Várias zoonoses virais acometem equídeos causando quadros neurológicos, entre as quais a raiva e as encefalites equinas do Leste (EEE) e Oeste (WEE). O diagnóstico clínico geralmente não é conclusivo, o que torna imprescindível o diagnóstico laboratorial. Dados do Laboratório de Diagnóstico de Raiva do Instituto Pasteur de São Paulo, entre os anos 2000 e 2010, mostram que aproximadamente 75% das amostras enviadas foram negativas para raiva, ressaltando a relevância da realização de um diagnóstico diferencial para as encefalites equinas causadas por alfavírus. Os objetivos do estudo foram testar a adequação do uso de multiplex hemi-nested RT-PCR para o diagnóstico de raiva, EEE e WEE em amostras de sistema nervoso central de equídeos e realizar uma análise de custo das reações de cada técnica. Foram utilizados os primers 21G, 304 e 504 dirigidos ao gene N do vírus da raiva, e os primers cM3W, M2W, nEEE e nWEE dirigidos ao gene NSP1 dos vírus da EEE e WEE. Procedeu-se a um estudo preliminar dos primers e de seu uso em uma hemi-nested RT-PCR, avaliando a temperatura ótima de anelamento, a sensibilidade e especificidade analíticas e a reprodutibilidade da técnica em amostras de campo positivas para raiva e para EEE. A partir do protocolo estabelecido na reação de hemi-nested RT-PCR, realizaram-se variações de concentração de reagentes no protocolo para a reação de multiplex hemi-nested RT-PCR. Após o estabelecimento do protocolo para esta reação, os mesmos testes para verificação da sensibilidade e especificidade analíticas e da reprodutibilidade foram realizados, comparando-se os resultados com os obtidos pela hemi-nested RT-PCR. No teste de limiar de detecção, a sensibilidade analítica foi semelhante para as duas técnicas, obtendo-se 10&#45;1,7 para os três vírus padrão CVS, EEEV e WEEV. No teste de limiar de detecção utilizando uma amostra com os três vírus verificou-se uma alta especificidade dos primers, sendo que na reação de multiplex hemi-nested RT-PCR foi possível detectar simultaneamente os três vírus padrão. Não houve diferença nas proporções de amostras detectadas como positivas para raiva obtidas pelas duas técnicas, analisando-se pelo teste exato de Fisher (P=1,0000). No entando, para amostras de campo positivas para EEE, a proporção de amostras detectadas como positivas pela hemi-nested RT-PCR foi maior do que a proporção obtida pela multiplex hemi-nested RT-PCR (P<0,0001). Apesar de não ter sido possível o uso de amostras de campo positivas para WEE nesse estudo, os resultados sugerem que seria possível a detecção pela multiplex hemi-nested RT-PCR. Estes dados sugerem que a técnica de multiplex hemi-nested RT-PCR poderia ser aplicada para detecção de raiva e WEE, mas com limitações para a detecção de EEE. Pela análise de custo dos reagentes, o valor de uma reação de multiplex hemi-nested RT-PCR é semelhante ao de uma hemi-nested RT-PCR, podendo representar uma economia de pelo menos 49,17%. / Several viral zoonoses affect the equids causing neurological diseases, including rabies and Eastern and Western equine encephalitides (EEE and WEE). Clinical diagnosis is often not conclusive, in a way that laboratory diagnosis is essential. Data from the Laboratory of Rabies Diagnosis at the Pasteur Institute of São Paulo, between 2000 and 2010, demonstrate that approximately 75% of submitted equid samples were negative for rabies, emphasizing the importance of achieving a differential diagnosis for equine encephalitis caused by alphaviruses. The aims of this study were to test the suitability of using multiplex hemi-nested RT-PCR for the diagnosis of rabies, EEE and WEE in equids central nervous system samples and to perform a cost analysis of the reactions of each technique. We used the primers 21G, 304 and 504 directed to the N gene of rabies virus, and the primers cM3W, M2W, nEEE and nWEE directed the NSP1 gene of WEE and EEE viruses. A preliminary study of the primers was carried out, as well as their use in a hemi-nested RT-PCR, evaluating the optimal annealing temperature, the analytical sensitivity and specificity and the