Vetiver grass or Chrysopogon zizanioides (L.) Roberty (1960) is a sterile grass which can regenerate vegetatively from clumps of the rootstock. This, as well as its vigorous and deep root system and flood tolerance makes it an ideal candidate for the use in soil remediation and erosion control. In South Africa, Hydromulch (Pty) Ltd. is part of the landscape, soil reclamation and erosion control industry. The company uses vetiver grass on a wide scale and has accumulated a collection of isolates to serve as possible germ lines for industrial use. Due to the different approaches in environmental management as well as environmental factors, a variety of ecotypes form during the planting and acclimatisation of this genus. Chrysopogon nigritanus (Benth.) Veldkamp (1999), which is a native species to Africa, is closely related to C. zizanioides and differs only slightly from C. zizanioides on a morphological level. The major difference between the two species is that C. nigritanus is able to seed freely and thus the use of this species should be avoided. The need arose to screen other non-fertile plants to uncover additional genotypic variety to enable diversification of vetiver plantings. The aim of this study was to characterise the genotype of 19 isolates of vetiver obtained from Hydromulch (Pty) Ltd. via sequencing analyses of three DNA fragments, ITS, ndhF and rbcL. In addition, the radial root anatomy was also investigated and compared with the genetic analyses. According to the results generated during this study, very little or no genotypical differences exist amongst the different isolates available from the Hydromulch (Pty) Ltd. plant collection. Only in the case of the ITS inference were differences observed between three of the studied isolates. There was no significant difference between the different isolates based on the root anatomy, with the exception of two of the studied isolates which formed starch granules. / MSc (Botany), North-West University, Potchefstroom Campus, 2014

Vetiver grass or Chrysopogon zizanioides (L.) Roberty (1960) is a sterile grass which can regenerate vegetatively from clumps of the rootstock. This, as well as its vigorous and deep root system and flood tolerance makes it an ideal candidate for the use in soil remediation and erosion control. In South Africa, Hydromulch (Pty) Ltd. is part of the landscape, soil reclamation and erosion control industry. The company uses vetiver grass on a wide scale and has accumulated a collection of isolates to serve as possible germ lines for industrial use. Due to the different approaches in environmental management as well as environmental factors, a variety of ecotypes form during the planting and acclimatisation of this genus. Chrysopogon nigritanus (Benth.) Veldkamp (1999), which is a native species to Africa, is closely related to C. zizanioides and differs only slightly from C. zizanioides on a morphological level. The major difference between the two species is that C. nigritanus is able to seed freely and thus the use of this species should be avoided. The need arose to screen other non-fertile plants to uncover additional genotypic variety to enable diversification of vetiver plantings. The aim of this study was to characterise the genotype of 19 isolates of vetiver obtained from Hydromulch (Pty) Ltd. via sequencing analyses of three DNA fragments, ITS, ndhF and rbcL. In addition, the radial root anatomy was also investigated and compared with the genetic analyses. According to the results generated during this study, very little or no genotypical differences exist amongst the different isolates available from the Hydromulch (Pty) Ltd. plant collection. Only in the case of the ITS inference were differences observed between three of the studied isolates. There was no significant difference between the different isolates based on the root anatomy, with the exception of two of the studied isolates which formed starch granules. / MSc (Botany), North-West University, Potchefstroom Campus, 2014

