Phenolic compounds in water and the implications for rapid detection of indicator micro-organisms using ß-D-Galactosidase and ß-D-Glucuronidase
- Authors: Abboo, Sagaran
- Date: 2009
- Subjects: Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3978 , http://hdl.handle.net/10962/d1004037 , Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Description: Faecal contamination in water is detected using appropriate microbial models such as total coliforms, faecal coliforms and E. coli. Βeta-D-Galactosidase (β-GAL) and Beta-D-glucuronidase (β-GUD) are two marker enzymes that are used to test for the presence of total coliforms and E. coli in water samples, respectively. Various assay methods have been developed using chromogenic and fluorogenic substrates. In this study, the chromogenic substrates chlorophenol red β-D-galactopyranoside (CPRG) for β-GAL and p-nitrophenyl-β-D-galactopyranoside (PNPG) for β-GUD were used. Potential problems associated with this approach include interference from other organisms present in the environment (e.g. plants, algae and other bacteria), as well as the presence of certain chemicals, such as phenolic compounds in water. Phenolic compounds are present in the aquatic environment due to their extensive industrial applications. The USA Enviromental Protection Agency (EPA) lists 11 Priority Pollutant Phenols (PPP) due to their high level of toxicity. This study investigated the interfering effects of the eleven PPP found in water on the enzyme activities of both the β-GAL and β-GUD enzyme assays. The presence of these PPP in the β-GAL and β-GUD enzyme assays showed that over and underestimation of activity may occur due to inhibition or activation of these enzymes. Three types of inhibition to enzyme activities were identified from double reciprocal Lineweaver-Burk plots. The inhibition constants (Ki) were determined for all inhibitory phenolic compounds from appropriate secondary plots. Furthermore, this study presented a validated reverse phase high performance liquid chromatography (RP-HPLC) method, developed for the simultaneous detection, separation and determination of all eleven phenolic compounds found in the environment. This method demonstrated good linearity, reproducibility, accuracy and sensitivity. Environmental water samples were collected from rivers, streams, industrial sites and wastewater treatment plant effluent. These samples were extracted and concentrated using a solid phase extraction (SPE) procedure prior to analysis employing the newly developed HPLC method in this study. Seasonal variations on the presence of the PPP in the environment were observed at certain collection sites. The concentrations found were between 0.033 μg/ml for 2,4-dinitrophenol in a running stream to 0.890 mg/ml for pentachlorophenol from an tannery industrial site. These concentrations of phenolic compounds found in these environments were able to interfere with the β-GAL and β-GUD enzyme assays.
- Full Text:
- Date Issued: 2009
A review of asbestos resources
- Authors: Abbott, Paul
- Date: 1983
- Subjects: Asbestos Asbestos -- Geology Silicate minerals Mineralogy Chrysotile
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4910 , http://hdl.handle.net/10962/d1001570
- Full Text:
- Date Issued: 1983
Genetic and biological characterisation of a novel South African Plutella xylostella granulovirus (PlxyGV) isolate
- Authors: Abdulkadir, Fatima
- Date: 2014
- Subjects: Diamondback moth , Diamondback moth -- Control -- South Africa , Plutellidae -- Control -- South Africa , Baculoviruses , Cruciferae -- Diseases and pests -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4113 , http://hdl.handle.net/10962/d1013059
- Description: The diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is an important pest of cruciferous crops worldwide. The prolonged use of synthetic chemical insecticides as a primary means of control has resulted in the development of resistance in pest populations. In addition, the pest has also evolved resistance to the bacterial insecticidal protein of Bacillus thuringiensis which is also widely used as a method of control. Baculoviruses are considered as effective alternatives to conventional methods of control when incorporated into integrated pest management (IPM) programmes. These viruses target the larval stages of insects, are generally host-specific and are safe for use in the environment. This study aimed to isolate a baculovirus from a laboratory-reared P. xylostella colony, characterise it genetically and then evaluate its virulence against neonate and fourth instar larvae. A laboratory colony of P. xylostella was established using pupae and asymptomatic larvae collected from a cabbage plantation outside Grahamstown in the Eastern Cape province of South Africa. The colony flourished in the laboratory due to prime conditions and availability of food. The duration of development from egg to adult was determined by observation and imaging of the various life stages. The mean developmental time from egg to adult was observed to be 14.59 ± 0.21 days. The population of the insects increased rapidly in number leading to overcrowding of the insect colony, and hence appearance of larvae with viral symptoms. Occlusion bodies (OBs) were extracted from symptomatic larval cadavers and purified by glycerol gradient centrifugation. Analysis of the purified OBs by transmission electron microscopy revealed the presence of a granulovirus which was named PlxyGV-SA. The virus isolate was genetically characterised by restriction endonuclease analysis of the genomic DNA, and PCR amplification and sequencing of selected viral genes. The complete genome sequence of a Japanese P. xylostella granulovirus isolate, PlxyGV-Japan, has been deposited on the GenBank database providing a reference strain for comparison with DNA profiles and selected gene sequences of PlxyGV-SA. BLAST analysis of the granulin gene confirmed the isolation of a novel South African PlxyGV isolate. Comparison of the restriction profiles of PlxyGV-SA with profiles of PlxyGV-Japan and other documented PlxyGV profiles obtained by agarose gel electrophoresis revealed that PlxyGV-SA is a genetically distinct isolate. The data obtained from the sequencing and alignment of ecdysteroid UDP-glucosyltransferase (egt), late expression factor 8 (lef-8) and late expression factor 9 (lef-9) genes with those of PlxyGV-Japan also showed that PlxyGV-SA is a genetically different isolate. In order to determine the biological activity of PlxyGV-SA against neonate and fourth instar P. xylostella larvae, surface dose bioassays were conducted. The median lethal concentration of the virus required to kill 50% (LC₅₀) and 90% (LC₉₀) of the larvae was estimated by feeding insects with a range of doses. In addition, the time to kill 50% of the larvae (LT₅₀) was determined by feeding insects with the LC₉₀ concentration. Larval mortality was monitored daily until pupation. The data obtained from the dose response assays were subjected to probit analysis using Proban statistical software. The time response was determined using GraphPad Prism software (version 6.0). The LC₅₀ and LC₉₀ values for the neonate larvae were 3.56 × 10⁵ and 1.14 × 10⁷ OBs/ml respectively. The LT₅₀ was determined to be 104 hours. The neonate larvae were found to be more susceptible to infection than the fourth instar larvae with the same virus concentration. The concentrations used for the neonate larvae assay did not have a significant effect on the fourth instar as no mortality was recorded. This is the first study to describe a novel South African PlxyGV isolate and the results suggest that PlxyGV-SA has significant potential for development as an effective biopesticide for the control of P. xylostella in the field.
