Thesis (MSc (Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The ostrich industry in South Africa is currently threatened by respiratory disease in feedlot ostriches which causes a dramatic loss in production. Ms01, Ms02 and Ms03 were identified as the three ostrichspecific mycoplasmas to be associated with this respiratory disease in ostriches of South Africa. The ostrich-specific mycoplasmas have a major impact on ostrich production and for this reason there is a serious need for treatment for these infections. For this reason, the ostrich industry has undertaken an investigation into the development of vaccines against mycoplasma infections. In this study, an approach to DNA vaccine development will be investigated and applied, specifically for the ostrich mycoplasma Ms02. Firstly, the whole genome of Ms02 was sequenced using GS FLX sequencing technology. The contiguous sequences obtained from the whole-genome sequencing were analysed bioinformatically which included the annotation of the contiguous sequences and the subsequent search for a vaccine candidate gene for the development of a DNA vaccine. The P100 gene of Ms02, which showed a high degree of homology with the P100 gene of the human pathogen M. hominis, was chosen as a vaccine candidate gene for the development of a DNA vaccine. The P100 gene was successfully cloned and subsequently modified by means of site-directed mutagenesis to correct for alternative codon usage, where after the modified P100 gene was subcloned into the mammalian expression vector, pCI-neo for vaccination trials in the near future. / AFRIKAANSE OPSOMMING: Die volstruisbedryf van Suid-Afrika is tans bedreig deur 'n respiratoriese siekte in voerkraal volstruise wat lei tot aansienlike verliese in volstruisproduksie. Ms01, Ms02 en Ms03 is geïdentifiseer as die drie volstruis-spesifieke mikoplasmas wat 'n rol speel in hierdie respiratoriese siektes van volstruise in Suid- Afrika. Die drie volstruis-spesifieke mikoplasmas het 'n groot impak op die produksie van volstruise en om hierdie rede is daar 'n ernstige behoefte aan 'n behandeling van hierdie infeksies. Ten einde mikoplasma infeksies in volstruise te voorkom, het die Suid-Afrikaanse volstruisbedryf 'n ondersoek geloods na moontlike strategieë vir entstof ontwikkeling. In hierdie studie, is 'n benadering van DNA entstof ontwikkeling ondersoek en toegepas, spesifiek teen die volstruis mikoplasma Ms02. Eerstens, is die volledige Ms02 genoomvolgorde bepaal deur gebruik te maak van GS FLX volgordebepalingstegnologie. Die gedeeltelike volgordes verkry vanaf die heelgenoom volgordebepaling is bioinformaties geanaliseer wat die annotering van die gedeeltelike volgordes asook die soektog vir 'n kandidaat entstof geen vir die ontwikkeling van 'n DNA entstof ingesluit het. Die P100 geen van Ms02, wat hoë homologie met die P100 geen van die menslike patogeen M. hominis getoon het, is gekies as die kandidaat entstof geen. Die P100 geen is suksesvol gekloneer en gemodifiseer deur middel van setelgerigte mutagenese om die P100 geen geskik te maak vir die invoeging in die soogdier ekspressie vektor, pCI-neo vir toekomstige entstofproewe.

Thesis (MSc)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: The GnRH receptor is a G-protein-coupled receptor in pituitary gonadotrope cells. Binding of its ligand, GnRH, results in synthesis and release of gonadotropin hormones luteinizing hormone (LH) and follicle stimulating hormone (FSH). Steroidogenic factor 1 (SF-1), a transcription factor, binds to specific sites in the promoter region of gonadotropin genes, and thus regulates transcription of these genes. The promoter region of the GnRHreceptor gene contains two SF-1-like binding sites, one at -14 to -8 (site 1) and another at -247 to -239 (site 2), relative to the methionine start codon. The role played by these two SF-1-like sites in basal transcription of the mouse GnRH receptor (mGnRH-R) gene in a pituitary precursor gonadotrope cell line, aT3 cells, was the first area of investigation during this study. Luciferase reporter constructs containing 580 bp of mGnRH-R gene promoter were prepared, where SF-1-like sites were either wildtype or mutated. Four such constructs were made, i.e. wildtype (LG), site 1 mutant (LGM1), site 2 mutant (LGM2) and mutated site 1 plus site 2 (LGM1/2). These constructs were transfected into aT3 cells to determine the effect of mutations of sites 1 and/or 2 on the basal expression of the mGnRH-R gene. Mutation of either site 1 or site 2 had no effect on basal expression of the mGnRH-R gene. It was found that only upon simultaneous mutation of both sites 1 and 2, a 50% reduction in basal transcription took place. The implications of this is that SF-1 protein seems to only require one intact DNA-binding site, to mediate basal transcription of the mGnRH-R gene, suggesting that these two sites lie in close proximity during basal transcription. The effect of the protein kinase A (PKA) pathway on the endogenous mGnRH-R gene was also investigated by incubating non- , transfected aT3 cells with the PKA activators, forskolin and 8-Br-cAMP. Similar incubations were also performed on the wild type and mutated site 1 constructs transfected into pituitary gonadotrope aT3 cells. It was found that forskolin and 8-Br-cAMP were able to increase endogenous mGnRH-R mRNA levels in a concentration-dependent fashion, showing that endogenous GnRH receptor gene expression is stimulated via a protein kinase A pathway. Similar results were obtained with the wildtype promoter construct, showing that the protein kinase A pathway stimulates transcription of the promoter. This effect was only seen with wild type and not with the mutated site 1. These results are consistent with a role for a SF-1-like transcription factor in mediating the protein kinase A effect via binding to the site 1 at position -14 in the GnRH receptor gene. A separate investigation was performed to determine whether 25-hydroxycholesterol (25-0HC) is a ligand for SF-1, by incubating aT3 cells transfected with the various constructs with 25-0HC. Results show a dose-dependant response, with an increase in gene expression at 1 μM and a decrease at higher concentrations, for both mutant and wild type constructs. This suggests that, if SF-1 is indeed the protein binding to sites 1 and 2, then 25-0HC is not a ligand for SF-1 protein in aT3 cells and that the effect of 25-0HC on the mGnRH-R gene is not mediated via site 1. The results indicate that these decreases of expression at the higher concentrations may be due to cytotoxic effects. Towards the end of the study the laboratory obtained a luminoskan instrument with automatic dispensing features. Optimisation studies on the luciferase and β-Gal assays were performed on the luminoskan in a bid to decrease experimental error. It was found that automation of these assays resulted in a decrease in experimental error, showing that future researchers could benefit substantially from these optimisation studies. / AFRIKAANSE OPSOMMING: Die GnRH reseptor is 'n G proteïen-gekoppelde reseptor in pituitêre gonadotroopselle. Binding van die ligand, GnRH, lei tot die sintese en vrystelling van die gonadotropien hormone, luteïniserende hormoon (LH) en follikel stimulerende hormoon (FSH). Steroidogeniese faktor-t (SF-1) is 'n transkripsie faktor wat aan spesifieke areas in die promotergebied van die gonadotropien hormone bind, en dus transkripsie van hierdie gene reguleer. Die promotergebied van die GnRH reseptor geen bevat twee SF-1 bindings areas, een by -14 to -8 (area 1) asook by -247 to -239 (area 2), relatief to die metionien beginkodon. Die rol wat hierdie twee SF-1 areas speel in basale transkripsie van die muis GnRH reseptor (mGnRH-R) geen in 'n pituïtêre voorloper gonadotroop sellyn, aT3 selle, was die eerste gebied van ondersoek gedurende hierdie studie. Plasmiede bestaande uit die 580 basispaar mGnRH-R promoter verbind aan 'n lusiferase geen is vervaardig, waar SF-1-soortige areas enersyds onveranderd gelaat is, of gemuteer is. Vier sulke plasmiede is vervaardig, nl. onveranderd (LG), area 1 mutant (LGM1), area 2 mutant (LGM2) en gemuteerde area 1 plus area 2 (LGM1/2). Hierdie plasmiede is gebruik om aT3 selle te transfekteer om die effek van mutasies van areas 1 en/of 2 op die basale ekspressie van