Master of Science / Department of Diagnostic Medicine/Pathobiology / A. Sally Davis / Rift Valley fever virus (RVFV) is a mosquito-borne, zoonotic Phlebovirus that is a significant threat to ruminants and humans. RVFV is categorized as an overlap Select Agent by the Department of Health and Human Services and US Department of Agriculture. Therefore, the study of RVFV’s pathogenesis and the development of novel diagnostic tools for the prevention and control of outbreaks and virus spread is crucial. RVF is endemic to sub-Saharan Africa but has spread beyond the continent to the Arabian Peninsula indicating the competence of the virus to emerge in new areas. Thus, the high likelihood of RVF’s spread to other non- endemic countries also spurs the need for development and implementation of rapid diagnostic tests and surveillance programs. In the US, RVFV is a Select Agent, requiring BSL-3 enhanced containment practices for research work. First, we developed a method for the detection of RVFV RNA by reverse transcriptase real-time PCR (RT-qPCR) using non-infectious, formalin- fixed, paraffin-embedded tissues (FFPET). The results from FFPET RT-qPCR were compared to prior results for fresh-frozen tissues (FFT) RT-qPCR, as well as immunohistochemistry and histopathology completed on the same FFPET blocks. We developed a novel technique using a rapid and low cost magnetic bead extraction method for recovery of amplifiable RVFV RNA from FFPET. FFPET RT-qPCR can serve as an alternative tissue-based diagnostic test, which does not require a BSL-3 research facility. Second, we assessed the diagnostic accuracy and precision of a recombinant RVFV nucleoprotein based competitive ELISA (cELISA) assay to detect RVFV antibodies. The cELISA results were compared to the virus neutralization test, the gold standard serological assay for RVFV. This prototype cELISA is easy to implement, sensitive, specific, and safe test for the detection of antibodies to RVFV in diagnostic and surveillance applications. RVF is an important transboundary disease that should be monitored on a regular basis. The diagnostic tests developed and validated in this thesis could be used in endemic or non-endemic countries for the early detection of RVF and assist with the implementation of countermeasures against RVFV.

Bovine tuberculosis is a global cause for concern in livestock, free-ranging wildlife, zoological collections and the human population. Large amount of time, effort and resources are spent on its diagnosis and control methods. This study was aimed at determining the sensitivity and specificity of the IS6110 specific PCR test on formalin fixed, paraffin embedded (FFPE) tissue blocks, compared to that of the gold standard method culture and to differentiate M. bovis from other members of the M. tuberculosis complex using the RD4 region of difference specific PCR test. A total of 141 FFPE tissue blocks of wild animals from game reserves, the National Zoological Gardens and routine tuberculosis (TB) surveys in Kruger National Park were tested. Among the 50 known TB positive samples (35 M. bovis culture positive, twelve M. tuberculosis culture positive and three diagnosed tuberculosis positive on histopathology examination) the IS6110 PCR had an overall sensitivity of 22%. The positive predictive value of the IS6110 test (91.67%) was quite high implying that although sensitivity was low, one can be highly confident that a positive test result is a true reflection of the positive disease status. The overall sensitivity of the RD4 PCR was 20%. The positive predictive value of the RD4 test (41.67%) was low, implying that a positive test result may be unreliable. The sensitivities of the M. tuberculosis and M. bovis culture positive samples were compared and a significant difference was noted. Sensitivities of the IS6110 and RD4 assays in M. tuberculosis culture positive samples were 66.67% and 33.33%, respectively; sensitivities of the IS6110 and RD4 assays in M. bovis culture positive samples were 8.57% and 17.14%, respectively. Difference in bacterial load in tissues infected with the two mycobacterial species may account for this finding (i.e. M. bovis infections have a lower bacteria load). Of the 91 known TB negative samples, the specificity of the IS6110 (98.90%) and RD4 (84.62%) PCR tests were high, but the negative predictive