Ce mémoire de thèse s'intéresse à la conception de systèmes temps-réel en s'appuyant sur la méthode formelle RT-Lotos, extension temporelle à l'algèbre de processus Lotos. Il aborde plusieurs points relatifs à la spécification, la validation et l'ordonnancement de systèmes concurrents sujets à des contraintes logiques et temporelles. La première partie propose un éventail de méthodes formelles pour la spécification et la validation de systèmes temps-réel. Elle présente également le langage RT-Lotos et la technique de vérification formelle associée basée sur une analyse d'accessibilité. Elle détaille finalement un ensemble de travaux concernant l'automate temporisé (appelé un DTA) dérivé d'une spécification RT-Lotos, avec comme objectifs d'exécuter des simulations rapides, et de s'interfacer avec des outils de vérification de type model-checker. La deuxième partie présente une étude sur la notion de cohérence temporelle et propose une technique ainsi qu'un modèle formel pour exploiter sous un nouvel angle des informations issues de la vérification formelle par analyse d'accessibilité. Cette approche propose de raffiner le graphe des régions, d'en élaguer certaines branches jugées non souhaitables, d'extraire les dates de tir possible des actions, et de présenter ces informations sous la forme d'un nouveau type d'automate temporisé (appelé un TLSA) ayant pour vocation l'ordonnancement dans le temps des actions d'un système. Enfin, la troisième partie se penche sur les liens possibles entre méthodes formelles et semi-formelles. Dans ce cadre, nous proposons une sémantique formelle pour les diagrammes UML s'appuyant sur RT-Lotos, après avoir défini une extension temps-réel à UML (appelée TURTLE). Ainsi, nous définissons une méthodologie qui s'inscrit dans les techniques de développement industriel classiques et qui permet une vérification formelle de systèmes temps-réel.

La symbiose constitue une force évolutive majeure permettant de nombreuses adaptations des partenaires, en particulier dans la réponse des hôtes aux agents pathogènes. La bactérie endosymbiotique Wolbachia ( -protéobactérie) confère ainsi à certains insectes une résistance aux agents pathogènes humains dont ils sont les vecteurs. Chez le crustacé isopode Armadillidium vulgare, la présence de Wolbachia altère l'immunocompétence de son hôte en diminuant le taux d'hémocytes circulants (THC) et en augmentant la septicémie naturelle. La présence de Wolbachia dans les hémocytes et les organes hématopoïétiques a soulevé de nombreuses questions quant aux conséquences que cela entraîne sur le fonctionnement du système immunitaire et sur l'immunocompétence d'A. vulgare. Nous avons donc étudié l'impact de cette symbiose sur les hémocytes, l'immunocompétence et l'expression de gènes de l'immunité. Ainsi Wolbachia est présente dans plus d'un tiers des hémocytes (hybridation in situ fluorescente) et sa présence diminue la proportion d'hémocytes granulaires circulants (cytométrie en flux) chez les animaux âgés d'un an, sans affecter le THC à cet âge. L'activité phénoloxydase diminue avec l'âge et le statut symbiotique. En revanche, la présence de Wolbachia semble protéger les hémocytes de l'apoptose et augmenter l'immunocompétence d'A. vulgare lors d'une infection par Listeria ivanovii. Enfin, la quantification de l'expression des gènes de l'immunité, identifié après l'établissement du premier transcriptome de référence d'isopode (projet ANR EndoSymbArt), a révélé une tendance à la sous-expression au niveau de l'animal entier et des ovaires mais à la sur-expression dans les tissus immunitaires. La présence deWolbachia modifie donc les caractéristiques du système immunitaire aux niveaux cellulaire et humoral ainsi que l'immunocompétence d'A. vulgare. L'étude de nouveaux paramètres permettra d'établir si la présence de Wolbachia constitue réellement un avantage pour son hôte ou si au contraire la bactérie présente un coût parasitaire important.

