Estima-se que a prevalência global da população mundial com hepatite C é de 3%. Pouco se sabe sobre a resposta ao tratamento com respeito à resistência viral. Algumas mutações no fragmento de 109 aminoácidos da NS5B são associadas com resistência ao interferon (IFN) e ribavirina (RBV). Estudos moleculares e clínicos identificaram fatores associados com o hospedeiro e vírus relacionados associada com a resposta ao tratamento, tal como o gene que codifica a IL-28B. Este estudo foi dividido em duas fases, cujos objetivos foram caracterizar a frequência de mutações que conferem resistência ao HCV e avaliar a relevância das mutações em pacientes Respondedores (R) ou Não Respondedores (NR) ao tratamento e caracterizar geneticamente as populações sobre polimorfismos genéticos nos SNPs da IL-28B em relação ao prognóstico da resposta ao tratamento. As amostras dos pacientes foram submetidas a testes de genotipagem e carga viral. As sequências geradas foram comparadas no BLAST e no banco de dados Los Alamos HCV. Realizamos o alinhamento das sequências homólogas e as mutações identificadas. Com base no genótipo e carga viral determinamos a classificação dos pacientes de acordo com a resposta à terapia. O DNA genômico foi isolado a partir de sangue periférico para a realização da tipagem de SNPs de IL-28B. A metodologia utilizada foi de PCR em tempo real utilizando sondas TaqMan SNP específico. A análise dos dados foi realizada utilizando GraphPad Prism com qui-quadrado, risco relativo (RR), Odds Ratio (OR) e intervalo de confiança de 95%, com um nível de significância de P <0,05. Foi encontrado na primeira fase deste estudo uma taxa significativa mutações associadas ao tratamento nas amostras estudadas. A prevalência de mutações associadas à resistência ao IFN e RBV bem como a novos medicamentos antivirais localizados no fragmento de 109 aminoácidos da NS5B foi examinado em 69 indivíduos infectados naïve no Rio de Janeiro, Brasil. Na segunda fase, as mutações foram clinicamente relevantes. Desde então, procuramos observar as diferenças entre melhor ou pior prognóstico de acordo com a imunogenética que mostrou diferenciação entre os grupos R e NR ao tratamento em relação ao prognóstico da resposta terapêutica. Quando as diferenças entre as sequências da NS5B e a resposta ao tratamento foram consideradas verificou-se que associada a mutação R254K, estava a C316N que poderia conduzir a uma não resposta à terapia no genótipo 1b. Os nossos dados também suportaram forte associação de IL-28B rs12979860, com elevada probabilidade de resposta à terapia de IFN + RBV. Nossos dados evidenciam a presença de pacientes virgens de tratamento que abrigam mutações de resistência previamente descritas na literatura. A análise dos fatores preditores de resposta virológica mostrou que a predição de boa resposta ou não ao tratamento e ainda da progressão da doença é dependente de uma importante interação entre a genética viral e a do hospedeiro. Fato este importante para que no momento de avaliação de diagnóstico e conduta terapêutica, o médico possa tomar medidas apropriadas para o tratamento de cada paciente individualmente independentemente do genótipo do HCV em questão. / It is estimated that the overall prevalence of the average world population with hepatitis C is 3%. Little is known about the treatment response with respect to viral resistance. Some mutations in the 109-aminoacid fragment of NS5B are associated to Interferon (IFN) and Ribavirin (RBV) resistance. Molecular and clinical studies have identified factors associated with the host and related viruses associated with response to treatment, as the gene encoding IL-28B. This study was divided into two phases whose objectives were to characterize the frequency of mutations conferring resistance to HCV viral evaluating the relevance of these in Responders (R) or Non-Responders (NR) patients to treatment and to characterize genetically the populations regarding genetic polymorphisms SNPs IL-28B in relation to prognosis of response to treatment for HCV. Patient samples were subjected to tests for genotyping and viral load. The sequences generated were compared in the BLAST and the Los Alamos database