparation for Single Nucleotide Polymorphism (SNP) analysis --- p.41 / Chapter 3.2.1 --- Isolation of Peripheral Blood Mononuclear Cell (PBMC) from buffy coat from blood of normal control group --- p.41 / Chapter 3.2.2 --- Preparation for NHL and DLBCL samples from paraffin-embedded sections for DNA extraction --- p.42 / Chapter 3.2.3 --- DNA extraction for SNP analysis --- p.42 / Chapter 3.3 --- SNP analysis by Restriction Fragment Length Polymorphism (RFLP) --- p.43 / Chapter 3.3.1 --- Amplification of target site by PCR --- p.43 / Chapter 3.3.2 --- SNP analysis --- p.45 / Chapter 3.4 --- Determination of haplotypic frequency --- p.50 / Chapter 3.5 --- Classification of DLBCL by immunohistochemistry --- p.50 / Chapter 3.5.1 --- Staining pattern of CD10 --- p.53 / Chapter 3.5.2 --- Staining pattern of Bcl-6 --- p.54 / Chapter 3.5.3 --- Staining pattern of CD138 --- p.55 / Chapter 3.5.4 --- Staining pattern of MUM1/IRF4 --- p.56 / Chapter 3.6 --- Statistical Analysis --- p.57 / Chapter Chapter 4: --- Results --- p.58 / Chapter 4.1 --- SNPs of IL-10 promoter in normal controls --- p.58 / Chapter 4.1.1 --- Allelic Frequencies and genotype distributions --- p.58 / Chapter 4.1.2 --- Haplotypic Frequencies of normal controls --- p.58 / Chapter 4.2 --- SNP of the IL-10 promoter in non-Hodgkin's lymphomas --- p.59 / Chapter 4.2.1 --- Allelic frequencies and genotype distributions --- p.59 / Chapter 4.2.2 --- Haplolypic frequencies --- p.61 / Chapter 4.4 --- SNPs of the IL-10 promoter in DLBCL --- p.62 / Chapter 4.4.1 --- Allelic frequencies and genotype distributions --- p.62 / Chapter 4.4.2 --- Haplotypic frequencies --- p.64 / Chapter 4.5 --- SNP of the IL-10 promoter in different subtypes of DLBCL --- p.65 / Chapter 4.5.1 --- Classification of DLBCL by immunohistochemistry --- p.65 / Chapter 4.5.2 --- SNP of the IL-10 promoter in Germinal Center DLBCL (GC-DLBCL) --- p.67 / Chapter 4.5.2.1 --- Allelic frequencies and genotype distributions --- p.67 / Chapter 4.5.1.2 --- Haplotypic frequencies --- p.69 / Chapter 4.5.2 --- SNP of the IL-10 promoter in Activated Germinal Center DLBCL (AGC-DLBCL) --- p.70 / Chapter 4.5.2.1 --- Allelic frequencies and genotype distributions --- p.70 / Chapter 4.5.2.2 --- Haplotypic frequencies --- p.72 / Chapter 4.5.3 --- SNP of the IL-10 promoter in Activated non-Germinal Center DLBCL (ANGC-DLBCL) --- p.73 / Chapter 4.5.3.1 --- Allelic frequencies and genotype distributions --- p.73 / Chapter 4.5.3.2 --- Haplotypic frequencies --- p.75 / Chapter 4.5.4 --- SNP of the IL-10 promoter in Unclassified DLBCL (UC-DLBCL). --- p.76 / Chapter 4.5.4.1 --- Allelic frequencies and genotype distributions --- p.76 / Chapter 4.5.4.2 --- Haplotypic frequencies --- p.78 / Chapter 4.6 --- Summary of SNP of the IL-10 promoter in DLBCL subtypes --- p.79 / Chapter 4.7 --- Overall survival analysis --- p.80 / Chapter 4.7.1 --- Clinical data of DLBCL --- p.80 / Chapter 4.7.2 --- Cox Proportional Hazards Regression Analysis in DLBCL --- p.81 / Chapter Chapter 5: --- Discussion --- p.88 / Chapter 5.1 --- SNP for low IL-10 production in Hong Kong population --- p.88 / Chapter 5.2 --- NHL in low IL-10 production population --- p.90 / Chapter 5.2.1 --- The relationship between IL-10 and NHL --- p.90 / Chapter 5.2.2 --- Allelic frequencies and haplotype of the IL-10 promoter in NHL --- p.90 / Chapter 5.3 --- Classification of DLBCL --- p.91 / Chapter 5.3.1 --- Current prognostic analysis --- p.91 / Chapter 5.3.2 --- DLBCL subtypes distribution in Hong Kong is different from Caucasian --- p.92 / Chapter 5.4 --- IL-10 and DLBCL --- p.93 / Chapter 5.5 --- SNP of IL-10 promoter in DLBCL subtypes --- p.94 / Chapter 5.5.1 --- Allelic frequencies and haplotype of DLBCL subtypes --- p.94 / Chapter 5.5.2 --- Rare haplotypes were discovered in DLBCL --- p.94 / Chapter 5.6 --- Overall survival Analysis --- p.95 / Chapter 5.6.1 --- Univariate Cox Proportional Hazards Regression Analysis --- p.95 / Chapter 5.6.2 --- Bivariate Cox Proportional Hazards Regression Analysis --- p.96 / Chapter Chapter 6: --- Conclusion --- p.97 / References --- p.99

Apolipoprotein E (apoE) is a lipid transport protein which plays a key role in lipid metabolism. In addition to the well known polymorphic coding alleles epsilon2, epsilon3 and epsilon4, APOE promoter single nucleotide polymorphisms (SNPs) have also been reported to modify disease susceptibilities in humans. / In a case-control study involving 710 Chinese type 2 diabetes and 198 non-diabetic subjects, genotyping of three SNPs (-491A/T, -219G/T and +113G/C) within the APOE proximal promoter identified that -491A was associated with increased risk for type 2 diabetes in women (OR=2.44, 95%CI=1.15-5.19, p=0.017). However, the three tested SNPs were not associated with the risk of diabetic nephropathy (DN). Yeast one-hybrid screening of the human brain cDNA library using the polymorphic DNA sequences spanning the APOE promoter -491 site as the 'baits' identified one of the interacting transcription factors being the activating transcription factor 4 (ATF4). Electrophoretic-mobility-shift assay confirmed the physical interaction of the purified recombinant ATF4 protein and APOE promoter -491 A/T spanning region (-521 to -461). The binding of ATF4 to the -491T-containing sequence was stronger than that of the -491A-containing sequence. Chromatin immunoprecipitation (ChIP) assay further confirmed the interaction between ATF4 and APOE promoter -491-spanning region in vivo. The functional significance of APOE -491A/T polymorphism was supported by the dual-luciferase reporter assay showing that -491 A to T single nucleotide substitution significantly decreased the activity of the cloned APOE promoter (-1019 to +407) in human kidney (293), liver (WRL-68) and astrocyte (U-87) cell lines. Further analysis showed that ATF4 over-expression significantly down-regulated the activities of the cloned APOE promoter. The suppression of ATF4 on APOE promoter with -491A allelic form was significantly stronger than that with -491T allelic form in 293 cells (p&lt;0.05). Interestingly, overexpression of recombinant ATF4 stimulated endogenous APOE transcription by about 10% in WRL-68 cells. / In conclusion, APOE promoter -491A/T polymorphism modifies the risk of type 2 diabetes in Hong Kong Chinese women. The -491A/T polymorphism controls APOE promoter activity and is interactive with transcription factor ATF4. / My thesis project aimed at testing two hypotheses: (1) APOE promoter SNPs associate with the risks of type 2 diabetes and diabetic nephropathy, (2) APOE promoter SNPs modify transcriptional control of the gene. / Geng, Hua. / "September 2007." / Source: Dissertation Abstracts International, Volume: 69-08, Section: B, page: 4559. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (p. 140-151). / 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.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 93-101).