Rozprawy doktorskie: „Real-time PCR”

1

Crane, Bryan Lee 1976. "Real time PCR measurement by fluorescence anisotropy". Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/30347.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, February 2005.
Page 230 blank.
Includes bibliographical references (p. 181-190).
Real-time polymerase chain reaction (PCR) is the gold-standard for quantitation in both mutation and gene expression analyses. Already this technique has found valuable clinical application in disease diagnosis and progression evaluation. As the number of known gene-disease correlations continues to rise, there will be increased demand for higher throughput and decreased cost for these analyses. Present real-time PCR measurement is based upon the fluorescent intensity of either intercalating dyes or oligonucleotide probes. Intercalating dye methods suffer from a lack of binding specificity, while probe methods are expensive and require increased assay optimization. In this thesis, a new method is presented for monitoring real-time PCR that utilizes the fluorescent anisotropy (FA) of labeled primers. FA, when measured at constant temperature, is indicative of the molecular mass to which the fluorophore is attached. Specificity is improved with the FA method over the use of intercalating dyes since the selective binding of primers is required for signal change. Assay complexity and cost are reduced compared to fluorogenic probe methods since the probes are eliminated. The design of a prototype instrument, which successfully implements this new method, is presented. Instrument and assay performance are compared to intercalating dye assays run in commercially available instrumentation. Theoretical limits on performance are also presented and compared to experimental results. Excellent repeatability and linearity are observed with respect to these benchmarks. This new method, having both high specificity and low optimization complexity, is expected to be particularly applicable to the demanding robustness requirements of nano-scale PCR.
by Bryan Lee Crane.
Ph.D.

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Rozales, Franciéli Pedrotti. "Real time-pcr e nested-pcr no diagnóstico da tuberculose pulmonar". reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2013. http://hdl.handle.net/10183/72990.

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A tuberculose (TB) é um importante problema de saúde pública, portanto, é necessário o desenvolvimento de novas ferramentas para a detecção rápida e confiável do Mycobacterium tuberculosis, prevenindo a transmissão da TB. O objetivo deste estudo foi avaliar dois testes moleculares para detecção de bactérias do Complexo Mycobacterium tuberculosis (MTBC) diretamente de amostras clínicas. Foi realizado um estudo transversal, no qual foram selecionadas 124 amostras respiratórias. As amostras foram avaliadas por dois testes moleculares “in house” para detecção do MTBC: NESTED-PCR (NPCR) e Real Time PCR (RT-PCR) ambos com primers para o IS6110. As amostras também foram avaliadas por um teste direto (pesquisa de BAAR). Os resultados foram comparados com a cultura para M.tuberculosis e também com os resultados da cultura juntamente com dados clínicos. Uma amostra comercial com quantificação de DNA conhecida foi utilizada para determinação do Limite de Detecção (LOD) dos testes moleculares. O LOD foi de 1 cópia/μL para o RT-PCR e de 25 cópias/μL para o NPCR. O BAAR apresentou baixa sensibilidade - SE - (40%) e alta especificidade - SP - (94%). Ambos os ensaios moleculares, apresentaram elevada SE e SP (RT-PCR 98% e 91%, NPCR 86% e 93%, respectivamente) em relação à cultura. Quando comparamos os resultados frente a cultura juntamente com os dados clínicos, a SE e a SP foram de 90% e 97% para a RT-PCR e de 80% e 99% para a NPCR, respectivamente. Houve um pequeno decréscimo da SE dos métodos moleculares, quando comparados com a cultura mais os dados clínicos em relação à cultura isoladamente, no entanto, a SP foi consideravelmente elevada para os três métodos avaliados. Avaliamos o custo dos insumos para os ensaios moleculares: o custo do NPCR foi de $ 17.77/teste enquanto que o custo do RT-PCR foi de $ 15.76/teste. Em relação ao tempo de execução dos testes o RT-PCR foi mais rápido (2 horas) do que o NPCR (4 horas). Este estudo confirma que técnicas de PCRs podem ser muito úteis para o diagnóstico rápido da TB respiratória, com altas taxas de SP. Ele também pode ser muito importante para a exclusão de diagnóstico, considerando o alto VPN encontrados no nosso estudo. Os resultados demonstraram que os ensaios moleculares visando IS6110 do M. tuberculosis podem ajudar a melhorar o diagnóstico da TB pulmonar, com muitos potenciais efeitos positivos para a gestão clínica e de controle da doença.
Tuberculosis (TB) remains as an important public health problem worldwide. Therefore, the rapid detection of M. tuberculosis is of primary importance to effectively reduce transmission among patients. The aims of this study were to evaluate two molecular tests to detect M. tuberculosis complex (MTBC) directly from clinical samples. The study included 124 respiratory samples which were evaluated by two in house molecular assays for MTBC detection: Nested PCR (NPCR) and Real Time PCR (RT-PCR). The respiratory samples were also evaluated by the direct test (AFB assay). The results were compared with the results of culture and also compared with the culture results plus clinical data of patients. We used a commercial DNA sample with known quantification to establish the Limit of Detection (LOD). The LOD was 1 copy/μL for RT-PCR and 25 copies/μL for NPCR. The AFB assay presented low sensitivity – SE - (40%) and a high specificity - SP – (94%). Both molecular assays, RT-PCR and NPCR presented high SE and SP (RT-PCR 98% and 91%, NPCR 86% and 93%, respectively) compared to culture. When the results of the molecular tests were compared to the culture plus clinical data the SE and SP were 90,20% and 97,26% for RT-PCR and 80,39% and 98,63% for the NPCR, respectively. It was possible to observe a slight decrease of SE of the molecular methods in comparison to culture plus clinical data in relation to culture; however, the SP was increased, since many cases of TB could not be confirmed by culture. Furthermore we evaluated the cost of molecular assays: the NPCR cost was $17.77/test while the RT-PCR cost was $15.76/test. The RT-PCR test was faster (2 hours) than the NPCR (4 hours) to be performed. Our study confirms that PCRs may be useful for rapid diagnosis of respiratory TB, with high SP rates. It may also be very important to exclude such diagnosis, considering the high NPV found in our study. In summary, PCRs targeting IS6110 of MTB improve the accuracy of the diagnosis of pulmonary TB, with many potential positive effects for clinical management and control of the disease.

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Pires, Elisabete Sofia Videira. "Real-Time PCR, High Resolution Melting - aplicações forenses". Master's thesis, Universidade de Aveiro, 2012. http://hdl.handle.net/10773/10747.

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Mestrado em Biologia Molecular e Celular
Apontada como a maior revolução científica na área forense desde a descoberta das impressões digitais, a identificação humana por meio da análise do DNA tornou-se uma poderosa ferramenta de investigação, auxiliando na elucidação de casos forenses, baseando-se cientificamente na existência de polimorfismos genéticos ao longo do genoma em indivíduos diferentes, que faz com que cada pessoa possua um código genético único. Com a introdução da real-time PCR nas investigações forenses, tornou-se possível uma análise sensível e específica de regiões polimórficas tanto no genoma nuclear como no mitocondrial, a partir de quantidades ínfimas de DNA obtidas de amostras altamente degradadas ou com baixo número de cópias. A quantificação do DNA é um procedimento importante na análise forense e deve ser efetuado, previamente, a qualquer análise de DNA. A união entre a bioinformática e a genética forense propiciou a criação de métodos de análise específicos, como a HRM, muito útil na genotipagem de SNPs, de extrema importância na investigação forense. Foi elaborada uma revisão bibliográfica com o objetivo de conhecer as aplicações forenses da real-time PCR e os respetivos métodos, tendo se confirmado então a aplicabilidade deste método na área forense.
Listed as the greatest revolution in forensic science since the discovery of fingerprints, identification by analyzing human DNA has become a powerful research tool, helping to elucidate forensic cases, scientifically based on the existence of genetic polymorphisms throughout the genome at different individuals, which causes that each person has a unique genetic code. With the introduction of real-time PCR in forensic investigations, it became possible a sensitive and specific analysis of polymorphic regions both in the mitochondrial and nuclear genome, from minute quantities of DNA obtained from samples highly degraded or low copy number. The quantification of DNA is an important procedure in forensic analysis and must be made in advance to any DNA analysis. The union between forensic genetics and bioinformatics led to the creation of specific analysis methods, such as HRM, very useful in scanning and genotyping of SNPs, of utmost importance in forensic investigation. A literature review has been prepared in order to meet the forensic applications of real-time PCR and related methods, and so been confirmed the applicability of this method in the forensic field.

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Dunkley, Kingsley Delroy. "Modulation of cell yields and genetic responses of Salmonella fermentation and colonization in the gastrointestinal ecology of avian species". [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1187.

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Andalo, Alice. "Analisi quantitativa dell'espressione genica mediante real-time rt-pcr". Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amslaurea.unibo.it/8450/.