reproducibility of the technique in positive field samples for rabies and EEE. From the protocol established for the hemi-nested RT-PCR, variations in reagents concentrations for the multiplex hemi-nested RT-PCR protocol were perfomed. After establishing the protocol for this reaction, the same tests to verify the analytical sensitivity and specificity and reproducibility were performed and the results compared to those obtained by hemi-nested RT-PCR. In the detection threshold test, the analytical sensitivity was similar for both techniques, resulting in 10&#45;1.7 for the three virus standard CVS, and EEEV WEEV. In the detection threshold test using a sample with the three viruses, a high specificity of the primers was verified and the multiplex hemi-nested RT-PCR was able to detect the three viruses simultaneously. There was no difference in the proportions of samples detected as positive for rabies obtained by both techniques, according to the Fisher exact test (P = 1.0000). However, for EEE positive field samples, the proportion of samples detected as positive by the hemi-nested RT-PCR was higher than the proportion obtained by multiplex hemi-nested RT-PCR (P <0.0001). Although it was not possible to use WEE positive field samples in this study, the results suggest that its detection would be possible by multiplex hemi-nested RT-PCR. Thus, data suggest that the multiplex hemi-nested RT-PCR technique could be applied to detect rabies and WEE, but with limitations for the EEE detection. For the analysis of reagent costs, the cost of one multiplex hemi-nested RT-PCR is similar to one hemi-nested RT-PCR, and may represent a saving of 49,17% at least.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A raiva é uma enfermidade infectocontagiosa causada por um Lyssavirus, que acomete os mamíferos, inclusive o homem, está presente em todos os continentes com exceção da Antártida. Os cães ainda são considerados os principais responsáveis pela manutenção e transmissão da raiva para o homem. Porém, nos últimos anos os morcegos hematófagos e não hematófagos têm ganhado destaque como potenciais transmissores de raiva para animais e humanos nas Américas. Em 2010, o Brasil registrou três casos de raiva humana, sendo um causado por agressão de morcego. Recentemente, várias epidemias de raiva humana transmitida por morcegos hematófagos foram relatados na região Amazônica. No estado de Roraima até a presente data não há registro de casos de raiva humana. O presente estudo teve o objetivo de detectar a presença e circulação do vírus rábico em quirópteros no estado de Roraima, bem como identificar as espécies de morcegos envolvidas na pesquisa. A técnica Transcriptase Reversa seguida da reação em Cadeia pela Polimerase foi utilizada para a detecção do vírus rábico, utilizando tecido cerebral de morcegos que foram coletados pelas equipes de vigilância epidemiológica e ambiental, da Secretaria de Saúde e Agência de Defesa Sanitária de Roraima. Os morcegos foram identificados utilizando chaves dicotômicas disponíveis para morcegos do Brasil e de outros países sul americanos. No total foram analisadas 94 amostras de morcegos, as quais apresentaram resultados negativos para raiva pela técnica da RT-PCR, no entanto, não é possível afirmar que o vírus rábico não circule em Roraima. Por outro lado, o presente estudo identificou 19 espécies de morcegos distribuídas em seis famílias, sendo uma família (Vespertilionidae) e cinco espécies de quirópteros (Diaemus youngi, Noctilio albiventris, Myotis nigricans, Eptesicus diminutus e Cynomops planirostris) ainda sem relato de ocorrência para Roraima. Morcegos hematófagos foram identificados em cinco municípios. Ressaltando que este trabalho foi um passo inicial e que novos estudos precisam ser desenvolvidos, aprimorando as estratégias de coletas a fim de monitorar a presença do vírus da raiva no Estado. / Rabies is an infectious disease that affects mammals, including human beings. Present on all continents except Antarctica. It is caused by a Lyssavirus. Dogs are considered responsible for the maintenance and