A PCR Differentiation Method, a hybrid of the US EPA and MOE methods, for quantifying human infectious C. parvum/C. hominis as a group and non-human infectious C. andersoni/C. muris was developed. Primers and probe sets targeting the hsp70 gene were designed for C. andersoni/C. muris; those for C. parvum/C. hominis were obtained from the MOE method. Results showed that C, andersoni/C. muris primers were specific for C. andersoni/C. muris oocysts, while those for C. parvum/hominis primers detected C. parvum/hominis and C. meleagridis. All primers were then used to quantify oocysts from urban and agricultural environmental water samples in Kitchener/Waterloo. Human infectious Giardia lamblia was also incorporated into this study. C. parvum/C. hominis and Giardia lamblia were detected at urban and agricultural areas, whereas C. andersoni/C. muris was only detected at agricultural sites. The PCR Differentiation Method is a reliable method for quantifying Cryptosporidium and Giardia lamblia in environmental water samples. / Best in Science Program of the Ontario Ministry of the Environment, Natural Sciences and Engineering Council (NSERC) of Canada Discovery Grants

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-06-25T21:03:51Z No. of bitstreams: 1 Cristiane Santos Nascimento Uso de método de biologia molecular....pdf: 1323686 bytes, checksum: caf3acf13d85858d02cc05e45a821e9c (MD5) / Made available in DSpace on 2012-06-25T21:03:51Z (GMT). No. of bitstreams: 1 Cristiane Santos Nascimento Uso de método de biologia molecular....pdf: 1323686 bytes, checksum: caf3acf13d85858d02cc05e45a821e9c (MD5) Previous issue date: 2011 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil / INTRODUÇÃO: A leishmaniose visceral humana (LVH) é uma importante causa de morbidade e mortalidade no Brasil. Apesar dos avanços no conhecimento da epidemiologia da LVH, ainda existem lacunas importantes nas informações sobre os principais reservatórios desta zoonose. A técnica validada para avaliação da infectividade de reservatórios, xenodiagnóstico, é um método laborioso, demorado e difícil de executar, portanto, inapropriado para a triagem de grande número de animais. A padronização de método capaz de quantificar a carga parasitária presente em diferentes tecidos pode oferecer respostas importantes sobre a epidemiologia e a prevenção da LVH. OBJETIVO: Avaliar a carga parasitária em diferentes amostras biológicas de cães naturalmente infectados por Leishmania chagasi, utilizando método de biologia molecular quantitativo, PCR real-time (qPCR). MÉTODOS:Entre nov/2004 e abr/2007, foram realizados seis inquéritos soro-epidemiológicos em duas áreas endêmicas para LVH. Os cães soropositivos foram eutanasiados e submetidos a: exame de cultura, parasitológico direto e exame histológico para confirmação da infecção. Amostras de sangue periférico e fragmento de pele foram coletadas em todos os animais para determinação da carga parasitária. Adicionalmente, coletou-se também swab da conjuntiva, aspirado de medula óssea e linfonodo para realização do teste de qPCR nos cães incluídos no último inquérito (abr/2007). A técnica de qPCR foi padronizada utilizando um par de primers LEIF e LEIR e sonda LEIP selecionados no gene SSu rRNA. A seleção dos primers e sonda foi realizada utilizando o programa Primer Express (Perkin-Elmer-Applied Biosystems). A sonda fluorogênica foi sintetizada utilizando uma molécula FAM ligada na extremidade 5‟ e TAMRA ligada à extremidade 3‟(Perkin-Elmer -Applied Biosystems). Para determinar a carga parasitária foi realizada curva padrão com o DNA obtido da cultura de L. chagasi em concentrações variando de 101 a 107 parasitas/ml. Cada ponto da curva foi testado em triplicata. RESULTADOS: Dos 98 cães soropositivos identificados, foi detectado DNA de Leishmania em 57% das amostras de sangue total, em 56% das amostras de pele e em 100% das amostras de medula óssea, linfonodos e swab da conjuntiva. A