HCV. We conducted the alignment of homologous sequences and mutations identified. Based on virological parameters genotype and viral load determined the classification of patients according to response to therapy. Genomic DNA was isolated from peripheral blood for carrying out the typing of SNPs of IL-28B. The methodology used was real-time PCR using TaqMan probes specific SNPs. Data analysis was performed using GraphPad Prism with chi-square, relative risk (RR), Odds Ratio (OR) and confidence interval of 95% with a significance level of P <0.05. To study these biological parameters we associated the responsive patients, non-responders, the viral load, genotype, and IL-28B polymorphism to treatment outcome. We found in the first phase of this study a significant rate of treatment-associated mutations in the samples studied. The prevalence of mutations associated to resistance to interferon and ribavirin (IFN/RBV) as well new antiviral drugs located in the 109 aminoacid fragment of NS5B was examined in 69 Hepatitis C Virus drug naïve (HCV)-infected individuals in Rio de Janeiro, Brazil. In the second phase, the mutations revealed clinically relevant from the gene in question. Since then, we seek to observe the differences between better or worse prognosis according to immunogenetic showed that differentiation between the immunogenetics of the groups R and NR to treatment in relation to prognosis of therapeutic response. When the differences between the NS5B sequences at baseline and the treatment response were considered we found that R254K associated with C316N mutations could lead to a non-response to IFN-RBV therapy in genotype 1b. Our data also strong support the association of rs12979860 IL-28B polymorphism with high probability of response to IFN + RBV therapy. Our data highlight the presence of HCV genotypes from drug naïve patients harboring resistance mutations previously described in literature. The analysis of predictors virologic response demonstrated that the prediction of better or worse therapy response and further the disease progression is dependent of a significant interaction between viral and host genetics. This fact is important for diagnosis evaluation and clinical therapeutic, the medico can take appropriate measures to treat each individual patient irrespective of the genotype of HCV in question.

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

Submitted by Verônica Esteves (vevenesteves@gmail.com) on 2017-09-28T17:28:41Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertação Carolina Barbara - AVALIAÇÃO DE POLIMORFISMOS NO.pdf: 2844302 bytes, checksum: d3ce9355ae4a9633c9b9e0c88ce683c5 (MD5) / Approved for entry into archive by Verônica Esteves (vevenesteves@gmail.com) on 2017-09-28T17:29:03Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertação Carolina Barbara - AVALIAÇÃO DE POLIMORFISMOS NO.pdf: 2844302 bytes, checksum: d3ce9355ae4a9633c9b9e0c88ce683c5 (MD5) / Made available in DSpace on 2017-09-28T17:29:03Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertação Carolina Barbara - AVALIAÇÃO DE POLIMORFISMOS NO.pdf: 2844302 bytes, checksum: d3ce9355ae4a9633c9b9e0c88ce683c5 (MD5) Previous issue date: 2012 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Fundação Oswaldo Cruz. Instituto Nacional de Controle de Qualidade em Saúde (INCQS-Fiocruz) / Cerca de 10-15% das causas de mortalidade e morbidade materna em países desenvolvidos e 37% das causas de morte obstétricas diretas no Brasil podem ser associadas à pré-eclâmpsia. A pré-eclâmpsia é uma patologia multissistêmica definida por uma hipertensão associada a uma proteinúria, após a 20ª semana de gestação. As manifestações clínicas desta doença podem se apresentar como uma síndrome materna ou fetal e de acordo com a gravidade podem ser classificadas em leve ou severa e de início precoce ou tardio. Apesar do conhecimento limitado sobre esta patologia, existem fortes evidências de envolvimento do componente genético na etiologia da pré-eclâmpsia. O fator de crescimento epidérmico (EGF) desempenha um papel importante na regulação do crescimento, proliferação e diferenciação celular, através da ligação ao seu receptor, o EGFR. Acredita-se que