Development of a binary positive and negative protein fragment complementation assay using yeast cytosine deaminase

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

Understanding Adolescents’ Positive and Negative Developmental Experiences in Sport

The purpose of this study was to gain understanding of adolescents’ positive and negative developmental experiences in sport. Twenty-two purposefully sampled adolescent competitive swimmers participated in a semistructured qualitative interview. Content analysis led to the organization of meaning units into themes and categories (Patton, 2002). Athletes suggested their sport involvement facilitated many positive developmental experiences (i.e., related to challenge, meaningful adult and peer relationships, a sense of community, and other life experiences) and some negative developmental experiences (i.e., related to poor coach relationships, negative peer influences, parent pressure, and the challenging psychological environment of competitive sport). Findings underline the important roles of sport programmers, clubs, coaches, and parents in facilitating youths’ positive developmental experiences in sport, while highlighting numerous important directions for future research. Implications for coach training and practice are outlined.

Informing the structure of subjective well-being through examining changes in life satisfaction, positive affect, and negative affect

Subjective well-being (SWB) refers to how individuals evaluate and experience their lives in positive ways, and encompasses global judgments of life satisfaction (LS), as well as the frequency of positive and negative affect (PA and NA, respectively) in one’s life. To inform the current ambiguity concerning the structure of SWB, the aim of this Masters thesis was to evaluate the structure of SWB based on whether the three components of SWB change together or independently naturally, over time and following experimental manipulation. In Study 1, associations among changes in LS, PA, and NA were evaluated using a longitudinal approach tracking natural changes in the components over periods of three months and three years. Results indicated that change in one component was related to change in the other two components. In Study 2, an experimental design was used to manipulate each SWB component individually, and evaluate changes in all three components following each manipulation. Manipulation materials designed to target LS only were effective (i.e., led to heightened focus on LS, and not PA or NA) and created an increase in both LS and PA. Manipulation materials designed to target PA and NA only were not effective (i.e., led to heightened focus on the target component, as well as on LS). Furthermore, in both studies the strength of an individual’s SWB (assessed in terms of structural consistency and structural ambivalence in Study 1 and Study 2, along with subjective ambivalence in Study 2) did not consistently moderate the degree to which changes in the components were associated with one another. Together, these findings indicate that the structure of SWB may be complex and dynamic, rather than static. Alternatively, the components of SWB may not be easily manipulated in isolation of one another. Implications for existing structural models of SWB are discussed.

Looking beyond the negatives: A time period analysis of positive cognitions, negative cognitions, and working alliance in cognitive-behavior therapy for panic disorder

Time period analysis was used in an international sample of clients ( N = 106) to demonstrate that cognitive - behavioral therapy (CBT) for panic disorder is associated with specific changes in both negative and positive cognitions during the treatment period. In the first 6 weeks of the treatment phase, working alliance failed to predict changes in panic severity, whereas changes in panic self-efficacy and catastrophic misinterpretation of bodily sensations predicted rapid symptom relief. In the last 6 weeks of treatment, higher doses of CBT were associated with further changes in positive and negative cognitions. The findings can be interpreted as suggesting that the role of the working alliance in CBT for panic disorder is to facilitate cognitive change.

Examining invisible social control as predictor of daily smoking and negative affect after a self-set quit date

Objectives: The dual-effects model of social control proposes that social control leads to better health practices, but also arouses psychological distress. However, findings are inconsistent in relation to health behavior and psychological distress. Recent research suggests that the most effective control is unnoticed by the receiver (i.e., invisible). There is some evidence that invisible social control is beneficial for positive and negative affective reactions. Yet, investigations of the influence of invisible social control on daily smoking and distress have been limited. In daily diaries, we investigated how invisible social control is associated with number of cigarettes smoked and negative affect on a daily basis. Methods: Overall, 99 smokers (72.0% men, mean age M = 40.48, SD = 9.82) and their non-smoking partners completed electronic diaries from a self-set quit date for 22 consecutive days within the hour before going to bed, reporting received and provided social control, daily number of cigarettes smoked, and negative affect. Results: Multilevel analyses indicated that between-person levels of invisible social control were associated with lower negative affect, whereas they were unrelated to number of cigarettes smoked. On days with higher-than-average invisible social control, smokers reported less cigarettes smoked and more negative affect. Conclusions: Between-person level findings indicate that invisible social control can be beneficial for negative affect. However, findings on the within-person level are in line with the assumptions of the dual-effects model of social control: Invisible social control reduced daily smoking and simultaneously increased daily negative affect within person.

