Thesis (MSc)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Cryotherapy is one of the popular treatments used to alleviate muscle soreness, especially in the competitive sports arena. However, the therapeutic use of cryotherapy is unsubstantiated because of a lack of proper investigations in the literature, especially a hypothesised effect on muscle recovery. Thus, our aims were to characterise satellite cell (SC) activity in human subjects with delayed onset muscle soreness (DOMS) and to shed light on the effect of cryotherapy on SC activity. DOMS was induced in six male subjects (24 ± 3 years) by completion of a downhill-run (DHR) protocol (5 x 8 min bouts, 2 min rest between bouts) at 70 or 80% of their individual peak treadmill speed. Ice application was applied to only one leg per subject for 3 days: 30 min every 2 hours, 5 times per day. In total 5 muscle biopsies were obtained from each subject: 1 baseline and 4 post-DHR. Post-DHR biopsies: 1 from each leg on day 1 and 7 (1st group, n=3) and 1 from each leg on day 2 and 9 (2nd group, n=3). DOMS was successfully induced as indicated by significant increases in muscle soreness at days 1 and 2 post-DHR (P < 0.01), and creatine kinase activity at day 1 post-DHR (P < 0.01). No difference in muscle soreness was found between treated and untreated legs. SC quiescence and activation were characterised by their expression of the cell surface markers CD34 and CD56 respectively. No significant change in quiescent SC was observed in the untreated or treated legs over time. However, at day 1 post-DHR the number of quiescent SC was significantly lower in the untreated compared with the treated leg (P < 0.05). There was a significant increase in activated SC numbers at day 2 post-DHR in the untreated leg, which was sustained up to day 9 post-DHR (P < 0.01). However, no such increase was found in biopsies taken on days 1 and 7. Also, no change was found in the treated leg, however a significant difference between the number of activated SC in untreated and treated legs on days 2 and 9 post-DHR (P < 0.01) was seen. No significant effect of DOMS or ice treatment was observed for the expression of the myogenic regulatory factors, MyoD and myogenin. C2C12 cell cultures induced to differentiate, however, did stain using these antibodies. This is the first study to report an effect of cryotherapy at the tissue level. In conclusion, this study highlights many unanswered questions on the SC response to DOMS at tissue level, and lays a good foundation for future studies. / AFRIKAANSE OPSOMMING: Kreoterapie is een van die gewilde behandelings wat gebruik word om spierseerheid te verlig, veral in die kompeterende sport arena, maar die gebruik van kreoterapie is onbevestig as gevolg van ‘n gebrek aan voldoende ondersoeke in die literatuur, veral ‘n hipotese oor die effek op spier-herstel. Ons doelstellings was dus om satellietsel (SC) aktiwiteit te ondersoek in mens proefpersone met vertraagde aanvang spierseerheid (DOMS) en ook om lig te werp op die effek van kreoterapie op SC aktiwiteit. DOMS was in ses mans proefpersone (24 ± 3 jare) geїnduseer deur voltooїng van ‘n afdraend-hardloop (DHR) protokol (5 x 8 min rondtes, 2 min rus tussen rondtes) teen 70 of 80% van elkeen se individuele maksimum trapmeul-spoed. Ys was vir 3 dae op net een been per proefpersoon aangewend: 30 min elke 2 ure, 5 keer per dag. 5 spierbiopsies in totaal was van elke proefpersoon verkry: 1 basislyn en 4 post-DHR. Post-DHR biopsies: 1 van elke been op dae 1 en 7 (1ste groep, n=3) en 1 van elke been op dae 2 en 9 (2de groep, n=3). DOMS was suksesvol geїnduseer soos aangedui deur die betekenisvolle verhogings in spierseerheid op dae 1 en 2 post-HR (P < 0.01) en kreatien kinase aktiwiteit op dag 1 post-DHR (P < 0.01). Geen verskil in spierseerheid is gevind tussen die onbehandelde en behandelde bene nie. SC dormansie en aktivering was gekarakteriseer deur die onderskeidelike uitdrukking van die sel oppervlak merkers CD34 en CD56. Geen betekenisvolle verandering is in SC dormansie in die onbehandelde en behandelde bene waargeneem nie, maar op dag 1 post-DHR was die getal dormante SC betekenisvol laer in die onbehandelde been as in die behandelde been (P < 0.05). Daar was ‘n betekenisvolle verhoging in die getalle geaktiveerde SC op dag 2 post-DHR in die onbehandelde been wat volgehou was tot op dag 9 post-DHR (P < 0.01), maar so ‘n verhoging was nie in biopsies wat op dae 1 en 7 geneem is gevind nie. Daar is ook geen verandering in die behandelde been gevind nie, maar ‘n betekenisvolle verskil in die getal geaktiveerde SC is tussen die onbehandelde en behandelde bene op dae 2 en 9 post-DHR gevind(P < 0.01). Geen betekenisvolle effek van DOMS en ys-aanwending vir die uitdrukking van die miogeniese (myogenic) regulatoriese faktore, MyoD en myogenin, is waargeneem nie. C2C12 sel kulture wat geїnduseer is om te differensieer het wel gekleur vir hierdie antiliggame. Dit is die eerste studie wat ‘n effek van kreoterapie op weefselvlak rapporteer. Ten slotte, hierdie studie beklemtoon baie onbeantwoorde vrae oor die SC respons op DOMS op weefselvlak en dit lê ‘n goeie grondslag neer vir toekomstige studies.

Thesis (MScMedSc)--Stellenbosch University, 2012. / Includes bibliography / ENGLISH ABSTRACT: In this thesis, research results are reported on the role of dipalmitoyl phosphatidyl choline (DPPC) and DPPC-liposomes on the in vitro permeability characteristics of various antimycobacterial drugs across porcine bronchial tissue. The permeability flux values of the different compounds (isoniazid, ofloxacin and moxifloxacin) and their relevant DPPC formulations were determined using a continuous flow through perfusion system. Mean steady state flux values were compared statistically by means of a t-test at a significance level of 5% as well as an F-test using whole curve comparisons. The results indicated that the different formulations of drug and their DPPC combinations retard the permeation of drug through bronchial tissue. However, moxifloxacin permeation was significantly enhanced when in a DPPC-liposomal formulation. These results demonstrate the important role that molecular weight, electrostatic charge, partitioning of the molecules in DPPC and DPPC-liposomes play in transmembrane diffusion. In addition, the effect of individual drugs and their DPPC combinations on the surface tension lowering property of DPPC was evaluated. The results obtained showed minimal decreases in the surface tension lowering capability of DPPC; however, the minimal increases in surface tension do not alter the integrity of DPPC to a large extent. Drug susceptibility testing of Mycobacterium tuberculosis cultures against the individual antitubercular drugs and their DPPC combinations was done by using the Radiometric BACTEC 460TB™ system. Drug-entrapped DPPC liposomes were tested at concentrations comparable to their relative minimum inhibitory concentrations (MIC). The results for the BACTEC assay indicated that the mycobacteria were susceptible to the developed drug entrapped liposomes; of which their encapsulation efficiencies for the relevant drugs were approximately ± 50%. It was concluded that drug-entrapped DPPC liposomes could fulfill the dual role of pulmonary drug delivery and alveolar stabilization due to antiatelectatic effect of DPPC which can improve the distribution of anti-tubercular drugs in the lung / AFRIKAANSE OPSOMMING: Hierdie tesis doen verslag oor navorsingsresultate met betrekking tot die rol van dipalmitoïel-fosfatidiel-cholien (DPPC) en DPPC-liposome in die in vitro-permeasiekenmerke van verskeie antimikobakteriese middels oor vark- brongiale weefsel. Die permeasievloedwaardes van die verskillende verbindings (isoniasied, ofloksasien en moksifloksasien) en hul betrokke DPPC-formules is met behulp van ’n deurlopende-deurvloei-perfusiestelsel bepaal. Gemiddelde vloedwaardes in ’n bestendige staat is statisties vergelyk met behulp van ’n t-toets op ’n beduidendheidsvlak van 5%, sowel as ’n F-toets met behulp van heelkurwevergelykings. Die resultate dui daarop dat die verskillende middelformules en hul DPPC-kombinasies middelpermeasie oor brongiale weefsel vertraag. Tog is die permeasie van moksifloksasien aansienlik versterk in ’n DPPC-liposomale formule. Hierdie resultate bevestig die belangrike rol van molekulêre gewig, elektrostatiese lading, die verdeling van molekules in DPPC sowel as DPPC-liposome in transmembraandiffusie. Daarbenewens is die uitwerking van individuele middels en hul DPPC-kombinasies op die oppervlakspanningsverligtingsvermoë van DPPC beoordeel. Die resultate toon minimale afnames in die oppervlakspanningsverligtingsvermoë van DPPC. Die minimale toenames in oppervlakspanning het egter meestal geen noemenswaardige effek op die integriteit van DPPC gehad nie. Voorts is die vatbaarheid van Mycobacterium tuberculosis-kwekings vir die individuele anti-tuberkulêre middels en hul DPPC-kombinasies met behulp van die radiometriese BACTEC 460TB™-stelsel getoets. Middel-ingeslote DPPC-liposome is getoets in konsentrasies wat met hul relatiewe minimum inhibisiekonsentrasies (MIK) vergelyk kan word. Die resultate van die BACTEC-toets toon dat die mikobakterieë vatbaar was vir die ontwikkelde middel-ingeslote liposome, met ’n enkapsuleringsdoeltreffendheid van ongeveer 50% vir die betrokke middels. Die studie kom tot die gevolgtrekking dat middel-ingeslote DPPC-liposome die dubbele rol van pulmonêre middel-lewering en alveolêre stabilisering kan vervul weens die anti-atelektatiese werking van DPPC, wat die verspreiding van anti-tuberkulêre middels in die long kan verbeter.

