Magister Scientiae - MSc (Microbiology)

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Mineralogy and chemical mobility in a weathered ash dump site, South Africa
(University of the Western Cape, 2010) Ojo, Olufunke Idowu; Akinlua, A; Petrik, L.F.; Scheepers, A.C.T
Coal fly ash generated from coal fired plants poses potential health risks to humans and plants in the environment due to the surface enrichment of the ash with various toxic trace elements during combustion. Only a small portion of the fly ash produced every year as a result of the increase in the demand for electricity, is being utilized. The bulk of the ash is disposed of in ash dams and landfills. Rain water as well as waste water from the ash slurry serves as leaching medium for the toxic elements into the environment, especially into the groundwater. This study aims at understanding the chemical and mineralogical omposition of the weathered fly ash, the distributive pattern of species down the ash dump, the various mineral phases with which the elements are associated and the change in mineralogy as a result of weathering over time. Methods employed in this study included the use of XRF and total acid digestion of the samples followed by ICP AES/MS analysis of the leachates to identify and quantify the major, minor and trace elements in the ash samples, pore water chemistry of the samples to determine the species soluble in water at various horizons in the drilled core, XRD and SEM/EDS to determine the mineralogy and morphology of the fly ash samples and a 5 step sequential extraction procedure to understand the various mineral phases with which the elements in the fly ash are associated. Fly ash samples were obtained from a core drilled to 32 m at Kragbron in the Free State Province of South Africa. Geology of the area falls under the Karoo Supergroup and the study site is underlain with Jurassic dolerite rock of the Karoo Supergroup. The ash was disposed at the dump as slurry in a layered form. The bulk chemical composition as determined by XRF showed AhO3, SiO2, Fe2O3 and CaO as the major oxide constituents in the fly ash samples. Kragbron ash belongs to Class F according to ASTM C618, as the sum of the percentage composition of SiO2, AhO3 and Fe2O3 revealed by XRF was greater than 70 % and the lime content was less than 10 %. Loss on ignition values in most of the samples (between 15 m and 22 m) was higher than specified by ASTM C618. This was as a result of the different coals used in the combustion units at the power stations. Comparison between the results obtained from XRF and the ICP analysis of the fly ash digestates was good in some of the elements. Al, Si and Na concentration was higher with XRF than with ICP. This was expected because the elements are present in reasonable amounts in fly ash. The concentration of Ca, Fe, Mg, K and Ti was higher with ICP than with XRF. This ought not to be as these elements are also present in appreciable quantities in fly ash. Results obtained with XRF showed more accuracy because the technique gives total composition of the solid sample and chances of contamination are minimal. Results obtained from XRD showed mullite, quartz and calcite to be the major crystalline mineral phases identified in most of the ash samples. Hematite and calcite were observed at 22 m depth in the ash dump. The inclusion of hematite at 22 m could be due to mixing with parts of the bedrock during the initial construction of the ash dump as hematite was not identified in the previous depths. Mullite, quartz, anorthite and diopside were the minerals identified at 23 m. The presence of mullite also indicates a mixture of ash and bedrock components. Literature revealed the bedrock to be dolerite. Major minerals revealed by XRD from 24 m to 32 m were quartz, diopside and anorthite commonly found in dolerites. The pH pattern observed in the profile showed strong weathering at the surface of the dump between 1 m and 5 m and it was alkaline for all the samples. Electrical conductivity (EC) was ery high at 16 m depth and the trend coincided with that which was observed in Ca, Na, K, Ba, so/- and are indicating the presence of these elements in highly soluble forms at that depth. Al was observed in high concentrations at 15 m and 18 m due to its presence in soluble hydroxide form. Se, As, Cr, Zn, Cu and V showed a considerable release in the fly ash pore water leachates. Ti, Pb, Co, Fe, Mn and Mg were present in water insoluble phases in the fly ash samples.
The identification of regulatory Elements in pseudomonas aeruginosa and p. putida responsive to specific heavy metals.
