Les plantes adaptent leur croissance en fonction des facteurs environnementaux dont la gravité qui est un facteur constant. Une modification de l’orientation de la plante par rapport à l’axe de la gravité, i.e. une inclinaison induit une réponse de redressement : le gravitropisme. Pour les parties aériennes le gravitropisme est négatif, c’est-à-dire que les plantes vont adapter leur croissance dans la direction opposée à la gravité. Chez les arbres, le redressement est assuré par à la formation asymétrique d’un bois aux propriétés physico-chimiques particulières appelé le bois de réaction. Des récepteurs kinases pourraient participer à la perception et à la réponse précoce au stimulus gravitropique qu’est l’inclinaison. Parmi ces familles protéiques, les kinases associées à la paroi (WAK) sont des candidats intéressants. La liaison de ces protéines à la paroi permettrait de percevoir les déformations qui sont supposées se produire par l’inclinaison de la tige. Nous avons alors identifié et caractérisé pour la première fois la famille WAKs chez une espèce ligneuse, le peuplier, qui est composée de 175 membres. L’étude d’accumulation des transcrits WAKs a permis d’identifier les gènes WAKs qui s’expriment dans la tige puis l’expression de ces gènes a été suivie lors d’une cinétique après inclinaison. Il s’avère que les gènes WAKs sont faiblement exprimés et que 25% des gènes présentent une expression différentielle après inclinaison. Ces données transcriptomiques suggèrent que les WAKs participeraient aux événements cellulaires précoces après l’inclinaison de tiges chez le peuplier. Enfin, une étude plus approfondie a été initiée sur PtWAK70 qui est localisée dans le jeune xylème et le phloème secondaire. Nous avons également généré des outils moléculaires dont l’objectif est d’identifier les interacteurs potentiels de la partie apoplastique de PtWAK70. / Plants adapt their growth to environmental factors whose gravity is a continuous one. A modification of plant orientation by tilting leads to a straightening response: gravitropism. For aerial parts, plants will adapt their growth upward (negative gravitropism). In trees, straightening is accomplished through asymmetric formation of reaction wood which exhibits modifications in its physicochemical properties. Receptors-like kinases could play a role in both perception and early response to a gravitropic stimulus. Among them, Wall-Associated Kinases (WAKs) are interesting candidates because they are bind to the cell wall. They could detect wall deformations that are supposed to occur after tilting of the stem. We identified and characterized for the first time in a woody species (poplar) the largest WAKs family with 175 members. An extensive study of WAKs transcripts accumulation was carried out to identify genes expressed in woody stem. These genes expressions were analyzed during a kinetic after tilting. WAKs genes were overall weakly expressed but 25% of analyzed genes showed a modulation in their transcript accumulation after tilting. This suggests they could play a role in early events after tilting of poplar stems. Lastly, a deeper study was initiated on PtWAK70 which is localized in young xylem and secondary phloem. We generated molecular tools to identify potentials interactors of PtWAK70 apoplastic part.

The mechanism by which prostate cancer progresses from androgen dependence (AD) to androgen independence/castration resistance (AI/CR) is currently a major focus of prostate cancer-related research. Prostate cancers that progress to a state of AI/CR are typically resistant to most standard types of treatments. Due to its primary role in driving normal prostate cell growth and proliferation, the androgen receptor (AR) is believed to play a key role in progression. Coregulators, or any proteins which may either enhance or abrogate AR activity, are considered to be one of the potential mechanisms by which AR function may become impaired. Cyclin G-associated kinase (GAK) was initially identified as a potential coregulator of AR in a Tup 1 repressed transactivation system. A LNCaP cDNA library was screened for proteins which interacted with the NH2-terminus of AR. GAK was isolated from three independent library clones using two different AR baits (AR 1-549 and AR 1-646). This interaction was confirmed via GST pulldown and coimmunoprecipitation experiments, and preliminary luciferase assays suggested that GAK activates AR in a hormone dependent manner. In this study, my objectives were to validate GAK’s role as a coregulator of AR and to determine if overexpressing GAK affects progression to AI. In vitro luciferase assays whereby GAK was either overexpressed or knocked down in both LNCaP and PC3 cells did not significantly affect AR activity. Xenograft experiments utilizing a doxycycline (DOX) inducible lentiviral LNCaP-GAK overexpressing stable cell line demonstrated that while GAK may not play a significant role in modulating AR activity, it may adopt a more subtle role enhancing tumour take and tumour volume growth rate in vivo. While these results could not confirm GAK to be a direct coregulator of AR, it is entirely possible that GAK may influence prostate cancer progression, albeit indirectly. Recent publications report a growing amount of evidence suggesting GAK’s involvement in the critical cellular process of clathrin coated vesicle endocytosis, the dysregulation of which could potentially indirectly affect AR regulated genes.