Thesis (MScMedSc (Pathology. Chemical Pathology))--University of Stellenbosch, 2010. / Bibliography / ENGLISH ABSTRACT: The aetiology of multiple sclerosis (MS) remains largely unknown, due to its multifactorial nature with environmental and genetic factors contributing to the risk. Several investigations highlighted the important role of the genetic component influencing disease susceptibility and progression. In the present study genetic variations in the MTHFR (1298 A>C and 677 C>T) and HFE (845 G>A) genes previously, shown to affect folate and iron metabolism respectively, were studied in the context of MS. The aim of the study was to contribute the laboratory component of a pathology supported genetic testing approach used to identify a subgroup of MS patients with altered nutritional requirements due to genetic susceptibilities. The study population included 90 patients with a clinical diagnosis of MS and 49 control individuals, without any signs or symptoms of the disease, drawn from the same age- and population group. Three mutation detection systems were compared in terms of accuracy, sensitivity, cost effectiveness and ease of operation in relation to the MTHFR and HFE gene mutations analysed. Analytical validity of the genetic assays was an important consideration; therefore the respective real-time polymerase chain reaction (RT-PCR) methods were compared with direct DNA sequencing as the gold standard. The methodology included use of the ABI™ 7900HT, the Roche LightCycler® 480 II system and the Corbett Rotor-Gene™ 6000 5-plex HRM. The same genotype results were obtained for the DNA samples tested with the three RT-PCR methods. In terms of cost effectiveness, ease of operation and optimization, the Corbett Rotor-Gene™ 6000 5-plex HRM thermal cycler, with use of the ABI™ TaqMan Genotyping assays was found to be the most efficient for mutation detection using relatively small sample batches. Following successful standardization of the RT-PCR assays, genotype-phenotype correlation studies was performed in a subset of 43 MS patients with available data. Biochemical tests were previously done on blood samples at the National Health Laboratory Service (NHLS) chemical pathology laboratory at Tygerberg Academic Hospital. A novel finding of this study was that heterozygotes and homozygotes for mutation 1298 A>C in the MTHFR gene presented with lower serum iron levels (12.37 ± 5.91 μmol/l) in comparison to subjects without the C-allele (18.64 ± 7.15 μmol/l; P = 0.02). Furthermore, C-reactive protein (CRP) levels were found to be marginally significantly higher (P = 0.07) in the MTHFR 1298 A>C mutation-positive heterozygotes compared to subjects without the C-allele (6.65 ± 4.96 mg/l vs 2.93 ± 2.31 mg/l), linking inflammation to the presence of the MTHFR 1298 A>C mutation. In comparison, the MTHFR 677 C>T as well as the HFE 845 G>A mutation showed no correlation with transferrin saturation, ferritin, haemoglobin or CRP levels. The absence of increased iron status in HFE mutation carriers was in accordance previous findings suggesting altered iron metabolism in MS patients with this mutation. For the first time, high-throughput assays for functional polymorphisms in the MTHFR and HFE genes can now be offered as a routine service at the Tygerberg Academic Hospital. This application is used in combination with blood biochemistry tests as part of a comprehensive gene-based, pathology supported screening and intervention program aimed at improved quality of life in patients diagnosed with MS. / AFRIKAANSE OPSOMMING: Die etiologie van meervoudige sklerose (MS) is nog grootendeels onbekend, as gevolg van die multifaktoriale aard van die siekte, met omgewings- en genetiese faktore wat bydra tot die risiko. 'n Aantal ondersoeke het reeds die belangrikheid van die genetiese komponent vir die vatbaarheid vir die siekte en die progressie daarvan beklemtoon. In die huidige studie was genetiese variasies in die MTHFR (1298 A>C en 677 C>T) en HFE (845 G>A) gene bestudeer wat voorheen getoon het dat dit foliensuur- enystermetabolisme respektiewelik in die konteks van MS affekteer. Die doel van die studie was om die laboratorium komponent van 'n patologie-ondersteunde genetiese toets daar te stel wat gebruik kan word om 'n subgroep van MS pasiënte te identifiseer wat veranderderde voedingsbehoeftes het as gevolg van genetiese vatbaarheid. Die studiepopulasie het bestaan uit 90 pasiënte met 'n kliniese diagnose van MS en 49 kontroles sonder enige tekens of simptome van die siekte, wat ingesluit is vanuit dieselfde ouderdoms- en populasiegroep . Drie mutasie analise sisteme was vergelyk in terme van akkuraatheid, sensitwiteit, kostedoeltreffendheid en gemak van gebruik met betrekking tot die MTHFR en HFE geen mutasies. Analitiese geldigheid van die genetiese toetse was 'n belangrike oorweging; daarom was die onderskeie rieëltyd polimerase kettingreaksie (RT-PKR) metodes vergelyk met direkte DNA volgordebepaling as die goue standaard. Die metodologie het die ABI™ 7900HT, die Roche LightCycler® 480 II sisteem en die Corbett Rotor-Gene™ 6000 5-plex HRM ingesluit. Dieselfde genotipe resultate was met die verskillende metodes verkry vir die DNA monsters wat getoets is met die drie RT-PKR metodes. Wat betref kostedoeltreffendheid, gemak van gebruik en optimisering, was die gebruik van die Corbett Rotor-Gene™ 6000 5-plex HRM Thermal Cycler, met die ABI™ TaqMan Genotyping essays die mees effektief vir mutasie opsporing van relatief klein getalle monsters. Nadat die RT-PKR toetse suksesvol gestandardiseer was, was genotipe-fenotipe korrelasies uitgevoer in 'n subgroep van 43 MS pasiënte met die beskikbare data. Biochemiese toetse was voorheen gedoen op die betrokke bloedmonsters by die Nationale Gesondheid Laboratorium Diens (NHLS) se chemiese patologie laboratorium by Tygerberg Akademiese Hospitaal. 'n Nuwe bevinding van hierdie studie was dat heterosigote en homosigote vir die MTHFR 1298 A>C mutasie gepresenteer het met laer serum yster vlakke (12.37 ± 5.91 μmol/l) in vergelyking met individue sonder die C-alleel (18.64 ± 7.15 μmol/l; P = 0.02). Verder was die C-reaktiewe proteien (CRP) marginaal betekenisvol hoër (P = 0.07) in die MTHFR 1298 A>C heterosigote in vergelyking met individue sonder die C alleel (6.65 ± 4.96 mg/l vs 2.93 ± 2.31 mg/l), wat aandui dat inflammasie verhoog mag wees in die teenwoordigheid van die MTHFR 1298 A>C mutasie. In vergelyking hiermee het die MTHFR 677 C>T sowel as die HFE 845 G>A mutasies geen korrelasie met transferrien versadiging, ferritien, hemoglobien of CRP-vlakke getoon nie. Die afwesigheid van verhoogde yster status in MS pasiënte met die HFE mutasie was in ooreenstemming met vorige bevindinge wat veranderde ystermetabolisme in MS pasiënte met hierdie mutasie aangedui het. Vir die eerste keer is hoë deurvoer genetiese toetse nou vir funksionele polimorfismes in die MTHFR en HFE gene beskikbaar as 'n roetiene diens by die Tygerberg Akademiese Hospitaal. Dit kan gebruik word saam met bloed biochemiese toetse as deel van 'n omvattende geen-gebaseerde, patologie ondersteunde intervensie program wat daarop gemik is om die kwaliteit van lewe van pasiënte gediagnoseer met MS te verbeter. / Medical Research Council

Thesis (MPhil)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Aim - The aim of this study was to explore second year medical students’ perceptions of their early clinical experiences with a view to improving curriculum development so as to enhance early clinical training programmes at Stellenbosch University (SU). Methodology - A qualitative, interpretive study, based on semi-structured focus group discussions with second year medical students was conducted in order to capture the relevant data that would provide information about their attitudes, feelings, beliefs and views on their early clinical learning experiences during their first year of studying medicine at SU. Thirty seven students participated in four focus group discussions after a process of selection of candidates using purposive sampling methods and stratification criteria to obtain the research sample. The interviews were moderated by an external facilitator, and were audiotaped and transcribed verbatim. The data transcripts were analysed and manually coded, and four broad categories with subthemes which illustrated the findings of the study, were identified and decided upon by the researcher and verified by the supervisor. Results - Early clinical exposure was generally positively perceived by students. It fostered a sense of vocation and feeling like real doctors, leaving students motivated and enhancing their learning interest. Early clinical skills training