<p>This dissertation reports the development of a scale to measure childrens' and adolescents' self-perceptions regarding their involvement in those physical activities typical of youth. Self-efficacy theory is used as a perspective from which to view these perceptions. The test-retest reliability, and both the construct and predictive validity of this scale are investigated and established. The development and testing of a Participation Questionnaire and a Teacher's Evaluation form are also reported herein.</p> / Doctor of Philosophy (PhD)

<p>During Herpes Simplex Virus type 1 (HSV-1) infections, many viral proteins are synthesized and several have proven or suspected roles in regulating viral gene expression. To facilitate the study of the individual activity of one such protein, ICP4, the ICP4 gene was cloned in a plasmid vector, and expresser cell lines containing 5-30% of infected cell levels of ICP4 were established. The ICP4 is functional, correctly processed, and located in the cell nuclei. The endogenous ICP4 gene retained its capacity to respond to viral trans-acting factors, since its expression after superinfection with HSV-2 mimicked that of the viral gene. Although cells infected with lCP4 mutant viruses overproduce ICP4 and other immediate-early proteins, cell lines synthesizing a mutant form of ICP4 did not overproduce this protein, suggesting that autoregulation of the lCP4 gene requires more than 30% of the infected cell level of ICP4 or, alternatively, requires the presence of other viral proteins. After superinfection in the presence of an inhibitor of protein synthesis, the endogenous ICP4 is capable of transactivating viral early genes encoding thymidine kinase, lCP6, ICP8, gB, gD, and gE. In contrast, the early gene for the viral alkaline exonuclease, the early-late gene for VP5 and the late genes for p40 and gC, respond poorly or not at all. This demonstrates that most early genes can be induced by ICP4 in the absence of other viral immediate-early proteins, but that early-late and late genes require supplementary factors.</p> / Doctor of Philosophy (PhD)

It has been demonstrated that retinal photoreception among mammals extends beyond rods and cones to include a small number of intrinsically photosensitive retinal ganglion cells (pRGCs), which are capable of responding to light due to expression of the melanopsin (OPN4) photopigment. OPN4 may have therapeutic potential if ectopically expressed in the degenerate retina in cases where photoreceptors are lost, but the other molecules involved in this light induced transduction cascade are less well characterized. Therefore I sought to probe further the mechanism of OPN4 mediated light sensitivity by siRNA mediated knock down of specific molecules in two mice models in which complete loss of rods and cones renders them almost exclusively dependent on the OPN4 pathway for light sensitivity. I generated siRNA probes against the long transcript variant of murine Opn4 mRNA and first tested these probes on the murine Neuro2A (N2a) cell line, before assessing effects in C3H/HeN rd and rodless/coneless rd/rd cl mice. siRNA was injected intravitreally into one eye and pupillometry was assessed, combined with molecular analyses at various timepoints. Reverse transcription polymerase chain reaction (RT-PCR) analysis in N2a cells confirmed Opn4 knockdown and immunolabelling techniques identified >85% silencing with siRNA. Pupil responses in the rd and rd/rd cl mice were inhibited by the siRNA injections in vivo which confirmed the functional effect of Opn4 silencing detected by molecular analysis. I therefore present a novel reproducible in vivo model in which siRNA induced silencing of the melanopsin pathway can be assessed by pupillometry and compared to levels of mRNA and protein at specific timepoints. Probes against other putative candidate genes, such as TRPC3, may unravel the molecular interactions of this pathway. This may help in future to induce light sensitivity in other retinal neurons in patients who are completely blind from photoreceptor loss.