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Il primo capitolo di questo lavoro di tesi introduce i concetti di biologia necessari per comprendere il fenomeno dell’espressione genica. Il secondo capitolo descrive i metodi e le tecniche di laboratorio utilizzate per ottenere il cDNA, il materiale genetico che verrà amplificato nella real-time PCR. Nel terzo capitolo si descrive la tecnica di real-time PCR, partendo da una descrizione della PCR convenzionale fino a delineare le caratteristiche della sua evoluzione in real-time PCR. Si prosegue con la spiegazione del principio fisico alla base della tecnica e delle molecole necessarie (fluorofori e sonde) per realizzarla; infine si descrive l’hardware e il software dello strumento. Il quarto capitolo presenta le tecniche di analisi del segnale che utilizzano metodi di quantificazione assoluta o relativa. Infine nel quinto capitolo è presentato un caso di studio, cioè un’analisi di espressione genica con real-time PCR condotta durante l’esperienza di tirocinio presso il laboratorio ICM. e delle molecole necessarie (fluorofori e sonde) per realizzarla; infine si descrive l’hardware e il software dello strumento. Il quarto capitolo presenta le tecniche di analisi del segnale che utilizzano metodi di quantificazione assoluta o relativa. Infine nel quinto capitolo è presentato un caso di studio, cioè un’analisi di espressione genica con real-time PCR condotta durante l’esperienza di tirocinio presso il laboratorio ICM.

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Dörries, Hans-Henno. "Entwicklung von Real-Time-PCR-Nachweissystemen für getränkerelevante Hefen". [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=979663938.

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Hartmann, Britta. "Entwicklung einer Real-time-PCR-Nachweismethode für Yersinia enterocolitica". [S.l.] : [s.n.], 2007. http://edoc.ub.uni-muenchen.de/archive/00006660.

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Hartmann, Britta. "Entwicklung einer Real-Time PCR-Nachweismethode für Yersinia enterocolitica". Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-66603.

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Malatji, Dikeledi Petunia. "Detection of Babesia rossi genotypes using real-time PCR". Diss., University of Pretoria, 2011. http://hdl.handle.net/2263/31138.

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Babesia rossi is the most virulent Babesia species in dogs occurring in South Africa and is associated with severe clinical manifestation and mortalities. Babesia rossi is highly pathogenic and reacting dogs requires treatment to prevent mortalities. Mild, uncomplicated forms of the disease are effectively treated with antibabesial drugs. Complicated forms of the disease are difficult to treat with high mortality rate.This results in the disease being of economic importance in South Africa. There is a lack of information regarding the relationship between parasite genotype and disease phenotype. The broad objective of this study is to detect B. rossi genotypes using real-time PCR. This test is a method that can be used to monitor amplicon formation throughout the PCR reaction and to estimate the initial concentration of target DNA in samples. Polymerase chain reaction, sequencing and phylogenetic analysis were used to determine the genotype detection of Babesia rossi isolated from infected dogs in South Africa. The correlation between the parasite genotype and disease phenotype was also investigated. Correlation between B. rossi Erythrocyte Membrane Antigen (BrEMA1) genotypes and age of dogs was studied in 44 cases. A total of 101 blood samples were tested using the reverse line blot (RLB) assay. Ninety six percent hybridized to the Babesia rossi species-specific probe. Our findings demonstrate that the most encountered (BrEMA1) genotype is genotype29, followed by genotype28 and genotype19, with genotype29 associated with most of the severe clinical signs diagnosed compared to genotype19. The number of cases caused by genotype19 was low, constituting 22% of the cases. This is comparable with the 2009 report where genotype19 appeared highly prevalent and virulent, whereas the prevalence of genotype28/29 appeared moderate. In this dissertation, we present the first report on the detection of an amplification product of BrEMA1 genotypes using real-time PCR. Samples which were below the detectable limit of conventional PCR and could not be sequenced probably due to low parasitaemia were also used and real-time PCR provided the ability to detect B. rossi positive animals. This was able to detect 10 BrEMA1 genotypes. However, it was not reliable enough in differentiating between various BrEMA1 genotypes. When evaluating the relationship between BrEMA1 genotypes, clinical manifestation and age of the dogs, collapse was found to be a poor prognostic sign in dogs with babesiosis. Genotype29 was associated with most of the collapsed cases and with high number of the dogs that died. Although B. rossi can infect dogs of all ages, young dogs showed to be more susceptible to canine babesiosis than older dogs. This is in agreement with the survey carried out from the Onderstepoort Veterinary Academic Hospital (OVAH) in 1994. Since B. rossi is the most pathogenic species of the large babesias of dogs, the ability to manage the disease is dependent on rapid detection of the organism. Real-time PCR test is indeed a quicker method to confirm diagnoses of B. rossi infected dogs. It can detect B. rossi infection at a low DNA concentration (0.185 ng/μl) which provides a major advantage in detecting B. rossi infection in field blood samples.
Dissertation (MSc)--University of Pretoria, 2011.
Veterinary Tropical Diseases
MSc
Unrestricted

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Zhang, Yan. "Frequent RASSF1A gene promoter hypermethylation in breast cancer". [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:289-vts-63611.

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Landgraf, Maria. "Detection of food relevant filamentous fungi by real time PCR". [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=98023946X.

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Tolardo, Aline Lavado. "Desenvolvimento e aplicação de RT-PCR em tempo real para Vesiculovirus brasileiros". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/17/17138/tde-21102015-110512/.

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Os Vesiculovirus são um gênero de vírus de RNA da família Rhabdoviridae que inclui os sorotipos Carajás, Cocal, Marabá, Piry, Alagoas e Indiana. Estes são causadores de estomatite vesicular em ruminantes e doença febril humana no Brasil. As vesiculoviroses e suas epidemiologias são pouco conhecidas em seres humanos. Ainda, os Vesiculovirus (VSV) são pouco diagnosticados no homem e em animais pela escassez de métodos laboratoriais diagnósticos. Por isso, objetivamos neste trabalho desenvolver e testar uma RT-PCR em tempo real, pelo método SYBR Green, visando à detecção de VSV brasileiros. Primers que amplificam parte do gene da proteína G dos VSV foram utilizados no teste o qual mostrou-se capaz de detectar genomas dos VSV Piry, Indiana, Alagoas e Carajás. O método foi usado para testar amostras séricas de pacientes com doença febril aguda, de bovinos, de equinos e de macerados de artrópodos. A RT-PCR em tempo real mostrou-se 100 vezes mais sensível que a RT-PCR convencional para Vesiculovirus e também, permitiu detectar até 10 cópias de RNA do vírus Piry. Ainda, a RT-PCR em tempo real para Vesiculovirus mostrou-se capaz de diagnosticar e quantificar o VSV Alagoas nas amostras séricas de bovinos e de equinos. Portanto, a RT-PCR em tempo real desenvolvida neste trabalho, provavelmente, será muito útil no diagnóstico e também, em futuras pesquisas, que permitirão ampliar o conhecimento epidemiológico, ainda pouco conhecido, sobre os Vesiculovirus.
The Vesiculovirus is a Rhabdoviridae family genre of RNA virus that includes serotypes Carajás, Cocal, Maraba, Piry, Alagoas and Indiana. These are causes of vesicular stomatitis in ruminants and human febrile illness in Brazil. The vesiculoviroses and its epidemiology are little known in humans. Still, Vesiculovirus (VSV) are poorly diagnosed in humans and laboratory animals by the lack of diagnostic methods. Therefore, we proposed in this work to develop and test a real-time RT-PCR by SYBR Green method, focusing on the detection of Brazilian VSV. Primers that amplify part of the VSV G protein gene were used in the test which proved capable of detecting genomes of VSV Piry, Indiana, Alagoas and Carajás. The method was used to test serum samples from patients with acute febrile disease, cattle, horses and macerated arthropods. Real time RT-PCR showed to be 100 times more sensitive than conventional RT-PCR for Vesiculovirus and also was possible to detect up to 10 RNA copies of the Piry virus. Also, the real-time RT-PCR for Vesiculovirus proved able to diagnose and quantify Alagoas VSV in serum samples from cattle and horses. Therefore, the real-time RT-PCR developed in this work will probably be very useful in the diagnosis and in future research, which will increase the epidemiological knowledge, as it is still little known about the Vesiculovirus.

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Steyn, HC, A. Pretorius i CME McCrindle. "A quantitative real-time PCR assay for Ehrlichia ruminantium using pCS20". Elsevier, 2008. http://encore.tut.ac.za/iii/cpro/DigitalItemViewPage.external?sp=1000379.