transmission of rabies to humans. But in recent years the bats have become a potential source of transmitting rabies to animals and human beings in the Americas. In 2010, Brazil recorded three cases of human rabies. One of them was caused by an attack of bat. Recently, several outbreaks of human rabies transmitted by vampire bats were reported in the Amazon region, so far, in the state of Roraima there is no record of cases of human rabies. This study is aimed to detect the presence and circulation of rabies virus in bats in the state of Roraima, as well as to identify the species involved, it includes, also, the necessity of strengthen the network of epidemiological and environmental surveillance of rabies. The technique followed by reverse transcriptase polymerase chain reaction (RT-PCR) was used for virus research involving brain tissue of bats that were collected by teams of environmental and epidemiological surveillance, belonging to the Department of Health and the health protection agency of Roraima. Species of Bats were identified using dichotomous keys available for bats in Brazil and other Latin American countries. In total of 94 bat samples were analysed. The samples tested were negative for rabies. It can not be said, however, that the rabies virus does not circulate in Roraima. This research identified 19 species of bats distributed in six family. On the other hand, the research points to a richness and abundance of species of bats. This study identified one family (Vespertilionidae) and five species of bats (Diaemus youngi, Noctilio albiventris, Myotis nigricans, Eptesicus diminutus e Cynomops planirostris) not yet reported to the State. Vampire bats were identified in five municipalities. Considering the epidemiological and environmental importance of bats for ecosystems, this study is contributing to the increase of knowledge about both environmental surveillance of rabies and diversity of bats.

Rondônia apresenta área com rica diversidade de artrópodes, porém pouco se conhece sobre a transmissão de arbovírus por estas espécies. O presente trabalho visou detectar arbovírus, por meio da RT-PCR e da Duplex RT-PCR, nas espécies de dipteros coletados no Estado, bem como caracterizá-los pela reação de sequenciamento. A RT-PCR e a Duplex RT-PCR detectaram as suspensões dos vírus Mayaro e Oropouche até 104 e 101 TCID50/mL, respectivamente, porém o vírus Dengue 2 em pools contendo menos de três mosquitos infectados foi negativa. O controle endógeno foi detectado em 66,8 % das amostras, sendo que, em pools contendo entre um e três mosquitos, a detecção foi aproximadamente metade da detecção nos pools contendo entre 11 e 15. Em 0,66 % dos pools foi encontrado o vírus Oropouche e em outros 0,66 %, o vírus Cacipacoré. O vírus Oropouche foi detectado em Coquillettidia sp. e Deinocerites sp., enquanto o vírus Cacipacoré foi encontrado em Anopheles sp. e Culex sp. As técnicas possibilitaram a detecção dos arbovírus pesquisados nos pools coletados em Rondônia. / The Rondônia state has an area with rich arthropods diversity although the knowledge about the arboviruses transmition for these species is poor. The present work aimed to detect arboviruses through RT-PRC and RT-PCR Duplex in the diptera species collected in the region as well as their characterization through the sequence reaction. The RT-PRC and RT-PCR Duplex detected the Mayaro and Oropouche virus suspensions until 104 e 101 TCID50/mL respectively, although it was negative for the Dengue 2 virus in pools containing less than three infected mosquitoes. The endogenous control was detected in 66,8 % of samples and from pools containing from one to three mosquitoes the detection rate was approximately half from that obtained from pools with 11 to 15 mosquitoes. Oropouche virus was found in 0,66 % of pools and Cacipacore virus also in 0,66 % of pools. Oropouche virus was detected in Coquillettidia sp. and Deinocerites sp. while Cacipacoré virus was found in Anopheles sp. and Culex sp. The techniques allowed the detection of examined arboviruses in the pools collected from Rondonia.

