Dados de desenvolvimento ponderal de 3.844 bovinos da raça Nelore, criados em pastagens em duas fazendas do sudoeste do Brasil, dos quais 1.889 tiveram suas carcaças avaliadas por ultra-sonografia e 674 foram confinados por 90 a 120 dias e abatidos por volta dos 24 meses de idade tiveram análises de associação com dezenas de marcadores genéticos realizadas, visando detectar a associação desses marcadores com características economicamente relevantes. Foram analisadas as características de crescimento, peso ao nascer (PNAS), peso a desmama (PDES), peso ao sobreano (PSOB), ganho de peso pós-desmama (GP345), escores visuais de conformação frigorífica (CONF), precocidade de acabamento (PREC), musculosidade (MUSC) e de carcaça área de olho de lombo medida por ultra-sonografia (AOL_US), espessuras de gorduras medida por ultra-som na região lombar (EGS_US) e na picanha (EGP8). Adicionalmente, foram analisadas as características medidas post-mortem, relacionadas a qualidade de carcaça, peso de carcaça quente (PCQ), área de olho de lombo (AOL), espessura de gordura no músculo Longissimus dorsi (EGS) e as características ligadas à qualidade de carne, perdas por exsudação após 7, 14 ou 21 dias de maturação da carne (PEX7, PEX14, PEX21), perdas por cocção e maciez após os mesmos períodos de maturação (PCO7, PCO14 e PCO21, MAC7, MAC14 e MAC21), além de teor de lipídeos totais e colesterol em amostras após 7 dias de maturação. Os genótipos dos polimorfismos de base única (SNP) foram obtidos em laboratórios licenciados por empresa parceira, com uso de placas de micro-arranjos dessa empresa. Foram analisados os efeitos de substituição em análises de marcador único e multi-polimorfismos e os efeitos de aditividade e desvio de dominância de cada marcador genético. Vários dos polimorfismos de DNA analisados apresentaram ou fixação ou freqüências muito altas, maiores que 99%, de um dos alelos impossibilitando as análises de associação. No entanto, muitos outros polimorfismos apresentaram freqüências gênicas adequadas às análises de associação. Cada uma das características avaliadas apresentou, no mínimo, dois marcadores com efeitos significativos (P≤0,05) ou sugestivos (0,05<P≤0,20), o que indica que polimorfismos de DNA podem ser critérios adicionais e auxiliares nos processos seletivos ligados às 24 características de desenvolvimento ponderal, qualidade de carcaça e carne na raça Nelore. Como os efeitos de substituição alélica são responsáveis apenas por parte da determinação de cada característica, em geral uma pequena parte, recomenda-se que as previsões de efeitos de marcadores sejam feitas com análise conjunta dos mesmos. / Data on of 3,844 Nellore cattle, reared under pasture conditions on two different farms in southwestern Brazil, 1,889 of them measured by ultra-sound for carcass traits and 674 bulls finished in a feedlot for 90 to 120 days and slaughtered around 24 month of age were analyzed to verify the association with genetic markers (DNA Single nucleotide polymorphism or SNP) with the objective of detecting association of those markers with traits economically important relevant for Brazilian beef business. Growth traits considered were birth weight (PNAS), weaning weight (PDES), yearling weight, measured at 18 mo (PSOB), weight gain after weaning (GP345), visual scores for carcass conformation (CONF), finishing (PREC) and muscle (MUSC). Carcass traits, measured by ultra-sound were ribeye area (AOL_US), backfat (EGS_US) and fat depth at rump (EGP8). Additionally, carcass traits measured after slaughter were hot carcass weight (PCQ), ribeye area (AOL), fat depth on Longissimus muscle (EGS). Meat quality traits were measured after 7, 14 and 21 days of ageing: weep loss (PEX7, PEX14 and PEX21), shrink loss (PCO7, PCO14 and PCO21) and tenderness (MAC7, MAC14 and MAC21). Total lipids and cholesterol content on samples aged for 7 days, were, also, included on the analysis. The genotypes of DNA markers were carried out in laboratories licensed by a private company using its micro-array panels. Allele substitution effects were estimated in single or multi-polymorphism analysis. Additive and dominance effects were also estimated. Many DNA polymorphisms analyzed showed to be fixed or the frequencies for one of the alleles were too high, more than 99 %. In those cases, analysis could not be performed. However, for many others polymorphisms there was observed variability on allele frequencies what make possible to do the association analysis. All traits analyzed were influenced by, at least, two polymorphisms with statistically significant (P≤0,05) or suggestive (0,05<P≤0,20) effects, thus DNA polymorphisms can be used as additional and auxiliary criteria on selection process of those 24 traits related to animal growth, carcass and meat quality in Nellore cattle. As allele substitution effects explain only a small part of the phenotype, the results of this paper suggest that the effect of those markers should be considered together.

