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Complex diseases are driven by multiple risk factors, including genetic variants, environmental exposures and interactions between the two. The advent of GWAS in 2005 and subsequent methodological advances have increased our knowledge of the genetic risk factors underpinning complex diseases. In addition, some research exploring genotype-environment interaction (GxE) effects has been conducted, revealing that multiple environments are linked to interaction effects at a single locus for a given trait. However, correlation between these identified environments renders interpretation of the results difficult. This, together with the collation of large-scale biobanks that contain a multitude of phenotypic and environmental data (facilitating an increase in the number of GxE effects detected) has generated the need for methods that jointly account for GxE at multiple environments. Such methods may also increase the power to detect interaction effects by aggregating modest or weak GxE effects across environments and in addition enable additional phenotypic variance to be explained. Thus, the aim of this thesis is to provide suitable methods to identify variants subject to GxE effects, jointly accounting for multiple environmental exposures and explore these effects across a range of phenotypes using the UK Biobank data. In Chapter 2, I describe the structured linear mixed model (StructLMM), a novel computationally efficient multivariate GxE framework. This model can be used to test for interaction or association effects. The latter accounts for possible heterogeneity in variant effects across individuals due to differences in environmental exposures, thus enabling the detection of variant effects that might otherwise be masked due to the presence of interaction effects. I show through the use of simulation experiments that StructLMM is robustly calibrated and in general, better powered than existing interaction and association tests. In Chapter 3, I present an application of StructLMM, where I identify significant interaction effects with 64 lifestyle-based factors for BMI using the UK Biobank data. In addition, I show that the StructLMM association test can be used to identify loci with genotype-environment contributions. Subsequently, I explore characteristics of loci with significant interaction effects, including the fraction of the genetic variance that is explained by GxE and the environmental profiles that increase or decrease phenotypic risk, using methods that are implemented as part of StructLMM. In Chapter 4, I apply the StructLMM interaction test to multiple cardiometabolic traits using the UK Biobank data, facilitating exploration of shared GxE architecture. Additionally, I provide preliminary estimates of the amount of phenotypic variation that can be explained by GxE effects, relative to marginal association effects. Taken together, the work in this thesis demonstrates the need and advantages of jointly modelling interaction effects at multiple environments, providing a new computationally efficient method to achieve this. Combined with the recent and ongoing generation of large biobanks, further research in this field has the potential to advance our understanding of complex traits and diseases.

The JAK/STAT pathway is a highly evolutionarily conserved signal transduction pathway, whose activation can lead to a broad range of cellular outcomes. The pathway is used repeatedly during multiple developmental stages and in adult tissue, and therefore tight regulation is required to enable accurate responses in a context specific manner. Internalisation and endocytic trafficking of signalling components provides a mechanism whereby spatial compartmentalisation can enable distinct signalling outputs. Within this study I have investigated the role of endocytosis in the regulation of the Drosophila melanogaster JAK/STAT pathway, and demonstrated that internalisation and endocytic trafficking differentially regulates target genes. Although the JAK/STAT pathway is transcriptionally competent and can regulate the expression of particular targets when the activated receptor is at the cell surface, receptor endocytosis and localisation to distinct endosomes is required for the expression of other targets. This appears to be context-dependent, as high levels of ligand stimulation overcomes endocytic regulation. STAT92E, the Drosophila JAK/STAT transcription factor, is a target of endocytic regulation. Although it is efficiently activated and undergoes nuclear translocation when endocytosis is perturbed, it is not capable of regulating a subset of target genes and therefore further STAT92E interacting partners and/or post translational modification must be required to fine-tune its transcriptional competency during endocytic trafficking. Utilising mass spectrometry I identified a novel STAT92E phosphorylation site, at threonine 702. Mutation of this threonine to prevent its phosphorylation, resulted in inhibition of STAT92E signalling and nuclear translocation, and also prevented phosphorylation of a highly conserved tyrosine residue at position 704, which is crucial for ligand activated JAK/STAT signalling outputs. Therefore, this study has enhanced our understanding of mechanisms that can modulate JAK/STAT activity. I have revealed an important role for endocytosis in fine- tuning Drosophila JAK/STAT signalling outputs and also identified a novel phosphorylation site which is crucial in the activity of STAT92E.

Craniosynostosis is a disease that afflicts approximately 1 in 2500 children worldwide. It is caused by the premature fusion of the cranial sutures which normally function as proliferation centres allowing the expansion of the skull during the growth of the brain and facial region. Affected children have major abnormalities including underdevelopment of the midface, limb defects, raised intracranial pressure, breathing problems as a result of airway restriction and severe learning difficulties. In 1994 a mutation in the Fibroblast Growth Factor Receptor 2 (FGFR2) gene was found in patients with Crouzon syndrome, one of the craniosynostoses and subsequently mutations in FGFRs 1-3 have accounted for many of these syndromes. Very little is known to date about the mechanisms which generate normal and abnormal phenotypes and in this Thesis, a model system has been used to elucidate the developmental pathways responsible. A grafting technique has been used to manipulate developing embryonic chick crania and perturb morphogenesis. Implantation of beads soaked in the ligand FGF-2 did not affect normal cranial development at biological concentrations. In the limb bud however, these same beads elicited dramatic changes in morphogenesis demonstrating that these beads are biologically active. Implantation of beads soaked in a neutralising antibody to FGF-2 resulted in a graded response. When a single bead is implanted thereby reducing the active levels of endogenous FGF-2 protein, the grafts grew to a massive size as a result of increased cell division in the tissue. By using a technique to detect proliferating cell nuclei immunohistochemically it is clear that in these large grafts almost all nuclei are undergoing cell division whereas in control grafts the opposite is the case. With greater inactivation of FGF-2 protein (2-3 antiFGF-2 loaded beads implanted) further bone differentiation was blocked and the level of cell proliferation was reduced below background levels. It is proposed that a multi-stage signalling cascade operates within the skull such that at low levels of FGF, proliferation occurs and at higher levels, these cells are further induced to differentiate into bone. Conversely, when FGF is blocked and the amount available to receptors is reduced, cranial bone morphogenesis is prevented. These results relate to the clinical situation since the majority of mutations in FGFRs in patients with craniosynostosis are thought to result in increased receptor activation equivalent to an increase in FGF signalling. Hence the effect is premature differentiation of cranial sutures into bone.

