Malaria vaccine research has been battling with persistent challenges, including polymorphisms of vaccine antigens, difficulties with production processes, and limited immune protection against the disease. Intrinsically unstructured proteins (IUPs) are a fairly newly classified group of proteins that have no stable 3D structure and are generally heat-resistant. They usually contain low complexity regions and repetitive sequences, both of which are distinct characteristics of the malaria proteome. Surprisingly, some of the vaccine candidates that have been extensively studied were later reported to have unstructured regions, some of which serve as targets of protective immunity. In keeping with their interesting immunological profiles and their unique properties, which are exceptionally beneficial for vaccine production, malarial IUP antigens may be good vaccine candidates. This PhD project has the following aims:- 1) to develop a synthetic unstructured protein antigen based on the Block 2 region of MSP-1, named the MSP-1 hybrid 2) to characterize a novel vaccine antigen derived from the MSP-3.3 protein, namely an IUP region of PF10_0347 gene product, for its potential as a vaccine candidate 3) to develop a second-generation vaccine by combining the MSP-1 hybrid, with two allelic variants of MSP-2, to overcome antigenic polymorphism and strain-specific immune responses 4) to validate protocols for IUP identification from proteins extracted from the malaria parasite. This study showed that 1) MSP-1 hybrid production was scalable, yielding high protein yields with comparable immunological properties to small-scale production. MSP-1 hybrid was shown to be compatible with different adjuvants, and elicited specific antibodies covering the whole range of Block 2 allelic diversities. 2) A novel antigen, MSP-3.3C, an IUP based on the 3’ region of the PF10_0347 gene, was cloned, expressed and purified. Anti-MSP3.3C antibodies showed very strong parasite growth inhibitory effects in vitro. 3) The MSP-multihybrid antigen was expressed using simple techniques, but only at low levels. It contains epitopes from all three parasite antigen components, and is recognized by specific naturally acquired antibodies. 4) an unconventional 2D gel technique was tested as a method of malaria parasite IUP identification. Plans for further validation of this technique were discussed.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Escherichia coli est une espèce bactérienne à multiples facettes. En effet, certaines souches sont présentes à l’état commensal au niveau intestinal, ou sont utilisées comme probiotiques. À l’inverse, d’autres souches sont responsables d’infections intestinales ou extra-intestinales chez l’Homme et les animaux à sang chaud. Les souches d’E. coli pathogènes extra-intestinales (ExPEC) sont responsables de nombreuses maladies infectieuses (méningites néo-natales, infections urinaires, septicémies ou infections respiratoires). Plusieurs facteurs de virulence ont été identifiés chez les souches ExPEC (adhésines, invasines…) et notamment la protéine IbeA, mise en évidence dans une souche isolée d’un cas de méningite néo-natale humaine. Le gène ibeA est retrouvé chez différentes souches ExPEC, dont certaines d’origine aviaire. Il est localisé au sein de l’îlot génomique GimA, sur un des quatre opérons de cet îlot, entre ibeR codant un potentiel régulateur et ibeT codant un potentiel antiporteur. La protéine IbeA a été décrite comme jouant un rôle dans l’invasion bactérienne des cellules endothéliales microvasculaires de cerveau humain (HBMEC). Afin de mieux comprendre le rôle d’IbeA dans le processus infectieux et l’invasion cellulaire, nous avons étudié l’implication d’IbeA dans l’adhésion de la souche ExPEC d’origine aviaire BEN2908 puis tenté de déterminer la localisation de cette protéine et son lien avec la protéine IbeT. L’étude phénotypique comparative de la souche BEN2908 et de son mutant ?ibeA nous a montré qu’IbeA intervenait dès le stade de l’adhésion aux HBMEC. Des tests d’adhésion en absence des fimbriae de type 1 (adhésine majeure de notre souche) nous ont montré que dans ce contexte, IbeA n’avait pas d’action sur l’adhésion. Ce résultat nous a suggéré qu’il pouvait y avoir une baisse d’expression des fimbriae de type 1 à la surface bactérienne dans un mutant ?ibeA, ce que nous avons montré par dots blots. Pour comprendre comment IbeA entraînait une modification de l’expression des fimbriae de type 1, nous nous sommes intéressés au contrôle de l’expression des gènes de l’opéron fim. Nous avons ainsi montré que le promoteur de ces gènes, localisé sur un élément invertible, était préférentiellement dans une orientation ne permettant pas la transcription des gènes fim dans un mutant ?ibeA. Nous avons ensuite mis en évidence chez le mutant ?ibeA une baisse de l’expression des gènes fimB et fimE qui codent pour deux recombinases participant au contrôle de l’orientation de l’élément invertible. Ces baisses d’expression de fimB et fimE pourraient expliquer la diminution d’expression des fimbriae de type 1 dans le mutant ?ibeA. Enfin, des phénotypes similaires à ceux du mutant ?ibeA ont été observés chez un mutant ?ibeT. La localisation d’IbeA est indispensable pour comprendre comment cette protéine peut agir sur l’expression des recombinases FimB et FimE. Nous avons localisé IbeA dans le compartiment cytoplasmique, mais l’incertitude sur la fonctionnalité d’IbeA dans les constructions génétiques utilisées nécessite de confirmer ces premiers résultats. Enfin, nous avons recherché un rôle métabolique pour IbeA et IbeT étant données les homologies d’IbeT avec des transporteurs de composés carbonés. Nous avons observé qu’un mutant ?ibeT présentait un retard de croissance par rapport à la souche sauvage et au mutant ?ibeA dans des cultures en milieu minimum avec du fumarate, du succinate, du malate ou de l’aspartate comme seule source de carbone. Ces résultats suggèrent un lien entre le métabolisme de certains dicarboxylates, l’expression des fimbriae de type 1 et les protéines IbeA et IbeT. Ils ouvrent de nombreuses perspectives pour la compréhension du mécanisme d’action d’IbeA et IbeT. / Escherichia coli is bacterial species with multiple facets. Indeed, some strains are present at a commensal state in the intestinal tract of humans and warm-blooded animals, or are used as probiotics. Conversely, other strains are responsible for intestinal or extra-intestinal infections in Humans and warm-blooded animals. Extra-intestinal pathogenic E. coli (ExPEC) strains are responsible for multiple infectious diseases (neonatal meningitis, urinary tract infections, septicaemias or respiratory infections). Several virulence factors have been identified in ExPEC strains (adhesins, invasins,…) and notably the IbeA protein, originally identified in a strain isolated from a case of human neonatal meningitis. The ibeA gene is found in different ExPEC strains, of including strains avian origin. It is located on one of the four operon of the GimA genomic island, between ibeR coding a putative regulator and ibeT coding a putative antiporter. The IbeA protein is known for its role in bacterial invasion of human brain microvascular endothelial cells (HBMEC). In order to better understand the role of IbeA in the infectious process and cellular invasion, we have studied the involvement of IbeA in adhesion of the avian pathogenic E. coli strain BEN2908 and attempted to determine the localisation of this protein and its link with the IbeT protein. The comparative henotypic study of strain BEN2908 and its ?ibeA mutant showed that IbeA was involved in the adhesion to HBMEC. Adhesion tests in the absence of type 1 fimbriae ( the major adhesin of our strain) showed that IbeA did not have a direct role in adhesion in this context. This result suggested there could be a decrease in type 1 fimbriae expression at the bacterial surface in the ?ibeA mutant. This was demonstrated by dot blots. To understand how IbeA led to a modification of type 1 fimbriae, we investigated the role of IbeA in the control of the expression of genes that belong to the fim operon. Thus we showed that the promoter of these genes, located on an invertible element, was preferentially in an orientation preventing transcription of the fim genes in the ?ibeA mutant. Then, we highlighted in the ?ibeA mutant, a decrease of expression of the fimB and fimE genes encoding two recombinases involved in the orientational control of invertible element. These decreases of fimB and fimE expression could explain the reduction of type 1 fimbriae expression in the ?ibeA mutant. Lastly, phenotypes similar to that of the ?ibeA mutant were observed in a ?ibeT mutant. The localisation of IbeA is necessary to understand how this protein can act on fimB and fimE expression. We localised IbeA in the bacterial cytoplasm, but the doubt on the functionality of IbeA in the genetic constructions used demands that these results be confirmed. Finally, we have looked for a metabolic role for IbeA and IbeT, given the IbeT homology with carbon compound transporters. We have observed that, in minimal broth with fumarate, succinate, malate or aspartate as sole carbon sources, the ?ibeT mutant presented a lower growth rate than the wild type strain and ?ibeA mutant. Altogether, these results suggest a link between metabolism of dicarboxylates, type 1 fimbriae expression and IbeA and IbeT proteins. They open numerous perspectives for the comprehension of IbeA and IbeT mechanisms.