Osteoarthritis (OA) is a common, multifactorial disease that is characterized by focal degeneration of the smooth articular cartilage in any of the synovial joints. Although the underlying molecular mechanisms for OA are still not fully understood, epidemiological studies have evidenced a significant genetic component to OA susceptibility. Genome-wide linkage scans and large-scale association studies have had success in unraveling the genetic architecture underlying OA with the identification of a number of susceptibility genes. In this work, functional analyses are reported of OA associated polymorphisms within two susceptibility genes: BMP5 and GDF5, both members of the TGF-β superfamily of secreted proteins. The extent of differential allelic expression (DAE) of BMP5 in human mesenchymal tissues was first examined with significant differences in BMP5 allelic output observed (allelic ratios exceeding 4:1 in the tissues of some donors). Significant variability in allelic expression within the different tissues of donors was also observed, suggesting that polymorphism in cis-regulation of BMP5 expression is common and that there is a considerable effect of tissue specific elements on BMP5 expression. DAE was then used as a phenotype to map tissue-specific cis-regulatory polymorphisms with the identification of a single nucleotide polymorphism (SNP) located downstream of BMP5 that was significantly associated with DAE as well as OA, suggesting that variability in cis-regulation of BMP5 is important in OA susceptibility. Moreover, the functional effect of a previously identified OA associated microsatellite within intron 1 of BMP5 was investigated using luciferase reporter assays and electrophoretic mobility shift assays (EMSAs) with significant differences observed both in the ability of various microsatellite alleles to modulate BMP5 promoter activity and to bind GATA-3 nuclear proteins, further suggesting a role for variability in BMP5 expression in OA susceptibility that may in part be due to altered GATA-3 binding. Finally, functional characterization of a previously reported OA associated SNP in the 5′ UTR of GDF5 is presented in which EMSAs show differential binding of nuclear factors between the two SNP alleles, strengthening the possible functional contribution of this SNP to OA susceptibility. Overall, this work demonstrates that polymorphism in cis-regulation is likely to play a role in OA susceptibility.

Common mycobacterial diseases, including tuberculosis and leprosy, contribute to major mortality and morbidity worldwide. Despite evidence of an important role of host genetic factors in susceptibility to these infections, few compelling genetic associations have been identified with previous candidate gene and linkage approaches. This thesis investigates the genetic factors of human immunity to these mycobacterial diseases using a high-throughput approach of association testing. To assess genetic susceptibility to tuberculosis, I have conducted a genome-wide association study in the Gambian population as part of the Wellcome Trust Case Control Consortium (WTCCC). The study reveals the region flanking CADM1 as a potential susceptibility locus. Combining this study with a Ghanaian cohort further implicates two genetic loci at chromosome 18q11.2 (P = 9.2x10⁻⁹) and PARD3B (P = 1.4x10⁻⁶). For leprosy, I have performed a gene-centric association study in the New Delhi Indian population. Evidence of significant association was observed in the HLA-DRB1/DQA1 (P = 4.9x10⁻¹⁴) and TLR1 (P = 1.7x10⁻⁹) loci. These studies identify important genomic regions that may be involved in immunity to tuberculosis and leprosy. Further analysis revealed a significant immunogenetic overlap between tuberculosis and leprosy. This provides proof-of-principle for the subsequent aggregate analysis for mycobacterial susceptibility, which suggests that the steroid biosynthesis pathway may be important in anti-mycobacterial immunity. This thesis represents one of the largest studies to identify the genetic factors for human immunity against mycobacteria. These novel findings will further enhance vaccine and pharmaceutical efforts into prevention and treatment of these mycobacterial diseases.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common heritable trait whose prevalence mirrors geographic patterns of historic malaria endemicity, is thought to confer a selective advantage owing to partial protection conferred against malaria. Direct evidence supporting this malaria protection hypothesis in the form of clinical association studies remains controversial, however, as conflicting results have been reported with respect to the strength and specificity of a protective effect, if any, conferred to carriers of G6PD deficiency-associated alleles. This thesis examines genetic diversity at the G6PD locus, and then considers how such variation impacts both immediate molecular phenotypes and multifactorial clinical phenotypes. First, Chapter 3 presents a survey of variation at G6PD in several malaria-endemic areas, while Chapter 4 describes a novel technique for polymorphism discovery using pooled massively parallel sequencing. Next, in Chapters 5 and 6, I evaluate the link between genetic variation at the locus and G6PD enzyme activity, identifying major and minor determinants of G6PD deficiency state in an association study conducted in Kenya, and demonstrating a new technique for assaying G6PD deficiency at the level of an individual erythrocyte in a pilot project in Mali. Finally, Chapter 7 addresses the malaria protection hypothesis directly by conducting a fine-mapping case-control association study of severe malaria in the Gambia, where I found that G6PD deficiency alleles exhibited differential direction of association with respect to two important clinical syndromes-- trending towards risk conferred to severe malarial anemia, and protection with respect to cerebral malaria. Overall, these findings suggest that future clinical association studies should consider heterogeneity at the genetic level, as well as at the level of molecular and clinical phenotypes in order to achieve a better mechanistic understanding of the relationship between G6PD deficiency and severe malaria.