Humans are continuously challenged by harmful endogenous and xenobiotic substances. Detoxification is the ability to neutralise and remove these substances from the body. Glycine N-acyltransferase, EC 2.3.1.13 (GLYAT) is a key enzyme in detoxification. GLYAT catalyses an amino acid (glycine) conjugation reaction in phase II of detoxification. It is expected that, similar to what has been observed in the Cytochrome P450 enzymes, variations within the GLYAT gene may lead to altered enzyme activity that may affect the efficacy of detoxification. The aim of this study was to identify genetic variations within the GLYAT gene of a cohort of individuals whose GLYAT activity has been biochemically characterized. Biochemical profiles of phase I and II detoxification of a number of individuals was screened to select those with possible aberrant GLYAT activity. Eighteen selected individuals agreed to participate in the study. The 23.21 kb GLYAT gene of the participants was amplified in four fragments and sent for pyrosequencing (Roche GS FLX titanium) at Inqaba Biotec. The results were analysed with the Lasergene software package from DNAStar (Madison, Wisconsin, USA). A total of 94 variations were identified from the Next Generation Sequencing data. Of these three found in the exons were known variations and four variations located in the exons were novel. A total of 62 known and 25 novel variations were identified in the introns of the GLYAT gene. Sanger sequencing verified 70.29% (68 in total) of the variation, which included 12 novel variations, of which one is located in exon six. Real-time quantitative PCR (qPCR) experiments were conducted and the data analysed using CopyCaller software to identify copy number variations within the cohort. It was found that participant 17 may have multiple copies of parts of the 3-terminal end of the gene (exons five and six), which might have an effect on GLYAT activity. Variations could possibly affect GLYAT activity, but the data was inconclusive and must be confirmed. Some of the variations could possibly affect GLYAT activity, but no correlation could be made between the variations identified during this study and the cohort’s detoxification ability. Further studies needs to be conducted to establish the effect of the variations in combination with one another on GLYAT activity. If some of these variations affect GLYAT activity such data might shed some light on variations observed between the glycine conjugation ability of individuals. Such information could eventually be of value in treatment of inborn errors of metabolism. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

Humans are continuously challenged by harmful endogenous and xenobiotic substances. Detoxification is the ability to neutralise and remove these substances from the body. Glycine N-acyltransferase, EC 2.3.1.13 (GLYAT) is a key enzyme in detoxification. GLYAT catalyses an amino acid (glycine) conjugation reaction in phase II of detoxification. It is expected that, similar to what has been observed in the Cytochrome P450 enzymes, variations within the GLYAT gene may lead to altered enzyme activity that may affect the efficacy of detoxification. The aim of this study was to identify genetic variations within the GLYAT gene of a cohort of individuals whose GLYAT activity has been biochemically characterized. Biochemical profiles of phase I and II detoxification of a number of individuals was screened to select those with possible aberrant GLYAT activity. Eighteen selected individuals agreed to participate in the study. The 23.21 kb GLYAT gene of the participants was amplified in four fragments and sent for pyrosequencing (Roche GS FLX titanium) at Inqaba Biotec. The results were analysed with the Lasergene software package from DNAStar (Madison, Wisconsin, USA). A total of 94 variations were identified from the Next Generation Sequencing data. Of these three found in the exons were known variations and four variations located in the exons were novel. A total of 62 known and 25 novel variations were identified in the introns of the GLYAT gene. Sanger sequencing verified 70.29% (68 in total) of the variation, which included 12 novel variations, of which one is located in exon six. Real-time quantitative PCR (qPCR) experiments were conducted and the data analysed using CopyCaller software to identify copy number variations within the cohort. It was found that participant 17 may have multiple copies of parts of the 3-terminal end of the gene (exons five and six), which might have an effect on GLYAT activity. Variations could possibly affect GLYAT activity, but the data was inconclusive and must be confirmed. Some of the variations could possibly affect GLYAT activity, but no correlation could be made between the variations identified during this study and the cohort’s detoxification ability. Further studies needs to be conducted to establish the effect of the variations in combination with one another on GLYAT activity. If some of these variations affect GLYAT activity such data might shed some light on variations observed between the glycine conjugation ability of individuals. Such information could eventually be of value in treatment of inborn errors of metabolism. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