This project was designed to develop a method for the collection of environmental samples during prolonged Norovirus (NoV) outbreak investigations, and to develop real-time RT-PCR assays to analyze environmental samples for GI and GII noroviruses. The collection and processing of environmental samples could provide epidemiological data to facilitate investigations of prolonged NoV outbreaks and could guide public health NoV intervention strategies. Real-time RT-PCR assays for the detection of GI and GII NoVs were developed by adapting the State Hygienic Laboratory clinical GI and GII assays to the AB 7500 Fast platform. Analysis of the GI assay performance yielded a dilution curve slope = 3.28, R2 = 0.999 and a calculated amplification efficiency of 102%. The GII assay yielded a dilution curve slope = 3.39, R2 = 0.999 and a calculated amplification efficiency of 97%. Amplification efficiencies determine the sensitivity and the limit of detection of real-time RT-PCR assays. Optimum efficiencies range from 95%-105%, with a 100% efficiency indicating exponential amplification of targeted nucleic acid. To develop a method for the collection of environmental samples, multiple swab types were tested to determine their ability to recover NoV from laboratory spiked environmental surfaces. It was determined that foam swabs moistened with viral transport media were most effective in recovering NoV from spiked surfaces. A field test of the environmental sampling method was conducted by sampling environmental surfaces in four restaurants in one Iowa community. NoVs were not detected in the environmental samples. The collection and processing of environmental samples when conducting an investigation of a prolonged NoV outbreak could provide additional information on the epidemiology of NoV transmission and infection.

Infectious bronchitis virus (IBV) is a member of family Coronaviridae and is classified into group 3 of the Coronaviruses. The virus is a single-stranded positive-sense RNA virus with a genome of 27kbp. IBV is a highly infectious disease of chickens that results in high morbidity with moderate to severe mortality depending on the strain involved, age of the birds, and immune status of the chickens. Multiple worldwide investigations indicate that differentiation within the S1 glycoprotein gene can lead to serotype variation within the IBV species. In this study 46 isolates collected over two years from broiler and broiler breeder flocks and eight historical isolates were analyzed. Forty one isolates originated from the KwaZulu-Natal region whilst the remaining thirteen were isolated from 4 other poultry-dense provinces. The S1 gene was sequenced and compared to determine variation between South African isolates, as well as global sequences submitted to Genbank. The results indicate the division of isolates analyzed into 2 different clades of IBV within the province. The most prevalent genotype was similar to IBV Mass strain detected in 79% of the full S1 sequences. Variation up to 22.3% was detected within local strains, supporting the hypothesis that multiple IBV serotypes may co-circulate in the same region simultaneously. Additionally, more conservation was observed among Mass serotypes versus QX-like serotypes, implying that vaccine use can influence the variability within the IBV population. Higher variability was found in the first half of the S1 gene in comparison to the last half of the S1 gene. This is in agreement with previous findings that the hypervariable regions of the S1 gene are located within the first 450 base pairs. This study offers the first published consolidation of IBV isolates from South Africa and identifies variation within the IBV population of the SA broiler flock. Previous publications list four or five IBV isolates whilst this study describes variation found in 54 isolates spanning 32 years. In addition this study provides the insight into the prevalence of IBV variation in poultry flocks due to the large number of isolates. The comparative use of geno- and serotyping for South African IBV isolates is also described for the first time in this study. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Veterinary Tropical Diseases / unrestricted

Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local production and implementation of molecular testing. Here, we provide detailed methods and validation of a molecular toolkit that can be readily produced and deployed using laboratory equipment available in LMICs. Our results show that lab-scale production of enzymes and nucleic acids can supply over 50,000 tests per production batch. The optimized one-step RT-PCR coupled to CRISPR-Cas12a-mediated detection showed a limit of detection of 102 ge/μL in a turnaround time of 2 h. The clinical validation indicated an overall sensitivity of 80%–88%, while for middle and high viral load samples (Cq ≤ 31) the sensitivity was 92%–100%. The specificity was 96%–100% regardless of viral load. Furthermore, we show that the toolkit can be used with the mobile laboratory Bento Lab, potentially enabling LMICs to implement detection services in unattended remote regions. / Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica / Revisión por pares

Der Folsäureantagonist Methotrexat (MTX) wird zur Behandlung onkologischer und rheumatoider Erkrankungen eingesetzt. Die Aufnahme des Methotrexats in die Zielzelle ist dabei Vorraussetzung für die Bindung an seine intrazellulären Zielstrukturen und erfolgt über verschiedene Transportsysteme. In diesem Zusammenhang ist bei entsprechenden Plasma-konzentrationen von MTX der Reduced Folate Carrier (RFC1) von besonderer Bedeutung. 1994 konnte erstmals die cDNA dieses Transporters aus Maus- und Hamstergewebe isoliert werden. Die cDNA für einen mit dem RFC1 identischen hepatozellulären MTX-Transporter der Ratte wurde 2000 kloniert. Vorhergehende Gen-Expressionsstudien zeigten, dass die RFC1-mRNA ubiquitär gebildet wird. Die Proteinexpression wurde jedoch bisher nur in ausgewählten Geweben der Maus untersucht. Systematische Arbeiten, in denen in vergleichender Weise sowohl die RFC1 Gen- als auch die Proteinexpression in allen Geweben mit einer möglichen Relevanz für die Folat- und Antifolataufnahme, Speicherung und Eliminierung untersucht werden, fehlten bisher. Insbesondere die Expression des RFC1-Proteins der Ratte (rRFC1) mittels immunologischer Verfahren ist bisher nicht beschrieben worden. Ziel dieser Arbeit war es daher, die Gen- und Proteinexpression des rRFC1 in ausgewählten Geweben der Ratte darzustellen. Dieses schließt die Generierung spezifischer Antiseren gegen den rRFC1 als ersten Schritt mit ein. Es wurden geeignete antigene Aminosäuresequenzen des rRFC1 bestimmt und die entsprechenden cDNA Sequenzen wurden amplifiziert und in einen geeigneten Expressionsvektor kloniert. Rekombinante rRFC1 Fusionsproteine konnten mittels E. coli Zellen hergestellt und anschließend aufgereinigt werden. Nachfolgend wurden entweder die rRFC1 Fusionsproteine oder die rRFC1 spezifischen Peptide, welche von dem Affinitätspeptid separiert worden waren, für die Immunisierung von Kaninchen verwendet Drei Antiseren mit ausreichender Reaktivität und Spezifität konnten gewonnen und mittels Affinitätschromatographie aufgereinigt werden. Die erhaltenen Antiseren sind gegen die intrazellulären N- und C-terminalen Regionen (ID1, ID7) bzw. gegen die erste extrazelluläre Schleife (OD1) gerichtet. In Western-Blot Studien konnte mittels dieser Antiseren für den rRFC1, der in transfizierten Nierenepithelzellen (MDCK-rRFC-HA) stabil exprimiert wurde, ein Molekulargewicht von 71 kD für die glykosylierte Form und von 53 kD für die unglykosylierte Form ermittelt werden. Weiter konnte belegt werden, dass das Protein in MDCK-rRFC1-HA Zellen überwiegend in der glycosylierten Form vorliegt. Mittels RT-PCR Analysen wurde die Genexpression des rRFC1 in allen untersuchten Geweben nachgewiesen. Besonders hohe mRNA-Gehalte waren in Thymus, Niere und Milz vorhanden, während in Herz- und Muskelgewebe sowie in Leukozyten nur ein Signal nahe der Nachweisgrenze detektierbar war. Durch immunhistologische