Orientador: Hélio José Montassier / Banca: Clarice Weins Arns / Banca: Adolorata Aparecida Bianco Carvalho / Resumo: A bronquite infecciosa das galinhas (BIG) é uma doença infecciosa que está amplamente disseminada entre as criações avícolas brasileiras e é uma das enfermidades virais que mais têm causado perdas econômicas na atualidade. Portanto, a rápida detecção e identificação do agente causal são imprescindíveis para que medidas eficazes de controle sejam prontamente tomadas. Para tanto, é necessário que os métodos de diagnóstico empregados sejam sensíveis, específicos, rápidos e também de baixo custo. Nesse contexto, a técnica de RTPCR em tempo real abordada no presente estudo permitiu a amplificação de duas regiões de hipervariabilidade do gene S1 de 17 estirpes diferentes do vírus da BIG (VBI), que foram testadas, mas não foi capaz de amplificar nenhum dos RNAvírus heterólogos analisados (vírus da doença de Newcastle, pneumovírus aviário e vírus da doença de Gumboro). Com essa mesma técnica foi possível fazer a diferenciação em grupos geneticamente distintos, de estirpes do VBI através de análises das curvas de dissociação de fragmentos amplificados a partir das regiões de hipervariabilidade gênica I e II do gene S1. A RT-PCR em tempo real desenvolvida apresentou maior sensibilidade na detecção do VBI em amostras teciduais, quando comparada à técnica padrão de Isolamento Viral em ovos embrionados de galinha... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The avian infectious bronchitis virus (IBV) is an infectious disease widely spread in Brazilian commercial poultries where causes significant economical losses. Rapid and accurate diagnosis of the IBV strain involved in a field outbreak is necessary to establish an effective control of this disease. The real-time RT-PCR performed in this study to amplify two hypervariable regions of S1 gene, was able to detect 17 IBV strains, e.g., nine reference strains (including Massachussets, Connecticut, JMK, SE 17 and Iowa serotypes) and eight Brazilian field isolates, whilst non-related avian viral pathogens such as Newcastle disease virus, Avian Pneumovirus and Gumboro disease virus were not detected. The differentiation between IBV strains was accomplished using the melting curve analysis of the amplified fragments corresponding to the hypervariable regions I and II of S1 gene. The real-time RT-PCR developed here showed a higher rate of IBV detection in tissue samples of experimentally infected chickens, when compared to the goldstandard technique of Viral Isolation in embryonated chicken eggs, and the same rate of detection was found for the conventional RT-PCR... (Complete abstract, click electronic access below) / Mestre

Les épisodes de mortalité massive de l’huître creuse Crassostreae gigas observés sur les côtes françaises depuis 2008 ont été associés à certaines espèces appartenant au genre bactérien Vibrio. Ces mortalités, particulièrement intenses et rapides au cœur des lagunes méditerranéennes, atteignent 80 à 100% de la production ostréicole remettant ainsi en cause la pérennité de cette activité. Une surveillance environnementale de ces bactéries apparait donc essentielle et nécessite la mise au point de méthodes d’analyse innovantes, alternatives aux techniques couramment employées, afin de permettre un suivi rapide et en temps réel des Vibrio dans les milieux aquatiques côtiers.Dans ce contexte, l’objectif de cette thèse a été de concevoir des outils analytiques de type génocapteurs pour la détection et la quantification des Vibrio dans les écosystèmes aquatiques. Dans un premier temps, un système basé sur un format d’hybridation « sandwich » reposant sur l’intercalation des acides nucléiques cibles entre une sonde capture immobilisée et une sonde signal marquée, couplé à une détection optique, a été élaboré. Après optimisation des conditions expérimentales, le test développé s’est avéré très sensible avec une limite de détection de 5 ng.µL-1 d’acides nucléiques, ainsi qu’hautement spécifique du genre Vibrio. La méthode a ensuite été appliquée avec succès à la détection des Vibrio dans des échantillons environnementaux, collectés dans la lagune de Salses-Leucate. Un second format d’hybridation, basé sur la compétition entre les acides nucléiques cibles et la sonde capture pour la sonde signal, a ensuite été envisagé en utilisant aussi bien une transduction optique qu’électrochimique. En parallèle, des méthodes de PCR quantitative en temps réel ont été mises au point afin de servir de références pour la validation des génocapteurs. / Mass mortality events affecting the Pacific oyster Crassostreae gigas on French coasts since 2008 have been associated to some Vibrio species. These mortalities, particularly severe and sudden in the mediterranean lagoons, can reach 80 to 100% of the oyster production threatening the sustainability of this activity. An environmental monitoring of these bacteria appears essential and, for this purpose, innovative analytical methods have to be developed as alternative to classical techniques, in order to allow the rapid and in real time monitoring of Vibrio in the coastal aquatic environments. In this context, the objective of the thesis was to design genosensors as analytical tools for Vibrio detection and quantification in aquatic ecosystems. In a first step, a system based on a « sandwich » hybridization format, in which nucleic acid targets were bound between an immobilized capture probe and a labeled signal probe, coupled with an optical detection method, was developed. After experimental condition optimization, the test showed high sensitivity with a limit of detection of 5 ng.µL-1 of nucleic acids and was highly specific to Vibrio spp. The method was then successfully applied to Vibrio detection in environmental samples collected in Salses-Leucate lagoon. A second hybridization format, based on a competition between the targeted nucleic acids and the capture probe for the signal probe has been considered using both optical and electrochemical transductions. Concurrently with the development of genosensors, quantitative real-time PCR have been designed as reference methods.