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Heartwater is a tick borne disease that affects ruminants and wild animals in Africa south of the Sahara. It is caused by Ehrlichia ruminantium and transmitted by the tick Amblyomma hebraeum. The protocols currently used to detect heartwater take several days to complete. Here, we describe the development of a pCS20 quantitative real-time PCRTaqMan probe assay to detect E. ruminantium in livestock blood and ticks from the field. The assay is based on the conserved pCS20 gene region of E. ruminantium that contains two overlapping genes, rnc and ctaG [Collins, N.E., Liebenberg, J., De Villiers, E.P., Brayton, K.A., Louw, E., Pretorius, A., Faber, F.E., Van Heerden, H., Josemans, A., Van Kleef, M., Steyn, H.C., Van Strijp, M.F., Zweygarth, E., Jongejan, F., Maillard, J.C., Berthier, D., Botha, M., Joubert, F., Corton, C.H., Thomson, N.R., Allsopp, M.T., Allsopp, B.A., 2005. The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. PNAS 102, 838–843]. The pCS20 quantitative real-time PCRTaqMan probe was compared to the currently used pCS20 PCR and PCR/32P-probe test with regards to sensitivity, specificity and the ability to detect DNA in field samples and in blood from experimentally infected sheep. This investigation showed that the pCS20 quantitative real-time PCRTaqMan probe was the most sensitive assay detecting seven copies of DNA/ml of cell culture. All three assays, however, cross react with Ehrlichia canis and Ehrlichia chaffeensis. The pCS20 real-time PCR detected significantly more positive field samples. Both the PCR and pCS20 real-time PCR could only detect E. ruminantium parasites in the blood of experimentally infected sheep during the febrile reaction. The PCR/32P-probe assay, however, detected the parasite DNA 1 day before and during the febrile reaction. Thus, because this new quantitative pCS20 real-time PCRTaqMan probe assay was the most sensitive and can be performed within 2 h it is an effective assay for epidemiological surveillance and monitoring of infected animals.

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Dib, Cristina Corsi. "Emprego da reação em cadeia pela polimerase em tempo real para o controle de eficiência de bacterinas anti-leptospirose". Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-27092012-164459/.

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A estirpe Fromm de Leptospira interrogans sorovar Kennewicki foi utilizada para produção de uma bacterina experimental anti-leptospirose. A extração do RNA total utilizado para transcrição reversa e quantificação dos antígenos LigA e LipL32 por PCR em Tempo Real, foi efetuada a partir de alíquotas colhidas das diluições da bacterina antes da sua inativação, as quais foram armazenadas à temperatura de -80ºC. O volume restante da bacterina foi inativado em banho-maria à 56ºC e mantido à temperatura de -20ºC para avaliação da sua potência em hamsters bem como da detecção e quantificação dos antígenos LigA e LipL32 em ensaios de ELISA Indireto e ELISA Sanduíche Indireto. Os resultados do ensaio de potência em hamsters demonstraram que a bacterina foi aprovada de acordo com as exigências dos padrões internacionais de qualidade até a diluição 1/6400, protegendo os hamters contra a infecção letal frente ao desafio com a diluição 10-6 (100 doses infectantes 50%/ 0,2mL). Os resultados das reações de Real Time PCR detectaram 3,2 x 103 e 2,3 x 101 cópias do mRNA que codifica a proteína LigA, na bacterina pura e diluída a 1:200, respectivamente. Apenas oito cópias do mRNA que codifica a proteína LipL32 foram detectadas na amostra de bacterina pura. Os ensaios com ELISA Indireto não detectaram a proteína LigA na amostra de bacterina inativada, mas demonstraram a detecção da proteína LipL32 até a diluição 1/1600 da bacterina. Os ensaios de ELISA Sanduíche Indireto apresentaram reações cruzadas nas placas controle, e, portanto seus resultados não puderam ser considerados nas análises. Os resultados da real time PCR não puderam ser correlacionados com o teste de potência em hamsters, mas os ensaios de ELISA Indireto para a proteína LipL32 demonstraram resultados condizentes com os apresentados pelo teste de potência em hamsters oferecendo uma possível alternativa in vitro para avaliação de potência de bacterinas anti-leptospirose.
Leptospira interrogans serovar Kennewicki strain Fromm was used for the production of a experimental leptospirosis bacterin. The extraction of total RNA used for reverse transcription and quantification of the antigens LigA and LipL32 for Real Time PCR was performed from the aliquots harvested of bacterin dilutions before inactivation that were separated and maintained at -80ºC. The remaining volume of bacterin was inativated at 56ºC and maintained at -20ºC for the evaluation bacterin potency in hamsters and detection and quantification of LigA and LipL32 antigens by Indirect ELISA assay and Indirect Sandwich ELISA. The results of potency assay in hamsters demonstrated that the bacterin was approved by the international patterns of quality until dilution 1/6400, protecting the hamters against lethal infection challenge by the dilution 10-6 (100 infectious doses 50%/0,2 mL). The results of Real Time PCR detected 3,2 x 103 e 2,3 x 101 copies of mRNA that encodes the LigA protein, in samples of pure bacterin and diluted 1:200, respectively. Few eight copies of mRNA that encodes LipL32 protein were detected in pure bacterin samples. Indirect ELISA assays not detected LigA protein in inactivated bacterin samples, but demonstrated LipL32 protein detection until dilution 1:1600 of bacterin. Indirect Sandwich ELISA presented cross-reaction in control plates, so the results cannot be considerated in the analysis. The results of real time PCR cannot be correlated with the potency assay in hamsters but Indirect ELISA assay for protein LipL32 demonstrated that the results were suitable with the results presented by the potency assay in hamsters offering a possible in vitro alternative for the evaluation of leptospirosis bacterins potency.

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Pantchev, Alexandra. "Spezies-spezifischer Nachweis von Chlamydien bei Haustieren mittels Real-Time PCR". Giessen VVB Laufersweiler, 2010. http://geb.uni-giessen.de/geb/volltexte/2010/7676/index.html.

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Wilhelm, Jochen. "Entwicklung real-time-PCR-basierter Methoden für die moderne DNA-Analytik". [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=96787775X.

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Tichopád, Aleš. "Quantitative real-time RT-PCR based transcriptomics improvement of evaluation methods /". [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972765069.

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Afshari, Kashanian Elisa. "Detection of celery (Apium graveolens) in food with Real-Time PCR". Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7130.

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Directive EC 2003/89/EC of the European Parliament and of the Council states that certain

ingredients and products derived there of known to cause allergen reactions must always be

declared. Furthermore labelling is mandatory irrespective of the amount included. The National

Food Administration therefore needs methods for monitoring the presence of allergens in food.

Methods already exist for most of the allergens on the EU-list, but an operational method for

celery (Apium graveolens) is missing.

A specific DNA-method was developed, based on TaqMan Real-Time PCR with the celery

mannitol dehydrogenase gene as target sequence. The analysis was started with homogenisation

of the sample followed by extraction of DNA. The Real-Time PCR method was shown to be

specific for celery, producing a 113 bp fragment with two celery varieties and negative results

with other closely selected species commonly present together with celery in food products (12

samples). The detection limit was 2-20 pg DNA, which corresponds to 1-7 haploid genome

copies. When evaluated with model samples of celery in meat, a detection limit of less than

0,01 % was determined. When used to analyse food products from the market, six out of seven

products declared to contain celery were correctly identified as positive.

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Ikuta, Koji, Toshio Sasao, Yuya Okuda, Kenji Watamura i Masashi Ikeuchi. "Development of New Biochemical IC Chip-Set for Real-Time PCR". IEEE, 2009. http://hdl.handle.net/2237/13926.

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Benninghoff, Myrna. "Etablierung und Evaluierung eines molekularen Wurmdiagnostikverfahrens (Real-Time-PCR) in Tansania". Diss., Ludwig-Maximilians-Universität München, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:19-182939.