(University of Western Cape, 1999) Africander, Nolan Lindsay; Brozel, Volker S
Heavy metals constitute a group of about sixty-five elements having a density greater than five (Gadd and Griffiths, 1978). Some metals, for example lead, copper, and nickel are extremely precious and profitable to man due to its widespread application in industry. As there has been an increase in heavy metal demand, necessary development of elegant and efficient methods for their isolation were also required. These methods, which led to an increase in industrial development, also resulted in an increase in the complexity and variety of heavy metals polluting the environment (Morby,1996
An assessment of the virulence of listeria spp. isolated from raw milk and raw chicken
(University of the Western Cape, 1994) Howard, R.L; Hastings, J.W; Gouws, P
Listeria a f~rn__e pathogen is the etiological agent of the deadly disease listeriosis. Although, the virulence traits of international isolates of Listeria are well studied, nothing is known about the virulence traits of Listeria found in raw milk and raw chicken in the Western Cape, South Africa. Therefore, the aim of this study was to isolate Listeria from raw milk and raw chicken in the Western Cape, South Africa, in order to determine the virulence nature of such Listeria isolates
Bioinformatics and polymerase chain reaction: Tools to determine the host specificity of Salmonella typhi murium
(University of the Western Cape, 2002) Davids, R; Gouws, P.A
The nucleotide primer pair, Redl and Red2, was designed from the nucleotide sequence obtained from the NCBI database (Fig. 2.1). This nucleotide sequence encodes for the Salmonella typhimurium invasion gene D protein (sigD) and invasion gene E protein (sigE) genes. The Sa/monella and the non-Salmonella serovars used were subjected to PCR conditions at various annealing temperatures (T.) (Tables 2.4, 2.5,2.6). This was performed in order to optimize the PCR. Plasmid DNA PCR amplicons (350bp) detected S.braenderup and S.gallinarum at 53oC (Fig. 2.7) and at 56oC, S.braenderup at 54oC and S.gatlinarum at 55oC. PCR of the plasmid DNA did however not detect Salmonella typhimurium, the serotype it was designed to detec
Cloning and sequence analysis of the gene coding for a Leuconostoe Bacteriocin
(University of the Western Cape, 1994) Felix, Joseline V.; Hastings, J.W; Smith, A.A
Previous studies have shown that Leuconostoc (Lc.) carnosum Tal la produces a bacteriocin that has been designated leucocin B-Tal la [Papathanasopoulos, 1993, M.Sc thesis, University of the Witwatersrandl. Leucocin B-Talla is active against Listeria nnnocytogenes and several lactic acid bacteria. An 8.9 MDa plasmid in Leuconostoc carnosum Tal1a hybridised to a 36-meroligonucleotide probe (JF-1) that is homologous to the amino-terminal sequence of the leucocin A-UAL187 structural gene. A library of Lc. carnosum Talla plasmid DNA was constructed by partial digestion of DNA with ^lar3A and ligation into the BamHl site of pUC1l8. A plasmid (pJF8.1), containing a 4.9 kb insert was identified by Southern blotting and hybridisation to JF-l. A subclone of this plasmid, with a 2.3 kb insert (pJF5.5), was generated by internal deletion of a 2.6 kb Xbal fragment and religation of the plasmid. Sequence analysis of pJF8.1 and pJF5.5 revealed the presence of two open reading frames (ORF). ORFI codes for a protein of 61 amino acid residues. This protein product is proposed to be the prepeptide of a 37 amino acid bacteriocin, leucocin B-Ta11a, by virtue of DNA sequence homology to leucocin A-UALI87 [Hastings et al., 1991. J. Bacteriol 173:749L-7500]. The 24 amino acid residue amino-terminal extension, possibly cleaved during processing of the prepeptide may function as a leader peptide. The aminoterminal extension of leucocin B-Talla differed trom the similar region in Ieucocin A-UAL187 by seven residues. The predicted protein of the ORF2 consists of 113 amino acids and is identical to the amino acid sequence of the cognate ORF of the leucocin A-UAL187 operon. Expression of leucocin B- Talla was attempted in Escheichia coli JMl03 transformed with pJF8.1 and pJF5.5. Results of inhibition studies with various cell fractions of the transformed strains showed that no bacteriocin was produced by these transformants.
Adenine nucleotides and selected chemical Parameters as potential markers for fertility assessment
(University of the Western Cape, 1997) Burger, D J G; Van der Horst, G
Diagnostic andrology with its descriptive approach to the diagnosis of defective sperm for the last 40 years has focused mainly on the macro- and microscopic appearance of the ejaculate. More emphasis has recently been placed on the quantification of biochemical components in semen and sperm. In this regard, substances can be measured more accurately and in some cases as multi-components in the same run. The value of bioenergetics of sperm as a marker for fertility assessment is a controversial topic in the literature. What complicates this issue is the relatively new information on how adenosine triphosphate (ATP), as the major high energy molecule, can be synthesized from other sources which c/as, until recently, unknown. This study attempts to investigate the role of adenine nucleotides as potential markers in semen for fertility assessment using the Tygerberg strict criteria. In this study a reverse phase liquid chromatography (RPLC) technique was developed which measures all the nucleotides in a single run. Because the cycle of energy yielding and energy consuming processes operate simultaneously, it is difficult to assess the energy status of spermatozoa by only measuring the ATP concentrations as suggested in the literature. In this study all the adenine nucleotides and their relative ratios were measured. The results did not show significant differences using the Tygerberg strict criteria of morphology evaluation. This is in line with some workers who indicate that there is no value in measuring ATP levels and correlating this with fertilization. This study furthermore indicates that the breakdown products of ATP and the different adenine nucleotide ratios do not correlate positively with morphology and fertilization in the IVF and GIFT procedures using the Tygerberg strict criteria of morphology. As an application of the technique preliminary experiments indicated that the duration of incubating semen or spermatozoa is important when measuring nucleotides. An unknown product, that relates to motility, is formed during the incubation period of 18 hours (absent after 40 minutes). It was also shown in this preliminary study that the ATP/ADP ratio is the most sensitive biochemical parameter for changes in motility and that the older concept of the adenylate energy charge (AEC) is not a good indicator of the energy status of spermatozoa. The experiments with the energy related enzymes Lactate dehydrogenase and Creatine kinase versus the morphological groups, have been proved not to be predictive. The sperm membrane enzyme y-glutamyl transferase which also correlates negatively with the Tygerberg morphological groups could be more informative if the number of the P Pattern group (<4o/o) were increased. This membrane enzyme could be of more value than previously realized, since it may relate to the lipid peroxidation of sperm which are extremely susceptible to oxidative stress.
Listeria in food and water in the Western Cape
(University of the Western Cape, 1998) Leonard, Carmen Myra; Brozel, V. S.
