Bibliography: leaves 116-130. / Hereditary macular degeneration describes a group of conditions causing macular pathology. Stargardt disease (STGD) is the most common inherited juvenile macular dystrophy characterised by severed reduction of central visual acuity and normal peripheral vision. The ABCA4 (adenosine triphosphate binding cassette transporter) gene is the only gene implicated in the autosomal recessive (ar) form of the STGD phenotype, while one genetic locus and one gene have been shown to be causative of the autosomal dominant form.

Includes bibliographical references (p. 231-279). / It is generally accepted that a linear relationship exists between heart rate/ workload and oxygen consumption and that heart rate thus accurately reflects workload and exercise intensity. As such, coaches and athletes commonly use heart rate to prescribe exercise and monitor changes in training status. Some studies have however, indicates that heart rate may not always be an accurate indicator of training status under all conditions, due to the possible influence of other variables. However, as measuring heart rate has been shown to be a reliable, accurate, inexpensive and practical method to monitor changes in training status, the purpose of this study was therefore to further explore ans clarify the heart/ workload relationship under a variety of different trainig and testing conditions.

Includes bibliographical references / Background: Mental health disorders represent a major public health problem in most countries around the world. In South Africa, the lifetime prevalence of psychiatric disorders is 30.3%, with substance-use disorders and mood disorders being the second and third most prevalent classes of lifetime disorders, respectively. Bipolar disorder (BD) has a lifetime prevalence of 1.4% and alcohol use disorder (AUD) a lifetime prevalence of 30.3%, and they are frequently comorbid. Both of these disorders have a relatively high heritability, yet the exact genetic basis of each remains unknown. Genetic variants within the hypothalamic-pituitary-adrenal (HPA)-axis and glutamatergic pathways have previously been implicated in both phenotypes. The aim of this project was to investigate the aetiology of BD and AUD, using high-throughput genomic technologies, bioinformatics, brain-imaging and environmental measures. An additional aim was to assess the genetic aetiology of BD-AUD comorbidity. Methods: For the genetic analysis underlying BD, a South African 'Afrikaner' family was investigated. Whole-genome sequencing (WGS) and whole-genome linkage analysis was performed for individuals with BD Type I (BDI) and unaffected family members using the Illumina HiSeq2000 and Affymetrix Axiom TM Genome-wide CEU 1 Array, respectively. For the AUD analysis, two groups were investigated; a South African adolescent group comprising 80 individuals with AUD and 80 controls, and a group of 8123 individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort. The South African group of adolescents were genotyped using the Illumina Infinium iSelect custom 6000 BeadChip, childhood trauma data was obtained and brain magnetic resonance images were collected for a subset of this group. Genotype data on HPA-axis genes were obtained from a previous study for the ALSPAC cohort. The fourth group of individuals investigated in this thesis comprised 233 individuals with BD-AUD comorbidity from the Systemic Treatment Enhancement Program for BD (STEP-BD). Genotype data for genes from the glutamatergic and HPA-axis pathways were obtained from a previous study conducted on these individuals. Results: The chromosomal regions 6p25, 10p14-10p15.1, 11q23-11q25, and 13q21-22 scored the highest LOD scores for BD and the most over-represented pathway in the affected family members was the T-cell receptor signalling pathway. In the South African adolescent group, circadian rhythm genes were associated with AUD and childhood trauma predicted alcohol use in adolescence. The gene-imaging analysis identified a SNP in the glutamate receptor, ionotropic, N-methyl D-aspartate 2B (GRIN2B) gene as being associated with brain volume in the left orbitofrontal cortex and posterior cingulate. HPA-axis genes did not show an association with AUD and no significant gene x environment interactions were detected for AUD in the ALSPAC cohort. Single variants in the glutamatergic genes and HPA-axis were not associated with BD-AUD comorbidity. However, from the gene-based analysis, the glutamatergic gene PRKCI was associated with BD-AUD comorbidity. Conclusions: It appears that disruption in immune-related genes may contribute to the development of BD in an Afrikaner family. No significant gene x environment interactions were detected for adolescent AUD. The circadian pathway and childhood trauma may play a role in the development of adolescent AUD. Differential brain volume and BD-AUD comorbidity may be characterised by variation in the glutamatergic pathway. These pathways and the interactions between them should be further investigated in BD and AUD.