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Hintergrund: Von den weltweit mehr als zwei Milliarden mit Würmern (griech. Helminthen) infizierten Menschen sind schätzungsweise etwa 22 Millionen zusätzlich mit HIV koinfiziert und verbleiben durch die krankheitsbedingte Produktivitäts- und Leistungsminderung in einer Abwärtsspirale. Trotz großangelegter globaler Versuche, Helminthosen mit präventiven Massenbehandlungen einzudämmen, gibt es weiterhin großen Forschungs- und Handlungsbedarf. Eine sensitivere und zuverlässigere Diagnostikmethode als die klassische Stuhlmikroskopie ist dringend erforderlich. Problemstellung und Zielsetzung: Etablierung eines molekularen Wurmdiagnostikverfahrens (Multiplex-Real- Time-Polymerase Chain Reaction) am Mbeya Medical Research Center (MMRC)-Labor im einkommensschwachen Tansania zur Detektion verschiedener Helminthen im Stuhl und direkter Vergleich mit der Merthiolat- Jod-Formalin (MIF)-Mikroskopie sowie dem derzeitigen Diagnostikgoldstandard der Kato-Katz (KK)-Mikroskopie. Klärung der Frage, ob das neue Verfahren wirklich sensitiver und für weitere Untersuchungen einsetzbar ist. Prüfung der Wirksamkeit von zur Massenbehandlung eingesetzten Medikamenten und Untersuchung von Besonderheiten bei HIV-Helminthen-koinfizierten Probanden mit Hilfe des neuen Verfahrens. Material und Methoden: Zwischen 2008 und 2011 Probensammlung, Erhebung der HI-Viruslast und CD4-Zellzahl, Stuhlmikroskopie nach der MIF- und KK-Methode, sowie Etablierung, Validierung, Durchführung und Evaluierung der Real-Time-PCR (RT-PCR) für 179 Probanden in Mbeya, Tansania. 118 Studienteilnehmer wurden nach einer Einmalgabe von 400 mg Albendazol gegen intestinale Nematoden und 40 mg/kg Praziquantel gegen Schistosomeninfektionen mit der Mikroskopie sowie der RT-PCR nachuntersucht. Zusammenfassung 108 Ergebnisse: Bei fast allen Probanden lagen laut WHO-Klassifikation leichte Infektionen vor. Eine externe sowie interne Qualitätskontrolle bestätigte die Validität unserer RT-PCR. Der Methodenvergleich ergab eine hohe Diskordanz zwischen den einzelnen Verfahren. Die RT-PCR wies 2,2 mal mehr Infektionen als MIF und 1,4 mal mehr Infektionen als KK nach. Bei etwa 17% der untersuchten Probanden lag ein Polyparasitismus vor. Mit der RT-PCR wurden mehr Mischinfektionen nachgewiesen. Ein niedriger Cycle Threshold (CT) korrelierte mit einer hohen Eizahl und umgekehrt. Die Infektionsstärke bei HIV-Wurmkoinfizierten Probanden unterschied sich nicht von der HIV-negativer Probanden. HIV-Positive schieden trotz ihrer Immunschwäche nicht weniger Schistosomeneier am Tag aus als Nichtinfizierte. Ein Polyparasitismus lag bei HIV-Positiven (37% Mischinfektionen) nicht häufiger als bei HIV-Negativen (43% Mischinfektionen) vor. Schlussfolgerung und Ausblick: Die RT-PCR erwies sich als wesentlich sensitiver als die Mikroskopie bei der Detektion von Hakenwürmern und Schistosomeninfektionen; nicht aber bei Askarideninfektionen. Als alleinig eingesetztes Diagnostikverfahren am MMRC hat sie daher keinen Bestand. Sie wird für zukünftige Studien als sensitives Zweitverfahren, das Hakenwurm-, Schistosomen- und Mischinfektionen besser nachweisen kann, neben der klassischen Kato-Katz-Mikroskopie Anwendung finden. Durch diese Arbeit konnte der Grundstein für die Diagnostik zukünftiger Studien am MMRC gelegt werden, die im Rahmen des IDEA-Projektes, einer großen afrikanisch-europäischen Forschungsinitiative, die unter anderem wurminduzierte Immunantworten in Bezug auf Koinfektionen mit HIV, Malaria und Tuberkulose und den Einfluss von Würmern auf Impfstoff-induzierte Immunantworten untersucht, durchgeführt werden. Es sollten weitere Studien zur Sensitivität der verwendeten RT-PCR-Protokolle an anderen Standorten durchgeführt werden. In Mbeya wurde das Verfahren nach meiner Abreise erfolgreich weitergeführt, sodass inzwischen fast 1000 Stühle mit der RT-PCR untersucht worden sind.

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Kelley, Erin, Elizabeth Driebe, Kizee Etienne, Mary Brandt, James Schupp, John Gillece, Jesse Trujillo i in. "Real-time PCR assays for genotyping of Cryptococcus gattii in North America". BioMed Central, 2014. http://hdl.handle.net/10150/610059.

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BACKGROUND:Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak, C. gattii has been identified outside of its previously documented climate, habitat, and host disease. Genotyping of C. gattii is essential to understand the ecological and geographical expansion of this emerging pathogen.METHODS:We developed and validated a mismatch amplification mutation assay (MAMA) real-time PCR panel for genotyping C. gattii molecular types VGI-VGIV and VGII subtypes a,b,c. Subtype assays were designed based on whole-genome sequence of 20 C. gattii strains. Publically available multilocus sequence typing (MLST) data from a study of 202 strains was used for the molecular type (VGI-VGIV) assay design. All assays were validated across DNA from 112 strains of diverse international origin and sample types, including animal, environmental and human.RESULTS:Validation revealed each assay on the panel is 100% sensitive, specific and concordant with MLST. The assay panel can detect down to 0.5 picograms of template DNA.CONCLUSIONS:The (MAMA) real-time PCR panel for C. gattii accurately typed a collection of 112 diverse strains and demonstrated high sensitivity. This is a time and cost efficient method of genotyping C. gattii best suited for application in large-scale epidemiological studies.

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Hipólito, Janayna Roriz. "Diagnóstico molecular para malária por nestedpcr e pcr em tempo real". Universidade Federal do Amazonas, 2006. http://tede.ufam.edu.br/handle/tede/2242.

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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.

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Elfaitouri, Amal. "Development of Real-Time PCR Based Methods for Detection of Viruses and Virus Antibodies". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7320.

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Pang, Zhenyi. "Non-alcoholic fatty liver disease : real-time PCR analysis of gene expression /". [St. Lucia, Qld.], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe.pdf.

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Andréasson, Hanna. "Sensitive Forensic DNA Analysis : Application of Pyrosequencing and Real-time PCR Quantification". Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5775.

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The field of forensic genetics is growing fast and the development and optimisation of more sensitive, faster and more discriminating forensic DNA analysis methods is highly important. In this thesis, an evaluation of the use of novel DNA technologies and the development of specific applications for use in forensic casework investigations are presented.

In order to maximise the use of valuable limited DNA samples, a fast and user-friendly Real-time PCR quantification assay, of nuclear and mitochondrial DNA copies, was developed. The system is based on the 5’ exonuclease detection assay and was evaluated and successfully used for quantification of a number of different evidence material types commonly found on crime scenes. Furthermore, a system is described that allows both nuclear DNA quantification and sex determination in limited samples, based on intercalation of the SYBR Green dye to double stranded DNA.

To enable highly sensitive DNA analysis, Pyrosequencing of short stretches of mitochondrial DNA was developed. The system covers both control region and coding region variation, thus providing increased discrimination power for mitochondrial DNA analysis. Finally, due to the lack of optimal assays for quantification of mitochondrial DNA mixture, an alternative use of the Pyrosequencing system was developed. This assay allows precise ratio quantification of mitochondrial DNA in samples showing contribution from more than one individual.

In conclusion, the development of optimised forensic DNA analysis methods in this thesis provides several novel quantification assays and increased knowledge of typical DNA amounts in various forensic samples. The new, fast and sensitive mitochondrial DNA Pyrosequencing assay was developed and has the potential for increased discrimination power.

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Muradrasoli, Shaman. "Detection and Quantification of Variable Viral RNA by Real-Time PCR Assays". Doctoral thesis, Uppsala universitet, Klinisk virologi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9193.

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As the area of nucleic acid based technologies develops, so will our understanding of how structural variations in DNA and RNA pathogens are associated with disease. The overall goal of this thesis is the development of broadly targeted measurement techniques for variable viral RNA by Real-Time PCR (here referred to as quantitative reverse transcriptase PCR, QRT-PCR). In papers I & II, broadly targeted and specific QRT-PCRs were used to study expression of endogenous and exogenous betaretrovirus sequences in human tissues. Results from human tissues demonstrated endogenous betaretrovirus expression in a tissue-specific manner, highest in reproductive tissues. Despite the high sensitivity, no exogenous betaretrovirus was found in human breast cancer samples. The limits of primer and probe degeneracy for detection of a diverse set of retroviral sequences was evaluated. These methods are useful for further investigations on the pathophysiological contribution(s) of endogenous betaretrovirus and to investigate whether an exogenous betaretrovirus is involved in human breast cancer. In papers III & IV, we developed and applied broadly targeted one-step QRT-PCRs for influenza viruses and coronaviruses. In addition to the generic primers, two novel probe design strategies were used in order to be able to broadly amplify these diverse sets of viruses: A triplex system for simultaneous detection and quantification of influenza A, B and C (3QRT-PCR and further developed 3QRT-PCR-MegB; where MegB stands for MegaBeacon) based on TaqMan® and MegB probes, and a pan-CoV QRT-PCR, based on three TaqMan® probes i.e., degeneracy was distributed on three probes. Probe fault tolerance was thus increased in two ways, either with short probes with/without locked nucleic acid (LNA) nucleotides concentrated to conserved stretches, or with long probes (MegB), compensating mismatching positions with many matching ones. Clinical samples, negative by antigen detection with immunofluorescence (IFA), were influenza A positive with 3QPCR-MegB. Avian pooled samples, negative with an earlier pan-CoV QPCR, came out positive with the triple-probe system. Assay evaluation with clinical samples and reference strains revealed good clinical diagnostic potential. Thus, the thesis describes several strategies to counteract sequence variation of RNA viruses and describes a set of broadly targeted QRT-PCRs useful for scientific screening or diagnostics of betaretroviruses and respiratory viruses.

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Mohamed, Nahla. "Molecular Diagnosis of Common Viral Infectious Diseases Based on Real-Time PCR". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7118.

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Andréasson, Hanna. "Sensitive forensic DNA analysis : application of pyrosequencing and real-time PCR quantification /". Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5775.

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Chan, Chi-chiu Elvin, i 陳志超. "Molecular characterization of toxigenic clostridium difficile by multiplex and real-time PCR". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46631392.

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Leopold, Luciana Eleanor Dittmer Dirk Peter. "Development of real-time PCR assays for the quantitative detection of herpesviruses". Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1487.