Listeria are glam positive non-spong rods that were found in diverse environments including water, seafood, dairy products and vegetables. Outbreaks of listeriosis due to the consumption of foods contaminated L.monocytogenes, coupled with the high mortality rate and the nsk posed to immuno compromised individuals have resulted in more focus being placed on Listeria-free products. Although most recorded Listeria outbreaks have been linked to contaminated food, most of these foods have a previous history of soil and / or water contact but little is known regarding its prevalence in soil and water. The aim of the work reported here was to ascertain the prevaluice and diversity of Listeria and bacteria that could be regarded as Listeria in various foods and in natural and irrigation waters in order to develop a reliable and conclusive detection method. Various methods including conventional culturing selective techniques, immunological methods and a variety of polymerase cham reaction methods have been developed for the detection of Listeria. In this study, preminary physiological tests were utilized to detect Listeria from 108 natural and irrigation water samples, 34 dairy samples, 33 raw and processed fish samples and 30 vegetable samples. After these preliminary tests, one-hundred and twelve isolates were found to be gram positive non-sporing rods that could hydrolyse aescuhn. These isolates were further tested using both genotypical (PCR with primers directed at the 165 rRNA gene and the invasive associated protein gene ) and phenotypical (BIOLOG and whole-cell protein analysis). The whole protein profiles divided the various isolates into two main divisions namely, Listeria and ListeriaJike organisms. A diverse selection of Listeria and, Listerio-like strarns, some of which are very distant from currently accepted members of the genus, were isolated. Dalry products (especially soft cheeses), seafoods and water isolates clustered in separate niches within the Listeria division. The majority of vegetables, however, were mainly contaminated by Listeria-like organisms and not true Listeria. The presence of these Listeria in a Iocal river was of some concernsince the local children used the river as a swimming facility. Some isolates from the river, although related to the type strains, were separate from typical Listeria. Thus, the possibility exists that this group could be a new species or subspecies. The development of a l65 rDNA primer set (CLis2 and CLis4) for the detection is reported. All isolates that contained the invasive associated protein (iap) gene resulted in a PCR product of l.5kb and those that contained the 165 rRNA gene resulted in a product of 0.68kb Although these primer sets could detect most Listeria, they could not detect all. The development of more selective media for the preliminary detection of Listeria and the reduction in the number of physiologrcal tests, were recommended as well as the optimisation of the l65 rRNA PCR for the direct detection of Listeria rn food products.
The effect of maternal nicotine exposure on rat lung tissue morphology. ' a light and electron microscopic study
(University of the Western Cape, 1991) Woolward, Keryn Miles; Maritz, G. S.
The infants of women who smoke during pregnancy have a lower birth mass than those born of women who abstain. Animal studies reveal that reduced growth due to maternal nicotine exposure during gestation is accompanied by lung hypoplasia. Biochemical analysis suggests that these lungs contain more cells which implies that lung damage occurs. In this study we examined the in vivo effects of maternal nicotine exposure (lmg/Kg/day), the equivalent of 32 cigarettes per day, on the following parameters of fetal and neonatal Wistar rat lung:(i) the content and distribution of glycogen in fetal and neonatal lung (ii) the status of connective tissue in neonatal lung (iii) the cell composition of the alveoli in neonatal lung. Fetal rat lungs of ages 17, 18, 19 and 20 days and neonatal lungs of 1, 7, 14 and 21 day old pups were used. Light microscope techniques and special stains were used to investigate glycogen, connective tissue, macrophage numbers and morphological status of the lungs. Fetal rat lungs of ages 17, 18, 19 and 20 days and neonatal lungs of 1, 7, 14 and 21 day old pups were used. Light microscope techniques and special stains were used to investigate glycogen, connective tissue, macrophage numbers and morphological status of the lungs. Transmission electron microscope (TEM) techniques were employed to investigate the characteristics and composition of the alveolus The results show clearly that maternal nicotine exposure elevates pulmonary alveolar macrophage numbers'(PAM's) and lung glycogen levels. The quantity of elastic fibres in 1 day old neonates was significantly reduced but no changes in the quantity of reticulin and collagen fibres was observed. As a result of this change in connective tissue status, emphysema-like lesions and alveolar collapse was evident in the lungs of nicotine-exposed pups. TEM investigations revealed that changes to the composition of alveoli occurred. These included increased numbers of type II pneumocytes with high numbers of lamellar bodies with degenerative changes. Thickening of the blood-air barrier was also observed. The effect of maternal nicotine exposure has been documented in this study. However, it has not been possible to pinpoint the mechanisms involved but explanations have been proposed. Further research is required to elucidate the mechanisms by which nicotine produces these effects. Information thus obtained could help prevent the harmful effects to the fetus and neonate caused by smoking during pregnancy.
The effect of diet on the mucus histochemistry and adjacent histology of the digestive tract in Vervet monkeys.
(University of the Western Cape, 1993) Woodroof, Colin William; van der Horst, G.