- Full Text:
- Date Issued: 2014
The implementation and evaluation of a service-learning component in a second year undergraduate organic chemistry course
- Authors: Abel, Sarah Ruth
- Date: 2011 , 2010-10-03
- Subjects: Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4393 , http://hdl.handle.net/10962/d1006008 , Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Description: The project describes the action research implementation, and evaluation of learning, of a service-learning component in a second year undergraduate organic chemistry course. The research aims to explore the learning that takes place in a service-learning context while utilizing an action research methodology within the critical theory paradigm. This occurs in response to the world-wide call for Higher Education to produce people with civic competencies and responsiveness to the society in which they live (Boyer 1996). Educating young Chemists to see the importance of their knowledge and their responsibilities in society is an important pedagogical step in the effort to cross boundaries and make connections between people communities (Eyler and Giles 1999). The goal of this project was to explore and categorize the learning that takes place in a service-learning context and discover how these areas of learning impact the awareness of the parties involved with regard to the discipline of chemistry as well as social issues. The project makes use of Kolb‘s (1984) Experiential Learning Theory, and Eyler and Giles‘ (1999) categories of learning in service-learning and results indicate that service-learning can be a powerful pedagogical tool to increase learning in chemistry as well as in the areas of critical thinking, personal and social development, reflection and citizenship. Students‘ perceptions of themselves, their discipline and their responsibility to society were transformed by their experience of service-learning in their undergraduate chemistry course.
- Full Text:
- Date Issued: 2011
Photosynthetic and growth response of C₃ and C₄ subspecies of Alloteropsis semialata to nitrogen-supply
- Authors: Abraham, Trevor Ian
- Date: 2008
- Subjects: Photosynthesis , Plants -- Effect of nitrogen on , Growth (Plants) , Plant ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4182 , http://hdl.handle.net/10962/d1003750 , Photosynthesis , Plants -- Effect of nitrogen on , Growth (Plants) , Plant ecology
- Description: The greater photosynthetic nitrogen use efficiency (PNUE) of C4 compared with C3 plants may explain the relative success of C4 grasses in nutrient poor environments. This study compared the responses in photosynthetic parameters, leaf nitrogen and biomass allocation between the C3 and C4 subspecies of Alloteropsis semialata supplied soil nitrogen at three levels. Photosynthesis was assessed by means of CO2 response curves and the leaf nitrogen content assayed. Plants were destructively harvested, leaf areas determined and the dry biomass of functional plant components was measured. Results confirmed that the higher PNUE of C4 plants allowed them to accumulate more biomass than C3 plants at the high nitrogen level, despite smaller leaf areas. The greater productivity of C4 plants enabled them to invest more in storage and sexual reproduction than in leaves when compared to the C3 plants. In contrast the C3 plants invested biomass in less efficient and more nitrogen demanding leaves and bigger root systems. PNUE and photosynthetic rates were not significantly affected by nitrogen-limitation in either subspecies and the major response was a decrease in biomass accumulation and an increase in biomass allocation to roots. This altered root to shoot ratio was accompanied by a lowered allocation to sexual reproduction in the C4 subspecies, but an unaltered allocation to leaves, while in the C3 subspecies there was a decrease in leaf allocation. In a further experiment, the C4 subspecies was supplied three levels of nitrogen provided as nitrate, or alternatively as ammonium plus nitrate, and leaves were excised to within 5 cm of the ground at the start of treatment. Prior to flowering, photosynthesis was assessed by means of CO2 response curves and the plants were destructively harvested. Leaf areas and the dry biomass of functional plant components were determined, and at levels of nitrogen supply higher than those found in savanna soils the rate of photosynthesis was increased. Leaf re-growth was reduced by severe nitrogen limitation and co-provision of nitrate and ammonium had no significant effect other than increased tillering. Both subspecies of Alloteropsis semialata are adapted to nutrient poor environments and maintain photosynthetic rates by reducing leaf area. The C4 subspecies is likely to show greater resilience in disturbance-prone environments by exploiting its higher PNUE to allocate greater resources to storage and sexual reproduction, while the C3 subspecies is usually found in environments with closed canopies which favour vegetative growth, and allocate greater resources to leaves and roots.