Includes bibliographical references (leaves 200-220). / The main aims of the series of studies comprising this thesis were to investigate the effect of altered endogenous carbohydrate (CHO) availability, achieved primarily by pre-exercise dietary manipulation and antecedent exercise exposure, on interindividual variability in metabolic and hormonal responses to dynamic, steady-state exercise. Further, this thesis examined the impact of altered blood glucose availability on fatigue development during prolonged exercise. In this regard, it was hypothesized that endogenous CHO availability and the associated metabolic sequelae would impact on effort perception during exercise and fatigue development.

Includes bibliographical references (p. 235-243). / The aim of this thesis is to evaluate both abnormal and normal fluid balance during exercise. The central theme permeating all investigations is an underlying desire to understand exercise-associated hyponatremia. This thesis reflects a journey of scientific investigation primarily launched by outcomes from the 1st International Consensus Development Conference on Exercise-Associated Hyponatremia. Each individual investigation directly follows from the results of the previous investigation. Hence, the journey towards a greater understanding of exercise-associated hyponatremia went full circle and ultimately encompassed the spectrum of fluid regulation and dysregulation during exercise. This thesis begins with a brief overview of the literatur which services to intertwine previous knowledge with new knowledge gained from each successive study. A review of the literature on exercise-associated hyponatremia opens the first chapter and lays the foundation for the follwoing eight investigations. This thesis closes with a final summary of the literature which defends fluid balance physiology as the ultimate guide for developing more "physiologically appropriate" fluid replacement strategies. More specifically, the first two chapters document the abnormal regulation of serum sodium concentration during exercise.