Made available in DSpace on 2016-01-26T12:51:43Z (GMT). No. of bitstreams: 1 sidneypinheirojunior_tese.pdf: 1185692 bytes, checksum: 2cae9b38515819abe487b6260ac74acc (MD5) Previous issue date: 2012-03-27 / Background Outstanding, among the factors associated to cholelithiasis after bariatric surgery, are those related to metabolism and synthesis of lipoproteins, such as apolipoprotein E (ApoE) and protein from cholesterol ester transfer protein (CETP). Methods - 220 patients have been part of the study, 114 (G1) with cholelithiasis postoperatively and 106 (G2) without cholelithiasis in over 8 months period, including the analysis of apoE-Hha I and CETP-TaqIB polymorphisms per PCR / RFLP and biochemical profile [total cholesterol (TC), lipoprotein cholesterol fraction of low (LDL), high (HDLc) and very low density (VLDLc), triglycerides (TG) and glucose levels. It was accepted level of significance for P <0.05. Results - Preoperatively, it was observed that in G1 54% of the patients with the APOE*4 allele had serum altered levels of LDL. Postoperatively, there was a decrease (P <0.001) of LDL with TG in G2 (85.3 ± 32.1 mg / dL, P <0.0001) and glucose (G1 = 83.2 ± 10.7 mg / dL; G2 = 84.7 ± 11.5 mg / dL, P <0.0001 for both), TC and LDL and HDL cholesterol increased only in G2 (P <0.0001). The B1 allele was related to decreased (P <0.01) of TC, LDLc and TG postoperatively in both groups, in addition to lowering glucose levels and increase HDL cholesterol only in G2 (P <0.0001). The genotype APOE*_/4 in G2 was associated with decreased levels of TC, LDL, TG and glucose levels and increased levels of HDL cholesterol (P<0.01) postoperatively. Conclusions - This study does not confirm the association of apoE-Hha-I and CETP-TaqIB with gallstones in the late postoperative period after bariatric surgery. However, B1 allele seems to enhance the action of bariatric surgery in the control of dyslipidemia effectively reducing levels of TC, LDL and TG, with additional benefit to those without gallstones by decreasing blood glucose levels and also increase HDL cholesterol. The relationship of APOE*4 with increased LDLc preoperatively only in G1 suggests its association with cholelithiasis in the late postoperative bariatric surgery, which should be evaluated in prospective studies. / Introdução- Destacam-se entre os fatores associados à colelitíase após cirurgia bariátrica, aqueles relacionados a metabolismo e síntese de lipoproteínas plasmáticas, como apolipoproteína E (apo E) e proteína de transferência do éster de colesterol (CETP). Objetivos-Avaliar a associação das variantes genéticas apoE-Hha I e CETP-TaqIB na colelitíase e sua influência no perfil bioquímico,além de perfil antropométrico e co-morbidades em pacientes com obesidade mórbida após cirurgia bariátrica. Métodos- Foram estudados 220 pacientes: 114 (G1) com colelitíase no pós-operatório e 106 (G2) sem colelitíase, em período >8 meses, incluindo a análise dos polimorfismos apoE-HhaI e CETP-TaqIB por PCR/RFLP e perfil bioquímico [colesterol total (CT), fração de colesterol de lipoproteína de baixa (LDLc), alta (HDLc) e muito baixa densidade (VLDLc), triglicérides (TG) e glicemia], além do índice de massa corporal (IMC), cintura abdominal (CA), hipertensão e diabete melito. Admitiu-se nível de significância para P<0,05. Resultados- Houve semelhança entre os grupos para os genótipos de apoE-HhaI e CETP-TaqIB. O genótipo APOE*3/3 prevaleceu em ambos os grupos (G1: 65% e G2:73%; P=0,204), enquanto genótipos APOE*_/4 destacaram-se em G1 (23% versus 16%; P=0,269). Para CETP o alelo B1 prevaleceu em G1 (0,59) e G2 (0,62; P=0,558). O perfil bioquímico, com valores recomendados já no pré-operatório em ambos os grupos, exceto para TG (141,4±75,4; 159,3±90,9mg/dL, respectivamente, P=0,123) e glicemia (113,0±53,2; 105,8±34,3mg/dL, respectivamente; P=0,262), mostrou decréscimo (P<0,001) no pós-operatório para todas as variáveis, incluindo TG (respectivamente, 89,0±34,6mg/dL; 85,3±32,1mg/dL; P<0,0001 para ambos) e glicemia (respectivamente, 83,2±10,7mg/dL; 84,7±11,5mg/dL; P<0,0001 para ambos). Níveis de HDLc mostraram acréscimo no pós-operatório apenas em G2 (52,5±14,7 versus 43,0±11,9; P<0,0001). Em G1, 54% dos pacientes portadores do alelo APOE*4 tinham níveis séricos alterados de LDLc no pré-operatório. O genótipo APOE*3/3, em G1, associou-se com decréscimo nos níveis de CT, LDLc, TG e glicemia e aumento nos níveis de HDLc (P<0,01). O mesmo ocorreu para genótipos APOE*_/4, em G2. O alelo B1 relacionou-se com decréscimo (P<0,01) de CT, LDLc e TG no pós-operatório em ambos os grupos, além de redução de glicemia e aumento de HDLc apenas em G2 (P<0,0001).Ambos os grupos mostraram redução nos valores de IMC e CA, além de hipertensão e diabete melito. Conclusões: Variantes de apoE-HhaI e CETP-TaqIB não diferenciam os grupos com e sem colelitíase no pós-operatório tardio de cirurgia bariátrica. Presença de APOE*4 relacionada com aumento de LDLc no pré-operatório, sugere sua influência no desenvolvimento de colelitíase no pós- operatório tardio, a ser confirmado em estudos prospectivos. CETP-Taq IB, representado pelo alelo B1 parece potencializar a ação da cirurgia bariátrica no controle do perfil bioquímico, particularmente em G2 com aumento de HDLc e decréscimo da glicemia. Além disso, independente da presença de colelitiase, a cirurgia bariátrica controla também doenças crônicas como diabete melito e hipertensão arterial.