- Full Text:
- Date Issued: 2008
Relative contribution of wild foods to individual and household food security in the context of increasing vulnerability due to HIV/AIDS and climate variability
- Authors: Abu-Basutu, Keitometsi Ngulube
- Date: 2014
- Subjects: Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4774 , http://hdl.handle.net/10962/d1010864 , Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Description: Wild foods are an integral component of the household food basket, yet their quantified contribution to food security relative to other sources in the context of HIV/AIDS, climate change and variability remains underexplored. This study was carried out in Willowvale and Lesseyton which are rural communities in the Eastern Cape province of South Africa. Willowvale is a relatively remote, medium-rainfall coastal community, while Lesseyton is a peri-urban low rainfall inland community. Qualitative and quantitative methods were used to collect data from 78 HIV/AIDS afflicted households with 329 individuals and 87 non-afflicted households with 365 individuals in the two study sites. Households were visited quarterly over 12 months to assess food acquisition methods, dietary intake and quality, and levels of food security, and to determine strategies employed by households to cope with droughts. The wild foods investigated were wild meat, wild birds, wild fish, wild mushrooms, wild leafy vegetables and wild fruits. Diets were moderately well-balanced and limited in variety, with cereal items contributing 52 % to total calorie intake. Mid-upper arm circumference measurements showed that all respondents were adequately nourished. The bulk of the food consumed by households was purchased, with supplementation from own production, wild vegetables and wild fruits. In Willowvale, wild vegetables comprised 46 % of overall vegetable consumption for afflicted households and 32 % for non-afflicted households, while own fruit production comprised 100 % of fruit consumption. In Lesseyton, wild vegetables comprised only 6 % and 4 % of vegetable consumption for afflicted and non-afflicted households, while wild fruit comprised 63 % and 41 % for afflicted and non-afflicted households. More than 80 % of respondents from both afflicted and non-afflicted households had sufficient daily kilocalories, although the majority of afflicted households felt they were food insecure and sometimes collected wild foods as one of their multiple coping strategies. Hunting and gathering of wild foods was associated with site, household affliction status, gender, age and season. More than 80 % of respondents ate wild vegetables and said they were more drought tolerant than conventional vegetables, making them the most consumed wild food and approximately 16 % of respondents ate wild birds, making them the least consumed wild food. Approximately 14 % of respondents from afflicted households in Willowvale sold wild fish, whilst 34 % of respondents from afflicted households and 7 % from non-afflicted households sold wild fruits in Lesseyton. Strategies adopted by households to cope with droughts were different between the two study sites, and households in Willowvale used a wider range of strategies. Given the devastating effects of HIV/AIDS coupled with the drawbacks of climate change and variability on food security, wild foods represent a free and easy way for vulnerable households to obtain food.
- Full Text:
- Date Issued: 2014
Isolation and structure elucidation of halogenated metabolites from Portieria hornemannii and Portieria tripinnata
- Authors: Adam, Mohammed
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64674 , vital:28591
- Description: The red marine algal genus, Portieria, is known to produce a number of potent cytotoxic compounds with anticancer potential. The most important anticancer lead produced by this genus is the compound halomon. Unfortunately, the lack of sufficient quantities of this compound hampered its further development. Two Portieria species, Portieria hornemannii and Portieria tripinnata, are found along the South African coastline. Recent studies, based on DNA analysis, suggest that Portieria hornemannii may in fact be divided into several cryptic species. The current project is part of a larger study designed to investigate the use of secondary metabolites to identify new marine algal species. In this study 1H NMR profiles of the organic extracts of selected Portieria spp were compared in order to identify new species. Selected compounds were then isolated and characterised as potential chemotaxonomic markers. Four halogenated monoterpenes were isolated from Portieria hornemannii. Two of these were new compounds 4-(3-bromo-4-chloro-4-methylpentyl)-3-chlorofuran-2(5H)-one, which were isomers of each other. The two known compounds had been previously isolated from Portieria hornemannii samples off the Madagascar coast. These compounds could prove to be useful as chemotaxonomic marker compounds, as they have never been isolated from any other species of marine algae. Three known halogenated monoterpenes were isolated from Portieria tripinnata. These compounds had been previously isolated from different species of marine algae and therefore, could not serve as chemotaxonomic marker compounds for this species of marine alga. Further work needs to be done on Portieria tripinnata, with regards to its chemistry, as it is a species of marine algae that has not been previously researched.
- Full Text:
- Date Issued: 2015
Photosynthetic and growth responses of C3 and C4 grasses to short- duration sunflecks and resultant consequences for their performance in understory environments
- Authors: Adams, Claire Elizabeth
- Date: 2017
- Subjects: Understory plants -- Effect of light on , Grasses -- Effect of light on -- South Africa , Erharta -- Effect of light on , Brachiara -- Effect of light on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5016 , vital:20753
- Description: Low C4 grass species abundance in understory environments is thought to be as a result of their high-light requirements, lack of photosynthetic advantage relative to C3 species in cooler environments, and an inability to adequately utilise sunflecks. This study sets out to investigate this theory, hypothesizing that C3 grass species outperform C4 grass species under the canopy, not as a result of quantum efficiency temperature effects, but as a result of C4 species inability to utilize short-duration sunflecks. Short sunflecks could result in a breakdown in assimilate movement between the mesophyll (MSC) and bundle sheath (BSC) cells. The role of BSC leakiness, stomata and PSII efficiency on the ability of C3 and C4 Alloteropsis semialata to utilize short-duration sunflecks was investigated using gaseous exchange and chlorophyll fluorescence techniques, while the growth of both subspecies under a simulated flecking-light environment tested whether these measured responses translated into effects on growth. As C3 grasses are known to possess higher levels of stomatal conductance in relation to C4 species, results showed that C3 A. semialata was able to utilize short-duration sunflecks as a result of increased stomatal conductance and an ability to induce photosynthesis under various light flecking conditions. In contrast, C4 A. semialata was unable to utilize sunflecks possibly as a result of energetic limitations of the carboxylation mechanism (PSII) and not because of increased bundle sheath leakiness. These photosynthetic responses translated into growth differences when both types were grown in an artificially flecking light environment. The photosynthetic differences noted for C3 and C4 A.semialata were also evident in shade adapted understory grasses; Erharta erecta (C3), Dactylotenium australe (C4) and Brachiaria chusqueoides (C4). As photosynthetic induction was marginally more rapid in all species relative to A. semialata it suggests some degree of adaptation in shade grasses, however the inability of the C4 species to utilise short sunflecks remained. As a result, it was hypothesized that C3 shade adapted E. erecta and C4 B. chusqueoides, co-inhabiting the same forest understory, are able to do so because of differences in light micro-environments associated with each species. However, canopy openness and light profiles determined for theses micro-climates showed no differences and that both species have persisted within a relatively stable understory environment. The coexistence was possible as the understory was supplied with a significant proportion of its daily light in flecks sufficiently long as to not compromise C4 productivity. A survey of 10 species of grasses under various canopy densities and in the open showed a strong negative linear relationship between canopy openness and the rate at which photosynthesis was induced by flecking light, which has not been shown before. This did not result from the phylogenetic relationship between species and could be shown for a single species (E. erecta) growing in a range of light environments. This demonstrates that C4 grasses, despite adaptation, would be limited from sunfleck environments if a significant proportion of the daily light available consists of flecks of short-duration. The generation of such environments may occur as a result of woody thickening and could help explain the observed decline in C4 grasses under these conditions.