values of 69.67% and 65.81%, respectively, suggest that the probability of negative test results being incorrect still exists. The resultant sensitivity was increased when parallel interpretation was applied to histopathology examination and the IS6110 or RD4 PCR tests and when applied to the IS6110 and RD4 PCR tests. Both histopathology examination and PCR tests produce rapid results and their combination can be used in routine diagnostics. The RD4 PCR assay was unable to distinguish M. bovis from other members of the MTB complex and based on the findings of this study the RD4 PCR cannot add value to the diagnosis of suspect tuberculosis samples at this stage, but successful troubleshooting relating to 1) extraction method, 2) DNA inhibitors, 3) contamination and 4) multisampling protocol, may enable its use in future. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Veterinary Tropical Diseases / Unrestricted

Philosophiae Doctor - PhD / Tumour-specific protein markers are usually present at elevated concentrations in patient biopsy tissue; therefore tumour tissue is an ideal biological material for studying cancer proteomics and biomarker discovery studies. To understand and elucidate cancer pathogenesis and its mechanisms at the molecular level, the collection and characterisation of a large number of individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardised methods of formalin fixation and paraffin embedment, these archived, FFPE tissues are important collections of pathology material, often accompanied by important metadata, such as patient medical history and treatments. FFPE tissue blocks are conveniently stored under ambient conditions for decades, while retaining cellular morphology due to the modifications induced by formalin. / 2022

No / The identification of proteins involved in tumour progression or which permit enhanced or novel therapeutic targeting is essential for cancer research. Direct MALDI analysis of tissue sections is rapidly demonstrating its potential for protein imaging and profiling in the investigation of a range of disease states including cancer. MALDI-mass spectrometry imaging (MALDI-MSI) has been used here for direct visualisation and in situ characterisation of proteins in breast tumour tissue section samples. Frozen MCF7 breast tumour xenograft and human formalin-fixed paraffin-embedded breast cancer tissue sections were used. An improved protocol for on-tissue trypsin digestion is described incorporating the use of a detergent, which increases the yield of tryptic peptides for both fresh frozen and formalin-fixed paraffin-embedded tumour tissue sections. A novel approach combining MALDI-MSI and ion mobility separation MALDI-tandem mass spectrometry imaging for improving the detection of low-abundance proteins that are difficult to detect by direct MALDI-MSI analysis is described. In situ protein identification was carried out directly from the tissue section by MALDI-MSI. Numerous protein signals were detected and some proteins including histone H3, H4 and Grp75 that were abundant in the tumour region were identified

O Herpesvírus equino tipo -1 (EHV-1) pertence ao gênero Varicellovírus da subfamília Alphaherpesvirinae pertencente à Família Herpesviridae. É um vírus envelopado, de DNA linear fita dupla, composto por 76 genes distintos. O EHV-1 é responsável por grandes prejuízos econômicos na equinocultura mundial. Responsável por doença neonatal fatal, mieloencefalopatia, rinopneumonite e abortamento, encontra-se amplamente distribuído pela população equina do território nacional. O objetivo do presente estudo foi o de padronizar uma reação em cadeia pela polimerase (PCR) para detecção do EHV-1 em tecidos incluídos em parafina a fim de permitir estudos retrospectivos em arquivos de amostras histopatológicas. Assim, foram inoculados experimentalmente 12 camundongos com 21 dias de idade da linhagem CH3/Rockfeller com três diferentes isolados de EHV-1, dois provenientes da Argentina e um do Brasil. Esses animais foram observados por quatro dias e, após sacrifício por sobre dose de uma associação de ketamina e xilazina, foram submetidos à necropsia e colhidos o pulmão e sistema nervoso central (SNC). Os órgãos colhidos foram divididos em duas partes aproximadamente iguais: uma mantida a -20ºC até processamento e a outra fixada em formalina 10% tamponada