This study is an exploratory evaluation of a multi-support peer mentoring process for young people with disabilities. Peer mentors, who were 4 young adults with a range of disabilities, made weekly phone calls to 12 young adults with disabilities as part of the Project TEAM intervention. The peer mentors had two primary methods of support: 1) a script with verbatim instructions of what to say, and 2) a supporter, who provided one on one support during the process. In total, there were 82 phone calls between 12 mentor trainee dyads. The audio for these calls was independently coded by 2 raters for the following criteria: mentor achieving objectives, mentor using the script, mentor using the supporter and trainee demonstrating engagement. The frequency of each code was transformed to a percentage to allow for comparisons between mentors. The evaluation found that mentors achieved a high percentage of objectives, that trainees in the program were consistently engaged, and that each peer mentor used supports in a unique way. A chi square found that there is a significant relationship between using supports and achieving objectives. The significance appears to be driven by a larger than expected number of peer mentors who did not meet objectives when not utilizing supports. Overall, the evaluation found that young people a range of disabilities can serve successfully as peer mentors when given support and that young people with disabilities can engage in a phone based mentoring process. This study can help inform future revisions to the peer mentoring program by tailoring the types of supports to each mentors individual preferences.

Background: The purpose of this study was to examine the impact of a culturally sensitive, cognitive-behavioral family treatment (CBFT) for pediatric patients with Sickle Cell Disease (SCD) to improve pain symptoms, health-related quality of life, functionality, depression, and coping strategies. Individual cognitive-behavioral treatment has been shown previously to be effective at improving pain symptoms, functionality, adaptive coping, and health care utilization, but such benefits have not yet been shown for SCD patients. The present study aimed to address this limitation by modifying the intervention to both include the family and to utilize culturally sensitive practices, which may be particularly relevant for this population. Methods: A non-concurrent multiple baseline design was used to assess the effectiveness of the intervention. A sample of 4 children (ages 8 to 12) and 4 adolescents (ages 13 to 15) participated in the intervention. Manualized treatment consisted of five sessions (including child and parent) that targeted problem-solving skills, cognitive processes, coping strategies, goal setting, and family processes. Outcomes of interest including health-related quality of life, functionality, psychological adjustment, and coping strategies, were assessed by child and parent report at pre-treatment (baseline), post-treatment, and 2-, 4-, and 6-month follow-up. Participants completed daily diaries to quantify pain, anxiety, and functionality. Results: Repeated-measures general linear model analyses were run separately for all outcome variables. A significant main effect of time was found for youth-reported HRQoL, F(4, 20) = 4.6, p=.01, depressive symptomatology, F(4, 20) = 4.5, p=.01, and parent-reported Internalizing, F(4, 16) = 3.4, p=.03, Externalizing, F(4, 16) = 7.2, p=.00, and Total Behavior Problems, F(4, 16) = 7.7, p=.00 from baseline to 6-month post-treatment. The mean frequency of pain symptoms also decreased for five of the eight participants (i.e., visual inspection of the daily diaries from baseline to treatment). Conclusions: These results suggest the potential for clinical gains through the incorporation of culturally sensitive and family-based practices into existing cognitive-behavioral interventions for SCD. The symptomatic improvements observed in the present study indicate gains in both specific domains (i.e., pain), as well as general psychological outcomes (i.e., improvements in depression, health-related quality of life, internalizing and externalizing behaviors).

The substantial emotional impact of trauma on children, adolescents and their caregivers has been amply documented within the general disaster literature. However, research addressing the specific psychological impact of residential fire on child and family functioning is still considered to be in its infancy. The present study adapted the Transactional Stress and Coping (TSC) model for this purpose. This was an extension of the TSC model from the child chronic health to the trauma literature. The TSC model proposes that child and adolescent adjustment (i.e., in the present study, symptoms levels of PTSD, depression, anxiety) following a residential fire will be mediated by both child and adolescent adaptational processes (i.e., cognitive appraisal and coping methods), as well as family processes (i.e., family conflict and parent psychopathology). While the TSC was not supported, several preliminary results were found. Results indicated that family conflict (β = .289, p < .05) may have mediated the relationship between children’s overall adjustment at 4-months and parent-report of child internalizing symptoms at 11-months post-fire (β = .235, p > .05). Avoidant coping strategies (β = .294, p < .05) also may have mediated the relationship between child anxiety/depression at 4-months and PTSD symptoms at outcome (β = .246, p > .05). Furthermore, an interaction effect was found between parent report of child and adolescent internalizing symptoms and children and adolescents’ self-reports of religious avoidance. Finally, a moderation effect was also found between children and adolescents’ self-reports of their overall adjustment and self-reports of their active coping strategies. These results suggest a transactional relationship among family environmental variables and individual child adaptational processes which may predict adjustment outcomes.