este fator esteja relacionado com a regulação do crescimento e da função placentária durante a gestação. Variações na sequência do DNA desses genes podem levar a uma alteração nos níveis de transcrição gênica e, como consequência, ser responsável por mudanças nos níveis de produção e/ou atividade desses fatores. O polimorfismo EGF +61 G>A está associado com a produção in vitro da proteína EGF e os polimorfismos EGFR -216 G>T e -191 C>A estão correlacionados a mudanças na atividade do promotor e na expressão de RNAm desse gene. O objetivo geral do nosso estudo foi avaliar uma possível associação entre polimorfismos funcionais nos genes EGF (+61 G>A) e EGFR (-216 G>T e -191 C>A) e a susceptibilidade à pré-eclâmpsia severa na população de gestantes do Estado do Rio de Janeiro, através de um estudo caso-controle. Como objetivos específicos, além de analisarmos uma possível interação entre os polimorfismos no desenvolvimento da pré-eclâmpsia severa, buscamos associar os polimorfismos ao histórico familiar da doença. O estudo foi composto por dois grupos, pareados por etnia: um grupo caso composto por 98 mulheres com pré-eclâmpsia severa e um grupo controle com 98 mulheres saudáveis. Os polimorfismos EGF (+61 G>A) e EGFR (-216 G>T e -191 C>A) foram avaliados pela reação em cadeia da polimerase seguida por análise de polimorfismos por tamanho de fragmentos de restrição (PCR-RFLP). As variáveis categóricas, frequências alélicas e genotípicas foram comparadas através do teste do exato de Fisher, e o teste t de Student foi utilizado para comparação das variáveis contínuas em cada grupo. Os resultados demonstram que o alelo A do polimorfismo -191 do gene EGFR está associado com a susceptibilidade à pré-eclâmpsia severa (p<0,05). Não houve associação significativa entre os outros polimorfismos (EGF +61 G>A e EGFR -216 G>T) e a susceptibilidade à pré-eclâmpsia severa (p>0,05), assim como também não foi encontrada relação entre a interação dos polimorfismos, histórico familiar e o desenvolvimento da pré-eclâmpsia severa. Além desses resultados, também foram encontradas diferenças significativas ao avaliarmos as características demográficas e clínicas entre os grupos. Este é o primeiro estudo a avaliar associações entre pré-eclâmpsia severa e os polimorfismos -216 G>T e -191C>A do gene EGFR e o primeiro estudo na população brasileira a investigar a associação do polimorfismo EGF +61 G>A e a doença. Com esse achado, podemos sugerir que o polimorfismo, o -191C>A do gene EGFR, possa ser o responsável por alguma regulação na produção do EGFR, e que através dessa regulação possa desempenhar algum papel importante na susceptibilidade à pré-eclâmpsia severa em mulheres do Estado do Rio de Janeiro. / About 10-15% of maternal deaths in development countries and approximately 37% of direct obstetrics deaths in Brazil can be assigned to preeclampsia. Preeclampsia is a multisystem disorder that usually occurs after 20 week of pregnancy and it is determined by the presence of hypertension associated with proteinuria. The clinical findings of preeclampsia can manifest as either a maternal syndrome or fetal syndrome. In addition, the preeclampsia can be classified as mild to severe, and in early or late-onset preeclampsia. Despite the limited knowledge of this pathology, there is a strong evidence of involvement of the genetic component in the etiology of preeclampsia. The epidermal growth factor (EGF) plays an important role in regulating cell growth, proliferation and differentiation, through binding its receptor, EGFR. Evidences suggest that this growth factor and its receptor are involved in growth regulation of placental function during the pregnancy. Variations in the DNA sequence in the EGF and EGFR genes can lead to an altered gene transcription and consequently can be responsible for changes in production and/or activity of these factors. The EGF +61 G>A polymorphism is significantly associated with in-vitro EGF protein production and the EGFR -216 G>T and -191 C>A polymorphisms are correlated with changes in promoter activity and expression of EGFR mRNA. The aim of this study was to verify the association between EGF +61 G>A, EGFR -216 G>T and -191 