Submitted by Ana Lúcia Torres (bfmhuap@gmail.com) on 2017-09-28T15:32:12Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Clarissa Fontoura dissertação final 2013.pdf: 4771397 bytes, checksum: c43a071b5dc04dfd4428016dfecf98f9 (MD5) / Approved for entry into archive by Ana Lúcia Torres (bfmhuap@gmail.com) on 2017-09-28T15:32:31Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Clarissa Fontoura dissertação final 2013.pdf: 4771397 bytes, checksum: c43a071b5dc04dfd4428016dfecf98f9 (MD5) / Made available in DSpace on 2017-09-28T15:32:31Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Clarissa Fontoura dissertação final 2013.pdf: 4771397 bytes, checksum: c43a071b5dc04dfd4428016dfecf98f9 (MD5) Previous issue date: 2013 / University of Iowa / A fissura labial com ou sem fissura palatina (FL/P) é uma anomalia craniofacial muito comum em humanos e pode ocorrer como característica de um quadro sindrômico ou isolada quando os indivíduos afetados não apresentam qualquer anomalia estrutural associada. A etiologia da FL/P é complexa, com a contribuição de componentes genéticos e ambientais. Diversos genes/loci candidatos a FL/P foram sugeridos nos últimos anos, contudo, discrepâncias entres os resultados são comumente encontradas. Recentemente, os genes WNT3, WNT9B, PBX1, TP63, e ARGHAP29 foram citados como possíveis genes candidatos à etiologia das FL/P devido à importante função que exercem durante o desenvolvimento craniofacial. O objetivo deste trabalho foi avaliar a associação entre polimorfismos nestes genes com o fenótipo de FL/P em uma população brasileira. Para tanto, setenta famílias, constituídas por um indivíduo afetado e seus pais não afetados, foram examinadas clinicamente e amostras de saliva foram coletadas para estudos moleculares. Um total de 20 polimorfismos distribuídos nos genes WNT3, WNT9B, PBX1, P63, e ARGHAP29 foram estudados com relação à associação com FL/P utilizando-se o método de TaqMan. O teste de desequilíbrio de transmissão (TDT) foi utilizado para detectar a associação de alelos em cada marcador nos indivíduos com FL/P, através do programa Family-Based Association Test (FBAT). O nível de significância foi determinado em P ≤ 0,05. Houve associação positiva entre FL/P para os genes ARGHAP29 (rs1048854), TP63 (rs4575879) e WNT9B (rs1530364) com FL/P. Não foi detectada associação entre alelos e genótipos de WNT3 e PBX1 com FL/P. Estes resultados sugerem que ARGHAP29, TP63 e WNT9B podem estar envolvidos na etiologia da FL/P na população estudada / Cleft lip with or without cleft palate (CL/P) is a common craniofacial anomaly in humans, and may occur as part of a syndrome or isolated, when the affected individuals do not present any associated structural anomalies. The etiology of CL/P is complex, with both genetic and environmental factors involved. Several genes /loci have been suggested in the past years although discrepancies among results are often found. Previous studies have demonstrated that WNT3, WNT9B, PBX1, TP63, and ARGHAP29 may be involved in the etiology of the CL/P due to the important function of these genes during craniofacial development. The aim of this study was to evaluate the association between polymorphisms in these genes and CL/P in a Brazilian population. Seventy families, composed by an affected individual and their unaffected parents, were examined clinically and saliva samples were collected for molecular analyses. A total of 20 polymorphisms distributed in WNT3, WNT9B, PBX1, TP63, and ARGHAP29 were investigated using the TaqMan method. The Family-Based Association Test (FBAT) and the transmission disequilibrium test (TDT) were used to verify the association between each marker allele and CL/P. The level of significance was established at P ≤ 0.05. Positive associations were detected between CL/P and three markers in ARGHAP29 (rs1048854), TP63 (rs4575879) and WNT9B (rs1530364) genes. No association was detected between CL/P and markers in WNT3 and PBX1. These results suggest that ARGHAP29, WNT9B and TP63 may be involved in the etiology of CL/P in the studied population

Dados de desenvolvimento ponderal de 3.844 bovinos da raça Nelore, criados em pastagens em duas fazendas do sudoeste do Brasil, dos quais 1.889 tiveram suas carcaças avaliadas por ultra-sonografia e 674 foram confinados por 90 a 120 dias e abatidos por volta dos 24 meses de idade tiveram análises de associação com dezenas de marcadores genéticos realizadas, visando detectar a associação desses marcadores com características economicamente relevantes. Foram analisadas as características de crescimento, peso ao nascer (PNAS), peso a desmama (PDES), peso ao sobreano (PSOB), ganho de peso pós-desmama (GP345), escores visuais de conformação frigorífica (CONF), precocidade de acabamento (PREC), musculosidade (MUSC) e de carcaça área de olho de lombo medida por ultra-sonografia (AOL_US), espessuras de gorduras medida por ultra-som na região lombar (EGS_US) e na picanha (EGP8). Adicionalmente, foram analisadas as características medidas post-mortem, relacionadas a qualidade de carcaça, peso de carcaça quente (PCQ), área de olho de lombo (AOL), espessura de gordura no músculo Longissimus dorsi (EGS) e as características ligadas à qualidade de carne, perdas por exsudação após 7, 14 ou 21 dias de maturação da carne (PEX7, PEX14, PEX21), perdas por cocção e maciez após os mesmos períodos de maturação (PCO7, PCO14 e PCO21, MAC7, MAC14 e MAC21), além de teor de lipídeos totais e colesterol em amostras após 7 dias de maturação. Os genótipos dos polimorfismos de base única (SNP) foram obtidos em laboratórios licenciados por empresa parceira, com uso de placas de micro-arranjos dessa empresa. Foram analisados os efeitos de substituição em análises de marcador único e multi-polimorfismos e os efeitos de aditividade e desvio de dominância de cada marcador genético. Vários dos polimorfismos de DNA analisados apresentaram ou fixação ou freqüências muito altas, maiores que 99%, de um dos alelos impossibilitando as análises de associação. No entanto, muitos outros polimorfismos apresentaram freqüências gênicas adequadas às análises de associação. Cada uma das características avaliadas apresentou, no mínimo, dois marcadores com efeitos significativos (P&le;0,05) ou sugestivos (0,05&lt;P&le;0,20), o que indica que polimorfismos de DNA podem ser critérios adicionais e auxiliares nos processos seletivos ligados às 24 características de desenvolvimento ponderal, qualidade de carcaça e carne na raça Nelore. Como os efeitos de substituição alélica são responsáveis apenas por parte da determinação de cada característica, em geral uma pequena parte, recomenda-se que as previsões de efeitos de marcadores sejam feitas com análise conjunta dos mesmos. / Data on of 3,844 Nellore cattle, reared under pasture conditions on two different farms in southwestern Brazil, 1,889 of them measured by ultra-sound for carcass traits and 674 bulls finished in a feedlot for 90 to 120 days and slaughtered around 24 month of age were analyzed to verify the association with genetic markers (DNA Single nucleotide polymorphism or SNP) with the objective of detecting association of those markers with traits economically important relevant for Brazilian beef business. Growth traits considered were birth weight (PNAS), weaning weight (PDES), yearling weight, measured at 18 mo (PSOB), weight gain after weaning (GP345), visual scores for carcass conformation (CONF), finishing (PREC) and muscle (MUSC). Carcass traits, measured by ultra-sound were ribeye area (AOL_US), backfat (EGS_US) and fat depth at rump (EGP8). Additionally, carcass traits measured after slaughter were hot carcass weight (PCQ), ribeye area (AOL), fat depth on Longissimus muscle (EGS). Meat quality traits were measured after 7, 14 and 21 days of ageing: weep loss (PEX7, PEX14 and PEX21), shrink loss (PCO7, PCO14 and PCO21) and tenderness (MAC7, MAC14 and MAC21). Total lipids and cholesterol content on samples aged for 7 days, were, also, included on the analysis. The genotypes of DNA markers were carried out in laboratories licensed by a private company using its micro-array panels. Allele substitution effects were estimated in single or multi-polymorphism analysis. Additive and dominance effects were also estimated. Many DNA polymorphisms analyzed showed to be fixed or the frequencies for one of the alleles were too high, more than 99 %. In those cases, analysis could not be performed. However, for many others polymorphisms there was observed variability on allele frequencies what make possible to do the association analysis. All traits analyzed were influenced by, at least, two polymorphisms with statistically significant (P&le;0,05) or suggestive (0,05&lt;P&le;0,20) effects, thus DNA polymorphisms can be used as additional and auxiliary criteria on selection process of those 24 traits related to animal growth, carcass and meat quality in Nellore cattle. As allele substitution effects explain only a small part of the phenotype, the results of this paper suggest that the effect of those markers should be considered together.