carga parasitária em sangue periférico e swab da conjuntiva não ultrapassou 103 parasitas/ml sendo mais comumente detectado 1 a 10 parasitas/ml. Por outro lado, em pele, medula óssea e linfonodos a carga parasitária passou de 104 parasitas/ml, além disso, as quantidades de DNA detectadas se distribuíram com maior freqüência na categoria acima de 104 parasitas/ml, notadamente em amostras de linfonodos. CONCLUSÕES: O qPCR apresentou alta sensibilidade nas amostras biológicas estudadas, particularmente em linfonodos , medula óssea e pele. Nossos resultados indicam que o qPCR pode ser utilizado numa variedade de amostras biológicas para a quantificação da carga parasitária de cães naturalmente infectados por Leishmania sp. Estudos de validação do qPCR para avaliar a capacidade de reservatórios da LV, em lugar do xenodiagnóstico, e para investigar o papel do qPCR na triagem de cães em programas de controle/prevenção da LV devem ser conduzidos. / INTRODUCTION: Human visceral leishmaniasis (LVH) is an important cause of morbidity and mortality in Brazil. Despite advances in knowledge of the epidemiology of LVH, there are still important gaps in information on the main reservoirs of this zoonotic disease. The validated technique for assessing the infectivity of reservoirs, xenodiagnosis, is laborious, time consuming and difficult to implement, therefore, inappropriate for screening large numbers of animals. A standardized method to quantify the parasite load present in different tissues may provide important answers on the epidemiology and prevention of LVH. OBJECTIVE: To assess the parasite load in different biological samples from dogs naturally infected by Leishmania chagasi using a molecular biology quantitative method, real-time PCR (qPCR). METHODS: From nov/2004 to apr/2007, six seroepidemiological surveys were conducted in two endemic areas for LVH. The seropositive dogs were euthanized and submitted to: culture, direct parasitological and histological examination to confirm infection. Blood samples and skin fragments were collected in all animals to determine the parasite load. Additionally, conjuntival swabs, bone marrow and lymph node aspirates were also collected to do qPCR in dogs included in the last survey (apr/2007). The qPCR technique was standardized using a pair of primers and probe and LEIF /LEIR and LEIP selected in the SSU rRNA gene. The selection of primers and probe was performed using the program Primer Express (Perkin-Elmer-Applied Biosystems). The fluorogenic probe was synthesized using a FAM molecule attached at the 5 'end and TAMRA linked to the 3' end (Perkin-Elmer-Applied Biosystems). In order to determine the parasite load a DNA standard curve was plotted with DNA obtained from L. chagasi culture in concentrations ranging from 101 to 107 parasites/ ml. Each point on the curve was tested in triplicate. RESULTS: Of the 98 seropositive dogs identified Leishmania DNA was detected in 57% of the whole blood samples, 56% of the skin samples and 100% of bone marrow, lymph nodes and conjuntival swabs samples. The parasite load in peripheral blood and conjuntival swab did not exceed 103 parasites/ml, and was more commonly in the range of 1-10 parasites /ml. On the other hand, skin, bone marrow and lymphnode parasite burden exceeded 104 parasites / ml, in addition, the quantities of DNA detected were distributed more frequently in the category above 104 parasites/ml, especially in lymphnodes samples. CONCLUSIONS: qPCR showed high sensitivity in biological samples studied, particularly in lymphnodes, bone marrow and skin. Our results indicate that qPCR could be used in a variety of biological samples to quantify the parasite load in dogs naturally infected by Leishmania sp. qPCR validation studies to assess potential reservoirs for VL (replacing xenodiagnosis), and to investigate the role of qPCR in dog screening programs for the control/prevention of LV should be conducted.