die mGnRH-R geen te ondersoek. Daar is gevind dat mutasies van areas 1 of 2 geen effek op basale ekspressie op die bogenoemde geen gehad het nie. Slegs tydens gelyktydige mutasie van areas 1 en 2 het 'n 50% vermindering in basale transkripsie plaasgevind. Die implikasies hiervan is dat die SF-1 proteïen blykbaar slegs een volledige DNA-bindingsarea benodig om basale transkripsie van die mGnRH-R geen te reguleer. Dit wil dus voorkom of hierdie twee areas baie na aan mekaar geposisioneer is tydens basale transkripsie. Die effek van die proteïen kinase A (PKA) roete op die natuurlike mGnRH-R geen is ook ondersoek tydens inkubasie van nie-getransfekteerde aT3 selle met die PKA akiveerders, forskolin en 8-Br-cAMP. Soortgelyke inkubasie is ook gedoen op die onveranderde en gemuteerde area 1 plasmiede wat in aT3 selle getransfekteer is. Daar is gevind dat forskolin en 8-Br-cAMP daarin geslaag het om die natuurlike mGnRH-R geen mRNA vlakke op 'n konsentrasie-afhanklike wyse te vermeerder. Hierdie resultaat dui daarop aan dat die natuurlike mGnRH-R geen se ekspressie gestimuleer kan word via 'n proteïen kinase A roete. Soortgelyke resultate is verkry met die onveranderde promoter plasmied en dit wys ook daarop dat proteïen kinase A transkripsie deur die promoter kan stimuleer. Hierdie effek was slegs aanwesig met die onveranderde en nie met die gemuteerde area 1 plasmied nie. Die resultate stem ooreen met 'n rol vir SF-1 transkripsie faktor in die regulering van proteren kinase A effek deur middel van binding aan die area 1 by posisie -14 in die GnRH-R geen. 'n Afsonderlike ondersoek is gedoen om vas te stel of 25-hidroksiecholesterol (25-0HC) 'n ligand vir SF-1 is deur getransfekteerde aT3 selle met 25-0HC te inkubeer. Resultate toon 'n dosis-afhanklike respons met 'n verhoging in geen ekspressie by 1 μM en 'n verlaging met hoër konsentrasies vir beide onveranderde en gemuteerde plasmiede. Dit impliseer dat, indien SF-1 wel die faktor is wat aan areas 1 en 2 bind, 25-0HC nie die ligand vir SF-1 proteren in aT3 selle is nie en dat die effek van 25-0HC op die mGnRH-R geen nie gereguleer word via area 1 nie. Die verlaging in ekspressie gevind by die hoër konsentrasies is dalk die gevolg van sitotoksiese effekte. Teen die einde van die studie het die laboratorium luminoskan toerusting met outomatiese pipettering verkry. Optimiseringstudies van die lusifirase en β-Galtoetse is met die luminoskan gedoen in 'n poging om eksperimentele foute te minimaliseer. Daar is gevind dat outomatisering van hierdie toetse wel gelei het tot 'n verlaging in eksperimentele foute. Toekomstige navorsers kan dus grootliks voordeel trek uit hierdie optimiseringstudies.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The Hodgkin-Huxley model, created in 1952, was one of the first models in computational neuroscience and remains the best studied neuronal model to date. Although many other models have a more detailed system description than the Hodgkin-Huxley model, it nonetheless gives an accurate account of various high-level neuronal behaviours. The fields of computational neuroscience and Systems Biology have developed as separate disciplines for a long time and only fairly recently has the neurosciences started to incorporate methods from Systems Biology. Metabolic Control Analysis (MCA), a Systems Biology tool, has not been used in the neurosciences. This study aims to further bring these two fields together, by testing the feasibility of an MCA approach to analyse the Hodgkin-Huxley model. In MCA it is not the parameters of the system that are perturbed, as in the more traditional sensitivity analysis, but the system processes, allowing the formulation of summation and connectivity theorems. In order to determine if MCA can be performed on the Hodgkin-Huxley model, we identified all the discernable model processes of the neuronal system. We performed MCA and quantified the control of the model processes on various high-level time invariant system observables, e.g. the action potential (AP) peak, firing threshold, propagation speed and firing frequency. From this analysis we identified patterns in process control, e.g. the processes that would cause an increase in sodium current, would also cause the AP threshold to lower (decrease its negative value) and the AP peak, propagation speed and firing frequency to increase. Using experimental inhibitor titrations from literature we calculated the control of the sodium channel on AP characteristics and compared it with control coefficients derived from our model simulation. Additionally, we performed MCA on the model’s time-dependent state variables during an AP. This revealed an intricate linking of the system variables via the membrane potential. We developed a method to quantify the contribution of the individual feedback loops in the system. We could thus calculate the percentage contribution of the sodium, potassium and leak currents leading to the observed global change after a system perturbation. Lastly, we compared ion channel mutations to our model simulations and showed how MCA can be useful in identifying targets to counter the effect of these mutations. In this thesis we extended the framework of MCA to neuronal systems and have successfully applied the analysis framework to quantify the contribution of the system processes to the model behaviour. / AFRIKAANSE OPSOMMINMG: Die Hodgkin-Huxley-model, wat in 1952 ontwikkel is, was een van die eerste modelle in rekenaarmagtige neurowetenskap en is vandag steeds een van die bes-bestudeerde neuronmodelle. Hoewel daar vele modelle bestaan met ’n meer uitvoerige sisteembeskrywing as die Hodgkin-Huxley-model gee dié model nietemin ’n akkurate beskrywing van verskeie hoëvlak-sisteemverskynsels. Die twee velde van sisteembiologie en neurowetenskap het lank as onafhanklike dissiplines ontwikkel en slegs betreklik onlangs het die veld van neurowetenskap begin om metodes van sisteembiologie te benut. ’n Sisteembiologiemetode genaamd metaboliese kontrole-analise (MKA) is tot dusver nog nie in die neurowetenskap gebruik nie. Hierdie studie het gepoog om die twee velde nader aan mekaar te bring deurdat die toepasbaarheid van die MKA-raamwerk op die Hodgkin-Huxley-model getoets word. In MKA is dit nie die parameters van die sisteem wat geperturbeer word soos in die meer tradisionele sensitiwiteitsanalise nie, maar die sisteemprosesse. Dit laat die formulering van sommasie- en konnektiwiteitsteoremas toe. Om die toepasbaarheid van die MKA-raamwerk op die Hodgkin-Huxleymodel te toets, is al die onderskeibare modelprosesse van die neurale sisteem geïdentifiseer. Ons het MKA toegepas en die kontrole van die model-prosesse op verskeie hoëvlak, tydsonafhanklike waarneembare sisteemvlak-eienskappe, soos die aksiepotensiaal-kruin, aksiepotensiaal-drempel, voortplantingspoed en aksiepotensiaal-frekwensie, gekwantifiseer. Vanuit hierdie analise kon daar patrone in die proseskontrole geïdentifiseer word, naamlik dat die prosesse wat ’n toename in die natriumstroom veroorsaak, ook sal lei tot ’n afname in die aksiepotensiaal-drempel (die negatiewe waarde verminder) en tot ’n toename in die aksiepotensiaal-kruin, voortplantingspoed en aksiepotensiaalfrekwensie. Deur gebruik te maak van eksperimentele stremmer-titrasies vanuit die literatuur kon die kontrole van die natriumkanaal op die aksiepotensiaaleienskappe bereken en vergelyk word met die kontrole-koëffisiënte vanuit die modelsimulasie. Ons het ook MKA op die model se tydsafhanklike veranderlikes deur die verloop van die aksiepotensiaal uitgevoer. Die analise het getoon dat die sisteemveranderlikes ingewikkeld verbind is via die membraanpotensiaal. Ons het ’n metode ontwikkel om die bydrae van die individuele terugvoerlusse in die sisteem te kwantifiseer. Die persentasie-bydrae van die natrium-, kalium- en lekstrome wat tot die waarneembare globale verandering ná ’n sisteemperturbasie lei, kon dus bepaal word. Laastens het ons ioonkanaalmutasies met ons modelsimulasies vergelyk en getoon hoe MKA nuttig kan wees in die identifisering van teikens om die effek van hierdie mutasies teen te werk. In hierdie tesis het ons die raamwerk van MKA uitgebrei na neurale sisteme en die analise-raamwerk suksesvol toegepas om die bydrae van die sisteemprosesse tot die modelgedrag te kwantifiseer.

