Studies towards the synthesis of novel, coumarin-based HIV-1 protease inhibitors
- Authors: Rashamuse, Thompho Jason
- Date: 2008
- Subjects: Coumarins , Protease Inhibitors , HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Heterocyclic compounds -- Derivatives
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4359 , http://hdl.handle.net/10962/d1005024 , Coumarins , Protease Inhibitors , HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Heterocyclic compounds -- Derivatives
- Description: A series of the Baylis-Hillman adducts have been obtained by reacting protected O-benzylated and unprotected substituted salicylaldehydes with methyl acrylate or tertbutyl acrylate, respectively, using DABCO as catalyst. Treatment of the Baylis-Hillman adducts with HCl in a mixture of acetic acid and acetic anhydride afforded the corresponding 3-(chloromethyl)coumarin derivatives with yields of up to 94%. Similar use of HI afforded the corresponding 3-(iodomethyl)coumarins but, depending on the reaction time, the reduced 3-methyl analogues could also be obtained. Arbuzov reactions of the 3-(halomethyl)coumarin derivatives have been undertaken to afford 4-phosphorylated and 1’-phosphorylated derivatives, regioselectivity being dependent on the halide-leaving group. The 3-(chloromethyl)coumarin derivatives have been subjected to nucleophilic (SN) attack by benzylamine to give the corresponding 3- [(benzylamino)methyl]coumarin derivatives in yields of up to 74%. Further treatment of the 3-[(benzylamino)methyl]coumarin derivatives with chloroacetyl chloride afforded the chloroacetamide derivatives, which exhibit hindered rotation about the amine C(O)-N bond. The acetamide derivatives have also been subjected to Arbuzov reaction conditions to afford the phosphorylated derivatives in yields of up to 86%. In a preliminary modelling study, hydrolysed analogues of the synthesized phosphorylated derivatives have been docked into the active site of the HIV-1 protease enzyme using the Cerius-2 Ligandfit software module to provide an insight into potential receptor-ligand hydrogen bonding interactions.
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Synthesis, photochemical and photophysical properties of gallium and indium phthalocyanine derivatives
- Authors: Chauke, Vongani Portia
- Date: 2008
- Subjects: Phthalocyanines , Photochemotherapy , Electrochemistry , Gallium , Indium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4375 , http://hdl.handle.net/10962/d1005040 , Phthalocyanines , Photochemotherapy , Electrochemistry , Gallium , Indium
- Description: The syntheses of octasubstituted and unsusbstitituted Gallium(III) chloride and indium(III) chloride phthalocyanines (GaPc and InPc), their photophysical, photochemical and nonlinear optical parameters are hereby presented. The photocatalytic oxidation of 1-hexene using the synthesized GaPc and InPc complexes as well as electrochemical characterization is also presented in this thesis. Fluorescence quantum yields do not vary much among the four Ga complexes, except for complex 21c; therefore it was concluded that the effect of substituents is not significant among them. Solvents however, had an effect on the results. Lower Φ[subscript F] values were obtained in low viscosity solvents like toluene, relative to highly viscous solvents, such as DMSO. The triplet quantum yields were found to be lower in DMSO than in DMF and toluene. The rate constants for fluorescence, intersystem crossing and internal conversion as well as fluorescence and triplet lifetimes are reported. Photodegradation and singlet oxygen quantum yields have also been reported. There was no clear correlation between the latter parameters. It was however established that the four gallium MPcs were stable, within the allowed stability range for phthalocyanines. High quantum yields of triplet state (Φ[subscript T] ranging from 0.70 to 0.91 in dimethysulfoxide, DMSO) and singlet oxygen generation (Φ[subscript greek capital letter delta], ranging from 0.61 to 0.79 in DMSO) were obtained. Short triplet lifetimes 50 to 60 μs were obtained in DMSO). Calculated non-linear parameters of these complexes are compared with those of the corresponding GaPc derivatives and tetrasubstituted GaPc and InPc complexes. The optical limiting threshold intensity (I[subscript lim]) values for the InPc and GaPc derivatives were calculated and compared with those of corresponding tetrasubstituted InPc and GaPc complexes. The octasubstituted were found to be better optical limiters. Photocatalytic oxidation of 1-hexene by GaPc (21a-c) and InPc (22a-c) derivatives is also presented. The photocatalytic oxidation products for 1-hexene were 1,2- epoxyhexane and 1-hexen-3-ol. The % conversion values of 1-hexene and % selectivity of 1,2-epoxyhexane were generally higher for InPc derivatives. Even though InPc derivatives showed better photocatalytic results than GaPc derivatives, the former were less stable relative to the latter. Both type I and type II mechanism were implicated in the photocatalysis mechanism.
