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Exploration into the use of aptamers as cross-reactive receptors was the focus of this work. Cross-reactivity is of interest for developing assays to identify complex targets and solutions. By exploiting the simple chemistries of aptamers, we hope to introduce a new class of receptors to the science of molecular discrimination. This manuscript first addresses the use designed aptamers for the identification of variants of HIV-1 reverse transcriptase. In this research aptamers were immobilized on a platform and were used to discriminate four variants of HIV-1 reverse transcriptase. It was found that not only could the array discriminate HIV-1 reverse transcriptase variants for which aptamers were designed, it would also discriminate variants for which no aptamers exist. A panel of aptamers was used to discriminate four separate cell lines, which were chosen as examples of complex targets. This aptamer panel was used to further explore the use of aptamers as cross-reactive sensors. Forty-six aptamers were selected from the literature that were designed to be specific to cells or molecules expected to be in the surface of cells. This panel showed differential binding patterns to each of the cell types, displaying cross-reactive behavior. During the course of this research, we also developed a novel ratiometric method of using aptamer count derived from next-generation sequencing as a method for discrimination. This is in lieu of the more commonly used fluorescent signals. Finally the use of multiple signals for pattern recognition routines was further explored by running various models using artificial data. Various situations were applied to replicate different possible situation which might arise when working with macromolecular interactions. The purpose of this was to advance the communities understanding and ability to interpret results from the pattern recognition methods of PCA and LDA. / text

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The socio-economic and geographical distribution of malaria overlaps with that of many parasitic helminths and in these areas co-infections are common. Co-infection with helminths can influence disease outcome causing either exacerbation or amelioration of malaria. Understanding the complex host-parasite interactions that lead to these different disease outcomes is important for the success of control programmes aimed at these parasites. The immune system has evolved diverse types of response (e.g. T-helper 1 (Th1) and T-helper 2 (Th2)) to efficiently combat infection with ‘microparasites’ and helminths respectively. When faced with co-infection however, the need for the host to multitask means it must manage these counter-regulatory responses. In this study a murine model of malaria-hookworm (Plasmodium chabaudi- Nippostrongylus brasiliensis) co-infection was utilised to investigate how changes in T-helper bias affect malaria disease outcome. Antibody isotypes were used as indicators of Th1/Th2 bias and revealed that helminth co-infection reduced the malaria-specific Th1 response. Counter-intuitively this resulted in ‘protection’ from malaria with co-infected mice having reduced peak P. chabaudi parasitaemia and suffering less severe anaemia. In addition to providing a measure of Th1/Th2 bias, analysis of antibody responses revealed the occurrence of cross-reactive antibodies. The potential for these crossreactive antibodies to influence disease outcome was investigated but in this murine model resource-mediated mechanisms of parasite regulation appear to be responsible for the ‘protection’ that co-infection affords. The question of why cross-reactive antibodies are produced has important immunological and ecological implications. Cross-reactive responses may arise through some physiological constraint on the immune mechanisms that usually result in antibody-specificity. However experiments designed to investigate if the specificity of antibodies is constrained by availability of antigen suggest that this is not the case in the model system used here. There is also the possibility that production of cross-reactive antibodies represents an evolutionary optimal strategy for a host faced with unpredictable exposure to a variety of parasites. However a major finding of this study indicates these two taxonomically distinct parasite species share antigens, which in itself is crucial to understanding host-parasite interactions in a co-infection setting. The main findings of this thesis are relevant to co-infection studies in general and the implications for both evolutionary and applied biology are discussed.