Submitted by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-12-01T19:00:57Z No. of bitstreams: 1 Tese - José Maria Cabral.pdf: 2564703 bytes, checksum: 7c12bbf1d7242ebf4c86cdbdfcc713e1 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-12-01T19:01:29Z (GMT) No. of bitstreams: 1 Tese - José Maria Cabral.pdf: 2564703 bytes, checksum: 7c12bbf1d7242ebf4c86cdbdfcc713e1 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-12-01T19:01:46Z (GMT) No. of bitstreams: 1 Tese - José Maria Cabral.pdf: 2564703 bytes, checksum: 7c12bbf1d7242ebf4c86cdbdfcc713e1 (MD5) / Made available in DSpace on 2016-12-01T19:01:46Z (GMT). No. of bitstreams: 1 Tese - José Maria Cabral.pdf: 2564703 bytes, checksum: 7c12bbf1d7242ebf4c86cdbdfcc713e1 (MD5) Previous issue date: 2013-11-28 / Hunter syndrome, or mucopolysaccharidosis II is one of the seven types of MPSs, lysosomal storage diseases inserted in the inborn errors of metabolism universe. Mutations in iduronate-2-sulfatase gene (IDS) cause deficiency of the homonymous enzyme activity and define the accumulation of GAG heparan and dermatan sulfate in the lysosomes, leading to dysfunction of cells, tissues and organs and clinical manifestations of wide phenotypic variety. The measures of the IDS gene expression in leukocytes by PCR in real time relative values evaluated by cDNA, were low in all five patients amazonenses in repeated tests, including in subjects with symptoms suggestive and no biochemical evidence. The partial sequencing of genomic DNA by choice of exon 9, home region of most mutations in Brazilian patients, to verify the presence of point mutation in all patients allowed to question the standard status gold of biochemical measurement of IDS enzyme for diagnosis. The use of PCR real time, via high-resolution melting analysis (HRM), proved to be useful for the identification of women with the mutant allele. Sequencing and HRM should be inserted in the flowchart for the confirmation of the disease with the accuracy of the advantages of early diagnosis and genetic counseling in more scientific basis. Plasma levels of manganese (Mn++) and B vitamins (pyridoxine and cobalamin) proved the deficiency of these items in patients and families, denouncing nutritional deficiency. Discusses the hypothesis that hipomanganesemia is directly related to low activity of IDS enzyme. The hypovitaminosis B6 and B12, in turn, can be related to hiperhomocistinemia / hypomethylation and changes in the methylation pattern of the IDS gene, further modifying gene expression and phenotypic defining multiple frames. This study advances the understanding of epigenetic accustomed processes to Hunter syndrome and justifies the development of new research in which a broader approach to validate low-cost therapeutic measures that are established in early childhood, pre-symptomatic, may prove to be able to modify the natural history of the disease to ensure greater efficiency of enzyme therapy and more favorable clinical outcome. / A Síndrome de Hunter ou Mucopolissacaridose II representa um dos sete tipos de MPSs, doenças de depósito lisossômico inseridas no universo dos erros inatos do metabolismo. Mutações no gene iduronato-2-sulfatase (IDS) causam deficiência da atividade da enzima homônima e definem o acúmulo de GAGsheparan e dermatan sulfato nos lisossomos, levando à disfunção de células, tecidos e órgãos e manifestações clínicas de ampla variedade fenotípica. As medidas da expressão do gene IDS em leucócitos através da PCR em tempo real, avaliadas pelos valores relativos de cDNA, foram baixas em todos os cinco pacientes amazonenses, em testes repetidos,inclusive no indivíduo com clínica sugestiva e sem comprovação bioquímica.O sequenciamento parcial do DNA genômico por escolha do éxon 9, região sede da maioria das mutações em pacientes brasileiros,ao constatar a presença