There is a need for defined models of human nutritional disorders partly because serious misconceptions about models are common amongst researchers. Historically a large variety of species has been used including primates, pigs, rats, lagomorphs. Advantages various small carnivores and and disadvantages are not well known and availability is a major factor. In 1753 John Hunter used pigs to study bone growth in one of the first scientifically controlled nutrition experiments (Kobler 1960). Rats were most likely the first animals to be bred specifically for scientific purposes and there is evidence that they were used in nutrition experiments during the late eighteenth century (Kobler 1960). Experience with carcinogenesis in animals has shown the great diversity of results which may possibly be obtained from different species (Lave et al. 1988). This is pertinent to nutritional research as there is an established link between diet and cancer. The selection of a suitable substitute to attempt to model possible human response to a variety of procedures is dependent upon criteria among which the following are possibly the more important. Availability; this is of great importance in Southern Africa where the cost of importation of exotic species. must be taken into account. Du Plessis (1981) referred to the fact that our indigenous primates were a valuable resource. A second consideration must be the cost the selected animal in a scientifically acceptable environment. Keeping animals of maintaining and ethically for research purposes in an uncontrolled environment could well lead to erroneous conclusions being made. Thirdly the cost of a research program in which animals are used may be increased if there is insufficient knowledge of the model selected. A paucity of knowledge available about an animal may affect the viability of an experiment. The need for precise information regarding the effects of extended term dietary supplementation of experimental animals has been noted by Fincham et. al. (1987) . Additionally the selected animal should preferably have similar dietary requirements to man, and have a life span which will enable extended term investigations.
An investigation of the effects of donor age on some haematological characteristics of the Wistar rat (Rattus Norwegicus)
(University of the Western Cape, 1986) Wesso, Iona; Van der Horst, G.
Knowledge of haematological 'normdata', of experimental animals, and the biological variables that affect it is essential in order to recognise variations from the normal. In addition, the haemopoietic system may be regarded in principle as good material for studies of the cellular events associated with ageing. These considerations, together with the well documented effects of age on various physiological processes, prompted an investigation into the effects of donor age on several blood parameters. Review of the literature revealed that age-related changes in blood parameters have been reported for several species, but the documentation thereof is incomplete, inconsistent and inconclusive in many respects. Blood samples from male Wistar rats of nine different biological ages, ranging from birth to 96 weeks of age, were analysed for haematological and biochemical parameters. These included the blood cell counts, erythrocytic indices, haemoglobin concentration, haematocrit, erythrocytic 2,3-diphosphoglycerate and adenosine triphosphate levels, and erythrocytic glucose 6-phosphate dehydrogenase and pyruvate kinase activities. Data was obtained which demonstrates that all blood parameters measured underwent significant, although not al~ays regular, age-related changes. These changes were found to be more marked during the first month of life than at any other period. Evidence is also presented to show that the depressed haemoglobin concentration during the early postnatal life may not imply a condition of 'physiologic anaemia' as was previously thought. Since the blood profile exhibits only slight changes from about 24 weeks of age, it does not seem that the haemopoietic system of the old rat deteriorates significantly as to constitute a limiting factor for the animal's life. However, the importance of taking an animal's age into account when blood parameters constitute experimental results is emphasised. The second phase of this study involved a detailed investigation of the effect of the animal's age on erythrocytes in particular. These cells have limited life-spans, and are often used as models in studies of cellular ageing. Special emphasis was therefore placed on comparing the relative effects of host and cellular ageing on the properties of these cells. Erythrocytes from rats between one and 48 weeks of age were separated into two populations by a modification of the conventional density gradient centrifugation technique. The two populations were assumed to differ in mean cell age and were analysed for erythrocytic indices, phosphate ester concentrations and the activities of glucose 6-phosphate dehydrogenase and pyruvate kinase. Evidence is presented to show that ageing rat erythrocytes exhibit a decrease in volume, phosphate ester content and enzyme activities while the cellular haemoglobin concentration increases. Differences in the mean cell age however, does not seem to account for the donor-age-related effects observed in the whole blood parameters. Rather, the significant differences found in the characteristics of similarly aged red cells, between variously aged donors, demonstrate that the biological age of the organism influences the red cells and probably the ageing thereof in vivo. The contribution of the changing status of the erythrocyte's environment of progressively older animals, to alterations which take place in the ageing red cell is discussed.