Le foisonnement filamenteux est un problème récurant dans de nombreuses stations d'épuration à boues activées. L'objectif de ces travaux est d'améliorer la compréhension des mécanismes physiologiques et moléculaires impliqués dans la filamentation des microorganismes, afin de pouvoir orienter de futures stratégies de lutte contre le phénomène de bulking. Sphaerotilus natans, qui peut croître réversiblement sous forme monocellulaire ou filamenteuse, a été utilisée comme bactérie modèle pour cette étude. Différents types de cultures, ainsi que des suivis par cytométrie en flux et marquage au cFDA/SE, ont montré que les diverses souches de S. natans adoptent des morphologies différentes et que les filaments croissent par divisions cellulaires successives et non par un chaînage des bactéries. Une analyse par RT-QPCR a mis en évidence que l'expression du gène sthA augmente fortement après induction de la filamentation et reste ensuite à un niveau élevé. Une comparaison de l'expression protéique des formes monocellulaire et filamenteuse, par LC-MS-MS, a permis d'identifier des protéines impliquées dans la filamentation, et notamment dans la synthèse de la gaine. La concentration intracellulaire en ARNr, mesurée par RT-QPCR, varie durant la croissance de S. natans et d'autres microorganismes, entraînant une diminution importante de l'intensité du marquage FISH, mesurée par cytométrie en flux. L'utilisation de la technique FISH pour quantifier des microorganismes est donc remise en question, d'autant plus dans des matrices aussi complexes que les boues activées. Ces observations mettent également en doute l'hypothèse, émise en utilisant ce mode de quantification, d'une déstructuration des filaments consécutive à un retour à des conditions de culture plus favorables.

<p>In the field of transplantation, the increasing deficit of human donors have lead to an interest in animals as an alternative source of organs and tissues. </p><p>Different <i>in vitro </i>systems and rodent models of xenotransplantation were used to examine the most significant barriers that have to be overcome, before isolated islets of Langerhans from pigs can be used as a cure for insulin-dependent diabetes mellitus in humans.</p><p>In clinical transplantation, islets are infused into the liver through the portal vein. During this procedure the islets are susceptible to harmful innate reactions triggered in blood. Adenoviral vectors generating transgenic expression of human complement regulatory proteins were evaluated in pig islets and shown to confer protection against acute complement-mediated damage. </p><p>Transplanted islets escaping this immediate destruction will be targets of a cellular immune response. Using a new mouse model of islet xenograft rejection, it was demonstrated that macrophages, effector cells in the rejection, were part of an MHC-restricted xenospecific immune response mediated by T cells. In a strain of knockout mice it was further shown that this process can proceed in the absence of an important signalling system, mediated by Toll-like receptors, between cells in innate and adaptive immunity. These findings illustrate some of the mechanistic differences compared to cellular islet allograft rejection which partly explain why immunosuppressive drugs used in clinical allotransplantation is not sufficient for preventing xenograft rejection. </p><p>Porcine endogenous retroviruses (PERV) remain a safety concern in xenotransplantation. Characterization of PERV in pig islets indicated that virus expression is low <i>in vitro </i>but increases during the immediate time period following transplantation. This suggests that antiviral therapies administered at the time of transplantation could be used for preventing the risk of PERV transmission after xenotransplantation.</p>

<p>Reverse transcriptase (RT) is a crucial enzyme for retrovirus replication, and its presence in the virion is indispensable for infectivity. This thesis illustrates the use of RT activity assays as tools for quantitation and characterization of different retroviruses, particularly HIV. </p><p>A non radioactive assay, using microtiter plates, for the RT of Moloney murine leukemia virus (MMuLV) was developed. Assay conditions for MMuLV and HIV-1 RT, together with isozyme specific RT activity blocking antibodies, were shown useful for discrimination between RTs from different retrovirus genera. RT activity assay for HIV-1 was found to quantitate different subtypes more equally efficient than p24 antigen assays did.</p><p>Viral load (VL), the amount of HIV particles in the blood, is an important marker of the clinical status of an infected person. A method for VL determination based on RT activity (ExaVir Load) was developed. After plasma pretreatment, to inactivate cellular DNA polymerases, virions in patient plasma were immobilized on a gel, which was washed to remove disturbing factors. The virions were lysed with a detergent containing buffer and the lysate eluted. Finally, the RT activity in the lysate was determined and found to correlate strongly to VL by RNA according to a PCR based standard method (Roche Amplicor 1.5). The second version of the method was able to measure VL down to approximately 400 HIV-1 RNA copies/ml. The usefulness of RT from the VL procedure for determination of susceptibility towards anti-HIV drugs was demonstrated, and the results were in agreement with genotypic data. </p><p>Due to its technical simplicity, and ability to detect a broad range of HIV-1 subtypes, ExaVir Load and the drug susceptibility application are interesting for clinical use, particularly but not only in resource limited settings. The concept is also potentially useful for research purposes, e.g. in combination with specific RT assay conditions.</p>

