Mseleni Joint Disease (MJD) is a crippling osteoarthropathy of unknown aetiology endemic to southern African Bantu-language speakers in a remote region of Northern KwaZulu-Natal, South Africa. Effective management of MJD has been hindered by limited insight into risk factors, explanatory models or treatment-seeking behaviours in those affected. Until MJD is better understood, disability, unemployment and dependence on social assistance grants and family income for subsistence will remain a reality for those affected. A mixed methods study was conducted with the aims of examining risk factors, explanatory models and treatment-seeking behaviours associated with MJD. The distribution, differential diagnosis and treatment of MJD were statistically analysed using medical records (n=723), MJD-patient surveys (n=37) and a meta-analysis. Socio-economic and cultural risk factors were assessed from surveys (n=99) and census publications. Interviews with MJD patients (n=6), nurses (n=7) and doctors (n=9) were qualitatively analysed for themes pertaining to perceptions, experiences and treatment-seeking for MJD. A point prevalence of 9% was estimated. Women were nearly twice as likely to have MJD than men (OR= 1.89; p=0.03) and the likelihood of MJD increased almost three-fold in those older than 50 years (OR= 2.83; p<0.01). Age was a confounder of the association between gender and MJD, as the sample was skewed in the representation of elderly women. MJD was only detected in patients older than 35 years, indicative of a later onset age than previously reported. The prevalence of MJD in settlements along tar and concrete roads, with access to public transport but limited piped water was suggestive of environmental risk factors or differential access to hospital-based care. Explanatory models of MJD were supernatural (witchcraft or ancestral displeasure); natural (nutritional deficiencies, 'genetics' and/or environmental); and/or social (gender-based practices and lifestyle). MJD patients described supernatural and natural aetiologies, and conceptualised disability as an inevitable reality. Consequently, patients reported taking few measures to prevent joint immobility, focussing instead on immediate symptomatic relief. Psychosocial and systemic barriers to treatment were suggestive of a disconnect between traditional African healing and Western biomedicine. This work demonstrates the value of the biocultural approach in identifying spatial, ecological, social and cultural processes that shape population patterns of health and disease.

Includes abstract. / Includes bibliographical references (p. 203-244). / The aetiology of obesity is complex, and in addition to intrinsic factors such as the biology of individuals (presented as genetics, age, gender) that contribute to the high obesity epidemic, there are behavioural determinants, along with economic, socio-cultural and environmental factors which are largely extrinsic, that either directly or indirectly influence the development of obesity, therefore are called “obesogenic” (Swinburn et al., 2005; Egger and Swinburn, 1997). In South Africa, these “obesogenic” factors have been only partially explored, and as such, there are gaps in our knowledge. We are also not certain of the extent to which the language, culture and age influence these afore-mentioned factors. As such, this dissertation focused on finding and adapting culturallysensitive and age-appropriate instruments to better understand these obesogenic factors in South African women and girls.

Bibliography: leaves 170-187. / Osteological, dental, and molecular analyses were conducted on remains from seven historical archaeological sites within South Africa. The emphasis was on the collection of lifestyle data for the purpose of adding to the unwritten history of indigenous South African peoples and to give voice to a once forgotten group of peoples. The demographic distribution reveals three different community dynamics: the Griqua sample are a pastoralist group incorporating some agricultural activities, the Colesberg individuals are an indigenous group resembling a migrant workers population living on the margins of society, and the Wolmaransstad demographics are suggestive of a Zabantu labouring community. All individuals are relatively healthy with low rates of dental disease and trauma and share similar growth patterns to living populations. However all of these individuals display high frequencies of porotic hyperostosis and cribra orbitalia, skeletal manifestations of iron deficiency anaemia. Many theories about the occurrence of anaemia are discussed and the hypothesis that, in these individuals, it is related to infection by the smallpox virus is investigated through the analysis of ancient DNA.

Includes bibliographical references (p. 228-241). / The present thesis examined the hypothesis that self-paced exercise performance and pacing strategies are regulated by a complex intelligent system in advance of a failure to maintain homeostasis in one or more physiological systems. In the first study, ten trained cyclists performed 20 km cycling time-trials in hot (35°C) and cool (15°C) conditions. The power output was reduced in the heat despite core temperatures that were sub-maximal and not different from those measured in the cool condition. Significantly, the reduction in power output was associated with a lower IEMG activity in the active muscle, suggesting that the brain recruited less muscle even at sub-maximal body temperatures. Thus, self-paced exercise in the heat was regulated in advance of thermoregulatory failure. This model was then applied to conditions where the oxygen content of the air was elevated (yperoxia). Eleven subjects performed 20km time-trails, and it was found that a higher power output was maintained throughput hyperoxic (F₁O₂0.21), and that the IEMG activity was elevated in hyperoxia. The subjective rating of perceived exertion (RPE), measured using the Borg scale, was similar in both this and the first study, despite differences in power output. It was suggested that the RPE may play a mediatory role.