Les réponses des cellules T CD4 (Thelper, TH) jouent un rôle clé dans l'immunité antivirale. Cependant, celles générées par l'infection au VIH et les vaccins candidats sont variables. Des données chez la souris et l'humain suggèrent que des réponses TH antivirales peuvent être générées avant l'exposition à l'antigène spécifique par réaction croisée avec d'autres microorganismes et influencer les réponses TH ultérieures. Les réponses TH au VIH chez des individus séronégatifs seront investiguées et comparées à celles de sujets infectés. Une haute prévalence de réponses TH prolifératives au VIH a été observée chez des sujets VIH-. Gag montre une légère prédominance sur les autres protéines du VIH Env, Nef et Pol (33% des donneurs VIH- ont une réponse contre Gag >1% par test CFSE), mais qui diffère de l’immunodominance observée chez les donneurs VIH+. Malgré les réponses prolifératives plus petites chez les donneurs VIH-, des lignées cellulaires de TH spécifiques pour Gag ou Env ont pu être générées. Un marquage intracellulaire a validé leur spécificité et leurs fonctions montrant des réponses dominées par l'expression de TNF et CD40L comparativement à celles dérivées de donneurs VIH+ produisant beaucoup d’IFN-γ. L’affinité antigénique varie chez les sujets VIH-, mais peut être améliorée chez certains donneurs en optimisant la présentation antigénique. Une cartographie d’épitopes pour Env gp41 à identifier des épitopes reconnus par les TH. Les résultats montrent la présence de TH spécifiques au VIH chez une proportion de donneurs séronégatifs. Ces cellules pourraient influencer le développement de réponses vaccinales et spécifique au VIH durant l’infection aiguë. / CD4+ T cell (Thelper, TH) responses play a key role in antiviral immunity. However, HIV-specific TH responses generated either by infection or by vaccine candidates are highly variable. Studies in mice and humans suggest that antiviral TH responses can be generated before exposure to the specific viral pathogen through cross-reactivity with other microorganisms These pre-existing responses may influence development of TH responses upon pathogen or immunogen exposure. We investigated HIV-specific TH responses in HIV-uninfected individuals (UD) and compared them to those of HIV-infected donors (HI). The prevalence of HIV-specific proliferative TH responses in UD was surprisingly high: 33% of UD had a robust Gag response >1% by CFSE assay. While Gag was more frequently targeted than the alternative HIV proteins Env, Nef and Pol, we did not observe the strong Gag immunodominance pattern seen in HI. Proliferative responses were overall lower in UD than HI, but strong expansion was occasionally observed. We derived Gag- and Env-specific short-term TH cell lines from UD and used intracellular staining to confirm their specificity and functions. TNF-α and CD40L dominated TH responses in UD lines, contrasting with HI lines that were robust IFN- producers. Functional affinity in UD was variable and could be improved in some subjects by optimization of antigen presentation. Gp41 epitope mapping identified peptides recognized by TH from UD. The results show that functional HIV-specific CD4 T cells exist in a substantial proportion of UD. Such pre-existing CD4 T cell could impact development of virus-specific TH responses at the time of acute HIV infection and influence responses to vaccine candidates.

L'objectif de cette thèse est d'explorer les applications potentielles d'un système de langue électronique basée sur des récepteurs combinatoires à réactivités croisées et l'imagerie par résonance de plasmons de surface, pour l'analyse et la discrimination de différents milieux complexes et de bactéries. L'étude de milieux complexes a été réalisée sur des échantillons de différentes natures comme le vin, la bière et le lait d'origines végétale et animale. Les expériences ont démontré que notre système de langue électronique est capable de répondre avec une bonne sélectivité à ces milieux complexes et qu'il génère ainsi des profils continus 2D et des images 3D, propres à chaque échantillon. La différentiation et la classification de ces divers types de boissons ont été réalisées grâce à ces signatures 2D et 3D. Le dispositif a également prouvé son efficacité pour le suivi du vieillissement du lait. Une seconde étude a été dédiée à l'application du système pour la détection de bactéries. Dans un premier temps, des paramètres fluidiques ont été optimisés comme la forme et la profondeur de la cuve ou le débit fluidique, en raison de la morphologie variable des bactéries, considérées ici comme des objets biologiques complexes et volumineux. Dans un second temps, le système s'est révélé performant pour l'analyse de bactéries et a montré la possibilité de quantifier ces analyses. En effet, la langue électronique a permis la discrimination de différentes bactéries selon leur genre, leur espèce et en fonction des souches grâce aux profils continus 2D et aux images 3D. / The objective of this PhD thesis is to explore the potential applications of the electronic tongue, based on combinatorial cross-reactive receptors and surface plasmon resonance imaging, for analysis and discrimination of different complex mixtures and bacteria. In this work, various complex mixtures of different nature such as wine, beer, and milk (either animal-based or plant-based) are used. It has been demonstrated that the electronic tongue is capable of responding differently to theses samples with good selectivity. For each of them, it can generate characteristic continuous 2D profile and 3D image, based on which the differentiation and classification of the complex mixtures have been carried out. Furthermore, it has been illustrated that the electronic tongue is efficient for monitoring the deterioration of milk. In the second part of this thesis, the electronic tongue has been applied for detection and analysis of bacteria. At first, some fluidic parameters have been optimized due to the variable morphology of these complexes and large biological objects. Under optimized experimental conditions, the electronic tongue is effective for analysis of bacteria with the possibility for quantification. Thereafter, the electronic tongue has allowed for the discrimination of different bacteria according to their genus, species and strains based on continuous 2D profiles and 3D images.