Hearing Loss (HL) is one of the highest contributors to disability worldwide. The highest incidence of the disease is seen in developing countries, such as those in subSaharan Africa (SSA). Patients affected with disabling HL are reported to be more than 466 million worldwide. The causes of HL can either be environmental or genetic with each contributing about 50% towards all cases, in many settings. In developing countries, the environment might contribute more due to poor health services and infrastructure available to the population. In the absence of environmental causes, there is a genetic component at play, that is largely unknown in African populations. Up to 70% of HL of genetic origin are non-syndromic (NS). The mode of inheritance is recessive in nearly 77% of non-syndromic HL. Up to date, more than 100 genes have been associated with HL harbouring more than 1000 causative variants. In many populations of European and Asian descent, pathogenic variants in GJB2 (connexin gene 26) and GJB6 (connexin gene 30) are a major contributor to autosomal recessive non-syndromic hearing loss (ARNSHL). Comprehensive hearing health care programs should cover genetic causes by providing molecular testing, and genetic counselling, specifically SSA where genes and mutations causing HL remain largely unknown. The aim of this project was thus to uncover the genetic causes of HL among patients’ cohorts from Cameroon and South Africa. This was addressed by 1) sequencing common variants in the most relevant genes in other populations (GJB2 and GJB6), 2) using a targeted gene panel to resolve HL in 10 multiplex families from Cameroon presenting with ARNSHL and negative for GJB2 and GJB6 mutations screening, 3) screening novel variants found in known genes in a cohort of 82 singleplex HL cases from Cameroon and South Africa, and lastly, 4) using Whole Exome sequencing to explore the two unresolved multiplex cases with and subsequent findings confirmed by functional studies, and also screened in 80 singleplex HL cases. The following findings are reported: GJB6, GJA1 mutations screening and literature review No GJA1 or GJB6 mutation was not found in multiplex and simplex cases of HL in both Cameroonians and South Africans. The review of the literature confirms that the prevalence of GJB2- or GJB6-related NSHL is approximating to zero in most subSaharan African populations. Targeted Exome Sequencing (OtoSCOPE) The targeted genes, panel that included 116 genes, was able to resolve 7 of 9 families (77.8%) which were successfully sequenced, with one family failing to be sequenced. The causative variants identified in the 7 resolved families were : 1) compound heterozygous c.5806_5808delCTC and c.5880_5882delCTT in MYO7A; 2) compound heterozygous c.646T>A (p.Phe216Ile) and c.38G>A (p.Arg13His) in LOXHD1; 3) homozygous c.766-2A>G in OTOF; 4) a deletion and a complex copy number variation in STRC; 5) compound heterozygous c.1678G>A (p.Asp560Asn) and c.2007C>A(p.Asp669Glu) in SLC26A4; 6) Homozygous c.1996C>T(p.Arg666Stop) in MYO7A; 7) compound heterozygous c.6399C>A(p.Asp2133Glu) and c.2000T>C (p.Met667Thr) in CDH23. Five out of 12 variants were novel. Screening of these causative variants in known genes, in 82 singleplex HL cases from Cameroon and South Africa was unable to resolve any of the cases: the variants were in either heterozygous in low frequency or absent. Bioinformatic pathways exploration of SNP data of known HL genes revealed an extensive network within the HL genes, with 10 identified as important nodes, including MYO7A. Most HL genes were found to be involved in two biological processes which were sensory perception of mechanical stimulus (GO: 0050954, p= 1.430e-8) and sound (GO: 0007605, p = 1.246e-8). The molecular functions of variants found within these genes were found to mostly fall within the binding (GO: 0005488) and/or structural molecule activity (GO: 0005198). Whole Exome sequencing Whole exome sequencing was performed on four of the nine multiplex families: the two families that were unresolved by targeted panel sequencing, and two previously resolved families that were used as positive controls for the variant annotation and filtering pipeline. The results were the resolution of 3/4 families, including the two- positive control. The previously unresolved “family 8” was found to harbour a novel variant within the GRXCR2 gene, a gene only associated with HL once before. The c.251delC variant was revealed through in silico studies to cause a premature stop codon at position 116 due to its frameshift effect. The screening of this variant in our cohort of 80 singleplex cases revealed one other unrelated HL patient harbouring this causative variant. Due to the limited literature on the gene and its protein, in silico studies were used to show the predicted secondary structure folding of the protein as well as potential protein binding regions. Analysis showed that the predicted loss of a stable region of the protein as well as that of a putative binding domain could explain the pathogenic nature of the variant. In vitro studies showed that the variant hindered the detection of the protein by way of a DDK tag downstream in the plasmid. Additionally, GFP-Tagged GRXCR2 showed altered expression pattern in the variant when compared to the wildtype. In summary, our data has revealed the efficacy of using next generation sequencing tools in resolving HL among sub-Saharan African patients as opposed to the single candidate gene approach. In our quest, we have employed two widely used strategies, targeted panel and whole exome sequencing (WES), both of which have had great successes in various populations. The targeted approach was able to resolve 77.8% of our families but did not detect variants for two of the families revealing the presence of other variants harboured in rarely associated gene not captured or included on the panel. This prompted for the use of a more comprehensive approach such as WES. These results corroborated with those of two families previously resolved by targeted exome sequencing. Additionally, one of the previously unresolved family was now resolved. This showed that WES was sensitive enough to detect variants in known HL genes but comprehensive enough to detect variants in other regions of the exome which have not been associated with HL or rarely associated with HL. The benefit of WES also extends to the contribution of exomic data from patients of African descent as there is an underrepresentation of this group in exome repositories as well as genomic or SNP databases. To the best of our knowledge, this is the first study to use WES to resolve HL in patients of African descent. The other benefit of such a venture is the use of this data not only for patients in SSA but also those in the diaspora. In conclusion, we have successfully demonstrated the feasibility of using NGS tools in identifying causative variants in HL patients in SSA. Additionally, we have shown that WES is a more suitable approach to trying to resolve HL in Africa. Therefore, the data strongly support that genetic studies on families segregating HL in SSA could be the next frontier of HL genetic research, of global importance through discovering novel variants in known genes, and potentially novel genes. These studies will improve HL genetic diagnosis, retrospective counselling and testing, prevention and care including future prediction of treatment outcomes in sub-Saharan Africans, and in people of African descent.

