As doenças respiratórias agudas (DRAs) são as causas mais comuns de morbidez e mortalidade infantil mundial, podendo ser causadas por uma grande variedade de microorganismos. A fim de se detectar os vírus respiratórios mais comumente associados às infecções agudas do trato respiratório e traçar seu perfil epidemiológico, utilizamos um protocolo de GS RT-PCR (GeneScan Transcrição Reversa-Reação em Cadeia da Polimerase) para a rápida detecção simultânea do, vírus influenza A e B, parainfluenzavirus tipo 1, 2 e 3, picornavirus, metapneumovirus e o adenovírus. As amostras clínicas foram colhidas de crianças menores de cinco anos de idade, apresentando sintomas respiratórios, no Hospital Universitário (HU) da Universidade de São Paulo (USP), durante o ano de 2003. O GS RT-PCR se mostrou uma metodologia sensível e específica, capaz de detectar uma diversidade maior de agentes infecciosos do trato respiratório em relação à Imunofluorescência Indireta (IFI), reduzindo neste estudo a porcentagem de amostras negativas de 69,9% (235 amostras) para 22% (74 amostras). / A reverse transcription polymerase chain reaction (RT-PCR) assay based on automated fluorescent capillary electrophoresis and GeneScan software analysis was used to detect nine common respiratory viruses in clinical specimens from young children. Assays for human respiratory syncytial virus (HRSV), human parainfluenza viruses 1, 2, and 3, influenza A and B viruses, human metapneumovirus, adenovirus and picornavirus were incorporated into a screening PCR standard assay format. The optimized assay panel was used to test 336 respiratory specimens obtained from children hospitalized with acute respiratory illness (ARI) that had been previously tested by viral culture and indirect immunofluorescence staining (IIF). GS RT-PCR showed be a sensitive and specific methodology, able to detect a larger diversity of respiratory viruses regarding IFI, reducing in this study the percentage of negative samples of 69,9% (235 samples) to 22% (74 samples).

PCR und Fluoreszenz - DNA - Fragment - Analyse zum Nachweis einer monoklonalen B-Zell-Population zur Diagnostik der kutanen B-Zell Lymphome (CBCL) Der Nachweis einer monoklonalen B-Zell Population mittels PCR hat sich seit ca. zehn Jahren ergänzend zu Klinik und Histopathologie in der Diagnostik der kutanen B-Zell Lymphome etabliert. Zu diesem Zweck wurden Primer für die IgH Framework-Regionen (FR1, 2, 3), die Leader-Sequenz und für die JH-Region sequenziert. Alle Primervarianten führen zur Amplifikation der hochvariablen CDR-3 Region, welche für jede B-Zelle spezifisch ist. Die Kapillarelektrophorese mit fluoreszenzmarkierten PCR-Produkten an automatischen Sequenziergeräten (z. B. Genescan ABI Prism 310) ermöglicht eine exakte Größenbestimmung des jeweiligen Fragmentes und ist daher in diesem Zusammenhang die geeignetste Methode. Zunächst wurden alle relevanten Primer mit der Simulationssoftware Oligo hinsichtlich ihrer Bindungseigenschaften geprüft. Danach wurden ausgewählte Primer-Sets an 58 in Paraffin eingebetteten und an 5 Kryoproben von sicher diagnostizierten CBCL-Patienten getestet. Die fluoreszenzmarkierten Produkte wurden mit dem Sequenziergerät ABI Prism 310 analysiert. Die ungeschachtelte FR3/JH-PCR konnte nur in 30% und zusammen mit der halbgeschachtelten FR3/JH-PCR nur in 37% der Fälle klonale B-Zellen nachweisen. Die Detektionsrate erhöhte sich auf 54% unter Einbeziehung der geschachtelten FR1/JH-PCR und schließlich auf 60% mit einer zusätzlichen geschachtelten FR2/JH-PCR. Das Auftreten von Pseudoklonen (variierende Größe des klonalen Peaks bei Wiederholung der PCR) bei den geschachtelten PCR machte eine Prüfung auf Reproduzierbarkeit der Ergebnisse unbedingt erforderlich. Die höchste Rate an Pseudoklonen zeigte die FR2/JH-PCR. Aufgrund der schlechten Qualität der IgH Leader-PCR konnten mit in Paraffin-eingebetteten Proben keine Amplifikate erzeugt werden. Zusammenfassend ist zu sagen, daß gemeinsame Verwendung der in dieser Arbeit entwickelten PCR eine Sensitivitätssteigerung von 30% auf 60% ermöglichen. / Clonality detection in cutaneous B-cell lymphomas (CBCL) using immunoglobulin heavy chain gene PCR assays and fluorescence PCR-fragment analysis on automated DNA sequencer Detection of clonally expanded immunoglobulin heavy chain (Igh) gene rearrangements by PCR and subsequent electrophoresis is increasingly used in the diagnosis of cutaneous B-cell lymphomas (CBCL). To this end, primers for the three Igh framework regions (FR1,2, 3), the leader sequence and the Jh region are applied, all amplifying the highly variable IgH third complementary region (CDR3) Recently, fluorescence PCR-fragment analysis on automated DNA sequencers (GeneScan analysis, GSA), providing an exact sizing has been applied as appropriate seperation technique in this context. We have evaluated all Igh primers hitherto known by a PC primer analysis program. Then, fluorescently labeled products generated from DNAs of 58 paraffin embedded and 5 frozen lesional skin biopsies of confirmed CBCL cases using the primer sets selected, were analysed by GSA on the ABI 310 Prism instrument. Single round or seminested FR3/JH-PCR showed clonal B-cells only in 30 or 37% of cases, respectively. This fraction was increased to 54% including a nested FR1/JH-PCR, and, to 60% applying a supplementary nested FR2/JH-PCR. However false clonal results, indicated by peaks of varying sizes from repeated PCR, have been received by nested PCR, mostly by FR2/JH. Obviously due to their poor quality, the IgH leader-PCR has not yielded amplification products from paraffin-derived DNAs. Our data show that the FR3/JH-PCR only is not sufficient for detecting B-cell clonality in CBCL, but following inclusion of additional IgH-PCR, an increase of detection rate up to 60% is possible. A substantial number of cases still fail to show clonality.