<p>Drugs and other foreign compounds must often be metabolised before they can be excreted from the body. One enzyme system that is responsible for this is the cytochrome P450 gene family (CYP). In this thesis, new sensitive molecular techniques have been used to study the human gene expression of some CYP enzymes, as well as the P-glycoprotein transporter (P-gp). The aim was to evaluate whether tissues other than the liver, e.g. the blood, could be used to assess an individual's drug metabolic capacity. Another aim was to investigate the gene expression in relation to the liver transplant process and a third aim was to evaluate the expression in gastrointestinal mucosa in both normal and inflamed mucosa.</p><p>We evaluated the CYP gene expression in paired specimens of liver and blood but found no correlation in the expression patterns of these two tissues. Instead, we found the opposite pattern, where, for example, CYP1B1 had the highest expression in the blood but the lowest in the liver and CYP2E1 was the enzyme with the highest expression in the liver. In an investigation of the expression of four different CYP enzymes and P-gp in liver transplants before and during the first year after transplantation, we found that the levels of all the CYP enzymes but not P-gp increased with time. We also found that the expression of CYP3A4 was inversely related to the normalised plasma levels of the immunosuppressive drugs cyclosporine and tacrolimus.</p><p>In the gastrointestinal tract, CYP2E1 was the enzyme with the highest mRNA expression compared with CYP3A4, CYP3A5 and the transporter P-gp. CYP3A4 has its highest expression in the duodenum compared with the expression in the stomach and the colon. CYP3A5 is expressed at a higher level than CYP3A4 in the colon. P-gp expression levels increase through the gastrointestinal tract to the left colon. Gene expression levels of CYP2E1 and CYP3A4 decrease in severely inflamed rectal mucosa. </p><p>In conclusion, this is a sensitive method for studying gene activity in a clinical situation, even though at this point we are not able to use blood or gastrointestinal mucosa as “surrogate” tissue to estimate an individual’s drug metabolic capacity. The studies in liver transplants and gastrointestinal mucosa are unique in that the gene expression is investigated during a clinical course of events.</p>

In the field of transplantation, the increasing deficit of human donors have lead to an interest in animals as an alternative source of organs and tissues. Different in vitro systems and rodent models of xenotransplantation were used to examine the most significant barriers that have to be overcome, before isolated islets of Langerhans from pigs can be used as a cure for insulin-dependent diabetes mellitus in humans. In clinical transplantation, islets are infused into the liver through the portal vein. During this procedure the islets are susceptible to harmful innate reactions triggered in blood. Adenoviral vectors generating transgenic expression of human complement regulatory proteins were evaluated in pig islets and shown to confer protection against acute complement-mediated damage. Transplanted islets escaping this immediate destruction will be targets of a cellular immune response. Using a new mouse model of islet xenograft rejection, it was demonstrated that macrophages, effector cells in the rejection, were part of an MHC-restricted xenospecific immune response mediated by T cells. In a strain of knockout mice it was further shown that this process can proceed in the absence of an important signalling system, mediated by Toll-like receptors, between cells in innate and adaptive immunity. These findings illustrate some of the mechanistic differences compared to cellular islet allograft rejection which partly explain why immunosuppressive drugs used in clinical allotransplantation is not sufficient for preventing xenograft rejection. Porcine endogenous retroviruses (PERV) remain a safety concern in xenotransplantation. Characterization of PERV in pig islets indicated that virus expression is low in vitro but increases during the immediate time period following transplantation. This suggests that antiviral therapies administered at the time of transplantation could be used for preventing the risk of PERV transmission after xenotransplantation.

Reverse transcriptase (RT) is a crucial enzyme for retrovirus replication, and its presence in the virion is indispensable for infectivity. This thesis illustrates the use of RT activity assays as tools for quantitation and characterization of different retroviruses, particularly HIV. A non radioactive assay, using microtiter plates, for the RT of Moloney murine leukemia virus (MMuLV) was developed. Assay conditions for MMuLV and HIV-1 RT, together with isozyme specific RT activity blocking antibodies, were shown useful for discrimination between RTs from different retrovirus genera. RT activity assay for HIV-1 was found to quantitate different subtypes more equally efficient than p24 antigen assays did. Viral load (VL), the amount of HIV particles in the blood, is an important marker of the clinical status of an infected person. A method for VL determination based on RT activity (ExaVir Load) was developed. After plasma pretreatment, to inactivate cellular DNA polymerases, virions in patient plasma were immobilized on a gel, which was washed to remove disturbing factors. The virions were lysed with a detergent containing buffer and the lysate eluted. Finally, the RT activity in the lysate was determined and found to correlate strongly to VL by RNA according to a PCR based standard method (Roche Amplicor 1.5). The second version of the method was able to measure VL down to approximately 400 HIV-1 RNA copies/ml. The usefulness of RT from the VL procedure for determination of susceptibility towards anti-HIV drugs was demonstrated, and the results were in agreement with genotypic data. Due to its technical simplicity, and ability to detect a broad range of HIV-1 subtypes, ExaVir Load and the drug susceptibility application are interesting for clinical use, particularly but not only in resource limited settings. The concept is also potentially useful for research purposes, e.g. in combination with specific RT assay conditions.

