Introdução: Variações genéticas podem influenciar a relação entre ácidos graxos (AG) do plasma e concentração plasmática de biomarcadores inflamatórios. Objetivo: Verificar a associação entre polimorfismos de nucleotídeo único (SNP) presentes nos genes da proteína C reativa (PCR), fator de necrose tumoral (TNF) e interleucina (IL)-10 e AG do plasma e seus efeitos sobre a concentração plasmática de biomarcadores inflamatórios em um estudo de base populacional ISACapital. Métodos: Foram coletadas informações sociodemográficas, de estilo de vida, de atividade física (IPAQ longo), hábito de fumar e beber, bem como amostras de sangue de 281 indivíduos (20 a 59 anos), oriundos de um estudo de base populacional (ISA-Capital). A partir do plasma, foram determinadas as concentrações de IL1, IL6, IL8, IL10, TNF, IL12p70, adiponectina, PCR, proteína quimiotática para macrófagos solúvel (sMCP)1, molécula de adesão intercelular solúvel (sICAM)1 e molécula de adesão celular vascular solúvel (sVCAM)1 por meio da técnica multiplex de imunoensaio e o perfil de ácidos graxos por cromatografia gasosa. O DNA genômico foi extraído e realizada a genotipagem dos SNP presentes no gene da PCR (rs1205, rs1417938, rs2808630), TNF (rs1799964, rs1799724, rs1800629 e rs361525) e IL10 (rs1800871, rs1800896 e rs1800872) pela ténica TaqMan Open Array. Foi realizada análise multivariada de cluster com base nos 11 biomarcadores inflamatórios, permitindo agrupar os indivíduos em grupo inflamado e cluster não inflamado. Resultados: Os indivíduos que possuíam os genótipos GA+AA do SNP -238 G>A (rs361525) do gene do TNF- apresentaram concentrações plasmáticas de TNF-, IL-1, IL-6, IL-10 e IL-12 aumentadas quando comparados com indivíduos homozigotos dominantes. Além disso, homozigotos recessivos do SNP e/i boundary C>T (rs1554286) do gene da IL-10 apresentaram maior concentração plasmática de IL-1 e de TNF- e menor de MCP-1 em relação aos indivíduos homozigotos dominantes. O grupo inflamado apresentou idade, circunferência da cintura, pressão arterial significantemente maiores que o grupo não inflamado. Em relação aos AG do plasma, o grupo inflamado apresentou concentração plasmática de AG palmítico (C16:0), razões AG saturados (SFA)/AG ômega-6 (n-6) e SFA/ AG poli-insaturados (PUFA) e atividade estimada da enzima estearoil CoA desaturase (SCD) aumentadas e concentrações plasmática de PUFA, n- 6 e AG araquidônico (AA) e atividade estimada da enzima delta-5-dessaturase (D5D) reduzidas em comparação com o grupo não inflamado. Interações SNP-AG plasmáticos estatisticamente significante foram detectadas entre o SNP +1919 A>T (rs1417938) do gene da PCR e C16:1n-7, SFA/n-6 e SFA/PUFA; entre o SNP +3872 G>A (rs1205) do gene da PCR e C16:1n-7; entre o SNP e/i boundary C>T (rs1554286) do gene da IL-10 e atividade estimada da enzima D6D; e entre o SNP -1082 A>G (rs1800896) do gene da IL-10 e C18:0, C14:0 e atividade estimada da enzima D5D. Conclusão: Os SNP analisados possuem associações com biomarcadores inflamatórios e os ácidos graxos plasmáticos palmítico, SFA/n-6, SFA/PUFA, SCD-18 foram associados positivamente com um padrão inflamatório, enquanto PUFA, n-6, ácido araquidônico e D5D foram negativamente associados. Dentre as interações encontradas, o AG palmitoleico e a razão SFA/PUFA interagiram com +1919 A>T (rs1417938), e os AG esteárico e mirístico e D5D com -1082 A>G.. / Introduction: Genetics variation can influence the relation between fatty acids (FA) and inflammatory biomarkers levels. Objective: To verify the association between Single Nucleotide Polymorphisms (SNP) in adiponectin, C-Reactive Protein (CRP), Tumor Necrosis Factor (TNF)- and Interleukin (IL)-10 genes and plasma fatty acids and their effects to a systemic inflammatory pattern at a population-based study. Methods: Sociodemographics information, life style, physical activity (IPAQ long form), smoking and drinking habits, as well as blood samples of 281 individuals (20 years 59 years) participants of a population based study (ISA-Capital). Plasma IL1, IL6, IL8, IL10, TNF, IL12p70, adiponectin, CRP, soluble monocyte chemoattractant protein-1 (sMCP-1), soluble intercellular adhesion molecule-1 (sICAM-1) and soluble vascular cell adhesion molecule 1 (sVCAM-1) levels were measured using a multiplex immunoassay and the fatty acid profile was measured by gas chromatography. The DNA was extracted and genotyping of SNP in CPR gene (rs1205, rs1417938, rs2808630), TNF (rs1799964, rs1799724, rs1800629 e rs361525) and IL10 (rs1800871, rs1800896 e rs1800872) was analyzed by TaqMan Open Array. Multivariate cluster analysis was applied on 11 inflammatory biomarkers, allowing to group individuals in inflammatory (INF) or non-inflammatory (NINF) group. Results: Individuals with GA+AA genotypes of SNP -238 G>A (rs361525) of TNF- gene had higher levels of TNF-, IL-1, IL-6, IL-10 and IL-12 compared to GG genotype. Besides that, recessive homozygous of SNP e/i boundary C>T (rs1554286) of IL-10 gene presented higher level of IL-1 and TNF- and lower level of sMCP-1 in relation to dominant homozygous. The INF group had significantly higher age, waist circumference, blood pressure, and total cholesterol than NINF group. Concerning fatty acid profile, INF group had palmitic acid (C16:0), saturated fatty acid (SFA)/omega-6 (n-6) polyunsaturated fatty acid (PUFA) ratio, SFA/PUFA and estimated enzyme activity of stearoyl-CoA desaturase (SCD) levels higher and PUFA, n-6, arachidonic acid and estimated enzyme activity of delta-5 desaturase (D5D) levels lower than NINF group. Significantly interactions were found between of SNP +1919 A>T (rs1417938) of PCR and C16:1n-7, SFA/n-6 and SFA/PUFA; between SNP +3872 G>A (rs1205) of PCR gene and C16:1n-7; between SNP e/i boundary C>T (rs1554286) of IL-10 and estimated enzyme activity of delta-6 desaturase (D6D); and between SNP -1082 A>G (rs1800896) of IL-10 gene and C18:0, C14:0 and estimated D5D activity. Conclusion: The SNP analyzed have associations with inflammatory biomarkers, and plasma palmitic, SFA/n-6, SFA/PUFA, SCD- 18 were positively associated with inflammatory pattern, while PUFA, n-6, arachidonic acid and D5D were negatively associated. Interactions were founded with palmitoleic and SFA/PUFA with +1919.A>T (rs1417938), and stearic and myristic acids and D5D with 1082 A>G.