Lui, Ming Yin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 117-129). / Abstracts in English and Chinese. / Acknowledgement --- p.I / Abstract --- p.III / Abstract in Chinese --- p.V / List of Abbreviations --- p.VII / List of Figures --- p.X / List of Tables --- p.XII / Table of Contents --- p.XIII / Chapter Chapter 1: --- Introduction / Chapter 1.1 --- Overview on type 2 diabetes --- p.1 / Chapter 1.1.1 --- Definition of diabetes --- p.1 / Chapter 1.1.2 --- Diagnostic criteria --- p.2 / Chapter 1.1.3 --- Prevalence and societal impact --- p.2 / Chapter 1.1.4 --- Risks factors for type 2 diabetes --- p.4 / Chapter 1.1.4.1 --- Metabolic syndrome --- p.4 / Chapter 1.1.4.2 --- Genetics of type 2 diabetes --- p.6 / Chapter 1.1.4.3 --- "Environmental risk factors, lifestyle and energy imbalance" --- p.8 / Chapter 1.1.5 --- Pathophysiology of type 2 diabetes --- p.9 / Chapter 1.1.5.1 --- Insulin secretion and signaling --- p.9 / Chapter 1.1.5.1.1 --- Insulin Secretion --- p.9 / Chapter 1.1.5.1.2 --- Insulin signaling --- p.11 / Chapter 1.1.5.2 --- Natural history of type 2 diabetes --- p.12 / Chapter 1.1.5.3 --- Insulin resistance --- p.13 / Chapter 1.1.5.4 --- Impairment in insulin secretion --- p.15 / Chapter 1.1.5.5 --- Endocannabinoid system: A new target for energy balance and metabolism --- p.16 / Chapter 1.1.5.6 --- Effects of diabetes mellitus and its complications --- p.16 / Chapter 1.2 --- Biology of prostacyclin synthase (PTGIS) --- p.18 / Chapter 1.2.1 --- Molecular information of PTGIS --- p.18 / Chapter 1.2.2 --- Transcriptional control of PTGIS --- p.19 / Chapter 1.2.3 --- Protein structure of PGIS --- p.21 / Chapter 1.2.4 --- Sub-cellular localization and tissue distribution --- p.22 / Chapter 1.2.5 --- Function of PGIS --- p.25 / Chapter 1.2.5.1 --- Function of PGI2 in blood vessels --- p.26 / Chapter 1.2.5.2 --- Role of PGh in embryo development --- p.26 / Chapter 1.2.5.3 --- Role of PGI2 in apoptosis --- p.27 / Chapter 1.2.5.4 --- Targeted knock-out mice phenotype --- p.27 / Chapter 1.2.6 --- Relationship between PTGIS and diseases --- p.28 / Chapter 1.2.6.1 --- Genetic association --- p.28 / Chapter 1.2.6.2 --- Inactivation and tyrosine nitration of PGIS by peroxynitrite --- p.29 / Chapter 1.3 --- Biology of peroxisome proliferator-activated receptor delta (PPARD) --- p.30 / Chapter 1.3.1 --- Molecular information of PPARD --- p.30 / Chapter 1.3.2 --- Transcriptional control of PPARD --- p.31 / Chapter 1.3.3 --- Translational control and protein structure --- p.32 / Chapter 1.3.4 --- Sub-cellular localization and tissue expression --- p.35 / Chapter 1.3.5 --- Function of PPARδ --- p.37 / Chapter 1.3.5.1 --- Mechanisms of action --- p.37 / Chapter 1.3.5.2 --- Ligands for PPARδ --- p.38 / Chapter 1.3.5.3 --- PPARδ in lipoprotein metabolism --- p.39 / Chapter 1.3.5.4 --- PPARδ action in adipose tissue --- p.39 / Chapter 1.3.5.5 --- PPARδ action in skeletal and cardiac muscle --- p.40 / Chapter 1.3.5.6 --- PPARδ action in liver --- p.42 / Chapter 1.3.5.7 --- PPARδ and endocannabinoid system --- p.42 / Chapter 1.3.5.8 --- PPARδ action in inflammation --- p.43 / Chapter 1.3.5.9 --- Targeted knock-out mice phenotype --- p.44 / Chapter 1.3.5.10 --- Disease association --- p.44 / Chapter 1.4 --- Functional relationship of PGIS and PPARδ: possible role in energy metabolism --- p.46 / Chapter 1.5 --- Methods for studying genetics of type 2 diabetes and linkage analysis results --- p.47 / Chapter 1.5.1 --- Genome-wide scan --- p.47 / Chapter 1.5.2 --- Candidate gene approach --- p.48 / Chapter 1.6 --- Hypothesis and objectives --- p.49 / Chapter 1.7 --- Long-term significance --- p.49 / Chapter Chapter 2: --- Association Study of Prostacyclin Synthase and Peroxisome Proliferator-Activated Receptor Delta Gene Polymorphisms with Type2 Diabetes and Related Metabolic Traits / Chapter 2.1 --- Introduction and research design --- p.50 / Chapter 2.2 --- Study population --- p.52 / Chapter 2.2.1 --- Ethics approval --- p.52 / Chapter 2.2.2 --- Subjects --- p.52 / Chapter 2.2.3 --- Clinical assessments --- p.52 / Chapter 2.3 --- Materials and methods --- p.55 / Chapter 2.3.1 --- DNA samples --- p.55 / Chapter 2.3.2 --- Marker selection --- p.55 / Chapter 2.3.3 --- Genotyping --- p.57 / Chapter 2.3.4 --- Statistical analysis --- p.59 / Chapter 2.4 --- Results and Discussion --- p.60 / Chapter 2.4.1 --- Clinical characteristics of the study population --- p.60 / Chapter 2.4.2 --- Genotyping and LD analysis --- p.60 / Chapter 2.4.3 --- Association with type 2 diabetes and related metabolic traits --- p.61 / Chapter 2.4.3.1 --- Single SNP association with type 2 diabetes --- p.61 / Chapter 2.4.3.2 --- Single SNP association with metabolic traits --- p.64 / Chapter 2.4.3.3 --- Gene-gene interaction on type 2 diabetes --- p.74 / Chapter 2.4.3.4 --- Gene-gene interaction on metabolic traits --- p.74 / Chapter 2.5 --- Limitation and improvement --- p.79 / Chapter 2.6 --- Conclusions --- p.79 / Chapter Chapter 3: --- Functional Studies of Prostacyclin Synthase rs508757-A/G Intronic Polymorphism / Chapter 3.1 --- Introduction and research design --- p.80 / Chapter 3.2 --- Materials and methods --- p.81 / Chapter 3.2.1 --- Bioinformatics --- p.81 / Chapter 3.2.1.1 --- Cross-species alignment --- p.81 / Chapter 3.2.1.2 --- BLAST search and open reading frame prediction --- p.81 / Chapter 3.2.1.3 --- Transcription factor binding sites prediction --- p.82 / Chapter 3.2.2 --- PCR amplification from cDNA --- p.82 / Chapter 3.2.3 --- Culture of mammalian cell --- p.83 / Chapter 3.2.3.1 --- Cell line --- p.83 / Chapter 3.2.3.2 --- Medium and supplement --- p.83 / Chapter 3.2.3.3 --- Cell culture wares --- p.83 / Chapter 3.2.3.4 --- Cell culture conditions --- p.84 / Chapter 3.2.4 --- Construction of reporter vectors with rs508757 flanking sequence --- p.84 / Chapter 3.2.4.1 --- Cloning and vector preparation --- p.84 / Chapter 3.2.4.2 --- Site-directed mutagenesis --- p.84 / Chapter 3.2.5 --- Dual-luciferase reporter assay --- p.85 / Chapter 3.2.5.1 --- Transfection of VSMC --- p.85 / Chapter 3.2.5.2 --- Cell lysis and luminescence measurement --- p.86 / Chapter 3.2.6 --- Circular Dichroism --- p.87 / Chapter 3.2.6.1 --- Introduction to DNA quardruplex structure and circular dichroism --- p.87 / Chapter 3.2.6.1.1 --- DNA quardruplex --- p.87 / Chapter 3.2.6.1.2 --- Circular dichroism --- p.88 / Chapter 3.2.6.2 --- Circular dichroism measurement --- p.89 / Chapter 3.2.6.2.1 --- DNA samples --- p.89 / Chapter 3.2.6.2.2 --- CD spectroscopy --- p.89 / Chapter 3.2.7 --- Statistical analysis --- p.90 / Chapter 3.3 --- Results and Discussion --- p.91 / Chapter 3.3.1 --- Cross-species alignment --- p.91 / Chapter 3.3.2 --- BLAST search and ORF prediction --- p.92 / Chapter 3.3.3 --- PCR results on testing the presence of a new transcript --- p.93 / Chapter 3.3.4 --- Effect of rs508757 flanking sequence on SV40 promoter activity --- p.94 / Chapter 3.3.5 --- Circular dichroism experiment on rs508757 flanking sequence --- p.96 / Chapter 3.3.6 --- DNA slipping model --- p.98 / Chapter 3.3.7 --- Transcription factor binding site prediction --- p.99 / Chapter 3.4 --- Limitation and improvement --- p.107 / Chapter 3.5 --- Conclusions --- p.107 / Chapter Chapter 4: --- "General Discussion, Conclusion and Future Perspectives" / Chapter 4.1 --- General discussion --- p.108 / Chapter 4.2 --- Future perspectives --- p.115 / Chapter 4.2.1 --- "Association on type 2 diabetes and molecular interaction between transcription factors, PTGIS and PPARD" --- p.115 / Chapter 4.2.2 --- Association with diabetic nephropathy --- p.115 / Chapter 4.2.3 --- Study tissue or cell type specific actions of PGIS and PPARδ --- p.116 / Chapter 4.3 --- Conclusions to my project --- p.116 / Chapter Chapter 5: --- Bibliography --- p.117 / Appendix --- p.130

Wong, Yun Sze. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 142-162). / Abstracts in English and Chinese. / Abstract (in English) --- p.ii / Abstract (in Chinese) --- p.vi / Acknowledgement --- p.ix / Statement of Work --- p.x / Table of Contents --- p.xi / List of Tables --- p.xiv / List of Figures --- p.xvi / Glossary of Terms and Abbreviations --- p.xviii / Chapter Section I: --- Introduction --- p.1 / Chapter Chapter 1: --- General Overview of Asthma --- p.2 / Chapter 1.1 --- Asthma definition and its phenotype --- p.2 / Chapter 1.2 --- Asthma epidemiology and its prevalence in past decades --- p.4 / Chapter 1.3 --- Hygiene hypothesis and asthma development --- p.8 / Chapter 1.4 --- Asthma pathogenesis and innate immunity --- p.12 / Chapter 1.5 --- The environmental factors and genetic makeup in relation with asthma --- p.17 / Chapter Chapter 2: --- Study Plan and Obj ective --- p.21 / Chapter Section II: --- Literature Review --- p.24 / Chapter Chapter 3: --- Indoor Environmental factors of Asthma --- p.25 / Chapter 3.1 --- Overview of the indoor environmental factors --- p.25 / Chapter 3.2 --- House dust endotoxin --- p.27 / Chapter 3.2.1 --- Determinants of endotoxin exposure in home environment --- p.21 / Chapter 3.2.2 --- Protective role of endotoxin in allergy and asthma development --- p.29 / Chapter 3.2.3 --- Deleterious effect of endotoxin exposure in asthma: the dark side --- p.31 / Chapter 3.3 --- Allergen --- p.34 / Chapter 3.3.1 --- Allergens: an update --- p.34 / Chapter 3.3.2 --- Determinants of allergens in home environment --- p.35 / Chapter 3.3.3 --- Allergens avoidance: environmental intervention --- p.36 / Chapter 3.4 --- Nitrogen dioxide --- p.40 / Chapter 3.4.1 --- Determinants of indoor nitrogen dioxide and its relation with gas cooking --- p.40 / Chapter 3.4.2 --- The adverse effects of nitrogen dioxide on respiratory symptoms --- p.41 / Chapter 3.4.3 --- Reactive nitrogen species and nitrosative stress in asthma --- p.42 / Chapter Chapter 4: --- CD14 Single Nucleotide Polymorphisms and Asthma --- p.45 / Chapter 4.1 --- Overview of CD14 receptor --- p.45 / Chapter 4.2 --- Action of CD14 receptor in endotoxin response --- p.47 / Chapter 4.3 --- Relation of CD14 with asthma --- p.48 / Chapter 4.3.1 --- Associations between CD14 polymorphisms and asthma phenotypes --- p.48 / Chapter 4.3.2 --- Endotoxin switch concept: from gene to gene - environment --- p.52 / Chapter Section III: --- Study Core --- p.55 / Chapter Chapter 5: --- Methodology in indoor environment investigation and its result --- p.57 / Chapter 5.1 --- Study Population --- p.57 / Chapter 5.2 --- Home Visiting Protocol --- p.60 / Chapter 5.2.1 --- The International Study of Asthma and Allergies in Childhood (ISAAC) --- p.60 / Chapter 5.2.2 --- ISAAC questionnaire --- p.61 / Chapter 5.2.3 --- House dust collection procedures --- p.62 / Chapter 5.2.4 --- Indoor nitrogen dioxide measurements --- p.65 / Chapter 5.2.4.1 --- Ogawa passive sampler --- p.65 / Chapter 5.2.4.2 --- Preparation and measurement procedures --- p.66 / Chapter 5.2.4.3 --- Indoor nitrogen dioxide quantification --- p.67 / Chapter 5.3 --- House