e posteriormente incluída em parafina. A extração foi realizada com nove fragmentos contínuos de 4µm cada, a partir do protocolo de extração com proteinase K/ fenol/ clorofórmio. Foi realizada avaliação da sensibilidade analítica da PCR com oito diluições na base 10 para os três isolados utilizados. A amplificação do DNA viral foi realizada utilizando primers direcionados para a ORF64. A fim de descartar a eventual presença de inibidores da reação de PCR e assegurar a adequada extração de DNA, foram incluídos primers direcionados para o gene da beta-actina. A PCR mostrou-se capaz de amplificar DNA viral alvo numa diluição de até 10-5, sendo positiva entre 10-1 a 10-2 DICT50/25µL. Com a PCR padronizada, foi possível detectar o DNA do EHV-1 em: a) 100% (12/12) das amostras de pulmão congeladas e 100% (12/12) das amostras de pulmão incluídas em parafina; b) em 91% (11/12) das amostras de SNC congeladas e 41% (5/12) das amostras de SNC incluídas em parafina. A aplicação da PCR padronizada em uma coleção de amostras incluídas em parafina do Laboratório de Anatomia Patológica do IB/SP, colhidas de cinco casos de abortamento em equinos, revelou que o DNA do EHV-1 foi detectado em: a) um caso em que originalmente foi possível isolar o EHV-1; b) em 4/4 amostras que revelaram-se originalmente negativas. Com base nos resultados obtidos, foi possível concluir que a PCR padronizada teve bom desempenho na detecção de DNA viral em amostras incluídas em parafina de animais experimentalmente infectados e, provavelmente, uma sensibilidade diagnóstica mais elevada que os métodos utilizados para o diagnóstico do EHV-1 na coleção de amostras de equino testada. / The equine herpesvirus type 1 (EHV-1) belongs to Varicellovírus genus, Alphaherpesvirinae subfamíly of the Herpesviridae Famíly. It is an enveloped virus, double stranded linear DNA, composed of 76 distinct genes. The EHV-1 is responsible for great losses in horsebread world. Responsible for neonatal death, mieloencephalopaty, rinopneumonite and abortion, it is widely distributed into brasilian equine population. The purpose of this study was to standardize a polymerase chain reaction (PCR) for EHV-1detection in paraffin- embedded tissues allowing retrospective studies based on the collection histopatological samples. Thus, 12 mice (CH3/Rockfeller) with 21 days of age were inoculated with 3 different isolates of EHV-1, 2 from Argentina and one from Brazil. These mice were observed for 4 days and, after sacrifice by overdose of a combination of ketamine and xylazina, it were subjected to necropsy and collected the lung and central nervous system (SNC). The collected tissues were divided into 2 approximately equal parts: 1one stored at -20ºC until processing, and another set at 10% buffering formalin and later paraffin-embedded. The extraction was performed with continuous 9 fragments of 4µm each, using the extration protocol with proteinase K/ fenol/ clorofórmio. The assessment of analytical sensitivity of PCR were determined using 8 dilutions for all 3 virus isolates. The viral DNA amplification was performed using primers targeted to ORF64. In order to rule out the possible presence of PCR inhibitors and to ensure adequate extraction of DNA, primers directed to the gene for beta-actin were included It was possible to amplify viral DNA until 10-5 dilution, corresponding to 10-1 to 10-2 DICT50/25µL. With the standardized PCR, it was possible to detect the EHV-1 DNA in: a) 100% (12/12) of lung frozen sample and 100% (12/12) of the paraffin-embedded lung; b) 91% (11/12) of the frozen CNS and 41% (5/12) CNS paraffin-embedded. Moreover, the standardized PCR was tested in a collection of paraffin-embedded specimens from Pathological Anatomy Laboratory od Biological Institute Sao Paulo State, taken 5 cases of the abortion in horses. It were possible to detect EHV-1 DNA in: a) 1 sample from a case in that originally was possible to isolate the EHV-1, b) 4/4 sample originally negative diagnosed. Based on these results, it is possible to conclude that the standardized PCR performed well for detection viral DNA in paraffin-embedded tissues of experimentally infected animals, and probably a higher diagnostic sensitivity than the methods used for diagnosis of EHV-1 in the collection samples tissues tested for equine.

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.