- Full Text:
- Date Issued: 2017
A study of a class of invariant optimal control problems on the Euclidean group SE(2)
- Authors: Adams, Ross Montague
- Date: 2011
- Subjects: Matrix groups Lie groups Extremal problems (Mathematics) Maximum principles (Mathematics) Hamilton-Jacobi equations Lyapunov stability
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5420 , http://hdl.handle.net/10962/d1006060
- Description: The aim of this thesis is to study a class of left-invariant optimal control problems on the matrix Lie group SE(2). We classify, under detached feedback equivalence, all controllable (left-invariant) control affine systems on SE(2). This result produces six types of control affine systems on SE(2). Hence, we study six associated left-invariant optimal control problems on SE(2). A left-invariant optimal control problem consists of minimizing a cost functional over the trajectory-control pairs of a left-invariant control system subject to appropriate boundary conditions. Each control problem is lifted from SE(2) to T*SE(2) ≅ SE(2) x se (2)*and then reduced to a problem on se (2)*. The maximum principle is used to obtain the optimal control and Hamiltonian corresponding to the normal extremals. Then we derive the (reduced) extremal equations on se (2)*. These equations are explicitly integrated by trigonometric and Jacobi elliptic functions. Finally, we fully classify, under Lyapunov stability, the equilibrium states of the normal extremal equations for each of the six types under consideration.
- Full Text:
- Date Issued: 2011
An investigation into the potential immunogenicity of various extracts of the South African bont tick Amblyomma hebraeum
- Authors: Adamson, Deborah Jane
- Date: 1993
- Subjects: Amblyomma -- South Africa , Ticks -- South Africa , Ticks -- Control -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4127 , http://hdl.handle.net/10962/d1015640
- Description: Rabbits and goats were inoculated with crude, membrane-associated and soluble components extracted from unengorged adult females and nymphs of the bont tick Amblyomma hebraeum. Inoculation provided some protection against nymphal infestation, however it had little effect on adult feeding. Histological examination of adults fed on inoculated hosts showed evidence of gut damage. Skin provocation testing with tick extracts elicited a Type I immediate hypersensitivity which was influenced by antihistamine. A delayed skin reaction was also evident. Whether this was attributable to Type III Arthus reaction or Type IV cell-mediated hypersensitivity was not determined. A comparative histological study of sites of tick extract injection, on inoculated and naive hosts, demonstrated the role of eosinophils in the hosts response to tick feeding. Serological examination revealed elevated anti-A hebraeum lgG titres following inoculation. These titres were found to decrease in the ten weeks after inoculation, despite the hosts being repeatedly infested with A hebraeum. Although the IgG titres of naive control hosts increased after each tick infestation, they failed to reach the titres achieved through inoculation. Western blot analysis of serum from inoculated hosts recognized most of the A. hebraeum proteins against which it was screened.