The mechanism by which prostate cancer progresses from androgen dependence (AD) to androgen independence/castration resistance (AI/CR) is currently a major focus of prostate cancer-related research. Prostate cancers that progress to a state of AI/CR are typically resistant to most standard types of treatments. Due to its primary role in driving normal prostate cell growth and proliferation, the androgen receptor (AR) is believed to play a key role in progression. Coregulators, or any proteins which may either enhance or abrogate AR activity, are considered to be one of the potential mechanisms by which AR function may become impaired. Cyclin G-associated kinase (GAK) was initially identified as a potential coregulator of AR in a Tup 1 repressed transactivation system. A LNCaP cDNA library was screened for proteins which interacted with the NH2-terminus of AR. GAK was isolated from three independent library clones using two different AR baits (AR 1-549 and AR 1-646). This interaction was confirmed via GST pulldown and coimmunoprecipitation experiments, and preliminary luciferase assays suggested that GAK activates AR in a hormone dependent manner. In this study, my objectives were to validate GAK’s role as a coregulator of AR and to determine if overexpressing GAK affects progression to AI. In vitro luciferase assays whereby GAK was either overexpressed or knocked down in both LNCaP and PC3 cells did not significantly affect AR activity. Xenograft experiments utilizing a doxycycline (DOX) inducible lentiviral LNCaP-GAK overexpressing stable cell line demonstrated that while GAK may not play a significant role in modulating AR activity, it may adopt a more subtle role enhancing tumour take and tumour volume growth rate in vivo. While these results could not confirm GAK to be a direct coregulator of AR, it is entirely possible that GAK may influence prostate cancer progression, albeit indirectly. Recent publications report a growing amount of evidence suggesting GAK’s involvement in the critical cellular process of clathrin coated vesicle endocytosis, the dysregulation of which could potentially indirectly affect AR regulated genes.

The mechanism by which prostate cancer progresses from androgen dependence (AD) to androgen independence/castration resistance (AI/CR) is currently a major focus of prostate cancer-related research. Prostate cancers that progress to a state of AI/CR are typically resistant to most standard types of treatments. Due to its primary role in driving normal prostate cell growth and proliferation, the androgen receptor (AR) is believed to play a key role in progression. Coregulators, or any proteins which may either enhance or abrogate AR activity, are considered to be one of the potential mechanisms by which AR function may become impaired. Cyclin G-associated kinase (GAK) was initially identified as a potential coregulator of AR in a Tup 1 repressed transactivation system. A LNCaP cDNA library was screened for proteins which interacted with the NH2-terminus of AR. GAK was isolated from three independent library clones using two different AR baits (AR 1-549 and AR 1-646). This interaction was confirmed via GST pulldown and coimmunoprecipitation experiments, and preliminary luciferase assays suggested that GAK activates AR in a hormone dependent manner. In this study, my objectives were to validate GAK’s role as a coregulator of AR and to determine if overexpressing GAK affects progression to AI. In vitro luciferase assays whereby GAK was either overexpressed or knocked down in both LNCaP and PC3 cells did not significantly affect AR activity. Xenograft experiments utilizing a doxycycline (DOX) inducible lentiviral LNCaP-GAK overexpressing stable cell line demonstrated that while GAK may not play a significant role in modulating AR activity, it may adopt a more subtle role enhancing tumour take and tumour volume growth rate in vivo. While these results could not confirm GAK to be a direct coregulator of AR, it is entirely possible that GAK may influence prostate cancer progression, albeit indirectly. Recent publications report a growing amount of evidence suggesting GAK’s involvement in the critical cellular process of clathrin coated vesicle endocytosis, the dysregulation of which could potentially indirectly affect AR regulated genes. / Medicine, Faculty of / Pathology and Laboratory Medicine, Department of / Graduate