T-cell reprogramming through targeted CD4-coreceptor and T-cell receptor expression on maturing thymocytes by latent Circoviridae family member porcine circovirus type 2 cell infections in the thymus

Although porcine circovirus type 2 (PCV2)-associated diseases have been evaluated for known immune evasion strategies, the pathogenicity of these viruses remained concealed for decades. Surprisingly, the same viruses that cause panzootics in livestock are widespread in young, unaffected animals. Recently, evidence has emerged that circovirus-like viruses are also linked to complex diseases in humans, including children. We detected PCV2 genome-carrying cells in fetal pig thymi. To elucidate virus pathogenicity, we developed a new pig infection model by in vivo transfection of recombinant PCV2 and the immunosuppressant cofactor cyclosporine A. Using flow cytometry, immunofluorescence and fluorescence in situ hybridization, we found evidence that PCV2 dictates positive and negative selection of maturing T cells in the thymus. We show for the first time that PCV2-infected cells reside at the corticomedullary junction of the thymus. In diseased animals, we found polyclonal deletion of single positive cells (SPs) that may result from a loss of major histocompatibility complex class-II expression at the corticomedullary junction. The percentage of PCV2 antigen-presenting cells correlated with the degree of viremia and, in turn, the severity of the defect in thymocyte maturation. Moreover, the reversed T-cell receptor/CD4-coreceptor expression dichotomy on thymocytes at the CD4(+)CD8(interm) and CD4SP cell stage is viremia-dependent, resulting in a specific hypo-responsiveness of T-helper cells. We compare our results with the only other better-studied member of Circoviridae, chicken anemia virus. Our data show that PCV2 infection leads to thymocyte selection dysregulation, adding a valuable dimension to our understanding of virus pathogenicity.

Acoustic and Magnetic Techniques for the Isolation and Analysis of Cells in Microfluidic Platforms

Cancer comprises a collection of diseases, all of which begin with abnormal tissue growth from various stimuli, including (but not limited to): heredity, genetic mutation, exposure to harmful substances, radiation as well as poor dieting and lack of exercise. The early detection of cancer is vital to providing life-saving, therapeutic intervention. However, current methods for detection (e.g., tissue biopsy, endoscopy and medical imaging) often suffer from low patient compliance and an elevated risk of complications in elderly patients. As such, many are looking to “liquid biopsies” for clues into presence and status of cancer due to its minimal invasiveness and ability to provide rich information about the native tumor. In such liquid biopsies, peripheral blood is drawn from patients and is screened for key biomarkers, chiefly circulating tumor cells (CTCs). Capturing, enumerating and analyzing the genetic and metabolomic characteristics of these CTCs may hold the key for guiding doctors to better understand the source of cancer at an earlier stage for more efficacious disease management.

The isolation of CTCs from whole blood, however, remains a significant challenge due to their (i) low abundance, (ii) lack of a universal surface marker and (iii) epithelial-mesenchymal transition that down-regulates common surface markers (e.g., EpCAM), reducing their likelihood of detection via positive selection assays. These factors potentiate the need for an improved cell isolation strategy that can collect CTCs via both positive and negative selection modalities as to avoid the reliance on a single marker, or set of markers, for more accurate enumeration and diagnosis.