Drugs and other foreign compounds must often be metabolised before they can be excreted from the body. One enzyme system that is responsible for this is the cytochrome P450 gene family (CYP). In this thesis, new sensitive molecular techniques have been used to study the human gene expression of some CYP enzymes, as well as the P-glycoprotein transporter (P-gp). The aim was to evaluate whether tissues other than the liver, e.g. the blood, could be used to assess an individual's drug metabolic capacity. Another aim was to investigate the gene expression in relation to the liver transplant process and a third aim was to evaluate the expression in gastrointestinal mucosa in both normal and inflamed mucosa. We evaluated the CYP gene expression in paired specimens of liver and blood but found no correlation in the expression patterns of these two tissues. Instead, we found the opposite pattern, where, for example, CYP1B1 had the highest expression in the blood but the lowest in the liver and CYP2E1 was the enzyme with the highest expression in the liver. In an investigation of the expression of four different CYP enzymes and P-gp in liver transplants before and during the first year after transplantation, we found that the levels of all the CYP enzymes but not P-gp increased with time. We also found that the expression of CYP3A4 was inversely related to the normalised plasma levels of the immunosuppressive drugs cyclosporine and tacrolimus. In the gastrointestinal tract, CYP2E1 was the enzyme with the highest mRNA expression compared with CYP3A4, CYP3A5 and the transporter P-gp. CYP3A4 has its highest expression in the duodenum compared with the expression in the stomach and the colon. CYP3A5 is expressed at a higher level than CYP3A4 in the colon. P-gp expression levels increase through the gastrointestinal tract to the left colon. Gene expression levels of CYP2E1 and CYP3A4 decrease in severely inflamed rectal mucosa. In conclusion, this is a sensitive method for studying gene activity in a clinical situation, even though at this point we are not able to use blood or gastrointestinal mucosa as “surrogate” tissue to estimate an individual’s drug metabolic capacity. The studies in liver transplants and gastrointestinal mucosa are unique in that the gene expression is investigated during a clinical course of events.

Hypoxia Inducible Factor-1α in Renal Cell Carcinoma Departments of Surgical and Perioperative Sciences, Urology and Andrology; Radiation Sciences, Oncology; Medical Biosciences, Pathology; and Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden Background: Renal cell carcinoma (RCC) accounts for approximately 2-3% of all human cancers. A distinguished feature of RCC is vascularisation and among the three dominating RCC types conventional RCC (cRCC) generally is more vascularised than papillary RCC (pRCC) and chromophobe RCC (chRCC). Angiogenesis is a critical step in tumour progression controlled by a balance involving molecules that have positive and negative regulatory activity. A balance distorted by metabolic stress such as hypoxia, acidosis, and inflammation. Hypoxia-Inducible Factor 1α (HIF-1α) is a key transcription factor in angiogenesis and tumour progression, targeting more than a 100 genes involved in vascular growth and regulation, iron metabolism and erythropoesis, collagen matrix formation, regulation of extracellular pH, glucose uptake and metabolism, proliferation, apoptosis, differentiation, and cell viability. Methods: Tumour tissue and corresponding kidney cortex from nephrectomised RCC patients was used in order to characterize HIF-1α expression and one of its target genes, Glucose Transporter 1 (GLUT-1). All tumour samples were thoroughly described regarding tumour type, TNM stage, nuclear grade, tumour size, vein invasion, and patient survival. Utilizing RT-PCR, Westen Blot and Tissue micro array (TMA) we studied HIF-1α mRNA and protein expression as well as GLUT-1 protein expression, correlating them to each other and clinicopathological parameters. Results: Using Western Blot, HIF-1α protein expression differed significantly between the different RCC types and kidney cortex. In cRCC, high expression of HIF-1α was an independent prognostic factor for favourable prognosis. TMA is a useful method to analyze HIF-1α protein expression in RCC. HIF-1α levels were significantly lower in locally aggressive cRCC and patients with high levels of HIF-1 tended to have a better prognosis. GLUT-1 levels were higher in cRCC than in other RCC types and for cRCC a correlation to HIF-1α was seen. HIF-1α mRNA levels were significantly lower in cRCC compared to other RCC types and kidney cortex. An inverse correlation between HIF-1α protein expression and mRNA levels was observed. Summary: These results demonstrate a discrepancy between RCC types, highlighting the need to separately evaluate biological events in different RCC types. Overexpression of HIF-1α protein is not necessarily all bad and translational regulation appears more critical than anticipated. Further studies are encouraged to clarify angiogenic pathways in RCC.