Alpacas were first introduced into South Africa during the year 2000. They are valuable because of the fine quality wool they produce which has much better insulation properties than that of merino wool fibres. Alpacas are also used to act as guards of sheep herds against predators. During 2008, blood samples from an alpaca that died acutely with severe lung oedema, respiratory distress and froth exuding from the nose were received at Elsenburg Veterinary Laboratory. The alpaca was from a herd of 23 alpacas of a British veterinarian in the Montagu district in the western Cape. Virus isolation attempts on the blood produced infrequent embryo mortalities. Embryonated chicken egg (ECE) material was send to the Virology Department at the Onderstepoort Veterinary Institute (OVI). A bluetongue virus (BTV) PCR performed at the diagnostic PCR laboratory at OVI on the ECE material was positive. Further intra-venous (IV) inoculations in ECE produced embryo mortalities on two consecutive days, the 8th and 9th November. The dead embryos were harvested separately and named and treated as two separate virus samples, Alp8 and Alp9 which were further passaged on baby hamster kidney (BHK) cells. The BTV virus neutralisation tests (VNT) performed at the Office International des Epizooties (OIE) Laboratory on both Alp8 and Alp9 were negative. Because of the close serological relationship between BTV and epizootic haemorrhagic disease virus (EHDV), an EHDV VNT was also performed and was also negative. In the light of the negative VNT and the positive BTV PCR results, more in-depth molecular analyses were performed. RNA was purified from tissue culture material and agarose gel electrophoresis (AGE) performed. Both Alp8 and Alp9 had a typical orbiviral electrophoretic profile, but their respective profiles were different. A sequence-independent reverse transcriptase PCR amplification method generated ample complementary DNA (cDNA) of both samples for sequencing. Sanger sequencing was used to partially sequence genome segments 5 (NS1) and 2 (VP2). BLAST analysis of the partial information of the genome segments 5 (NS1) of Alp8 confirmed it as being a BTV and Alp9 as being an EHDV. BLAST analysis of the deduced amino acid sequence generated of VP2 of both Alp8 and Alp9 established that these samples were possibly new serotypes of BTV and EHDV respectively. The complete genome of both Alp8 and Alp9 was sequenced with next generation 454 Pyrosequencing. This confirmed the partial sequencing results. BLAST analysis of the complete sequence of S2 (VP2) of Alp8 showed that it has 73 % nucleotide and 77 % deduced amino acid identity to BTV15. In contrast the nucleic acid sequence of genome segment S2 (VP2) of Alp9 had no nucleotide sequence identity to any virus, but its deduced amino acid sequence had 71 % amino acid identity to EHDV2. Hyper immune guinea pig (GP) serum prepared against the putative new BT (Alp8) and EHD (Alp9) virus serotypes were tested for serological cross-reactivity against the 24 OIE reference antigen strains of BTV and the 8 OIE reference antigen strains of EHDV. Alp8 had a neutralising antibody (NAb) titre of > 32 against BTV15. Alp9 did not cross react with any of the OIE BTV and EHDV strains. Six out of the remaining 22 alpacas on the farm had NAbs to a greater or lesser extend against Alp8 (BTV) and Alp9 (EHDV) viruses, which confirmed that the viruses were also present in other alpacas in the herd. Very few cases of EHDV in alpacas have ever been reported in literature. A small scale pilot vector susceptibility study showed that vector competence of C. imicola for both Alp8 and Alp9 was low, below 2 %. The fact that neutralising antibodies to Alp8 and Alp9 were detected in other alpacas in the herd raises the question as to whether there are other Culicoides species circulating in the area that could vector the viruses. In conclusion, the results from the serological and virological analyses as well as the nucleic acid sequence data of the genomes of two virus samples, Alp8 and Alp9, from an alpaca that died in the Montagu district in the western Cape identified Alp9 as a definite new serotype of EHDV and Alp8 as a possible new serotype of BTV most closely related to BTV15. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