C>A polymorphisms and susceptibility to severe preeclampsia in the population of Rio de Janeiro through a case-control design. The specific objectives were to assess the association between these polymorphisms and the history family of preeclampsia, and also to analyze a possible interaction among these polymorphisms on the development of severe preeclampsia. The study was composed by two groups matched by ethnicity: the case group with 98 women with severe preeclampsia and the control group with 98 healthy women. Polymerase chain reaction restriction fragment length polymorphism analyses (PCR-RFLP) were performed to genotype EGF +61 G>A, EGFR -216 G>T and -191 C>A polymorphisms. Categorical variables, allelic and genotype frequencies were compared in each group applying Fisher´s exact test and a Student t test was used for continuous variables. The results showed that the A allele of the -191 C>A polymorphism of the EGFR gene is associated with susceptibility to severe preeclampsia (P<0,05). There were no significant association between severe preeclampsia and +61 G>A EGF and -216 G>T EGFR polymorphisms (P>0,05), as well as no correlation was found between the interaction of these polymorphisms, history family and the development of severe preeclampsia. We also found differences when we evaluated demographic and clinical characteristics between the two groups. This is the first study to assess the associations between -191 C>A and -216 G>T EGFR genetics polymorphisms and severe preeclampsia and the first study in Brazilian population to investigate the association between +61 G>A EGF polymorphism and severe preeclampsia. These findings suggest that the polymorphism-191C>A of the EGFR gene may be responsible for some regulation in the production of the EGFR, and that through this regulation this polymorphism might play an important role in the susceptibility to severe preeclampsia in women from Rio de Janeiro.

Polimorfismos em genes de receptores Toll-like (TLR) podem modular o risco de desenvolvimento de infecção, inflamação crônica e câncer. O objetivo deste estudo foi investigar a associação de polimorfismos em TLR ao risco aumentado de desenvolvimento de câncer de cabeça e pescoço, o carcinoma epidermóide (CEC) de boca e de laringe, e lesões bucais com potencial de transformação maligna, como o líquen plano oral (LPO), incluindo lesões idiopáticas e lesões liquenóides (LLO). Para tal foi conduzido um estudo caso-controle com 40 pacientes com CEC de boca, 35 com CEC de laringe, 175 com LPO (129 idiopático e 46 LLO) e 89 controles saudáveis, todos de origem basca. Oito SNP nos TLR1, TLR2, TLR4, TLR6, TLR9 e TLR10 foram genotipados por ensaios TaqMan® ou pirosequenciamento. A análise estatística por meio do teste qui-quadrado mostrou que a variante A, para o SNP TLR2-rs4696480 aumentou significativamente o risco para o desenvolvimento de CEC de boca (p=0.03) e LLO (p=0.0223). O genótipo AT representa risco de desenvolvimento de CEC de boca aumentado em 5.3 vezes quando comparado ao genótipo TT (OR=5.3, IC95%=1.19-13.63), e genótipo AA em 6.6 vezes (OR=6.6, IC95%=1.30-33.89). Quanto ao desenvolvimento de LLO, o genótipo AT representa um aumento no risco de 4.6 vezes comparado ao genótipo TT (OR=4.6, IC95%=1.55-13.38) e o genótipo AA em 4.1 vezes (OR=4.1, IC95%=1.33-12.88). Embora os genótipos AT e AA ocorram com significativa frequência no grupo LPO idiopático (p=0.045), este SNP não foi correlacionado estatisticamente à susceptibilidade de desenvolvimento deste. O SNP TLR2-rs4696480 pode ser relevante para o risco de desenvolvimento de CEC de boca e LLO nesta população, incentivando novos estudos sobre a possível associação destes grupos de doenças e SNP no gene do TLR2, colaborando com a demonstração de polimorfismos de TLR como marcadores úteis do prognóstico e prevenção do câncer de boca. / Polymorphisms in toll-like receptor (TLR) genes may modulate the risk of infection, chronic inflammation and cancer. This study investigated whether TLR polymorphisms were associated with an increased risk of head and neck cancer, including oral (OSCC) and laryngeal squamous cell carcinoma (LSCC); and oral premalignant disorders such as oral