Suite aux contraintes environnementales imposées à la production classique d’électricité, les énergies à caractère renouvelable se développent très vite grâce aux politiques gouvernementales. En pratique, la nature des sources primaires étant aléatoire, l’introduction d’énergie renouvelable dans un réseau électrique peut impacter le fonctionnement du système électrique et la qualité de la puissance. L’utilisation des méthodes probabilistes dans la planification du système électrique s’avère alors nécessaire pour un système électrique composé d’une quantité importante de sources peu prévisibles. Cependant, ces méthodes probabilistes sont actuellement limitées à la planification long-terme à cause de leur temps de calcul élevé. Dans le cadre de cette thèse, une nouvelle approche probabiliste basée sur un couplage entre la formule des probabilités totales et la méthode de fiabilité du premier ordre est proposée pour l’évaluation de la fiabilité du système électrique à court terme. Elle prend en compte la probabilité de défaillance non prévue des composants du système, l’incertitude dans les prévisions de la production renouvelable et de la consommation. A l’aide de cette méthode, les indicateurs permettant de quantifier la fiabilité de fonctionnement du système électrique et l’utilisation des ressources renouvelables peuvent être déterminés. Grâce à ces indicateurs, la fiabilité du système électrique intégrant des énergies renouvelables peu prévisibles peut être évaluée. Le temps de calcul faible de la méthode permet de l’utiliser pour valider la planification court-terme, qui est faite un jour à l’avance pour la journée considérée (J). / Following the environmental constraints to conventional power generation, renewable energy character grows very quickly thanks to government policies. In practice, the nature of primary sources is random, the introduction of renewable energy in an electrical network may impact the operation of the power system and the quality of the power. The use of probabilistic methods in planning the power system becomes necessary for a power system consisting of a large amount of less predictable sources. However, these probabilistic methods are currently limited to long-term planning due to their high computation time. In this thesis, a new probabilistic approach based on a coupling between the law of total probability and the first order reliability method is proposed to evaluate the reliability of the power system in short-term. It takes into account the probability of unanticipated failure of system components, the uncertainty in forecasts of renewable generation and consumption. With this method, the indicators used to quantify the reliability of the power system and the use of renewable resources can be determined. Therefore, the reliability of the power system incorporating less predictable renewable energy can be evaluated. The low computation time of the method allows it to be used to validate the short term planning, which is made one day in advance to the considered day (J).

The goal of this thesis is to design and implement a modern parser generator. The result is a program that reads description of some context-free LALR(1) grammar and semantic actions from an input file. To output files the program generates source codes in several target modern object-oriented programming languages for implementation of the syntax analyzer which, when parsing the language corresponding to the given grammar, executes the given semantic actions. Powered by TCPDF (www.tcpdf.org)

Syftet med detta projekt var att konstruera en mindre variant av pQlacZ-1 för att senare kunna använda den som reportervektor i Ideonella dechloratans. pQlacZ-1 är en plasmid som är 17,1 kbp stor, som skulle kunna användas som reportervektor i  Ideonella dechloratans för att kunna undersöka olika promotorsekvenser. Detta är möjligt eftersom pQlacZ-1 är en broad host range plasmid och saknar promotorsekvensen för lacZ genen. Ett problem med pQlacZ-1 är dess storlek vilket gör den svår att transformera, och då speciellt i Ideonella dechloratans som är svår att transformera överhuvudtaget. En stor del av projektet har lagts på att ta reda på hur pQlacZ-1 ser ut i detalj, då detta inte finns väl beskrivet. Även efter denna studie saknas information om ett fragment för att få en helt klar bild över hur plasmiden är uppbyggd. Efter att ha ställt upp en hypotes om hur plasmiden ser ut så identifierades ett område som kunde klyvas bort och det var fragmentet med lacA och lacY. Detta gjordes  genom en dubbelklyvning med SalI och BstBI. Den nya mindre varianten av plasmiden har jag valt att kalla pQlacZ-1cc och den ska teoretiskt sett vara ca 13427 bp stor, vilket bör göra den lättare att jobba med. Ytterligare arbete behövs för att verifiera konstruktionen i pQlacZ-1cc. / The aim with this project was to design a smaller version of pQlacZ-1 in order to later use it as a reporter vector in Ideonella dechloratans.  