Mycobacteriosis is a common disease of laboratory zebrafish (Danio rerio). Different infection patterns occur in zebrafish depending on mycobacterial species. Mycobacterium marinum and M. haemophilum produce virulent infections associated with high mortality, whereas M. chelonae is more wide spread and not associated with high mortality. Identification of mycobacterial infections to the species level provides important information for making management decisions. Observation of acid-fast bacilli in histological sections or tissue imprints is the most common diagnostic method for mycobacteriosis in fish, but only allows for diagnosis to the genus level. Mycobacterial culture, followed by molecular or biochemical identification is the traditional approach for species identification, but recently it has been shown that DNA of diagnostic value can be retrieved from paraffin blocks. Type of fixative, time in fixative before processing, species of mycobacteria, and severity of infection were investigated as parameters to determine if the hsp gene PCR assay (primer set HS5F/hsp667R) could detect and amplify mycobacterial DNA from paraffin-embedded zebrafish. Whole zebrafish were experimentally infected with either M. chelonae or M. marinum, and then preserved in 10% neutral buffered formalin or Dietrich's fixative for 3, 7, 21 and 45 days. Subsequently, fish were evaluated by H&E and Fite's acid-fast stains to detect mycobacteria within granulomatous lesions. The PCR assay was quite effective, and obtained PCR product from 75% and 88% of the M. chelonae and M. marinum infected fish, respectively. Fixative type, time in fixative, and mycobacterial species showed no statistical relationship with the efficacy of the PCR test. Regarding natural transmission, zebrafish are capable of contracting mycobacterial infections by feeding on infected fish tissue, but other natural routes have not been clearly elucidated. Free living amoebae have been shown to be vectors for mycobacteria and their virulence is enhanced when residing in these protozoans. Paramecium caudatum are commonly used as a first food for zebrafish, and I investigated this ciliate's potential to serve as a vector of Mycobacterium marinum and M. chelonae. The ability of live P. caudatum to transmit these mycobacteria to larval, juvenile and adult zebrafish was evaluated. Infections were defined by histologic observation of granulomas containing acid-fast bacteria in extraintestinal locations. In both experiments, fish fed paramecia containing mycobacteria became infected at a higher incidence than controls. Larvae (exposed at 4 days post hatch) fed paramecia with M. marinum exhibited an incidence of 30% (24/80) and juveniles (exposed at 21 days post hatch) showed 31% incidence (14/45). Adult fish fed gelatin diets containing bacteria within paramecia or mycobacteria alone for 2 wk resulted in infections when examined 8 wk after exposure: M. marinum OSU 214; in paramecia 47% (21/45; 3.5 x 10⁵ dose/fish/day), M. marinum CH in paramecia 47% (9/19; 3.6 x 10⁵ dose/fish/day), M. chelonae in paramecia 38% (5/13; 3.5 x 10⁵ dose/fish/day). I investigated the ability of mycobacteria to persist within paramecia, as this has previously been demonstrated in amoebae. Gram negative bacteria ingested by paramecia were processed within an hour. In contrast, I determined using GFP-labeled Mycobacterium marinum that mycobacteria can persist within paramecia digestive vacuoles. The concentration of M. marinum at 1 hour was similar to that at the time of ingestion. Twenty-four hours post-ingestion and later there was significant decline in M. marinum concentrations compared to time of ingestion, but M. marinum continued to persist inside digestive vacuoles for up to one week. My results demonstrate for the first time that Paramecium caudatum can act as a vector for mycobacteria. This provides a useful animal model for evaluation of natural mycobacterial infections and demonstrates the possibility of mycobacterial transmission in zebrafish facilities via contaminated paramecia cultures. / Graduation date: 2013 / Access restricted to the OSU Community at author's request from April 2, 2013 - April 2, 2015

