Philosophiae Doctor - PhD / This thesis has been placed under a long term embargo. Forensic and population genetic parameters were investigated in the Botswana population using autosomal and Y-chromosome short tandem repeat markers. AmpFlSTR Profiler plus markers were used to investigate the genetic diversity and forensic parameters in 773 individuals from Botswana from the reference database of the Botswana Police. The levels of polymorphism found using the AmpFlSTR Profiler Plus markers showed that the nine loci that make up the AmpFlSTR Profiler Plus can differentiate individuals for forensic casework in the Botswana population. AmpFlSTR Identifiler autosomal STR markers were used to investigate the population structure according to ethno-linguistics and geography 990 individuals from Botswana that serve as a reference database for the Botswana Police. Using pairwise genetic distances (Fst), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and the landscape genetics software TESS, ethno-linguistics were found to have a greater influence on population structure than geography. The patterns of population structure found using these markers highlight the need for regional reference databases that include both ethnolinguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications. The 17 Y-chromosomal short tandem repeats found in AmpFlSTR Y-filer and a highly discriminatory Y-STR genotyping system (the Y-STR 10-plex developed in the Forensics DNA Laboratory at the University of the Western Cape) were analysed in 249 unrelated male individuals from Botswana. Rst, multi-dimensional scaling (MDS) and AMOVA were used to investigate population differentiation in Botswana. The discrimination capacity (DC) was found to be higher using the Y-STR 10-plex as compared to the 17 markers in the Y-filer genotyping system. No geographic regional or ethnic differentiation was observed between the Northern and Southern regions of Botswana using both marker systems. Regional and ethnic variation can be useful in forensic working hypotheses. Cluster analysis using the highly discriminatory Y-STR 10-plex haplotypes may provide information about ancestry and haplogroup information. / National Research Foundation (NRF)

Os pacientes infectados pelo vírus da imunodeficiência humana (HIV) freqüentemente apresentam alterações digestivas, sendo o esôfago um alvo comum de lesões estruturais. A etiologia infecciosa é a mais freqüente neste grupo de pacientes. Múltiplos agentes já foram implicados como causadores de lesões esofágicas. As infecções virais são uma das principais causas de tais lesões, sendo os vírus mais implicados o citomegalovirus (CMV) e o vírus herpes simples (HSV). Muitas lesões ulceradas permanecem sem diagnóstico etiológico, mesmo após exaustiva investigação, sendo denominadas úlceras idiopáticas ou aftosas. Os métodos de diagnóstico usuais são demorados e pouco sensíveis. Assim, nosso estudo tem como principal objetivo estudar o papel do método da reação em cadeia da polimerase (PCR) no diagnóstico destas lesões. Durante o período de outubro de 1996 a outubro de 1997, foram estudados 79 pacientes HIV-positivos, que foram submetidos ao exame de endoscopia digestiva alta por indicação clínica. Estes foram submetidos a 89 exames endoscópicos, sendo colhidas 96 biópsias, as quais foram armazenadas em nitrogênio líquido (50) ou em freezer a –70oC (46). O DNA foi extraído usando método baseado na lise hipotônica, digestão com proteinase K, extração com fenol-clorofórmio e precipitação em etanol. Uma quantidade fixa foi usada para amplificação em ciclador térmico, utilizando primers específicos para CMV, Herpesvirus, HPV, HIV, Haemophilus ducreyi, Treponema pallidum e as micobactérias M. tuberculosis, M. avium e M. intracellulare. O produto final foi submetido a uma eletroforese em gel de agarose e corado com brometo de etídeo. A endoscopia não revelou alterações esofágicas em 26 exames (29,2%). As alterações observadas foram monilíase esofágica em 33 exames (37,1%), úlceras em 22 (24,7%); esofagite em 10 (11,2%) e áreas lugol-negativas em 9 (10,1%). A PCR resultou positiva para o CMV em 19 amostras (19,8%), para o Herpes em 4 (4,2%), para o HPV em 17 (17,7%), para o HIV em 37 (38,5%) e para o H. ducreyi em 3 (3,1%). Nenhuma amostra foi positiva para o T. pallidum e para micobactérias. No estudo de 29 amostras de 22 úlceras esofágicas a PCR detectou o CMV em 9 amostras (31%), o Herpes em 3 (10,3%), o HPV em 6 (20,7%), o HIV em 19 (65,5%) e o H. ducreyi em 2 (6,9%) e em 8 (36,4%) não foi detectado nenhum agente. O CMV foi detectado com freqüência nas úlceras esofágicas, sendo difícil diferenciar se havia infecção ativa ou latente. O HIV teve uma incidência elevada nas biópsias de úlceras, o que pode sugerir um possível papel etiológico deste agente em tais lesões. O HPV foi o terceiro agente mais freqüente, mas não foi possível caracterizá-lo como causador de lesões esofágica ulceradas. A PCR apresentou potencial para tornar-se um método útil na investigação das lesões esofágicas em pacientes infectados pelo HIV. / Patients infected by Human Immunodeficiency Virus (HIV) usually present digestive abnormalities and the esophagus is a common target of structural lesions. Infections are the most frequent cause of esophageal lesions in these patients. Several agents were already implied in this process. Viral infections are one of the main causes of such lesions and cytomegalovirus (CMV) and herpes simplex virus (HSV) were the most involved agents. Many ulcerated lesions persist without etiologic diagnosis even after exhaustive investigation, being denominated idiopathic or aphthous ulcers. The usual diagnostic methods are difficult and have low sensitivity. Thus, the main objective of our study was to evaluate the role of the polimerase chain reaction (PCR) method in the diagnosis of these lesions. During the period of October of 1996 to October of 1997, 79 HIV-positive patients were studied. They were submitted to upper digestive endoscopies, which were indicated on clinical basis. These patients were submitted to 89 upper digestive endoscopies, being obtained 96 biopsies, which were stored in liquid nitrogen or in a 70oC freezer. DNA was extracted using a method based on hypotonic lyses, proteinase K digestion, extraction with phenol-chloroform and precipitation in ethanol. A fixed amount was used for amplification in thermal cycler, using specific primers for CMV, herpesvirus, human papillomavirus (HPV), HIV, Haemophilus ducreyi, Treponema pallidum, Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium intracellulare. The final products were submitted to an electrophoresis in agarose gel and stained with ethidium bromide. The endoscopies did not reveal esophageal alterations in 26 exams(29,2%). The abnormalities observed were esophageal candidiasis in 33 exams (37,1%), ulcers in 22 (24,7%); esophagitis in 10 (11,2%) and lugol-negative areas in 9 (10,1%). The PCR was positive to CMV in 19 samples (19,8%), for Herpes in 4 (4,2%), for HPV in 17 (17,7%), for HIV in 37 (38,5%) and for the H. ducreyi in 3 (3,1%). No sample was positive for T. pallidum or micobacterium. In the study of the esophageal ulcers by PCR, CMV was detected in 9 samples (31%), Herpes in 3 (10,3%), HPV in 6 (20,7%), HIV in 19 (65,5%), H. ducreyi in 2 (6,9%) and any agent was detected in 8 samples (36,4%). CMV was frequently detected in esophageal ulcers, being difficult to differentiate between active and latent infections. The HIV had an elevated incidence in ulcer biopsies, which may suggest a possible etiologic role of this virus in such lesions. HPV was the third more frequent agent, but it was not possible to attribute the esophageal lesions to that virus. In conclusion, this study suggests that the PCR can be an useful method in the investigation of esophageal lesions in HIV infected patients.

