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No. of bitstreams: 1 Danielle Albuquerque Pires Rocha.pdf: 1640322 bytes, checksum: 517abde36a5e28961792c6d782a3d48b (MD5) Previous issue date: 2012-06-25 / FAPEAM - Fundação de Amparo à Pesquisa do Estado do Amazonas / The lack of precision and speed in the laboratory diagnosis of some sexually transmitted infections (STI) are commom problems faced by professionals working in this area. Additionally, the lack of some of them in the public health system become more difficult to elucidate the diagnosis. Because of these difficulties, the STI are underdiagnosed, being treated indiscriminately, using only clinical diagnosis. The molecular diagnostic methods have arisen in recent years as an excellent alternative to fill some of the gaps left by traditional methods. The aim of this research was to study the epidemiology of some sexually transmitted pathogens at molecular level, using molecular biology techniques in women attended in public health system in the city of Coari, Amazonas, Brazil. Samples were collected from 361 women for cervical cytology (Pap Smear) and molecular examination. We carried out molecular diagnosis using the technique of Polymerase Chain Reaction (PCR) and real-time PCR for some sexually transmitted pathogens, which were: Human Papillomavirus, Herpes Simplex Virus 2, Human Cytomegalovirus, Chlamydia trachomatis, Neisseria gonorrhoeae and Thichomonas vaginalis. The results showed that 47.8% of these women were infected by any of the pathogens. There was a high prevalence of infection with Human Papilomavirus (29.1%), followed by T. vaginalis (12.7%), Human Cytomegalovirus (8.3%), C. trachomatis (6.4%), N. gonorrhoeae (1.4%) and Herpes Simplex Vírus 2 (0.6%). The prevalence of HPV type in the infected women was HPV 16 (58.1%), followed by HPV 58 (20.0%). The satisfactory slides for cytological diagnosis (n=321) showed that 7 women (2.1%) showed abnormal cytology (ASCUS, LSIL and HSIL), 5 of them being infected by HPV. There were no statistically significant associations between sexually transmitted infections and the variables related to socio-demographics, medical history and sexual behavior. / A falta de precisão e rapidez no diagnóstico laboratorial de algumas doenças sexualmente transmissíveis (DST) são problemas enfrentados pelos profissionais que atuam nesta área. Além dessas dificuldades inerentes aos testes, a falta de alguns deles na rede pública de saúde dificultam ainda mais a elucidação de diagnósticos. Por causa dessas dificuldades, as DST são subdiagnosticadas, sendo tratadas indiscriminadamente, valendo-se apenas do diagnóstico clínico. Os métodos moleculares de diagnóstico têm surgidos nos últimos anos como uma excelente alternativa para preencher algumas dessas lacunas deixadas pelos métodos tradicionais. Esta pesquisa teve como finalidade estudar a epidemiologia de alguns patógenos sexualmente transmissíveis a nível molecular, valendo-se para isso de técnicas de biologia molecular, em mulheres atendidas na Atenção Primária à Saúde do Município de Coari, Amazonas (AM). Foram colhidas amostras cervicais de 361 mulheres para exame citológico (Papanicolaou) e exame molecular. Foi realizado o diagnóstico molecular através da técnica de Reação em Cadeia da Polimerase (PCR) e PCR em tempo real para alguns patógenos sexualmente transmissíveis, que foram: Papilomavírus Humano, Herpes Vírus Simples 2, Citomegalovírus Humano, Chlamydia trachomatis, Neisseria gonorrhoeae e Trichomonas vaginalis. Os resultados obtidos mostraram que 47,8% dessas mulheres estavam infectadas por algum dos patógenos estudados. Constatou-se alta prevalência de infecção por Papilomavírus Humano (29,1%), seguida pelo T. vaginalis (12,7%), Citomegalovírus Humano (8,3%), C. trachomatis (6,4%), N. gonorrhoeae (1,4%) e Herpes vírus Simples 2 (0,6%). O tipo prevalente de HPV nas mulheres infectadas foi o HPV 16 (58,1%), seguido pelo HPV 58 (20,0%). As lâminas citológicas satisfatórias para diagnóstico (n=321) mostraram que 7 mulheres (2,1%) exibiram alterações citológicas (ASCUS, LSIL e HSIL), estando 5 delas contaminadas pelo HPV. Não foram encontradas associações estatisticamente significativas entre as infecções por patógenos sexualmente transmissíveis e variáveis relacionadas à condições sócio-demográficas, história clínica e comportamento sexual.

FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / Queijo de Coalho à um dos produtos lÃticos mais consumidos no Nordeste do Brasil. No estado do CearÃ, sua produÃÃo à considerada tradicional e apresenta bastante significÃncia econÃmica e social. O queijo de Coalho à tradicionalmente feito com leite cru, o que representa um risco em potencial para a saÃde do consumidor, devido à possibilidade de veiculaÃÃo de microrganismos patogÃnicos. O processo de pasteurizaÃÃo do leite, alÃm de destruir os microrganismos patogÃnicos, reduz tambÃm as bactÃrias Ãcido lÃticas (BAL) que sÃo os microrganismos responsÃveis pelas propriedades sensoriais dos alimentos fermentados. AlÃm do mais, a substituiÃÃo das BAL endÃgenas por fermento lÃtico comercial tem levado a perdas nas propriedades sensoriais do queijo. Este trabalho teve por objetivo identificar, pela tÃcnica da ReaÃÃo em Cadeia da Polimerase (PCR), BAL dos gÃneros Lactococcus e Lactobacillus, previamente identificadas bioquimicamente, isoladas de leite, massa de queijo e queijos de Coalho artesanais produzidos no estado do CearÃ. Os 44 isolados selecionados apresentavam propriedades tecnolÃgicas de interesse para fabricaÃÃo de queijo de Coalho como: capacidade de acidificar o leite, baixa atividade proteolÃtica, capacidade de produÃÃo de aroma e capacidade de tolerÃncia ao NaCl na concentraÃÃo de 3%. As PCR identificaram 20,4% dos isolados como Lactococcus lactis subsp. lactis e 27,3% como Lactobacillus paracasei. Nenhum isolado de Lactobacillus plantarum teve sua identificaÃÃo confirmada pela tÃcnica molecular. Ao todo, 47,7% dos isolados foram confirmados pela PCR, assegurando que estes microrganismos podem ser usados na fabricaÃÃo de queijo de Coalho a partir de leite pasteurizado, mantendo as caracterÃsticas sensoriais tÃpicas deste produto. Este estudo mostra a importÃncia da implantaÃÃo de tÃcnicas moleculares aumentando a qualidade e a eficiÃncia na identificaÃÃo de microrganismos. / Coalho Cheese is one of the dairy products more consumed in Northeast of Brazil. In Cearà state, its fabrication is traditional and has social and economic importance. Traditionally, it is made with raw milk, which represents potential risk for consumers health due to the possibility of foodborne pathogens transmission. The milk pasteurization process eliminates pathogenic microorganisms, but also reduces the lactic acid bacterias (LAB) â the microorganism responsible for sensorial characteristics of fermented foods. Moreover, the substitution of indigenous LAB by commercial lactic ferment has led to losses in the sensorial properties of the cheese. This work aimed to identify, by Polymerase Chain Reaction (PCR), LAB of the genus Lactococcus and Lactobacillus, previously biochemical identified, isolated from milk, curd and traditional Coalho cheeses produced in the state of CearÃ. The forty-four strains selected presented interesting technological properties for the Coalho cheese manufacture: ability to acidify the milk, low proteolytic activity, ability to produce flavor and ability to tolerate 3% NaCl. The PCR identified 20,4% of the isolates as Lactococcus lactis subsp. lactis and 27,3% as Lactobacillus paracasei. No one Lactobacillus plantarum was identified by the molecular technique employed. A total of 47.7% of the isolates were confirmed by PCR, assuring that these microorganisms can be used for Coalho cheese manufacture made from pasteurized milk, preserving the typical characteristics of this product. This work shows the relevance of molecular approaches, increasing the quality and efficiency in the microorganisms identification.