The technologies proposed herein offer a unique set of strategies to focus, sort and template cells in three independent microfluidic modules. The first module exploits ultrasonic standing waves and a class of elastomeric particles for the rapid and discriminate sequestration of cells. This type of cell handling holds promise not only in sorting, but also in the isolation of soluble markers from biofluids. The second module contains components to focus (i.e., arrange) cells via forces from acoustic standing waves and separate cells in a high throughput fashion via free-flow magnetophoresis. The third module uses a printed array of micromagnets to capture magnetically labeled cells into well-defined compartments, enabling on-chip staining and single cell analysis. These technologies can operate in standalone formats, or can be adapted to operate with established analytical technologies, such as flow cytometry. A key advantage of these innovations is their ability to process erythrocyte-lysed blood in a rapid (and thus high throughput) fashion. They can process fluids at a variety of concentrations and flow rates, target cells with various immunophenotypes and sort cells via positive (and potentially negative) selection. These technologies are chip-based, fabricated using standard clean room equipment, towards a disposable clinical tool. With further optimization in design and performance, these technologies might aid in the early detection, and potentially treatment, of cancer and various other physical ailments.

A role for the alpha-chain connecting peptide motif in mediating TCR-CD8 cooperation.

To generate peripheral T cells that are both self-MHC restricted and self-MHC tolerant, thymocytes are subjected to positive and negative selection. How the TCR discriminates between positive and negative selection ligands is not well understood, although there is substantial evidence that the CD4 and CD8 coreceptors play an important role in this cell fate decision. We have previously identified an evolutionarily conserved motif in the TCR, the alpha-chain connecting peptide motif (alpha-CPM), which allows the TCR to deliver positive selection signals. Thymocytes expressing alpha-CPM-deficient receptors do not undergo positive selection, whereas their negative selection is not impaired. In this work we studied the ligand binding and receptor function of alpha-CPM-deficient TCRs by generating T cell hybridomas expressing wild-type or alpha-CPM-deficient forms of the T1 TCR. This K(d)-restricted TCR is specific for a photoreactive derivative of the Plasmodium berghei circumsporozoite peptide(252-260) IASA-YIPSAEK(ABA)I and is therefore amenable to TCR photoaffinity labeling. The experiments presented in this work show that alpha-CPM-deficient TCRs fail to cooperate with CD8 to enhance ligand binding and functional responses.

Dissecting cell cycle protein complexes using the pptimized yeast cytosine deaminase protein-fragment complementation assay “You too can play with an edge”