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Synthesis, photophysics and electrochemical study of tin macrocycles
- Authors: Khene, Mielie Samson
- Date: 2008
- Subjects: Electrochemistry , Photochemistry , Phthalocyanines , Macrocyclic compounds , Spectrum analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4376 , http://hdl.handle.net/10962/d1005041 , Electrochemistry , Photochemistry , Phthalocyanines , Macrocyclic compounds , Spectrum analysis
- Description: Three non-peripherally substituted tin(IV) macrocylic compounds, octahexylphthalocyaninato dichlorotin(IV) (35a), octahexyltetrabenzo-5,10,15-triazaporphyrinato dichlorotin(IV) (35b) and octadecylphthalocyaninato dichlorotin(IV) (35c) were synthesized and their photophysical and electrochemical behaviour studied. Complex (35b), containing a CH group in place of one of the aza nitrogen atom of the phthalocyanine core, shows a split Q band due to its lower symmetry. The triplet state quantum yields were found to be lower than would be expected on the basis of the heavy atom effect of tin as the central metal for phthalocyanine derivatives (35a and 35c). In contrast, (35b) shows a triplet quantum yield ΦT = 0.78. The triplet state lifetimes were solvent dependent, and were higher in THF than in toluene. Cyclic voltammetry and spectroelectrochemistry of the complexes revealed only ring based redox processes. This thesis also reports on the microwave syntheses of tetrasulphonated tin phthalocyanine and tetrasulphonated tin α,β,γ-tetrabenzcorrole. The latter was only formed at low ratios (< 1:8) of 4-sulfophthalic acid to urea. Both complexes are aggregated in aqueous media, but can be partly or fully disaggregated by the addition of Triton X-100. The SnTSTBC complex has lower triplet life times and yields, while binding constant and quenching (of bovine serum albumin) constant are lower for SnTSTBC, compared to SnTSPc. Finally Non-peripherally (α) tetra- (40) and octa-(38a) substituted dodecyl-mercapto tin(IV) phthalocyanines where synthesized and the electrochemical behavior studied. Cyclic voltammetry and spectroelectrochemistry show ring-based reductions for (38a) and (40); the former shows two ring oxidations, while the latter shows only one ring based oxidation. The adsorption kinetics of (38a) and (40) on a gold electrode have been investigated by electrochemical impedance spectroscopy (EIS). The equilibrium constant (K) for the adsorption and the Gibbs free energy ΔG(ads) of the self-assembled monolayer (SAMs) were evaluated based on the Frumkin isotherm. The interaction factor between adsorbate –adsorbate molecules is also discussed.
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Temperature dependence of the HartRAO pointing model
- Authors: Copley, Charles Judd
- Date: 2008
- Subjects: Astronomical instruments , Observatories -- South Africa , Telescopes , Astronomical observatories , Astronomy -- Data processing , Antennas (Electronics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5491 , http://hdl.handle.net/10962/d1005277 , Astronomical instruments , Observatories -- South Africa , Telescopes , Astronomical observatories , Astronomy -- Data processing , Antennas (Electronics)
- Description: This thesis investigates control aspects of the Hartebeeshoek Radio Astronomy Observatory (HartRAO) antenna. The installation of a new 22 GHz receiver has required the pointing accuracy to be improved to less than 4 mdeg. The effect of thermal conditions on the the HartRAO antenna pointing offset is investigated using a variety of modelling techniques including simple geometric modelling, neural networks and Principal Component Analysis (PCA). Convincing results were obtained for the Declination pointing offset, where applying certain model predictions to observations resulted in an improvement in Declination pointing offset from 5.5 mdeg to 3.2 mdeg (≈50%). The Right Ascension pointing model was considerably less convincing with an improvement of approximately from 5.5 mdeg to 4.5 mdeg (≈20%) in the Right Ascension pointing offset. The Declination pointing offset can be modelled sufficiently well to reduce the pointing offset to less than 4 mdeg, however further investigation of the underlying causes is required for the Right Ascension pointing offset.