Untersuchungen konnten die rRFC1 Proteinexpression und beträchtliche Unterschiede in der Signalintensität bestätigt werden. Zusätzlich konnten neue Informationen über die unterschiedliche subzelluläre Lokalisation gewonnen werden: so konnte eine starke Expression des Transporters in der apikalen Membran von Dünn- und Dickdarmmukosa dargestellt werden, während die ebenfalls starke Färbung in der Niere auf den Bereich der basolateralen Membran der Tubuli beschränkt war. In der Leber war eine Expression mittlerer Intensität im Bereich der Lebertrias erkennbar. Während in der Milz nur in der roten Pulpa das RFC1-Protein detektiert wurde, konnten im Thymus sowohl in der Rinde als auch im Mark positive Zellen nachgewiesen werden. Im Hoden konnte der Transporter in den Sertoli-Zellen dargestellt werden. Eine starke Expression des Transporters wurde im Gehirn im Bereich der apikalen Membran der Ependymzellen des Plexus choroideus nachgewiesen. In der Skelettmuskulatur und im Herzgewebe beschränkte sich die Expression des rRFC1 auf das Perimysium des Muskelgewebes und auf kleinere Gefäße des Muskel- und Herzgewebes. In dieser Arbeit konnte somit gezeigt werden, dass der RFC1 der Ratte ubiquitär exprimiert wird, wobei die Expressionsstärke jedoch stark variiert. Die beobachtete Gewebslokalisation des RFC1 belegt sowohl dessen zentrale Rolle in der Folathomöostase als auch in der MTX vermittelten Organtoxizität und Pharmakokinetik, insbesondere bei der intestinalen Resorption sowie der hepatischen und renalen Exkretion.

Im Graduiertenkolleg „Schlachttierbelastung und Produktsicherheit“ der Veterinärmedizinischen Fakultät der Universität Leipzig sollten in interdisziplinärer Zusammenarbeit Erkenntnisse zum Verhalten transportbelasteter Schlachtschweine in Bezug auf bakterielle Translokationsprozesse erarbeitet werden. Es wurden Mastschweine aus herkömmlichen Mastbetrieben definierten Belastungssituationen ausgesetzt , geschlachtet und untersucht. Dabei sollten physiologische, pathologisch-anatomische, immunologische, lebensmittel- und fleischhygienische, bakteriologische, virologische sowie ethologische Fragestellungen bearbeitet werden. Ziel war es festzustellen, ob eine Belastung der Tiere (u.a. durch den Transport) Auswirkungen auf die Produktqualität hat und ob durch eine Translokation pathogener Erreger ein Risiko für die Gesundheit des Verbrauchers besteht. Im Teilprojekt des Institutes für Virologie wurde untersucht, ob Rotavirus-Infektionen von Schlachtschweinen unter der Problematik der Belastung ein mögliches Infektionsrisiko für den Menschen darstellen. Um die zu erwartende niedrige Konzentration von Rotaviren in Organen von Schlachtschweinen nachweisen zu können, wurde eine kompetitive RT-PCR zum Nachweis von Rotaviren der Gruppe A verschiedener Spezies entwickelt. Dazu wurde ein sogenannter Kompetitor synthetisch hergestellt, welcher als interne oder externe Reaktionskontrolle eingesetzt wurde. Zum einen diente er der Überprüfung des ordnungsgemäßen Verlaufes einer RT-PCR, zum anderen wurde er zur Herstellung von Standards verwendet. Die RT-PCR wurde anschließend in eine „Real time“ RT-PCR umgewandelt. Sowohl mit der herkömmlichen als auch mit der „Real-time“ RT-PCR konnten 10 spezifische RNA-Moleküle in einer Probe nachgewiesen werden. In einer SPF-Schweineherde, welche einer Belastung infolge eines Tiertransports ausgesetzt war, konnten mit Hilfe der RT-PCR klinisch gesunde intermittierende Rotavirus-Ausscheider entdeckt werden. Bei einigen dieser Tiere gelang der Nachweis der Virusausscheidung über einen Zeitraum von drei Monaten. Nach der Schlachtung wurden in Organen des lymphatischen Systems bei zwei Schweinen sehr geringe Konzentrationen an rotavirus-spezifischer RNA detektiert. Infektiöses Virus konnte daraus allerdings nicht isoliert werden. Auch in einer Mastschweineherde konnte bei einigen Tieren Rotavirus-spezifische RNA im Kot nachgewiesen werden. Ein Infektionsversuch dieser Tiere mit Salmonella typhimurium konnte keine Reaktivierung der Rotavirus-Infektion auslösen. Aufgrund des