- Full Text:
- Date Issued: 1993
Isolation, propagation and rapid molecular detection of the Kalahari truffle, a mycorrhizal fungus occurring in South Africa
- Authors: Adeleke, Rasheed Adegbola
- Date: 2007 , 2013-04-03
- Subjects: Truffles -- Kalahari Desert , Fungi -- Identification , Mycorrhizal fungi -- South Africa , Edible fungi -- South Africa , Mushroom culture -- South Africa , Fungi -- Cultures and culture media -- South Africa , Truffles -- South Africa , Truffles -- Lifecycles , Mycorrhizal fungi -- Lifecycles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3889 , http://hdl.handle.net/10962/d1002951 , Truffles -- Kalahari Desert , Fungi -- Identification , Mycorrhizal fungi -- South Africa , Edible fungi -- South Africa , Mushroom culture -- South Africa , Fungi -- Cultures and culture media -- South Africa , Truffles -- South Africa , Truffles -- Lifecycles , Mycorrhizal fungi -- Lifecycles
- Description: Terfezia pfeilii is an edible mycorrhizal fungus that thrives in the Kalahari Desert of southern Africa. It is best known by desert dwellers for its flavour and as a source of nutrition. Although the genus Terfezia is generally regarded as being an ectomycorrhizal mycobiont, the exact mycorrhizal type formed by T. pfeilli and its' associated host plants remains uncertain. Discovery of the host plants for T. pfeilii would first be required in order to further investigate the life cycle and cultivation of this truffle. This study focussed on the isolation of mycelia from the ascocarp, optimising the growth conditions of the mycelial cultures, rapid molecular identification of T. pfeilii, investigation of potential helper bacteria and mycorrhizal synthesis experiments. T. pfeilii ascocarps were harvested from the Spitskop Nature Reserve in Upington, South Africa. Ascocarps were successfully identified using both morphological and molecular methods. Despite the delayed growth mostly caused by contaminating microorganisms, the isolation of T. pfeilii mycelia culture was successful. Molecular techniques were used to confirm the identity of the pure culture. Further studies were conducted on ways to improve the growth conditions of the mycelial culture on Fontana medium. An optimum temperature of 32°C, the addition of Bovine Serum Albumin as a nitrogen source and a pH of 7.5 significantly improved the growth of T. pfeilii in vitro. A rapid PeR-based molecular method was developed to speed up the identification of T. pfeilii. Specific primers that can exclusively amplify the ITS region of T. pfeilii were designed and used to identify both the ascocarps and the mycelial culture. The specificity of these primers was confirmed by their inability to amplify DNA from the isolates of contamining fungi obtained during the isolation process. Molecular comparison was made to confirm the reclassification of South African samples of T. pfeilii as Kalaharituber pfeilii as proposed by Ferdman et al.,(2005). However, in this study, the name T. pfeilii has been retained. A total of 17 bacterial isolates were obtained from the fruiting bodies of T. pfeaii and these were tested for stimulation of mycelial growth in vitro, indole production and phosphate solubilising capabilities. Bacterial isolates that showed potential to be Mycorrhization Helper Bacteria (MHB) were identified as Paenibacillus sp., Bacillus sp. and Rhizobium tropici. Selected plant seedlings were inoculated with T. pfeilii cultures or ascocarp slurry in order to re-establish the mycorrhizal association. After 8 months, light microscopy observations revealed an endomycorrhizal type association between Cynodon dactylon and T. pfeilii. This was confirmed with molecular analysis using specific T. pfeilii ITS primers. After 15 months, molecular methods confirmed Acacia erioloba as another host plant. These results have provided essential information paving the way for further investigation into the life cycle and biology of the Kalahari truffle. , KMBT_363 , Adobe Acrobat 9.53 Paper Capture Plug-in
- Full Text:
- Date Issued: 2007
Marine anti-malarial isonitriles : a synthetic and computational study
- Authors: Adendorff, Matthew Ralph
- Date: 2011 , 2010-05-17
- Subjects: Isocyanides , Isocyanates , Marine pharmacology , Antimalarials , Antimalarials -- Development , Drug development
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4398 , http://hdl.handle.net/10962/d1006674 , Isocyanides , Isocyanates , Marine pharmacology , Antimalarials , Antimalarials -- Development , Drug development
- Description: The development of Plasmodium falciparum malarial resistance to the current armoury of anti-malarial drugs requires the development of new treatments to help combat this disease. The marine environment is a well established source of potential pharmaceuticals. Of interest to us are isonitrile, isocyanate and isothiocyanate compounds isolated from marine sponges and molluscs which have exhibited nano-molar anti-plasmodial activities. Through quantitative structure-activity relation studies (QSAR), a literature precedent exists for a pseudoreceptor model from which a pharmacophore for the design of novel anti-malarial agents was proposed. The current theory suggests that these marine compounds exert their inhibitory action through interfering with the heme detoxification pathway in P. falciparum. We propose that the computational methods used to draw detailed conclusions about the mode of action of these marine compounds were inadequate. This thesis addresses this problem using contemporary computational methodologies and seeks to propose a more robust method for the rational design of new anti-malarial drug compounds that inhibit heme polymerization to hemozoin. In order to investigate the interactions of the marine compounds with their heme targets, a series of modern computational procedures were formulated, validated and then applied to theoretical systems. The validations of these algorithms, before their application to the marine compound-heme systems, were achieved through two case studies. The first was used to investigate the applicability of the statistical docking algorithm AutoDock to be used for the exploration of conformational space around the heme target. A theoretical P. falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR) enzyme model, constructed by the Biochemistry Department at Rhodes University, provided the ideal model to validate the AutoDock program. The protein model was accordingly subjected to rigorous docking simulations with over 30 different ligand molecules using the AutoDock algorithm which allowed for the docking algorithm’s limitations to be ascertained and improved upon. This investigation facilitated the successful validation of the protein model, which can now be used for the rational design of new PfDXR-inhibiting anti-plasmodial compounds, as well as enabling us to propose an improvement of the docking algorithm for application to the heme systems. The second case study was used to investigate the applicability of an ab initio molecular dynamics algorithm for simulation of bond breaking/forming events between the marine compounds and their heme target. This validation involved the exploration of intermolecular interactions in a naturally occurring nonoligomeric zipper using the Car-Parrinello Molecular Dynamics (CPMD) method. This study allowed us to propose a model for the intermolecular forces responsible for zipper self-assembly and showcased the CPMD method’s abilities to simulate and predict bond forming/breaking events. Data from the computational analyses suggested that the interactions between marine isonitriles, isocyanates and isothiocyanates occur through bond-less electrostatic attractions rather than through formal intermolecular bonds as had been previously suggested. Accordingly, a simple bicyclic tertiary isonitrile (5.14) was synthesized using Kitano et al’s relatively underutilized isonitrile synthetic method for the conversion of tertiary alcohols to their corresponding isonitriles. This compound’s potential for heme detoxification inhibition was then explored in vitro via the pyridine-hemochrome assay. The assay data suggested that the synthesized isonitrile was capable of inhibiting heme polymerization in a similar fashion to the known inhibitor chloroquine. Attempts to synthesize tricyclic analogues of 5.14 were unsuccessful and highlighted the limitation of Kitano et al’s isonitrile synthetic methodology.