lichenoid disease (OLD), including oral lichen planus (OLP) and oral lichenoid lesions (OLL). This case-control study included 40 OSCC, 35 LSCC, 175 OLD (129 OLP and 46 OLL) patients and 89 healthy controls, all of them from the Basque Country. Genetic polymorphisms in TLR1, TLR2, TLR4, TLR6, TLR9, and TLR10 were genotyped by TaqMan® assays or pyrosequencing. Chi-square analysis showed that the variant A for the SNP TLR2-rs4696480 increased OSCC (p=0.03) and OLL (p=0.0223) risk significantly. AT genotype increases the risk of developing an OSCC by 5.3 times compared with TT genotype (OR=5.3, 95%CI=1.19-13.63), and the AA by 6.6 times (OR=6.6, 95%CI=1.30-33.89). AT genotype increases the risk of developing OLL by 4.6 times compared with TT genotype (OR=4.6, 95%CI=1.55-13.38) and the AA by 4.1 times (OR=4.1, 95%CI=1.33-12.88). Although these mutated genotypes were significantly frequent in the OLP group (p=0.045), this SNP was not correlated with OLP susceptibility. TLR2-rs4696480 polymorphism may be relevant to OSCC and OLL susceptibility in this population; encouraging further studies to assess the possible association of this group of potentially malignant disorders and oral cancer with TLR2 SNP, which may help to demonstrate that TLR polymorphisms may be useful markers to prognosis and cancer prevention.

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.

The peroxisome is a subcellular organelle that carries out a diverse range of metabolic functions, including the b-oxidation of very long chain fatty acids, the breakdown of peroxide and the a-oxidation of fatty acids. Disruption of peroxisome metabolic functions leads to severe disease in humans. These diseases can be broadly grouped into two categories: those in which a single enzyme is defective, and those known as the peroxisome biogenesis disorders (PBDs), which result from a generalised failure to import peroxisomal matrix proteins (and consequently result in disruption of multiple metabolic pathways). The PBDs result from mutations in PEX genes, which encode protein products called peroxins, required for the normal biogenesis of the peroxisome. PEX1 encodes an AAA ATPase that is essential for peroxisome biogenesis, and mutations in PEX1 are the most common cause of PBDs worldwide. This study focused on the identification of mutations in PEX1 in an Australasian cohort of PBD patients, and the impact of these mutations on PEX1 function. As a result of the studies presented in this thesis, twelve mutations in PEX1 were identified in the Australasian cohort of patients. The identified mutations can be broadly grouped into three categories: missense mutations, mutations directly introducing a premature termination codon (PTC) and mutations that interrupt the reading frame of PEX1. The missense mutations that were identified were R798G, G843D, I989T and R998Q; all of these mutations affect amino acid residues located in the AAA domains of the PEX1 protein. Two mutations that directly introduce PTCs into the PEX1 transcript (R790X and R998X), and four frameshift mutations (A302fs, I370fs, I700fs and S797fs) were identified. There was also one mutation found in an intronic region (IVS22-19A>G) that is presumed to affect splicing of the PEX1 mRNA. Three of these mutations, G843D, I700fs and G973fs, were found at high frequency in this patient cohort. At the commencement of these studies, it was hypothesised that missense mutations would result in attenuation of PEX1 function, but mutations that introduced PTCs, either directly or indirectly, would have a deleterious effect on PEX1 function. Mutations introducing PTCs are thought to cause mRNA to be degraded by the nonsense-mediated decay of mRNA (NMD) pathway, and thus result in a decrease in PEX1 protein levels. The studies on the cellular impact of the identified PEX1 mutations were consistent with these hypotheses. Missense mutations were found to reduce peroxisomal protein import and PEX1 protein levels, but a residual level of function remained. PTC-generating mutations were found to have a major impact on PEX1 function, with PEX1 mRNA and protein levels being drastically reduced, and peroxisomal protein import capability