Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2014-12-01T16:24:52Z No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-12-04T14:30:35Z (GMT) No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-12-04T14:30:35Z (GMT). No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-01-23 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Brazil was the first country to introduce the pneumococcal conjugate 10valent vaccine into the National Immunization Program for infants, in 2010. The nasopharyngeal colonization by Streptococcus pneumoniae occurs early in life. It is the first step for the development of invasive diseases. So far no study has evaluated the impact of vaccination on the reduction on pneumococcal carriage. The evaluation of the impact of vaccination should based on technologies with high accuracy. In this investigation we applied molecular technologies, recently developed, to ascertain pneumococcal nasopharyngeal colonization and serotypes. Objectives: (i) to compare the prevalence of S. pneumoniae nasopharyngeal colonization by using real-time PCR (RT-PCR) and multiplex PCR, and culture (“gold standard”) in children residing in Goiania municipality; (ii) to evaluate the simultaneous colonization by different serotypes by using the multiplex PCR technique. Methods: A household populationbased survey was carried out between October/2010 and March/2011 by using a systematic sampling, weighted by census tract. Based on previous studies, the sample size was calculated taking into account an estimated 50% of pneumocococcal carriage. A total of 1,437 nasopharyngeal swabs were collected from children less than 24 months of age. Broth-enriched culture of nasopharynx specimens followed by pneumococcal isolation by both, culture and RT-PCR targeting the lytA gene (S. pneumoniae) were performed. Pneumococcal carriage was defined for RT-PCR Cycle threshold (Ct) < 35.0, and therefore all samples were submitted to multiplex PCR to detect serotypes. ROC curve (Receiver Operating Characteristics) were built up to identify Ct values predicted of S. pneumoniae positive culture. Results: The prevalence of pneumococcal carriage by RT-PCR (56.9%) was statistically higher (p< 0,001), compared to that obtained by culture (39.3%), regardless of the vaccination status. Among the 818 positive children/samples by RT-PCR, in 54.2% of them it was possible to detect the serotype. Simultaneous colonization by different types was found in 6.9% of the children. Ct values Ct33.0 showed the best accuracy (91.4%) to predict positive pneumococcal culture (Sensitivity=88% and Specificity=81.2%). When using Ct values  32.0 we found the best accuracy of multiplex PCR in detecting serotypes (Sensitivity =90% and Specificity =84,7%). Conclusion: Our findings suggest that RT-PCR and multiplex PCR techniques showed great potential to be used in evaluating the vaccination impact. Further studies are needed to evaluate the cost-effectiveness of using these technologies on a large scale. / O Brasil foi o primeiro pais a introduzir a vacina pneumocócica conjugada, 10-valente (PCV10), no Programa de Imunização infantil, em 2010. A colonização nasofaringeana pelo Streptococcus pneumoniae ocorre na infância e é etapa obrigatória para desenvolvimento da doença invasiva. Até o momento nenhum estudo avaliou o impacto da vacinação na redução do estado de portador. Para avaliação do impacto de vacinas deve-se utilizar tecnologias de alta acurácia. Este estudo utiliza técnicas moleculares, recentemente desenvolvidas, para detecção de pneumococo e sorotipos de secreção nasofaringeana.Objetivos: (i) Comparar a prevalência de colonização nasofaringeana por S. pneumoniae pelas técnicas de PCR em tempo real (RT-PCR) e cultura (―padrão-ouro‖) em crianças residentes em Goiânia no primeiro ano de introdução da PCV10; (ii) avaliar a colonização simultânea por pneumococo por diferentes sorotipos por meio da reação de PCR multiplex. Métodos: Um inquérito populacional domiciliar foi conduzido de outubro/2010 a março/2011, com coleta de 1.437 swabs nasofaríngeos de crianças < 24 meses de idade. A amostragem foi sistemática, ponderada por setor censitário, com tamanho da amostra calculado para prevalência esperada de 50% de portador. O isolamento do pneumococo foi realizado a partir do caldo enriquecido (meio STGG). A cultura foi realizada pela semeadura do caldo em placas de Agar sangue de carneiro. A RT-PCR foi direcionada para o gene lytA do pneumococo, utilizando como positividade valores do ciclo da PCR (Ct-Cycle threshold) <35,0. A reação de PCR multiplex para sorotipagem foi realizada para amostras com valores de Ct<35,0. Foram construídas curvas ROC (Receiver Operating Characteristics) para identificação de valores de Ct preditivos de cultura positiva e de tipo capsular. Resultados: A prevalência de pneumococo obtida pela RT-PCR foi de 56,9%, estatisticamente maior do que a prevalência de 39,3% obtida pela cultura (p< 0,001), independente da situação vacinal da criança. Dentre as 818 crianças positivas pela RT-PCR, em 54,2% delas foi possível detectar-se o tipo capsular. Cocolonização por diferentes sorotipos foi encontrada em 6,9% (100/1.437) das crianças. Valores de Ct33,0 apresentaram a melhor acurácia (91,4%) na predição de cultura positiva para pneumococo (sensibilidade/S=88% e especificidade/E=81,2%). Para detecção de sorotipos a melhor acurácia da PCR multiplex foi para valores de Ct32,0 (S=90% e E=84,7%). Conclusão: Os resultados sugerem que as técnicas de PCR em tempo real e multiplex apresentam grande potencial para serem utilizadas em estudos de avaliação de impacto da vacinação, respectivamente no portador e nos sorotipos vacinais. Estudos deverão ser conduzidos para se avaliar o custo-benefício da utilização desta tecnologia em larga escala.