- Full Text:
- Date Issued: 2011
Studies towards the development of novel antimalarial agents
- Authors: Adeyemi, Christiana Modupe
- Date: 2015
- Subjects: Antimalarials , Malaria , Drug resistance , Drug development , Enzyme inhibitors , Plasmodium
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54645 , vital:26596
- Description: Considerable efforts have been made in the modification of existing antimalarial drugs, and the support of incentive programmes have led to a drastic decrease in malaria cases reported by WHO during the past 6 years. However, the development of drug resistance threatens the eradication of this deadly disease and has prompted research on the synthesis of novel antimalarial drugs. Our research has involved the design and synthesis of novel benzylated phosphonate esters as potential 1-deoxy-D-xylose-5-phosphate reductoisomerase (DXR) inhibitors. A series of amidoalkylphosphonate esters were obtained by reacting various 3-subsituted anilines and heterocyclic amines with chloroalkanoyl chlorides and reacting the resulting chloroalkanamides with triethyl phosphite using Michaelis-Arbuzov methodology. Benzylation of the phosphonate esters afforded a series of novel N-benzylated derivatives in good yields and these compounds were fully characterised by NMR and HRMS methods. Several approaches to the introduction of a benzyl group at the C-2 position of the phosphonate ester derivatives have been explored, leading unexpectedly to the isolation of unprecedented tetrahydrofuranyl derivatives. Studies towards the preparation of potential bi-functional PfDXR / HIV-1 RT inhibitors have also been initiated. Preliminary in silico docking studies of selected non-benzylated and benzylated phosphonated derivatives into the Pf-DXR active-site has provided useful insight into the binding potential of these ligands. Bioassays have revealed a very low toxicity for all the synthesised phosphonated compounds and a number of these ligands also exhibit a promising inhibitory activity against the Plasmodium parasite.
- Full Text:
- Date Issued: 2015
Structural bioinformatics analysis of the Hsp40 and Hsp70 molecular chaperones from humans
- Authors: Adeyemi, Samson Adebowale
- Date: 2014
- Subjects: Structural bioinformatics , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Biomolecules
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4171 , http://hdl.handle.net/10962/d1020962
- Description: HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70 isoforms will interact. We attempted to use bioinformatics to identify residues involved in the specificity of the interaction between the J domain from HSP40 and the ATPase domain from the HSP70 isoforms from humans. A total of 49 HSP40 and 13 HSP70 sequences from humans were retrieved and used for subsequent analyses. The HSP40 J domains and HSP70 ATPase domains were extracted using python scripts and classified according to the subcellular localization of the proteins using localization prediction programs. Motif analysis was carried out using the full length HSP40 proteins and Multiple Sequence Alignment (MSA) was performed to identify conserved residues that may contribute to the J domain – ATPase domain interactions. Phylogenetic inference of the proteins was also performed in order to study their evolutionary relationship. Homology models of the J domains and ATPase domains were generated. The corresponding models were docked using HADDOCK server in order to analyze possible putative interactions between the partner proteins using the Protein Interactions Calculator (PIC). The level of residue conservation was found to be higher in Type I and II HSP40 than in Type III J proteins. While highly conserved residues on helixes II and III could play critical roles in J domain interactions with corresponding HSP70s, conserved residues on helixes I and IV seemed to be significant in keeping the J domain in its right orientation for functional interactions with HSP70s. Our results also showed that helixes II and III formed the interaction interface for binding to HSP70 ATPase domain as well as the linker residues. Finally, data based docking procedures, such as applied in this study, could be an effective method to investigate protein-protein interactions complex of biomolecules.
- Full Text:
- Date Issued: 2014
Research projects
- Authors: Adusei-Owusu, James
- Date: 2001
- Subjects: Constructivism (Education) , Review literature , College students -- Study and teaching , Teaching -- Methods , Competency based education -- Eastern Cape (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:1740 , http://hdl.handle.net/10962/d1003624 , Constructivism (Education) , Review literature , College students -- Study and teaching , Teaching -- Methods , Competency based education -- Eastern Cape (South Africa)
- Description: RESEARCH PROJECTS: 1 RESEARCH PROJECT ONE: A literature review: Constructivism: An alternate approach to teaching and learning. Abstract The constructivist perspectives on learning have helped enhance science educators' understanding of how students make sense of their lived experiences. Constructivism purports to be a transformation of the traditional curriculum. As such this article starts with a brief overview of behaviorism: the scientific approach to education. The main tenets underlying constructivism, how constructivism guides educators to change their classroom practice, and the implications to science teaching have been reviewed. 2 RESEARCH PROJECT TWO (Empirical study): Being Constructive: College students' learning of work and heat as aspects of the energy concept based a constructivist approach. Abstract This study is an extension of a literature review on constructivism as an alternate teaching and learning approach discussed in research project one. It is an empirical study concerning the use of a learning module based on a constructivist approach to develop pre-service student teachers' understanding of work and heat as aspects of the energy concept. The data consisted mainly of transcripts of students' interviews, written responses to questionnaires designed in the form of a worksheet, and comments from non-participant observers and students. The results seem to suggest that a carefully designed learning module based on a constructivist teaching and learning approach may be a valuable tool in developing pre-service student teachers' understanding of work and heat. 3 RESEARCH PROJECT THREE (Empirical study): A College in transition: A case study of the readiness of a college in the Eastern Cape province to implement Outcomes-Based Education in an Education Development centre. Abstract Curriculum 2005 premised on Outcomes-Based Education is the new curriculum framework for South Africa. It signifies a paradigm shift in education from the traditional 'telling-listening' relationship between the teacher and the learner to one that emphasises leamer-centred approach to the teaching process. Teachers, though recognized as crucial to the educational transformation process in the country have also being identified as ill-equipped to meet the challenges posed by Outcomes-Based Education. This study starts with a brief overview of the South African curriculum and the main tenets underlying Outcomes-Based Education. The institutional conditions and whether the lecturers at a college in the Eastern Cape province perceive the need for a change in their classroom practice were also investigated. Bearing in mind the need for further research to validate the findings of this study, positive indicators that emerged from the study suggest the readiness of the college to implement Outcomes-Based Education at the proposed Education Development Centre.