The influence of nicotine exposure on the male reproductive system
(University of the Western Cape, 1993) Naidu, Thulasimala; van der Horst, Gerhard
It is well documented that cigarette smoking and nicotine exposure create widespread physiological disorders in humans and animals. The primary tobacco constituent that is responsible for the toxicological consequences associated with the effects of tobacco smoke is nicotine (Van Lancker 1977). After maternal nicotine exposure, the fetal gonads and lungs are the principle sites of nicotine damage (Szuts et al. 1978, Mosier & Jansons 1972). Whilst the fetal lung has received widespread attention in this regard (Maritz 1988), the testis has never been studied. Therefore, I have chosen to explore the effects of maternal nicotine exposure on the testis of male offspring by evaluating various aspects of the male reproductive tract. It is believed that, in adult male smokers (Rosenberg 1987, Handelsman et al. 1984) and sexually mature animals (Mattison 1982) that are exposed to nicotine, male fertility may be compromised. However, these studies provide conflicting data on single parameters. It was therefore my objective to identify the effect of nicotine exposure on the male reproductive tract and to establish possible sites through which these effects may be mediated in adult male rats. The influence of nicotine was then investigated in male offspring after maternal nicotine treatment (MNT), and in sexually mature adult males after direct adult nicotine treatment (ANT). In the former experiment (MNT), 7 day pregnant rats were exposed to Img nicotine/kg body weight/day. Therefore, these offspring were indirectly exposed to nicotine during fetal development and early neonatal development. After weaning the animals were divided into two groups. One group did not receive further treatment (withdrawn group), whilst the other group was continually treated till adulthood (nicotine group), after which both groups were sampled together with the control. In the latter experiment (ANT), the animals were treated daily for 3 weeks and were sampled as above (MNT animals). The fundamental parameter investigated in both experiments to assess reproductive status was sperm quality (motility and morphology). Thereafter, it was necessary to establish a possible site where the effects of nicotine would occur. Testicular growth, epididymal structure, and plasma testosterone content were measured as probable localities of nicotine's effect. The results signify that maternal nicotine exposure poses a greater threat to the male reproductive system than adult nicotine exposure. In the MNT experiment, progressive sperm motility of the nicotine and withdrawn groups were 1.7% and 3.4% respectively. The proportion of abnormal sperm was 72% in each of the above groups. The lower quality sperm that is evident after nicotine exposure implies that the fertilizing ability of the animals may be impaired during adulthood. The data on testicular growth indicates that nicotine exposure during early development results in slower testicular development until maturity. The epididymal lining of these animals also increased after nicotine exposure, indicating increased cellular activity. However, these results from testicular and epididymal studies are inconclusive and need further work. In the ANT experiment, progressive sperm motility of the nicotine group was 1.2%, whilst the proportion of abnormal sperm was 58%. No other parameter was affected after nicotine exposure to adult animals. From the above data it is evident that nicotine exposed animals were subject to greater nicotine damage after maternal nicotine exposure during early development. Moreover, within the maternal nicotine treated experiment, the withdrawal of nicotine after weaning did not appear to reverse the injurious effects of nicotine that were established during early development. These effects were evident since the nicotine and withdrawn groups showed similar levels of damage in all instances. The most profound effects after adult nicotine exposure and maternal nicotine exposure were on sperm quality. The probable site of sperm impairment appears to be via retarded testicular growth and possibly, structural status of the epididymis after maternal nicotine exposure. The results from adult nicotine exposure however, suggest that sperm cells may be directly affected by nicotine exposure. An epidemiological survey was included to validate the basic conclusions established in animal research when compared to clinical data from human patients. No statistically significant changes were observed in this study between the patient's spermiogram results versus his smoking habits, and, that of his mother. From the level of significance it was concluded that cigarette smoking does not appear to be a cause of impaired fertility in already infertile patients. However, the data does suggest that cigarette smoking may well be a precipitating agent in male infertility. Experimentally, nicotine exposure impairs the male reproductive system to some extent. The effects of which are irreversible after indirect exposure (MNT) during development and may begin with poor testicular development. The effects of adult nicotine exposure implies that nicotine exposure in mature animals (ANT) acts directly on sperm cells to incapacitate them. It is well advised that cigarette smoking should be curbed in pregnant women and in adult males to alleviate contributing effects to male infertility.
The evaluation of the imp act of interventions by a physiotherapist on intellectually imp aired and physically disabled children and their caregivers in two community groups in peri-urban Cape Town
(University of the Western Cape, 2008) Behr, Janice; Mpofu, R M B
Physiotherapy services for disabled children and their families have conventionally been received at a hospital or school for children with special educational needs in the main towns and cities of South Africa. Community-Based Rehabilitation (CBR) programmes were proposed and established as an additional approach to Institutional-Based Rehabilitation to address the need for accessible resources for these families. In this study the author evaluated two CBR programmes for disabled children and their main caregivers in two separate low socioeconomic peri-urban areas of Cape Town. The programme, a weekly group meeting, included physiotherapy interventions to assist the development and functional abilities of the children by means of activities that the caregivers could include in daily home care. They handled their own children following demonstrations and correction of handling skills by the author. The majority of the caregivers were mothers. Their children, less than 13 years old, were severely intellectually impaired. Some with concomitant physical disabilities. The author implemented the interventions of the CBR programme and she required to understand the impact on the particpants in a study using qualiative research methods. In the pilot programme the attendant members were individually interviewed, after her withdrawal, for their opinions of the outcomes. Evaluation documentation.ofjheir children and CBR programme records were related to the caregivers' responses. From the pilot study experiences the author felt that additional methods of data collection would result in a greater understanding of the impacts of the interventions. Expanded methods of research were utilised in the study of the second group. During the interventions at group meetings the author used field notes to record observations. Participant observation allowed the author to analysis the responses of the participants. Focus group interviews assisted in understanding external factors influencing the participants as well as their needs. Individual interviews, after the closure of the CBR programme, allowed the participants to express their views of the interventions. Documentation of the individual evaluation of each child was related to the views expressed by the caregivers. Common meanings and themes were explored in the analysis of the various data collected. Analysis revealed that interventions of education and training for the caregivers improved their knowledge and understanding of the impairments and disability of their children. The children benefited functionally from their families increased skills and knowledge. Through discussion with other families at group meetings, the caregivers had an understanding of other disabilities in children and developmental outcomes possible for their own child. The caregivers were more confident to address the negative perceptions of disability in their communities. It is recommended that physiotherapists implementing any interventions for disabled children should ensure that the caregivers are partners in planning and selection of interventions and that their needs are addressed. Community participation in Community-Based Rehabilitation programmes was required for the participants to become self-reliant and solve their own needs as well as for the programme to be sustainable. This was demonstrated in only one of the programmes.