La pyriculariose, maladie causée par le champignon phytopathogène Magnaporthe oryzae, affecte gravement le riz qui constitue l'aliment de base de plus de la moitié de la population mondiale. La connaissance des mécanismes de résistance est nécessaire pour guider la sélection variétale. Au cours de ce travail, une synthèse de la littérature a permis de recenser plus de 60 gènes régulateurs du riz impliqués dans la résistance du riz à différents agents pathogènes. Nous avons complété ces données en étudiant le rôle in planta de huit de ces régulateurs. Un rôle central du facteur de transcription OsWRKY28 a pu être établi et le rôle du récepteur CEBiP a été démontré. Ce travail a aussi exploré l'éventuelle implication d'une nouvelle famille de récepteurs, les Wall-Associated Kinases (WAK) dans la résistance chez le riz. Ce travail montre l'implication des WAK dans la résistance à M. oryzae. Alors que la transcription de la plupart de ces gènes est induite au cours de l'infection, celle du gène WAK112d est réprimée. La régulation transcriptionnelle précoce observée pour certains gènes WAK est déclenchée par la chitine et sous contrôle partiel du récepteur CEBiP et d'OsWRKY28. L'étude de mutants d'insertion et de lignées de surexpression a permis de montrer le rôle positif de trois gènes WAK et le rôle négatif du gène WAK112d dans la résistance. Des approches biochimiques seront nécessaires pour comprendre le mode de fonctionnement de ces récepteurs et pour les relier aux autres systèmes de défense connus. / Rice blast disease, caused by the fungus Magnaporthe oryzae, is one of the most serious diseases on rice which is the staple food of more than the half of the world population. Improving our knowledge of resistance mechanisms is necessary to guide breeding programs. In this study, we reviewed over 60 rice gene regulators involved in resistance against various pathogens. We completed these data by analyzing the role of eight of these regulators. A pivotal role for the transcription factor OsWRKY28 has been established and the role of the CEBiP receptor in planta has been demonstrated. This work also shows the implication of some WAKs in rice blast resistance. Whereas the transcription of most of these genes is induced, transcription of the OsWAK112d gene is repressed upon infection. The early transcriptional regulation observed for some OsWAK genes is triggered by chitin and partially under CEBiP and OsWRKY28 regulation. Analysis of insertion mu tants and over-expressor lines revealed a positive role for three OsWAK genes and a negative role for OsWAK112d gene in rice blast resistance. Biochemical studies will be essential to understand how these receptors work and to connect them to other known defense systems.

No description available.

