Une attention croissante est portée aux cascades multi enzymatiques pour l’élaboration de procédés de synthèse plus efficaces. Cependant, le contrôle de l’expression hétérologue de plusieurs gènes dans un même hôte s’avère difficile et peut mener à un déséquilibre du flux réactionnel. Pour exploiter au mieux les avantages d’une cascade in vivo, il est nécessaire d’ajuster les activités de chaque étape, et de construire des catalyseurs cellulaires capables de programmer la stœchiométrie des enzymes. Nous avons développé dans ce projet une approche originale pour moduler le ratio de deux enzymes in cellulo en jouant sur le nombre de copies de plasmides par cellule (PCN). Nous avons choisi comme modèle un système autosuffisant associant une Alcool Déshydrogénase (ADH) et une Baeyer-Villiger MonoOxygenase (BVMO), NADP(H)-dépendantes. Plusieurs plasmides recombinants portant les deux gènes ont été conçus et combinés dans E. coli. Les souches de co-expression construites ont été comparées en termes de PCN, de production d’enzymes et d’activité. Nous avons montré l’importance d’un choix judicieux de la combinaison de plasmides ainsi que l’existence d’une corrélation entre ratios d’enzymes et activité. Nos biocatalyseurs s’étendent sur une gamme allant du système inactif à un système affichant un TTN d’environ 6000. Ce système a permis la synthèse de lactones d’intérêt industriel, la dihydrocoumarine et la caprolactone, à partir d’indanol et de cyclohexanol. Enfin, sur ce modèle de combinaison de plasmides, trois nouveaux biocatalyseurs cellulaires, associant l’ADH à diverses BVMOs, ont été créés afin d’élargir la gamme d’esters et de lactones synthétisables à partir d’alcools. / Growing attention is paid to multienzymatic cascades to develop more efficient synthetic processes. However, in in cellulo process, the control of the simultaneous heterologous expression of several genes in the same host is often difficult and can lead to imbalances in the reaction flow. To exploit the benefits of cascades, activities of each step have to be adjusted and thus, cellular biocatalysts capable of programming enzymes stoichiometry have to be constructed. In this work, to modulate the stoichiometry of two enzymes in vivo, we developed an original approach based on the copy number per cell of plasmids (PCN) used as vectors. The PCN is regulated in bacteria by three main mechanisms leading, according to the replicon, to low, medium or high PCN. As proof of concept, we chose a self-sufficient system combining an Alcohol Dehydrogenase (ADH) and a Baeyer-Villiger MonoOxygenase (BVMO), both NADP(H)-dependent. Several recombinant plasmids harboring both genes were designed and combined in E. coli. Coexpression strains constructed were compared in terms of PCN, enzyme production and activity. We showed the importance of a judicious choice of plasmids combination and the existence of a correlation between enzymes ratios and activity. Our biocatalysts ranged from an inactive system to a system with a TTN of about 6000. This system allowed the synthesis of lactones of industrial interest, dihydrocoumarin and caprolactone, via double oxidation of indanol and cyclohexanol. Finally, based on this plasmids combination model, three new cellular biocatalysts combining ADH with various BVMOs were designed to broaden the range of esters and lactones synthesizable from alcohols.

Ophiostoma novo-ulmi is the causal agent of Dutch elm disease (DED) which has had a severe impact on the urban landscape in Canada. This research program focused on developing molecular genetic strategies to control this pathogenic fungus. The first strategy involved the development of RNA interference (RNAi) for the down-regulation of genes involved in pathogenicity. An efficient RNAi cassette was developed to suppress the expression of the endopolygalacturonase (epg1) locus which encodes a cell-wall degrading enzyme. This epg1-RNAi cassette significantly reduced the amount of polygalacturonase activity in the fungus and resulted in almost complete degradation of epg1 mRNA. The need for a native promoter to selectively down-regulate specific gene loci was addressed by developing a carbon-catabolite regulated promoter (alcA) to drive the expression of the epg1-RNAi cassette. The expression of an alcA-driven epg1-RNAi cassette resulted in the down-regulation of epg expression under glucose starvation but normal levels of expression in high glucose. The expression could therefore be controlled by culture conditions. The second strategy explored the potential of using dsRNA viruses to vector disruptive RNAi cassettes. An isolate of O. novo-ulmi strain 93-1224 collected in the city of Winnipeg, was infected by two dsRNA mitoviruses which upon sequence characterization were named OnuMV1c and OnuMV7. To assess the transmissibility of this dsRNA virus the infected isolate 93-1224 was paired with three naive isolates of the related fungi O. ulmi and O. himal-ulmi. Through the use of nuclear and mitochondrial markers it was determined that the virus OnuMV1c may not rely on mitochondrial fusion for transmission but may have a cytoplasmic transmission route. This investigation of gene expression and manipulation has provided tools to help understand gene regulation in O. novo-ulmi. It has also added to our knowledge of mitoviruses, their transmission and potential use as a biological control. By enhancing our understanding of transmissible hypovirulence this work contributes to efforts to develop a new approach to target DED as well as a potential model for the control of other fungal diseases. / Graduate / 0307 / 0306 / 0369 / jscarneiro@hotmail.com