led to students’ professional development, acquiring the technical skills of a doctor, familiarisation with basic clinical terminology, and normal clinical findings which prepared them for later clinical studies. The new setting of practical learning in a simulated environment required students to adapt to small group learning and student clinical demonstrations which developed new learning styles and study skills. Some of the challenges that students encountered in the transition to clinical learning were, understanding the new subject of clinical medicine, having limited background knowledge to acquire basic clinical skills, and student clinical demonstrations. Although the strategy of peer physical examination was perceived to be effective, some ethical dilemmas emerged for students in terms of autonomy, and no opportunities available to practice on female models. Acting as a simulated patient proved to have both positive and negative outcomes on students’ skills acquisition. Factors that had a negative outcome on clinical skills learning were limited practice opportunities due to high student to teacher ratios per clinical session, and the variability of teaching content and practical techniques taught by various clinical tutors with different teaching strategies. The most stressful experience for students was the OSCE since it was a new method of assessment. Stress was attributed to uncertainty about the correct clinical content and techniques resulting from the teaching variability, while performance anxiety during the exam was related to inappropriate examiner behaviour. The OSCE was a positive learning experience because its format simulated the hospital setting which fostered students’ critical thinking abilities and time management. Conclusion - Early clinical exposure and practice have a great impact on junior medical students’ academic growth, and have positive learning outcomes. However, further development by the faculty in the areas of didactic skills, addressing the ethical issues related to student clinical demonstrations, and supporting students to enable a smooth transition to clinical learning will enhance and optimise their early clinical training.

Dissertation (PhD)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: Obsessive-compulsive disorder is a severe, debilitating psychiatric disorder for which the underlying molecular aetiology still remains unclear. Evidence from family studies have suggested that OCD may be caused by a complex interplay of environmental and genetic factors. In order to identify the genetic factors that mediate OCD susceptibility, several genetic association studies have been undertaken, which have yielded inconsistent findings. Moreover, the majority of these studies have focused on a small number of candidate genes that encode components of the serotonin and dopamine neurotransmitter pathways. However, based on the complexity of clinical manifestations observed in OCD, it is likely that its pathogenesis is mediated by a broader complex of interrelated neurotransmitter systems and signal transduction pathways; consequently there is a need to identify and assess novel candidate genes. One method of identifying such novel OCD candidate genes is by utilising knowledge of diseases with phenomenological overlap with OCD, which lend themselves to better genetic dissection through linkage analysis and animal studies. Genetic loci for such disorders, identified though linkage analysis, could potentially harbour novel OCD candidate genes, while genes implicated through animal models may lead to the identification of additional susceptibility genes through delineation of pathways by, for instance, interactome analysis. One such disorder is schizophrenia, which manifests overlap in both symptoms and brain circuits with OCD. In schizophrenia, in addition to several case-control association studies having been performed, linkage data, studies of chromosomal aberrations and animal models have led to the identification of many chromosomal regions that may contain genes involved in its aetiology and thus may also contain OCD candidate genes. In the present investigation, this approach was employed using previously reported schizophrenia susceptibility loci to identify novel OCD candidate genes. All genes residing in each of these loci were catalogued and individually analysed using a battery of bioinformatic techniques in order to assess their potential candidature for OCD susceptibility. These analyses yielded 13 credible OCD candidate genes.Additional candidates were sought using information regarding a well-defined schizophrenia animal model, the heterozygous reeler mouse, that exhibits neurodevelopmental, neuroanatomical and behavioural abnormalities, similar to those displayed by patients with schizophrenia. The phenotype of these mice is caused by a mutation in Reln, which encodes reelin, a large extracellular matrix protein that plays a pivotal role in the ordered migration of neurons during the development of laminar brain structures. The fact that both reelin protein and mRNA levels have been shown to be reduced in post-mortem brain sections of schizophrenic patients, coupled with the observed behaviour and neurochemical similarities between the heterozygous reeler mouse and schizophrenic patients suggests that reelin may be involved in the pathogenesis of schizophrenia and hence also OCD. Furthermore, genes encoding proteins that interact with reelin may thus also be considered plausible candidate genes for both schizophrenia and OCD. For this reason, novel reelin-interacting proteins were sought using the N-terminal reeler-domain of reelin, a domain only found in proteins involved in neuronal migration, as “bait” in a yeast twohybrid screen of a foetal brain cDNA library. Putative reelin ligands were subsequently reevaluated using co-immunopreciptitation and mammalian two-hybrid analysis to corroborate the yeast two-hybrid findings. Results of these analyses showed that WDR47, a WD40-repeat domain protein, interacts with reelin via its reeler-domain; therefore, the gene encoding this ligand protein, as well as RELN itself, was also considered a credible OCD candidate gene. Each of the candidate genes identified using the afore-mentioned strategies were assessed for their potential role in the aetiology of OCD by case-control association studies of a cohort of Afrikaner OCD patients and control individuals. Statistically significant associations were detected for two genes, DLX6 and SYN3, with the disorder. These associations are exciting as they may point to novel mechanisms involved in OCD development. The identification of WDR47 as a novel reelin-interacting protein has significant implications for our understanding of reelin-dependant signalling. Using this protein as the starting point, further novel components of the reelin signalling pathway may be unravelled, an investigation which may lead to the identification of novel roles for reelin in neurodevelopment. Such novel components may, of course, also be considered OCD and schizophrenia candidate genes, which may, in turn, augment the existing knowledge of the pathophysiologies of OCD, schizophrenia and other neurodevelopmental disorders. Taken together, the current study yielded exciting results that warrants follow-up investigation in future. The identification of DLX6 and SYN3 as novel OCD susceptibility genes as well as the identification of WDR47 as a reelin-interacting protein may provide investigators with alternative avenues of research into potential pathological mechanisms involved both in OCD and schizophrenia, which may ultimately lead to alternative pharmacotherapy. / AFRIKAANSE OPSOMMING: Obsessiewe kompulsiewe steuring (OKS) is `n ernstige, verswakkende psigiatriese steuring waarvan die onderliggende molekulêre etiologie steeds onbekend is. Bewyse verkry vanuit familiestudies het voorgestel dat OKS moontlik veroorsaak word deur `n komplekse interaksie van omgewings en genetiese faktore. Om die genetiese faktore te identifiseer wat OKS vatbaarheid veroorsaak, is `n hele aantal genetiese assosiasie studies onderneem, wat teenstrydige resultate gelewer het. Wat meer is, die grootste hoeveelheid van hierdie studies het gefokus op `n klein aantal kandidaatgene wat vir komponente van die serotonien en dopamine neurotransmittor weë enkodeer. Dit is egter, gebaseer op die kompleksiteit van die kliniese manifestasies wat waargeneem word in OKS, heel moontlik dat die patogenisiteit van die siekte bemiddel word deur `n breër kompleks van interverwante neurotransmittor sisteme en seintransduksie weë. Daar is dus `n behoefte na die identifikasie en