de mutação pontual em todos os pacientes estudados, permitiu questionar o status de padrão ouro das dosagens bioquímicas da enzima IDS para o diagnóstico. O emprego da PCR real time, via análise de fusão de alta resolução (HRM), mostrou-se útil para a identificação das mulheres portadoras do alelo mutante. Sequenciamento e HRM devem ser inseridos no fluxograma para a confirmação da doença com as vantagens da precisão do diagnóstico precoce e do aconselhamento genético em bases mais científicas. As dosagens plasmáticas de manganês (Mn++) e de vitaminas do complexo B (piridoxina e cobalamina) comprovaram a deficiência desses itens em pacientes e familiares, denunciando carência nutricional. Discute-se a hipótese de que a hipomanganesemia esteja diretamente relacionada à baixa atividade da enzima IDS. As hipovitaminoses B6 e B12, por sua vez, podem estar relacionadas à hiperhomocistinemia/hipometilação e alterações no padrão de metilação do gene IDS, modificando ainda mais a expressão do gene e definindo quadros fenotípicos múltiplos. Este estudo avança no entendimento dos processos epigenéticosafeitos à síndrome de Hunter e justifica o empreendimento de novas pesquisas, nas quais uma abordagem mais ampla possa validar medidas terapêuticas de baixo custo que se instituídas em idade mais tenra,pré-sintomática,podem revelar-se capazes de modificar a história natural da doença aogarantir maior eficiência da terapia enzimática e evolução clínica mais favorável.

<p>Chlamydia and gonorrhea are major causes of sexually transmitted infections (STI) in adolescents worldwide. The infections are caused by <em>Chlamydia trachomatis</em> or <em>Neisseria gonorrhoeae, </em>bacteria with clinical manifestations such as urethritis, prostatitis and epididymitis among men, and urethritis, cervicitis and upper genital tract infection (i.e. pelvic inflammatory disease) among women. However, in many cases of genital tract infection, the etiology remains uncertain. In light of this, <em>Mycoplasma genitalium</em> was somewhat accidentally isolated in 1980 after prolonged incubation of urogenital specimens from men with non-gonococcal urethritis. Following the initial isolation in 1980, repeated attempts have been made to recover the extremely fastidious organism from clinical samples by culture techniques, but isolates have been rare and difficult to obtain. With the development of PCR methods in the early 1990s, detection of <em>M. genitalium</em> infection became more feasible.</p><p>The aim in paper <strong>I</strong> was to compare three different PCR assays (conventional and real-time 16S rRNA gene PCR as well as real-time <em>Mycoplasma genitalium</em> adhesin protein (MgPa) gene PCR) for detection of <em>M. genitalium</em>. The study also determined the prevalence of <em>M. genitalium</em>. Clinical specimens collected from STI attendees, 381 men and 298 women, were used to determine the prevalence of <em>M. genitalium</em> and 213 of these specimens were used in the PCR comparative study. The prevalence of <em>M. genitalium</em> infection in men and women was 27/381 (7.1 %) and 23/298 (7.7 %) respectively. In the PCR comparative study, <em>M. genitalium </em>DNA were detected in 61/76 (80.3 %) of true-positive specimen by conventional 16S rRNA gene PCR, in 52/76 (68.4 %) by real-time 16S rRNA gene PCR and in 74/76 (97.4 %) by real-time MgPa gene PCR. Hence, real-time MgPa gene PCR is well suited for clinical diagnosis of <em>M. genitalium</em> in urogenital specimens from men and women.