FBXW7 encodes the substrate recognition component of an SCF E3 ubiquitin ligase complex. This complex regulates the degradation of multiple targets, such as Notch1, c-Jun, c-Myc and cyclin E, that function in critical developmental and cancer pathways. FBXW7 mutations are found in cancers of diverse tissue origins, with one of the highest mutation rates in the colorectrum. FBXW7 mutations are typically missense mutations that disrupt the substrate recognition domain at critical arginine propellor-tips. Mutations are often mono-allelic suggesting that FBXW7 is not a typical tumour supressor gene. Despite this, most of the evidence on FBXW7 function to date comes from null systems. Several Fbxw7 -null mouse models have been generated and suffer homozygous embryonic lethality due to disrupted vascular development. Conditional Fbxw7-null mice have been created but do not in general reflect the mutation spectrum found in human tumours. In order to analyse the functional effects of Fbxw7 propellor-tip missense mutations, mice carrying a commonly-occurring Fbxw7 R482Q mutation were generated. This propellor-tip mutation was knocked-in constitutively and whilst heterozygous mice developed normally in utero, they died perinatally due to defective lung development. Cleft palate and eyelid fusion defects were also observed with incomplete penetrance. Fbxw7 substrates were screened in embryonic lungs and significantly elevated protein levels of Klf5 and Tgif1 were observed. The Fbxw7 R482Q mutation was also conditionally knocked-in in the gut. In the heterozygous state, large adenomas in the small intestine were observed at a low multiplicity, in approximately 30% of mice at an age greater than 300 days. Upregulation of Wnt signalling and Ctnnb1 mutations have been identified in a selection of these tumours. Breeding the Fbxw7^R482Q allele onto Apc-mutant backgrounds led to accelerated morbidity, in which compound R482Q/Apc-mutant mice exhibited polyps of increased number and size. Elevated protein levels of Fbxw7 substrates Klf5 and Tgif1 were observed in adenoma and normal intestinal tissue from these mice. In vitro work using epitope-tagged murine wildtype and propellor-tip mutant Fbxw7 proteins showed that they were capable of dimerising, opening the prospect of investigating a dominant negative mechanism of action. To conclude, an Fbxw7 propellor-tip mutation studied in vivo resulted in both disrupted embryonic development and intestinal tumorigenesis and was distinct from Fbxw7 -null alleles.

Cerebral ischemia elicits a wide range of events, including complex activation of various intracellular signaling pathways. This study aims to investigate the expression of vascular endothelial growth factor (VEGF) and the activation pattern of mitogen-activated protein kinases (MAPK) in reponse to focal cerebral ischemia. Furtermore, the functional roles of the p38 MAPK and the Src family kinases (SFKs) are investigated with specific signal transduction inhibitors in the rat in vivo. VEGF was found upregulated in several cell types including neurons, glia and vascular cells after both permanent and transient cerebral ischemia. VEGF-receptor 1 (VEGFR1) was expressed in a similar manner, while VEGFR2 expression was more restricted and confined to endothelial cells and glia.The main MAPK pathways, including extracellular-regulated kinase (ERK), c-jun N-terminal kinase (JNK) and p38, were differentially activated by cerebral ischemia. ERK activation was present in blood vessels, suggesting a potential role in neovascularization. JNK was also activated in blood vessels in the infarcted hemisphere, possibly reflecting an interaction with ERK, whereas p38 activity was absent in vessels. In neurons, ERK was activated in cortical cells up to days of survival, while no substantial JNK or p38 activation was seen in ischemic neurons. Invading macrophages showed distinct activation of p38 and to some extent also JNK but not ERK. Glia showed activation of all MAPK to a variable extent. Pretreatment with the p38-inhibitor SB203580 before transient cerebral ischemia (ischemia-reperfusion) was investigated with magnetic resonance imaging (MRI). The experiment group suffered worse infarcts and blood-brain barrier (BBB) damage than controls, which contrasts to previous studies. The results might be attributed to interference with protective effects of the vehicle or with preconditioning mechanisms. The SFK-inhibitor PP2 significantly reduced infarct size after cerebral ischemia-reperfusion, which is consistent with previously reported effects in permanent ischemia. Due to the multifunctional role of SFKs, it cannot be easily concluded in exactly what cellular context(s) SFKs are of importance to cerebral ischemia. In conclusion, the VEGF and MAPK systems of extra- and intracellular signaling are activated in focal cerebral ischemia. Manipulation of p38 as well as SFK in vivo can influence the course of transient cerebral ischemia, which may be of significance to the understanding of the pathology of cerebral ischemia and to the development of therapeutic strategies.