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

Orientador: Flávia Lombardi Lopes / Resumo: O melhoramento genético em bovinos visa a seleção de características para facilitar o manejo, a qualidade da carne, a resistência a doenças e a adaptação ao meio ambiente. Polimorfismos de nucleotídeo único (SNPs) podem gerar grandes efeitos sobre essas características fenotípicas. Os microRNAs são pequenos RNAs não-codificadores que atuam como reguladores da expressão pós-transcricional através de sua ligação a mRNAs alvo. No presente estudo, realizamos o cruzamento de dados entre ~56 milhões de SNPs contra todas as seqüências conhecidas de miRNA bovino e analisamos in silico, seus possíveis efeitos. Seguindo a predição dos alvos, mostramos que 82% dos alvos foram alterados como consequência dos SNPs que ocorrem na região de seed de miRNAs maduros. Em seguida, identificamos variações na Energia Livre Mínima (MFE) que representam a capacidade de alterar a estabilidade das moléculas e, consequentemente, a maturação dos miRNAs. Também encontramos 129 SNPs em miRNAs, que alteraram sua predição com alvos, ocorrendo em regiões de QTL e, por último, a análise dos escores de conservação evolutiva para cada locus de SNP sugeriu que eles têm uma função biológica conservada através do processo evolutivo. Nossos resultados sugerem que os SNPs em microRNAs têm o potencial de alterar os fenótipos bovinos e são de grande valor para a pesquisa de melhoramento genético, bem como para a produção. / Abstract: Genetic improvement of cattle is aimed at selection of characteristics to facilitate the handling, quality of the meat, resistance to diseases and adaptation to the environment. Single nucleotide polymorphisms (SNPs) can generate large effects on these phenotypic characteristics. MicroRNAs are small non-coding RNAs that act as regulators of posttranscriptional expression through their binding to target mRNAs. In the present study, we scanned ~56 million SNPs against all known bovine miRNA sequences and analyzed in silico, their possible effects. Following target prediction, we show that 82% of targets were altered as a consequence of SNPs that occur in the seed region of mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE) which represent the capacity to alter molecule stability and, consequently, the maturation of the miRNAs. We have also found 129 SNPs in miRNAs, with altered target prediction, occurring in QTL regions and, lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to alter bovine phenotypes and are of great value for genetic improvement research, as well as production. / 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