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The cryopreservation potential and ultrastructure of Agulhas sole Austroglossus pectoralis spermatozoa
- Authors: Markovina, Michael Zeljan
- Date: 2008
- Subjects: Spermatozoa , Spermatozoa -- Cryopreservation , Aquaculture , Fishes -- Breeding , Soleidae , Flatfishes , Agulhas Current (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5251 , http://hdl.handle.net/10962/d1005094 , Spermatozoa , Spermatozoa -- Cryopreservation , Aquaculture , Fishes -- Breeding , Soleidae , Flatfishes , Agulhas Current (South Africa)
- Description: As the estimated market demand for the Agulhas sole Austroglossus pectoralis exceeds the annual catch from trawlers, this species is a potential aquaculture candidate. Broodstock conditioning and gamete preservation is part of research and development aiming at establishing a breeding protocol for a new aquaculture species. Based on a literature review of the morphology of pleuronectiform spermatozoa, this study was designed firstly, to contribute to the field of spermatozoan morphology by describing the ultrastructure of A. pectoralis spermatozoa. This was followed by an experiment to cryopreserve mature spermatozoa to provide baseline data for future studies on this and related species. The testis of A. pectoralis was a paired structure encased in a membrane, the tunica albuginea. The primary testis was located on the dorsal surface of the rib cage and the secondary testis on the ventral side. The testis was of an unrestricted spermatogonial type, based upon observations of spermatogonia along the entire length of the lobule. Mature spermatozoa of A. pectoralis had an acrosome-free ovoid head 1.68 ± 1.6μm in length and 1.7 ± 1.6μm in diameter, a short mid-piece of 0.5 ± 0.1μm in length, containing 7 irregularly shaped mitochondria forming a ring-like structure at the base of the nucleus. The flagellae were 47.4 ± 4.8μm in length, most with two plasma membrane lateral fin-like projections. However, some flagellae had either zero or three lateral fin projections. Cross-sections of the flagellae showed an axenome with a 9+2 microtubule configuration. The proximal and distal centriols were coaxal, situated deep within the nuclear fossa. The structure of A. pectoralis spermatozoa conformed to the type 1 ect-aquasperm, also found in externally fertilizing species. This type has been suggested to be the plesiomorphic form in Neopterigians. Finally, this study contributed to a cryopreservation protocol for A. pectoralis spermatozoa by testing the two cryoprotectants dimethyl sulphoxide (DMSO) and glycerol. Glycerol, at a concentration of 10%, offered better cryoprotection than DMSO. This was established using flow cytometry analysis of post-thaw nuclear membrane integrity after 64 days of storage in liquid nitrogen. The toxicity of DMSO to isolated cellular proteins may have resulted in DMSO-treated sperm having the highest percent (35.2% ± 3.2%) of non-viable cells compared with 23.0% ± 2.5% and 27.8% ± 3.4% for glycerol and the control, respectively. The presence of sucrose in the Modified Mounib Medium extender solution may explain why 45.5% ± 5% of the sperm cells were potentially viable in the control treatment. Initially, the white margined sole Dagatichthys marginatus (Soleidae) was selected as the most suitable candidate for flatfish aquaculture in South Africa. Thus, the aim of this study was to investigate the cryogenic potential and ultrastructure of D. marginatus spermatozoa. However, due to a skewed sex ratio, there were not enough males available to study this species. A skewed sex ratio is common amongst soleids, thus, the need to develop effective cryopreservation methods and to develop an understanding of sperm morphology so that the best time for cryopreservation can be chosen. In conclusion, this first description of spermatozan morphology of A. pectoralis contributed to our understanding of soleid sperm ultrastructure. In addition, a comparison of testis appearance between fish sampled just prior to spawning season and fish with mature sperm provided information on the spawning season of this species. The findings from the cryopreservation experiment suggested that glycerol was a feasible cryoprotectant for this species when sperm was prepared under field conditions.
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The development and evaluation of a custom-built synchronous online learning environment for tertiary education in South Africa
- Authors: Halse, Michelle Louise
- Date: 2008 , 2008-02-23
- Subjects: Education, Higher -- South Africa -- Computer-assisted instruction , Universities and colleges -- Computer networks -- South Africa , Internet in higher education -- South Africa , Distance education -- South Africa -- Computer-assisted instruction , Computer-assisted instruction -- South Africa , Computer science -- Study and teaching (Higher) -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4636 , http://hdl.handle.net/10962/d1006545 , Education, Higher -- South Africa -- Computer-assisted instruction , Universities and colleges -- Computer networks -- South Africa , Internet in higher education -- South Africa , Distance education -- South Africa -- Computer-assisted instruction , Computer-assisted instruction -- South Africa , Computer science -- Study and teaching (Higher) -- South Africa
- Description: The Departments of Computer Science and Information Systems at Rhodes University currently share certain honours-level (fourth year) course modules with students from the corresponding departments at the previously disadvantaged University of Fort Hare. These lectures are currently delivered using video-conferencing. This was found to present a number of problems including challenges in terms of implementing desired pedagogical approaches, inequitable learning experiences, student disengagement at the remote venue, and inflexibility of the video-conferencing system. In order to address these problems, various e-learning modes were investigated and synchronous e-learning were found to offer a number of advantages over asynchronous e-learning. Live Virtual Classrooms (LVCs) were identified as synchronous e-learning tools that support the pedagogical principles important to the two universities and to the broader context of South African tertiary education, and commercial LVC applications were investigated and evaluated. Informed by the results of this investigation a small, simple LVC was designed, developed and customised for use in a predominantly academic sphere and deployment in a South African tertiary educational context. Testing and evaluation of this solution was carried out and the results analysed in terms of the LVC’s technical merits and the pedagogical value of the solution as experienced by students and lecturers/facilitators. An evaluation of this solution indicated that the LVC solves a number of the identified problems with video-conferencing and also provides a flexible/customisable/extensible solution that supports highly interactive, collaborative, learner-centred education. The custom LVC solution could be easily adapted to the specific needs of any tertiary educational institute in the country, and results may benefit other tertiary educational institutions involved in or dependant on distance learning.