ondersoek van nuwe kandidaatgene. Een metode om sulke nuwe OKS kandidaatgene te identifiseer, is deur die gebruik van bestaande kennis oor siektes wat fenomenologiese ooreenkomste het met OKS, siektes wat makliker geneties ontleed kan word deur koppelingsanalises en dierestudies. Genetiese lokusse vir sulke versteurings, geïdentifiseer deur koppelingsanalises, het die potensiaal om nuwe OKS kandidaatgene in te sluit, terwyl gene wat geïmpliseer word deur dierestudies mag lei tot die identifisering van bykomende vatbaarheidsgene deur die ondersoek van weë deur, byvoorbeeld, interaktoom analises. `n Voorbeeld van so `n versteuring is skisofrenie, wat in manifestasie oorvleuel in beide simptome en breinstroombane met OKS. In skisofrenie het, addisioneel tot verskeie geval-kontrole assosiasiestudies wat gedoen is, koppelingsdata, studies van chromosomale afwykings en dierestudies gelei tot die identifikasie van verskeie chromosomale gebiede wat gene mag bevat wat betrokke kan wees in die etiologie van die siekte, en dus ook OKS kandidaatgene mag bevat. In die huidige ondersoek is hierdie benadering gevolg en is gebruik gemaak van voorheen gerapporteerde skisofrenie vatbaarheidslokusse om nuwe OKS kandidaatgene te identifiseer. Alle gene wat in hierdie lokusse voorkom is gekatalogiseer en individueel geanaliseer deur gebruik te maak van `n battery van bioinformatika tegnieke om hul potensiaal as kandidate vir OKS vatbaarheid te bepaal. Hierdie analise het 13 geloofwaardige OKS kandidate opgelewer. Addisionele kandidate is gesoek deur inligting van `n goed gedefinieerde skisofrenie dieremodel te gebruik, naamlik die heterosigotiese “reeler” muismodel, wat neuro-ontwikkelings-, neuroanatomiese- en gedragsabnormaliteite vertoon, soortgelyk aan dié wat voorkom by pasiënte met skisofrenie. Die feit dat daar aangetoon is dat beide reelin protein en bRNS vlakke verlaag is in post-mortem brein seksies van skisofrenie pasiënte, gekoppel aan die gedrags- en neurochemiese ooreenkomste wat gesien word tussen heterosigotiese “reeler” muise en skisofrenie pasiënte, stel voor dat reelin betrokke is by die patogenese van skisofrenie en dus ook OKS. Vir hierdie rede is nuwe proteïene gesoek wat `n interaksie met reelin toon, deur gebruik te maak van die N-terminale reeler-domein van reelin, `n domein wat slegs gevind word in proteïene wat betrokke is by neuronale migrasie, as “aas” in `n gis-twee-hibried sifting van `n fetale brein cDNS biblioteek. Vermeende reelin ligande is vervolgens herevalueer deur gebruik te maak van koimmunopresipitasie en soogdier twee-hibried analises om die gis-twee-hibried bevindings te bevestig. Resultate van hierdie analises het getoon dat daar interaksie is tussen WDR47, `n WD40-herhalingsdomein protein, met reelin via sy reeler-domein. Die geen wat hierdie ligand protein enkodeer, sowel as RELN self, is dus beskou as ‘n geloofwaardige OKS kandidaatgeen. Elkeen van die kandidaatgene wat geïdentifiseer is deur gebruik te maak van bogenoemde strategieë is ondersoek vir `n potensiële rol in die etiologie van OKS deur gebruik te maak van geval-kontrole assosiasie studies met `n groep Afrikaner OKVS pasiënte en kontrole individue. Statisties-betekenisvolle assosiasies met die versteuring is vasgestel vir twee gene, DLX6 en SYN3. Hierdie assosiasies is opwindend aangesien hul nuwe meganismes betrokke by OKS ontwikkeling mag aantoon. Die identifikasie van WDR47 as ‘n nuwe protein wat interaksie met reelin vertoon, het betekenisvolle implikasies vir die verstaan van reelin-afhanklike seining. Deur hierdie proteïn as die beginpunt te gebruik kan vêrdere nuwe komponente van die reelin seinweg ontdek word, `n ondersoek wat mag lei tot die identifisering van nuwe funksies vir reelin in neuro-ontwikkeling. Sulke nuwe komponente mag, natuurlik, ook in aanmerking kom as OKS en skisofrenie kandidaatgene, wat op sy beurt weer die bestaande kennis van die patofisiologie van OKS, skisofrenie en ander neuro-ontwikkelings versteurings mag verbreed. In samevatting, hierdie studie het opwindende resultate gelewer wat opvolgondersoeke in die toekoms regverdig. Die identifikasie van DLX6 en Syn3 as nuwe OKS vatbaarheidsgene, sowel as die identifisering van WDR47 as ‘n protein wat interaksie vertoon met reelin, mag aan navorsers alternatiewe navorsingsweë voorsien om die moontlike patologiese meganismes wat betrokke is by beide OKS en skisofrenie te ondersoek, wat uiteindelik mag lei tot alternatiewe farmakoterapie.

Thesis (PhD)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: Ischaemic preconditioning (PC) is the phenomenon whereby a short episode of coronary occlusion followed by reperfusion protects the myocardium against a subsequent period of prolonged (also called index or sustained) ischaemia. Even though the exact mechanism of PC remains to be established, it implies that the heart has an endogenous protective mechanism against ischaemia which, if identified, may have important clinical implications. The importance of establishing the mechanism of PC lies in the potential to convert this biological phenomenon into a therapeutic modality to be used clinically. If mediated by certain components of a signal transduction pathway, such a goal will be achievable. Several triggers and signal transduction pathways have been implicated in the mechanism of protection induced by PC: for example, receptor-dependent endogenous triggers (such as adenosine and opioids) and receptor-independent endogenous triggers (such as free radicals and calcium). However, the involvement of both the ~-adrenergic signalling pathway as well as nitric oxide (NO) in PC has not been defined. It has been suggested that all triggers are linked to a common final pathway, for example, activation of protein kinase C (PKC) and/or the mitogen-activated kinases (MAPKs), in particular p38 MAPK. However, the role of the latter is still controversial. The aim of this study was to: (A) characterize changes in the cyclic nucleotides, cAMP and cGMP, and p38 MAPK occurring during the entire experimental procedure in an attempt to gain insights into the possible mechanisms involved in ischaemie PC (Chapter 3); (8) establish the significance of the changes observed in cAMP and cGMP by pharmacological manipulation of their respective pathways (Chapters 4 and 5); (C) establish the role of p38 MAPK in ischaemie PC: trigger or mediator involvement (Chapter 6). Isolated perfused working rat hearts were preconditioned by 3 x 5 min global ischaemia, interspersed by 5 min reperfusion, followed by 25 min global ischaemia and 30 min reperfusion. Functional recovery during reperfusion was used as end-point. Hearts were freeze-clamped at different times during the PC protocol, sustained ischaemia, as well as during reperfusion. Tissue cyclic nucleotides (cAMP and cGMP), cyclic nucleotide phosphodiesterase (cAMP- and cGMP-PDE) activities, adenylyl cyclase and protein kinase A activities and p-adrenergic receptor characteristics were determined. p38 MAPK activation was also assessed by Western blotting, using dual phospho-p38 MAPK (Thr180ITyr182) antibody as well as activating transcription factor 2 (ATF2) activation. In addition, to evaluate the role of p38 MAPK in PC protection, the effect of inhibition of p38 MAPK activation, by 8B203580, was determined in adult isolated rat cardiomyocytes as well as in isolated perfused rat hearts. Based on the results obtained, it is proposed that during a multi-cycle ischaemie PC protocol triggers (presumably endogenous catecholamines and NO) are released which induce cyclic changes in cyclic nucleotides, cAMP and cGMP. Both these cyclic nucleotides transiently activate the downstream stress kinase, p38 MAPK, which may trigger further downstream adaptive processes. Furthermore, the sustained ischaemic period of PC hearts was characterized by attenuated cAMP and elevated cGMP levels, as well as attenuated activation of p38 MAPK, which was associated with cardioprotection. In addition, pharmacological attenuation of p38 MAPK activation during sustained ischaemia led to functional recovery. It is concluded that the cardioprotection of PC is due to attenuation of ischaemia-induced p38 MAPK activation. Pharmacological manipulation of this kinase should be considered as a therapeutic modality in the future. / AFRIKAANSE OPSOMMING: Isgemiese prekondisionering (PK) verwys na die verskynsel waardeur 'n kort, verbygaande episode van isgemie gevolg deur herperfusie, die miokardium teen 'n daaropvolgende langdurige periode van isgemie beskerm. Die presiese meganisme van beskerming van PK moet nog opgeklaar word, maar dit impliseer dat die hart oor 'n endogene beskermingsmeganisme beskik