Les techniques de biologie moléculaire ont pris au cours des 20 dernières années une place importante dans le diagnostic direct des pathogènes viraux. Notre travail a porté sur la mise en place et le développement d’une plate-forme de biologie moléculaire, au sein du laboratoire de virologie de l’hôpital de la Timone, pour répondre aux demandes et contraintes du diagnostic en milieu hospitalier. L’organisation de cette plate-forme a nécessité plusieurs étapes : la prévention des risques de contamination, l’aliquotage et le stockage des réactifs, l’automatisation des techniques d’extraction des acides nucléiques, la mise au point de témoins positifs synthétiques et de témoins internes et l’optimisation des protocoles de PCR. Cette approche optimisée du diagnostic moléculaire des infections virales a été appliqué notamment à la détection de la grippe pandémique A/H1N1v dans les laboratoires de routine hospitalière et d’urgence « Point Of Care ». La mise en place de cette plate-forme a fait progresser de manière considérable le diagnostic moléculaire du laboratoire. Elle nous permet actuellement de détecter un grand nombre de pathogènes (>80) et de réaliser des tests dans un format à haut débit (≈40 000 tests/an). Au total, cette plateforme est au coeur de la capacité du laboratoire pour réagir de manière rapide aux évènements d'émergence en mettant en place rapidement des procédures diagnostiques standardisées. Ces techniques ont été transférées à de nombreux autres laboratoires de virologie partenaires nationaux et internationaux. Nous envisageons maintenant son utilisation dans une approche syndromique avec notamment, le développement du diagnostic des virus respiratoires. / Molecular biology techniques have taken an important role in the direct diagnosis of viral pathogens over the last 20 years. Our work focused on establishing and developing a platform for molecular diagnosis in the laboratory of Virology (Timone Hospital) to meet the demands and constraints of diagnosis in hospitals. The organization of this platform required several steps: prevention of contamination risks, aliquoting and storage of reagents, automation techniques of nucleic acid extraction, development of synthetic positive controls and internal controls and optimization of PCR protocols. This optimized approach of the molecular diagnosis of viral infections has particularly been applied to the detection of pandemic influenza A/H1N1v in hospital laboratories for routine and emergency "Point Of Care." The implementation of this platform has significantly improved molecular diagnosis in our laboratory. It currently allows us to detect a large number of pathogens (> 80) and perform tests in a high-throughput (≈ 40,000 tests per year). In total, this platform is at the heart of the laboratory capacity to react quickly to emerging events by rapidly implementing standardized procedures. These techniques have been transferred to many other partners’ laboratories nationally and internationally. We are now considering its use in a syndromic approach including the development of the diagnosis of respiratory viruses.