As doenças respiratórias agudas (DRAs) são as causas mais comuns de morbidez e mortalidade infantil mundial, podendo ser causadas por uma grande variedade de microorganismos. A fim de se detectar os vírus respiratórios mais comumente associados às infecções agudas do trato respiratório e traçar seu perfil epidemiológico, utilizamos um protocolo de GS RT-PCR (GeneScan Transcrição Reversa-Reação em Cadeia da Polimerase) para a rápida detecção simultânea do, vírus influenza A e B, parainfluenzavirus tipo 1, 2 e 3, picornavirus, metapneumovirus e o adenovírus. As amostras clínicas foram colhidas de crianças menores de cinco anos de idade, apresentando sintomas respiratórios, no Hospital Universitário (HU) da Universidade de São Paulo (USP), durante o ano de 2003. O GS RT-PCR se mostrou uma metodologia sensível e específica, capaz de detectar uma diversidade maior de agentes infecciosos do trato respiratório em relação à Imunofluorescência Indireta (IFI), reduzindo neste estudo a porcentagem de amostras negativas de 69,9% (235 amostras) para 22% (74 amostras). / A reverse transcription polymerase chain reaction (RT-PCR) assay based on automated fluorescent capillary electrophoresis and GeneScan software analysis was used to detect nine common respiratory viruses in clinical specimens from young children. Assays for human respiratory syncytial virus (HRSV), human parainfluenza viruses 1, 2, and 3, influenza A and B viruses, human metapneumovirus, adenovirus and picornavirus were incorporated into a screening PCR standard assay format. The optimized assay panel was used to test 336 respiratory specimens obtained from children hospitalized with acute respiratory illness (ARI) that had been previously tested by viral culture and indirect immunofluorescence staining (IIF). GS RT-PCR showed be a sensitive and specific methodology, able to detect a larger diversity of respiratory viruses regarding IFI, reducing in this study the percentage of negative samples of 69,9% (235 samples) to 22% (74 samples).

Published information on the structure and regulation of H. pylori promoters is limited. The work presented in this thesis describes the cloning and characterisation of promoter regions from a clinical isolate of H. pylori, and the development of an alternative, non-radioactive method for verifying the location of transcriptional start sites of bacterial promoters. H. pylori 4187E promoters were randomly cloned into the promoter-trap vector pKK232-8 in Escherichia coli DH5α using two sets of restriction enzymes. Vector pKK232-8 contains a promoterless chloramphenicol acetyltransferase (CAT) gene. Seventy-four promoter-containing clones were isolated from selective media based on their resistance to chloramphenicol. The strength of each promoter was analysed qualitatively, using chloramphenicol minimum inhibitory concentrations, and quantitatively, using CAT assays following exposure of the clones to pH 4 and pH 7. Selected promoter fragments were subcloned into the GFP reporter vector pFPV25, containing a promoterless gfp gene. The subclones were exposed to buffered LB broth at pH 4, 5, 6, 7 and 8, for varying lengths of time, to study acid-induced regulation of gene expression. Subclones were examined qualitatively, using visual examination of GFP fluorescence and fluorescence microscopy, and quantitatively, using flow cytometry following acid shock. DNA sequences were determined for 61 of the 74 H. pylori promoters, and sequence alignments with the published H. pylori strains (26695 and J99) were performed. The transcriptional start site of 27 H. pylori promoter fragments was experimentally mapped using a fluorescence-based primer extension protocol developed by our group. Potential -35 and -10 sequences were identified for each promoter, and a new consensus sequence for H. pylori promoters was proposed based upon these results. This study has considerably expanded knowledge of H. pylori promoter sequences and transcriptional start sites based on those which also function in E. coli. It has also revealed several H. pylori promoters which appear to respond to acid stress