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Thesis (M.S.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Sep. 16, 2008). "... in partial fulfillment of the requirements for the degree of Master of Science in the Curriculum of Genetics and Molecular Biology." Discipline: Genetics and Molecular Biology; Department/School: Medicine.

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Ferreira, Karin Correa Scheffer. "Detecção do vírus da raiva em órgãos de morcegos do gênero Artibeus (Leach, 1821) por meio de RT-PCR, Hemi-Nested RT-PCR e Real Time RT-PCR". Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-19102012-132944/.

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Este estudo teve como objetivo detectar a presença do vírus da raiva em diferentes órgãos de morcegos do gênero Artibeus empregando as técnicas moleculares como RT-PCR, hnRT-PCR e Real Time RT-PCR. De aproximadamente 4000 espécimes de morcegos recebidas no Instituto Pasteur para o diagnóstico da raiva, foram selecionados 30 morcegos do gênero Artibeus, com resultados positivos para raiva pelas técnicas tradicionais de IFD e inoculação em células N2A utilizando suspensões feitas a partir do SNC. Para as técnicas moleculares, foram retirados glândulas salivares, bexigas urinárias, rins, pulmões e conteúdos fecais e ainda foram lavadas as calotas cranianas dos espécimes. Os órgãos e conteúdos fecais foram diluídos a 1:10 (P/V) e as bexigas urinárias a 1:20 (P/V). As suspensões foram inoculadas em células N2A para o isolamento viral. Foi realizada a extração do RNA total usando o TRIzol®, foram realizadas a transcrição reversa seguida da PCR e hnRT-PCR com utilização de primers específicos para o gene codificante da proteína N. A partir do produto da transcrição reversa foi realizada a técnica de Real Time RT-PCR, utilizando primers e sonda específicos para variante antigênica 3. Das 30 suspensões de lavado cerebral, 28 (93,33%) resultaram positivos, na inoculação em cultura de células, seguido de glândulas salivares (36,67%), bexigas (16,67%) e conteúdos fecais (3,33%). Os resultados encontrados da sensibilidade nas técnicas de RT-PCR, hnRT-PCR e Real Time RT-PCR foram 56,25%, 82,57% e 82,19% quando avaliadas as 180 amostras analisadas. A comparação das técnicas de hnRT-PCR e Real Time RT-PCR feita pelo teste exato de Fisher quanto a proporção de positivos detectados mostrou que para o lavado cerebral, órgãos e conteúdos fecais a proporção foi igual (P>0,05). Em relação à positividade os resultados encontrados nas técnicas de hnRT-PCR e Real Time RT-PCR foram 100% em lavado cerebral; 90% e 93,33% em glândulas salivares; 83,33% e 90% em bexigas; 80% e 93,33% em rins; 76,67% e 50% em pulmões e 43,33% em ambas as técnicas em conteúdos fecais. Esses resultados sugerem que tanto as técnicas de hnRT-PCR como Real Time RT-PCR podem ser utilizadas como métodos complementares para o diagnóstico da raiva e são sensíveis o bastante para o uso em estudos de patogênese. A técnica de Real Time RT-PCR realizada neste estudo se mostrou eficiente em detectar o RABV em diferentes órgãos e tecidos extraneurais com a vantagem de ser uma técnica mais rápida e sensível.
This study was aimed to detect the presence of rabies virus in different organs of the genus Artibeus bats using molecular techniques such as RT-PCR, hnRT-PCR, and the Real Time RT-PCR. From about 4,000 specimens of bats received for rabies diagnosis at the Pasteur Institute, 30 bats of the genus Artibeus were then selected. The selected bats presented positive results by the traditional DFA and N2A-cells inoculation test using brain tissue suspensions. Samples of salivary glands, urinary bladders, kidneys, lungs, and fecal contents and washings of the skulls were collected for the molecular techniques testing. The organs and the fecal contents were diluted at 1:10 (w/v) and the urinary bladder, at 1:20 (w/v) and these suspensions were inoculated into N2A cells for viral isolation. The extraction of the total RNA was performed by using TRIzol® and followed by the reverse transcription and the PCR and the hnRT-PCR were performed by using specific primers for the gene encoding the protein N. The product obtained by the reverse transcription technique was submitted to the Real Time RT-PCR technique, using primers and probe specific for antigenic variant 3 of the rabies virus. Of the 30 suspensions of the brain washings, 28 (93.33%) were positive in N2A cell culture inoculation, followed by the suspensions of the salivary glands (36.67%), bladders (16.67%) and fecal contents (3.33%). For the 180 samples evaluated, the results of sensitivity found for the RT-PCR, hnRT-PCR and Real Time RT-PCR techniques were 56.25%, 82.57%, and 82.19%, respectively. A comparison of hnRT-PCR and Real Time RT-PCR techniques performed by Fisher\'s exact test showed that the proportion of positives detected by the brain washings, organs and of the fecal content was non-significant (P> 0.05). Regarding the results found in hnRT-PCR and Real Time RT-PCR techniques, 100% positives were in brain washing, 90% and 93.33% in salivary glands, 83.33% and 90% in bladders, 80% and 93.33% in kidneys, 76.67% and 50% in lungs and 43.33% for both techniques on fecal contents. These results suggest that both hnRT-PCR and Real-Time PCR techniques can be used as complementary methods for the diagnosis of rabies and are sensitive enough for use in pathogenesis studies. The Real Time RT-PCR technique performed in this study proved to be faster and more sensitive and effective in detecting RABV in different organs and extra neural tissues of bats.

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Nascimento, Cristiane Santos. "Uso de método de biologia molecular quantitativo (PCR real-time) na avaliação da carga parasitária em cães naturalmente infectados por Leishmania sp". s. n, 2011. https://www.arca.fiocruz.br/handle/icict/4152.

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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.

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Rosa, Stefanie Ulrike. ""Real-Time-PCR-Untersuchungen zur Persistenz von infektiösen Toxoplasma-gondii-Dauerstadien in Rohwurst-Erzeugnissen"". Giessen VVB Laufersweiler, 2009. http://d-nb.info/996004408/04.

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Midena, Raquel Zanin. "Suscetibilidade antimicrobiana e protocolo de purificação de RNA para análise de expressão gênica de isolados clínicos de Fusobacterium nucleatum". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/25/25147/tde-26022016-143429/.

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Fusobacterium nucleatum é uma espécie bacteriana Gram-negativa, anaeróbia estrita e uma das espécies frequentemente encontradas nas infecções primárias do sistema de canais radiculares. Esta espécie tem grande importância na formação de biofilmes por ser uma ponte de união entre espécies que não são capazes de interagir. Os micro-organismos constituintes de biofilmes trocam material genético, aumentando a tolerancia dos mesmos e é quase impossível um isolado clínico ter os genes totalmente iguais à cepa padrão de coleções de cultura como da ATCC (American Type Culture Colection). O presente estudo investigou a espécie bacteriana anaeróbia Fusobacterium nucleatum isolada de canais radiculares, comparando-a com sua cepa de referência. Foi feito a comparação da suscetibilidade microbiana in vitro por meio de cultura microbiológica pelo método do E-test, com as cepas em crescimento planctônico e em biofilme. Também foi definido um protocolo de Purificação de RNA para esta espécie em ambas as condições de crescimento. As cepas clínicas de F. nucelatum foram isoladas por meio da cultura microbiológica de 23 pacientes que apresentavam dentes com infecção primária e periodontite apical visível em radiografia. Foi feito isolamento e identificação da espécie por série bioquímica com testes comerciais (Sistema Api, Bio-Meriéux, França) e PCR convencional, sendo no total 4 isolados clínicos investigados. Foi verificada a suscetibilidade antimicrobiana dos seguintes antibióticos: Amoxicilina, Amoxicilina + ácido clavulânico, Ampicilina, Azitromicina, Clindamicina, Eritromicina e Metronidazol. O protocolo para purificação de RNA foi feito com microesferas de zircônia, dispositivo bead beater, kit comercial RNeasy (Qiagen) e transcrição para DNA complementar (cDNA). A qualidade da purificação foi testada quanto a sua capacidade de amplificação pela reação em cadeia da polimerase em tempo real (qPCR) utilizando primer para o gene 16s RNA específico para F. nucelatum. Todas as cepas testadas foram 100% suscetíveis a Amoxicilina + ácido clavulânico, Ampicilina, Azitromicina, Clindamicina e Metronidazol. Ambos os tipos de crescimento bacteriano demonstraram resistência somente à eritromicina. O protocolo proposto para a purificação do RNA de F. nucelatum dos isolados em crescimento planctônico e em biofilme foi eficaz. A média do rendimento do RNA das amostras para as bactérias em crescimento planctônico foi de 514,2 ng/μL (DP ± 397,7) e para as amostras em biofilme foi de 377,1 ng/μL (DP± 144,1). Os valores encontrados sugerem uma boa qualidade de RNA, livre de contaminação por proteínas. Todas as cepas de Fusobacterium nucleatum isoladas de canais radiculares, assim como a cepa ATCC foram suscetíveis aos antibióticos testados, com exceção do antibiótico eritromicina em ambos os tipos de crescimento bacteriano. As bactérias em biofilme apresentaram aumento na tolerância frente aos agentes antimicrobianos, com diferença estatística. O protocolo estabelecido para a purificação do RNA de cepas de Fusobacterium nucleatum cultivadas em fase planctônica e em biofilmes teve êxito com amplificação por qPCR.
Fusobacterium nucleatum is a Gram-negative bacterial species, strict anaerobic and one of the species often found in primary infection of the root canal system. This species has great importance in biofilm formation to be a union bridge between species which are not able to act alone. The constituent microorganisms of the biofilm exchange each tother genetic material, increasing the strength of them. It is almost impossible for a clinical isolate have genes totally equal to a standard strain, such as strains of culture collections like ATCC (American Type Culture Collection). The present study investigated anaerobic bacterial species Fusobacterium nucleatum isolated from root canals, comparing them to the ATCC strain. The microbial in vitro susceptibility of biofilm and planktonic growth of the strains was compared by means of microbiological culture and the E-test method, with the antibiotics Amoxicillin, Amoxicillin + clavulanic acid, Ampicillin, Azithromycin, Clindamycin, Eritromycin and Metronidazole.. Also, a RNA Purification protocol for the strains under the same growth conditions was defined. Clinical isolates were obtained by microbiological samples of patients with teeth with pulp necrosis and apical periodontitis visible on radiographs. The species isolation and identification were performed using commercial biochemical tests (Sistema Api, Bio-Meriéux, France) and conventional PCR, obtaining four clinical isolates. The protocol for RNA purification was done with zirconia beads, bead beater device and commercial kit RNeasy (Qiagen) and transcribed into complementary DNA (cDNA). The quality of purification was tested for its ability of amplification by real time polymerase chain reaction (qPCR) using primer for the gene 16s RNA specific for F. nucleatum. All tested trains were 100% susceptible to amoxicillin + clavulanic acid, ampicillin, azithromycin, clindamycin and metronidazole. Both types of bacterial growth showed resistance to Erythromycin. Bacteria in biofilm showed a decrease in susceptibility to all antibiotics, but without statistical difference. The protocol proposed for the purification of RNA of F. nucleatum was effective, in the planktonic and the biofilm growth. The average yield of RNA samples for bacteria in planktonic growth was 514.2 ng /μL (SD ± 397.7) and the samples in biofilm was 377.1 ng / μL (SD ± 144.1). These found values suggest a good quality of RNA, free of protein contamination. The established protocol for the purification of the RNA of the Fusobacterium nucleatum strains, grown in biofilm and planktonic phase, had successfully amplified by qPCR.