Research suggests that the cyclic AMP (cAMP) signaling pathway including CREB-CRE regulated expression of various genes is implicated in the predisposition to and development of alcoholism in humans. Alcohol also induces changes in inflammatory and immune responses; these changes increase the incidence of pneumonias and other infections, which can negatively affect recovery from infections. Cyclic AMP (cAMP) is known for its immunosuppressive effects and is also required for proper development of the immune system. Previous work in our laboratory has demonstrated that ethanol enhances the activity of adenylyl cyclase (AC) in an isoform-specific manner; type 7 AC (AC7) is most enhanced by ethanol. Therefore, we hypothesize that the AC isoform expressed in the cells will play a role in ethanols effects on cAMP regulated gene expression. We further hypothesize that alcohol modulates cAMP signaling in immune cells by enhancing the activity of AC7; thus, AC7 may play a role in ethanols effects on immune function. Our objectives include: 1) evaluate the AC isoform specific effects of ethanol on cAMP regulated gene in NIH 3T3 cells by overexpressing two AC isoforms: AC3 and AC7; 2) employ immune cell lines endogenously expressing AC7, RAW 264.7 and BV-2, to further elucidate the role of AC7 in the effect of ethanol on cAMP regulated gene expression. To examine these objectives, time-lapse fluorescent resonance energy transfer (FRET) and cAMP accumulation assays were used to monitor cAMP levels within the cells. A reporter gene (luciferase) driven by an artificial promoter inducible with cAMP was utilized to evaluate the effect of ethanol on cAMP regulated gene expression. CREB phosphorylation and nuclear translocation of transducers of regulated CREB (TORCs) were examined by western blotting. Stimulation of AC activity by the addition of dopamine caused an increase in the reporter gene activity. Ethanol potentiated the increase of reporter gene activity in NIH 3T3 cells expressing AC7, while cells expressing AC3 did not respond to ethanol. Cyclic AMP pathway activation via stimulation with prostaglandin E1 (PGE1) showed an increase in cAMP and reporter gene expression in RAW 264.7 and BV-2 cells. The effect observed was potentiated in the presence of ethanol. Cyclic AMP analog, 8-Bromo-cAMP, induced luciferase activity was not significantly affected by ethanol. The level of CREB phosphorylation did not change by cAMP stimulation or in the presence of ethanol. However, there were significant changes in the TORC3 amount in nuclei depending on stimulation conditions. The results suggest that nuclear translocation of TORC3 may play a more critical role than CREB phosphorylation in the observed changes in the cAMP driven reporter gene activity. Furthermore, the ethanol effect on cAMP regulated reporter gene expression is due to a change in the amount of cAMP, which most likely results from the enhancement of AC7 activity by ethanol.

HLA-B27 and ERAP1 are the two strongest predisposing genetic factors to Ankylosing Spondylitis (AS). As a key aminopeptidase in MHC class I presentation, ERAP1 potentially contributes to AS pathogenesis through altering HLA-B27 peptide presentation. In this thesis, I first studied the effect of AS-associated ERAP1 variation on its enzyme activity in vitro. Trimming of two N-terminally extended HLA-B27 epitopes was decreased by K528R mutation; the effect of R725Q was however substrate-dependent. I also investigated the effects of ERAP1 silencing on the repertoire of peptides bound to HLA-B27 and on peptide presentation to Cytotoxic T lymphocytes (CTLs). In both HeLa.B27 and C1R.B27 cells, the proportion of 9mer peptides, the canonical MHC class I peptide length, was decreased by ERAP1 silencing whereas the percentage of longer peptides (11-13mer) was increased. Surprisingly, following ERAP1 silencing, C-terminally extended versions of 9mer and 10mer peptides were readily identified. In both HeLa.B27 and mouse fibroblasts expressing HLA-B27, ERAP1 silencing/knockout reduced recognition by KK10-specific HLA-B27-restricted CTLs following recombinant vaccinia viral infection or transfection with minigenes expressing KK10 precursors. Interestingly, KK10 CTL recognition following extended KK10 minigene transfection was reduced in the presence of the AS protective variant, K528R-ERAP1 compared to wildtype ERAP1. The effects of ERAP1 inhibition (Leucinethiol), silencing (siRNA & shRNA) and introduction in ERAAP-/- cells on cell surface HLA-B27 expression were also studied. My finding validates the role of ERAP1 and HLA-B27 interaction in AS pathogenesis indicated by GWAS. ERAP1 inhibition could potentially be used for treatment in AS and other ERAP1-associated diseases.