Thesis (MSc)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: Nanoscale visualisation of live cells and cellular components under physiological conditions has long been a goal in microscopy. The objective of this study was to validate the use of Atomic Force Microscopy (AFM) as a new tool in unravelling the mysteries of antimicrobial peptide mechanism of action. Using the simplest AFM imaging technique, we were able to analyse the influence of haemolytic melittin and anti-bacterial magainin 2 on different target membranes at nanometer resolution, without using fixing agents. First, magainin 2 was synthesised and purified by gel permeation chromatography and high performance liquid chromatography (HPLC). The purity of magainin 2 and melittin, isolated from bee venom (Sigma-Aldrich), was verified with electro spray ionisation mass spectrometry (ESI-MS). Second, dose-response experiments were used to determine the optimum peptide/target cell ratio that would allow interaction with the membrane without causing lysis. Third, peptide/target-cell samples were placed on silica plates and visualised using contact mode AFM. Images obtained of the cells before and after peptide treatment, showed distinct changes in cell membrane surface topology. We observed grooves, lesions, membrane collapse and vesiculation depending on the concentration, type of peptide and target-cell used, allowing us to make conclusions regarding the mechanism of action of melittin and magainin 2. In comparison with model membrane studies, our AFM results show that a peptide can function by more than one mechanism of action depending on the structural composition of the membrane, which appears to have specific segregated lateral organisation. Magainin 2 (non-toxic) selectively targets cell membranes using different mechanisms of action. In this way it can lyse bacterial membranes (anti-bacterial agent) using one mechanism, while using another mechanism to interact with mammalian cells at physiological concentrations, without destroying them. In contrast, melittin (toxic) is non-selective, and uses the same mechanism of interaction with bacterial and mammalian cells. In conclusion, we propose a new holistic model for the mechanism of action of antimicrobial peptides. / AFRIKAANSE OPSOMMING: Nanoskaal visualiseering van lewende selle en sellulêre komponente onder fisiologiese toestande is al 'n geruime tyd 'n mikpunt in mikroskopie. Die doel van hierdie studie was om antimikrobiese peptiede se meganisme van werking op teikenselle op nanoskaalvlak met AFM te visualiseer. Sonder om fikseermiddels by te voeg, het ons die eenvoudigste AFM tegniek gebruik om die effek van hemolitiese melittien en anti-bakteriële magainin 2 op verskillende teikenselle, in nanometer resolusie, waar te neem. Eerstens is Magainin 2 gesintesiseer en gesuiwer met behulp van gelpermeasie chromatografie en hoë doeltreffenheid vloeistof chromatografie (HPLC). Die suiwerheid van magainin 2 en kommersiële bye gif melittien, is bevestig met behulp van elektrosproei-ionisasie massaspektrometrie (ESI-MS). Tweedens, is dosis-respons eksperimente gebruik om die optimale peptied/teikensel verhouding te bepaal voordat membraanliese plaasvind. Derdens, is peptied/teikensel monsters op silika plate gevisualiseer met gebruik van kontak AFM. Die beelde van die selle, voor en na peptied behandeling, het duidelike veranderinge in seltopologie getoon. Ons het groewe, letsels, membraaninstorting en vesikulasie, afhangende van die konsentrasie peptied en teikensel gebruik, waargeneem. Dit het ons toegelaat om tot gevolgtrekkings te kom aangaande die meganisme van werking van melittien en magainin 2. In ooreenstemming met model membraan studies, het ons AFM resultate gewys dat 'n peptied veelvoudige meganismes van werking kan hê, afhangend van die strukturele samestelling van die membraan, wat klaarblyklik laterale segregasie toon. Magainin 2 (nie-giftig) is selektief ten opsigte van teikenselle omdat dit gebruik maak van verskillende meganismes van werking op bakteriële en soogdier selle. In teenstelling is melittien (giftig) nie-selektief, en gebruik dieselfde meganisme van werking op bakteriële en soogdierselle. Ten slotte, stel ons 'n nuwe model vir die meganisme van werking voor.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Due to a global lack of access to potable water, a problem particularly affecting people in developing countries and the poor, improvement on existing water purification methods are necessary to provide more cost effective, accessible and efficient methods of water purification. In drinking water systems, biofilms are a potential source of contamination, which can affect the biological stability and hygienic safety of water. In industrial water systems, biofilms can cause corrosion, resistance in flow systems and a decrease in efficiency of membranes. Nanotechnology has been identified as a technology to utilize in water purification problem solving. Alternatives to the use of chemical biocides and antibiotics need to be investigated therefore; the focus of this study was the fabrication and characterization of polymer nanofibers containing silver nanoparticles as biocide and anti-biofouling nanofibers with hydrolytic enzymes immobilized on the surface. The aim of this study was to synthesize and compare poly (vinyl alcohol) (PVA) nanofibers and poly (acrylonitrile) (PAN) nanofibers with silver nanoparticles to determine which type of fiber will be the most appropriate for application in water sanitation. The two types of fibers were to be compared based on morphology, silver nanoparticle content, physical distribution of silver nanoparticles, levels of silver leaching from the fibers in water, which could imply toxicity, and most importantly, anti-microbial efficacy. Back scattering electron images revealed that silver nanoparticles in PVA nanofibers were more evenly dispersed than in PAN nanofibers, but that PAN nanofibers had higher silver nanoparticle content. This was confirmed by energy dispersive X-ray (EDX) analysis. Both PVA and PAN nanofibers containing silver nanoparticles had excellent anti-microbial activity, with PVA nanofibers killing between 91% and 99% of bacteria in a contaminated water sample and PAN nanofibers killed 100%. When investigated by SEM, the biocidal effect of PAN nanofibers containing silver nanoparticles can be observed as morphological changes in the cell walls. Neither PVA nor PAN nanofibers leached silver into water. PVA is a non-toxic and biodegradable synthetic polymer, and PVA-silver nanofibers have excellent anti-microbial activity, making it applicable in water sanitation in an environmental conscious milieu. PAN nanofibers are more conductive to the formation of silver nanoparticles, have higher silver nanoparticle content, allowing the complete sanitation of pathogenically contaminated water samples. PAN nanofibers also have better longevity and strength in water, making it ideal for water filtration and sanitation in higher throughput systems. Furthermore, immobilized enzymes are being investigated as possible alternatives to inefficient conventional methods of controlling and removing biofilms from filtration systems. This