- Full Text:
- Date Issued: 2001
A structural study of the capsular antigen of Klebsiella serotype K43
- Authors: Aereboe, Michael
- Date: 1993
- Subjects: Polysaccharides , Klebsiella , Antigens , Enterobacteriaceae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3740 , http://hdl.handle.net/10962/d1003218 , Polysaccharides , Klebsiella , Antigens , Enterobacteriaceae
- Description: This thesis presents a detailed chemical and spectroscopic determination of the capsular, polysaccharide K-antigen isolated from the Klebsiella bacterium, serotype K43 (culture #2482). The repeating unit of the capsular polysaccharide was found to be of the "3 + 2" repeating unit type. A uronic acid was found as part of a disaccharide side chain and the main chain of the polysaccharide was found to be composed of a neutral trisaccharide of mannose and galactose. The work forms part of an ongoing research interest in bacterial polysaccharides of this laboratory and now completes the structural elucidation of all the Klebsiella K-antigens, bar three antigens which were originally assigned to other laboratories. These data together with the respective serological characteristics of each serotype are available to the molecular biologist, and may result in the production of: vaccine(s) against Klebsiella infections, diagnostic products and novel carrier molecules enabling targeted drug delivery.
- Full Text:
- Date Issued: 1993
Constituent processes of leaf senescence in Hordeum vulgare cv. Dyan
- Authors: Afitlhile, Meshack Mosimanegape
- Date: 1994
- Subjects: Leaves , Leaves -- Development
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4184 , http://hdl.handle.net/10962/d1003752
- Description: Changes in chlorophyll content, carotenoid content and composition, abscisic acid and phaseic acid levels, hydrolytic enzyme activity and polypeptide pattern were monitored during senescence of the primary attached leaves of Hordeum vulgare L. cv. Dyan. Senescence occurred due to the normal course of leaf development or was induced by incubation of leaves in darkness. Loss of chlorophyll and total leaf protein was retarded in light whereas it continued rapidly in leaves from dark-incubated seedlings. Chlorophyll alb ratio increased with the progression of senescence, suggesting that chlorophyll b was referentially degraded during this process. Loss of total protein coincided with enhanced activity of acid and neutral proteases. In contrast, loss of chlorophyll was not accompanied by an increase in· peroxidase activity, suggesting that this enzyme was not responsible for initiating chlorophyll breakdown. Carotenoid and abscisic acid levels were monitored in the same tissue extracts. The results obtained show that the increase in endogenous levels of abscisic acid, induced by senescence, correlated with enhanced epoxidation of the xanthophyll cycle, ie., increased conversion of zeaxanthin to antheraxanthin and all-trans-violaxanthin. In addition, an increase in abscisic acid levels occurred concomitant with a decrease in all-trans-violaxanthin and 9'-cis-neoxanthin, suggesting an apparent 1:1 relationship on a molar basis. It is therefore proposed that enhanced abscisic acid production, due to foliar senescence, arises from fluctuations in carotenoid turnover. Polypeptide patterns in isolated chloroplasts, purified thylakoid and stromal fractions were very similar for leaves incubated in either light or darkness. A decrease in intensity of bands was observed in isolated chloroplasts and stromal fractions. Intensity of bands in thylakoids remained unchanged with the progression of senescence. Protein standards of peroxidase and lipoxygenase co-migrated with proteins of the isolated chloroplast. Although tentative, some proteins of the chloroplast may be representative of precursors of hydrolytic enzymes which are known to increase during senescence.
- Full Text:
- Date Issued: 1994
Isolation and characterization of antiplasmodial metabolites from South African marine alga
- Authors: Afolayan, Anthonia Folake
- Date: 2008
- Subjects: Malaria -- Africa Antimalarials -- Therapeutic use Malaria -- Prevention Malaria -- Drug therapy Marine algae -- Therapeutic use Natural products -- Therapeutic use Plasmodium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3739 , http://hdl.handle.net/10962/d1003063
- Description: Malaria is one of the three most deadly diseases in Africa. Although there are available treatments, their efficacy has been greatly reduced over the past two decades due to the development of resistance to currently available drugs. This has necessitated the search for new and effective antimalarial agents. This project approached the search for new antimalarial compounds in two ways: (i) by screening natural products isolated from marine algae against the Plasmodium parasite and (ii) by modification of selected isolated active compounds to target 1-deoxY-đ-xylulose 5-phosphate reductoisomerase (DXR), an enzyme found in the nonmevalonate isoprenoid biosynthetic pathway of Plasmodium Jalciparum. It was envisaged that such a compound would exhibit dual action on the Plasmodium parasite. Extracts obtained from 22 marine algae were prefractionated by solvent partitioning and were screened for anti plasmodial activity against the chloroquine sensitive (CQS) P. Jalciparum D 10 strain. Overall, 50% of the algae screened produced at least one crude fraction with activity against P. Jalciparum. Extracts of the algae Sargassum heterophyllum, Plocamium cornutum, Amphiroa ephedrea and Pterosiphonia cloiophylla gave the most promising results. Fractionation of S. heterophyllum afforded three tetraprenyltoluquinols (3.1, 3.2 and 3.5) and an all-trans-fucoxanthin (3.6). Three new compounds (4.5, 4.6 and 4.7) and two known halogenated monoterpenes (4.1 and 4.4) were isolated from P. cornutum. Each of the isolated compounds from both S. heterophyllum and P. cornutum showed antiplasmodial activity with IC₅₀ values ranging from 2.0 - 15.3 μM for S. heterophyllum and 13 - 230 μM for P. cornutum. Attempts to synthetically modify halogenated monoterpene 4.4 by dihydroxylation and phosphorylation in order to inhibit the DXR enzyme was unsuccessful. However, the hemiterpene analogue (5.42) of the halogenated monoterpenes was successfully phosphorylated and dihydroxylated to give compound 5.45 which showed promising activity against DXR. The result obtained indicated that the proposed phosphorylation and dihydroxylation of the halogenated monoterpene 4.4 would result in the synthesis of a potent DXR inhibitor and therefore a potential antimalarial agent with dual mode of action on the Plasmodium parasite.