Parkinson's Disease (PD) is the second most common neurodegenerative disorder, clinically characterized by severe motor impairment and pathologically characterized by progressive loss of the dopaminergic neurons of the substantia nigra pars compacta (SNpc) as well as the formation of cellular aggregate deposits called Lewy Bodies. While some advances have been made in understanding the molecular underpinnings of the disorder, the molecular implications of common genetic factors increasing risk for PD have not been adequately studied. First identified by GWA studies in 2009, the GAK/DGKQ/IDUA region on chromosome 4p16.3 shows significant genetic association to risk for PD, and the GAK protein has been shown to be associated with the primary component of Lewy Bodies, a-synuclein. In order to determine which gene in the 4p16.3 region may account for the genetic association to PD and to understand the molecular consequences of that association, post-mortem cortical brain tissue from 29 PD and 49 control patients was RNA-sequenced and differential exon usage in the context of disease and risk variant carrier status was analyzed. Exons in the 3' region of GAK were found to be associated to case status, and notably exon 25 expression in GAK was associated with both case status and the risk variant. This exon was further observed to be associated to several genes previously shown to interact with GAK, including SNCA, which codes for a-synuclein. As a proxy for expression of the 3' region of GAK, exon 25 was assessed for genome-wide association, and genes showing association to the exon were involved in pathways related to synaptic transmission and neuronal function. In order to validate these findings, microarray analysis of primary rat cortical neurons in which GAK expression was reduced by shRNA transduction was performed. GAK expression in rat neurons was significantly inversely correlated to endogenous SNCA expression, and also exhibited association to pathways involved in synaptic transmission and mitochondrial function. Together, these findings suggest aberrant GAK expression related to genetic risk to be an important factor in the pathogenesis of PD through GAK's influence on SNCA expression and through dysregulation of important neuronal pathways.

Low dose endotoxemia is caused by several health conditions including smoking, alcohol abuse, high fat diets, and aging. Several studies have correlated low dose endotoxemia with increased risks of atherosclerosis, diabetes, and Parkinson's disease. Unlike high doses of endotoxin which induce a strong but transient induction of pro-inflammatory mediators, low doses of endotoxin result in a mild but chronic induction of pro-inflammatory genes. The central hypothesis of our study was that if low doses of endotoxin are capable of inducing mild prolonged inflammation, then a unique signaling circuit must be utilized. In the first study, the molecular mechanisms for the persistent induction of lipocalin 2 (LCN2) in response to 100 ng/mL of lipopolysaccharide (LPS) in kidney fibroblasts was examined. It appears that the intracellular signaling network responsible for the persistent induction of LCN2 requires both activator protein-1 (AP-1) and CCAAT/enhancer binding protein delta (C/ebpδ). Interleukin-1 receptor-associated kinase 1 (IRAK-1) is critical for LCN2 expression. In the second study, the molecular mechanisms governing the persistent induction of interleukin 6 (IL-6) upon a 50 pg/mL challenge of LPS in macrophages was examined. At this dose, only the persistent activation of cJun N-terminal kinase (JNK) and C/ebpδ was observed. IL-6 transcription requires the transient recruitment of activating transcription factor 2 (ATF2) and the persistent recruitment of C/ebpδ to the IL-6 promoter. In the third study, the molecular mechanisms that mediate LPS-induced priming was examined. The results demonstrate that macrophages are able to sense their prior history of exposure to LPS that result in either a priming or tolerance phenotype upon a secondary challenge of LPS. Results suggest that this sensing mechanism involves cross-talk between IRAK-1 and phosphoinositide-3-kinase (PI3K). Collectively, these studies indicate that JNK and C/ebpδ are the primary players responsible for the persistent expression of pro-inflammatory genes during low dose endotoxemia. IRAK-1 is a key intracellular signaling kinase that mediates signaling at low doses of LPS. IRAK-1 is not only critical for low dose induced expression, but also for LPS-induced priming. This research has revealed a novel signaling pathway that could provide new molecular targets for drug development against chronic inflammatory diseases. / Ph. D.