Les protéines sont les produits finaux de la machinerie génétique. Elles jouent des rôles essentiels dans la définition de la structure, de l'intégrité et de la dynamique de la cellule afin de promouvoir les diverses transformations chimiques requises dans le métabolisme et dans la transmission des signaux biochimique. Nous savons que la doctrine centrale de la biologie moléculaire: un gène = un ARN messager = une protéine, est une simplification grossière du système biologique. En effet, plusieurs ARN messagers peuvent provenir d’un seul gène grâce à l’épissage alternatif. De plus, une protéine peut adopter plusieurs fonctions au courant de sa vie selon son état de modification post-traductionelle, sa conformation et son interaction avec d’autres protéines. La formation de complexes protéiques peut, en elle-même, être déterminée par l’état de modifications des protéines influencées par le contexte génétique, les compartiments subcellulaires, les conditions environmentales ou être intrinsèque à la croissance et la division cellulaire. Les complexes protéiques impliqués dans la régulation du cycle cellulaire sont particulièrement difficiles à disséquer car ils ne se forment qu’au cours de phases spécifiques du cycle cellulaire, ils sont fortement régulés par les modifications post-traductionnelles et peuvent se produire dans tous les compartiments subcellulaires. À ce jour, aucune méthode générale n’a été développée pour permettre une dissection fine de ces complexes macromoléculaires. L'objectif de cette thèse est d'établir et de démontrer une nouvelle stratégie pour disséquer les complexes protéines formés lors du cycle cellulaire de la levure Saccharomyces cerevisiae (S. cerevisiae). Dans cette thèse, je décris le développement et l'optimisation d'une stratégie simple de sélection basée sur un essai de complémentation de fragments protéiques en utilisant la cytosine déaminase de la levure comme sonde (PCA OyCD). En outre, je décris une série d'études de validation du PCA OyCD afin de l’utiliser pour disséquer les mécanismes d'activation des facteurs de transcription et des interactions protéine-protéines (IPPs) entre les régulateurs du cycle cellulaire. Une caractéristique clé du PCA OyCD est qu'il peut être utilisé pour détecter à la fois la formation et la dissociation des IPPs et émettre un signal détectable (la croissance des cellules) pour les deux types de sélections. J'ai appliqué le PCA OyCD pour disséquer les interactions entre SBF et MBF, deux facteurs de transcription clés régulant la transition de la phase G1 à la phase S. SBF et MBF sont deux facteurs de transcription hétérodimériques composés de deux sous-unités : une protéine qui peut lier directement l’ADN (Swi4 ou Mbp1, respectivement) et une protéine commune contenant un domain d’activation de la transcription appelée Swi6. J'ai appliqué le PCA OyCD afin de générer un mutant de Swi6 qui restreint ses activités transcriptionnelles à SBF, abolissant l’activité MBF. Nous avons isolé des souches portant des mutations dans le domaine C-terminal de Swi6, préalablement identifié comme responsable dans la formation de l’interaction avec Swi4 et Mbp1, et également important pour les activités de SBF et MBF. Nos résultats appuient un modèle où Swi6 subit un changement conformationnel lors de la liaison à Swi4 ou Mbp1. De plus, ce mutant de Swi6 a été utilisé pour disséquer le mécanisme de régulation de l’entrée de la cellule dans un nouveau cycle de division cellulaire appelé « START ». Nous avons constaté que le répresseur de SBF et MBF nommé Whi5 se lie directement au domaine C-terminal de Swi6. Finalement, j'ai appliqué le PCA OyCD afin de disséquer les complexes protéiques de la kinase cycline-dépendante de la levure nommé Cdk1. Cdk1 est la kinase essentielle qui régule la progression du cycle cellulaire et peut phosphoryler un grand nombre de substrats différents en s'associant à l'une des neuf protéines cycline régulatrice (Cln1-3, Clb1-6). Je décris une stratégie à haut débit, voir à une échelle génomique, visant à identifier les partenaires d'interaction de Cdk1 et d’y associer la cycline appropriée(s) requise(s) à l’observation d’une interaction en utilisant le PCA OyCD et des souches délétées pour chacune des cyclines. Mes résultats nous permettent d’identifier la phase(s) du cycle cellulaire où Cdk1 peut phosphoryler un substrat particulier et la fonction potentielle ou connue de Cdk1 pendant cette phase. Par exemple, nous avons identifié que l’interaction entre Cdk1 et la γ-tubuline (Tub4) est dépendante de Clb3. Ce résultat est conforme au rôle de Tub4 dans la nucléation et la croissance des faisceaux mitotiques émanant des centromères. Cette stratégie peut également être appliquée à l’étude d'autres IPPs qui sont contrôlées par des sous-unités régulatrices.