A espécie Escherichia coli constitui um grupo de bactérias tipicamente não patogênicas e que fazem parte do trato intestinal de humanos e animais. As amostras são sorotipadas com base em seus antígenos de superfície O (somático), H (flagelar) e K (capsular). O antígeno flagelar correspondente ao filamento é formado pela polimerização da flagelina, codificada pelo gene fliC. O presente trabalho empregou a técnica de PCR-RFLP para analisar os padrões de antígenos flagelares de 112 amostras de EPEC e STEC. Quatorze amostras não amplificaram o gene fliC, 17 tiveram seu antígeno flagelar determinado apenas por PCR-RFLP e 75 amostras tiveram seus antígenos flagelares confirmados por esta técnica. Três antígenos H com padrões irregulares foram clonados e sequenciados. Após o sequenciamento, inserções e remoções de nucleotídeos foram encontradas. Até o momento, poucos estudos utilizam um número abrangente de amostras de STEC e EPEC provenientes de diferentes animais para a determinação do antígeno H empregando a técnica de PCR-RFLP do gene fliC. De acordo com os resultados encontrados neste estudo, podemos concluir que a técnica de PCR-RFLP do gene fliC é mais rápida, menos trabalhosa e mais eficiente que a metodologia de sorotipagem clássica. / The Escherichia coli species consists of a group of typically non-pathogenic bacteria present in the intestinal tract of humans and animals. Strains are serotyped according to their O (somatic), H (flagellar) and K (capsular) surface antigens, in order to distinguish these microorganisms from the non-pathogenic members of the intestinal microbiota. The flagellar antigen corresponding to the filament is formed by the polymerization of the flagellin, codified by the fliC gene. This study employed the PCR-RFLP technique to analyze flagellar antigen patterns from 112 EPEC and STEC strains. Fourteen strains have not amplified the fliC gene, 17 had their flagellar antigen determined only by the PCR-RFLP and 75 strains had their flagellar antigen confirmed by this technique. Three H antigens with irregular patterns were cloned and sequenced. After sequencing, insertions and deletions of nucleotides were discovered. So far, few studies used a significant number of STEC and EPEC strains originated from different animals to determine H antigens employing the PCR-RFLP technique of the fliC gene. According to the findings of this study, we assumed that PCR-RFLP of the fliC gene is faster, less laborious and more efficient than classic serotyping methodology.

Magister Scientiae - MSc / Sexual assault is a significant problem facing the South African society. In this context, efficient but also affordable genotyping systems are needed for positive identification of criminals in incidences of sexual violence. The aim of this study was therefore to develop non-commercial Y-STR genotyping systems suitable for sexual assault cases in South Africa. Y-chromosome STR loci constituting the minimal haplotype are still the most widely used loci in investigating sexual assault cases despite the fact that DYS391 and DYS392 have shown low levels of polymorphism in Xhosa populations in Cape Town. The minimal haplotype was, therefore, further investigated in the Cape Muslim population. The Cape Muslim population generally exhibited high GD values among all the South African populations. These values were higher than 0.5 for most loci, and ranged from 0.447 for DYS391 to 0.957 for DYS385. The highest number of alleles in most loci was also recorded in this population. The overall assessment of the minimal haplotype has shown that this system is still a useful in investigating sexual assault case in many South African subpopulations. Therefore the exercise of internal validation of the minimal haplotype system was successfully carried out in the laboratory. The properties of additional novel and widely used STRs were also investigated in this study. Loci were successfully sequenced and allele nomenclature was assigned to them according to the ISFG guidelines. / South Africa