Identification of novel microRNAs as potential biomarkers for the early diagnosis of ovarian cancer using an in-silico approach
(University of the Western Cape, 2019) Zahra, Latib; Keyster, Marshall
Ovarian cancer (OC) is the most fatal gynaecologic malignancy that is generally diagnosed in the advanced stages, resulting in a low survival rate of about 40%. This emphasizes the need to identify a biomarker that can allow for accurate diagnosis at stage I. MicroRNAs (miRNAs) are appealing as biomarkers due to their stability, non-invasiveness, and differential expression in tumour tissue compared to healthy tissue. Since they are non-coding, their biological functions can be uncovered by examining their target genes and thus identifying their regulatory pathways and processes. This study aimed to identify miRNAs and genes as candidate biomarkers for early stage OC diagnosis, through two distinct in silico approaches. The first pipeline was based on sequence similarity between miRNAs with a proven mechanism in OC and miRNAs with no known role. This resulted in 9 candidate miRNAs, that have not been previously implicated in OC, that showed 90-99% similarity to a miRNA involved in OC. Following a series of in silico experimentations, it was uncovered that these miRNAs share 12 gene targets that are expressed in the ovary and also have proven implications in the disease. Since the miRNAs target genes contribute to OC onset and progression, it strengthens the notion that the miRNAs may be dysregulated as well. Using TCGA, the second pipeline involved analysing patient clinical data along with implementing statistical measures to isolate miRNAs and genes with high expression in OC. This resulted in 26 miRNAs and 25 genes being shortlisted as the potential candidates for OC management. It was also noted that targeting interactions occur between 15 miRNAs and 16 genes identified through this pipeline. In total, 35 miRNAs and 37 genes were identified from both pipelines.
Synthesis of One-Dimensional TiO2 Nanotube Arrays by Potentiostatic Anodisation
(University of the Western Cape, 2017) Tshaka, Anele; Cummings, Franscious
TiO2 nanomaterials, in particular nanotubes, are some of the most studied materials, as they are considerably important in technological and biological applications due to their unique electronic properties and biocompatibility. For example, vertically aligned TiO2 nanotubes play a crucial role in photovoltaics as they enhance the charge separation as a result of their excellent photo-catalytic properties in the presence of organic dye molecules, and provide a superior one-dimensional transport route compared to nanoparticle films. There are numerous techniques used to synthesise TiO2 nanotubes, such as chemical vapor deposition (CVD), template based techniques, anodisation, to name but a few. However, due to its non-toxicity environmental friendliness and cost-effectiveness, anodisation is the most common technique to synthesise TiO2 nanotubes. In addition anodisation allows for control over the morphology when tailoring the anodisation parameters such as voltage, concentration, temperature and duration. It is well-documented that the as-synthesised TiO2 nanotubes via anodisation technique are amorphous and require post-treatment at elevated temperature (above 280 degrees C) to induce crystallinity into anatase phase. Further increase in annealing temperature results in crystallisation in either rutile or mixed phase structure.
Parameters affecting the production of fumonisin B1 by fusarium verticillioides in culture
(University of the Western Cape, 2001) Keyser, Zanephyn; Klaasen, J.A
Fi1sarium verticillioides is a very important mycotoxin-produeing fungus associated with maize. Fverticillioides produces a group of mycotoxins known as fumonisins under suitable environmental conditions. A series of studies was designed to provide information regarding some of the factors associated with the production offumonisin B1 (FB1) in maize patties and MYRO liquid medium. Our investigation together with previous studies have detailed the important influence of several factors on the production of fumonisins by F verticillioides strains. To understand why these strains are able to produce these toxins, an investigation into the complex interaction that occurs between biotic and abiotic parameters and their impact on fumonisin production was necessary. The results reflect the interacting factors and the intraspecific differences between strains, which may also be present in field conditions. The parameters that were varied under a predetermined set of culture conditions, included initial moisture content of maize patty cultures, temperature, initial pH and the addition of the fumonisin precursors, L-alanine and L-methionineto the cultures. Investigations into the three-way interactions of initial maize patty moisture content (30 ml water to 30g of maize), L-methionine (0.3 %) and temperature (25°C), resulted in the highest yield ofFB1 (5777.26 μgig) produced by MRC 4316. In contrast, MRC 826 was negatively affected, producing lower levels ofFB1 (3492.24 μg/g), compared to MRC 4316 at an initial moisture content (20 ml water to 30 g maize), L-methionine (0.3 %) and 25 °C. An American strain of F verticillioides MRC 7424 (= NRRL 13616), produced the highest levels of FB, (116 μg/ml), while the South African isolates, MRC 4316 and MRC 826, produced lower FB1 levels (93 and 62 μg/ml, respectively) in MYRO liquid medium. In general, FB1 production in maize patty cultures far exceeded levels obtained in liquid shake cultures. It appears that not only the ability of a particular strain of F. verticillioides, but the interaction of a variety of physiological and nutritional factors and the culture medium, are important in the production of FB,. Thus, variation of a single factor such as temperature under field conditions due to seasonal change, may therefore have a major effect on fomonisin production. A chain reaction may occur when changes in moisture, pH, etc. take place, which may influence fumonisin production further. Lyophilisation of fungal cultures proves to be an excellent method to preserve a wide range of fungi over long periods of time. It is, however, necessary to determine the viability of conidia stored in lyophilised vials at 4 ° Con a regular basis. At present, plate count methods