Zoonose-Potentials von Rotaviren kann nach den Untersuchungen ein Infektionsrisiko für den Verbraucher durch eine endogene Kontamination von Schlachttieren mit Rotaviren nicht sicher ausgeschlossen werden. Die Untersuchungen zeigten auch, dass intermittierende Rotavirus-Ausscheider ein Infektionsrisiko für den Verbraucher darstellen, wenn z.B. bei der Schlachtung der Tiere oder bei der Verarbeitung des Fleisches dieser Tiere hygienische Grundregeln verletzt werden. Besonders gefährdet wären hierbei Neugeborene, Kinder, Senioren und immunsupprimierte Personen. Ein Ort einer Viruspersistenz in Organen konnte auch nach diesen Untersuchungen nicht gefunden werden. Dennoch scheint es, dass Rotaviren in der Natur oder in einer Population von Menschen oder Tieren persistieren. Durch ständige Neuinfektionen bzw. Reinfektionen empfänglicher Organismen haben Rotaviren so ihre Erhaltung gesichert. / Within the graduate programme “Schlachttierbelastung und Produktsicherheit” of the Veterinary Faculty of the University of Leipzig, the behaviour of slaughter swine exposed to the stress of transport was observed in an interdisciplinary collaboration concerning the translocation processes of bacteria. Fattened pigs from conventional pig fattening units were exposed to particular stress situations, and then slaughtered and examined. The following aspects of this process were investigated: physiology, pathological-anatomy, immunology, food and meat hygiene, bacteriology, virology and ethology. The aim of this study was to verify whether exposing the animals to stress situations (such as transport) influences the quality of the product and whether the translocation of pathogens represents a risk for consumer health. Within the sub-project of the Institute for Virology, analyses were made to verify whether rotavirus infections of slaughter swine exposed to stress situations represents a potential contamination risk for humans. In order to detect the expected low concentration of rotaviruses in the organs of slaughtered pigs, a competitive RT-PCR was developed as a test of rotaviruses for various group A species. To do this, a so-called competitor was synthetically created, which was used as an internal and external reaction control. On one hand, it was used to verify the regular course of an RT-PCR reaction, and on the other hand, it was implemented to develop standards. RT-PCR was then modified by means of a real time RT-PCR. Both with the conventional and with the real time RT-PCR, it was possible to detect 10 specific RNA molecules/ sample.With this new very sensitive and specific amplification process, it was possible to detect rotavirus-specific RNA in the excrement of people and of pigs, cows, horses, rabbits and monkeys. the evidence of the virus excretion was produced over a time period of three months. After slaughtering, low amounts of rotavirus specific RNA were found in the organs of the lymphatic system. There were no indications that any of these organs were infectious. Rotavirus specific RNA was also found in the excrement of some fattened pigs. An attempt to infect these animals with Salmonella typhimurium was unable to cause any reactivation of the rotavirus infection. An infection risk for the consumer through an endogenous rotavirus contamination of fattened pigs cannot be excluded with any degree of certainty on the basis of these analyses due to the zoonotic potential of rotaviruses. The analyses also showed that intermittent rotavirus excretors represent an infection risk for the consumer, if for example basic hygiene rules are broken during the slaughter or meat processing of these animals. At special risk may be new-borns, children, youth, the elderly and people suffering from immunodeficiency. These examinations could not find a specific place in the organs where the virus persists. Nevertheless, it seems that rotaviruses persist in the environment or in a population of people or animals. With constant new infections or re-infections of receptive organisms, rotaviruses seem to have assured their survival.