dust extraction --- p.69 / Chapter 5.4 --- House dust endotoxin measurement --- p.70 / Chapter 5.5 --- Allergen measurement --- p.72 / Chapter 5.6 --- Statistical Analysis --- p.75 / Chapter 5.7 --- Results --- p.77 / Chapter 5.7.1 --- Demographic data and subjects characteristics --- p.77 / Chapter 5.7.2 --- "Dust weight, endotoxin and allergen levels and their determinants in household" --- p.82 / Chapter 5.7.3 --- Indoor NO〕2levels and its determinant in household --- p.95 / Chapter 5.7.4 --- Associations between indoor environmental factors and respiratory health --- p.96 / Chapter 5.7.4.1 --- Clinical symptoms --- p.96 / Chapter 5.7.4.2 --- Exhaled NO levels --- p.101 / Chapter 5.7.4.3 --- Spirometric indices --- p.103 / Chapter Chapter 6： --- Methodology in genotyping CD14 polymorphisms and its result --- p.105 / Chapter 6.1 --- Study population --- p.105 / Chapter 6.2 --- Serum Total and allergen-specific IgE measurement --- p.106 / Chapter 6.3 --- CD14 Genotyping s --- p.107 / Chapter 6.3.1 --- Genotyping promoter SNPs ofCD14/-159 and -1359 --- p.107 / Chapter 6.3.2 --- Genotyping promoter SNP of CD14/-1619 --- p.109 / Chapter 6.3.3 --- Validation of genotyping by sequencing --- p.111 / Chapter 6.4 --- Statistical Analysis --- p.112 / Chapter 6.5 --- Results --- p.113 / Chapter 6.5.1 --- Subjects characteristics and clinical features. --- p.113 / Chapter 6.5.2 --- Associations between CD14 SNPs and asthma phenotypes --- p.114 / Chapter Chapter 7: --- Discussion --- p.120 / Chapter 7.1 --- Influence of indoor factors on asthmatic children --- p.120 / Chapter 7.2 --- CD14 polymorphisms in modifying asthma phenotypes --- p.135 / Chapter Chapter 8: --- Conclusion and Further Works --- p.138 / References --- p.141 / Appendix 1 Questionnaire / Appendix 2 Publications

La leucémie myéloïde chronique (LMC) est un syndrome myéloprolifératif rare traité par des inhibiteurs de tyrosine kinase, tel que l’imatinib. Malgré son efficacité, la résistance au traitement est un problème récurrent. Des variants génétiques responsables d’une altération de la mort cellulaire programmée (apoptose) pourraient notamment expliquer l’hétérogénéité de la réponse au traitement entre les patients. Dans un premier temps, l’objectif était de rechercher des variants candidats. Pour cela un panel de 45 gènes impliqués dans l’apoptose a été étudié par séquençage nouvelle génération chez 24 patients atteints de LMC, 12 répondeurs et 12 résistants au traitement par imatinib. A l’aide d’outils informatiques, 473 polymorphismes ont été détectés. Le nombre de patients étudiés étant limité, de nouvelles méthodes statistiques ont dû être développées pour analyser les résultats obtenus. Tout d’abord, les fréquences de survenue des variants chez les patients résistants et répondeurs ont été comparées aux fréquences observées dans la population générale et visualisées par une approche de statistiques descriptives. Cette stratégie a permis de réduire la liste à 95 polymorphismes pouvant être impliqués dans la résistance au traitement. Par la suite, les gènes ont été classés selon leur enrichissement en allèles variants. Au final, trois gènes candidats ont été choisis et séquencés chez 103 patients. Cette méthodologie, automatisée grâce à un algorithme informatique, a permis de mettre en évidence, un variant non synonyme dans le gène BCL RAMBO, retrouvé plus fréquemment chez les patients résistants de manière significative. Dans un second temps, l’objectif était de caractériser le rôle de ce variant dans la réponse à l’imatinib à l’aide de lignées cellulaires modifiées par la technologie CRISPR-Cas9. Des cellules n’exprimant plus la protéine ont été obtenues et ont permis de mettre en évidence le rôle majeur de la protéine BCL RAMBO dans l’inhibition de l’apoptose. Des lignées cellulaires portant le variant candidat ont également été créées à l’aide d’une nouvelle technique utilisant CRISPR-Cas9 : l’exon entier contenant le nucléotide d’intérêt a été remplacé par un exon modifié. La modification d’un acide aminé induite par le variant a été associé à une perte de la sensibilité au traitement par imatinib dans ces lignées, comme suggéré après séquençage des patients. Ces données indiquent que BCL-RAMBO, facteur anti-apoptotique dans une lignée modèle de LMC, pourrait devenir une nouvelle cible thérapeutique afin de surmonter la résistance à l’imatinib / Chronic myeloid leukemia (CML) is a rare myeloproliferative syndrome treated by tyrosine kinase inhibitors, such as imatinib. Despite its efficacy, resistance to treatment is a persistent clinical issue. Notably, genetic variants causing alterations in apoptosis may explain heterogeneity of imatinib sensitivity between patients. First, the goal was to look for candidate variants. For that purpose, a panel of 45 apoptotic genes was assessed by next-generation sequencing on 24 CML patients, 12 sensitive and 12 resistant to imatinib treatment. Using informatics tools, 473 polymorphisms were detected. As the number of sequenced samples was limited, novel statistical methods had to be developed to interpret the results. The variant frequency in resistant and sensitive patients was compared to variant frequency in the general population and visualized using descriptive statistics. This strategy allowed to obtain a restricted list of 95 polymorphisms that might be involved in resistance to the treatment. Then, genes were ranked according to variant allele enrichment. At the end, three candidate genes