Magister Scientiae - MSc / The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters. / South Africa

Magister Scientiae - MSc / The aim of the present study was to evaluate the power of discrimination and genetic (diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categories; Niger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa). / South Africa

Magister Scientiae - MSc / The aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South Africa; a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot® and Multiplex AS-PCR genotyping assays, and also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the Cape Metropolitan area. Two SNaPshot® Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific – PCR (MAS-PCR) genotyping system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan large numbers of samples for novel genetic variations. / South Africa

Isolation of plant DNA is complicated due to the presence of polyphenols, polysaccharides and other metabolites, that are isolated together with DNA. These compounds can affect the yield and quality of DNA and can inhibit a polymerase chain reaction (PCR). A modern, simple, and fast method of DNA isolation in molecular biology laboratories is magnetic separation based on reversible DNA immobilization on magnetic particles. These methods allow to obtain DNA of high quality and purity. In the experimental part, magnetic microparticles PGMA 2 mg/ml and magnetic nanoparticles functionalized by polylysine (PLL) 0,2 mg/ml were used for isolation of plant DNA from vegetables (carrots), fruits (pear, apple, lemon, mango) and heat treated food products for children (Hami first carrot, Nestlé fruit pocket, dmBIO pear carrot apple, Hello fruit snack with apples and Hello fruity snack with mango). The efficiency of separation of magnetic particles with bound DNA using a magnetic needle and a magnetic separator were compared. The quality and quantity of isolated DNA were verified by spectrophotometric analysis. The amplificability of isolated DNA was tested in a conventional PCR using primers specific for plant ribosomal DNA (rDNA). PCR products were analyzed by agarose gel electrophoresis. Major fluorescent bands were of 700, 350 and 220 bp corresponding to three different rDNA amplicons. DNA was isolated from heat treated food products for children in a PCR-ready quality. Only 220 bp long PCR products were detected, that indicated DNA degradation. The identity of PCR products was determined by restriction fragment lenght analysis (RFLP) using NlaIII enzyme cutting the rDNA subregion (ITS1) of Daucus carota (carrot). The digestion profiles were in a good agreement with those predicted from bioinformatic analysis confirming, thus, the specificity of the developed PCR method.

Polymerase chain reaction (PCR) is molecular diagnostic method which allows the identification of lactic acid bacteria used in food industry. In this work species-specific PCR primers (targeted on highly conserved 16S rDNA region) were used for identification of bacteria of species Streptoccocus thermophilus in 10 randomly commercially accessible fermented milk products and for identification of species Streptococcus thermophilus in 25 lyophilisates collected in Culture Collection of Dairy Microorganisms Laktoflora (CCDM, Tábor, Czech Republic). The PCR products (968 bp) were detected using electrophoresis in 1,2 % agarose gel. Bacterial DNA was isolated from crude cell lysates by magnetic carriers P(HEMA co GMA) containing carboxyl groups. DNA was reversibly bind on their surface in the presence of high concentrations of poly(ethylene glycol) (PEG 6000) and sodium chloride. Phenol extraction of DNA was used as control. Streptococcus thermophilus strains were identificated using PCR in all analysed samples.

The aim of this study was focused on the study of conditions of growth of strains Lbc. paracasei subsp. paracasei CCDM 211, Lbc. paracasei CCDM 212, Lbc. paracasei subsp. paracasei CCDM 213 and Lbc. salivarius CCDM 216 in media with different amount of carbon-source (glucose, lactose and whey). Next part of the experiment was dealed with study of conditions of bacteria growth at stress conditions (lower pH). The purity od bacterial culture was verified with help of streaking. Purity DNA isolated from bacteria was tested using agarose gel electrophoresis, DNA concentration was estimated spectrophotometricaly. The presence of bacteria of genus Lactobacillus was proved using polymerase chain reaction (PCR) with genus specific primers.