Made available in DSpace on 2014-07-29T15:30:42Z (GMT). No. of bitstreams: 1 dissertacao ana beatriz.pdf: 103876 bytes, checksum: dca149fa61a0329de409ef0e4cba735a (MD5) Previous issue date: 2007-10-11 / Introduction: the nasopharynx (NP) constitutes the primary ecological reservoir or source of dissemination of microorganisms as Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus and Gram-negative bacilli (GNB). Several studies demonstrated that asymptomatic nasopharyngeal (NP) carriage of pathogens is prevalent in young infants and precedes the development of invasive disease. Children in day-care centers act as an important vector for horizontal spread of the respiratory pathogens and GNB within the community. The infants are susceptible to condition of carrier and take a fundamental role in the epidemiology of respiratory infections. The nasopharyngeal flora becomes established during the first year of life and is densely colonized by a broad variety of microorganisms, commensal bacteria as well as potential pathogens that may cause infections. Epidemiologic studies demonstrate that many factors influence nasopharyngeal carriage rates: age, gender, season, acute respiratory illness, exposure to other children, socio-economic status, family size, warm-climate countries, passive smoking exposure, antibiotic therapy are risk factors of colonization of the NP by BGN. Objective: this study aimed to determinate the prevalence and susceptibility pattern of BGN isolated from NP of children less than five years old attending day-care centers at municipality of Goiânia. Methods: the investigation was conducted in the municipality of Goiânia as part of an ongoing prospective surveillance of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus in children of 62 day-care centers. The surveillance was carried out from August to December, 2005 and was collected 1192 samples. The nasopharyngeal specimens were collected with a transwab, extrathin and flexible, placed in Stuart transport medium tubes and transported to the Laboratory of Bacteriology of the Federal University of Goias-Institute of Tropical Pathology and Public Health to processing. The isolates were identified by colony morphology, Gram staining technique and according to standardized tests. Susceptibility tests were performed by the disk diffusion method. Results: a total of 106 (8,9%) Gram-negative bacilli were isolated and 13 species were identified. The species more prevalent were twenty-six (24,5%) Enterobacter aerogenes, seventeen (16,0%) K. pneumoniae, eleven (10,4%) E. coli, eight (7,5%) E. agglomerans and five (4,7%) Pseudomonas sp. It was observed that forty-three (57,3%) GNB were resistant to ampicillin; twenty (26,7%) to trimethoprim-sulfametoxazole; eighteen (24,0%) showed resistance to amoxicillin-clavulanic acid and nine (12,0%) presented resistance to tetracycline. The production of extended-spectrum beta-lactamase was not detected. Conclusion: in this study was demonstrated that young children attending in daycare centers at municipality of Goiania might be GNB carrier and therefore have a fundamental role in the dissemination of microorganisms involved in community-acquired infections. It is necessary that more studies be developed to establish strategies more effectives to minimize the problem of the nasopharyngeal colonization and communityacquired infections due to importance and seriousness that both represent in the public health. / Introdução: a nasofaringe (NF) constitui o reservatório ecológico primário ou fonte de disseminação de microrganismos como Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus e bastonetes Gram-negativos (BGN). Vários estudos demonstraram que colonização nasofaríngea assintomática é prevalente em crianças e precede o desenvolvimento de doença invasiva. Crianças que freqüentam creches atuam como um importante vetor para disseminação horizontal de patógenos respiratórios e BGN dentro da comunidade. As crianças são suscetíveis à condição de portador e assumem um papel fundamental na epidemiologia de infecções respiratórias. A microbiota da nasofaringe é formada durante os primeiros anos de vida e é densamente colonizada por uma variedade de microrganismos, bactérias comensais assim como patógenos que podem causar infecções. Estudos epidemiológicos demonstram que muitos fatores influenciam o padrão de colonização da NF por BGN: idade, sexo, estação do ano, infecções respiratórias, contato com outras crianças, condição sócio-econômica, tamanho das famílias, países tropicais, exposição passiva a fumantes e antibioticoterapia. Objetivo: este estudo objetivou determinar a prevalência e padrão de suscetibilidade de BGN isolados da nasofaringe de crianças menores de 5 anos de idade que freqüentam creches no município de Goiânia. Métodos: a investigação é parte de um sistema de vigilância ativa, prospectiva e populacional de Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus em crianças de 62 creches. O estudo foi realizado no período de agosto a dezembro de 2005 e foram coletadas 1192 amostras. As coletas de espécimes da nasofaringe foram realizadas com um transwab, extrafino e flexível, inoculado no meio modificado para trasporte de Stuart e enviado ao Laboratório de Bacteriologia da Universidade Federal de Goiás-Instituto de Patologia Tropical e Saúde Pública para processamento. Os isolados foram identificados pela morfologia da colônia, coloração de Gram e testes bioquímicos padronizados. O peril de suscetibilidade foi determinado pelo método de disco difusão. Resultados: um total de 106 (8,9%) BGN foram isolados da nasofaringe de crianças e 13 espécies foram identificadas. As espécies mais freqüentes: foram vinte e seis (24,5%) Enterobacter aerogenes, dezessete (16,0%) K. pneumoniae, onze (10,4%) E. coli, oito (7.5%) E. agglomerans, cinco (4,7%) Pseudomonas sp. Observou-se que quarenta e três (57,3%) BGN apresentaram resistência a ampicilina; vinte (26,7%) foram resistentes a sulfametoxazol-trimetoprim; dezoito (24,0%) mostraram resistência a amoxacilina-ácido clavulânico e nove (12,0%) apresentaram resistência a tetraciclina. Conclusão: no presente estudo observou-se que crianças que freqüentam creches no município de Goiânia podem ser portadores de BGN e, portanto, assumem um papel fundamental na disseminação de microrganismos envolvidos em infecções comunitárias. É necessário que mais estudos sejam desenvolvidos para estabelecer estratégias mais eficazes para minimizar o problema da colonização nasofaríngea e de infecções adquiridas da comunidade devido à importância e seriedade que ambas representam no cenário da saúde pública.