were chosen and sequenced for 103 CML patients. This methodology, automated using a computer algorithm, permitted to highlight a nonsynonymous variant in the BCL RAMBO gene, significantly found more often in resistant patients. Second, the objective was to characterize the role of this variant in response to imatinib using model cell lines modified by CRISPR-Cas9 technology. BCL-RAMBO knock-out cells were obtained and allowed to demonstrate the major role of BCL-RAMBO protein in apoptosis inhibition. Additionally, cell lines carrying the variant were created using a new CRISPR-Cas9 mediated technique: the whole exon carrying the nucleotide of interest was replaced with a variant exon. The amino acid change induced by the identified polymorphism was associated with a loss of sensitivity to imatinib treatment in these cell lines as suggested after patient sequencing. These data indicate that BCL-RAMBO, anti apoptotic factor in a CML cell line, could become a novel therapeutic target to overcome drug inefficacy for a subset of resistant patients.

In this work we have analyzed the variation of (i) several X chromosome polymorphic Alu insertions and (ii) several SNPs and microsatellites within and around the genomic regions of the genes coding for coagulation factors VII and XII (F7 and F12 respectively) in different human populations - mainly Mediterranean, but also from other geographic regions. Alu polymorphisms are very useful for anthropological studies to investigate the origin and genetic relationships between different human populations. In addition, there are certain mutations in the F7 and F12 genes that affect plasma levels of coagulation factors VII and XII, as well as the risk of cardiovascular diseases, with a high epidemiological relevance. The main conclusions of the thesis are the following: 1. Genetic differentiation among populations of northern Africa and southern Europe is low but significant. 2. For the same range of geographical distances in the Mediterranean, the genetic distances between populations from opposite coasts are longer than those between populations of the same coast, indicating that the Mediterranean may have acted as a barrier to gene flow between northern Africa and southern Europe. 3. Haplotype analysis of the F7 and F12 genomic regions has provided evidence of a higher sub-Saharan gene flow to northern Africa than to Southern Europe. This observation may be the result of the existence of a genetic barrier in the Mediterranean. 4. As shown by the principal component analysis, genetic differentiation between the studied populations in southern Europe is less pronounced than that in Africa. 5. Unlike previous studies, the genetic variation studied in this work showed that the Basques present no special genetic characteristics compared to other southern European populations. 6. According to the X chromosome Alu polymorphisms, the Egyptian Berbers from the Siwa Oasis appear as the most differentiated population within North African with a strong sub-Saharan influence. 7. The data indicate that, of all North African populations, the population of Monastir in Tunisia is genetically closest to Europe, possibly due to the historical background of the region and a less pronounced geographic isolation compared to other countries of northern Africa. 8. The genetic variation of both the X chromosome and, for the most part, the autosomal markers showed that the Berbers from the Maghreb (Asni and Khenifra) are significantly more differentiated among all North African populations. 9. The population distribution of the variation in the F7 gene promoter region shows no traits of positive selection in the Mediterranean region. On the contrary, there is strong evidence of positive selection in the indigenous population of Bolivia. 10. The lack of association between polymorphism FXII 46C> T and ischemic heart disease in the case-control study of Tunisia suggests that this polymorphism is not a universal risk factor for ischemic heart disease. / En esta tesis se ha analizado la variación que presentan (i) los polimorfismos Alu del cromosoma X y (ii) unos SNPs y microsatélites dentro y en torno a las regiones genómicas de los genes que codifican para los factores de coagulación VII y XII (F7 y F12 respectivamente) en distintas poblaciones humanas procedentes mayoritariamente del mediterráneo además de otras regiones geográficas. Los polimorfismos Alu son muy útiles para los estudios antropológicos que investigan el origen y las relaciones genéticas entre diversas poblaciones humanas. Asimismo, en los genes F7 y F12 se sitúan unas mutaciones que determinan los niveles plasmáticos de los factores de coagulación VII y XII y el desarrollo de enfermedades cardiovasculares, teniendo su distribución poblacional un alto interés epidemiológico. Las principales conclusiones de la tesis son las siguientes: 1. La diferenciación genética entre poblaciones del norte de África y sur de Europa es baja pero significativa. 2. Para del mismo rango de distancias geográficas en el mediterráneo, las distancias genéticas entre poblaciones procedentes de costas opuestas son más largas que entre poblaciones de la misma costa, indicando que el mar mediterráneo puede haber actuado como una barrera al flujo génico entre el norte de África y sur Europa. 3. El análisis de haplotipos de las regiones F7 y F12 ha proporcionado evidencias de un flujo génico subsahariano más elevado hacia el norte de África que el sur de Europa. Esta observación podría ser el resultado de la existencia de una barrera genética en el Mediterráneo. 