Searches for sequence similarity against a previously isolated and known ABA regulated partial geranium cDNA on GenBank and TIGR databases gave results indicating sequence similarities to both firefly luciferase and 4-coumarate:CoA Ligase (4-CL). To determine whether or not this geranium cDNA, and a root mRNA from Arabidopsis that hybridized with the geranium cDNA, is 4-CL, specific Arabidopsis 4-CL primers were used for expression analysis by RT-PCR of Arabidopsis 4-CL mRNA from Arabidopsis root tissue. The expression pattern of the Arabidopsis 4-CL mRNA was identical with the expression pattern of the mRNA that hybridized with the geranium cDNA. This matching expression pattern gives very strong evidence that our geranium cDNA is 4-CL like and that Arabidopsis 4-CL is downregulated during water stress by ABA. This is significant in that it has not previously been reported. Northern analysis and PCR product sequence analysis further confirmed this expression data.

Association of Mycobacterium avium subspecies paratuberculosis (MAP) with Crohn's disease (CD) and not with ulcerative colitis (UC), two forms of inflammatory bowel disease (IBD), has been vigorously debated in recent years. This theory has been strengthened by recent culture of MAP from breast milk, intestinal tissue and Blood from patients with active Crohn's disease. Culture of MAP from clinical samples remained challenging due to the fastidious nature of MAP including its lack of cell wall in infected patients. The advent of real time PCR has proven to be significant in infectious disease diagnostics. In this study, real time reverse transcriptase PCR (RT-PCR) assay based on targeting mRNA of the IS900 gene unique to MAP has been developed. All variables included in RNA isolation, cDNA synthesis and real time PCR amplification have been optimized. Oligonucleotide primers were designed to amplify 165 bp specific to MAP and the assay demonstrated sensitivity of 4 genomes per sample. In hope this real time RT-PCR may aid in the detection of viable MAP cells in Crohn's disease patients, a total of 45 clinical samples were analyzed. Portion of each sample was also subjected to 12 weeks culture followed by standard nested PCR analysis. The samples consisted of 17 cultures (originated from 13 CD, 1 UC and 3 NIBD subjects), 24 buffy coat blood (originated from 7 CD, 2 UC, 11 NIBD and 4 healthy subjects) and 4 intestinal biopsies from 2 CD patients. Real time RT-PCR detected viable MAP in 11/17 (65%) of iii suspected cultures compared to 12/17 (70%) by nested PCR including 77% and 84% from CD samples by both methods, respectively. Real time RT-PCR detected MAP RNA directly from 3/7 (42%) CD, 2/2 (100%) UC and 0/4 healthy controls similar to results following long term culture incubation and nested PCR analysis. Interestingly, real time RT-PCR detected viable MAP in 2/11 (13%) compared to 4/11 (26%) by culture and nested PCR in NIBD patients. For tissue samples, real time RT-PCR detected viable MAP in one CD patient with the culture outcome remains pending. This study clearly indicates that a 12-hr real time RT-PCR assay provided data that are similar to those from 12 weeks culture and nested PCR analysis. Consequently, use of real time In our laboratory, we previously demonstrated a possible downregulation in the Interferon-gamma receptor gene (IFNGR1) in patients with active Crohn's disease using microarray chip analysis. In this study, measurement of RNA by real time qRT-PCR indicated a possible downregulation in 5/6 CD patients compared to 0/12 controls. The preliminary data suggest that downregulation in INFGR1 gene, and the detection of viable MAP in CD patients provides yet the strongest evidence toward the linkage between MAP and CD etiology.