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Bernardes, Nara Thiers Cacciatori Galleti. "Desenvolvimento PCR em Tempo-Real em sistema TaqMan® para detecção de rotavírus em amostras clínicas de bovinos". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-26092016-103616/.

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A diarréia neonatal é o principal problema sanitário que acomete os bezerros nas primeiras semanas de vida, causando grandes prejuízos devido à morbidade, mortalidade, custos com tratamento e atraso no desenvolvimento. Os rotavírus são os mais importantes agentes virais causadores de gastroenterites em crianças e diarreia em diferentes espécies animais. Além do seu impacto econômico na produção animal, os bovinos podem atuar como reservatórios da diversidade genética e antigênica para humanos. Assim, o diagnóstico deste agente é fundamental para o desenvolvimento de medidas profiláticas mais especificas visando o seu controle. O objetivo deste trabalho foi desenvolver um método de PCR em Tempo Real para a detecção de rotavírus bovinos em sistema Taqman® tendo como alvo, a proteína não-estrutural 5 (NSP5). Para isso, 113 amostras de fezes bovinas foram coletadas de reabanhos do estado de São Paulo, e previamente testadas por PCR convencional. Para a padronização da PCR em Tempo Real, a estirpe padrão foi clonada, gerando um plasmídeo com 3x1010 cópias/reação. Como controle exógeno foi utilizado β-actina. O limite de detecção foi determinado por diluições seriadas na base 10, detectando até 6x101 cópias/µl. A curva padrão da PCR em Temo Real para a detecção do segmento codificador da proteína NSP5 teve como resultados, uma eficiência de 100,47%; com slope igual a -3,18 e R2 de 1,0. De um total de 113 amostras testadas pela PCR convencional 63 delas (55,7%) foram consideradas positivas para rotavírus. Dessas mesmas amostras testadas, 5 não amplificaram para β-actina e não foram incluídas nas análises posteriores. Para a PCR em Tempo Real o limite de detecção foi considerado o valor de 6x101 cópias/reação, sendo definido o ponto de corte o ciclo (Ct) de número 36 para o teste com a amostra viral a partir do DNA ligado em vetor plasmidial. Considerando-se o ponto de corte de 60 (6x101) cópias/reação, das 108 amostras testadas, 63 (58,3%) foram consideradas positivas ao teste. O valor de concordância obtido através do teste Kappa, a um intervalo de confiança de 95%, a partir dos resultados gerados entre os testes de PCR convencional e PCR em foi de 0.279 (baixa concordância). Os resultados obtidos nesse estudo demonstrou que o teste foi eficiente podendo ser utilizado para um diagnóstico rápido e eficiente do rotavirus do grupo A, aumentando assim o repertório dos testes já estabelecidos
Neonatal diarrhea is the main health problem affecting the calves in the first weeks of life, causing major losses due to morbidity, mortality, treatment costs and delayed development. Rotaviruses are the most important causative agents of viral gastroenteritis in children and in different animal species. In addition to its economic impact on livestock, cattle can act as reservoirs for genetic and antigenic diversity for human samples. Therefore, the diagnosis of this agent is critical to the development of more specific preventive measures for their control. The objective of this work is to develop a method of PCR for rotavirus detection in cattle using TaqMan® system targeting the 5 nonstructural protein (NSP5). For this, 113 samples of cattle feces were collected from farms of São Paulo, and previously tested by convencional PCR. To PCR standardization, the standard sample was cloned, generating plasmid 3x1010 copies/reaction. The β-actin was usede as exogenous control. The limit of detection was determined by serial dilutions, to detect 6 x101 copies/µl. The standard curve of PCR to encoding segment detection NSP5 protein had as a result, an efficiency of 108.5%; with slope equal to -3.18 and R2 equal 1.. From a total of 113 samples tested by conventional PCR 63 (55.7%) were positive for rotavirus. From these samples 5 not amplifyed for β-actin gene and were not included in subsequent analyzes. For detection limit of Real-Time PCR was considered the amount of 6x101 copies / reaction, the cut-off being defined cycle (Ct) number 36 to the test with a viral sample from the DNA ligated into plasmid vector. Considering the cut-off 60 (6x101) copies/reaction of the 108 samples tested, 63 (58.3%) were positive to the test. The correlation value obtained by the Kappa test, at a 95% confidence interval, based on results generated between the conventional and PCR testing PCR was 0.279 (low agreement). The results of this study demonstrated that the probe can be efficiently used for a fast and efficient diagnosis of rotavirus of group A, thereby enhancing the repertoire of the established tests

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Mozol, Ivan Miletovic. "Análise temporal da expressão gênica e atividade enzimática, relacionadas ao estresse oxidativo e proteômica de Eucalyptus grandis inoculados com Puccinia psidii". Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-13112013-151232/.

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A floresta plantada de eucalipto representa a maior porcentagem entre as florestas plantadas no Brasil, principalmente para a producao de papel e celulose. Porem, durante todo o seu desenvolvimento, o eucalipto sofre o ataque de diferentes patogenos, e entre eles esta o fungo Puccinia psidii causador da ferrugem, principal doenca do eucalipto em regioes tropicais. Assim, com o intuito de estudar alguns mecanismos de defesa da planta contra a infeccao do fungo, este trabalho visou analisar a expressao genica de enzimas relacionadas ao estresse oxidativo e a atividade das mesmas; e o proteoma de clones de eucalipto resistentes e suscetiveis, ao longo do processo de infeccao, colonizacao e multiplicacao do fungo nas plantas. Foi possivel observar diferencas na expressao dos genes em todos os horarios estudados, principalmente as 24 horas apos inoculacao com o fungo. Alem disso, com a analise do proteoma pode-se observar algumas proteinas de grande relevancia para este trabalho, como algumas relacionadas a estresse oxidativo e a resposta de defesa da planta.
The eucalyptus planted forest represents the major percentage among all planted forests in Brazil, mainly for the production of paper and cellulose. However, during its development, the eucalyptus can be attacked by a large number of different pathogens, like the fungus Puccinia psidii, the causer of the eucalyptus rust, main disease that affects the eucalyptus in tropical regions. Thus, in order to study some plant defense mechanisms against the infection of the fungus, this study aimed to analyse the gene expression of some enzymes related to oxidative stress and their activities, and the proteome of resistant and susceptible eucalyptus clones, during the process of infection, colonization and multiplication of the fungus in the plant. We could observe differences in the gene expression at all times studied, mostly at 24 hours after inoculation with the fungus. Besides, with the proteome analysis we could find the very relevant proteins for this study, for instance some proteins related to the oxidative stress and to the plant defense response.