Le rôle de la MAPK non-conventionnelle ERK3 dans le développement thymique

Les premières cellules progénitrices lympho-myéloïdes (LMPP) entrent dans le thymus et commencent leur processus de différenciation au stade double négatif (DN, CD4-CD8-). Après un réarrangement fonctionnel de la chaine bêta de leur récepteur des cellules T (RCT), les cellules reçoivent des signaux de différenciation, de prolifération, de survie et de sélection et passent au stade double positif (DP, CD4+CD8+). Ensuite, la chaine alpha du RCT est réarrangée et testée via les sélections positive et négative. Si le RCT reçoit un signal ni trop fort, ni trop faible, les cellules passent au stade simple positif où elles exprimeront soit la molécule CD4 ou CD8. ERK3, une MAPK non-conventionnelle, joue un rôle important dans le développement thymique. Des études précédentes ont démontré qu’une déficience en ERK3 diminue de 50 % la cellularité thymique et de 75% le nombre de cellules simples positives CD4 (CD4SP). Nous avons posé comme hypothèses qu’il y a une augmentation de l’apoptose chez les thymocytes DP de souris Erk3-/- et que cette déficience chez les thymocytes DP affecterait la sélection positive des cellules DP, réduisant ainsi le nombre de thymocytes CD4SP. Afin de vérifier la première hypothèse, nous avons regardé les niveaux d’apoptose grâce à la cytométrie en flux et par immunohistochimie. Dans les deux cas, nous étions incapables de détecter une différence du niveau d’apoptose chez les thymocytes DP entre les souris Erk3+/+ et Erk3-/-. Ensuite, nous nous sommes posés la question suivante : La demi-vie des thymocytes DP Erk3-/- était-elle plus courte que le type sauvage? La demi-vie des thymocytes DP a été mesurée à l’aide de l’étude des réarrangements secondaires de la chaine alpha du RCT par PCR semi-quantitatif et à l’aide de cultures de thymus fœtaux. En effet, ERK3 semble important pour prolonger la demi-vie des thymocytes DP. Ensuite, nous avons utilisé des marqueurs cellulaires différentiels (CD69, CD5 et RCT) pour regarder si les thymocytes DP sont capables de passer la sélection positive. En effet, il y a moins de thymocytes DP Erk3-/- qui sont CD69fort, CD5fort et RCTfort. Finalement, nous voulons savoir si les fonctions de ERK3 passent par MK5, son seul partenaire d’interaction connu à ce jour. Après la caractérisation du thymus de la souris Mk5-/-, nous observons que seulement la réduction du nombre de thymocytes CD4SP est identique à celle des thymocytes CD4SP de la souris Erk3-/-. En conclusion, ces résultats révèlent des fonctions importantes pour la molécule ERK3 lors du processus de sélection positive, le maintient de la demi-vie des thymocytes DP et lors de la régulation de développement thymique de manière MK5-dépendante et -indépendante.

Misregulation of the tumour suppressor gene CYLD drives hyperactivation of T cells leading to intestinal pathology

The tumour suppressor gene cyld is mutated in familial cylindromatosis, an autosomal-dominant condition that predisposes to multiple skin tumours. The deubiquitinase CYLD acts as a negative regulator of NF-κB signaling. To analyse the function of CYLD in vivo we used the CYLDex7/8 mice, which are characterized by loss of the full-length transcript and overexpression of a short splice variant of CYLD (sCYLD). In CYLDex7/8 mice the overexpression of sCYLD results in splenomegaly and lymphadenopathy. Additionally, the B cell population in spleen and lymph nodes is increased at the expense of T cells. Analysis of CYLDex7/8 T cells showed a significant reduction of CD4 single positive (SP) and CD8 SP T cells in the thymus and in the periphery. By investigating the impact of sCYLD in TCR signaling in thymocytes, we could demonstrate that sCYLD partially inhibited the activation of Zap70 and thereby negatively regulated TCR signaling. In vitro as well as in vivo we could show that CD4+ T cells displayed a hyperactive phenotype, proliferated to a better extent than WT cells and expressed high amounts of inflammatory cytokines such as IL-6 and IL-17A. Western Blots of steady state thymocytes and peripheral CD4+ T cells were performed, showing that the noncanonical pathway was highly upregulated visualized by the expression levels of RelB and p100 leading to a hyperactive phenotype of CD4+ T cells. In order to investigate the contribution of sCYLD in positive and negative selection in the thymus in vivo, the HY-TCR transgene (HYtg) was crossed to CYLDex7/8 mice. The analysis of CYLDex7/8 HYtg males revealed an increase in CD4+CD8+ DP as well as in CD8+ SP thymocytes, suggesting a less pronounced negative selection in CYLD mutant mice compared to HYtg control mice. Interestingly, the impaired negative selection in the thymus was accompanied by a strong colitis phenotype at early ages (4 weeks). Since medullary TECs (mTECs) play an important role in the late stage of T cell development by negatively selecting autoreactive thymocytes, the levels of mTECs in the medullary compartment was investigated. Of note, low numbers of mTECs were observed, combined with decreased expression levels of the mTEC markers UEA-1, keratin-5, claudin-3 and claudin-4. The reduction of mTECs in the medullary compartment could explain the inflammatory phenotype of CD4+ T cells in CYLDex7/8 mice leading to the severe intestinal pathology observed in these mice. Taken together, these results show an important role of sCYLD in T cell development and function as well as in NF-кB signaling of T cells.