Cette thèse de doctorat est une étude de la biologie et de la dynamique des microARN circulants, démontrant leur potentiel comme biomarqueurs pour l’amélioration de la surveillance et de l’évaluation pronostique dans le cancer. Il s’agit des ARN non codants simple-brin, d'environ 19-25 nt de longueur. Ils jouent un rôle clé dans la régulation de l'expression génomique au niveau post-transcriptionnel, en ciblant et réprimant la traduction des ARNm par complémentarité partielle avec leur 3'-UTR. Ils sont également libérés dans le milieu extracellulaire, la circulation et les liquides biologiques. Leur stabilité remarquable et leur diversité dans la circulation, ainsi que leur provenance maligne ou normale, en font des candidats biomarqueurs intéressants, reflétant potentiellement l'état et la dynamique d’une tumeur. Nous nous sommes focalisés sur les carcinomes ovariens (OvCa) et nasopharyngés (NPC), essayant d'élucider la relation entre les miARN plasmatiques et le pronostique des OvCa après une première ligne de traitement, ainsi que d’évaluer leur utilité dans la détection d’une réponse précoce des NPC au traitement. Le carcinome ovarien séreux est la malignité gynécologique la plus agressive. L'absence de symptômes précoces et l'insuffisance des moyens modernes pour détecter la maladie résiduelle et évaluer les résultats du traitement signalent le besoin de nouveaux biomarqueurs diagnostiques et pronostiques. En utilisant des prélèvements plasmatiques séquentiels OvCa avant et après traitement, nous avons étudié un groupe de miARN, en comparaison à des lésions pelviennes bénignes et des femmes en bonne santé. MiR-200b avait une concentration nettement plus élevée dans les échantillons malins avant traitement par rapport aux deux groupes non cancéreux. L'analyse pré- et post-traitement de miR-200b en parallèle avec le biomarqueur standard CA125 a révélé des variations distinctes et une corrélation significative de la variation de miR-200b avec le temps de rémission (PFS). Nous concluons que miR-200b pourrait éventuellement être utilisé comme biomarqueur supplémentaire pour l'estimation de la rémission à la fin du traitement. Le carcinome nasopharyngé (NPC) d'autre part est une tumeur constamment associée à une infection latente des cellules malignes par le virus d’Epstein-Barr (EBV), présentant une distribution géographique particulière. La position de la tumeur rend difficile l'approche chirurgicale, les biomarqueurs évaluant différentes approches thérapeutiques étant de grande importance. Etudiant une nouvelle forme orale de l'agent démethylant 5-azacytidine, démontrée prometteuse pour un tiers des patients NPC qui l’ont reçue, nous avons essayé d'évaluer son impact sur l'expression des miARN et des protéines virales. Malgré l'infection virale latente, les miARN viraux sont abondamment exprimés. En traitant pendant deux semaines quatre modèles de tumeur NPC développés in vivo, nous avons observé une réponse nette dose-dépendante dans les deux. L'analyse protéique a montré une induction de la protéine activatrice du cycle lytique BZLF1, renforçant les preuves antérieures d'induction partielle du cycle lytique viral par la 5-azacytidine. L'analyse des miARN a confirmé l'expression robuste des miARN BART et l'absence des miARN BHRF1 dans les NPC sans traitement. Lors du traitement, nous avons détecté les miR-BHRF1 à la fois dans la tumeur et le plasma des souris traitées. Cette induction a été validée par un traitement ultérieur d'une semaine qui a aussi mis en évidence l'induction de l’expression de l'ARNm de BHRF1, transcrit par le locus situé parmi les miARN BHRF1. Une induction de ces miARN a été observée après traitement par des agents de chimiothérapie, suggérant une utilité clinique potentielle des miR-BHRF1 comme biomarqueurs pour l’évaluation précoce de l’efficacité du traitement. Notre objectif actuel est de valider cette induction par chimiothérapie et étendre nos études au plasma humain. / This doctorate thesis provides an insight into the biology and dynamics of circulating microRNAs, demonstrating their potential to become crucial biomarkers for a better surveillance and prognosis of cancer. MicroRNAs (miRNAs) are small, single-stranded non-coding RNAs, 19-25 nt long, with a key role in the post-transcriptional regulation of gene expression, repressing the translation of target mRNAs through partial base-pair complementarity with their 3’-UTR. They can be released in the extracellular medium, being protected from RNases by association with various transporters and reach body fluids and circulation, participating in intercellular communication. Their remarkable stability and manageable diversity in circulation, as well as the fact that they derive from both malignant and normal cells make them very attractive biomarker candidates, potentially reflecting tumor state and dynamics. We have been focusing on ovarian (OvCa) and nasopharyngeal (NPC) carcinomas, attempting to elucidate the relation between plasma miRNAs and the prognosis of OvCa after first-line treatment, as well as to evaluate their use in the detection