pQlacZ-1 is a plasmid that is 17,1 kbp big, which might be used as a reporter vector in Ideonella dechloratans to investigate different promoter sequences. This is possible because pQlacZ-1 is a broad host range plasmid and lacks the promoter sequence of the lacZ gene. A problem with pQlacZ-1 is its size which makes it difficult to transform, and especially in Ideonella dechloratans which is difficult to transform at all. A large part of the project has been about finding out how pQlacZ-1 looks like in detail, as this is not well described. Even after this study information about one fragment is missing to get a completely clear picture of how the plasmid is constructed. After formulation of a hypothesis about how the plasmid is constructed, a section that could be removed was identified. The part of pQlacZ-1 that was removed was the lacA and lacY. This was done by a double digestion with SalI and BstBI. The new smaller version of the plasmid, is called pQlacZ-1cc. Theoretically it should be about 13427 bp, which should make it easier to work with. Additional work is required to verify the design of pQlacZ-1cc.

Leukemia is one of the most deadly diseases, responsible for the highest number of childhood cancer cases. Immunoglobulin-containing and proline-rich receptor-1 (IGPR-1) is a newly identified protein found to play an important role in human colon cancer and angiogenesis. The overall goal of this project was to assess IGPR-1 expression in leukemia cell lines and investigate its possible function in the NF-κB pathway, specifically the role of inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ) in the phosphorylation of IGPR-1. The NF-κB pathway, among others, plays a critical role in human-T-cell leukemia virus type 1 (HTLV-1) infected T-cells. Our preliminary results indicated that IGPR-1 is expressed in leukemia cell lines at variable levels. Further experiments demonstrated that IKKβ is involved in the phosphorylation of IGPR-1 as treatment of HEK-293 cells ectopically expressing IGPR-1 with an IKKβ inhibitor decreased IGPR-1 phosphorylation at Ser220. Likewise, cells treated with lipopolysaccharide (LPS), which is known to activate IKKβ, also stimulated the phosphorylation of IGPR-1 at Ser220. However, transfection of IGPR-1/HEK293 cells with Tax, an oncogene encoded by HTLV-1, decreased phosphorylation of IGPR-1 at Ser220. Taken together, our data indicates that activation of IKKβ in the NF-κB pathway stimulates phosphorylation of IGPR-1. / 2020-06-17T00:00:00Z

Type II diabetes is a major cause of blindness according to the World Health Organization (WHO, 2018). Diabetics are at risk of developing corneal diseases such as recurrent abrasions, ulcers, and erosions due to dysfunctional wound healing. Corrective surgeries or corneal transplants may be considered as a treatment in some, but not all, cases. The purinoreceptor P2X7 has been shown to be involved in cell-cell communication and in the restructuring of cytoskeletal actin, a necessary process for cell migration in wound healing. P2X7 relies on the binding of extracellular ATP for activation. Panx1 is a transmembrane protein whose primary role is for the release of intracellular ATP into the extracellular space. In healthy corneal epithelium, Panx1 localizes to the wound edge and forms clusters with the P2X7, which augments the wound healing response. This thesis looks at the localization of Panx1 in pre-diabetic murine corneal tissue. It was found that Panx1 is less expressed and does not localize to the wound edge to the extent as control corneas, therefore, creating less clusters with P2X7. Furthermore, preliminary studies that inhibit Panx1 with probenecid reduce the communication between cells, which is hypothesized as critical for migration of the tissue sheet and proper wound healing. / 2019-12-17T00:00:00Z