wat, indien geïdentifiseer, belangrike kliniese implikasies mag hê. Die belang van opklaring van die meganisme van PK lê daarin dat 'n biologiese verskynsel in 'n terapeutiese modaliteit vir kliniese gebruik, omgeskakel kan word. Sou dit deur bepaalde komponente van 'n seintransduksiepad gemedieër word, is so 'n doel bereikbaar. Verskeie stimuli en seintransduksiepaaie is in PK betrokke: byvoorbeeld, reseptorafhanklike endogene stimuli (soos adenosien en opioïde), asook reseptor-onafhanklike endogene stimuli (soos vrye radikale en kalsium). Die betrokkenheid van die padrenerge seintransduksiepad asook stikstofoksied (NO) in PK egter nog nie behoorlik evalueer nie. Dit is voorgestel dat alle stimuli op 'n finale algemene pad uitloop, soos byvoorbeeld die aktivering van protein kinase C (PKC) en/of die mitogeen-geaktiveerde kinases (MAPKs), spesifiek die p38 MAPKs. Laasgenoemde se rol in PK is steeds kontroversieël. Die doel van die studie was dus: (A) karakterisering van die veranderinge in die sikliese nukleotiede, cAMP en cGMP, en p38 MAPK wat tydens die hele eksperimentele prosedure plaasvind, in 'n poging om meer insig te verkry aangaande moontlike meganismes betrokke in isgemiese PK (Hoofstuk 3); (8) bepaling van die belang van die waargenome veranderinge in cAMP en cGMP deur hulonderskeie paaie farmakologies te manipuleer (Hoofstukke 4 en 5); (C) bepaling van die rol van p38 MAPK in PK: betrokkenheid as stimulus of mediator (Hoofstuk 6). Geïsoleerde, geperfuseerde werkende rotharte is geprekondisioneer deur blootstelling aan 3 x 5 min globale isgemie, afgewissel met 5 min herperfusie, gevolg deur 25 min globale isgemie en 30 min herperfusie. Funksionele herstel tydens herperfusie is as eindpunt gebruik. Harte is op verskillende tye tydens die PK protokol, volgehoue isgemie, asook herperfusie gevriesklamp. Weefsel sikliese nukleotiede (cAMP en cGMP), die aktiwiteit van sikliese nukleotied fosfodiesterases (cAMP- en cGMP-PDE), adeniel siklase en protein kinase A (PKA) asook die eienskappe van die p-adrenerge reseptor is gemeet. p38 MAPK aktivering is met Westerse oordragtegnieke bepaal, deur van dubbel gefosforileerde p38 MAPK (Thr180fTyr182) antiliggame asook geaktiveerde transkripsie faktor 2 (ATF2) gebruik te maak. Die rol van p38 MAPK in PK beskerming is evalueer deur die effek van inhibisie van p38 MAPK aktivering met SB 203580, in volwasse geïsoleerde rot kardiomiosiete asook in geïsoleerde geperfuseerde rotharte, te bepaal. Na aanleiding van die resultate, is voorgestel dat, tydens 'n multi-siklus isgemie PK protokol, stimuli (moontlik endogene katekolamiene en NO) vrygestel word wat die sikliese veranderinge in sikliese nukleotiede, cAMP en cGMP, veroorsaak. Beide hierdie sikliese nukleotiede aktiveer die distale stres kinase, p38 MAPK, op 'n betekenisvolle, maar verbygaande manier. Hierdie kinase mag verdere distale aanpassingsprosesse stimuleer. Die volgehoue isgemiese periode van PK harte is gekenmerk deur verminderde cAMP en verhoogde cGMP vlakke, asook verminderde aktivering van p38 MAPK. Hierdie veranderinge is met beskerming van die hart teen isgemie geassosieer. Daarbenewens, farmakologiese vermindering van p38 MAPK aktivering tydens volgehoue isgemie het tot verbeterde funksionele herstel gelei. Die gevolgtrekking is gemaak dat die beskermende effek van PK die gevolg is van verminderde aktivering van isgemies-geïnduseerde p38 MAPK. Farmakologiese manipulasie van hierdie kinase moet in die toekoms as terapeutiese modaliteit oorweeg word.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Rifampicin resistance in clinical isolates of Mycobacterium tuberculosis develops through selection of bacterial variants harbouring mutations in the rpoB gene. These mutations infer a fitness-cost in the absence of antibiotic pressure, however, fitness-levels of rifampicin-resistant strains can be restored by compensatory mutations in rpoA and rpoC. This study was the first to investigate the epidemiological relevance of these compensatory mutations in clinical M. tuberculosis isolates collected in South Africa. Through targeted DNA sequencing, we demonstrated a strong association between rpoC mutations and transmission, and the rpoB S531L mutation. Our study emphasises the epidemiological relevance of compensatory evolution in response to the emergence of rifampicin resistance, and illustrates how compensatory mutations may be selected as a function of epistatic interactions. Recently a hypothesis has been developed which suggests that the activation of efflux systems through exposure to rifampicin may explain the observed spectrum of rifampicin resistance phenotypes. To elucidate whether rifampicin dependent activation of efflux systems also increases energy production, the RNA expression profiles of candidate energy metabolism genes were investigated. This study demonstrated that rifampicin exposure induced an overall increase in the expression of energy metabolism genes. Our findings suggest that the response to rifampicin is not universal and may depend on other genomic mutations. From these results we conclude that the stress response induced by exposure to rifampicin increases the energy production which fuels efflux activity thereby enabling the cell to extrude rifampicin in an energy dependent manner. This also provides a platform to explain the mechanism by which the newly developed drug, TMC207, increases the rate of culture conversion when used in combination with second-line anti-TB drugs. We propose that inhibition of ATP synthesis by TMC207 will deprive the efflux pumps and transporter genes of energy, which will result in the accumulation of second-line anti-TB drugs within the bacilli, leading to more efficient binding of the second-line drugs to their targets and ultimately to cell death. To identify the genetic basis governing the level of rifampicin resistance, we sequenced the genomes of MDR clinical isolates and in vitro generated rifampicin resistant mutants. Only minor genetic changes in addition to the rpoB mutation were identified in the genomes of in vitro rifampicin resistant mutants which displayed varying levels of resistance. This suggests that these mutants may either use alternative regulatory mechanisms or have acquired SNPs outside the genetic regions investigated in this study to modulate rifampicin resistance levels. In contrast, the genomes of clinical MDR isolates from the Low Copy Clade showed considerable variability in genes involved in cell wall, cellular processes and lipid metabolism, while the genomes from the Beijing Clade displayed variability in genes known to confer drug resistance and compensatory mechanisms. These results suggest that the structure and processes of the cell wall, as well as lipid metabolism plays a critical role in determining the intra-cellular concentration of rifampicin. Finally, this study illustrated the complexity in the physiology of M. tuberculosis resistant to rifampicin, whereby multiple mechanisms are employed by the bacteria to modulate its resistance levels. / AFRIKAANSE OPSOMMING: Rifampisien weerstandigheid in kliniese isolate van Mycobacterium tuberculosis ontwikkel deur die seleksie van bakteriële variante wat mutasies in die rpoB geen het. Alhoewel hierdie mutasies lei tot „n afname in fiksheid van die bakterieë in die teenwoordigheid van antibiotika, kan die fiksheids vlakke van rifampisien weerstandige stamme herstel word deur vergoedende mutasies in rpoA en rpoC. Hierdie is die eerste studie wat die epidemiologiese relevansie van hierdie vergoedende mutasies in kliniese M. tuberculosis isolate wat in Suid-Afrika versamel is, ondersoek. Deur middel van doelgerigte DNA volgordebepaling het ons „n sterk assosiasie tussen rpoC mutasies en transmissie, en die rpoB S31L mutasie getoon. Hierdie studie beklemtoon die epidemiologiese relevansie van regstellende evolusie na aanleiding van die ontwikkeling van rifampisien weerstandigheid en illustreer hoe regstellende mutasies geselekteer mag word as „n funksie van epistatiese interaksies. „n Hipotese is onlangs ontwikkel wat voorstel dat blootstelling aan rifampisien uitvloei sisteme in die bakterium aktiveer, wat moontlik die waargenome spektrum van rifampisien weerstandige fenotipes kan verklaar. Ons het die RNA uitdrukkingsprofiele van kandidaat-energiemetabolisme gene ondersoek om te bepaal of rifampisien afhanklike aktivering van uitvloei sisteme ook energieproduksie verhoog. Hierdie studie demonstreer dat rifampisien-blootstelling „n algehele verhoging in die uitdrukking van energiemetabolisme gene induseer. Ons bevindinge stel voor dat die reaksie van die sel op rifampisien blootstelling nie universeel is nie, en