<p>Human endogenous retroviruses (HERVs) represent approximately 7% of the human genome. This investigation was focused on one particular HERV, ERV3, with the main purpose of characterising its gene expression patterns and genomic distribution of ERV3-like sequences. Furthermore, this careful expression study should provide insights into the biological role of HERVs. The impact of HERVs in health and disease is not yet clarified. ERV3 is expressed as three envelope (<i>env</i>) transcripts, of which two also contain a cellular gene, <i>H-plk</i> (human proviral linked <i>Krüppel</i>). ERV3 <i>env</i> expression was mainly investigated at the RNA level. The gene expression of two other HERVs, HERV-K and HERV-E was analysed and compared with ERV3 activity.</p><p>Real-time PCRs were developed and in combination with in situ hybridisation, it was found that ERV3 is expressed in a tissue- and cell-specific way. High levels of ERV3 mRNA (up to six times over Histone3.3) were demonstrated in placenta, sebaceous glands, foetal and adult adrenal glands, brown adipose tissue, corpus luteum, pituitary gland, thymus and testis. In monocytic cells including both normal monocytes and malignant U-937 cells, elevated mRNA levels were observed after retinoic acid (RA)-induced differentiation. ERV3-encoded Env protein was detected in selected cases, one following RA-treatment. In addition, several new ERV3-like sequences were discovered in the human genome. </p><p>ERV3 was found to have conserved open reading frames in contrast to other ERV3-like sequences in the human genome. This suggests that ERV3 may be involved in important cellular processes such as differentiation, cell fusion, immunomodulation and protection against infectious retroviruses. The developed techniques and obtained results will allow further studies of HERV expression to better correlate HERV activity to both normal development and disease. </p>

<p>In recent years molecular biology has become an integral part of the clinical laboratory. With an ever increasing number of methodologies and applications being presented each year it has increased our knowledge of how bacteria cause disease as well as our ability to predict disease outcome. </p><p>The main focus of this thesis has been to develop methods for identifying biomarkers and prediction methods for bacterial infectious diseases by taking advantage of the ever increasing possibilities of molecular biology. We applied cutting edge techniques in order to establish novel platforms for identifying and characterizing biomarkers of disease. </p><p>In paper one we describe a novel approach to measure levels of antibiotic resistance and viability of C. trachomatis, a method that is a clear improvement over existing techniques. In the second paper we describe the development of two assays designed to type pertussis toxin subunit 1 in circulating strains, in order to facilitate multi center studies for vaccine escape surveillance. In paper three we develop a novel microarray application designed to identify a large number of bacterial traits of H. pylori simultaneously with human genetic polymorphisms in order to identify a collection of risk factors that could be used as a prediction tool for gastric cancer risk. In the last paper we define the “antigenome” of H. pylori and identified 14 promising, previously unreported antigens as well as a number of potential biomarkers.</p><p>The platform technologies described in this collection of papers will hopefully help us identifying novel ways of fighting and predicting bacterial disease in future studies. </p>

<p>Genetic profiling is commonly performed on the autosomes using multiple DNA markers. Although routine forensic DNA analysis is robust and based on reliable technologies, samples with degraded or limited amounts of DNA often fail. In these cases, the analysis of mitochondrial DNA (mtDNA) can be very valuable due to the high copy number per cell. This thesis describes evaluation and modifications of existing technologies that are useful in forensic DNA typing, mainly focusing on mtDNA.</p><p>DNA quantities isolated from common evidence materials such as hairs, fingerprints and accessories were estimated using a real-time quantification assay. Knowledge of quantitative differences between materials can guide forensic scientists to perform the best analysis (Paper I).</p><p>The current mtDNA analysis is based on hypervariable region (HVI/HVII) sequencing, which is the most rigorous and time-consuming forensic DNA analysis. Therefore, we evaluated the possibility to exclude individuals by screening for non-matching samples using the rapid and easy mtDNA Linear Array Assay (Paper II). </p><p>The major disadvantage using mtDNA is the lower discrimination power compared to multiple nuclear DNA markers. In contrast to the nuclear genome, due to the uniparental (maternal) mode of inheritance, no individual has unique mtDNA. We investigated the possibility of increasing the discrimination power by using pyrosequencing technology to analyse parts of the coding region in addition to HVI/HVII (Paper III). Furthermore, the addition of coding mtDNA information was evaluated by comparing several recently published mtDNA coding region assays (Paper IV). </p><p>Mixtures of DNA are common in forensic genetics due to contribution of DNA from several individuals, contamination or heteroplasmy. To resolve mixtures we have developed a pyrosequencing-based assay for the accurate quantification of the mtDNA mixture components (Paper V).</p><p>In conclusion, this thesis describes several assays that are valuable in forensic genetics for DNA quantification, improved mtDNA analysis, and mtDNA mixture interpretation.</p>