remain the most valid technique for the detection of the viability of lyophilised conidia. Membrane-permeant nucleic acid-binding dyes (FUN-I) are viability stains that are relatively new flourescent probes for assessing the viability of metabolically active yeast cells. The purpose of this study was to microscopically determine the viability oflyophilised conidia of Fusarium and A lternaria species, using the yeast, Saccharomyces cerevisiae, as a control. FUN-1 viability stain was compared to two other staining methods, i.e. ethidium bromide (EB) and methylene blue (MB) and the viability of the conidia was compared to colony-forming units (CFU) on solid media as a control. For the purpose of determining or screening for percentage viability in a specific inoculum, results indicate that EB can be used in the case of lyophilised conidia, and MB in the case of freshly harvested conidia. Although FUN-I are recommended as a good way to determine the cell viability of a fungus, it needs relatively complicated procedures and has a time limit in which the stain can be used. The result of this study emphasize that the use of dyes to determine viability of lyophilised conidia require a critical definition of protocols for a specific fungal species, and that a good correlation with CFU needs to be demonstrated. The findings of this study could find useful applications in various studies on living and dead conidial populations. The diverse toxicological effects of fumonisins m animals and plants raised the possibility that fumonisins may also inhibit the growth of filamentous fungi. This study investigated the antifungal activity of FB1 to some h1sariu111 and other fungal species. The sensitivity of these fungi was tested by an agar-diffusion method on PDA plates. FB1 inhibited the myceliaJ growth of five of the nine fungi tested. The FB1-producing Fusarium species isolated from maize, i.e. F verticil/ioides, F glohosum and F proliferatum were resistant to FB1 even though a small inhibition zone at the highest FB1 concentration of 40mM was noted in the case of F. proliferatum. However, amongst two non-producing Fusarium spp. also isolated from maize, one (F subglutinans) was resistant and one (F graminearum) was sensitive. The most sensitive fungi tested were non-producing species not isolated from maize, i.e. A lternaria alternata, Botrytis cinerea and Penicillium expansum. The minimum inhibitory concentration ofFB1 ranged between 0.25-0.SmM for A. alternata, 1-SmM for P. expansum and B. cinerea and 5-1 OmM for F. graminearum, while the other fungi tested showed no sensitivity to FB1. This is the first report on the antifungal activity ofFB1 to filamentous fungi. Another study investigated the effect of FB1 on the germination of freshly harvested conidia of Fusarium and some other fungal species. The FB1 -producing F'usarium species isolated from maize, i. e. F vertici llioides, F. globosum and F. prolifer alum showed a decrease in germ tube length with an increase in FB1 concentrations. This indicated that these fungi can tolerate their own toxic metabolite to a ce11ain extent. However, amongst the two non-fumonisin producing Fi1sarium spp. examined, i.e. F. subglutinans and F. graminearum, isolated from maize, F. subglutinans was induced to genninate faster in the presence ofFB1 but soon developed stunted germ tubes, while F graminearum developed shorter germ tubes compared to the control cultures. The most sensitive fungi tested were species not isolated from maize, i.e. A. alternata, B. cinerea and P. expansum, which did not germinate at higher FB1 concentrations at all. Statistical analyses showed that the inhibiting effect of FB1 was highly significant (P <0.001). The conidial germination bioassay was more sensitive in the detection of the antifungal activity ofFB1 than the petri dish bioassay. The minimum inhibitory concentrations of FB1 for visible mycelial growth were closely comparable to those obtained from conidial germination. Results of these studies provide considerable information on the parameters affecting the production of FB1 and will be of great benefit in further studies focussing on fumonisin prodnction.
Reliability of panoramic radiographs to determine the vertical position of the impacted third molar root tip from the inferior alveolar canal
(2013) Fauzi, Azizah Ahmad; Parker, Mohamed Ebrahim; Norval, E J
Nowadays, the availability of radiographic modalities from conventional radiography to more advanced approaches such as medical computed tomography as well as cone beam computed tomography have been useful in providing insights of relevant anatomy prior to surgical procedures. The increased popularity of cone beam computed tomography has prompted interest in the utility of this approach for diagnostic application in dentistry, including the assessment of the proximity of impacted mandibular third molars to the inferior alveolar canal. It is important to understand the reliability of conventional panoramic radiograph in the assessment of this criterion since it is more commonly used as first line radiographic approach due to its availability and lower radiation dose. This study is aimed to investigate the reliability of conventional panoramic radiograph in the evaluation of the proximity of impacted mandibular third molar root tip to the inferior alveolar canal by correlating the results with cone beam computed tomography. A retrospective study of forty nine patients who underwent panoramic radiography as well as cone beam computed tomography for examination of impacted mandibular third molars was conducted. Two observers were participated in all image evaluation. In this study, both observers recorded statistically significant differences in the measurement of the apices of vertically impacted third molars and the inferior alveolar canal from panoramic radiographs and cone beam computed tomography images. The low reliability of panoramic radiograph to assess the vertical proximity between these two anatomical structures suggests the importance of additional assessment with cone beam computed tomography in cases where panoramic radiograph shows superimposition of the third molar root on the roof of the canal, presence of root below the roof of the canal and presence of bone height of less than one millimetre separating the third molar from the inferior alveolar canal.