moontlik ook afhanklik is van ander genomiese mutasies. Uit hierdie resultate kan ons aflei dat die stres respons wat geïnduseer word deur rifampisien-blootstelling energieproduksie verhoog, wat weer die uitvloei aktiwiteit aanvuur, en gevolglik die sel in staat stel om rifampisien op „n energie-afhanklike wyse uit te dryf. Dit bied ook „n basis om die meganisme te verklaar waardeur die nuwe middel, TMC207, die tempo van kultuuromskakeling verhoog wanneer dit saam met tweede-linie anti-TB middels gebruik word. Ons stel voor dat die inhibisie van ATP sintese deur TMC207 die uitvloeipompe en transporteerder gene van energie ontneem. Gevolglik veroorsaak dit „n ophoping van tweedelinie anti-TB middels binne-in die bakterium, wat geleentheid bied vir meer effektiewe binding tussen die middels en hulle teikens en uiteindelik seldood veroorsaak. Ons het DNA volgordes bepaal van die genome van MDR kliniese isolate en in vitro selekteerde rifampisienweerstandige mutante om sodoende die genetiese grondslag waarop die vlak van rifampisienweerstandigheid beheer word, te identifiseer. Slegs klein verskille, bo en behalwe die rpoB mutasie, is geïdentifiseer in die genome van in vitro rifampisien weerstandige mutante wat verskillende vlakke van weerstandigheid getoon het. Dit dui aan dat hierdie mutante of ander regulatoriese meganismes gebruik, of hulle het enkelnukleotied polimorfismes buite die genetiese area wat in hierdie studie ondersoek is, waarmee rifampisien weerstandigheid gemoduleer word. In teenstelling hiermee het die genome van kliniese MDR isolate van die “Low Copy Clade” aansienlike variasie getoon in gene wat betrokke is by die selwand, sellulêre prosesse en lipiedmetabolisme. Verder het die genome van die Beijing genotipe variasie in gene getoon wat betrokke is by middelweerstandigheid en regstellende meganismes. Hierdie resultate dui aan dat die struktuur en prosesse van die selwand, asook lipiedmetabolisme, „n kritiese rol speel in die bepaling van die intrasellulêre konsentrasie van rifampisien. Opsommend, hierdie studie toon verskeie meganismes aan wat deur die bakterieë gebruik word om weerstandigheidsvlakke te moduleer en die kompleksiteit van die fisiologie van M. tuberculosis wat weerstandig is teen rifampisien. / The National Research Foundation (NRF) / South African Medical Research Council (MRC) / Harry Crossley Foundation

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: This study is the first of its kind to highlight the importance of using the latest state of the art technology available in the field of proteomics as a complementary tool to characterize the proteome of members of the Mycobacterium tuberculosis Beijing lineage which have been linked to outbreaks and drug resistance of Tuberculosis (TB). Our label-free comparative analysis of two closely related M. tuberculosis strains with different transmission patterns and levels of virulence highlighted numerous factors that may alter metabolic pathways leading to hyper-virulence whereby the strain was able to rapidly replicate in the host and cause extensive disease. This comparative analysis clearly demonstrated that both instrumentation and analysis software impacts on the number of proteins identified and thereby the interpretation of the proteomic data. These proteomes also served as substrates for the discovery of phosphorylation sites, a field of research that reflects a significant knowledge gap in the field of M. tuberculosis. By using differential separation techniques in combination with the state of the art mass spectrometry we described the phosphorylation sites on 286 proteins. This was the first study to document phosphorylation of tyrosine residues in M. tuberculosis. By this means, our data set further extend and complement previous knowledge regarding phosphorylated peptides and phosphorylation sites in M. tuberculosis. Using advanced mass spectrometry methods we further investigated the impact of the in vivo evolution of rifampicin resistance on the proteome of a rifampicin-resistant strain containing a S531L rpoB mutation. We identified the presence of overabundant proteins which could provide novel insight into potential compensatory mechanisms that the bacillus uses to reduce susceptibility to anti-TB drugs. Our findings suggest that proteins involved in a stress response may relate to an altered physiology enabling the pathogen to tolerate and persist when exposed to anti-TB drugs. Together this suggests that structural changes in the RNA polymerase precipitated a cascade of events leading to alterations of metabolic pathways. In addition, we present the first comprehensive analysis of the effect of rifampicin on the proteome of a rifampicin resistant M. tuberculosis isolate suggesting that rifampicin continues to influence the biology of M. tuberculosis despite the presence of an rpoB mutation. Our analysis showed alterations in the cell envelope composition and allowing the bacterium to survive in a metabolically dormant/persistent growth state. The results presented in this study illustrate the full potential of using a proteomic approach as a complementary molecular technique to select promising candidate molecules and genes for further characterization using the tools of molecular biology. / AFRIKAANSE OPSOMMING: Die huidige studie is ‘n eerste van sy soort, deur die nuutste gevorderde tegnologie in die proteomika veld te gebruik. Die proteoom van lede van die Mycobacterium tuberculosis Beijing stam, wat die oorsaak is van tuberkulose (TB) uitbrake en ook weerstandige TB, is gekarakteriseer. Ons merkervrye vergelykende analise van twee naby verwante M. tuberculosis stamme met verskillende vlakke van oordraagbaarheid en virulensie, beklemtoon verskeie faktore wat metaboliese paaie mag verander, wat kan ly tot hiper-virulensie, wat die TB-stam in staat stel om vinniger te repliseer in die gasheer en ‘n uitgebreide siektetoestand kan veroorsaak. Die analise het duidelik gewys dat die toerusting wat gebruik word, sowel as die sagteware ‘n invloed kan hê op die hoeveelheid proteïne wat geïdentifiseer kan word en daardeur intrepretasie van proteomika data kan beïnvloed. Hierdie proteome dien as substrate vir die ondekking van fosforilasie setels, ‘n veld van navorsing wat dui op ‘n gaping in ons kennis van M. tuberculosis. Deur gebruik te maak van differensiële skeidingstegnieke en moderne spektrometrie beskryf ons fosforileringsetels in 286 proteine. Hierdie is die eerste studie wat fosforilasie van tirosien residue in M. tuberculosis beskryf. Hierdeur komplimenteer en brei ons data die huidige kennis oor gefosforileerde peptiede en fosforilasie setels in M. tuberculosis uit. Deur gebruik te maak van gevorderde massa spektrometriese tegnieke het ons verder ook die impak van in vivo evolusie van rifampicin weerstandigheid op die proteoom van ‘n rifampicin weerstandige TB-stam met die algemene S531L rpoB mutasie ondersoek. Ons het proteïne geïdentifiseer wat in groot hoeveelhede voorkom en kan nuwe insigte gee tot potensiele kompenserende meganismes wat deur die bacillus gebruik word om vatbaarheid vir anti-TB middels te verminder. Ons bevindings dui daarop dat proteïene betrokke in ‘n stresreaksie mag lei tot ‘n verandering in fisologie wat die patogeen in staat stel om anti-TB middels te verdra en te volhard in die teenwoordigheid van sulke middels. Saam impliseer dit dat ‘n ketting van gebeure wat lei tot veranderinge in metaboliese paaie, word vooraf gegaan deur strukturele veranderinge in die RNS polimerase. Tesame hiermee bied ons ook die eerste omvattende analise aan van die effek wat rifampicin op die proteoom van ‘n rifampicin weerstandige M. tuberculosis isolaat het, en wat aan die hand doen dat rifampicin voordurend die biologie van M. tuberculosis beïnvloed, ten spyte van die teenwoordigheid van ‘n rpoB mutasie. Ons analise dui op veranderinge in die samestelling van die selomhulsel wat die bakterie toelaat om te oorleef in ‘n metabolies dormante staat. Die resultate wat in hierdie studie aangebied word illustreer die volle potensiaal van ‘n proteomiese benadering as komplementêre molekulêre tegniek om belowende kandidaat molekules en gene te kies vir verdere karakterisering, deur gebruik te maak van molekulêre tegnieke. / The National Research Foundation (RSA), / Norwegian Research Council (Norway) / National Institute of Health –Forgarty (USA) / Southern Africa Consortium for Research Excellence-Welcome Trust (SACORE) (United Kingdom) / Kwazulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) (USA)