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The development of a putative microbial product for use in crop production
- Authors: Gumede, Halalisani
- Date: 2008
- Subjects: Agricultural productivity , Agriculture -- Economic aspects , Microbial products , Bacterial diseases of plants , Biological pest control agents , Lettuce -- Diseases and pests , Crops -- Nutrition , Bacillus (Bacteria) , Phytopathogenic microorganisms -- Control
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3945 , http://hdl.handle.net/10962/d1004004 , Agricultural productivity , Agriculture -- Economic aspects , Microbial products , Bacterial diseases of plants , Biological pest control agents , Lettuce -- Diseases and pests , Crops -- Nutrition , Bacillus (Bacteria) , Phytopathogenic microorganisms -- Control
- Description: The challenges faced by the agricultural sector especially around improving production yields using environmentally friendly solutions have received market attention. Biological intervention can range from application of biological products to enhance the nutritional value of crops or to control plant pathogens. Biostart, a biological product that demonstrated growth enhancement when applied in lettuce crops is currently in the market. The product is comprised of a consortium of bacterial isolates (Bacillus licheniformis, Brevibacillus laterosporus and Bacillus laterosporus) but the contribution of the individual isolates to growth enhancement had not been elucidated. Green house experiments on lettuce seedlings with individual and mixed treatments were commissioned to determine such contribution. There was either no or marginal growth enhancement observed in the experiments. The results showed that the product was effective as a consortium and not as individual isolates. Further isolation and screening for potential Bacilli with antifungal properties was undertaken. An isolate identified as Bacillus subtilis that demonstrated inhibition against a wide spectrum of fungi, and especially the phytopathogenic Verticillium dahliae and Fusarium oxysporum, was successfully identified. The isolate was cryo-preserved and cultivated to significant levels at bench scale. A characterized comparison of different putative products with known systematic fungicide showed potential application even of heat treated products. The product showed control V. dahliae when tested in green houses with potatoes and tomatoes as test crops. This isolate has been targeted for further development as a biological control product.
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The effect of restricted environments on selected postural, physiological and perceptual responses
- Authors: Wolfe, Amy
- Date: 2008
- Subjects: Human engineering , Posture , Human mechanics , Work environment , Human beings -- Effect of environment on , Musculoskeletal system -- Wounds and injuries , Industrial safety , Work -- Physiological aspects , Stress (Physiology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5115 , http://hdl.handle.net/10962/d1005193 , Human engineering , Posture , Human mechanics , Work environment , Human beings -- Effect of environment on , Musculoskeletal system -- Wounds and injuries , Industrial safety , Work -- Physiological aspects , Stress (Physiology)
- Description: Manual lifting tasks are the predominant means of transporting materials in industry with many of these tasks being performed in confined spaces. Research has tended to focus on the biomechanical implications of working in small spaces with a decided lack of information about the physiological and perceptual responses in these environments. This holistic study therefore investigated the manner in which the human operator responded to conditions where the ceiling height was lowered and reach demands increased. Thirty-two young physically active male subjects (age: 21.55yr; stature: 1810mm) were recruited to complete a 2-way repeated measures experiment during which four lifting protocols where different combinations of ceiling height (‘normal’ or reduced to 1460mm in height) and reach demands (400mm or 800mm) were tested. A crude postural analysis was conducted while physiological responses were detailed and continuously monitored. Perceptual responses were also assessed. The tasks with a ‘normal’ ceiling height (mean compression forces: 2615N; mean shearing forces: 388N) and the greatest reach distance (mean compression forces: 3655N; mean shearing forces: 386N) placed individuals under the highest strain. Mean heart rate (HR) responses were significantly lower (p < 0.05) in the URN condition when compared to the RF condition. Furthermore, HR responses were statistically significantly affected by the height of the ceiling and the reach depth. Statistically significant differences (p< 0.05) in mean tidal volume (VT) occurred in the least (URN) and most (RF) restrictive conditions. Statistically significant differences (p < 0.05) in mean VE were evident between URN and URF, between URN and RF and between RN and RF. Ceiling height and reach demands had a statistically significant effect on all respiratory responses. There was a statistically significant difference in mean oxygen consumption (VO2) between the URN and all other conditions, and between the most restricted task (RF) and all other conditions. Both the effect of ceiling height and reach demands had a statistically statistically significant impact on VO2. Respiratory quotient (RQ) was significantly higher when loads were moved over 800mm compared to 400mm yet ceiling height did not have a statistically significant effect on RQ. Mean energy expenditure was significantly higher in the RF condition compared to the two least restrictive conditions (URN and RN). Statistically significant differences in EE were also evident between URN and RN, and between URN and URF. EE was significantly affected by reductions in ceiling height and increases in reach demands. Perceptually, the RF task (mean ‘Central’ RPE of 11) was perceived to place significantly greater cardiorespiratory demands on the operator compared to the URN (CRPE: 10) and RN (CRPE: 10) conditions. Statistically significant differences in perceived musculoskeletal strain only occurred between URN and RF. The effect of reach was perceived to have a statistically significant effect on both cardiovascular and musculoskeletal demands whereas ceiling height only had a statistically significant effect on musculoskeletal demands. The greatest discomfort was experienced in the lower back with the most intense discomfort occurring in the RN condition.