Includes bibliographical references (p. 216-249). / The temperature responses to exercise have been a much investigated topic of intense research interest over the past 50 years. More recently, the effects of fluid ingestion on temperature regulation have been the focus of this area. The aim of this thesis is to undertake research to evaluate what has become the established dogma in this field and to determine whether a new model might better explain thermoregulation in humans during endurance exercise.

Includes bibliographical references (leaves 115-128). / Generally, the factors contributing to success or failure of axon regeneration lie in the intrinsic properties of the injured neurons, as well as the surrounding microenvironment of the transected axon. Mammalian neurons may lack the intrinsic ability to survive after trauma, or to re-express genes required for axonal regrowth. Moreover, several proteins inhibitory to neurite growth, such as Tenascin-R (TN-R) and Nogo-A, have been identified in mammals. These proteins are associated with oligodendrocytes and myelin and are considered major inhibitory components of the CNS environment.

Includes bibliographical references. / Musculotendinous stiffness or elasticity is difficult to measure in vivo. Therefore, various procedures have been used in an attempt to quantify the contribution of the elastic properties of muscle and tendon to stretch shortening cycle performance. The results are variable, perhaps as a result of the different techniques utilised. Although several studies have suggested an association between a more compliant muscle-tendon complex, and enhanced stretch shortening cycle performance, this interpretation is not conclusive and needs further testing with particular attention being focused on the non-invasive, in vivo measurement of musculotendinous stiffness. Accordingly, the primary goal of this dissertation was to identify the relationship between the mechanical characteristics of the muscle-tendon complex, in particular tendon stiffness, and stretch shortening cycle muscle function.

Includes bibliographical references (p. 177-213). / The aim of this thesis was to examine the effect of various antecedent exposures and physiological pertubations on the relationship between the perceptual (perceived exertion), the physiological (metabolic milieu), and the performance (overall exercise performance) during both open and closed loop exercise at either a self-placed or constant workload.

Activity-based training (ABT) represents the current standard of care in neurological rehabilitation centers around the world. However, innovative rehabilitation techniques have been developed including robotic locomotor training (RLT). The conceptual basis for RLT initially appeared promising; a rehabilitation modality that removes the need for intensive assistance from therapists, whilst facilitating safe and effective over-ground ambulation. However, small sample sizes and a lack of homogeneity across studies have resulted in an underpowered evidence base supporting the efficacy of RLT for SCI rehabilitation. Thus, this randomized control pilot study aimed to investigate the effects of RLT compared to ABT on functional capacity, secondary complications, and psychological well-being in people with SCI after 24-weeks of rehabilitation. Participants with chronic, traumatic motor incomplete SCI were randomized into two intervention groups: RLT (n = 8) and ABT (n = 8) groups. RLT involved solely walking in the Ekso bionic suit. ABT involved a variety of resistance, cardiovascular and flexibility training combined with regular weight-bearing in the standing position. Outcome measures, including functional strength, ambulatory function, pain, spasticity, bladder/bowel, bone density, body composition, quality of life (QoL) and depression were tested at baseline, 6, 12 and 24-weeks of the intervention. There were no significant differences between the intervention groups for lower or upper extremity motor scores (UEMS effect size (ES) = 0.30; LEMS ES = 0.07), back strength (ES = 0.14) and abdominal strength (ES = 0.13) after training. However, both groups showed a significant increase of 2.00 points in UEMS and a significant increase in abdominal strength from pre- to post intervention. Only the RLT group showed a significant change in LEMS, with a mean increase of 3.00 [0.00; 16.5] points over time. Distance walked in the Functional Ambulatory Inventory (SCI-FAI) increased significantly (p = 0.02) over time only for the RLT group. Therefore, the RLT showed promising evidence for potentially inducing functional strength changes and improvements in ambulatory function after 24 weeks of training. There was some evidence to support RLT to induce bowel improvements in individuals with SCI and both interventions appeared to reduce urinary incontinence and improve bladder function (p = 0.04). Total spasticity and pain intensity were similar between groups (p = 0.25; p = 0.96). However, pain interference ratings significantly increased from pre-post intervention for both groups (p = 0.05). RLT prevented the progressive decline of bone mineral density usually occurring in the SCI population, as hip BMD was maintained during RLT; however, it was significantly reduced (p = 0.04) during ABT, with a mean reduction of 0.06 [-0.34, 0.22] g/cm2 (5%) from pre to post intervention. No change in leg fat-free soft tissue mass (FFSTM) occurred between groups or over time (p = 0.32), however, there was a significant 7% increase in arm FFSTM over time for both groups (p < 0.01). The ABT group was more effective (ES = 1.02) in reducing central and peripheral adiposity, with a significant decrease in visceral adipose tissue (VAT) (p = 0.04) and gynoid FM (p = 0.01) over time. Both groups reported increased QoL and decreased depression ratings over time, with the RLT group having a significant change in the general life and physical health domains, p = 0.03, respectively. This pilot trial offers promising evidence for the effectiveness of RLT for improving functional and ambulatory capacity, reducing secondary complications, and potentially improving QoL in people with incomplete SCI. Thus, this dissertation adds substantial weight to the lacking evidence base on the effects of RLT, by incorporating a large homogenous sample, comprehensive testing procedures and an extended intervention period within South Africa.