4. Como han mostrado los análisis de componentes principales, la diferenciación genética interpoblacional en la parte europea del mediterráneo es menos pronunciada que en la parte Africana. 5. A diferencia de estudios anteriores, la variación genética estudiada en este trabajo mostró que los vascos no presentaron ninguna posición genética especial con respecto a otras poblaciones del sur de Europa. 6. Según los polimorfismos Alu del cromosoma X, los bereberes egipcios del Oasis de Siwa aparecen como la población más diferenciada dentro del norte de África y con una fuerte influencia subsahariana. 7. Todos los datos afirman que, de todas las poblaciones del norte de África, la población de Monastir en Túnez es la más cercana genéticamente a Europa, posiblemente debido a los antecedentes históricos de la región y a un aislamiento geográfico menos pronunciado en comparación con otros países del norte de África. 8. La variación genética del cromosoma X, pero sobretodo de los marcadores autosómicos, mostró que los bereberes procedentes del Magreb (Asni y Khenifra) son notablemente los más diferenciados en el conjunto de las poblaciones norteafricanas examinadas. 9. La distribución poblacional de la variación en la región promotora del gen F7 no presenta rasgos de selección positiva en la región mediterránea. En cambio, hay evidencias sólidas de una la selección positiva en la población indígena de Bolivia. 10. La falta de asociación entre el polimorfismo FXII 46C>T y la cardiopatía isquémica en el estudio caso-control de Túnez sugiere que dicho polimorfismo no es un factor de riesgo universal de la cardiopatía isquémica.

Acute lymphoblastic leukemia (ALL) is the most common type of cancer affecting children in the world and in our country. The exact molecular etiology of the disease still remains to be elucidated. This study hypothesized that four genes, namely CYP2E1*5B, *6, and *7B, NQO1*2 SNPs, GSTM1 null and GSTT1 null, alone or in combination, could contribute to the risk of development of childhood ALL. Also interactions of these polymorphisms with non-genetic risk factors were investigated. The genotyping of these polymorphisms were done on 209 healthy subjects, and 185 patients with childhood ALL, in Turkish population. Venous blood samples were collected and genomic DNA was isolated from these samples. Genotyping was done by PCR-RFLP techniques. In the case-control analyses for the risk of development of childhood ALL, only GSTT1 null was found to be associated with the development of disease (OR= 1.8, p=0.01). CYP2E1*5B and *6 combination showed an increased risk of 2.7 fold (p= 0.04). Also co-presence of CYP2E1*6-GSTT1 and CYP2E1*7B-GSTT1 polymorphisms increased the risk significantly above 4.0 fold. The risk increased more to 7.6 fold, when CYP2E1*5B,*6 and GSTT1 null were considered together, with borderline significance (p=0.04). When interaction of exposure to cigarette smoke and genetic polymorphisms were investigated, NQO1*2 and GSTM1 null were turned out to be significant risk factors for the development of disease when the parental or child&rsquo / s postnatal exposure to cigarette smoke was considered. This study presented several new findings to the literature in terms of genetic epidemiology of childhood ALL. The present work would also contribute to public health in determining the susceptibility of the Turkish population to childhood ALL.

Genetische Einflüsse stellen in der Ätiologie der Alzheimer-Demenz (AD) eine zentrale Rolle dar. In den letzten Jahren konnte eine Vielzahl neuer Kandidatengene entdeckt werden, die in sogenannten Genome-wide association studies (GWAS) eine signifikante Assoziation zur AD zeigten. Inwieweit diese neu entdeckten Polymorphismen auch die Progressionsgeschwindigkeit der AD beeinflussen, ist bislang jedoch nur unzureichend untersucht. Das Ziel dieser Arbeit war es daher, die 11 Polymorphismen mit der stärksten Assoziation zur AD in einem Kollektiv von 42 AD-Patienten hinsichtlich des Einflusses auf die Progressionsgeschwindigkeit zu untersuchen. Dazu wurde bei den Studienteilnehmern der Punktverlust im Mini-Mental-Status-Test (MMST) innerhalb eines Jahres gemessen. Unter den Polymorphismen wurde zusätzlich nach möglichen prädiktiven genetischen Markern für die „rapid-progressive AD“ (MMST-Verlust > 5 Punkte/Jahr) gesucht. Für den untersuchten rs541458-Polymorphismus des PICALM-Gens ließ sich bei C-Allel-Trägern eine signifikant höhere durchschnittliche MMST-Progression als bei Nicht-C-Trägern nachweisen (p = 0,039). Beim rs5930-Polymorphismus des LDLR-Gens konnte zudem für weibliche G-Allel-Träger eine signifikant erhöhte MMST-Progression gezeigt werden (p = 0,040). Prädiktive Marker für die rapid-progressive AD konnten nicht nachgewiesen werden. Der AG-Genotyp des untersuchten BIN1-Polymorphismus (rs744373) war jedoch signifikant häufiger in der langsamen Gruppe (≤ 5 Punkte Verlust im MMST/Jahr) anzutreffen (p = 0,026). Da bisher keine vergleichbaren Studien vorliegen, sind weitere Untersuchungen mit weitaus größeren Teilnehmerzahlen nötig, um die Ausprägung dieser möglichen Effekte genauer zu bestimmen. Die Möglichkeit, die gefundenen Polymorphismen als prognostische Marker zu verwenden und somit das Risiko des Krankheitsverlaufes zu bestimmen, hätte sowohl für Patienten und ihre Angehörigen als auch für die behandelnden Ärzte große Bedeutung.