Weak Affinity Chromatography (WAC) is a technology that was developed to analyse weak (KD > 10-5 M) although selective interactions between biomolecules. The focus of this thesis was to develop this method for various applications in the drug development process.   Fragment Based Drug Discovery is a new approach in finding new small molecular drugs. Here, relatively small libraries (a few hundreds to a few thousands of compounds) of fragments (150 – 300 Da) are screened against the target. Fragment hits are then developed into lead molecules by linking, growing or merging fragments binding to different locations of the protein’s active site. However, due to the weakly binding nature of fragments, methods that are able to detect very weak binding events are needed. In this thesis, WAC is presented as a new robust and highly reproducible technology for fragment screening. The technology is demonstrated against a number of different protein targets – proteases, kinases, chaperones and protein-protein interaction (PPI) targets. Comparison of data from fragment screening of 111 fragments by WAC and other more established technologies for fragment screening, such as surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR), validates WAC as a screening technology. It also points at the importance of performing fragment screening by multiple methods as they complement each other.   Other applications of WAC in drug development are also presented. The method can be used for chiral separations of racemic mixtures during fragment screening, which enables affinity measurements of individual enantiomers binding to the target of interest. Further, analysis of crude reaction mixtures is shown. By these procedures, the affinity of the product can be assessed directly after synthesis without any time-consuming purification steps. In addition, a high performance liquid chromatography (HPLC) system for highly efficient drug partition studies was developed by stable immobilization of lipid bilayer disks – lipodisks – on a high performance silica support material. These lipodisks are recognized model membranes for drug partition studies. A WAC system with incorporated membrane proteins into immobilized lipodisks has also been produced and evaluated with the ultimate objective to study affinity interactions between ligands and membrane proteins. / Ett läkemedel utövar sin funktion genom att påverka aktiviteten hos ett protein i kroppen då det binder till dess aktiva säte. Förändringen i aktivitet leder till fysiologiska förändringar i kroppen beroende på vilken funktion proteinet har. Med läkemedelsmolekyl avses här en liten organisk molekyl. Fragment-baserad läkemedelsutveckling är en ny metod for att ta fram nya läkemedel. Metoden fungerar genom att man bygger läkemedelsmolekyler utifrån mindre fragment som binder till målproteinet. Fragmenten hittar man genom att screena hela bibliotek av olika fragment mot samma målprotein för att urskilja de som binder till proteinets aktiva säte. Fördelen med den här metoden är bl. a. att med mindre molekyler som utgångspunkt kan en större del av antalet möjliga kombinationer av atomer representeras med ett mindre antal fragment än för större molekyler. Normalt utgörs ett fragmentbibliotek enbart av några hundra till några tusen substanser. Eftersom fragmenten är små har de få interaktionspunker och binder relativt svagt. De svaga bindningarna är svåra att se och mycket känsliga metoder behövs.   Svagaffinitetskromatografi är en vätskekromatografisk metod som utvecklades för att studera svaga men mycket selektiva bindningar mellan biomolekyler. Den här avhandlingen syftar till att utveckla metoden för olika användningsområden inom läkemedelsutveckling, främst som en ny metod för fragment-screening. Här mäter man interaktionen mellan ett protein och ett fragment. Proteinet kopplas till ett material som sedan packas i en kolonn i formen av en cylinder. När provet pumpas igenom kolonnen kommer de analyter med affinitet till proteinets aktiva säte att fördröjas på kolonnen i relation till hur starkt de interagerar med målproteinet.   I den här avhandlingen presenteras fragment-screening med svagaffinitetskromatografi gentemot ett antal olika typer av målproteiner. Resultatet överensstämmer väl med andra metoder för fragment-screening. Analys av reaktionsblandningar med svagaffinitetskromatografi demonstreras också. Därmed kan bindningen mellan en produkt i en reaktionsblandning och ett målprotein mätas direkt utan föregående uppreningssteg av reaktionsblandningen. Lipodiskar är små diskformade modellmembran som kan användas för att bl. a. mäta hur effektivt läkemedlet tas upp i kroppen vid behandling. Ett system med immobiliserade lipodiskar i en kolonn utvecklades med det framtida målet att kunna arbeta med membranproteiner med svagaffinitetskromatografi.   Detta arbete utgör en del i att utveckla svagaffinitetskromatografi som en lättillgänglig och relativt billig metod för användning inom industrin och akademin för läkemedelsutveckling.

No description available.