Background: Several variants have been associated with the risk of musculoskeletal soft tissue injuries, suggesting a role for genetics in the aetiology of chronic Achilles tendinopathy (AT) and anterior cruciate ligament (ACL) ruptures. Genetic risk modifiers have primarily been identified using a hypothesis driven candidate gene approach. However, the ability to identify all risk-conferring variants using this approach alone is limited. Therefore, the primary aim of this thesis was to further define the molecular signatures of musculoskeletal soft tissue injuries mapping to specific genes. The genes encoding the tenascin-C glycoprotein (TNC, chromosome 9), the α1 chain of type XXVII collagen (COL27A1, chromosome 9), matrix metalloproteinase 3 (MMP3, chromosome 11) and the α1 chain of type I collagen (COL1A1, chromosome 17) were previously associated with the risk of injury and were therefore prioritised for further interrogation. Variants within these regions, which had either been previously associated with injury risk or prioritised from the list of new candidates identified by whole exome sequencing (WES) through the application of a customised tiered filtering strategy, were genotyped in several self-identified white AT and ACL rupture cohorts. The second aim of this study was to determine whether the observed risk-associated variants in the self-identified white cohorts were similar to those underpinning injury in the ancestrally admixed South African Coloured cohort, using ACL ruptures as the phenotypic model. The specific objectives of this thesis were: • To select well-phenotyped participants to be sequenced using an extended whole exome sequencing platform • The development and application of a reusable bioinformatics analyses pipeline involving a customised, tiered filtering strategy to select candidates for interrogation from the list of variants identified by WES. The TNC, COL27A1, MMP3 and COL1A1 genes were prioritised for further interrogation using this approach. • To test the association between the selected candidate variants and the risk of chronic AT and ACL ruptures using a case-control genetic association study design. The candidates selected from the list of variants identified by WES included: TNC rs1061494 (T>C), rs2104772 (T>A) and rs1061495 (T>C) and COL27A1 rs2567706 (A>G), rs2241671 (G>A) and rs2567705 (A>T). In addition, several variants previously associated with the risk of injury including TNC rs1138545 (C>T), MMP3 rs3025058 (5A>6A), rs679620 (G>A), rs591058 (C>T) and rs650108 (G>A) and COL1A1 rs1107946 (G>T) and rs1800012 (G>T), were also prioritised for investigation in additional injury cohorts. • To functionally annotate the prioritised variants using a host of in silico bioinformatic analyses tools. Methods Whole exome sequencing and data processing: Ten asymptomatic controls and ten chronic AT cases were selected for sequencing. Controls were older than 47 years of age, were physically active and had not reported any previous tendon or ligament injuries. Cases were younger than 35 years of age, had suffered chronic, bilateral Achilles tendinopathy and/or reported several Achilles tendon injuries. Paired-end WES was performed on the Illumina HiSeq 2000/2500 platform at 30X coverage. A customised, tiered filtering strategy was developed to screen for candidate variants. All candidate variants were confirmed using Sanger Sequencing and genotyped, together with the other prioritised variants in the larger injury cohorts. Case-control genetic association studies Achilles tendon injury cohorts: Three cohorts were independently recruited from South Africa (SA), Australia (AUS) and the United Kingdom (UK). The South African White (SAW)- Achilles tendon injury cohort consisted of 165 controls (SAW-CONAT), 123 cases with chronic Achilles tendinopathy (SAW-TEN) and 47 cases with acute Achilles tendon ruptures (SAWRUP). The UK-Achilles tendon injury cohort consisted of 130 controls (UK-CON), 87 cases with chronic Achilles tendinopathy (UK-TEN) and 35 cases with acute Achilles tendon rupture (UKRUP). The AUS-Achilles tendon injury cohort included 210 