of early response of NPC tumors to treatment. Serous epithelial ovarian carcinoma is the most frequent ovarian and the most aggressive gynecologic malignancy. The absence of early symptoms and the insufficiency of modern means to accurately map residual disease and assess treatment outcome highlight the need for new diagnostic and prognostic biomarkers. Using sequential plasma samples from OvCa patients before and after first-line treatment, we studied a pre-selection of miRNAs, comparing them to samples from benign pelvic lesions and healthy women. MiR-200b exhibited a distinct higher concentration in malignant samples before treatment compared to both non-cancerous groups. Pre- and post-treatment assessment of miR-200b in parallel with the standard biomarker CA125 revealed distinct variations and a significant correlation of miR-200b variation with the progression-free survival (PFS) of the patient. We suggest that miR-200b could eventually be used as a supplementary biomarker for estimation of the remission upon treatment completion. Nasopharyngeal carcinoma (NPC) on the other hand is a tumor consistently associated to latent Epstein-Barr virus (EBV) infection of the malignant cells, presenting a unique geographical incidence pattern. The deep position of the tumor makes it tough to access surgically, with biomarkers assessing different therapeutic approaches being greatly needed. Studying a new oral form of the demethylating agent 5-azacytidine, proven to be promising for one third of NPC patients receiving it as a monodrug, we attempted to identify impact of the drug on the expression of viral miRNAs and proteins. Despite the latent viral infection, viral miRNAs are abundantly expressed, attracting interest in EBV-associated malignancies. Treating four in vivo developed NPC tumor models for two weeks, we observed clear response in two of them, in a dose-dependent manner. Protein analysis showed an induction of the immediate-early lytic protein BZLF1, solidifying previous evidence of partial activation of the viral lytic cycle by 5-azacytidine. MiRNA analysis confirmed robust expression of BART and absence of BHRF1 miRNAs at baseline status of NPC. Upon treatment, we observed an induction of BHRF1 miRNAs in both tumor and plasma of treated mice. This induction was successfully validated in a following one-week treatment and completed by a recorder de novo expression of the BHRF1 mRNA, transcribed within the BHRF1 miRNA loci. A weaker induction of BHRF1 miRNAs was also recorded after treatment with standard chemotherapeutic agents, suggesting a potential clinical utility of these miRNAs as circulating biomarkers for detection of early response to treatment. We are further working to confirm this induction by chemotherapy and extend our study to plasma samples derived from treated patients.

This thesis is the construct of a computational system for studying the nasopharyngeal carcinoma (NPC) using high-throughput sequencing data. The system involves several components, including discovery of gene fusion in NPC cell line, construction of Esptein-Barr virus (EBV) genome, and evaluation on contaminated sequencing data alignment approaches. We successfully discovered a gene fusion (UBR5-ZNF423) in a NPC cell line (C666-1) which was verified by lab experiments and found in 8.3% of primary tumors. It was discovered the regulation of this gene affect the growth of cancer cell. We constructed the EBV genome in C666-1. It serves as an important reference for studying this important NPC cell line, which was the only NPC cell line in the world for a long time. We also evaluated three mapping approaches. Two of them are designed to filter out potential mouse contamination reads on human sequencing data, which can originate from NPC human-in-mouse xenografts. We found that special care should always be applied to contaminated data. Although direct mapping can give acceptable results if in most cases, the combined-based approached is suggested. It can effectively reduce false positive variants and maintain good enough numbers of true positive variants. Filtering approach is an alternative to the combined-based approach that can also effectively reduce contamination when memory is not sufficient. / 本論文利用電腦有系統地研究鼻咽癌，當中的數據利用了高通量測序技術來定序。其中章節包括在鼻咽癌胞系中尋找融合基因、組建潛藏於人體可引致鼻咽癌的EB病毒基因組、還有評價幾種可處理受污染序列的序列排列方法。我們成功地在鼻咽癌胞系（C666-1）中發現出一個融合基因（UBR5-ZNF423），並在實驗中確定此成果，其中發現在原發腫瘤中有8.3%的樣本中找出此融合基因。此外，也發現這融合基因調控會影響到癌細胞的生長。C666-1鼻咽癌胞系在過往有一段很長的時間裡，都是全世界唯一的鼻咽癌胞系，因此它有非常重要的參考價值，在此研究，我們組建了在C666-1裡的EB病毒基因組，使它作為研究C666-1的參考樣本。另外，我們評價了三種處理排列的方法，其中兩種的設計能過濾部分人類序列數據當中老鼠基因組的污染，老鼠基因組的污染可以來自於異種移植，即把人類癌細腫瘤移植於老鼠身上種植，我們建議在情況許可下都使用特殊的處理方法而不是直接作序列排列。直接作序列排列數據雖然已有合理的表現，但相比之下組合基因組式序列排列方法能有效減少錯誤肯定的遺傳變異，並同時保留足夠多正確肯定的遺傳變異，所以組合基因組式序列排列方法應在情況許可下都使用它。過濾式序列排列方法也是一種特殊的處理方法，它也能有效減少錯誤肯定的遺傳變異，它對記憶體的需求比組合基因組式序列排列方法少，可在電腦的記憶體不足時使用它。 / Tso, Kai Yuen. / Thesis M.Phil. Chinese University of Hong Kong 2014. / Includes bibliographical references (leaves 112-120). / Abstracts also in Chinese. / Title from PDF title page (viewed on 24, October, 2016). / Detailed summary in vernacular field only.