Bibliography: leaves 162-190. / The present study was initiated with the aim of elucidating the molecular genetic basis of the RP phenotype segregating in a large SA family of British origin. The family is one of the largest pedigrees from which DNA is archived in the Department, and the pedigree structure and ADRP phenotype will be discussed in detail in chapter two.

Includes abstract. / Includes bibliographical references (p. 221-240). / Current evidence indicates that schoolboy cricketers are at a high risk of injury to the lumbar spine. This is particularly relevant in the case of fast bowlers who bowl with a high degree of shoulder counter-rotation. There, however, is a lack of evidence in the literature with respect to injury research of all cricketing disciplines, as fast bowlers receive the most attention. After reviewing the literature it was evident that the effect of a cricket-specific lumbar stabilisation exercise intervention in an attempt to reduce lower back pain and alter other physiological variables, had never been studied. Previous interventions in cricketers have focused only on fast bowlers in an attempt to decrease the degree of shoulder counter-rotation. However, these studies either took two years to observe a decrease or were unsuccessful.

Includes abstract. / Includes bibliographical references. / Ingestion of a high carbohydrate (CHO) diet (7-10 g CHO/kg body mass) for 3 days, typically referred to as ‘CHO-loading’, is a commonly recommended dietary practice for endurance sporting events lasting >90 minutes. CHOloading effectively maximizes muscle glycogen stores and has been shown to enhance prolonged exercise performance. However, the body’s glycogen stores are limited, therefore a dietary strategy that would not only increase CHO availability but also ‘spare’ muscle glycogen during exercise may be more beneficial during prolonged exercise compared to a standard CHO-loading diet. Preliminary studies in which athletes ingested a high fat diet (4-4.6 g fat/kg body mass) for 5-6 days followed by 1 day of CHO-loading have been shown to increase fat oxidation and ‘spare’ muscle glycogen during prolonged exercise compared to a high CHO diet. However, the effectiveness of a high fat diet followed by CHO-loading has not been tested in self-paced endurance and ultra-endurance events. Further, there is little available evidence concerning the pre-event habitual dietary practices of ultra-endurance athletes. It is possible that athletes and cyclists competing in endurance and ultra-endurance events have diets which may differ in macronutrient content compared to that typically recommended for endurance events. As a result, athletes may not respond in a similar way to diets typically recommended for endurance and ultra-endurance events, such as CHO-loading. The aims of this thesis were therefore: (1) to characterize the habitual dietary intakes of sub-elite male cyclists before and during an ultra-endurance event; (2) to investigate the effects of different dietary strategies aimed at increasing carbohydrate availability and ‘sparing’ muscle glycogen (e.g. CHO-loading and fat-adaptation), on substrate utilization and exercise performance during simulated endurance and ultra-endurance exercise; and (3) to investigate the individual responsiveness of athletes to these dietary strategies.

Includes bibliographical references. / Prospective motion correction methods using an optical system, diffusion-weighted prospective acquisition correction, or a free induction decay navigator have recently been applied to correct for motion in diffusion tensor imaging. These methods have some limitations and drawbacks. This article describes a novel technique using a three-dimensional-echo planar imaging navigator, of which the contrast is independent of the b-value, to perform prospective motion correction in diffusion weighted images, without having to reacquire volumes during which motion occurred, unless motion exceeded some preset thresholds. Water phantom and human brain data were acquired using the standard and navigated diffusion sequences, and the mean and whole brain histogram of the fractional anisotropy and mean diffusivity were analyzed.