Salmonella species is the etiologic agent of salmonellosis, which is a zoonotic infection that is characterized by diarrhea and systemic infection. Contaminated foods are usually the vehicles of Salmonella transmission along the food supply chain. Asymptomatic food production animals and effluents also contribute to contamination of meat. Antimicrobials have contributed significantly to treatment of salmonellosis. However, uncontrolled antimicrobial use is among the causes of antibiotic resistance, which results in treatment failure. The aim of this research study was to determine the extent of Salmonella spp contamination during the cattle slaughtering process in South African rural abattoirs (n = 23), water and cattle feaces. In addition, the aim was to determine antimicrobial resistance profiles of the Salmonella spp isolates. The specific objectives were: i) to establish the occurrence and distribution of Salmonella spp on cattle carcasses, hides, and intestinal contents and environmental samples using classical microbiology and molecular techniques; ii) to determine the Salmonella serovars using serotyping; and iii) to determine antimicrobial resistance patterns and multidrug resistance among the Salmonella isolates using the Kirby-Bauer disc diffusion method. Materials and Classical microbiology techniques were used to analyze cattle faeces (n = 400), hides (n = 67), intestinal contents (n = 62), carcass sponges (n = 100), and water from the abattoirs (n = 75) for the presence of Salmonella spp. Further confirmation of the Salmonella isolates was done using Polymerase Chain Reaction whereby the invA gene was targeted. A total of 92 Salmonella spp isolates were recuperated. The 92 Salmonella were serotyped as described in the White-Kauffmann-Le Minor scheme. The 92 Salmonella spp isolates were further subjected to antimicrobial susceptibility examination towards the following antimicrobials: ampicillin (10μg), cefotaxine (30μg), kanamycin (30μg), oxytetracycline (30μg), and enrofloxacin (5μg) by using the Kirby-Bauer disk diffusion procedure. All the isolates carried the invA genes. The average Salmonella spp occurrence on carcasses, hides, and intestinal contents was 35.37% (n = 81). Eleven of the faecal samples (2.75%) tested positive for Salmonella spp. The Salmonella serovar that occurred more frequently was S. Enteritidis. Different serovars that were recognized on carcasses were not automatically found on the hides and intestinal contents. The incompatible frequency of the different Salmonella serovars on carcasses, intestinal contents and hides means that in addition to carriage on hides and in intestinal contents, new external causes that did not form part of this study also play a vital role concerning carcass contamination. Most Salmonella spp (n = 66; 71.7%) isolates were resistant to a minimum of one antimicrobial with main resistance detected towards oxytetracycline (51.90%). This emphasizes on the call for wise antimicrobial use at some stage in animal production and strict sanitation for the duration of slaughtering. Briefly, cattle slaughtered in South African rural abattoirs harboured different types of Salmonella serovars that were resistant to antimicrobials, which could be a public health risk and danger. The outcome should support policymakers with determining the effectiveness of existing sanitary measures during cattle slaughtering in rural abattoirs, which is vital from socio-economic, public health, and epidemiological perspectives. / College of Agriculture and Environmental Sciences

In the food industry, it is very important to take care of the quality, safety and organoleptic properties of the products supplied. For this reason, food must be checked. However, not all information can be found using conventional techniques such as immunoassays, chromatographic techniques, etc. DNA-based techniques can be used for these cases where traditional procedures are insufficient. Among them, the best known technique is PCR. The aim of the thesis was to isolate DNA from vegetable samples (broccoli, beetroot, carrot and pepper). DNA was isolated using the magnetic particle method and the traditional CTAB method. Both methods were able to isolate the DNA from the vegetable samples in quality and at a concentration suitable for PCR, where the 35S rDNA gene region was amplified (more precisely about 700 bp of the 18S-ITS1-5,8S region). After amplification, the PCR products were subjected to restriction reactions and the results compared to bioinformatic analysis. These steps have succeeded in finding suitable enzymes for diferentiation of PCR products from the tested vegetable species.

The effectiveness of magnetic microparticles in isolation of DNA from Lactobacillus rhamnosus CCM 1825T and DNA from chicken erythrocytes were studied in diploma thesis. Magnetic HEMA based microparticles coated by carboxylic groups and hyperbranched styrene-divinylbenzene particles (IMC AS ČR, Prague, Czech Republic) were used for DNA isolation. Magnetic microparticles Dynabeads® DNA DIRECT™ Universal (Dynal, Norway) based on polystyrene and MPG® Uncoated (PureBiotech, USA) based on magnetic glass were used as a control. The dependence of amount of eluted DNA on concentration of DNA in the base solution and the dependence of amount of eluted DNA on concentration of magnetic microparticles were studied. The affinity of magnetic microparticles to RNA for various concentrations of RNA solution was studied, too. The ability of tested particles to isolate DNA from real samples was validated using milk product Actimel. The quality of isolated DNA of Lactobacillus genus was proved using genus specific PCR.