study demonstrates the covalent immobilization of two industrial proteases and an amylase enzyme onto polymer nanofibers widely used in filtration membranes. Confirmed by FTIR, these nanofibers were successfully activated by amidination, allowing the covalent immobilization of respectively two serine proteases and an α-amylase onto the fibers. When inspected visually, fibers largely retained their original morphology after activation and enzyme immobilization. Immobilized enzymes were, however visible as aggregated particles on the nanofiber surfaces. The large surface area to volume ratio provided by the nanofibers as immobilization surface, allowed sufficient amounts of enzymes to be immobilized onto the fibers so that all enzymes retained above 80% of the specific activity of the free enzymes. For each of the immobilized enzymes, just below 30% of initial activity was retained after 10 repeated cycles of use. Fibers with immobilized enzymes on their surface did not support the growth of biofilms, as opposed to plain nanofibers, which did support the growth of biofilms. When considering the combined advantages of this effective immobilization process, the robustness of the enzymes used in this study, and their effectiveness against biofilms in their immobilized state, a valuable addition has been made to technology available for the control of biofilm formation on filtration membranes, and could potentially be employed to control biofilm formation in water filtration systems. A combination of anti-microbial and anti-biofouling nanofibers into a single nanofiltration product may prove to be highly applicable in water sanitation systems. / AFRIKAANSE OPSOMMING: As gevolg van 'n wêreldwye gebrek aan toegang tot drinkbare water, 'n probleem wat veral mense in ontwikkelende lande en armes raak, is dit van belang dat bestaande metodes van watersuiwering verbeter word om voorsiening te maak vir meer koste-effektiewe, toeganklike en doeltreffende metodes van watersuiwering. In drinkwater stelsels is biofilms 'n potensiële bron van besoedeling, wat die biologiese stabiliteit en die higiëniese veiligheid van water beïnvloed. In industriële waterstelsels kan biofilms tot die verwering van pyplyne lei, weerstand in die stroomstelsels veroorsaak en 'n afname in die doeltreffendheid van membrane veroorsaak. Nanotegnologie is geïdentifiseer as 'n tegnologie wat aangewend kan word in watersuiwerings probleemoplossing. Alternatiewe vir die gebruik van chemiese antimikrobiese middels moet dus ondersoek word. Hierdie studie fokus dus op die vervaardiging en karakterisering van polimeer nanovesels met silwer nanopartikels wat ingesluit is as antimikrobiese middel en anti-biofilm vesels met hidrolitiese ensieme geïmmobiliseer op die oppervlak. Die doel van hierdie studie was om poli (viniel alkohol) (PVA) nanovesels en poli (akrielonitriel) (PAN) nanovesels te sintetiseer waarby silwer nanopartikels ingesluit is, en te bepaal watter tipe vesel die mees geskikte sal wees vir die gebruik in water sanitasie. Die twee tipes vesels is met mekaar vergelyk gebaseer op morfologie, silwer nanopartikel inhoud, fisiese verspreiding van silwer nanopartikels, vlakke van silwer uitloging vanuit die vesels in water, wat toksisiteit tot gevolg kan hê, en die belangrikste, antimikrobiese effektiwiteit. Terug verstrooiing elektron beelde het aan die lig gebring dat die silwer nanopartikels in PVA nanovesels meer eweredig versprei was as in PAN nanovesels, maar dat PAN nanovesels 'n hoër silwer nanopartikel inhoud gehad het. Dit is bevestig deur “energy dispersive X-ray” (EDX) analise. Beide PVA en PAN nanovesels met silwer nanopartikels het uitstekende antimikrobiese aktiwiteit getoon, met PVA vesels wat tussen 91% en 99% bakterieë in besoedelde water monsters kon doodmaak en PAN vesels wat 100% bakterieë kon uitwis. Wanneer vesels ondersoek is met ʼn skandeer elektronmikroskoop (SEM), kon die antimikrobiese effek van PAN vesels met silwer nanopartikels as morfologiese veranderinge in die selwande waargeneem word. Nie PVA of PAN nanovesels loog silwer uit in water nie. PVA is 'n nie-toksiese en bioafbreekbare sintetiese polimeer, en PVA-silwer nanovesels het uitstekende antimikrobiese aktiwiteit, wat dit van toepassing maak op water sanitasie in ʼn omgewings bewuste milieu. PAN vesels is meer gunstig tot die vorming van silwer nanopartikels, en het 'n hoër silwer nanopartikel inhoud, dus word patogeen besoedelde water volledig gesteriliseer. PAN vesels het ook 'n beter langslewendheid en weerstandige sterkte in water, wat dit ideaal vir water filtrasie en sanitasie in hoër deursettings stelsels maak. Geïmmobiliseerde ensieme word ook ondersoek as moontlike alternatiewe tot ondoeltreffende konvensionele metodes van beheer en die verwydering van biofilms uit water stelsels. Hierdie studie toon die kovalente immobilisasie van twee industriële proteases en 'n amilase ensiem op polimeer vesels wat gebruik word in filtrasie membrane. Bevestig deur FTIR, is PAN vesels suksesvol geaktiveer deur amidinasie, sodat die kovalente immobilisasie van onderskeidelik twee serien proteases en 'n α-amilase op die vesels moontlik is. Met visuele ondersoek kan gesien word die vesels behou grootliks hul oorspronklike morfologie na aktivering en ensiem immobilisasie. Geïmmobiliseerde ensieme is egter sigbaar as saamgevoegde deeltjies op die nanovesel oppervlaktes. Die groot oppervlakarea: volume-ratio van die vesels wat dien as immobilisasie oppervlak, laat toe dat voldoende hoeveelhede van ensieme geïmmobiliseer word sodat alle ensieme meer as 80% van die spesifieke aktiwiteit van die vrye ensieme behou. Vir elk van die geïmmobiliseer ensieme, is net minder as 30% van die aanvanklike aktiwiteit behou na 10 siklusse van hergebruik. Vesels met geïmmobiliseerde ensieme op hul oppervlaktes het nie die groei van biofilms ondersteun nie, in teenstelling met gewone vesels, sonder ensieme, wat die groei van biofilms ondersteun. As die gesamentlike voordele van hierdie doeltreffende immobilisasie proses, die robuustheid van die ensieme en hulle doeltreffendheid teen biofilms in hul geïmmobiliseerde toestand in ag geneem word, is ʼn waardevolle toevoeging gemaak tot tegnologie wat beskikbaar is vir die beheer van biofilm vorming op filtrasie membrane, en dit kan potensieel gebruik word om biofilm vorming filter stelsels te beheer. Die kombinasie van anti-mikrobiese en anti-biofilm vesels in ʼn enkele nanofiltrasie produk moet nagestreef word, omdat dit hoogs van toepassing sal wees in water sterilisasie stelsels.