Alpacas were first introduced into South Africa during the year 2000. They are valuable because of the fine quality wool they produce which has much better insulation properties than that of merino wool fibres. Alpacas are also used to act as guards of sheep herds against predators. During 2008, blood samples from an alpaca that died acutely with severe lung oedema, respiratory distress and froth exuding from the nose were received at Elsenburg Veterinary Laboratory. The alpaca was from a herd of 23 alpacas of a British veterinarian in the Montagu district in the western Cape. Virus isolation attempts on the blood produced infrequent embryo mortalities. Embryonated chicken egg (ECE) material was send to the Virology Department at the Onderstepoort Veterinary Institute (OVI). A bluetongue virus (BTV) PCR performed at the diagnostic PCR laboratory at OVI on the ECE material was positive. Further intra-venous (IV) inoculations in ECE produced embryo mortalities on two consecutive days, the 8th and 9th November. The dead embryos were harvested separately and named and treated as two separate virus samples, Alp8 and Alp9 which were further passaged on baby hamster kidney (BHK) cells. The BTV virus neutralisation tests (VNT) performed at the Office International des Epizooties (OIE) Laboratory on both Alp8 and Alp9 were negative. Because of the close serological relationship between BTV and epizootic haemorrhagic disease virus (EHDV), an EHDV VNT was also performed and was also negative. In the light of the negative VNT and the positive BTV PCR results, more in-depth molecular analyses were performed. RNA was purified from tissue culture material and agarose gel electrophoresis (AGE) performed. Both Alp8 and Alp9 had a typical orbiviral electrophoretic profile, but their respective profiles were different. A sequence-independent reverse transcriptase PCR amplification method generated ample complementary DNA (cDNA) of both samples for sequencing. Sanger sequencing was used to partially sequence genome segments 5 (NS1) and 2 (VP2). BLAST analysis of the partial information of the genome segments 5 (NS1) of Alp8 confirmed it as being a BTV and Alp9 as being an EHDV. BLAST analysis of the deduced amino acid sequence generated of VP2 of both Alp8 and Alp9 established that these samples were possibly new serotypes of BTV and EHDV respectively. The complete genome of both Alp8 and Alp9 was sequenced with next generation 454 Pyrosequencing. This confirmed the partial sequencing results. BLAST analysis of the complete sequence of S2 (VP2) of Alp8 showed that it has 73 % nucleotide and 77 % deduced amino acid identity to BTV15. In contrast the nucleic acid sequence of genome segment S2 (VP2) of Alp9 had no nucleotide sequence identity to any virus, but its deduced amino acid sequence had 71 % amino acid identity to EHDV2. Hyper immune guinea pig (GP) serum prepared against the putative new BT (Alp8) and EHD (Alp9) virus serotypes were tested for serological cross-reactivity against the 24 OIE reference antigen strains of BTV and the 8 OIE reference antigen strains of EHDV. Alp8 had a neutralising antibody (NAb) titre of > 32 against BTV15. Alp9 did not cross react with any of the OIE BTV and EHDV strains. Six out of the remaining 22 alpacas on the farm had NAbs to a greater or lesser extend against Alp8 (BTV) and Alp9 (EHDV) viruses, which confirmed that the viruses were also present in other alpacas in the herd. Very few cases of EHDV in alpacas have ever been reported in literature. A small scale pilot vector susceptibility study showed that vector competence of C. imicola for both Alp8 and Alp9 was low, below 2 %. The fact that neutralising antibodies to Alp8 and Alp9 were detected in other alpacas in the herd raises the question as to whether there are other Culicoides species circulating in the area that could vector the viruses. In conclusion, the results from the serological and virological analyses as well as the nucleic acid sequence data of the genomes of two virus samples, Alp8 and Alp9, from an alpaca that died in the Montagu district in the western Cape identified Alp9 as a definite new serotype of EHDV and Alp8 as a possible new serotype of BTV most closely related to BTV15. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