Micromethod of DNA isolation using magnetic particles is one of the modern technological methods used in DNA isolation, and makes the process simpler, more effective and faster. The main aim of this study was to isolate the DNA from various plant (tomato) food products, using different types of magnetic particles. The results were compared and the quantity, purity and the possibility of amplication of the isolated DNA among samples were found to be different. The DNA isolation method using magnetic particles P(HEMA-co-GMA) or HPS B-M-NH2 was shown to be the most effective in achieving the above mentiond parametres. DNAs from the analysed samples of plant food products were isolated in sufficient quantity and quality to be used in the conventional PCR. Differences in the possibility of the amplification of the isolated DNA stored at -20 °C during more than a half year were not found.

INTRODUÇÃO: A síndrome de Williams-Beuren (SWB; OMIM #194050) é causada por microdeleções em hemizigose de genes contíguos na região 7q11.23. Fácies típico, estenose aórtica supravalvar (EASV), deficiência intelectual, personalidade amigável e hiperacusia constituem as principais características da SWB. A deleção mais freqüente é de 1,55Mb, porém deleção de 1,84Mb também já foi descrita. Embora a técnica de hibridização in situ por fluorescência (FISH) ser amplamente utilizada na detecção da deleção, os marcadores microssatélites são considerados altamente informativos e de fácil manejo. OBJETIVOS: Testar os marcadores microssatélites para o diagnóstico da SWB, determinar o tamanho e origem parental da microdeleção, comparar as características clínicas entre os pacientes com diferentes tamanhos da deleção e origem parental. MÉTODOS: Foram estudados 97 pacientes com diagnóstico clínico de SWB utilizando cinco marcadores microssatélites: D7S1870, D7S489, D7S613, D7S2476 e D7S489_A. A partir do DNA genômico dos probandos e de seus genitores, foi realizada reação em cadeia da polimerase (PCR), seguida de eletroforese em gel de poliacrilamida desnaturante (uréia, com 7,5 M) e os resultados visualizados com coloração de prata. RESULTADOS E DISCUSSÃO: Com cinco marcadores juntos, o resultado foi informativo em todos os pacientes. O marcador mais informativo foi D7S1870 (78,4%), seguido por D7S613 (75,3%), D7S489 (70,1%) e D7S2476 (62,9%). A deleção foi encontrada em 84 (86,6%) pacientes e sua ausência em 13 (13,4%) pacientes. A deleção de 1,55 Mb foi observada em 76/84 pacientes (90,5%) e 1,84 Mb em 8/84 pacientes (9,5%). A origem parental da deleção foi materna em 44/84 pacientes (52,4%) e paterna em 40/84 pacientes (47,6%). Alterações oculares foram mais freqüentes em pacientes com deleção. Não houve diferença nos achados clínicos entre o tamanho ou a origem parental da deleção, exceto para EASV, presente em maior freqüência nos pacientes com deleção paterna. Os resultados por marcadores microssatélites foram concordantes com FISH positivos, no entanto, em dois pacientes com FISH negativos, a microdeleção foi detectada apenas pelos marcadores. CONCLUSÃO: O uso de cinco marcadores microssatélites selecionados foi informativo em todos os pacientes. Em dois casos, os marcadores foram mais eficientes que FISH, portanto pode ser considerado um método alternativo para o diagnóstico molecular da SWB / INTRODUCTION: Williams-Beuren syndrome (WBS; OMIM 194050) is caused by hemizygous contiguous gene microdeletions at 7q11.23. Typical facies, supravalvular aortic stenosis (SVAS), mental retardation, overfriendliness and hiperacusis comprise typical symptoms in WBS. The most common deletion is 1.55 Mb, however 1.84 Mb deletion also has been described. Although fluorescence in situ hybridization (FISH) is widely used in the detection of deletion, microsatellite markers are considered highly informative and easily manageable. PURPOSE: Test the microsatellite markers for the diagnosis of WBS, to determine the size and parental origin of microdeletion, compare the clinical characteristics between patients with different sizes of the deletion and parental origin. METHODS: We studied 97 patients with clinical diagnosis of WBS using five microsatellite markers: D7S1870, D7S489, D7S613, D7S2476 and D7S489_A. From the genomic DNA of probands and their parents was performed polymerase chain reaction (PCR), followed by electrophoresis on denaturing polyacrylamide gel (urea, 7.5 M) and the results