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Metabolic systems are open systems continually subject to changes in the surrounding environment that cause uctuations in the state variables and perturbations in the system parameters. However, metabolic systems have mechanisms to keep them dynamically and structurally stable in the face of these changes. In addition, metabolic systems also cope with large changes in the uxes through the pathways, not letting metabolite concentrations vary wildly. Quantitative measures have previously been proposed for "metabolic regulation", using the quantitative framework of Metabolic Control Analysis. However, the term "regulation" is so loosely used so that its content is mostly lost. These di erent measures of regulation have also not been applied to a model and comparably investigated prior to this study. Hence, this study analyses the usefulness of the di erent quantitative measures in answering di erent types of regulatory questions. Thus, the aim of this study was to distinguish the above mentioned aspects of metabolic regulation and to nd appropriate quantitative measures for each, namely dynamic stability, structurally stability, and homeostasis. Dynamic stability is the property of a steady state to return to its original state after a perturbation in a metabolite in the system, and can be analysed in terms of self and internal-response coe cients. Structural stability is concerned with the change in steady state after a perturbation of a parameter in the system, and can be analysed in terms of concentration-response coe cients. Furthermore, it is shown that control patterns are useful in understanding which system properties determine structural stability and to what degree. Homeostasis is de ned as the change in the steady-state concentration of a metabolite relative to the change in the steady-state ux through the metabolite pool following a perturbation in a system parameter, and co-response coe cients are proposed as quantitative measures of homeostasis. More speci cally, metabolite-ux coresponse coe cients allow the de nition of an index that quanti es to which degree a metabolite is homeostatically regulated. A computational model of a simple linear metabolic sequence subject to feedback inhibition with di erent sets of parameters provided a test-bed for the quantitative analysis of metabolic regulation. Log-log rate characteristics and parameter portraits of steady-state variables, as well as response and elasticity coe cients were used to analyse the steady-state behaviour and control properties of the system. This study demonstrates the usefulness of generic models based on proper enzyme kinetics to further our understanding of metabolic behaviour, control and regulation and has laid the groundwork for future studies of metabolic regulation of more complex core models or of models of real systems. / AFRIKAANSE OPSOMMING: Metaboliese sisteme is oop sisteme wat gedurig blootgestel word aan `n uktuerende omgewing. Hierdie uktuasies lei tot veranderinge in beide interne veranderlikes en parameters van metaboliese sisteme. Metaboliese sisteme besit egter meganismes om dinamies en struktureel stabiel te bly. Verder verseker hierdie meganismes ook dat die konsentrasies van interne metaboliete relatief konstant bly ten spyte van groot veranderinge in uksie deur die metaboliese pad waarvan hierdie metaboliete deel vorm. Kwantitatiewe maatstawwe is voorheen voorgestel vir "metaboliese regulering", gebaseer op die raamwerk van Metaboliese Kontrole Analise. Die onkritiese gebruik van die term "regulering" ontneem egter hierdie konsep van sinvolle betekenis. Voor hierdie studie is die voorgestelde maatstawwe van regulering nog nie toegepas op 'n model ten einde hulle met mekaar te vergelyk nie. Die huidige studie ondersoek die toepaslikheid van die verskillende maatstawwe om verskillende tipe vrae oor regulering te beantwoord. Die doelwit van hierdie studie was om aspekte van metaboliese regulering, naamlik dinamiese stabiliteit, strukturele stabiliteit en homeostase, te onderskei, asook om 'n gepaste maatstaf vir elk van die verskillende aspekte te vind. Dinamiese stabiliteit is 'n eienskap van 'n bestendige toestand om terug te keer na die oorspronklike toestand na perturbasie van die konsentrasie van 'n interne metaboliet. Hierdie aspek van regulering kan in terme van interne respons en self-respons koeffi siente geanaliseer word. Strukturele stabiliteit van 'n bestendige toestand beskryf die mate van verandering van die bestendige toestand nadat 'n parameter van die sisteem geperturbeer is, en kan in terme van konsentrasie-responskoeffisiente geanaliseer word. Verder wys hierdie studie dat kontrole patrone van nut is om vas te stel watter eienskappe van 'n sisteem die strukturele stabiliteit bepaal en tot watter mate. Homeostase word gede finieer as die verandering in die konsentrasie van 'n interne metaboliet relatief tot die verandering in die uksie deur daardie metaboliese poel nadat 'n parameter van die sisteem verander het. Vir die analise van hierdie aspek van regulering word ko-responskoe ffisiente as 'n maatstaf voorgestel. Meer spesi ek kan metaboliet- uksie ko-responskoeff siente gebruik word om `n indeks te de nieer wat meet tot watter mate 'n metaboliet homeostaties gereguleer word. 'n Rekenaarmatige model van 'n eenvoudige lineere metaboliese sekwens wat onderhewig is aan terugvoer inhibisie is gebruik om die verskillende aspekte van metaboliese regulering kwantitatief te analiseer met vier verskillende stelle parameters. Dubbel-logaritmiese snelheidskenmerke en parameter portrette van bestendige toestandsveranderlikes, asook van respons- en elastisiteit koeffisente is gebruik om die bestendige toestandsgedrag en kontrole eienskappe van die sisteem te analiseer. Hierdie studie demonstreer die nut van generiese modelle wat op korrekte ensiemkinetika gebaseer is om ons verstaan van metaboliese gedrag, kontrole en regulering te verdiep. Verder dien hierdie studie as grondslag vir toekomstige studies van metaboliese regulering van meer ingewikkelde kernmodelle of modelle van werklike sisteme. / National Research Foundation

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Infection of potatoes by viral pathogens causes reduced crop yield and subsequent economic loss. In South Africa Potato virus Y (PVY) and Potato leafroll virus (PLRV) are the two most destructive viruses infecting potatoes. Several other viral pathogens exist, including Potato virus X (PVX), Potato virus M (PVM), Potato virus A (PVA), Potato virus S (PVS), Potato mop-top virus (PMTV), Tomato spotted wilt virus (TSWV) and Potato spindle tuber viroid (PSTVd). Although the aforementioned pathogens are found infecting potatoes around the world, there are no published information pertaining to the prevalence of these viral agents in South Africa. Currently, the occurrence of PLRV infection in potatoes of South Africa has reached epidemic proportions. A previous phylogenetic investigation undertaken in our laboratory of South African PLRV isolates, using coat protein (CP) gene sequences, found large variation between native South African PLRV isolates and most other isolates from elsewhere in the world; with their nearest relatives being single isolates from Australia and North America. In this study the incidence of PVX, PVM, PVA, PVS, PMTV, TSWV and PSTVd was investigated. A large number of potato plant and tuber samples was collected and infected samples were identified with reverse transcriptase polymerase chain reaction (RT-PCR) amplification of the CP gene or the whole genome in the case of PSTVd. The amplified nucleic acid segments were sequenced, aligned with international reference sequences and analysed phylogenetically to determine their relative relationships with these reference sequences. The CP genes of PLRV isolates were sequenced and