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Numerous studies conducted internationally have identified and described several endemic methicillin-susceptible Staphylococcus aureus (MSSA) clones. However, only some of these clones are associated with methicillin resistance (CC5, CC8, CC22, CC30 and CC45). To date, studies reporting on the population structure of S. aureus isolated in South Africa represent limited demographic areas, focus on methicillin-resistant S. aureus (MRSA) only and have displayed little emphasis on virulence. This study was undertaken to elucidate the population structure of S. aureus isolated from specific clinical sources at Tygerberg hospital, and to investigate specific host-pathogen interactions of representative isolates. Consecutive non-repetitive clinical S. aureus isolates were collected over one year (September 2009/2010) with patient demographics and limited clinical information. Strains were typed by PFGE and molecular markers (spa, multi-locus sequence typing (MLST), agr, Staphylococcal Chromosome Cassette mec and Panton-Valentine leukocidin (PVL)). Representative isolates were selected and investigated for the presence of virulence genes, adherence (to immobilised fibronectin [Fn], fibrinogen [Fg], collagens IV [CnIV] and VI [CnVI]), cellular invasion and cell death induction. Statistical association were determined between all in vitro results and methicillin-resistance, clonality, patient HIV status and bacterial PVL status. Fifteen percent of the isolates (n = 367) were MRSA. Forty four present of isolates were PVL+. agr I-IV and SCCmec I-V were identified. The MSSA population was diverse: ST22 (dominant), ST1865 and ST121 were PVL+. ST45, ST1863 and ST15 were PVL-. PVL- MRSA were diverse: ST612-MRSA-IV (dominant), ST5-MRSA-I, ST239-MRSA-III, ST36-MRSA-II and ST22-MRSA-IV. The genes fnbA/B (fibronectin-binding protein A/B), clfA/B (clumping factor A/B), eap (extracellular adherence protein), nuc (nuclease), coa (coagulase) and hld (delta toxin) were detected in all representative isolates. The CC8 and CC6 isolates adhered strongly to all ligands (100-700% of control, ligand dependent), while isolates of CC45, CC22 and CC88 adhered strongly only to Fg and Fn. The CC30, CC15, and CC12 isolates adhered extremely strongly to CnIV (>300%) and CC8, CC15, and C6 to CnVI (>200%). Isolates from CC30, CC8, CC15, CC6, CC12, CC97, CC88 and CC45 were highly invasive (>100%). ST121 was non-invasive (>50%). Isolates of CC5, CC30 and CC121 were non-cytotoxic (<50%), while isolates of CC22, CC8, CC15, CC45 and CC88 were very cytotoxic (>70%). No significant difference was observed in adherence or cell death induction of MRSA vs. MSSA clones or between isolates from HIV+ vs. HIV- persons. PVL- isolates displayed higher cellular invasiveness than PVL+ isolates. The presence of ST612-MRSA-IV, ST22-MRSA-V and ST8-MRSA-V points to local SCCmec acquisition, as we found MSSA isolates with the same spa types. Numerous MSSA clones were prevalent, but do not appear to have a major common genetic background with MRSA. PVL was highly prevalent among MSSA, indicating acquisition of PVL genes independently of SCCmec. The abilities to adhere to specific immobilised ligands in vitro were diverse and grouped with the genetic background, while the vast majority of isolates were invasive and induced significant cell death. We can conclude that the population of S. aureus at Tygerberg hospital is composed of a vast number of MSSA and MRSA clones, which display varying patters of adherence to selected ligands and of which, the majority clones are invasive and cytotoxic. / AFRIKAANSE OPSOMMING: Talle internasionale studies het verskeie endemiese metisillien vatbare Staphylococcus aureus (MSSA) klone geïdentifiseer en beskryf. Slegs 'n paar van hierdie klone word geassosieer met metisillien weerstandigheid (Klonale kompleks (KK) 5, KK8, KK22, KK30 en KK45). Studies oor die bevolking struktuur van S. aureus geïsoleer in Suid-Afrika is tot dusver beperk tot demografiese gebiede, fokus slegs op metisillien-weerstande S. aureus (MRSA) en het min klem op virulensie geplaas. Hierdie studie is onderneem om die bevolking struktuur van S. aureus, geïsoleer vanaf spesifieke kliniese bronne, in die pasiëntpopulasie van Tygerberg-hospitaal te ondersoek en om ondersoek in te stel na spesifieke gasheer-patogeen interaksies van verteenwoordigende isolate. Opeenvolgende, nie-herhalende en suiwer kliniese S. aureus isolate is versamel oor ´n periode van een jaar (September 2009/2010), tesame met pasiënt demografiese- en beperkte kliniese inligting. Stamme is deur PFGE en molekulêre merkers (spa, MLST, agr, SCCmec en PVL) beskryf. Verteenwoordigende isolate is gekies en ondersoek vir die teenwoordigheid van virulensie gene, aanhegting ( aan geïmmobiliseerde fibronektien [Fn], fibrinogeen [Fg], kollageen IV [CnIV] en kollageen VI [CnVI]), sellulêre indringing en die induksie van seldood. Statistiese assosiasies is bepaal tussen alle in vitro resultate en methicillin-weerstandigheid, klonaliteit, pasiënt MIV status en bakteriese PVL status. Fyftien persent van die isolate (n = 367) was MRSA. Vier-en-veertig van die isolate was PVL+. agrI-IV en SCCmec I-V is geïdentifiseer. Die MSSA bevolking was divers: ST22 (dominant), ST1865 en ST121 PVL +. ST45, ST1863 en ST15 was PVL+. PVL- MRSA was divers: ST612-MRSA-IV (dominant), ST5-MRSA-I, ST239-MRSA-III, ST36-MRSA-II en ST22-MRSA-IV. Die gene fnbA/B (fibronektien A/B), clfA/B (klontings faktor A/B), eap (ekstrasellulêre aanhegtings protein), nuc (nukease), coa (koagulase) en hld (delta toksien) was aangetref in alle verteenwoordigende isolate. Isolate van KK8 en KK6 het sterk aan alle ligande (100-700% van kontrole, ligand-afhanklike) aangeheg, terwyl isolate van KK45, KK22 en KK88 slegs sterk aand fibronektien en fibrinogeen aangeheg het. Isolate van KK30, KK15, en KK12 het baie sterk aan CnIV (> 300%) aangeheg en KK8, KK15, en KK6 and CnVI (> 200%). Isolate van KK30, KK8, KK15, KK6, KK12, KK97, KK88 en KK45 was hoogs indringend (> 100%). ST121 was nie-indringende (> 50%). Isolate van KK5, KK30 en KK121 was nie-sitotoksiese (<50%), terwyl isolate van KK22, KK8, KK15, KK45 en KK88 baie sitotoksies was (> 70%). Geen betekenisvolle verskil is waargeneem in die aanhegting of seldood induksie van MRSA teenoor MSSA klone of tussen isolate van MIV+ teenoor MIV- persone nie. PVL- isolate het hoër sellulêre indringing as PVL+ isolate vertoon. Die teenwoordigheid van ST612-MRSA-IV, ST22-MRSA-V en ST8-MRSA-V verwys na die plaaslike verwerwing van SCCmec, aangesien ons MSSA isolate beskryf het met dieselfde spa-tipes. Talle MSSA klone was algemeen, maar het nie 'n beduidende genetiese agtergrond met MRSA vertoon nie. PVL was baie algemeen onder MSSA isolate en die PVL gene is dalk onafhanklik van SCCmec verkry. Die vermoë om aan spesifieke geïmmobiliseer ligande in vitro aan te heg was divers en groepeer met die genetiese agtergrond, terwyl die meerderheid van die isolate indringend was en kon betekenisvolle sel dood veroorsaak. Ons kan aflei dat die bevolking van S. aureus by die Tygerberg hospitaal saamgestel is uit 'n groot aantal van MSSA en MRSA klone, wat verskillende patrone van aanhegting aan geselekteerde ligande vertoon en waarvan die meeste klone indringende en sitotoksies is. / DFG/NRF International Research and Training Group (IRTG) 1522 “HIV and associated infectious diseases in Southern Africa” / National Research Foundation / Medical Research Council, Medi-Clinic / Harry Crossley Fund (Stellenbosch University) / Stellenbosch University