Choi, Pui Ying. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 101-122). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

Xu, Meng. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 112-129). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Wang, Yajun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 118-126). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.v / Table of Contents --- p.vi / List of Figures --- p.xi / List of Tables --- p.xii / Abbreviations and Symbols --- p.xiii / List of Publications and Sequence Submissions during the Study --- p.xv / Chapter Chapter One: --- General Introduction --- p.1 / Chapter Chapter Two: --- Literature Review --- p.8 / Chapter 2.1 --- DNA methylation --- p.8 / Chapter 2.1.1 --- Epigenetic changes --- p.8 / Chapter 2.1.2 --- Differential methylation pattern in normal and tumor cells --- p.10 / Chapter 2.2 --- TSGs --- p.13 / Chapter 2.2.1 --- "Cancer initiation, progression and cancer genes" --- p.13 / Chapter 2.2.2 --- TSGs could be inactivated through promoter hypermethylation --- p.14 / Chapter 2.3 --- NPC --- p.17 / Chapter 2.3.1 --- Epidemiology ofNPC --- p.18 / Chapter 2.3.2 --- Molecular genetic and epigenetic studies ofNPC --- p.19 / Chapter 2.3.3 --- NPC and chromosome 11q --- p.21 / Chapter 2.4 --- ESCC --- p.21 / Chapter 2.4.1 --- Epidemiology of ESCC --- p.22 / Chapter 2.4.2 --- Genetic and epigenetic studies of ESCC --- p.23 / Chapter 2.4.3 --- ESCC and chromosome 11q --- p.24 / Chapter 2.5 --- Chromosome 11q and other carcinomas --- p.24 / Chapter 2.5.1 --- Breast cancer --- p.24 / Chapter 2.5.2 --- Ovarian cancer --- p.25 / Chapter 2.5.3 --- Neuroblastoma --- p.26 / Chapter 2.5.4 --- Melanoma --- p.27 / Chapter 2.5.5 --- Multiple myeloma --- p.27 / Chapter 2.5.6 --- Lung Cancer --- p.27 / Chapter 2.6 --- Important candidate genes located at the project study 1 lq region --- p.28 / Chapter 2.6.1 --- ETS1 --- p.28 / Chapter 2.6.2 --- FLI1 --- p.29 / Chapter 2.6.3 --- P53AIP1 --- p.30 / Chapter 2.6.4 --- RICS --- p.30 / Chapter 2.6.5 --- BARX2 --- p.30 / Chapter 2.6.6 --- ST14 --- p.32 / Chapter 2.6.7 --- ADAMTS8 --- p.33 / Chapter 2.6.8 --- ADAMTS15 --- p.35 / Chapter 2.6.9 --- HNT --- p.36 / Chapter 2.6.10 --- OPCML --- p.36 / Chapter Chapter Three: --- Materials and Methods --- p.37 / Chapter 3.1 --- Cell lines and primary tumor samples --- p.37 / Chapter 3.2 --- Cell line demethylation treatment --- p.38 / Chapter 3.3 --- DNA and RNA extraction from cell lines and tissues --- p.39 / Chapter 3.4 --- Semiquantitative RT-PCR --- p.41 / Chapter 3.5 --- DNA bisulfite treatment --- p.42 / Chapter 3.6 --- Promoter analysis and identification of 5' CpG islands of target genes --- p.45 / Chapter 3.7 --- Methylation-Specific PCR (MSP) --- p.45 / Chapter 3.8 --- Bisulfite Genomic Sequencing (BGS) --- p.46 / Chapter 3.8.1 --- BGS PCR reaction --- p.46 / Chapter 3.8.2 --- TA cloning of the PCR products into the sequencing vector --- p.47 / Chapter 3.8.3 --- Plasmid mini-preparation on 96-well plate --- p.48 / Chapter 3.8.4 --- Plasmid sequencing --- p.49 / Chapter 3.9 --- Homozygous deletion detection --- p.50 / Chapter 3.10 --- Construction of expression plasmids --- p.51 / Chapter 3.10.1 --- The strategy of full length cDNA cloning --- p.51 / Chapter 3.10.2 --- Obtaining of full length covered cDNA by cloning PCR --- p.53 / Chapter 3.10.3 --- Ligation and transformation --- p.54 / Chapter 3.10.4 --- Mini preparation of plasmid in Eppendorf tubes --- p.54 / Chapter 3.10.5 --- Verification of correct inserts in the plasmid --- p.55 / Chapter 3.10.6 --- Subcloning --- p.55 / Chapter 3.10.7 --- Bacteria storage --- p.57 / Chapter 3.11 --- Colony formation assays (CFA) --- p.57 / Chapter 3.11.1 --- Midiprep of the transfection grade plasmid --- p.57 / Chapter 3.11.2 --- Transfection --- p.58 / Chapter 3.11.3 --- Selection of the transfected cells with G418 --- p.59 / Chapter 3.11.4 --- Colony staining --- p.60 / Chapter 3.12 --- Statistical analysis --- p.60 / Chapter Chapter Four: --- Results --- p.61 / Chapter 4.1 --- Narrow down the candidate genes for further study --- p.61 / Chapter 4.1.1 --- Define the study chromosome region --- p.61 / Chapter 4.1.2 --- Database search of all candidate genes --- p.61 / Chapter 4.1.3 --- Transcriptional expression analysis of the candidate genes --- p.63 / Chapter 4.1.4 --- Selection of the genes with tumor specific expression downregulation for further intensive study --- p.64 / Chapter 4.2 --- Further characterization of ADAMTS8 --- p.69 / Chapter 4.2.1 --- Tissue transcriptional expression panel --- p.69 / Chapter 4.2.2 --- Semiquantitative RT-PCR results in tumor cell lines --- p.70 / Chapter 4.2.3 --- Promoter CpG island identification and promoter methylation study --- p.70 / Chapter 4.2.4 --- Transcription reactivation by demethylation treatment --- p.72 / Chapter 4.2.5 --- High resolution promoter methylation analysis by BGS --- p.72 / Chapter 4.2.6 --- Detection of homozygous deletion --- p.73 / Chapter 4.2.7 --- Analysis of ADAMTS8 promoter methylation in clinical samples --- p.74 / Chapter 4.2.8 --- ADAMTS8 full length cDNA cloning --- p.74 / Chapter 4.2.9 --- Colony formation assay --- p.75 / Chapter 4.3 --- Further characterization of HNT --- p.80 / Chapter 4.3.1 --- Tissue transcriptional expression panel --- p.80 / Chapter 4.3.2 --- Semiquantitative RT-PCR results in tumor cell lines --- p.80 / Chapter 4.3.3 --- Promoter CpG island identification and promoter methylation study --- p.81 / Chapter 4.3.4 --- Transcription reactivation by demethylation treatment --- p.82 / Chapter 4.3.5 --- HNT full length cDNA cloning --- p.82 / Chapter 4.4 --- Further characterization of BARX2 --- p.87 / Chapter 4.4.1 --- Tissue transcriptional expression panel --- p.87 / Chapter 4.4.2 --- Semiquantitative RT-PCR results in tumor cell lines --- p.87 / Chapter 4.4.3 --- Promoter CpG island identification and promoter methylation study --- p.88 / Chapter 4.4.4 --- Transcription reactivation by demethylation treatment --- p.89 / Chapter 4.4.5 --- BARX2 full length cDNA cloning --- p.89 / Chapter 4.5 --- Further study of other downregulated genes --- p.92 / Chapter 4.5.1 --- FLII --- p.92 / Chapter 4.5.2 --- ADAMTS15 --- p.94 / Chapter 4.5.3 --- P53AIP1 --- p.97 / Chapter Chapter Five: --- Discussion --- p.100 / Reference List --- p.118 / Appendix I: Reagents Preparation Recipe --- p.127 / Appendix II: PCR Primers for cDNA Cloning --- p.129

Lou, Pak Kin. / Thesis (M.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 136-170). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.v / Table of Contents --- p.vi / List of Figures --- p.x / List of Tables --- p.xiii / List of Publications --- p.xv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1. --- Aims of Study --- p.1 / Chapter 1.2. --- Literature Review --- p.2 / Chapter 1.2.1. --- Nasopharyngeal Carcinoma --- p.2 / Chapter 1.2.1.1. --- Overview --- p.2 / Chapter 1.2.1.2. --- Histopathology --- p.2 / Chapter 1.2.1.3. --- Epidemiology --- p.3 / Chapter 1.2.1.4. --- Etiology --- p.5 / Chapter 1.2.1.4.1. --- Epstein-Barr Virus (EBV) Latent Infection --- p.5 / Chapter 1.2.1.4.2. --- Environmental Factors --- p.5 / Chapter 1.2.1.4.3. --- Genetic Factors --- p.6 / Chapter 1.2.1.5. --- Molecular Pathogenesis --- p.7 / Chapter 1.2.1.5.1. --- Chromosomal Alterations --- p.7 / Chapter 1.2.1.5.2. --- NPC-associated Tumour Suppressor Genes --- p.7 / Chapter 1.2.1.5.3. --- NPC-associated Oncogenes --- p.8 / Chapter 1.2.2. --- Epstein-Barr Virus --- p.9 / Chapter 1.2.2.1. --- Overview --- p.9 / Chapter 1.2.2.2. --- Lytic and Latent Infection of EBV --- p.9 / Chapter 1.2.2.3. --- EBV Latency Programs and Associated --- p.10 / Malignancies --- p.11 / Chapter 1.2.2.4. --- The Role of EBV in NPC --- p.12 / Chapter 1.2.3. --- NF-kB Signalling Pathways --- p.12 / Chapter 1.2.3.1. --- Overview --- p.12 / Chapter 1.2.3.2. --- Pathway Components --- p.12 / Chapter 1.2.3.2.1. --- NF-kB Subunits --- p.16 / Chapter 1.2.3.2.2. --- Inhibitors of kB (IkBs) --- p.16 / Chapter 1.2.3.2.3. --- IkB Kinases (IKKs) --- p.17 / Chapter 1.2.3.3. --- NF-kB Activation and Signalling --- p.17 / Chapter 1.2.3.3.1. --- The Canonical Pathway --- p.18 / Chapter 1.2.3.3.2. --- The Non-canonical Pathway --- p.18 / Chapter 1.2.3.3.3. --- Physiological Functions of NF-kB --- p.19 / Chapter 1.2.3.4. --- NF-kB Signalling and Tumourigenesis --- p.20 / Chapter 1.2.3.4.1. --- Oncogenic Activation of NF-kB in Hematological Malignancies --- p.20 / Chapter 1.2.3.4.2. --- Oncogenic Activation of NF-kB in Solid and Epithelial Tumours --- p.22 / Chapter Chapter 2 --- Material and Methods --- p.22 / Chapter 2.1. --- Tumour Specimens --- p.24 / Chapter 2.2. --- NPC Tumour Lines and Immortalized NP Cell Lines --- p.24 / Chapter 2.2.1. --- Cell Lines --- p.24 / Chapter 2.2.2. --- Xenografts --- p.27 / Chapter 2.3. --- DNA Sequence Analysis --- p.27 / Chapter 2.3.1. --- Genomic DNA Extraction --- p.27 / Chapter 2.3.2. --- Polymerase Chain Reaction (PCR) --- p.28 / Chapter 2.3.3. --- DNA Sequencing --- p.32 / Chapter 2.4. --- RNA Expression Analysis --- p.32 / Chapter 2.4.1. --- Total RNA Extraction and Reverse Transcription --- p.33 / Chapter 2.4.2. --- Quantitative Real-time Polymerase Chain Reaction (QRT-PCR) --- p.35 / Chapter 2.5. --- Protein Expression Analysis --- p.35 / Chapter 2.5.1. --- Total Protein Extraction --- p.35 / Chapter 2.5.2. --- Nuclear and Cytoplasmic Protein Isolation --- p.36 / Chapter 2.5.3. --- Western Blotting --- p.39 / Chapter 2.6. --- Immunohistochemical Staining --- p.41 / Chapter 2.7. --- Statistical Analysis --- p.41 / Chapter 2.8. --- Immunoprecipitation --- p.43 / Chapter 2.9. --- Electrophoretic Mobility Shift Assay (EMSA) and Supershift Assay --- p.44 / Chapter 2.10. --- Enzyme-Linked Immunosorbent Assay (ELISA) --- p.45 / Chapter 2.11. --- Plasmid Preparation --- p.45 / Chapter 2.11.1. --- Plasmids --- p.45 / Chapter 2.11.2. --- Bacterial Transformation and Plasmid DNA Extraction --- p.46 / Chapter 2.12. --- Transfections --- p.46 / Chapter 2.12.1. --- Transient Transfection --- p.46 / Chapter 2.12.2. --- Stable Transfection --- p.47 / Chapter 2.13. --- Immunofluorescence --- p.47 / Chapter 2.14. --- Cell Proliferation and Viability Analysis --- p.47 / Chapter 2.15. --- Small Interfering RNA (siRNA) Knockdown --- p.49 / Chapter 2.16. --- Expression Microarray --- p.49 / Chapter 2.16.1. --- Agilent Oligonucleotide Microarray --- p.50 / Chapter 2.16.2. --- Data Analysis --- p.51 / Chapter Chapter 3 --- Activation of NF-kB Signals in NPC --- p.51 / Chapter 3.1. --- Introduction --- p.52 / Chapter 3.2. --- Results --- p.52 / Chapter 3.2.1. --- Expression Pattern of NF-kB Subunits in NPC Tumour Lines --- p.55 / Chapter 3.2.2. --- Distinct NF-kB Complexes in NPC Tumour Lines --- p.60 / Chapter 3.2.3. --- Expression of NF-kB Subunits in NPC Primary Tumours --- p.67 / Chapter 3.3. --- Discussion / Chapter Chapter 4 --- Alterations of NF-kB Components in NPC --- p.71 / Chapter 4.1. --- Introduction --- p.72 / Chapter 4.2. --- Results --- p.72 / Chapter 4.2.1. --- Homozygous Deletion of IicBa and TRAF3 in NPC Tumour Lines --- p.76 / Chapter 4.2.2. --- Mutation of TRAF2 and A20 in NPC Tumour Lines / Chapter 4.2.3. --- Aberrant Expression of Multiple NF-kB Signalling Components in NPC Tumour Lines --- p.80 / Chapter 4.2.4. --- Expression of NF-kB Signalling Components in NPC --- p.85 / Primary Tumour --- p.92 / Chapter 4.3. --- Discussion --- p.99 / Chapter Chapter 5 --- Identification of Downstream Targets for NPC-associated NF-kB Signalling --- p.99 / Chapter 0.1. --- Introduction --- p.99 / Chapter 0.2. --- Results --- p.100 / Chapter 0.2.1. --- Target Genes Modulated by p50 --- p.100 / Chapter 0.2.2. --- Functional Annotation of p50 Target Genes --- p.105 / Chapter 0.2.3. --- Target Genes Modulated by RelB --- p.105 / Chapter 0.2.4. --- Functional Annotation of RelB Target Genes --- p.105 / Chapter 0.2.5. --- Functional Annotation of Genes Modulated by both p50 and RelB --- p.111 / Chapter 0.3. --- Discussion --- p.118 / Chapter Chapter 6 --- Functional Role of TRAF3 Inactivation in NPC --- p.118 / Chapter 0.1. --- Introduction --- p.118 / Chapter 0.2. --- Results --- p.118 / Chapter 0.2.1. --- Effect of TRAF3 Restoration on NF-kB Activity --- p.119 / Chapter 0.2.2. --- Effect of TRAF3 Expression on Cell Proliferation --- p.123 / Chapter 0.2.3. --- TRAF3 Expression Modulates Interferon Transcription in NPC Cells --- p.128 / Chapter 0.3. --- Discussion / Chapter Chapter 7 --- General Discussion --- p.132 / Chapter Chapter 8 --- Conclusion / Chapter Chapter 9 --- References / Appendix --- p.136

Tong Hung Man Joanna. / "June 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 137-149). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Made available in DSpace on 2014-07-29T15:26:20Z (GMT). No. of bitstreams: 1 TeseCristyaneBenicio2010.pdf: 531193 bytes, checksum: 9a3d68036fe340ca60db84cb20f7066b (MD5) Previous issue date: 2010-02-18 / Objectives (i) Present review article focusing on pneumococcal vaccines and carriage; (ii) to validate sequential multiplex PCR for identifying pneumococcal capsular serotypes from children attending day-care centers; (iii) determine the multilocus sequence typing; (iv) to identify the capsular types of multiple colonies of S. pneumoniae isolates from a single sample of nasopharyngeal secretions of children attending day-care centers