controls (AUS-CON) and 85 cases with chronic Achilles tendinopathy (AUS-TEN). Anterior cruciate ligament rupture cohorts: The first ACL rupture cohort consisted of 232 control participants (SAW-CONACL) and 234 cases with surgically diagnosed ACL ruptures (SAW-ACL), of which 135 were reportedly non-contact in mechanism (SAW-NON). All participants in this group were self-identified to be of South African White ancestry. The participants in the second South African ACL rupture cohort were of mixed ancestry and self-identified as being South African Coloured (SAC). This group consisted of 100 controls (SAC-CON) and 97 participants with surgically diagnosed ACL ruptures (SAC-ACL), of which 50 were reportedly non-contact in mechanism (SAC-NON). The TNC and COL27A1 genomic intervals were explored through the TNC rs1061494, rs1138545, rs2104772 and rs1061495 variants and the COL27A1 rs2567706, rs2241671 and rs2567705 variants in the SAW- and UK-Achilles tendon injury cohorts, in addition to the SAWand SAC-ACL rupture cohorts. The MMP3 locus was explored using the previous riskassociated rs3025058, rs679620, rs591058 and rs650108 variants in the AUS-Achilles tendon injury and SAW-ACL rupture cohorts. Chapter 5 explored the COL1A1 locus using the previous risk-associated COL1A1 rs1107946 and rs1800012 variants in the SAW- and UK-Achilles tendon injury cohorts, in addition to the SAW-ACL rupture and SAC-ACL rupture cohorts. Statistical analyses were performed using the R programming environment, with statistical significance set at PC) variant is predicted to overlap the sequence motifs of the muscle initiator nuclear protein, members of the myogenic family of transcription factors and RNA polymerase II subunit A. Furthermore, the rs1061494 variant demonstrated marked differences in its predicted pre-mRNA structure. The other TNC variant associated with injury risk, rs2104772 (T>A), was predicted to be deleterious by two independent annotation tools. The investigated COL27A1 variants were suggested to interact with several predicted enhancers of cellular function. However, this gene is still relatively uncharacterised in musculoskeletal soft tissue injuries, and therefore, these variants will require further interrogation. The 8kb MMP3 genomic interval demonstrated high levels of linkage disequilibrium. Furthermore, MMP3 was predicted to interact with the MMP12 gene mediated by chromatin looping. The COL1A1 rs1800012 (G>T) variant overlaps the recognition sequence of the Sp1 transcription factor in intron 1. This variant is also proposed to interact with the functional promoter variants, rs1107946 (G>T) and rs11327935 (indel/T). This interaction is suggested to be mediated by chromatin looping. Furthermore, the rare rs1800012 T allele is predicted to result in a looser mRNA conformation immediately surrounding the variant within the pre-mRNA sequence compared to the ancestral G allele. Conclusion: These results provide proof of concept for the use of WES and a customised tiered filtering strategy to identify and prioritise variants for further interrogation using traditional molecular techniques. This approach, utilising previous research to guide a targeted analysis of a WES dataset has highlighted the potential risk modifying effects of several new variants in the TNC and COL27A1 genes. Furthermore, haplotype analysis has implicated several signatures encompassing variants previously associated with risk of injury in the four investigated genes. Although no new candidate variants within the MMP3 and COL1A1 genes were independently associated with risk of injury, unique allele combinations were observed to co-segregate with an altered injury risk profile. Therefore, this study has genetically characterised several previously implicated loci and highlighted new sequence signatures, which may potentially contribute to the susceptibility of musculoskeletal soft tissue injuries. The next step would be to explore the functional significance of these sequence signatures in vitro; a process that would help further characterise the biological mechanisms underpinning the observed risk associations.