visualized with silver staining. RESULTS AND DISCUSSION: Using five markers together, the result was informative in all patients. The most informative marker was D7S1870 (78.4%) followed by D7S613 (75.3%), D7S489 (70.1%) and D7S2476 (62.9%). The deletion was found in 84 (86.6%) patients and absent in 13 (13.4%) patients. The deletion of 1.55 Mb was observed in 76/84 patients (90.5%) and 1.84 Mb in 8 / 84 patients (9.5%). The parental origin was maternal in 44/84 patients (52.4%) and paternal in 40/84 patients (47.6%). Abnormalities ocular were more frequent in the patients with a deletion. There were no clinical differences in relation to either the size or parental origin of the deletion, except for SVAS, present in more frequency in the patients with paternal deletion. The results for microsatellite markers were concordant with FISH positive, however, in two patients with negative FISH, the microdeletion was detected only by the markers. CONCLUSION: Using these five selected microsatellite markers was informative in all patients. In two cases, the markers were more efficient than FISH, thus can be considered an alternative method for molecular diagnosis in SWB

Made available in DSpace on 2015-04-11T13:38:22Z (GMT). No. of bitstreams: 1 francisca.pdf: 878093 bytes, checksum: 251097fdfe9003556935b61ec3a58ab8 (MD5) Previous issue date: 2012-06-27 / The human papillomavirus (HPV) is recognized as a major risk factor related to cervical cancer. The identification of HPV types of high risk can aid in the prevention of malignant lesions of the cervix. This study aims to determine and genotype HPV in women with a cytological result of ASC-US and LSIL. This is a cross-sectional study with an analytical component in women attended the Fundação Alfredo da Matta - FUAM. The patients were selected from the file examination of the Laboratory of Cytology of FUAM from January 2009 to July 2011 and requested to attend the DST clinic through active search in order to make a new collection of material for revaluation cytological, molecular detection and genotyping of HPV. Molecular detection was performed by Nested-PCR targeting the L1 region of the viral capsid. PCR products were analyzed on an agarose gel. Out of 100 patients selected, 70% (70/100) participated in the study, 34 of them had the cytological result of ASC-US and LSIL of 36. After reevaluation cytological 8 (11.4%) patients had cytology within normal limits, 33 (47.2%) inflammatory cytology, 22 (31.4%) ASC-US, 6 (8.6%) LSIL, 1 (1.4%) HSIL. HPV was identified in 28.6% (20/70) of the samples. Of the 20 patients HPV DNA-positive 1 had cytology within normal limits, 6 inflammatory cytology, 10 ASC-US and 2 LSIL and 1 HSIL. After the genotyping were identified the following HPV types 6, 16, 58, 61, 70, 83, 84 and 85. The most prevalent HPV 25% was HPV 58. The presence of HPV high-risk oncogenic stresses the importance of actions aimed at preventing the transmission of this virus and tracking of diseases in the city of Manaus. / O Papillomavírus humano (HPV) é reconhecido como o principal fator de risco relacionado do câncer cervical. A identificação de tipos de HPV de alto risco pode auxiliar na prevenção de lesões malignas do colo do útero. Este estudo tem como objetivo determinar e genotipar o HPV em mulheres com resultado citológico de Lesão Intraepitelial de Baixo grau (LSIL) e Células Escamosas Atípicas Significado Indeterminado (ASC-US). Trata-se de um estudo de corte transversal com componente analítico em mulheres atendidas na Fundação Alfredo da Matta - FUAM. As pacientes foram selecionadas a partir do arquivo de exames do Laboratório de Citologia da FUAM no período de janeiro de 2009 a julho de 2011 e solicitadas a comparecer ao ambulatório de DST por meio de busca ativa, a fim de fazer uma nova coleta de material para reavaliação citológica, detecção molecular e genotipagem do HPV. A detecção molecular foi realizada pela técnica de Nested-PCR tendo como alvo a região L1 do capsídeo viral. Os produtos da PCR foram analisados em gel de agarose. Do total de 100 pacientes selecionadas, 70% (70/100) participaram do estudo, sendo que 34 delas tinham resultado citológico de ASC-US e 36 de LSIL. Após reavaliação citológica 8(11,4%) pacientes apresentaram citologia dentro dos limites da normalidade, 33(47,2%) citologia inflamatória, 22(31,4) ASC-US, 6(8,6%) LSIL, 1(1,4%) HSIL. O HPV foi identificado em 28,6% (20/70) das amostras examinadas. Das 20 pacientes HPV-DNA positivas 1 caso apresentou citologia dentro do limite da normalidade, 6 citologia inflamatória, 10 ASC-US, 2 LSIL e 1 caso apresentou HSIL. Após a genotipagem foram identificados os seguintes tipos de HPV: 6, 16, 58, 61, 70, 83, 84 e 85. O HPV mais prevalente com 5 casos em 20 positivos foi o HPV 58. A presença do HPV de alto risco oncogênico destaca a importância de ações voltadas para a prevenção na transmissão desse vírus e no rastreamento das doenças relacionadas, na cidade de Manaus.