in Goiânia. Materials and Methods S. pneumoniae was obtained from health children less than 5 years old attending 62 day care centers of Goiânia. The laboratory procedures were performed according to WHO recommendations. Were selected 217 isolates (penicillin resistant and sensitive) for capsular typing by multiplex PCR technique. MLST was performed for 55 isolates representing the serotypes detected and the different susceptibility patterns for penicillin. Quellung reaction was used for typing isolates serotypes 6A, 6B, 18C and the isolates not typed by multiplex PCR. For 28 presumptive pneumococcal positive NP swabs, 3 colonies were picked to acess possible serotype diversity. Eighty four pneumococci were identified by conventionally procedure and multiplex PCR was performed. Results Serotypes were deduced for 177/217 (81.6%) of the pneumococcal. The most frequent serogroups/serotypes were 14, 6, 23F, 19F and 18. Multiple serotypes were detected in 13 specimens. Were found 19 MLST types and two new ST. Forty (18.4%) were not serotyped by the multiplex PCR and quellung reaction. The analysis of three colonies from the same NP permitted the detection of differente serotypes in 7/28 (25%) NP samples. Conclusion (i) The multiplex PCR is simple and cost-effective method for detecting multiple serotypes in nasopharyngeal isolates; (ii) and thus might be useful for the monitoring of pneumococcal colonization over time; (iii) the use of multiplex PCR can further broaden our understanding of the dynamics of pneumococcal carriage, including multiple serotypes, the effect of vaccination on carriage, and transmission, as well as surveillance of IPD and co-colonization. / Objetivos: (i) Apresentar uma revisão focando as vacinas pneumocócicas e o portador de S. pneumoniae na nasofaringe; (ii) realizar a tipagem capsular de pneumococos colonizadores de nasofaringe de crianças de creches pela técnica de multiplex PCR; (iii) identificar o perfil MLST dos pneumococos isolados na nasofaringe; (iv) identificar os tipos capsulares de múltiplas colônias de S. pneumoniae isolados de uma única amostra de secreção da nasofaringe de crianças que frequentam creches do município de Goiânia pela técnica de multiplex PCR. Material e Métodos: Um estudo de prevalência de portador de pneumococo foi conduzido de agosto a dezembro de 2005, em crianças de dois a 59 meses de idade, atendidas em 62 creches em Goiânia. Os procedimentos laboratoriais para isolamento e identificação dos pneumococos foram realizados de acordo com as técnicas recomendadas pela Organização Mundial de Saúde. Foram selecionados 217 isolados (resistentes e sensíveis à penicilina) para a tipagem capsular pela técnica de multiplex PCR. O perfil MLST foi realizado para 55 isolados, representando os sorotipos detectados e os diferentes perfis de suscetibilidade à penicilina. A reação de Quellung foi usada para tipar os sorotipos 6A, 6B e 18C e os isolados não tipados pelo multiplex PCR. Para a análise de múltiplas colônias de S. pneumoniae, utilizou-se 28 amostras positivas para pneumococo, das quais se recuperou 3 colônias de cada placa de ágar sangue, totalizando 84 colônias, que foram submetidas aos testes de tipagem fenotípica e caracterização capsular pela técnica de multiplex PCR. Resultados: Cento e setenta e sete sorotipos em duzentos e dezessete (177/217), totalizando 81,6% dos pneumococos foram tipados. Os sorotipos mais freqüentes foram 14, 6, 23F, 19F e 18. Foram identificadas múltiplas colônias em 13 amostras de nasofaringe. Foram observados 19 tipos MLST e dois novos tipos de seqüência (ST). Quarenta (18,4%) dos isolados não foram tipados pelo multiplex PCR e todos não tipados pela reação de Quellung. A análise de múltiplas colônias de S. pneumoniae pela técnica de multiplex PCR permitiu a detecção de mais de um tipo em 25% (7/28) das amostras. Conclusões: (i) O método de multiplex PCR mostrou-se seguro e simples na detecção de diferentes tipos capsulares incluídos na reação, além de mais barato; (ii) representou uma valiosa ferramenta em investigações de vigilância de pneumococos; (iii) Aplicação da técnica multiplex PCR permitiu o conhecimento da diversidade genética de pneumococos colonizadores da nasofaringe, detectando a dinâmica da colonização desta bactéria na população, incluindo a colonização por múltiplos sorotipos; a substituição ou mudança de sorotipo como resultado da vacinação; como também vigilância das doenças pneumocócicas invasivas.