Colorectal cancer (CRC) is a common malignancy which develops due to old age and lifestyle factors, low percent of patients afflicted by a genetic disorders. Half of all colorectal cancer patients are diagnosed after metastasis. The high rate of the late detection, emphasizes on the requirement of convenient and inexpensive diagnostic methods for comprehensive screening programs. The aim of this study was to discover proto-oncogenes mutation and assessment of tumor suppressor genes expression. Formalin fixed paraffin embedded (FFPE) histologically verified colorectal cancer samples were used. APC, KRAS and BRAF mutations were investigated using polymerase chain reaction (PCR) fragments and direct sequencing. Gene expression assessment of MLH1, MGMT and CDKN2A were achieved via quantitative polymerase chain reaction (qPCR). In the present study we could detect a novel transversion heterozygous mutation in APC gene codon 1365 in three patients. BRAF codon 600 mutation were detected in one patient. KRAS codon 12 mutation was discovered in one sample and also a novel transition mutation in codon 15 was detected in 6 patients. In 80% of cases, MLH1 and MGMT expression were undetectable, in remaining 20%, MLH1 expression were reduced, but MGMT showed both reduced and increased expression compared to control. In 100% of patients CDKN2A expression was undetectable. The rate of mutations in predetermined hotspot codons and amount of uncommon mutations into APC, BRAF and KRAS in Nepalese patients indicates the requirement of further investigation in CRC patients from that part of the world. Also, the expression rate of MLH1, MGMT, CDKN2A and deficiency of an information source emphasizes the necessity of whole genome CRC expression profiling data to comparison and conclusion. / <p>-</p> / -

O Herpesvírus equino tipo -1 (EHV-1) pertence ao gênero Varicellovírus da subfamília Alphaherpesvirinae pertencente à Família Herpesviridae. É um vírus envelopado, de DNA linear fita dupla, composto por 76 genes distintos. O EHV-1 é responsável por grandes prejuízos econômicos na equinocultura mundial. Responsável por doença neonatal fatal, mieloencefalopatia, rinopneumonite e abortamento, encontra-se amplamente distribuído pela população equina do território nacional. O objetivo do presente estudo foi o de padronizar uma reação em cadeia pela polimerase (PCR) para detecção do EHV-1 em tecidos incluídos em parafina a fim de permitir estudos retrospectivos em arquivos de amostras histopatológicas. Assim, foram inoculados experimentalmente 12 camundongos com 21 dias de idade da linhagem CH3/Rockfeller com três diferentes isolados de EHV-1, dois provenientes da Argentina e um do Brasil. Esses animais foram observados por quatro dias e, após sacrifício por sobre dose de uma associação de ketamina e xilazina, foram submetidos à necropsia e colhidos o pulmão e sistema nervoso central (SNC). Os órgãos colhidos foram divididos em duas partes aproximadamente iguais: uma mantida a -20ºC até processamento e a outra fixada em formalina 10% tamponada e posteriormente incluída em parafina. A extração foi realizada com nove fragmentos contínuos de 4µm cada, a partir do protocolo de extração com proteinase K/ fenol/ clorofórmio. Foi realizada avaliação da sensibilidade analítica da PCR com oito diluições na base 10 para os três isolados utilizados. A amplificação do DNA viral foi realizada utilizando primers direcionados para a ORF64. A fim de descartar a eventual presença de inibidores da reação de PCR e assegurar a adequada extração de DNA, foram incluídos primers direcionados para o gene da beta-actina. A PCR mostrou-se capaz de amplificar DNA viral alvo numa diluição de até 10-5, sendo positiva entre 10-1 a 10-2 DICT50/25µL. Com a PCR padronizada, foi possível detectar o DNA do EHV-1 em: a) 100% (12/12) das amostras de pulmão congeladas e 100% (12/12) das amostras de pulmão incluídas em parafina; b) em 91% (11/12) das amostras de SNC congeladas e 41% (5/12) das amostras de SNC incluídas em parafina. A aplicação da PCR padronizada em uma coleção de amostras incluídas em parafina do Laboratório de Anatomia Patológica do IB/SP, colhidas de cinco casos de abortamento em equinos, revelou que o DNA do EHV-1 foi detectado em: a) um caso em que originalmente foi possível isolar o EHV-1; b) em 4/4 amostras que revelaram-se originalmente