Human endogenous retroviruses (HERVs) represent approximately 7% of the human genome. This investigation was focused on one particular HERV, ERV3, with the main purpose of characterising its gene expression patterns and genomic distribution of ERV3-like sequences. Furthermore, this careful expression study should provide insights into the biological role of HERVs. The impact of HERVs in health and disease is not yet clarified. ERV3 is expressed as three envelope (env) transcripts, of which two also contain a cellular gene, H-plk (human proviral linked Krüppel). ERV3 env expression was mainly investigated at the RNA level. The gene expression of two other HERVs, HERV-K and HERV-E was analysed and compared with ERV3 activity. Real-time PCRs were developed and in combination with in situ hybridisation, it was found that ERV3 is expressed in a tissue- and cell-specific way. High levels of ERV3 mRNA (up to six times over Histone3.3) were demonstrated in placenta, sebaceous glands, foetal and adult adrenal glands, brown adipose tissue, corpus luteum, pituitary gland, thymus and testis. In monocytic cells including both normal monocytes and malignant U-937 cells, elevated mRNA levels were observed after retinoic acid (RA)-induced differentiation. ERV3-encoded Env protein was detected in selected cases, one following RA-treatment. In addition, several new ERV3-like sequences were discovered in the human genome. ERV3 was found to have conserved open reading frames in contrast to other ERV3-like sequences in the human genome. This suggests that ERV3 may be involved in important cellular processes such as differentiation, cell fusion, immunomodulation and protection against infectious retroviruses. The developed techniques and obtained results will allow further studies of HERV expression to better correlate HERV activity to both normal development and disease.

In recent years molecular biology has become an integral part of the clinical laboratory. With an ever increasing number of methodologies and applications being presented each year it has increased our knowledge of how bacteria cause disease as well as our ability to predict disease outcome. The main focus of this thesis has been to develop methods for identifying biomarkers and prediction methods for bacterial infectious diseases by taking advantage of the ever increasing possibilities of molecular biology. We applied cutting edge techniques in order to establish novel platforms for identifying and characterizing biomarkers of disease. In paper one we describe a novel approach to measure levels of antibiotic resistance and viability of C. trachomatis, a method that is a clear improvement over existing techniques. In the second paper we describe the development of two assays designed to type pertussis toxin subunit 1 in circulating strains, in order to facilitate multi center studies for vaccine escape surveillance. In paper three we develop a novel microarray application designed to identify a large number of bacterial traits of H. pylori simultaneously with human genetic polymorphisms in order to identify a collection of risk factors that could be used as a prediction tool for gastric cancer risk. In the last paper we define the “antigenome” of H. pylori and identified 14 promising, previously unreported antigens as well as a number of potential biomarkers. The platform technologies described in this collection of papers will hopefully help us identifying novel ways of fighting and predicting bacterial disease in future studies.

Genetic profiling is commonly performed on the autosomes using multiple DNA markers. Although routine forensic DNA analysis is robust and based on reliable technologies, samples with degraded or limited amounts of DNA often fail. In these cases, the analysis of mitochondrial DNA (mtDNA) can be very valuable due to the high copy number per cell. This thesis describes evaluation and modifications of existing technologies that are useful in forensic DNA typing, mainly focusing on mtDNA. DNA quantities isolated from common evidence materials such as hairs, fingerprints and accessories were estimated using a real-time quantification assay. Knowledge of quantitative differences between materials can guide forensic scientists to perform the best analysis (Paper I). The current mtDNA analysis is based on hypervariable region (HVI/HVII) sequencing, which is the most rigorous and time-consuming forensic DNA analysis. Therefore, we evaluated the possibility to exclude individuals by screening for non-matching samples using the rapid and easy mtDNA Linear Array Assay (Paper II). The major disadvantage using mtDNA is the lower discrimination power compared to multiple nuclear DNA markers. In contrast to the nuclear genome, due to the uniparental (maternal) mode of inheritance, no individual has unique mtDNA. We investigated the possibility of increasing the discrimination power by using pyrosequencing technology to analyse parts of the coding region in addition to HVI/HVII (Paper III). Furthermore, the addition of coding mtDNA information was evaluated by comparing several recently published mtDNA coding region assays (Paper IV). Mixtures of DNA are common in forensic genetics due to contribution of DNA from several individuals, contamination or heteroplasmy. To resolve mixtures we have developed a pyrosequencing-based assay for the accurate quantification of the mtDNA mixture components (Paper V). In conclusion, this thesis describes several assays that are valuable in forensic genetics for DNA quantification, improved mtDNA analysis, and mtDNA mixture interpretation.