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Introduction: Coronary heart disease (CHD) is the leading cause of death worldwide with 3.8 million men and 3.4 million women dying globally each year. Although existing myocardial reperfusion strategies such as thrombolysis and percutaneous coronary intervention (PCI), if applied in a timely manner, limit myocardial infarct size, the mortality and morbidity remains significantly high. Ischaemic preconditioning (IPC) may offer the potential to attenuate myocardial ischaemia/reperfusion injury through cardioprotective signaling pathways which is recruited at the time of myocardial reperfusion, thereby improving clinical outcomes in patients with coronary artery disease. Ischaemic preconditioning is a phenomenon whereby short intermittent episodes of coronary occlusion followed by reperfusion protect the myocardium against a subsequent period of sustained ischaemia. This protection is reflected in the limitation of infarct size and improved functional recovery of the ischaemic heart during reperfusion. Despite intensive research efforts, the promise of an effective cardioprotective strategy using the endogenous protective mechanisms of the heart which underlies IPC, has not yet been materialized. Although progress has been made in terms of signaling mechanisms in the preconditioned heart, the identification of the myocardial reperfusion phase as the critical “window” for cardioprotection, requires the elucidation of the signal transduction pathways during the reperfusion phase after IPC. In view of the above, the aims of the present study were to investigate: i. the involvement of the RISK pathway and p38 MAP kinase pathway in IPC during early and late reperfusion ii. the involvement of heat shock protein-27 (HSP-27), heat shock protein-70 (HSP-70), GSK-3β, CAMKII, AMPK and the transcription factor CREB in the context of IPC during early reperfusion iii. the involvement of autophagy and apoptosis during early and late reperfusion after IPC iv. the correlation of the protein kinases with the hemodynamic parameters of the heart v. the mechanism of IPC by means of two-dimensional (2D) proteomics Methods: The isolated perfused working rat heart model was used with functional recovery as end-point. Hearts were preconditioned (IPC) for 3x5 min global ischaemia, alternated with 5 min reperfusion. Hearts were subjected to 25 min sustained global ischaemia, followed by 5, 10, 15 or 30 min reperfusion when hearts were snap-frozen for western blotting analysis. Alternatively, hearts were reperfused for 30 min to record hemodynamic parameters and measure functional recovery. Non-preconditioned (Non-IPC) hearts were stabilized for 30 min and subjected to 25 min sustained global ischaemia followed by 5, 10, 15 or 30 min reperfusion when hearts were snap-frozen. Alternatively Non-IPC hearts were reperfused for 30 min to serve as control for the 30 min reperfused IPC group. Activation of the protein kinases was determined by western blotting analysis. For the proteomic study mitochondrial and cytosolic proteins were isolated from heart tissue and separated in the first dimension by isoelectric focusing, followed by separation in the second dimension by two dimensional gel electrophoresis. The PD Quest software programme was used to identify significantly expressed protein spots. Protein spots of interest were excised and subjected to in-gel digestion and the resulting peptides were analysed by mass spectrometry. Proteins were identified by Mascot and the Swiss Prot database. Results: Western blotting analysis demonstrated that the RISK pathway and p38 MAPK are activated very early in reperfusion, but the activation is not sustained during the reperfusion period. Autophagy is also upregulated during this early reperfusion phase; it is attenuated in the middle reperfusion phase and increase for a second peak of upregulation in the late reperfusion phase. In addition, we identified CAMKII as a novel marker of functional recovery in IPC after reperfusion. The proteomic analysis identified twenty differentially expressed mitochondrial and thirty six differentially expressed cytosolic proteins between Non-IPC and IPC hearts. Functions ascribed to the majority of these individual proteins were directly related to cardiac metabolism. Conclusion: Activation of the majority of the protein kinases investigated in the present study is associated with the hemodynamic parameters of the heart instead of functional recovery. Results indicated that the variable signaling patterns could be attributed to differences in heart rate and the effect thereof (ejection fraction, minimum and maximum rate of contraction), as a result of sympathetic stimulation due to psychological stress in the animals before slaughtering. Proteomics results demonstrated that IPC hearts which failed after ischaemia /reperfusion are metabolically compromised and “worse off” compared to non-IPC hearts. / AFRIKAANSE OPSOMMING: Inleiding: Koronêre hartsiekte is die vernaamste oorsaak van sterftes wêreldwyd met 3.8 miljoen mans en 3.4 miljoen vrouens wat jaarliks sterf. Alhoewel bestaande miokardiale herperfusie strategieë soos trombolise en perkutane koronêre intervensie (PKI), wanneer betyds toegepas, miokardiale infarktgrootte beperk, bly mortaliteit en morbiditeit steeds hoog. Isgemiese prekondisionering (IPK) beskik oor die potensiaal om miokariale isgemie/herperfusie skade te verminder deur beskermende seinoordragpaaie tydens miokardiale herperfusie te aktiveer en sodoende die pasiënte wat aan koronêre arterie siekte ly, se prognose te verbeter. Isgemiese prekondisionering verwys na die verskynsel waartydens kort episodes van isgemie opgevolg deur herperfusie, die miokardium teen ‘n daaropvolgende langdurige isgemiese insident beskerm. Hierdie beskerming word gereflekteer in die beperking van infarktgrootte en verbeterde funksionele herstel van die isgemiese hart tydens herperfusie. Ten spyte van intensiewe navorsingspogings is die presiese meganisme van endogene beskerming tydens IPK nog nie ten volle ontrafel nie. Die identifisering van die miokardiale herperfusie fase se kritiese “vensterperiode” van beskerming, noodsaak ‘n volledige analise van die seinoordragpaaie wat geaktiveer word tydens die herperfusie fase na IPK. In die lig van bogenoemde, was die doel van die huidige studie om die volgende te ondersoek: i. die betrokkenheid van die RISK seinoordragpad en p38 MAP kinase tydens vroeë en laat herperfusie na IPK ii. die betrokkenheid van “heat shock protein-27” (HSP-27), “heat shock protein- 70” (HSP-70), GSK -3β, CAMKII, AMPK en die transkripsie faktor, CREB, in die konteks van IPK tydens vroeë herperfusie iii. die betrokkenheid van outofagie en apoptose tydens vroeë en laat herperfusie na IPK iv. die korrelasie van die proteïenkinases met die hemodinamiese parameters van die hart v. die meganisme van IPK deur middel van twee dimensionele proteomika Metodes: Die geïsoleerde werkende rothart model, met funksionele herstel as eindpunt, is gebruik. Harte is geprekondisioneer (IPK) met 3x5 min globale isgemie, afgewissel met 5 min herperfusie. Daarna is harte blootgestel aan 25 min volgehoue globale isgemie, gevolg deur 5, 10, 15 of 30 min herperfusie, waartydens harte gevriesklamp is. Alternatiewelik, is harte blootgestel aan 30 min herperfusie ten einde funksionele herstel te meet en hemodinamiese parameters te registreer. Nie-geprekondisioneerde (Non-IPK) harte is gestabiliseer vir 30 min, waarna dit onderwerp is aan 25 min volgehoue globale isgemie, gevolg deur 5, 10, 15 of 30 min herperfusie, waartydens harte gevriesklamp is vir westelike klad analise. Alternatiewelik, is Non-IPK harte onderwerp aan 30 min herperfusie om te dien as kontrole vir die 30 min IPK groep. Aktivering van die proteïenkinases is bepaal deur westelike klad analise. Vir die proteomiese studie, is onderskeidelik mitokondriale en sitosoliese proteïene geïsoleer en geskei in die eerste dimensie met behulp van isoelektriese fokusering, gevolg deur skeiding in die tweede dimensie met behulp van twee dimensionele gel elektroforese. Die PDQuest sagteware program is gebruik om proteïenkolle te identifiseer wat statisties beduidende verskille toon. Proteïenkolle van belang is uitgesny en onderwerp aan in-gel tripsinering en die peptiede wat sodoende verkry is, is deur middel van massa spektrometrie geanaliseer. Proteïene is geïdentifiseer deur Mascot en die Swiss Prot databasis. Resultate: Westelike klad analise het aangetoon dat die RISK pad en p38 MAPK geaktiveer is tydens vroeë herperfusie, maar die aktivering word nie volgehou tydens die hele herperfusie periode nie. Outofagie word gestimuleer tydens die vroeë herperfusie fase; dit word onderdruk in die middel herperfusie fase en bereik ‘n tweede piek van stimulering in die laat herperfusie fase. Die proteomiese analise het onderskeidelik twintig differensieel gereguleerde mitokondriale proteïene en ses en dertig differensieel gereguleerde sitosoliese proteïene geïdentifiseer tussen Non-IPK en IPK. Die grootste persentasie van hierdie proteïene is direk betrokke by miokardiale energie metabolisme. CAMKII is geidentifiseer as ‘n unieke merker van funksionele herstel in IPK tydens reperfusie. Gevolgtrekking: Aktivering van die meeste van die proteïenkinases wat ondersoek is in die huidige studie, is geassosieer met die hemodinamiese parameters van die hart, in plaas van funksionele herstel. Die resultate het aangetoon dat die varierende patrone van kinase aktivering toegeskryf kan word word aan verskille in harttempo en die effek daarvan (ejeksie fraksie, minimum en maksimum tempo van kontraksie), as gevolg van simpatiese stimulasie toegeskryf aan sielkundige stres in die diere voor slagting. Proteomiese analise het getoon dat IPK harte wat faal na isgemie/reperfusie metabolies gekompromiseer is en “slegter daaraan toe” is, in vergelyking met Non-IPK harte.