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The feasibility of stock enhancement as a management tool for dusky kob (Argyrosomus japonicus) in South Africa
- Authors: Palmer, Ryan Michael
- Date: 2008
- Subjects: Argyrosomus -- South Africa , Argyrosomus -- Genetics , Fishery management -- South Africa , Fish stocking -- South Africa , Fisheries -- South Africa , Marine ecology -- South Africa , Fish culture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5281 , http://hdl.handle.net/10962/d1005125 , Argyrosomus -- South Africa , Argyrosomus -- Genetics , Fishery management -- South Africa , Fish stocking -- South Africa , Fisheries -- South Africa , Marine ecology -- South Africa , Fish culture -- South Africa
- Description: The dusky kob, Argyrosomus japonicus, is a popular South African “line fish” whose stocks have dwindled to dangerously low levels of between 1% and 4.5% of pristine spawner biomass per recruit. A. japonicus stocks are currently managed by means of minimum size restrictions and daily bag limits, and as a result of the inability of these measures to facilitate the recovery of the species over a realistic time frame, the need for an alternative management plan has become apparent. Given the status of the stock and management regime, stock enhancement appears to be an appropriate option to be investigated. This study evaluates the feasibility of stock enhancement as a possible management tool to assist with the recovery of this important South African linefish species. By evaluating the genetic and ecological implications related to stock enhancement, identifying a suitable tagging method for post-release monitoring, and evaluating the economic feasibility of such a programme, any fatal flaws would become immediately apparent. This coupled with the required framework for the development of a management plan for stock enhancement of A. japonicus provides direction further research and actions required in order to utilise stock enhancement as a management tool. Due to the nature of stock enhancement, there are several ecological and genetic issues that arise from such a programme. These issues were reviewed and the issues that were relevant to stock enhancement of A. japonicus identified. Ecological concerns that arose included those of competition, disease and seed quality, while genetic issues were concerned mainly in the possible loss of genetic variability and consequent reduction in fitness of the stock. Fortunately the technology exists to evaluate the effects and likelihood of these problems occurring as well as to minimise the likelihood of them occurring. By taking a scientific approach to stock enhancement, hatchery management, and release strategies can be manipulated in such a way as to minimise any negative effects that may be caused. Both ecological and genetic effects of stocking indicate a need for post-release monitoring of stock enhancement programmes. Stock enhancement requires a post-release monitoring programme, which in turn relies on an ability to distinguish between hatchery reared and wild fish. A study was conducted to evaluate the suitability of coded wire tags (CWT), visual implant fluorescent elastomers (VIFE), and oxytetracycline (OTC) as a means of distinguishing between hatchery reared and wild A. japonicus, for the purpose of a post-release monitoring programme. OTC appeared to be the most suitable as it produced 100% retention over a five month period compared to 62% and 61% for VIFE and CWT respectively. OTC is therefore suggested as a tagging method for the purpose of post-release monitoring of the stock enhancement of A. japonicus. To evaluate a possible funding option for stock enhancement of A. japonicus in South Africa, a willingness-to-pay survey, based on a “user pays” approach using recreational fishing permits as a vehicle for payment, included 102 recreational anglers in the Plettenberg Bay area. The survey showed that generally anglers were willing to pay more than the current amount for the recreational fishing permit. This promising result, coupled with the fact that there are approximately 450 000 recreational anglers leads to the belief that there is potential for a substantial increase in the funds generated for the Marine Living Resources Fund through recreational anglers. Stock enhancement should not be ruled out on the basis of economic feasibility yet as there is potential for it to be sustained by the users of the resource. An A. japonicus juvenile production costing model was created taking into account setup and running costs of a hatchery for A. japonicus, based on known parameters from existing facilities, and adjusting them to meet the requirements of a stock enhancement facility. Estimates varied according to the number and size of fish for release (values which can only be decided upon after further research), with setup estimated to be between R 10 000 000 and R 30 000 000 and annual running costs between R 2 400 000 and R 6 700 000 annually. These figures were dependant on the size and number of fish being produced, with production ranging between 100 000 and 5 000 000 fish of between 50 mm and 150 mm, and a broodstock of 150 individuals. Given the need for alternative management of A. japonicus in South Africa and the lack of evidence to suggest that it is an unfeasible option, this project has found no reason why further investigation into the use of stock enhancement for the management of A. japonicus should not proceed further provided the fishery is shown to be recruit limited. The technology and ability to overcome possible ecological and genetic problems exists, a suitable means of tagging for post-release monitoring exists, as does a realistic funding option. There is a substantial amount of research that must be done prior to stocking, for which a base framework is provided.