Helicoverpa armigera is an insect, causes important economical losses in crops. To reduce this loss, chemical insecticides such as pyrethroids have been commonly used against H. armigera in farming areas all over the world. However, excess and continuous usages of them cause resistance development in H. armigera. Insects develop resistance against applied insecticides by following three main mechanisms / by reducing the amount of insecticide entering into the insect body, developing insensitivity of the insecticide effective site and increasing detoxification metabolism of insecticides such as increased metabolism of them in midgut tissue of H. armigera. Therefore, changes in differentially expressed midgut proteins were analysed at protein level with two-dimensional gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) together with examine biochemical activity changes of certain detoxification enzymes such as esterases (EST) and glutathione S-transferases (GST). Moreover, transcriptional level analysis of certain genes from EST and GST systems together with cytochrome P450 monooxygenases (CYP450) system were done with quantitative real-time PCR method, too. According to the comparative proteome analysis, it was found that H. armigera field samples overcome pyrethroid stress mainly by increasing energy metabolism related proteins expressions such as ATP synthase, Vacuolar ATPase A and B and arginine kinase proteins. Furthermore, certain detoxification enzymes such as thioredoxin peroxidase and NADPH cytochrome P450 reductase were up-regulated in Mardin population, suggesting that they were actively participating in response to pyrethroid stress. NADPH cytochrome P450 reductase could play a role in detoxification of toxic pyrethroid metabolites such as 3-phenoxybenzaldehyde. However, while glutathione S-transferases (GSTs) were not found up-regulated in the comparative proteome analysis, biochemical assays (GST-CDNB, GST-DCNB and GST-PNBC) showed significant increases in enzyme activities in the Adana and in the Mardin field population, as compared to the susceptible strain. Furthermore, GST-DCNB and GST-PNBC activities showed significant increase in &Ccedil / anakkale population. As overcoming energy crisis may lead to an increase in oxidative stress, detoxification enzymes (GSTs and thioredoxin peroxidase) might be involved in pathways for eliminating toxic reactive oxygen species such as H2O2. Similarly, although esterases (EST) were not found as differentially expressed, biochemical assays for ESTs showed significant increases in enzymatic activities in the Adana and the Mardin field populations. Thus, ESTs are also proposed to be involved in developing resistance as an initiator of pyrethroid metabolism in H. armigera from Turkey. Quantitative real-time PCR results showed that while CYP9A14 gene expression was up-regulated in all analyzed field populations, CYP9A12 gene expression was up-regulated in both &Ccedil / anakkale and Mardin populations. CYP4S1 gene expression was also up-regulated only in Mardin field population. However, while CYP6B7 gene expression together with CYP9A12 and CYP4S1 genes expressions were down-regulated in Adana population, CYP6B7 gene expression was not significantly changed in both &Ccedil / anakkale and Mardin populations. In addition, GST, GSTX01 and ESTX018 gene expressions were not significantly changed in all field populations in comparison to susceptible population. Therefore, CYP9A14, CYP9A12 and CYP4S1 genes proposed to be involved in detoxification of toxic pyrethroid metabolites possibly through regulation of NADPH cytochrome P450 reductase. In conclusion, it is suggested that one of the main mechanisms of resistance development is increased energy metabolism in the midgut tissue of H. armigera which may be a general prerequisite for compensating the costs of energy-consuming detoxification processes.