phylogenetically investigated to determine how these new isolates compared relative to the previous findings from our laboratory. In addition, the complete genomes of two PLRV isolates were sequenced and phylogenetically investigated as a preliminary study to investigate the apparent increase of pathogenicity of certain variants of South African PLRV. Results obtained showed that only PVX and PVS were present in the samples collected and the incidences of these viruses were very low (2.0 and 1.1% respectively). The phylogenetic analyses of the CP genes, indicated that the PVX and PVS variants isolated in this study, were part of the dominant types of variants found worldwide. From the analyses of the PLRV CP and whole genome sequences, it was determined that many of the PLRV variants found in South Africa, are genetically distinctly different from those around the world. This warrants further investigation into the increased pathogenicity experienced with South African PLRV. / AFRIKAANSE OPSOMMING: Infeksie van aartappels deur virale patogene veroorsaak verlaagde opbrengs en gevolglike ekonomiese verlies. In Suid-Afrika is Aartappelvirus Y (PVY) en Aartappelrolblad virus (PLRV) die twee mees vernietigende virusse wat aartappels infekteer. Verskeie ander virale patogene, insluitend Aartappelvirus X (PVX), Aartappelvirus M (PVM), Aartappelvirus A (PVA), Aartappelvirus S (PVS), Aartappel "moptop" virus (PMTV), Kromnekvirus (TSWV) en Aartappel "spindle tuber" viroïed (PSTVd) kom ook wêreldwyd in aartappels voor. Alhoewel hierdie virusse aartappels wêreldwyd besmet, is daar geen gepubliseerde inligting met betrekking tot die voorkoms van hierdie virusse of die viroïed in Suid-Afrika nie. Tans het die voorkoms van PLRV infeksie in aartappels in Suid-Afrika epidemiese proporsies bereik. In 'n vorige filogenetiese ondersoek van die mantelproteïen (MP) nukleotiedvolgordes van Suid Afrikaanse PLRV isolate in ons laboratorium, is groot variasie tussen hierdie inheemse isolate en die meeste ander isolate van elders in die wêreld bevind. Die Suid Afrikaanse PLRV variante betree 'n unieke intermediêre posisie tussen die internasionale isolate en enkele isolate van Australië en Amerika. In hierdie studie is die voorkoms van PVX, PVM, PVA, PVS, PMTV, TSWV en PSTVd ondersoek. Groot aantal aartappelplant en -knol monsters is versamel en infeksie is getoets met tru-transkripsie polimerase kettingreaksie (RT-PCR) amplifisering van die MP geen, of die hele genoom in die geval van PSTVd. Die nukleïensuurvolgordes is bepaal en vergelyk met internasionale verwysingsvolgordes. Die relatiewe verhoudings tussen die bepaalde volgordes en die verwysingsvolgordes is geanaliseer met filogeneties ontledings. Die MP gene van PLRV isolate se volgordes is bepaal en filogeneties ontleed om hierdie nuwe isolate te vergelyk relatief tot vorige bevindinge in ons laboratorium. Die volledige genome van twee PLRV isolate se volgordes is bepaal en filogeneties ontleed as 'n voorlopige studie om die oënskynlike toename in patogenisiteit van Suid-Afrikaanse PLRV te ondersoek. Resultate het getoon dat slegs PVX en PVS teenwoordig was in die monsters wat versamel is en dat die voorkoms van hierdie virusse baie laag was (2.0% en 1.1% onderskeidelik). Die filogenetiese ontleding van die MP gene het aangedui dat die Suid Afrikaanse variante van PVX en PVS, geisoleer in hierdie studie, van die dominante tipes is wat mees gereeld internationaal voorkom. Uit die ontleding van die PLRV MP en heelgenoom volgordes, is vasgestel dat baie van die PLRV variante wat in Suid-Afrika aangetref word, geneties meer verskillend is as die van regoor die wêreld. Dus, regverdig dit, verdere ondersoek van die verhoogde patogenisiteit van Suid Afrikaanse PLRV variante.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: In the present-day competitive global market, wine industries are constantly aiming to improve the wine-making process,including the role of yeast. The most commonly used wine yeast is Saccharomyces cerevisiae, which is able to produce high quality wines, but problem fermentations do sometimes arise. The occurrence of stuck and sluggish fermentations pose a serious problem leading to loss of productivity and quality. Although the precise mechanism leading to stuck fermentations is unknown, they are often correlated with high fructose to glucose ratios in the wine-must. S. cerevisiae is a glucophylic yeast, indicating its preference for consuming glucose over fructose. Both these hexose sugars are present in unfermented wine must, mostly in equal concentrations. As fermentation progresses, glucose is consumed at a faster rate than fructose, leading to an increase in the fructose to glucose ratio. Yeast are left with the undesirable fructose at the later stages of fermentation, when the environmental stresses on the yeast can lead to stuck or sluggish fermentation. This residual fructose can lead to undesirable sweetness, as fructose is about twice as sweet as glucose. Even with the extensive research into yeast metabolism, there is as yet no definitive explanation as to why yeasts ferment glucose faster than fructose. This study aimed to investigate the mechanism responsible for the faster consumption of glucose over fructose of a commercially used wine yeast strain S. cerevisiae VIN 13. The first two steps of sugar metabolism, uptake and phosphorylation, were investigated as the possible sites of discrepancy in fermentation rates. Enzyme rates and affinities for both glucose and fructose as substrates for the relevant enzymes were experimentally determined. These kinetic parameter values were used to improve an existing model of yeast glycolytic pathway to model wine fermentations. The feasibility of constructing and validating a kinetic model of wine fermentations were investigated, by comparing model predicted fluxes with experimentally determined fluxes. Another aspect of this study was an investigation into the effect of hexose sugar type on fermentation profiles. Wine fermentations were done with only one hexose sugar as carbon source to determine if it has an effect on the flux through metabolism. This work succeeded in the construction of a kinetic model that distinguished between glucose and fructose as carbon source. The glucose was consumed faster than fructose, with control lying in the hexose transport step. It was also established that fermentation prfiles of fermentations with only one sugar was the same for both one sugar type fermentations. Fermentation with either glucose or fructose as the sole carbohydrate source had the same specfic production and consumption rates as normal fermentations with both sugars. Construction of detailed kinetic models can aid in the metabolic and cellular engineering of novel yeast strains. By identifying the importance of hexose transport, and thus the glucophilic character of the yeast, in flux control, yeast transporters can be targeted for strain improvement. This may in turn lead to more effective fermentation practices for controlling problem fermentations, or to the development of novel strains that utilizes fructose in the same manner as glucose, and in so doing lower the risk of stuck or sluggish wine fermentation. / AFRIKAANSE