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The impact of HIV/AIDS on rural children's reliance on natural resources within the Eastern Cape, South Africa
- Authors: McGarry, Dylan Kenneth
- Date: 2008
- Subjects: Natural resources -- South Africa -- Eastern Cape , AIDS (Disease) in children -- South Africa -- Eastern Cape , HIV infections -- South Africa -- Eastern Cape , AIDS (Disease) -- South Africa -- Eastern Cape , Children of AIDS patients -- South Africa -- Eastern Cape , Rural children -- South Africa -- Eastern Cape , Wild foods -- South Africa -- Eastern Cape , Food supply -- South Africa -- Eastern Cape , Children -- Social conditions -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4759 , http://hdl.handle.net/10962/d1007149 , Natural resources -- South Africa -- Eastern Cape , AIDS (Disease) in children -- South Africa -- Eastern Cape , HIV infections -- South Africa -- Eastern Cape , AIDS (Disease) -- South Africa -- Eastern Cape , Children of AIDS patients -- South Africa -- Eastern Cape , Rural children -- South Africa -- Eastern Cape , Wild foods -- South Africa -- Eastern Cape , Food supply -- South Africa -- Eastern Cape , Children -- Social conditions -- South Africa -- Eastern Cape
- Description: The role of natural resources in the lives of rural children impacted by HIV/AIDS remains unexplored. This study highlights wild food use by rural children vulnerable to the impacts of HIV/AIDS as an important and regular activity that supplements their domestic diets. This work found that with an increase in vulnerability to HIV/AIDS, children rely more on wild foods. Through an 18 month project in the Eastern Cape, using a broad quantitative and qualitative school and non-school survey, individual interviews, food diaries, participant observation, interactive photography, and other participatory techniques, a total of 850 children's coping strategies and livelihoods were examined. The quality of children’s domestic diets was, on average, 60% lower than the Food and Agricultural Organization (FAO) guidelines. However, 62% of the children interviewed were supplementing their diets with wild foods, 30% having over half their diet supplemented with wild foods. Dietary diversity showed a 13% increase when wild food supplementation occurred. While traditionally rural children rely on reciprocal networks during times of crisis, we found that these networks were eroding from the pressures of HIV/AIDS. Begging, for some children, was replaced by wild food collection and a significantly larger proportion of children more vulnerable to HIV/AIDS relied on wild foods more than did less vulnerable children. Considering the heightened nutritional and energy needs of children, combined with the impact of HIV/AIDS on household food access, wild foods represent the last freely attainable food sources available to them. Hunting and collection of wild food is a group activity, which was found to have valuable psychosocial benefits. Commercialisation of wild foods was observed among 38% of the children, with significantly more vulnerable children selling wild foods. The use of wild foods by rural children also had positive influences on the preservation of indigenous ecological knowledge.
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The potential roles of interactions between STAT3, Hsp90, and Hop in the maintenance of self-renewal in mouse embryonic stem cells
- Authors: Setati, Mokgadi Michael
- Date: 2008
- Subjects: Embryonic stem cells , Leukemia inhibitory factor , Cellular signal transduction , Heat shock proteins , Molecular chaperones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3981 , http://hdl.handle.net/10962/d1004040 , Embryonic stem cells , Leukemia inhibitory factor , Cellular signal transduction , Heat shock proteins , Molecular chaperones
- Description: Self-renewal of mouse embryonic stem (mES) cells is dependent upon the presence of leukemia inhibitory factor (LIF). LIF induces tyrosine phosphorylation and nuclear translocation of STAT3 (signal transducer and activator of transcription 3) which is thought to promote self-renewal by inducing key target genes. The molecular chaperone heat shock protein 90 (Hsp90) is involved in signal transduction pathways and regulates STAT3 activity in different cell types. However, the role of Hsp90 in regulating STAT3 activity in mES cells has not previously been investigated. The aim of this study was to investigate if Hsp90 interacts with STAT3 in mES cells and to determine if this interaction is important for the maintenance of self-renewal. It was found that when mES cells were cultured for 24.0 hours in the absence of LIF, the expression levels of total STAT3, tyrosine-phosphorylated STAT3 (pYSTAT3), and the pluripotency marker, Nanog, were down regulated. However, the expression level of Hsp90 was found to be slightly up-regulated over the same period. Significantly, it was found that the amount of STAT3 in differentiating mES cells available for binding to Hsp90 was decreased upon down-regulation of STAT3 by LIF withdrawal. Therefore, STAT3-Hsp90 interactions in mES cells were dependent on the presence of LIF, which suggested that the reduction in STAT3-Hsp90 interaction may have resulted from the low levels of STAT3. Despite a dramatic reduction in the expression levels of pYSTAT3 upon 24.0 hours of culture of mES cells in the presence of the STAT3 tyrosine phosphorylation inhibitor, cucurbitanin I, there was no obvious reduction in the levels of total STAT3, Oct-3/4 or Nanog. These results suggested that the levels of unphosphorylated STAT3 rather than pYSTAT3, maybe more important in the maintenance of mES cells self-renewal.