INTRODUÇÃO: A síndrome de Williams-Beuren (SWB; OMIM #194050) é causada por microdeleções em hemizigose de genes contíguos na região 7q11.23. Fácies típico, estenose aórtica supravalvar (EASV), deficiência intelectual, personalidade amigável e hiperacusia constituem as principais características da SWB. A deleção mais freqüente é de 1,55Mb, porém deleção de 1,84Mb também já foi descrita. Embora a técnica de hibridização in situ por fluorescência (FISH) ser amplamente utilizada na detecção da deleção, os marcadores microssatélites são considerados altamente informativos e de fácil manejo. OBJETIVOS: Testar os marcadores microssatélites para o diagnóstico da SWB, determinar o tamanho e origem parental da microdeleção, comparar as características clínicas entre os pacientes com diferentes tamanhos da deleção e origem parental. MÉTODOS: Foram estudados 97 pacientes com diagnóstico clínico de SWB utilizando cinco marcadores microssatélites: D7S1870, D7S489, D7S613, D7S2476 e D7S489_A. A partir do DNA genômico dos probandos e de seus genitores, foi realizada reação em cadeia da polimerase (PCR), seguida de eletroforese em gel de poliacrilamida desnaturante (uréia, com 7,5 M) e os resultados visualizados com coloração de prata. RESULTADOS E DISCUSSÃO: Com cinco marcadores juntos, o resultado foi informativo em todos os pacientes. O marcador mais informativo foi D7S1870 (78,4%), seguido por D7S613 (75,3%), D7S489 (70,1%) e D7S2476 (62,9%). A deleção foi encontrada em 84 (86,6%) pacientes e sua ausência em 13 (13,4%) pacientes. A deleção de 1,55 Mb foi observada em 76/84 pacientes (90,5%) e 1,84 Mb em 8/84 pacientes (9,5%). A origem parental da deleção foi materna em 44/84 pacientes (52,4%) e paterna em 40/84 pacientes (47,6%). Alterações oculares foram mais freqüentes em pacientes com deleção. Não houve diferença nos achados clínicos entre o tamanho ou a origem parental da deleção, exceto para EASV, presente em maior freqüência nos pacientes com deleção paterna. Os resultados por marcadores microssatélites foram concordantes com FISH positivos, no entanto, em dois pacientes com FISH negativos, a microdeleção foi detectada apenas pelos marcadores. CONCLUSÃO: O uso de cinco marcadores microssatélites selecionados foi informativo em todos os pacientes. Em dois casos, os marcadores foram mais eficientes que FISH, portanto pode ser considerado um método alternativo para o diagnóstico molecular da SWB / INTRODUCTION: Williams-Beuren syndrome (WBS; OMIM 194050) is caused by hemizygous contiguous gene microdeletions at 7q11.23. Typical facies, supravalvular aortic stenosis (SVAS), mental retardation, overfriendliness and hiperacusis comprise typical symptoms in WBS. The most common deletion is 1.55 Mb, however 1.84 Mb deletion also has been described. Although fluorescence in situ hybridization (FISH) is widely used in the detection of deletion, microsatellite markers are considered highly informative and easily manageable. PURPOSE: Test the microsatellite markers for the diagnosis of WBS, to determine the size and parental origin of microdeletion, compare the clinical characteristics between patients with different sizes of the deletion and parental origin. METHODS: We studied 97 patients with clinical diagnosis of WBS using five microsatellite markers: D7S1870, D7S489, D7S613, D7S2476 and D7S489_A. From the genomic DNA of probands and their parents was performed polymerase chain reaction (PCR), followed by electrophoresis on denaturing polyacrylamide gel (urea, 7.5 M) and the results visualized with silver staining. RESULTS AND DISCUSSION: Using five markers together, the result was informative in all patients. The most informative marker was D7S1870 (78.4%) followed by D7S613 (75.3%), D7S489 (70.1%) and D7S2476 (62.9%). The deletion was found in 84 (86.6%) patients and absent in 13 (13.4%) patients. The deletion of 