negativas. Com base nos resultados obtidos, foi possível concluir que a PCR padronizada teve bom desempenho na detecção de DNA viral em amostras incluídas em parafina de animais experimentalmente infectados e, provavelmente, uma sensibilidade diagnóstica mais elevada que os métodos utilizados para o diagnóstico do EHV-1 na coleção de amostras de equino testada. / The equine herpesvirus type 1 (EHV-1) belongs to Varicellovírus genus, Alphaherpesvirinae subfamíly of the Herpesviridae Famíly. It is an enveloped virus, double stranded linear DNA, composed of 76 distinct genes. The EHV-1 is responsible for great losses in horsebread world. Responsible for neonatal death, mieloencephalopaty, rinopneumonite and abortion, it is widely distributed into brasilian equine population. The purpose of this study was to standardize a polymerase chain reaction (PCR) for EHV-1detection in paraffin- embedded tissues allowing retrospective studies based on the collection histopatological samples. Thus, 12 mice (CH3/Rockfeller) with 21 days of age were inoculated with 3 different isolates of EHV-1, 2 from Argentina and one from Brazil. These mice were observed for 4 days and, after sacrifice by overdose of a combination of ketamine and xylazina, it were subjected to necropsy and collected the lung and central nervous system (SNC). The collected tissues were divided into 2 approximately equal parts: 1one stored at -20ºC until processing, and another set at 10% buffering formalin and later paraffin-embedded. The extraction was performed with continuous 9 fragments of 4µm each, using the extration protocol with proteinase K/ fenol/ clorofórmio. The assessment of analytical sensitivity of PCR were determined using 8 dilutions for all 3 virus isolates. The viral DNA amplification was performed using primers targeted to ORF64. In order to rule out the possible presence of PCR inhibitors and to ensure adequate extraction of DNA, primers directed to the gene for beta-actin were included It was possible to amplify viral DNA until 10-5 dilution, corresponding to 10-1 to 10-2 DICT50/25µL. With the standardized PCR, it was possible to detect the EHV-1 DNA in: a) 100% (12/12) of lung frozen sample and 100% (12/12) of the paraffin-embedded lung; b) 91% (11/12) of the frozen CNS and 41% (5/12) CNS paraffin-embedded. Moreover, the standardized PCR was tested in a collection of paraffin-embedded specimens from Pathological Anatomy Laboratory od Biological Institute Sao Paulo State, taken 5 cases of the abortion in horses. It were possible to detect EHV-1 DNA in: a) 1 sample from a case in that originally was possible to isolate the EHV-1, b) 4/4 sample originally negative diagnosed. Based on these results, it is possible to conclude that the standardized PCR performed well for detection viral DNA in paraffin-embedded tissues of experimentally infected animals, and probably a higher diagnostic sensitivity than the methods used for diagnosis of EHV-1 in the collection samples tissues tested for equine.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. It is a molecular and prognostic heterogeneous disease. Three main genetic subtypes are called germinal center-like DLBCL (GC-like DLBCL), non-germinal center-like DLBCL (nonGC-like DLBCL) and primary mediastinal B-cell lymphoma (PMBL). These subtypes can be reliably distinguished only with usage of gene expression profiling (GEP). The GEP method can be applied only when fresh frozen tissue is available. The method is technically difficult and expensive. Thus, it is not used routinely. Since the DLBCL subtypes differ in prognosis, it is extremely important to be able to distinguish them. The presented thesis is focused on distinguishing of PMBL diagnosis in the group of DLBCL. Easily stored formalin-fixed, paraffin-embedded tissue (FFPE) and gene expression analysis using real-time quantitative polymerase chain reaction (RTqPCR) are used. In the first step, PMBL and DLBCL cases were distinguished with an internationally accepted clinical-pathological method. The agreement between clinical-pathological diagnosis and GEP is only 76%. In the presented text a genetic algorithm for PMBL/DLBCL distinguishing is suggested. It uses three carefully chosen genes and their expression is measured with RTqPCR. Both, the...