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The status and prognosis of the smoothhound shark (mustelus mustelus) fishery in the Southeastern and Southwestern Cape coasts, South Africa
- Authors: Da Silva, Charlene
- Date: 2008
- Subjects: Osteichthyes -- South Africa Mustelus -- South Africa Sharks -- South Africa Fishery management -- South Africa Fisheries -- South Africa Chondrichthyes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5200 , http://hdl.handle.net/10962/d1003287
- Description: Global trends in commercially valuable teleost fisheries point to substantial deterioration in population size, offering limited potential for increased harvests. Consequently a shift in focus towards alternative fisheries has increased fishing effort towards targeting chondrichthyans as a possible solution to meet global demands. The life-history traits of chondrichthyans make them poor candidates for resolving economic and nutritional security as these make them particularly vulnerable to anthromorphic influences. Current fisheries management approaches based on centralized government intervention have proved inadequate. This failure of current management approaches is often linked with poor co-operation by industry with government when collecting fishery-dependent data. As management decisions are based on quantitative estimates from fishery assessment modes data collected are often of poor quality. Co-management with its implied power-sharing arrangement between government and fishing communities has been proposed as a more realistic alternative. The motivation within industry to collect high quality data can only be created with a feeling of ownership. The decline in linefish species in South Africa has led to increased exploitation of demersal sharks such as Mustelus mustelus. Their status as one of the target and by-catch species of South Africa's shark fisheries necessitated resource assessment. Age, growth, maturity and mortality calculations for M mustelus were made from data collected from 1983-2006. The maximum observed age for M mustelus was 25 years. Estimated von Bertalanffy growth parameters from observed length-at-age for combined sexes, females and males were L∞ = 1946.16 mm TL, K = 0.08 year⁻' , to = -3.63 year⁻'; L∞ = 2202.21mm, K = 0.05 year⁻', to = 4.67 years; and L∞ = 1713.19 mm TL, K = 0.08 year⁻' and to = -4.36 years, respectively. Instantaneous total mortality (Z) was estimated at 0.16 y⁻', whilst natural mortality (M) for M mustelus was estimated at 0.05 y⁻'. The age and length at 50% maturity was determined for combined sexes, females and males at 1216 mm TL corresponding to an age of 9.93 years, 1234 mm (TL) and 10.75 years, and 1106 mm TL and 9.1 years respectively. The smoothhound shark resource off the south-eastern and south-western Cape coast was assessed by three dynamic pool models; yield per recruit, spawner biomass per recruit and an extended yield and spawner biomass per recruit. Due to the longevity of elasmobranches the per-recruit model was extended over a 20 year time-frame to simulate resource responses to management options. Fo.1 was estimated as 0.034 year⁻' and F MAX was estimated as 0.045 year⁻'. FsB50 was estimated as 0.031. The extended per-recruit model tested the outcome of different management scenarios, Size and effort control showed the least probability of pristine biomass falling below 20% of current levels in 20 years (where selectivity was set at 3 years). The replacement yield model showed that the average catches over the past decade are 2.5 times higher than the replacement yield is on the South Coast and 1.30 on the West Coast. A more realistic level optimising yield would be at 0.05 with a selection pattern at 3 years, where the probability of the biomass falling to below 20% of pristine pre-exploited levels in twenty years becomes negligible. A comparison of the models showed that current catches need to be halved for exploitation of smoothhound sharks to be sustainable. The results of this study indicate a need for a management intervention for M mustelus in South Africa with regards to potential overexploitation and collection of quality data for further assessments. A demersal identification key was developed as part of this study, which should aid monitoring officials in accurately identifying shark logs for collecting data. This study showed how adopting a management plan with the inclusion of comanagement concepts would improve the quality of data collected and increase monitoring of fishing activities. The inclusion of co-management is possible due to the unique bottle neck created by few demersal shark processing facilities actively exporting shark. A fishery management plan was compiled proposing several management options including size and effort controls.