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Prates, Mirela Cristina Moreira. "Codetecção de bactérias em pacientes com adenoamigdalite crônica". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/17/17151/tde-22062015-152409/.

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As tonsilas palatinas e adenoides são órgãos linfoides epiteliais do trato respiratório superior, onde ocorre o primeiro contato entre antígenos inalados e células de defesa do hospedeiro. O tecido adenoamigdaliano está em contato constante com uma grande diversidade de bactérias e vírus, que se reflete na elevada taxa de detecção de patógenos bacterianos e virais nesses tecidos, mesmo que saudáveis. Infecções crônicas ou repetidas nas mucosas dos tecidos linfoides podem desencadear o desenvolvimento de um estado inflamatório crônico e a presença de hiperplasia tecidual. Esse estado está associado com inúmeras complicações como rinussinusites de repetição, ronco, obstrução nasal, disfunção da tuba auditiva, apnéia obstrutiva do sono, otite média, alterações do desenvolvimento facial, desenvolvimento comportamental. Por isso, este trabalho tem como objetivo principal analisar co-detecções das principais bactérias da microbiota respiratória humana (Streptococcus pneumoniae, Staphylococcus aureus, Haemophylus influenzae, Moraxella catahrralis e Pseudomonas aeruginosa) de pacientes com e sem adenoamigdalite crônica através da técnica de PCR em tempo real. Tivemos como principal bactéria detectada em nosso estudo H. influenzae, que foi encontrada em altos níveis na amígdala e adenoide. Já nas secreções, a bactéria de maior frequência encontrada foi S. pneumoniae. Os resultados de comparação entre os 2 grupos (pacientes com a doença e sem a mesma) não foram estatisticamente significantes, porém não menos importante, mostrando que os principais agentes comensais que colonizam o trato aéreo superior (Streptococcus pneumoniae, Haemophylus influenzae e Moraxella catahrralis) sao elevados em ambos os grupos, e que provavelmente não são fundamentais na fisiopatogenia da hipertrofia adenoamigdaliana/tonsilites de repetição. Como conclusão podemos observar que as bactérias H. influenzae, M. catarrhalis e S. pneumoniae tiveram altas frequências de detecção em amígadalas, adenoides e lavados nasofaríngeo de crianças sem hipertrofia tonsilar e sintomatologia de infecção respiratória. Além disso, não houve maiores frequências de detecção de bactérias presentes na microbiota em pacientes com hipertrofia tonsilar do que em controles e diferentemente das demais bactérias, houve concordância moderada ou boa nas detecções de M. catarrhalis e H. influenzae entre adenoide e amígdada de indivíduos sem sintomas respiratórios.
The tonsils and adenoids are lymphoid epithelial organs of the upper respiratory tract, where the first contact between inhaled antigens and host defense cells occurs. In fact, the adenoid and tonsillar tissue is in constant contact with a wide variety of bacteria and viruses, which is reflected in the high rate of detection of bacterial and viral pathogens in these tissues, even if healthy. Chronic or recurrent infections of mucosal lymphoid tissues may trigger the development of a chronic inflammatory condition and the presence of tissue hyperplasia. This condition is associated with numerous complications such as rinussinusites repeat, snoring, nasal congestion, Eustachian tube dysfunction, obstructive sleep apnea, otitis media, abnormal facial development, behavioral development. Therefore, this study aims to analyze co-detections of the major human respiratory microbiota bacteria (Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Moraxella catahrralis and Pseudomonas aeruginosa) in patients with and without chronic adenoamigdalite using the technique of real time PCR. We had the main bacteria detected in our study H. influenzae, which was found in high levels in the amygdala and adenoids. Already in the secretions, the bacterium most frequently found was S. pneumoniae. In conclusion we can see that the bacteria H. influenzae, M. catarrhalis, and S. pneumoniae had high frequency of detection in amígadalas, adenoids and nasopharyngeal washed children without tonsillar hypertrophy and symptoms of respiratory infection. In addition, there were no major frequency detection of bacteria present in the microbiota in patients with tonsillar hypertrophy than in controls, and unlike the other bacteria, there was moderate to good agreement in the detection of M. catarrhalis and H. influenzae between adenoid and amígdada of individuals without respiratory symptoms.

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Stenberg, Jenny. "Optimization and validation of the method lactose intolerance genotyping with real-time PCR". Thesis, Uppsala universitet, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-150810.

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Abstract Primary lactose intolerance has been associated with a single nucleotide polymorphism located upstream of the lactase gene. The most common diagnostic tests for lactose intolerance are time-consuming and the patient is not allowed to eat and drink for 12 hours before the test is carried out. A method that can establish the genotype would be an easier way of diagnosing lactose intolerance compared to fenotypic lactose intolerance tests. Optimization and validation of a previously published method was performed with real-time polymerase chain reaction. We used whole blood from de-identified blood donors. During the optimization and validation we used a positive control, genotype C/T from Laboratoriemedicin Västernorrland, Sundsvall. The whole-blood was extracted using the MagNa Pure LC instrument. The reagent used was KAPA PROBE FAST qPCR Master Mix. The optimized program for real-time PCR was established to be 95°C 3min [95°C x 3sec, 55°C x 20sec, detection, 72°C x 15sec] x 50 cycles. Optimal probe concentration was found to be 0.2µM and primer concentration will be 0.5µM. This genotyping method is a good first-stage screening test for lactoseintolerance. Before it can be used as a routine method further validation will be necessary in order to ensure that the evaluation of the results can be done in an easy and secure way.

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Batista, Ribrio Ivan Tavares Pereira. "Efeito do ácido linoléico conjugado TRANS-10, CIS-12 na regulação do acúmulo de lípides e expressão gênica em embriões produzidos in vitro". Universidade Federal de Juiz de Fora (UFJF), 2010. https://repositorio.ufjf.br/jspui/handle/ufjf/2507.

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FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais
A suplementação do ácido linoléico conjugado trans-10, cis-10 no meio de cultivo, representa uma importante alternativa para aumento da sobrevivência dos embriões após a criopreservação. No entanto este isômero de CLA no cultivo in vitro sem antioxidante pode aumentar a taxa apoptótica. O objetivo do presente estudo foi avaliar o efeito da adição CLA trans-10, cis-12 no cultivo in vitro de embriões sem antioxidante. Zigotos bovinos (n = 1.694) foram divididos em dois tratamentos: (T1) grupo controle, zigotos cultivados no meio CR2aa suplementado com soro fetal (n = 815); (T2) zigotos cultivados no meio CR2aa suplementado com soro fetal mais 100 µM CLA trans-10, cis-12. Os embriões foram avaliados quanto a desenvolvimento, quantidade de lípides e criotolerância. Transcritos dos RNA mensageiros (RNAm) dos genes selecionados foram mensurados pelo Real Time PCR. Suplementação de CLA trans-10, cis-12 não afeta significativamente a taxa de blastocisto (31,8% e 34,1% T1 e T2, respectivamente, p = 0,20) e nível dos RNAm dos genes relacionados com stress celular, apoptose e síntese de novo de ácido graxo. Quantidade de lípides e transcritos do RNAm do gene 1-acilglicerol-3-fosfato oaciltransferase 1 enzima relacionado a síntese de triglicérides foram significativamente reduzidos nos embriões cultivados na presença de CLA trans-10, cis-12 em comparação com o grupo controle. Teve aumento significativo na taxa de re-expansão dos blastocistos cultivados na presença de CLA trans-10, cis-12, após o descongelamento (34.4 e 56.3% para T1 e T2, respectivamente p = 0,002). Essa diferença não persistiu na taxa de eclosão (14,0% e 16,5% para T1 e T2, respectivamente, P = 0,62). Esses resultados mostram que o CLA trans-10, cis-12 reduz o acúmulo de lípides nos embriões pela redução nos níveis dos transcritos do gene 1-acilglicerol-3-fosfato o-aciltransferase 1 sem afetar a qualidade do embrião. Adicionalmente, este ácido graxo aumenta a taxa de re-expansão, no entanto, não melhora a taxa de eclosão.
Supplementation of conjugated linoleic acid trans-10, cis-10 in the culture medium, represents an important alternative to increasing the survival of embryos after cryopreservation. However the addition of culture media with CLA trans-10, cis-12 without antioxidant may increase the apoptotic rate. The aim of this study was to evaluate the effect of adding CLA trans-10, cis-12 in vitro culture of embryos without antioxidant. Bovine zygotes (n = 1,694) were divided into two treatments: (T1) control group, zygotes cultured in CR2aa medium supplemented with fetal calf serum (n = 815), (T2) zygotes cultured in CR2aa medium supplemented with fetal calf serum plus 100 µM CLA trans-10, cis-12. Embryos were evaluated for development, amount of lipids and cryotolerance. Transcripts of messenger RNA (mRNA) of selected genes were measured by real time PCR. Supplementation of CLA trans-10, cis-12 did not significantly affect the blastocyst rate (31.8% and 34.1% T1 and T2, respectively, p = 0,20) and the mRNA level of genes related to cell stress, apoptosis and de novo synthesis of fatty acid . Lipids and transcripts of the mRNA of the gene 1-acilglicerol-3-phosphate o-acyltransferase 1 enzyme related to the synthesis of triglycerides were significantly reduced in embryos cultured in the presence of CLA trans-10, cis-12 in comparison the control group. Had increased rate re-expansion of blastocysts cultured in the presence of CLA trans-10, cis-12, after thawing (34.4 and 56.3% for T1 and T2, respectively p = 0,002). This difference did not persist in the hatching rate (14.0 and 16.5% for T1 and T2, respectively, P = 0,62). These results show that the CLA trans-10, cis-12 reduces the accumulation of lipids in the embryos by reducing the levels of gene transcripts acilglicerol-1-3-phosphate oacyltransferase 1 without affecting the quality of the embryo. Additionally, this fatty acid increases the rate re-expansion, but does not improve the hatching rate.