Elevated concentrations of arsenic in groundwater pose a public health threat to millions of people worldwide. While arsenic is an established human carcinogen, a mode of action has yet to be determined for arsenic carcinogenesis. However, the oxidative stress and DNA repair pathways have been implicated in arsenic toxicity and have been hypothesized to underlie arsenic carcinogenesis. To date, few epidemiologic studies have evaluated genetic susceptibility to arsenical skin lesions based on single nucleotide polymorphisms (SNPs) in antioxidant enzyme or DNA repair genes. Utilizing cross-sectional data from the 2000-2002 survey of the Health Effects of Arsenic Longitudinal Study (HEALS) for 610 prevalent arsenical skin lesion cases and 1,079 randomly selected controls, I evaluated the associations of SNPs in genes encoding antioxidant enzymes and DNA repair enzymes on skin lesion prevalence. I also evaluated potential interactions between the SNPS as well as SNP-environment interactions in determining skin lesion prevalence. In the first study of this dissertation (Chapter 2), I assessed the relationship between SNPs in antioxidant enzyme genes and skin lesion prevalence, as well as possible interactions of these associations on the additive scale by various environmental factors. There were no statistically significant associations between these SNPs (SOD2, rs4880; CAT, rs1001179; GPX1, rs1050450; and MPO, rs2333227) and skin lesion prevalence. Additionally, there was no evidence of additive interaction by arsenic exposure levels, body mass index, smoking status, or fruit and vegetable intake with the SNPs in relation to skin lesion prevalence. However, there was marginal evidence that skin lesion prevalence was increased among individuals who carried 4 or more risk alleles compared to individuals carrying 0-3 risk alleles in these SNPs. Additionally, I observed a significant departure from additivity for the risk allele score and primary methylation index on skin lesion prevalence. In the second study of this dissertation (Chapter 3), I assessed the relationship between SNPs in DNA repair genes (OGG1, rs1052133; XRCC1, rs25487 and rs1799782; XRCC3, rs861539; ERCC2, rs1052559; ERCC5, rs17655; and LIG4, rs1805388) and skin lesion prevalence, as well as possible interactions of these associations on the additive scale by various environmental factors. In logistic regression models controlling for sex, age, and well water arsenic concentration, no associations were observed between measured SNPs and skin lesion prevalence. The results did not vary by arsenic exposure levels, body mass index, or smoking status. However, I did observe a significant inverse association of total fruit and vegetable consumption with skin lesion prevalence, and its additive interaction with the polymorphism in ERCC5. In the third study of this dissertation (Chapter 4), I utilized a multi-analytic approach to explore gene-gene, gene-environment, and higher-order interactions among 10 SNPs related to the oxidative stress and DNA repair pathways by MDR, CART, and logistic regression models. As shown in Chapters 2 and 3, none of these SNPs were associated with skin lesion prevalence, however, were evaluated for potential SNP-SNP interactions. MDR and CART modeling approaches were utilized for the selection of potential gene-gene and gene-environment interactions. Considerable overlap of the interactions detected by both these methods was observed, which were further evaluated by logistic regression. Results from logistic regression modeling, provided some evidence of these statistical interactions; however, their biological interpretation was limited. In summary, there was marginal evidence that skin lesion prevalence was increased among individuals who carried 4 or more risk alleles in genotyped SNPs related to the oxidative stress pathway compared to individuals carrying 0-3 risk alleles in these SNPs and, a significant departure from additivity was observed for the risk allele score and primary methylation index on skin lesion prevalence. Additionally, a significant inverse association of total fruit and vegetable consumption with skin lesion prevalence was observed and, a significant interaction between the polymorphism in ERCC5 and total fruit and vegetable intake was observed in relation to skin lesion prevalence on the additive scale. However, these finding require replication in other studies.

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<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.

Magister Scientiae - MSc (Biotechnology) / The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population. The first step was to design the multiplex system. This was done by using inhouse SNPs. A total of seven multiplexes were designed and optimised, each consisting of two, three or four different SNPs respectively. A total of 143 saliva and buccal samples were collected from male Johannesburg Coloureds. DNA was extracted from the saliva samples using an optimised organic method. DNA was extracted from the buccal samples using an optimised salting out method. DNA was successfully extracted from 77 of the male samples. A total of 69 samples were screened using Multiplex 1; of the 69 samples 56 samples were successfully screened to infer the paternal lineage of the samples. The results show that the most frequent haplogroup of the Johannesburg male samples was haplogroup CF (39%). The second most frequent haplogroup was haplogroup DE (38%). Under further analysis of haplogroup DE it was seen that 37% of those samples were derived for the haplogroup E1b1b.

Tracking seed dispersal using traditional, direct measurement approaches is difficult and generally underestimates dispersal distances. Variation in chloroplast haplotypes (cpDNA) offers a way to trace past seed dispersal and to make inferences about factors contributing to present patterns of dispersal. Although cpDNA generally has low levels of intraspecific variation, this can be overcome by assaying the whole chloroplast genome. Whole-genome sequencing is more expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among SNPs are lost in pooled samples and treating SNP frequencies as independent estimates of variation provides biased estimates of genetic distance. I have developed an application, CallHap, that uses a least-squares algorithm to evaluate the fit between observed and predicted SNP frequencies from pooled samples based on network topology, thus enabling pooling for chloroplast sequencing for large-scale studies of chloroplast genomic variation. This method was tested using artificially-constructed test networks and pools, and pooled samples of Lasthenia californica (California goldfields) from Whetstone Prairie, in Southern Oregon, USA. In test networks, CallHap reliably recovered network topologies and haplotype frequencies. Overall, the CallHap pipeline allows for the efficient use of resources for estimation of genetic distance for studies using non-recombining, whole-genome haplotypes, such as intra-specific variation in chloroplast, mitochondrial, bacterial, or viral DNA.