Palladium telluride quantum dots biosensor for the determination of indinavir drug
(2013) Feleni, Usisipho; Iwuoha, Emmanuel
Indinavir is a potent and well tolerated protease inhibitor drug used as a component of the highly active antiretroviral therapy (HAART) of HIV/AIDS, which results in pharmacokinetics that may be favourable or adverse. These drugs work by maintaining a plasma concentration that is sufficient to inhibit viral replication and thereby suppressing a patient’s viral load. A number of antiretroviral drugs, including indinavir, undergo metabolism that is catalysed by cytochrome P450-3A4 enzyme found in the human liver microsomes. The rate of drug metabolism influences a patient’s response to treatment as well as drug interactions that may lead to life-threatening toxic conditions, such as haemolytic anaemia, kidney failure and liver problems. Therapeutic drug monitoring (TDM) during HIV/AIDS treatment has been suggested to have a potential to reduce drug toxicity and optimise individual therapy. A fast and reliable detection technique, such as biosensing, is therefore necessary for the determination of a patient’s metabolic profile for indinavir and for appropriate dosing of the drugs. In this study biosensors developed for the determination of ARV drugs comprised of cysteamine self-assembled on a gold electrode, on which was attached 3-mercaptopropionic acid-capped palladium telluride (3-MPA-PdTe) or thioglycolic acid-capped palladium telluride (TGA-PdTe) quantum dots that are cross-linked to cytochrome P450-3A4 (CYP3A4) in the presence of 1-ethyl-3(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxysuccinimide. The quantum dots were synthesized in the presence of capping agents (3-MPA or TGA) to improve their stability, solubility and biocompatibility. The capping of PdTe quantum dots with TGA or 3-MPA was confirmed by FTIR, where the SH group absorption band disappeared from the spectra of 3-MPA-PdTe and TGA-PdTe. The particle size of the quantum dots (< 5 nm) was estimated from high resolution transmission electron microscopy (HRTEM) measurements. Optical properties of the materials were confirmed by UV-Vis spectrophotometry which produced absorption iii bands at ~320 nm that corresponded to energy band gap values of 3 eV (3.87 eV) for TGAPdTe (3-MPA-PdTe) quantum dots. The electrocatalytic properties of the quantum dots biosensor systems were studied by cyclic voltammetry (CV) for which the characteristic reduction peak at 0.75 V was used to detect the response of the biosensor to indinavir. Results for indinavir biosensor constructed with 3-MPA-SnSe quantum dots are also reported in this thesis. The three biosensors systems were very sensitive towards indinavir; and gave low limits of detection (LOD) values of 3.22, 4.3 and 6.2 ng/mL for 3-MPA-SnSe, 3-MPA-PdTe and TGA-PdTe quantum dots biosensors, respectively. The LOD values are within the ‘maximum plasma concentration’ (Cmax) value of indinavir (5 - 15 ng/mL) normally observed 8 h after drug intake.
Transcriptional regulatory networks in the mouse hippocampus
(University of the Western Cape, 2007) MacPherson, Cameron Ross; Bajic, Vladimir
Neurological diseases are socially disabling and often mortal. To efficiently combat these diseases, a deep understanding of involved cellular processes, gene functions and anatomy is required. However, differential regulation of genes across anatomy is not sufficiently well understood. This study utilized large-scale gene expression data to define the regulatory networks of genes expressing in the hippocampus to which multiple disease pathologies may be associated. Specific aims were: ident i fy key regulatory transcription factors (TFs) responsible for observed gene expression patterns, reconstruct transcription regulatory networks, and prioritize likely TFs responsible for anatomically restricted gene expression. Most of the analysis was restricted to the CA3 sub-region of Ammon’s horn within the hippocampus. We identified 155 core genes expressing throughout the CA3 sub-region and predicted corresponding TF binding site (TFBS) distributions. Our analysis shows plausible transcription regulatory networks for twelve clusters of co-expressed genes. We demonstrate the validity of the predictions by re-clustering genes based on TFBS distributions and found that genes tend to be correctly assigned to groups of previously identified co-expressing genes with sensitivity of 67.74% and positive predictive value of 100%. Taken together, this study represents one of the first to merge anatomical architecture, expression profiles and transcription regulatory potential on such a large scale in hippocampal sub-anatomy.
Functional analysis of the mouse RBBP6 gene using Interference RNA
(University of the Western Cape, 2007) Pretorius, Ashley; Jasper, D.; Rees, G.; Faculty of Science
The aim of this thesis was to investigate the cellular role of the mouse RBBP6 gene using the interference RNA (RNAi) gene targeting technology and also to understand the relevance of two promoters for the RBBP6 gene.
An in vitro study on the immunotoxicity of South African beer
(University of the Western Cape, 2008) Neethling, Michelle; Pool, Edmund J.; Faculty of Science
Traditionally brewed beers are of cultural and economic importance to many African nations. The presence of mycotoxins in African beer is a topic that needs to be addressed, since most African countries have a climate of high humidity and temperature that favours the growth of moulds. Mycotoxins challenge not only the health of animals and humans, but also the economy, especially in underdeveloped countries where contamination is most likely. Literature proves that mycotoxins depict various effects on the immune system including immunotoxicity. Beer analysis is therefore of utmost importance in order to evaluate organoleptic characteristics, quality, nutritional value as well as safety. The aims of this study involve the analysis and comparison of traditional and commercial beer in terms of physical characteristics, mycotoxin concentrations as well as effects on specific immune pathway biomarkers in order to elucidate possible immunotoxicity.

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