- Full Text:
- Date Issued: 2008
Biochemical characterisation of Pfj2, a Plasmodium falciparum heat shock protein 40 chaperone potentially involved in protein quality control in the endoplasmic reticulum
- Authors: Afolayan, Omolola Folasade
- Date: 2013
- Subjects: Plasmodium falciparum Endoplasmic reticulum Heat shock proteins Malaria , Mosquito-borne infectious disease
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3883 , http://hdl.handle.net/10962/d1001617
- Description: Plasmodium falciparum is a protozoan parasite that causes a severe form of malaria, a mosquito-borne infectious disease in humans. P. falciparum encodes a number of proteins to facilitate its life-cycle, including a type II heat shock protein 40 (Hsp40), Pfj2. Pfj2 shows a degree of homology to human ERdj5, a resident protein of the endoplasmic reticulum (ER) that promotes protein quality control by facilitating the degradation of misfolded proteins. The overall aim of this study was to further understand the function of Pfj2 in the P. falciparum cell by characterising it biochemically. A bioinformatic analysis of Pfj2 was carried out to enable the identification of a potential ER signal sequence and cleavage site. Furthermore, an analysis of Pfj2 protein sequence was performed to compare domain similarities and identities with typical type II Hsp40s namely, human ERdj5, S. cerevisiae Sis1, human Hsj1a and human DnaJB4. The method used included the insertion of the codon-optimised coding sequence for the processed ER form of Pfj2 into the prokaryotic expression vector, pQE30, to enable overproduction of a histidine-tagged protein. A 62 kDa His₆-Pfj2 was successfully expressed in Escherichia coli and purified using denaturing nickel affinity chromatography. ATPase assays were performed to determine the ability of His₆- Pfj2 to stimulate the chaperone activity of the ER Hsp70, also called immunoglobulin binding protein (BiP). Initial studies were conducted on readily available mammalian His₆-BiP as a control, which was shown to have an intrinsic activity of 12.07±3.92 nmolPi/min/mg. His₆- Pfj2 did not stimulate the ATPase activity of mammalian His₆-BiP, suggesting that it either could not act as a co-chaperone of mammalian His₆-BiP (specificity), or it required a misfolded substrate in the system. Therefore, ongoing studies are addressing the interaction of Pfj2 and misfolded substrates with P. falciparum BiP. The results of these studies will further our understanding of a poorly-studied parasite chaperone that represents a potential drug target for development of novel strategies for the control of a serious human disease
- Full Text:
- Date Issued: 2013
Perceptions and livelihood uses of an invasive alien tree (acacia dealbata) by rural communities in the Eastern Cape
- Authors: Agripa, Ngorima
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5326 , vital:20813
- Description: The negative impacts which invasive alien species have on ecosystems are well documented but there is paucity of information on their impacts on rural communities. Due to ecological impacts that may be associated with Acacia dealbata invasions the Agricultural Research Council Plant Protection Institute is considering releasing a biocontrol agent for A. dealbata. The actual social impacts of A. dealbata invasion and control are likely to be related to its importance in rural livelihoods. This thesis reports on the perceptions and livelihood uses of A. dealbata in the Eastern Cape. Three study sites were assessed, Matatiele, Mount Fletcher and Maclear. The study involved 150 household surveys, one focus group discussion and one transect walk at each site, key informant interviews and frequent house visits to acquire reliable data. Results show that 100 % of households in the three sites use Silver Wattle extensively for firewood. In Matatiele 64 %, 72 % in Mount Fletcher and 84 % of households in Maclear use Silver Wattle for fencing. To carve tools 76 % in Matatiele, 76 % in Mount Fletcher and 84 % households in Maclear use Silver Wattle. For medicinal purposes 18 % in Matatiele, 20 % in Mount Fletcher and 16 % in Maclear use Silver Wattle, whilst 78 % in Matatiele, 80 % in Mount Fletcher and 80 % in Maclear use it for fodder purposes. Many respondents felt that Silver Wattle is too abundant within their areas such that it now has many negative impacts associated with it. Perceptions of local people towards A. dealbata are neither static nor uniform, but are influenced by time since the invasion and now abundance of the species. There are no alternatives which provide the same services provided by Silver Wattle. Benefits and constraints due to A. dealbata invasion are experienced by everyone irrespective of wealth and gender. In conclusion, Silver Wattle is a valuable resource to these rural communities, but increasing abundance is incurring high costs to grazing resources and landscape accessibility.
- Full Text:
- Date Issued: 2017