abolished. Patients with two missense mutations showed the least impact on PEX1 function, patients with two PTC-generating mutations had a severe defect in PEX1 function, and patients carrying a combination of a missense mutation and a PTC-generating mutation showed levels of PEX1 function that were intermediate between these extremes. Thus, a correlation between PEX1 genotype and phenotype was defined for the Australasian cohort of patients investigated in these studies. For a number of patients, mutations in the coding sequence of one PEX1 allele could not be identified. Analysis of the 5' UTR of this gene was therefore pursued for potential novel mutations. The initial analyses demonstrated that the 5' end of PEX1 extended further than previously reported. Two co-segregating polymorphisms were also identified, termed –137 T>C and –53C>G. The -137T>C polymorphism resided in an upstream, in-frame ATG (termed ATG1), and the possibility that the additional sequence represented PEX1 coding sequence was examined. While both ATGs were found to be functional by virtue of in vitro and in vivo expression investigations, Western blot analysis of the PEX1 protein in patient and control cell extracts indicated that physiological translation of PEX1 was from the second ATG only. Using a luciferase reporter approach, the additional sequence was found to exhibit promoter activity. When examined alone the -137T>C polymorphism exerted a detrimental effect on PEX1 promoter activity, reducing activity to half that of wild-type levels, and the -53C>G polymorphism increased PEX1 promoter activity by 25%. When co-expressed (mimicking the physiological condition) these polymorphisms compensated for each other to bring PEX1 promoter activity to near wild-type levels. The PEX1 mutations identified in this study have been utilised by collaborators at the National Referral Laboratory for Lysosomal, Peroxisomal and Related Genetic Disorders (based at the Women's and Children's Hospital, Adelaide), in prenatal diagnosis of the PBDs. In addition, the identification of three common mutations in Australasian PBD patients has led to the implementation of screening for these mutations in newly referred patients, often enabling a precise diagnosis of a PBD to be made. Finally, the strong correlation between genotype and phenotype for the patient cohort investigated as part of these studies has generated a basis for the assessment of newly identified mutations in PEX1.

In the present study / ten autosomal human-specific Alu insertion polymorphisms / ACE, APO, A25, B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and TPA25 were analyzed in approximately 100 unrelated individuals from Anatolia. Alu insertion polymorphisms offer several advantages over other nuclear DNA polymorphisms for human evolution studies. The frequencies of the ten biallelic Alu insertions in Anatolians were calculated and all systems were found to be in Hardy-Weinberg equilibrium (p&gt / 0.05). By combining the results of this study with results of previous studies done on worldwide populations, the genetic distance (Nei&rsquo / s DA) between each pair of populations was calculated and neighbor joining trees were constructed. In general, geographically closer populations were found to be also genetically similar. Principal component analysis (PCA) was performed and Anatolia was found to be in the European cluster. As a result of PCA / it was concluded that FXIIIB, PV92 and ACE were the variables contributing the most to the explanation of the variation between the populations. Additionally / canonical variates analysis (CVA) concluded that the most discriminative markers for the groups of populations were PV92, D1, ACE and HS4.32. Pair-wise Fst values were also calculated between Anatolians and some of the populations for which the data was available. It was concluded that, Anatolians have non-significant pair-wise Fst values with Swiss and French Acadian populations. Lastly, heterozygosity vs. distance from centroid graph was constructed and it was found that Anatolians and India-Hindu had exactly the expected heterozygosity value predicted by the model of Harpending and Ward (1982).