South Africa has the highest prevalence of Foetal Alcohol Spectrum Disorders (FASD) worldwide. Despite the high prevalence of FASD in children and the resulting need for services, appropriate identification and management of most genetic and congenital disorders are critically lacking in South Africa. As a result of the established risk for communication delay from birth, young children with FASD need early communication intervention (ECI). There appears to be a dearth in research on the communication difficulties of local young children with FASD. Determining comprehensive communication profiles of young children may serve to emphasize their need for ECI. The main aim of the study was to present the distinctive communication profiles of a group of young children with FASD. The sub-aims entailed the description of their developmental histories, family/care-giving contexts, communication functioning and identifying developmental trends across the participants. A collective case study design following a quantitative approach was selected. The study was cross-sectional and descriptive statistics was used to describe the participants’ communication skills. A purposive sampling procedure was utilized as a limited number of participants could be found with a diagnosis of FASD. Five participants diagnosed with FASD, living in the Gauteng area, between the ages of 4 to 58 months took part in the study. The empirical study comprised of two phases. Phase 1 entailed the development of the Interview Schedule, the Assessment Protocol and the conduction of a pilot study. Phase 2 comprised the data collection, analysis and interpretation of results. The results of the study indicated that all five participants presented with incomplete case histories obtained from the foster parents and general developmental delays. According to the Four-Level Early Communication Assessment Framework the greatest delays included all aspects of communication skills. A developmental trend of the combined communication profiles of the participants indicated an increase in delay with an increase in chronological age. The participants presented with complex multiple neuro-developmental needs to be viewed within a developmental systems and ecological framework. Based on the results of this study the diverse roles of the speech-language therapist working with young children with FASD and their families were identified. A framework for interdisciplinary service delivery to this population was suggested. The study succeeded in the attempt to provide a comprehensive, in-depth description of a group of the five participants’ unique communication skills. In addition the study also highlighted the shortage of services, e.g. limited early identification and services dedicated to families affected by alcohol related problems. The study is of value to the speech-language therapist in the clinical and research domain. Future research is recommended to expand and support the findings. AFRIKAANS : Suid-Afrika vertoon die hoogste prevalensie van Fetale Alkohol Spektrumafwykings (FAS) wêreldwyd. Ten spyte van die hoë prevalensie van FAS in kinders en die voortspruitende behoefte aan dienste, is toepaslike identifikasie en hantering van die meeste genetiese en kongenitale afwykings in Suid-Afrika krities ontoereikend. As ‘n resultaat van die bevestigde risiko vir kommunikasie agterstand vanaf geboorte, benodig jong kinders met FAS vroëe kommunikasie intervensie (VKI). Daar blyk ‘n gaping in die navorsing aangaande die kommunikasie probleme van plaaslike jong kinders met FAS te wees. Omvattende kommunikasie profiele van jong kinders met FAS kan die behoefte aan VKI dienste beklemtoon. Die hoofdoel van die studie was om die kommunikasie profiele van ‘n groep jong kinders met FAS voor te lê. Die sub-doelwitte het die beskrywing van hulle ontwikkelings geskiedenis, gesin/sorggewer konteks, kommunikasie funksionering en die identifisering van ontwikkelings neigings in al die deelnemers behels. ‘n Saamgestelde gevallestudie is geselekteer volgens ‘n kwantitatiewe navorsings benadering. Die studie is ‘n kruisdeursnee ontwerp en beskrywende statistieke is gebruik om die deelnemers se kommunikasie vaardighede te beskryf. ‘n Doelgerigte steekproef prosedure is gebruik omdat ‘n beperkte aantal deelnemers met ‘n diagnose van FAS gevind kon word. Die vyf deelnemers wat geselekteer was vir die steekproef was gediagnoseer met FAS, woonagtig in die Gauteng area en het binne die 0 – 5 jaar ouderdomsgroep geval. Die empiriese studie het uit twee fases bestaan. Fase 1 het die ontwikkeling