In order to investigate the effect of food restriction on fat mobilization in horses with impaction in left ventral colon during treatment, serum triglycerides, NEFA and total bilirubine (TB) were measured before and after treatment. On another side, the determination of alcohol dehydrogenase (ADH) activity in serum could facilitate the distinguishing of the non-strangulating intestinal obstruction from the potential fatal strangulation obstruction and could submit a new prognostic biochemical parameter for intestinal strangulation. With the intention of giving a highlight over the analgesic effect of Buscopan® compositum in horses with colic, it was attempted to investigate the effect of Buscopan® compositum on the intestinal motility of healthy conscious horses in different regions of intestine. A significant elevation of NEFA and TB was observed in horses with impaction in left ventral colon at admission. By relieving the impaction, there was a significant elevation of triglycerides in comparison to its level at admission. There was a significant increase in ADH activity in all horses with acute intestinal obstruction. ADH activity was significantly higher in horses with strangulation in comparison to non-strangulation obstruction. There was only a significant correlation between ADH and lactate in horses with non-strangulation obstruction and colon torsion. Only AST and GLDH were significantly increased in horses with colon torsion. ADH activity > 20 U/l had 80.56% specificity and 80.49% sensitivity for discriminating horses with intestinal strangulation from non-strangulation obstruction. ADH activity < 80 U/l had 94.44% specificity and 66.67% sensitivity for survival. Buscopan® compositum had an immediate, rapid and significant (p< 0.05) reduction of duodenal, cecal and left ventral colon contractions after application. Cecal and left ventral colon contractions restored rapidly their normal contractions after 30 min, while duodenal contractions returned to the normal rate after 120 min of Buscopan® compositum administration. The horses with impaction in left ventral colon are susceptible to fat mobilization during the period of treatment as a result of food restriction. It was characterized by a revisable hypertri-glyceridemia and hyperbililrubinemia. Serum ADH activity could have a useful clinical value in detecting the intestinal strangulation and predicting the prognosis in horses with intestinal strangulation. Buscopan® compositum at its therapeutic dosage has an immediate, potent, short-lived reductive effect on cecum and left ventral colon contractions but a minor, longer effect on the duodenal contractions. Therefore, it is thought to be more effective in treatment of spasmodic colic than in large colon impaction.:Contents I List of Abbreviations II 1 Introduction and Literature 1 2 Results 4 2.1 Publication 1: Triglyceride, free fatty acids and total bilirubin in horses with left ventral large colon impaction 4 2.2 Publication 2: Clinical evaluation of serum alcohol dehydrogenase activity in horses with acute intestinal obstruction 9 2.3 Publication 3: Effect of Buscopan® compositum on the motility of the duodenum, cecum and left ventral colon in healthy conscious horses 43 3 Discussion 60 4 Summary 68 5 Zusammenfassung 70 6 References 72 7 Acknowledgement 81 / Um den Effekt der Nahrungskarenz auf die Fettmobilisation bei Pferden mit Verstopfung der linken ventralen Längslagen des Kolons während der Behandlung zu untersuchen, wurden Triglyceride (TG), freie Fettsäuren (FFS) und Gesamtbilirubin (GB) bestimmt. Andererseits ermöglicht die Bestimmung der Aktivität der Alkoholdehydrogenase (ADH) im Serum die Unterscheidung zwischen einer nichtstrangulierenden intestinalen Obstruktion und einer potentiell tödlichen Strangulation. ADH kann somit als ein neuer prognostischer biochemischer Parameter für die intestinale Strangulation eingesetzt werden. Um den spasmolytischen Effekt von Buscopan compositum bei Pferden mit Kolik zu untersuchen, wurde der Effekt von Buscopan compositum auf die intestinale Kontraktion von gesunden Pferden in verschiedenen Regionen des Darmes getestet. Eine signifikante Erhöhung der FFS und des GB wurde bei Aufnahme von Pferden mit einer Verstopfung in der linken ventralen Längslagen festgestellt. Nach der Behandlung der Verstopfung konnte eine signifikante