</p><p>The aim in paper <strong>II</strong> was to determine whether a patients’ endocervical swab specimen can be transported in first void urine (FVU) as combined specimens in detection of <em>Mycoplasma genitalium </em>by real-time PCR. The study also compared two different DNA extraction methods (manual Chelex DNA extraction and automated BioRobot M48 DNA extraction) for observation of possible PCR inhibition. Clinical specimens collected from 329 women attending a STI clinic were used in the study. A total of 100 endocervical swab specimens transported in FVU was used in the PCR inhibition analysis. <em>M. genitalium</em> was detected in 25/329 (7.6 %) women. Endocervical swab specimens transported in FVU demonstrate higher sensitivity compared to both FVU alone and specimens transported in 2-SP medium detecting 24/25 (96 %), 22/25 (88 %) and 17/25 (68 %) of <em>M. genitalium</em> positive women, respectively. Automated BioRobot M48 DNA extraction was shown to be superior to manual Chelex extraction leaving no PCR inhibition and slightly higher DNA yield and/or better sensitivity. The results from these two studies are important knowledge in establishing the future diagnostic level of this STI in our county and also nationally.</p>

In recent years, foods produced by genetic engineering technology have been on the world food market. The biosafety aspects, regulations, and labelling of these foods are still contentious issues in most countries. It is necessary to have approval for the use of GMOs in the production of food. Thus, detection and quantification of GMOs play crucial role for developing regulations on GM foods. In this study, raw and processed maize samples were analysed for genetic modification using a DNA based detection method, the Polymerase Chain Reaction. Ten raw food and 18 processed maize food including maize flour, starch, corn flakes, maize chips were collected from different markets located in different places in Turkey. The samples were examined for the presence of genetic elements located in the majority of transgenic crops such as NOS terminator, CaMV 35S promoter, kanamycin resistance (KanR) gene, using conventional PCR with oligonucleotide sets targeting to novel genes. Furthermore screening was conducted via Real-Time PCR assay for NOS terminator and 35S promoter. For confirming the presence of Bt11 maize lines event specific primers were utilised. Quantification of Bt11 maize lines were performed via Real-Time PCR. The result indicates that foreign genetic elements were found in all analysed raw material. In six out of 10 raw material, presence of Bt11 gene were identified. GMO detection was also possible for maize flour and starch, however in processed material as corn starch, corn flakes, corn chips and pop corn, transgenes were not detected.

No description available.

Real-time PCR method is a type of PCR which allows continual monitoring of DNA amplification during every cycle of its process. It is mostly used for gene expression analysis. Based on the results of previous experiments, we decided to test out the effect of anticoagulants EDTA, heparin, sodium citrate and CPDA on the expression of selected genes of the immunological spectrum and further, to test how the time period between drawing the blood and processing of blood sample influences mRNA levels of selected genes that are determined by changes in gene expression and/or mRNA degradation. To quantify mRNA of the studied genes, we isolated total RNA from the peripheral blood leucocytes and transcribed it into cDNA by using the reverse transcription PCR. This cDNA served as a template for the real-time PCR. To examine the changes of the expression caused by the effect of each particular anticoagulants, peripheral blood derived from 10 volunteers was used (each donor's blood was taken into 3 vacuum tubes with EDTA, heparin and sodium citrate anticoagulant agents). Next to that, we obtained 10 buffy coat samples in transfusion blood bags with CPDA anticoagulant agent. Compared to blood cells influenced by one of the three anticoagulant agents present in vacuum tubes, cells from transfusion bags affected...