1.55 Mb was observed in 76/84 patients (90.5%) and 1.84 Mb in 8 / 84 patients (9.5%). The parental origin was maternal in 44/84 patients (52.4%) and paternal in 40/84 patients (47.6%). Abnormalities ocular were more frequent in the patients with a deletion. There were no clinical differences in relation to either the size or parental origin of the deletion, except for SVAS, present in more frequency in the patients with paternal deletion. The results for microsatellite markers were concordant with FISH positive, however, in two patients with negative FISH, the microdeletion was detected only by the markers. CONCLUSION: Using these five selected microsatellite markers was informative in all patients. In two cases, the markers were more efficient than FISH, thus can be considered an alternative method for molecular diagnosis in SWB

Microfabricated thermal cyclers for nucleic acid amplification by using polymerase chain reaction (PCR) have been demonstrated by several groups over the last decade, with improved cycling speed and smaller volumes when compared to conventional bench-top cyclers. However, high fabrication costs coupled with difficulties in temperature sensing and control remain impediments to commercialization. In this study we have used a silicon-glass device that takes advantage of the high thermal conductivity of silicon but at the same time utilizes minimum number of fabrication steps to make it suitable for disposable applications. The thermal cycler is based on noncontact induction heating developed in this group. The microchip reaction kinetics is studied for the first time in-situ during PCR, using a real-time fluorescence block that is capable of data acquisition every 0.7 s from the microchip. The fluorescence information from SYBR green I dye is used to optimize microchip amplification reactions and confirm the product by melting curve analysis. We have also developed a novel non-contact temperature sensing technique using SYBR green fluorescence that can be used for miniaturized PCR devices. The thesis is organized into the following chapters. In chapter 1 we introduce the basic biology ideas that are required to understand DNA amplification. DNA based analysis requires amplification of low initial concentrations to above detectable limits using a technique known as polymerase chain reaction (PCR). In this process, the sample is cycled through three thermal steps for 3040 times to produce multiple copies of DNA. In microchip PCR, conventional polypropylene tubes using 2050 µL volume are replaced by miniaturized devices using ~1 µL sample volumes. The device response improves in terms of ramp rate and total analysis time due to the small volume and smart design of the materials. In this chapter we summarize some of the issues important for miniaturized PCR devices and compare them with commercial tube PCR systems. In chapter 2 we describe the induction heating technique that was developed by our group for miniaturized devices. Induction heating is a noncontact heating technique unlike resistive heating which has been commonly used for microchip PCR. Though resistive heating is very efficient in terms of heat transfer efficiency, it is not suitable for disposable devices and requires multi-step microfabrication. Other non-contact heating techniques such as hot air and IR heating require larger size arrangements that are not suitable for miniaturized devices. The heating was verified by using a thermocouple soldered at the back of the secondary plate that was also used for feedback to the comparator circuit for control. The simple on-off circuit was able to control within ±0.1 ◦C with heating and cooling ramp rates of 25 ◦C/s and 2.5 ◦C/s respectively. In this chapter, we also describe the design and fabrication of the silicon-glass microchip fabricated in our lab. We have used silicon-glass hybrid device for PCR in which glass with a 2 mm drilled hole is anodically bonded to an oxidized silicon surface. The hole formed the static reservoir for 3 µL volume of amplification solution. During PCR, the solution needs to be cycled to high temperature of ~95 ◦C. Hence it was necessary to seal the tiny droplet of liquid against evaporation at this temperature. The devices after being filled by sample were covered by 4 µL of mineral oil to serve as an evaporation barrier. It was easy to recover the whole sample after amplification for further