Erhöhung der Konzentration von TG, bezogen auf die TG Konzentration bei Aufnahme in die Klinik, festgestellt werden. Bei Pferden mit akuter intestinaler Obstruktion wurde eine signifikante Erhöhung der Aktivität der ADH beobachtet. Die Aktivität der ADH war bei Pferden mit einer Strangulation signifikant höher als bei Pferden, die eine nichtstrangulierende Obstruktion des Darmes hatten. Bei Pferden mit einer nichtstrangulierenden Obstruktion oder einer Kolontorsion wurde eine positive Korrelation zwischen der ADH-Aktivität und der Laktatkonzentration im Serum festgestellt. Nur bei Pferden mit Kolontorsion waren die Aktivitäten von AST und GLDH signifikant erhöht. Für die Unterscheidung zwischen Pferden mit einer intestinalen Strangulation oder einer nichtstrangulierenden Obstruktion wurde für die ADH- Aktivität größer als 20 U/l eine Spezifität von 80,56% und eine Sensitivität von 80,49% ermittelt. Eine ADH-Aktivität kleiner 80 U/l zeigt, mit einer Spezifität von 94,44% und einer Sensitivität von 66,67%, eine günstige Prognose für das Überleben des Pferdes an. Nach Gabe von Buscopan® compositum trat eine sofortige schnelle und signifikante (p<0,05) Reduktion der Kontraktionen im Duodenum, Zäkum und den linken ventralen Längslagen ein. Die Kontraktionen des Zäkums und der linken ventralen Längslagen normalisierten sich schnell innerhalb von 30 min, wogegen die Kontraktionen des Duodenums erst 120 min nach der Applikation von Buscopan® compositum den Normalzustand erreichten. Pferde mit einer Verstopfung in der linken ventralen Längslagen des Kolons sind während der medizinischen Behandlung anfällig für Fettmobilisation aufgrund der reduzierten Futter-aufnahme. Dies ist gekennzeichnet durch eine reversible Hypertriglyceridämie und eine Hyperbilirubinämie. Die Aktivität von ADH im Serum kann ein nützlicher klinischer Parameter sein, um eine intestinale Strangulation zu identifizieren und bietet sich auch als prognostischer Marker bei intestinaler Strangulation an. Die Applikation von Buscopan® compositum in der therapeutischen Dosierung hat eine sofortige, potente und kurzzeitige Reduktion der Kontraktionen des Zäkums und der linken ventralen Längslage aber einen geringen und länger anhaltenden Effekt auf die duodenalen Kontraktionen zur Folge. Daraus folgt, dass Buscopan® compositum bei der Behandlung von Krampfkoliken effektiver ist als bei Verstopfungen des großen Kolons.:Contents I List of Abbreviations II 1 Introduction and Literature 1 2 Results 4 2.1 Publication 1: Triglyceride, free fatty acids and total bilirubin in horses with left ventral large colon impaction 4 2.2 Publication 2: Clinical evaluation of serum alcohol dehydrogenase activity in horses with acute intestinal obstruction 9 2.3 Publication 3: Effect of Buscopan® compositum on the motility of the duodenum, cecum and left ventral colon in healthy conscious horses 43 3 Discussion 60 4 Summary 68 5 Zusammenfassung 70 6 References 72 7 Acknowledgement 81

The proven ability to ferment Saccharomyces cerevisiae on a large scale presents an attractive target for producing chemicals and fuels from sustainable sources. Efficient and predominant carbon flux through to ethanol is a significant engineering issue in the development of this yeast as a multi-product cell chassis used in biorefineries. In order to evaluate diversion of carbon flux away from ethanol, combinatorial deletions were investigated in genes encoding the six isozymes of alcohol dehydrogenase (ADH), which catalyse the terminal step in ethanol production. The scarless, dominant and counter- selectable amdSYM gene deletion method was optimised for generation of a combinatorial ADH knockout library in an industrially relevant strain of S. cerevisiae. Current understanding of the individual ADH genes fails to fully evaluate genotype-by-genotype and genotype-by-environment interactions: rather, further research of such a complex biological process requires a multivariate mathematical modelling approach. Application of such an approach using the Design of Experiments (DoE) methodology is appraised here as essential for detailed empirical evaluation of complex systems. DoE provided empirical evidence that in S. cerevisiae: i) the ADH2 gene is not associated with producing ethanol under anaerobic culture conditions in combination with 25 g l-1 glucose substrate concentrations; ii) ADH4 is associated with increased ethanol production when the cell is confronted with a zinc-limited [1 μM] environment; and iii) ADH5 is linked with the production of ethanol, predominantly at pH 4.5. A successful metabolic engineering strategy is detailed which increases the product portfolio of S. cerevisiae, currently used for large-scale production of bioethanol. Heterologous expression of the cytochrome P450 fatty acid peroxygenase from Jeotgalicoccus sp., OleTJE, fused to the RhFRED reductase from Rhodococcus sp. NCIMB 978 converted free fatty acid precursors to C13, C15 and C17 alkenes (3.81 ng μl-1 total alkene concentration).