L'objectif de cette thèse est le développement d'une langue électronique avec une méthode simplifiée d'obtention de récepteurs à réactivité croisée. Ces récepteurs sont préparés par une approche combinatoire novatrice qui consiste au mélange et à l'auto-assemblage de deux disaccharides. Le couplage de ces récepteurs avec un système de détection d'imagerie par résonance des plasmons de surface nous a permis de réaliser une langue électronique capable de différencier des échantillons de différentes complexités, y compris des protéines pures et des mélanges complexes. Cela se fait grâce aux profils et images d'évolution continue, assimilés à des « empreintes digitales » des échantillons. D'un autre côté, ce système peut être utilisé en tant qu'outil pour la conception de surfaces biomimétiques 2D et 3D. Ce système est prometteur pour l'étude des interactions sucre-protéine et pour la préparation de nanovecteurs biomimétiques qui ciblent de façon spécifique des protéines d'intérêt. / L'objectif de cette thèse est le développement d'une langue électronique avec une méthode simplifiée d'obtention de récepteurs à réactivité croisée. Ces récepteurs sont préparés par une approche combinatoire novatrice qui consiste au mélange et à l'auto-assemblage de deux disaccharides. Le couplage de ces récepteurs avec un système de détection d'imagerie par résonance des plasmons de surface nous a permis de réaliser une langue électronique capable de différencier des échantillons de différentes complexités, y compris des protéines pures et des mélanges complexes. Cela se fait grâce aux profils et images d'évolution continue, assimilés à des « empreintes digitales » des échantillons. D'un autre côté, ce système peut être utilisé en tant qu'outil pour la conception de surfaces biomimétiques 2D et 3D. Ce système est prometteur pour l'étude des interactions sucre-protéine et pour la préparation de nanovecteurs biomimétiques qui ciblent de façon spécifique des protéines d'intérêt.

The treatment of human immunodeficiency virus (HIV-1) infection faces the challenge of drug resistance. The high mutation rate of HIV-1 allows it to develop resistance against all available drugs. New mechanisms of intervention that do not succumb to failure through resistance are thus being explored. Mutagens that increase the viral mutation rate are a promising class of drugs. They can drive HIV-1 past a critical mutation rate, called the error threshold, and induce a catastrophic loss of genetic information. The treatment duration for a mutagen to drive HIV-1 beyond this error threshold is not yet estimated. We devise a detailed stochastic simulation of HIV-1 infection to estimate this duration. The simulations predict that the required duration is inversely proportional to the difference between the mutation rate induced by a mutagen and the error threshold. This scaling is robust to changes in simulation parameters. Using this scaling, we estimate the required duration of treatment with mutagens to be many years. Unfortunately, all available drugs, including mutagens, fail to clear the infection because HIV-1 establishes a reservoir of latently infected cells harbouring silent HIV-1 integrated genomes. A new \shock and kill" strategy that aims to activate latent cells and render them susceptible to immune killing or viral cytopathicity and thus to eradicate the HIV-1 latent reservoir has been suggested. Several latency reversal agents (LRAs) have been developed. Individual LRAs fail to show any decline in the HIV-1 latent reservoir in clinical trials. Combinations of LRAs have been tested in a few in-vitro and ex-vivo experiments. It has been found that in combination LRAs act synergistically. Finding the drug concentrations that yield the maximum synergy may be helpful in achieving a sterilizing cure. Here, we develop an intracellular model to estimate these drug concentrations. We choose drugs from two different classes of LRAs and show that our model captures quantitatively recent in-vitro experiments of their activity individually and in combination. With this model, we estimate the concentrations of the drugs required to obtain the maximum synergy. Strong CD8+ T cell responses against viruses have been associated with low levels of viremia. Elite controllers of HIV-1, who are known to have low or undetectable viremia, mount a cross-reactive CD8+ T cell response against the pathogen which controls viral mutation-driven escape from immune activity. These cross-reactive responses are against specific epitopes of HIV-1. Our goal was to examine whether such epitopes could be identified systematically so that a cross-reactive immune response could be induced by using these epitopes as immunogens. Immune recognition of an epitope involves two parts: presentation of the epitope, or peptide, by the major histocompatibility complex (MHC) molecules in the host and high a finity binding of the peptide-MHC complex with a T cell receptor (TCR). Immune escape could occur at either of these steps. Here, we examined the first step. We devise the following procedure to identify peptides that sustain HLA binding despite mutations. First, from the full length HIV-1 (HCV) proteome, we identify viral peptides that bind tightly with MHC molecules using the software NetMHCpan2.8. Next, we pick the peptides and their complementary MHC molecules that yield tight binding and mutate the peptides bit by bit to examine whether binding was compromised. We identify several viral peptide-MHC pairs that display tight binding despite all possible single mutations of the peptides both with HIV-1 and HCV. These peptides present candidates which can be tested for their TCR binding and cross-reactive immunogenic potential.