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Binder, Michael. "Development of a Botrytis specific immunosensor : towards using PCR species identification". Thesis, Cranfield University, 2014. http://dspace.lib.cranfield.ac.uk/handle/1826/12110.

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Botrytis species affect over 300 host plants in all climate areas of the world, at both pre and post-harvest stages, leading to significant losses in agricultural produce. Therefore, the development of a rapid, sensitive and reliable method to assess the pathogen load of infected crops can help to prescribe an effective curing regime. Growers would then have the ability to predict and manage the full storage potential of their crops and thus provide an effective disease control and reduce post-harvest losses. A highly sensitive electrochemical immunosensor based on a screen-printed gold electrode (SPGE) with onboard carbon counter and silver / silver chloride (Ag/AgCl) pseudo-reference electrode was developed in this work for the detection and quantification of Botrytis species. The sensor utilised a direct sandwich enzyme-linked immunosorbent assay (ELISA) format with a monoclonal antibody against Botrytis immobilised on the gold working electrode. Two immobilisation strategies were investigated for the capture antibody, and these included adsorption and covalent immobilisation after self-assembled monolayer formation with 3-dithiodipropionic acid (DTDPA). A polyclonal antibody conjugated to the electroactive enzyme horseradish peroxidase (HRP) was then applied for signal generation. Electrochemical measurements were conducted using 3,3’, 5,5’-tetramethylbenzidine dihydrochloride / hydrogen peroxide (TMB/H2O2) as the enzyme substrate system at a potential of -200 mV. The developed biosensor was capable of detecting latent Botrytis infections 24 h post inoculation with a linear range from 150 to 0.05 μg fungal mycelium ml-1 and a limit of detection (LOD) as low as 16 ng ml-1 for covalent immobilisation and 58 ng ml-1 for adsorption, respectively. Benchmarked against the commercially available Botrytis ELISA kits, the optimised immuno-electrochemical biosensor showed strong correlation of the quantified samples (R2=0.998) ... [cont.].

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Jungebloud, Anke. "Untersuchung der Genexpression in Aspergillus niger mittels Echtzeit-PCR". Paderborn FIT-Verl. für Innovation und Technologietransfer, 2007. http://www.gbv.de/dms/bs/toc/533996201.pdf.

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Mangold-Gehring, Sandra. "Bestimmung der Interferon-gamma-Expression bei Baypamune-behandelten Hunden mittels "Real-Time PCR"". [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=97606524X.

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Thilo, Florian Nikolaus. "Nachweis und Quantifizierung von kolorektalen Tumorzellen in peripherem Blut mittels Real-time PCR". [S.l.] : [s.n.], 2001. http://www.diss.fu-berlin.de/2001/143/index.html.

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Lorenz, Andreas. "Quantitative Real-time PCR zum spezifischen Nachweis transrenaler DNA des Mycobacterium tuberculosis complex". Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-115143.

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Sharif, Sanaz. "Comparison of real-time PCR assays for screening of meticillin-resistant Staphylococcus aureus". Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-154460.

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Staphylococcus aureus belongs to the normal flora. Many healthy people are colonized by the bacterium mainly in the nose but also on the skin and on other mucous membranes without showing symptoms. After damage to the skin, the bacterium can enter the wound and cause infections. Methicillin-resistant S. aureus (MRSA) is resistant to b-lactam antibiotics such as penicillin and methicillin. The gene that gives resistance characteristic of MRSA is the mecA-gene. MRSA strains are spread in both hospitals and in the community, and it is important to identify these bacteria with rapid and sensitive methods. In this study, Taq Man RT-qPCR was compared with SYBR Green RT-qPCR (LightCycler480, Roche) to explore which method had the best sensitivity with the least working hours. In addition, Bullet for automated DNA extraction and CAS 1200 ™ for automated pipetting of the samples were evaluated. Twelve patient isolates and 232 patient samples for MRSA screening were included in the study. The results showed that the primers were of major importance for the outcome of the amplification. It was also shown that the Ct-values were clearly lower when the Bullet, CAS 1200 ™ and LightCycler480 were combined compared with manual DNA extraction, manual pipetting and the Rotor-Gene 6000. In future, the former method will be used by the laboratory when screening patient samples for MRSA.

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Pettersson, Erik. "Investigation of tissue factor mRNA levels in human platelets using real-time PCR". Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-180831.

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Tissue factor (TF), a 47 kDa glycoprotein, is the initiator of the extrinsic pathway of blood coagulation and consequently of the upmost importance when damage to blood vessel occurs. The source of TF in circulation has been investigated. However, the source of TF is still not clear. One theory is that platelets express and increases the expression of TF after stimulation and the aim of our report was to investigate whether platelets really are a source for TF in circulation. Using specific primers for TF mRNA, platelets in plasma from healthy volunteers and from patients suffering from cardiac infarction were analyzed by using real-time polymerase chain reaction (PCR). Gel electrophoresis was performed after amplification of TF mRNA to verify the results. The samples were negative for TF when using real-time PCR and the few positive all had cycle threshold (Ct) values above 35. The contamination by monocytes was analyzed by using real-time PCR, with primers for CD14 and showed low amounts. After analysis, our conclusion was that platelets do not express TF. Although some samples had positive real-time PCR, the Ct values were all above 35, meaning they had very few transcripts in the initial samples and that the biological importance is uncertain. Since contamination of CD14 positive cells were found in most samples it can’t be ruled out that the origin of the positive TF mRNA is from monocytes.

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Utokaparch, Soraya. "Development of a standardized quantitative real time PCR panel for respiratory viral diagnosis". Thesis, University of British Columbia, 2006. http://hdl.handle.net/2429/31339.

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Traditional viral diagnostics such as viral culture and various serological techniques tend to be slow, insensitive and labour-intensive. A large proportion of viral pathogens still go undetected using these techniques. This thesis concerns the development of a rapid and sensitive technique - standardized real-time quantitative PCR. Individual qPCR assays and synthetic plasmid controls were developed for 12 common respiratory viruses including influenza types A and B, parainfluenza (PIV)-l, -2 and -3, respiratory syncytial virus (RSV) A and B, metapneumovirus (MPV), human coronavirus (HCoV) 229E and OC43, human rhinovirus (HRV) and adenovirus. A reference gene assay using hypoxanthine phosphoribosyl transferase (HPRT) was also developed. A retrospective analysis on nasopharyngeal aspirates from patients previously diagnosed was conducted. The results demonstrated that the respiratory viral qPCR panel was sensitive, efficient, and had a large dynamic range of detection. Some cross-reactivity was noted for HRV with an enterovirus (coxsackievirus B3). HPRT proved to be a stable reference gene with the additional benefit that qPCR viral loads could be interpreted based on copy number per unit volume of specimen. One hundred culture negative specimens were examined and viral nucleic acid was amplified in 43 of them. There was a statistically significant relationship between viral load and whether or not the same specimen was positive by culture for influenza A , PIV-3, RSV A and B, HRV and adenovirus. Mean viral load was highest in patients with lower respiratory tract infections (LRTI) compared to those with fever or upper respiratory tract infections (URTI) and 95% confidence interval (CI) between these patients did not overlap. These results suggest that patients with more severe clinical disease had higher viral loads. This study highlights the developmental phase of a technique that has the potential to increase the detection rate of viral pathogens involved in respiratory illnesses.
Medicine, Faculty of
Medicine, Department of
Experimental Medicine, Division of
Graduate

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Gavrilenko, Andreas. "Entwicklung einer real-time multiplex multitube RT-PCR zur Differentialdiagnostik der klassischen Schweinepest". Giessen DVG-Service, 2006. http://deposit.d-nb.de/cgi-bin/dokserv?idn=981170897.

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Kraemer, Iris. "Untersuchungen zum Vorkommen von Enterobacter sakazakii in Speiseeis mit real-time-PCR-Verfahren". Diss., kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/8377/.

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Lagmo, Johan. "Development of a multiplex real time PCR assay to target bacteria causing meningitis". Thesis, Uppsala universitet, Klinisk mikrobiologi och infektionsmedicin, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-215641.

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