testing. Chapter 3 describes the development of a fluorescent block for SYBR green I dye (SG) used for real-time monitoring of the amplification. The block contains a blue LED for excitation, a dichroic beamsplitter, and silicon photodiode along with filters and focusing optics. Signal levels being weak, we incorporated lock-in detection technique. A TTL at 190 Hz was used to pulse the excitation source and detect the emission at the same frequency using a commercial lock-in amplifier. The block was first characterized using a commercial thermal cycler and polypropylene tubes with different dilution of initial template copy number, and the results crosschecked with agarose gel electrophoresis. Performing continuous monitoring every 0.7s within cycles, we discovered interesting features during extension which have not been studied previously. During the constant temperature extension step, the fluorescence shows a rise and then saturates until the temperature is cycled to the next set point. We have confirmed the same behavior in single cycle extension control experiments and established its connection with polymerase extension activity. We were thus able to extract the activity rate for two different kinds of polymerase in-situ during PCR. By monitoring PCR reactions with different fixed extension times, we were able to determine the optimum conditions for tube PCR. Chapter 4 implements the ideas of fluorescence monitoring from tube that was explained in the previous chapter for the silicon-glass microchip. Since the microchip uses parameters such as sample volume, ramp rates, stay time etc. which are different from tube PCR, we performed several initial test experiments to establish key capabilities such as low volume detection, 3 µL amplification, surface passivation of silicon-glass etc. The same fluorescence block was used to obtain DNA melting point information by continuously monitoring ds-DNA with SG while the temperature is ramped slowly (melting curve analysis). Depending on ds-DNA present, the fluorescence gives a melting temperature (TM ), which was used to calibrate the mix temperature with respect to the thermocouple sensor. After successfully calibrating the microchip, we confirmed complete chip PCR in silicon-glass devices using induction heater. The continuous monitoring of chip PCR gave similar curves as obtained previously for tubes except that the signal level was lower in silicon devices. Extension fluorescence information was used to find an optimum temperature for microchip that shows a maximum activity rate. Similarly the reaction time was optimized in-situ during PCR by using continuous fluorescence data in a feedback experiment. The commercial lock-in amplifier was also replaced by a homemade circuit to successfully pickup fluorescence signal from the microchip during melting curve analysis. In chapter 5, we describe a novel technique to sense the temperature from the microchip without touching the sample volume. Usually the temperature is monitored by a sensor spatially separated from the mix and it has always been challenging to measure the exact temperature accurately. Most of the sensors are not biocompatible and too large in size to be placed inside the small volume of liquid. We have developed a protocol that involves SG fluorescence with addition of excess sensor DNA to the amplification solution. The sensor DNA added into the mix is non specific to the primer used for amplification of the template. It therefore does not participate in the amplification and its number remains unchanged throughout the 3040 cycles of PCR. If the amount of sensor DNA is titrated accurately, it will saturate the fluorescence envelope which then shows very reproducible thermal response with cycling. We have used this thermal response of the fluorescence for feedback as a temperature sensor. The fluorescence feedback was shown to produce identical amount of product in comparison to thermocouple feedback. The product can also be verified by melting curve analysis if the sensor DNA is chosen carefully depending on the product. In this chapter we also discuss some preliminary experiments with smart devices that will use dye based temperature sensor and control along with fluorescence based amplification monitoring. Chapter 6 summarizes the thesis and discusses some of the future areas which can be explored in the field of microchip PCR devices.