Made available in DSpace on 2015-04-11T13:38:41Z (GMT). No. of bitstreams: 1 Dissertacao-Janaina Roriz Hipolito.pdf: 4312682 bytes, checksum: ecb7ef268b16e006660e9770d5f663b4 (MD5) Previous issue date: 2006-07-28 / Fundação de Amparo à Pesquisa do Estado do Amazonas / A malária é um problema de saúde pública na região Amazônica, mais de 200 mil casos dessa doença ocorrem anualmente no Amazonas, sendo 80% deles causados pelo P. vivax, que vem apresentando índices crescentes de morbidade, principalmente associados à diminuição da sensibilidade aos antimaláricos. Dentre as estratégias para combate e controle da doença, a identificação rápida e precisa da espécie é ferramenta indispensável para um tratamento apropriado, diminuição do risco de transmissão e melhor entendimento da epidemiologia desses parasitas. A técnica microscópica da gota espessa é a principal para diagnóstico da malária, entretanto, outros métodos vêm sendo testados, principalmente os moleculares que tem se mostrado mais sensíveis e específicos para detectar e diferenciar as espécies em baixas parasitemias. Avanços desse método, como a PCR em tempo real, permitem que o resultado do teste seja detectado simultaneamente a amplificação, diminuindo o tempo gasto para a realização do diagnóstico. Com o intuito de detectar molecularmente a malária, verificando a presença de plasmódios, o diagnóstico molecular foi realizado através das técnicas de PCR em tempo real e nested-PCR, para se fazer uma comparação desses dois métodos com o diagnóstico microscópico da gota espessa em 300 amostras criopreservadas, 200 coletadas no dia inicial do tratamento (D0), das quais 88% (176/200) eram provenientes de pacientes de Manaus, as 24 amostras restantes (12%) eram provenientes de localidades do interior do Amazonas: São Gabriel da Cachoeira (09), Tefé (08), Humaitá (04) e Careiro (03). Apenas 9% dessas amostras tinham diagnóstico microscópico de monoinfecção por P. falciparum e 91% (182/200) por P. vivax, não havia nenhuma amostra mista pelo diagnóstico microscópico. O diagnóstico molecular por nested-PCR confirmou a presença de DNA de plasmódio em 100% das amostras monoinfectadas. Adicionalmente, foram observadas infecções mistas, co-infecção de P. falciparum e P. vivax, em 19% (38/200) destas amostras. O diagnóstico molecular por PCR em tempo real (Lightcycler, Roche®) foi realizado em apenas 17% (34/200) dessas amostras. A co-positividade (sensibilidade) dos testes para P. vivax foi em média 71% e a co-negatividade (especificidade) 92%, para P. falciparum a co-positividade foi 91% e a conegatividade 79%. A concordância entre os testes foi regular. As 100 amostras restantes haviam sido coletadas no sétimo dia (D7) de tratamento e eram negativas pela microscopia. O diagnóstico molecular demonstrou 21% de positividade. Este estudo mostrou que muitas infecções mistas vêm sendo subestimadas para fins de avaliação epidemiológica, demonstrando que a sensibilidade e especificidade do diagnóstico molecular são superiores a do teste microscópico. O diagnóstico molecular seria então mais indicado como teste complementar no diagnóstico de pacientes com baixas parasitemias, na análise da quantidade de portadores assintomáticos, em estudo de infecções criptônicas e na avaliação da negativação da parasitemia para monitoramento terapêutico, e em estudos que visem a diminuição da transmissão pela existência de prováveis gametócitos persistentes após o tratamento. Entretanto, esse método não é indicado para rotina de diagnóstico de malária, uma vez que os resultados positivos por essa técnica não significam necessariamente que o paciente desenvolva a doença.

This study was carried out to analyze tomato samples and tomato seeds, purchased from different food markets of Turkey randomly, for the presence of genetic modification by using PCR method as it allows more specific detection. The DNAs of collected samples were isolated according to CTAB DNA extraction protocol and also with extraction kits. Screening tests of tomatoes were done by targeting 35S promoter, NOS terminator and NptII kanamycin resistance gene with eight different primer sets. Real time PCR is used to confirm 35S and NOS positives results obtained from conventional PCR. In this study, it was observed that 14 out of 35 seed samples, and 14 out of 40 fresh tomato samples which were screened had at least one transgenic element of 35S promoter, NOS terminator and NPTII kanamycin resistance gene indicating the possible presence of genetic modifications. After screening, gene specific studies were carried out for PG, sam-k indicating F type ripening delayed tomato and the 35 1 N lines respectively and cry1Ac genes inserted in 5345-1 insect resistant tomato line. PG and sam-k specific primers were not amplified in any of the samples investigated whereas 18 out of 75 samples were cry1Ac positive and 1 out of 75 samples was sam-k positive. Positives were confirmed by sequence analysis. Additionally, construct specific primers specific to 5345-1 and 35 1 N lines were designed. PCR amplicons indicate the existence of the construct sequence. In order to verify the results, PCR products were sent to sequence analysis

No description available.