van die onderhoud skedule, die assesserings protokol en die uitvoering van ‘n loodsstudie ingesluit. Fase 2 het die data insameling, analise en interpretasie van resultate behels. Die resultate van die studie het aangedui dat al die deelnemers gepresenteer het met onvolledige gevalsgeskiedenisse wat van hul pleegouers verkry is en ‘n algemene ontwikkelings agterstand. Volgens die Vier-Vlak Vroëe Kommunikasie Assesserings Raamwerk het die grootste agterstande alle aspekte van kommunikasie vaardighede behels. ‘n Ontwikkelings neiging vanuit die gekombineerde kommunikasie profiele van die deelnemers het ‘n toename in agterstand met ‘n toename in kronologiese ouderdom aangedui. Die deelnemers presenteer met veelvuldige neuro-ontwikkelings behoeftes wat binne die ontwikkelings sisteem en ekologiese raamwerk beskou moet word. Gebasseer op die resultate is die diverse rolle van die spraak-taalterapeut wat met jong kinders met FAS en hulle families werk, geïdentifiseer. ‘n Raamwerk vir interdissiplinêre dienslewering aan hierdie populasie word voorgestel. Die studie het geslaag in die poging om ‘n omvattende, in-diepte beskrywing van die deelnemers se unieke kommunikasie vaardighede te verskaf. Addisioneel het die studie ook die tekort aan dienste, naamlik beperkte vroëe identifikasie en dienste toegewy aan families geaffekteer deur alkohol verwante probleme, uitgelig. Die studie is van waarde vir die spraak-taalterapeut in die kliniese en navorsings domein. Toekomstige navorsing vir die uitbreiding en ondersteuning van die studie se bevindinge word aanbeveel. / Dissertation (MCommunication Pathology)--University of Pretoria, 2011. / Speech-Language Pathology and Audiology / Unrestricted

The maintenance schedule of generators in power plants needs to match the electricity demand and needs to ensure the reliability of the power plant at a minimum cost of operation. In this study, a comparison is made between the modified generator maintenance scheduling model and the classic generator maintenance scheduling model using the reliability objective functions. Both models are applied to a 21-unit test system, and the results show that the modified generator maintenance scheduling model gives better and more reliable solutions than the regular generator maintenance scheduling model. The better results of the modified generator maintenance scheduling model are due the modified and additional constraints in the modified generator maintenance scheduling model. Due to the reliable results of the modified generator maintenance scheduling model, a robust model is formulated using the economic cost objective function. The model includes modified crew and maintenance window constraints, with some additional constraints such as the relationship constraints among the variables. To illustrate the robustness of the formulated GMS model, the maintenance of the Arnot power plant in South Africa is scheduled with open-loop and closed-loop controllers. Both controllers satisfy all the constraints but the closed-loop results are better than the open-loop results. AFRIKAANS : Die onderhoudskedule vir kragopwekkers (OSK) in kragstasies moet kan voorsien in die vraag na elektrisiteit en moet die betroubaarheid van die kragstasie teen ’n minimum operasiekoste verseker. In hierdie studie word die betroubaarheidsdoelwitfunksie gebruik om ’n gewysigde onderhoudskeduleringsmodel vir kragopwekkers te vergelyk met die konvensionele onderhoudskeduleringsmodel. Beide modelle word toegepas op 'n 21-eenheid-toetsstelsel, en die resultate toon dat die gewysigde model ’n beter en meer betroubare oplossing bied as die konvensionele model. Die beter resultate van die gewysigde model is die gevolg van die gewysigde en bykomende beperkings in die gewysigde model. As gevolg van die betroubare resultate van die gewysigde onderhoudskeduleringsmodel word die koste-ekonomie-doelwitfunksie gebruik om ’n robuuste model te formuleer. Die model sluit gewysigde bemanning- en onderhoudvensterbeperkings in, met ’n paar bykomende beperkings soos die verhoudingsbeperkings tussen die veranderlikes. Om die robuustheid van die geformuleerde OSK-model te illustreer word die instandhouding van die Arnot kragstasie in Suid-Afrika geskeduleer met oop- en geslotelus-beheerders. Beide beheerders voldoen aan al die beperkinge, maar die geslotelusresultate is beter as die ooplusresultate. / Dissertation (MSc)--University of Pretoria, 2011. / Electrical, Electronic and Computer Engineering / Unrestricted