Being a Dissertation presented in fulfilment of the requirement governing the Degree of Master of Science in The School of Medicine, University of the Witwatersrand / Interleukin 1 (IL - 1) is a macrophage factor that exerts control over T cell activation. The experimental work presented in this dissertation consists of studies on IL - 1 production by monocytes which can be used as an in vitro correlate for monocyte function, as well as the effect of IL - 1 on immature T cells, that is, thymocytes. In accomplishing the studies presented in this dissertation, a two stage assay was employed. Firstly IL - 1 containing supernatants were produced by stimulated human peripheral blood adherent cells and secondly, the IL - 1 supernatants were assayed on mouse thymocyctes in which these supernatants caused mitogenesis. / IT2018

Thesis (Ph.D.)--University of the Witwatersrand, Faculty of Health Sciences, 2012. / The development of an effective HIV-1 vaccine is critical in mitigating the global HIV epidemic. Understanding the interplay between host immune functions, such as cellular memory differentiation, activation, inflammatory cytokine production and the virus, may provide key insight into anti-HIV immunity that can inform vaccine development. This PhD aims at understanding and identifying T cell memory, functional profiles and the effect of immune activation on in vivo HIV-1 control during primary/early infection. Furthermore, this study aims to examine and understand the potential mechanisms related to immune activation during primary HIV-1 infection. Use was made of a unique cohort of individuals recruited during primary HIV-1 infection and using a battery of assays to characterize and identify properties and mechanisms of T cell reactivity and activation. Multiparameter flow cytometry was used to measure memory differentiation (CD27 and CD45RO), activation (CD38, HLA-DR), proliferation (Ki67), and multiple cellular functions (CD107, IFNγ, IL-2, MIP-1β and TNFα) of total and antigen-specific CD4+ and CD8+ T cells from 15 HIV-1 and CMV-coinfected individuals followed over 15 months of HIV-1 infection. Plasma samples were used to measure markers associated with intestinal permeability (LBP, sCD14, I-FABP and IgM EndoCAb) and inflammation (IL-1β, IL-6, IL-7, IL-10, IL-12p70, TNFα and MCP-1). The differentiation profile of HIV-Gag specific memory CD4+ and CD8+ T cells was found to be mainly characterized by an early differentiated (ED) memory phenotype relative to CMV- specific CD4+ and CD8+ T cells. Moreover, the proportion of HIV-specific ED-memory CD4+ T cells inversely associated with viraemia, suggesting that HIV-1 antigen burden could be shaping the differentiation of HIV-specific memory CD4+ T cells during primary infection. Primary HIV-1 infection was also characterized by significantly elevated levels of activated and proliferating total and HIV-specific memory CD4+ and CD8+ T cells, which positively correlated with viraemia. Furthermore, upon sorting of total activated memory CD4+ T cells, these cells harboured more gag provirus DNA than non-activated memory cells, suggesting that activated memory CD4+ T cells support ongoing HIV-1 replication. When examining the relationship between memory differentiation and activation markers, the level of T cell activation was equally expanded across the different memory CD4+ T cell subpopulations, suggesting that memory differentiation of CD4+ T cells was unlikely driven per se by the level of T cell activation. In addition, when teasing out events that may result in T cell activation during primary HIV-1 infection using statistical models, plasma markers of microbial translocation and inflammation were found to correlate with immune activation. The lack of these associations in HIV-uninfected controls suggests that microbial translocation and inflammation were unlikely causative. Analysis of the polyfunctional profile of memory T cells during primary HIV-1 infection showed that HIV-specific CD4+ and CD8+ T cell responses are less polyfunctional relative to CMV-specific memory CD4+ and CD8+ T cell responses. Furthermore, the polyfunctional status of HIV-specific CD4+ T cells significantly correlated with viraemia at 3 months post-infection, indicating that the polyfunctionality of memory CD4+ T cells is likely driven by HIV-1 antigenemia. Overall, these observations suggest that HIV-1 antigenic burden appears to be a central driver of memory differentiation, activation/inflammation and polyfunctionality of T cells. Given the impact of HIV-1 viraemia on immune activation and memory T cell dysfunction (as measured by limited polyfunctional HIV-specific responses), preventing high levels of viral replication, with a vaccine or other early interventions may serve as an important strategy for delaying HIV-1 disease progression.