OPSOMMING: In die hedendaagse kompeterende wynmark is wynmakers aanhoudend besig om die wynmaak proses te verbeter en dit sluit die verbetering van wyngis in. Die mees algemeenste gebruikte wyngis is Saccharomyces cerevisiae, omdat dit wyn van gehalte produseer, maar probleem fermentasies kom wel voor. Die verskynsel van vasval of stadige fermentasies kan lei tot die verlies van produksie en kwaliteit. Die oorsaak van probleem fermentasies is gewoontlik veelvoudig, maar die verhouding van glukose tot fruktose in die wyn-mos kan ongunstig raak om fermentasies te onderhou. S. cerevisiae is 'n glukofiliese gis, wat sy voorkeur om glukose bo fruktose te gebruik beskryf. Albei hierdie heksose suikers is teenwoordig in ongefermenteerde wyn-mos, meestal in gelyke hoeveelhede. Soos fermentasies vorder word glukose vinniger verbruik as fruktose wat lei tot 'n toename in die fruktose tot glukose verhouding. Die gis moet dus die fruktose in die later stadium van fermentasie gebruik wanneer die omgewings druk op die gis kan lei tot probleem fermentasies. Die oorblywende fruktose kan lei tot ongewenste soetheid aangesien fruktose twee keer soeter is as glukose. Selfs met die ekstensiewe navorsing met betrekking tot gis metabolisme is daar nog nie 'n verduideliking hoekom gis glukose vinniger as fruktose gebruik nie. Hierdie studie het beoog om die meganisme wat lei tot die vinniger verbruik van glukose oor fruktose te ondersoek vir 'n kommersieël gebruikte gis S. cerevisiae VIN 13. Die eerste twee stappe van suiker metabolisme, suiker opname en fosforilasie, was ondersoek as die moontlike punt van die verskil in fermentasie tempo. Ensiem snelhede en affiniteite vir beide glukose en fruktose as substrate vir die ensieme van belang was eksperimenteel bepaal. Hierdie waardes is gebruik om 'n bestaande model van gis glikolise aan te pas vir wyn fermentasies. Die uitvoerbaarheid van saamstel en valideer van 'n kinetiese model van wyn fermentasies was ondersoek, deur model voorspelde fluksie waardes met eksperimentele fluksie waardes te vergelyk. 'n Ander aspek van die studie was die ondersoek van die effek van heksose suiker tipe op fermentasie profiel. Wyn fermentasies is gedoen met slegs een heksose suiker as koolstof bron om te bepaal of dit 'n invloed het op die fluksie deur metabolisme. Hierdie werk het daarin geslaag om 'n kinetiese model saamtestel wat onderskei tussen glukose en fruktose as koolstof bron. Die glukose is vinniger verbruik as fruktose, met beheer gesetel in die heksose opname stap. Dit was ook vasgestel dat fermentasie profiele van fermentasies met slegs een suiker nie verskil het vir fermentasies met slegs fruktose of glukose. Fermentasies met slegs een suiker het dieselfde spesifieke produksie en konsumpsie tempo gehad as die normale fermentasie met albei suikers. Die konstruksie van 'n gedetailleerde kinetiese model kan gebruik word in die metaboliese en sellulêre ontwikkeling van nuwe gisstamme. Deur die ontdekking van die belangrikheid van heksose opname in fluksie beheer, wat lei tot die glukofiliese karakter van gis, kan gis opname geteiken word vir gis ontwikkeling. Dit mag om die beurt lei tot meer effektiewe fermentasie praktyk in die beheer van probleem fermentasies, of die ontwikkeling van nuwe stamme wat fruktose in dieselfde manier as glukose benut, en sodoende die risiko van vasval of stadige wyn fermentasies verlaag. / National Research Foundation / Post-graduate Merit Bursary

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The South African ostrich industry is under enormous threats due to diseases contracted by the ostriches. H5N2 virus (avian influenza) outbreaks the past two years have resulted in thousands of ostriches having to be culled. However, the more silent respiratory infectious agents of ostriches are the three ostrich-specific mycoplasmas. Named Ms01, Ms02, and Ms03, these three mycoplasmas are responsible for dramatic production losses each year, due to their intrusive nature and the fact that no vaccines are currently available to prevent mycoplasma infections in ostriches. The use of antibiotics does not eradicate the disease completely, but only alleviates symptoms. The ostrich industry commissioned investigations into the development of three specific vaccines using the relatively novel approach of DNA vaccination. The concept of DNA vaccine development is based on the availability of complete genome sequences of the pathogen against which the vaccine is to be developed. This is necessary in order to identify vaccine candidate genes through comparative genomic studies. The Ms02 genome has previously been sequenced, resulting in 28 large contiguous sequences. This thesis used the technique of Thermal Asymmetric Interlaced Polymerase Chain Reaction (TAIL-PCR) to attempt assembly of these 28 contiguous sequences. The number was reduced to 14 large contiguous sequences, which were then subjected to repetitive sequence analysis and open reading frame analysis. Bioinformatic software was also used to predict the origin of replication. The extent of repeats in the Ms02 genome is illustrated, as well as the problems with genome assembly when dealing with repetitive-rich and A+T-rich genomes as those of mycoplasmas. Previous studies determined the mycoplasma oppA gene to be a good vaccine candidate gene, due to its cytadherent properties. This thesis describes the development of three DNA vaccines containing the Ms02 oppA gene, and a preliminary attempt to prove expression of one of these vaccines in a cell culture-based system. The DNA vaccine vectors pCI-neo, VR1012, and VR1020 were chosen for the vaccine development. The Ms02 oppA gene was also cloned into the prokaryotic expression vector pGEX-4T-1 in order to express the OppA protein for purification. The purified protein may be used in future serological tests in ostrich vaccination trials. In this study the protein was used to elicit anti-OppA rabbit antibodies, which were used to attempt detection of the pCI-neo-driven OppA protein expression in an MDA cell line in a transfection study. However, preliminary findings could not detect expression, but did indicate that the currently used colorimetric western blot technique may not be sensitive enough. It is suggested that different cell lines need to be investigated. Further optimisations are also required to decrease the observed non-specific binding. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse volstruisbedryf is onder geweldige druk vanweë siektes wat die volstruise bedreig. Die epidemie van die H5N2 virus (voëlgriep) in die afgelope twee jaar het veroorsaak dat duisende volstruise van kant gemaak moes word. Daar is egter nog ‘n bedreiging wat tot geweldige produksie verliese lei elke jaar: die respiratoriese infeksies wat versoorsaak word deur die drie volstruis mikoplasmas, genoem Ms01, Ms02 en Ms03. Geen entstowwe is tans beskibaar om die infeksies te voorkom nie, en behandeling met behulp van antibiotikas is nie effektief in die genesing van infeksie nie, maar help net om die simptome te verlig. Weens die erns van die saak, het die Suid-Afrikaanse volstruisbedryf ‘n ondersoek geloods na die ontwikkeling van enstowwe teen elkeen van die drie volstruis mikoplasmas. Die relatiewe nuwe benadering van DNA-entstof ontwikkeling was die strategiese keuse. Die beginsel van DNA-entstof ontwikkeling berus op die beskikbaarheid van die genoomvolgordes van die siekte-veroorsakende organisme waarteen die enstof ontwikkel word. Geskikte kandidaat entstof gene word so opgespoor met behulp van vergelykende studies met ander beskikbare genome. Die Ms02 genoomvolgorde is voorheen bepaal en word verteenwoordig deur 28 groot geenvolgorde fragmente. Die tegniek van Thermal Asymmetric Interlaced Polymerase Chain Reaction (TAIL-PCR) is gebruik om van die 28 fragmente aan mekaar te las. Die aantal fragmente is verminder na 14 groot geenvolgorde fragmente, wat vervolgens gebruik was om die omvang van herhalende volgordes in die genoom te bepaal, om nuwe leesrame te ondersoek, asook om die oorsprong van DNA replikasie op te spoor met behulp van bioinformatika sagteware. Die omvang van die herhalende aard van die Ms02 genoom word geïllustreer, asook die gepaardgaande probleme met die las van geenvolgorde fragmente wanneer met genome van veelvuldige herhalende volgordes, wat boonop A+T-ryk is, gewerk word, soos die van mikoplasmas. Vorige studies het die mikoplasma oppA geen geïdentifiseer as ‘n geskikte kandidaat entstof geen as gevolg van sy selaanhegting-eienskappe. Hierdie studie behels die invoeging van die Ms02 oppA geen in drie DNA-enstof vektore, naamlik pCI-neo, VR1012, en VR1020, asook die voorlopige poging om bewys van uitdrukking van een van die entstowwe in ‘n selkultuursisteem te bewerkstellig. Die geen is ook gekloneer in die prokariotiese ekspressie vektor pGEX-4T-1, ten einde die Ms02 OppA proteïen te isoleer. Die geïsoleerde proteïen kan in serologiese toetse in toekomstige volstruis enstof proewe gebruik word. In hierdie studie is die proteïen gebruik om konyn teenliggame teen dit op te wek, wat dan gebruik was om vir die pCI-neo-gedrewe ekspressie van die oppA geen te toets in ‘n selkultuur omgewing deur ‘n MDA sellyn te transfekteer. Die voorlopige resultate toon nie ekspressie van die OppA proteïen aan nie, maar het wel uitgelig dat die western blot tegniek wat tans gebruik word, dalk nie sensitief genoeg is nie. Dit kan belowend wees om ander tipes selle te toets. Verdere optimisering is ook nodig om die nie-spesifieke binding wat waargeneem is, te verlaag. / South African Ostrich Business Chamber

Thesis (MSc) Stellenbosch University, 2014 / ENGLISH ABSTRACT: In this study, the effect of the amino acid residues at positions 40 and 407 on the catalytic activity of porcine CYP17A1 was investigated. Porcine cofactor CYB5 was cloned from porcine liver tissue and its effect on the catalytic activity of porcine CYP17A1 was determined. The influence of rat, human and angora CYB5 on the lyase activity of porcine CYP17A1 was subsequently determined and compared to the influence of porcine CYB5. Wt porcine CYP17A1, which has residues Val40 and His407, catalysed the conversion of prog efficiently with ~50% prog converted to 17OHprog (~40%) and A4 (~10%) after 3 hr. After 24 hr, negligible levels prog remained with ~71% 17OHprog and ~25% A4 being produced. Low levels of 16OHprog were formed (~9%). The Leu105Ala mutation reduced wt 17α-hydroxylase activity, with 70% prog remaining after 24 hr while 16OHprog (~10%) levels remained unchanged. Porcine CYP17A1 with residues Leu40 and His407, exhibited similar catalytic activity towards prog as did wt porcine CYP17A1 (Val40 and His407 residues), while porcine CYP17A1 with residues Leu40 and Leu407 increased the formation of A4 2-fold to 54% at 24 hr and porcine CYP17A1 with residues Val40 and Leu407 resulted in the highest formation of A4 (90%). Wt porcine CYP17A1, while having converted 95% of the prog substrate, produces only ~16% A4 after 24 hr. In the presence of porcine CYB5, however, the lyase activity was stimulated with 85% of prog being converted to A4 and only 13% 17OHprog remaining. The lyase activity was also stimulated by CYB5 from other species, resulting in an increase in A4 production of 60.6%, 24% and 11.6% by rat, angora and human CYB5, respectively. The degree of lyase stimulation correlated to the percentage identity of the CYB5 amino acid sequences to porcine CYB5. While the Val and Leu residues at position 40 do not appear to influence the lyase activity of porcine CYP17A1 as prominently as the residue at position 407, it is the charged residue at 407 that plays a significant role in the production of A4, decreasing A4 production irrespective of the Val and the Leu residues at position 40. It would, furthermore, appear that the stimulation of lyase activity of CYP17A1 is the greatest when assaying this activity in the presence of CYB5 of the same species as was detected when co-expressing porcine CYP17A1 and porcine CYB5. / AFRIKAANSE OPSOMMING: In hierdie studie is die invloed van die aminosuurresidue by posisies 40 en 407 op die katalitiese aktiwiteit van vark CYP17A1 ondersoek. Vark CYB5 is geklooneer vanuit vark lewer weefsel en die effek van hierdie kofaktor op die katalitiese aktiwiteit van vark CYP17A1 is bepaal. Die invloed van rot, mens en angora CYB5 op die liase aktiwiteit van vark CYP17A1 is daarna bepaal en vergelyk met die invloed van vark CYB5. Vark CYP17A1-VH, (kodeer Val40 en His407), kataliseer die omskakeling van prog doeltreffend met ~50 % prog wat omgeskakel word na 17OHprog (~40%) en A4 (~10%) na 3 uur. Na 24 uur, is feitlik alle prog omgeskakel, met ~71% 17OHprog en ~25% A4 geproduseer. Lae vlakke 16OHprog is ook gevorm (~9%). Die Leu105Ala mutasie verminder 17α- hidroksilase aktiwiteit, met 70% prog wat na 24 uur nie omgesit is nie, terwyl 16OHprog (~10%) vlakke onveranderd gebly het. Vark CYP17A1-LH (kodeer Leu40 en His407), en CYP17A1-VH het diselfde katalitiese aktiwiteit teenoor prog getoon, terwyl vark CYP17A1-LL (kodeer Leu40 en Leu407) die vorming van A4 2-voudig verhoog het tot 54% na 24 uur. Vark CYP17A1-VL (kodeer Val40 en Leu407) se katalitiese aktiwiteit het gelei tot die hoogste vorming van A4 (90%). Alhoewel CYP17A1-VH, 95% van die prog substraat omgeskakel het is slegs ~16% A4 geproduseer na 24 uur. In die teenwoordigheid van vark CYB5 is die liase aktiwiteit egter gestimuleer, en is 85% van die prog substraat omgeskakel na A4 met slegs 13% 17OHprog teenwoordig na 24 uur. Die liase aktiwiteit is ook gestimuleer deur CYB5 van ander spesies, wat lei tot 'n toename in A4 produksie van 60,6% , 24% en 11,6% deur rot, angora en menslike CYB5, onderskeidelik. Daar is gevind dat daar’n sterk korrelasie is tussen die stimulering van die liase aktiwitieit en die persentasie aminosuur volgorde identiteit van CYB5 afkomstig vanaf die verskillende spesies. Terwyl die Val en die Leu aminosuurresidu op posisie 40 wel die liase aktiwitiet tot ‘n mate beȉnvloed, blyk dit uit die data dat die potitief gelaaide residue by 407 'n belangrike rol speel in die produksie van A4, en A4 produksie verlaag ongeag van die Val en die Leu residu by posisie 40. Dit wil ook verdermeer voorkom asof die stimulering van die liase aktiwiteit van CYP17A1 die hoogste is wanneer die ensiem gekataliseerde reaksie deurgevoer word in die teenwoordigheid van CYB5 en CYP17A1 afkomstig vanaf dieselfde spesies.