Cathepsin S dominates autoantigen processing in human thymic dendritic cells

The interaction of developing thymocytes with peptide-MHC complexes on thymic antigen presenting cells (APC) is crucial for T cell development, both for positive selection of "useful" thymocytes as well as negative selection of autoreactive thymocytes to prevent autoimmunity. The peptides presented on MHC II molecules are generated by lysosomal proteases such as the cathepsins. At the same time, lysosomal proteases will also destroy other potential T cell epitopes from self-antigens. This will lead to a lack of presentation on negatively selecting thymic antigen presenting cells and consequently, escape of autoreactive T cells recognizing these epitopes. In order to understand the processes that govern generation or destruction of self-epitopes in thymic APC, we studied the antigen processing machinery and epitope processing in the human thymus. We find that each type of thymic APC expresses a different signature of lysosomal proteases, providing indirect evidence that positive and negative selection of CD4(+) T cells might occur on different sets of peptides, in analogy to what has been proposed for CD8(+) T cells. We also find that myeloid dendritic cells (DC) are more efficient in processing autoantigen than plasmacytoid DC. In addition, we observed that cathepsin S plays a central role in processing of the autoantigens myelin basic protein and proinsulin in thymic dendritic cells. Cathepsin S destroyed a number of known T cell epitopes, which would be expected to result in lack of presentation and consequently, escape of autoreactive T cells. Cathepsin S therefore appears to be an important factor that influences selection of autoreactive T cells.

Inhibition of intrathymic T cell development by expression of a transgenic antagonist peptide

The mature T cell receptor (TCR) repertoire is shaped by positive- and negative-selection events taking place during T cell development. These events are regulated by interactions between the TCR and major histocompatibility complex molecules presenting self-peptides. It has been shown that many antagonist peptides are efficient at mediating positive selection. In this study we analyzed the effects of a transgene encoding an antagonist peptide (influenza NP34) that is presented by H-2Db in a Tap-1-independent fashion in mice expressing the influenza NP68-specific TCR F5. We find that the transgenic peptide does not mediate positive or negative selection in F5+Tap-1−/− mice, but inhibits maturation of CD8+ single positive thymocytes in F5+Tap-1+ mice without inducing signs of negative selection. We conclude that antagonism of antigen recognition occurs not only at the level of mature T cells but also in T cell development.

A new method for generating point mutations in bacterial artificial chromosomes by homologous recombination in Escherichia coli

Bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs), which contain large fragments of genomic DNA, have been successfully used as transgenes to create mouse models of dose-dependent diseases. They are also potentially valuable as transgenes for dominant diseases given that point mutations and/or small rearrangements can be accurately introduced. Here, we describe a new method to introduce small alterations in BACs, which results in the generation of point mutations with high frequency. The method involves homologous recombination between the original BAC and a shuttle vector providing the mutation. Each recombination step is monitored using positive and negative selection markers, which are the Kanamycin-resistance gene, the sacB gene and temperature-sensitive replication, all conferred by the shuttle plasmid. We have used this method to introduce four different point mutations and the insertion of the β-galactosidase gene in a BAC, which has subsequently been used for transgenic animal production.

Clonal deletion and the fate of autoreactive thymocytes that survive negative selection.

Clonal deletion of autoreactive thymocytes is important for self-tolerance, but the intrathymic signals that induce clonal deletion have not been clearly identified. We now report that clonal deletion during negative selection required CD28-mediated costimulation of autoreactive thymocytes at the CD4(+)CD8(lo) intermediate stage of differentiation. Autoreactive thymocytes were prevented from undergoing clonal deletion by either a lack of CD28 costimulation or transgenic overexpression of the antiapoptotic factors Bcl-2 or Mcl-1, with surviving thymocytes differentiating into anergic CD4(-)CD8(-) double-negative thymocytes positive for the T cell antigen receptor αβ subtype (TCRαβ) that 'preferentially' migrated to the intestine, where they re-expressed CD8α and were sequestered as CD8αα(+) intraepithelial lymphocytes (IELs). Our study identifies costimulation by CD28 as the intrathymic signal required for clonal deletion and identifies CD8αα(+) IELs as the developmental fate of autoreactive thymocytes that survive negative selection.