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The variability and predictability of the IRI shape parameters over Grahamstown, South Africa
- Authors: Chimidza, Oyapo
- Date: 2008
- Subjects: Ionosphere -- Mathematical models -- South Africa , Atmosphere, Upper -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5496 , http://hdl.handle.net/10962/d1005282 , Ionosphere -- Mathematical models -- South Africa , Atmosphere, Upper -- South Africa
- Description: The International Reference Ionosphere (IRI) shape parameters B0, B1, and D1 provide a representation of the shape of the F2 layer, the thickness of the F2 layer and the shape of the F1 layer of the ionosphere respectively. The aim of this study was to examine the variability of these parameters using Grahamstown, South Africa (33.3±S, 26.5±E) ionosonde data and determine their predictability by the IRI-2001 model. A further aim of this study was to investigate developing an alternative model for predicting these parameters. These parameters can be determined from electron density profiles that are inverted from ionograms recorded with an ionosonde. Data representing the B0, B1 and D1 parameters, with half hourly or hourly intervals, were scaled and deduced from the digital pulse sounder (DPS) ionosonde for the period April 1996 to December 2006. An analysis of the diurnal, seasonal, and solar variations of the behaviour of these parameters was undertaken for the years 2000, 2004 and 2005 using monthly medians. Comparisons between the observational results and that of the IRI model (IRI 2001 version) indicate that the IRI-2001 model does not accurately represent the diurnal and seasonal variation of the parameters. A preliminary model was thus developed using the technique of Neural Networks (NNs). All available data from the Grahamstown ionosonde from 1996 to 2006 were used in the training of the NNs and the prediction of the variation of the shape parameters. Inputs to the model were the day number, the hour of day, the solar activity and the magnetic index. Comparisons between the preliminary NN model and the IRI-2001 model indicated that the preliminary model was more accurate at the prediction of the parameters than the IRI-2001 model. This analysis showed the need to improve the existing IRI model or develop a new model for the South African region. This thesis describes the results from this feasibility study which show the variability and predictability of the IRI shape parameters.
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Toward the development of a rearing protocol for juvenile dusky kob, Argyrosomus japonicus (Pisces: Sciaenidae)
- Authors: Collett, Paul David
- Date: 2008
- Subjects: Argyrosomus -- South Africa , Mariculture -- South Africa , Fishes -- Nutrition -- South Africa , Fishes -- Growth -- South Africa , Fish trade -- South Africa , Sciaenidae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5325 , http://hdl.handle.net/10962/d1005171 , Argyrosomus -- South Africa , Mariculture -- South Africa , Fishes -- Nutrition -- South Africa , Fishes -- Growth -- South Africa , Fish trade -- South Africa , Sciaenidae
- Description: The South African mariculture industry is developing the rearing technology of indigenous fish species. Dusky kob (Argyrosomus japonicus) has high-quality flesh and a good market demand. Research is needed to determine the environmental requirements under which growth of dusky kob is optimised. This study assessed the effect of temperature, light intensity, feeding frequency and stocking density, respectively, on growth, feed conversion ratio (FCR) and survival of juvenile dusky kob within a weight range of 10-60 g fish⁻¹) in a series of four growth trials. The effect of temperature on growth and FCR was assessed at 14 temperatures from 17 to 28°C. The temperature for best growth was estimated to be 25.3 °C, while 21.4 °C was the temperature at which the best FCR was achieved. A growth trial testing the effect of light intensity on growth showed that light intensity did not affect growth in the range of 23 – 315 lx. Fish fed a restricted ration of 3.6% body weight per day (chapter 2) or 3.41% body weight per day (chapter 4) had a better FCR than fish fed to satiation. A trial to assess the effect of feeding frequency on growth and FCR showed that fish fed both two or three times daily grew better than those fed once daily. FCR was best in fish that were fed once or twice daily. Preliminary analysis of the results from a stocking density trial showed that stocking density in the range of 10 – 50 kg m⁻³ did not affect growth of juvenile dusky kob. It is recommended to culture dusky kob at a temperature of 25.3 - 21.4 °C at stocking densities up 50 kg m⁻³ to maximise growth. However, a study is needed to determine the environmental conditions needed to maximise profit under commercial conditions. The results allow the South African industry the opportunity to assess the culture potential of this species. In addition, the results will help develop protocols that can be used in other South African candidate aquaculture species such as silver kob, yellowtail, white-stumpnose and sole.
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Understanding and improving the residual efficacy of the cryptophlebia leucotreta granulovirus (Cryptogran)
- Authors: Kirkman, Wayne
- Date: 2008
- Subjects: Cryptophlebia leucotreta , Cryptophlebia leucotreta -- Control , Pests -- Biological control , Citrus -- Diseases and pests
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5794 , http://hdl.handle.net/10962/d1005482 , Cryptophlebia leucotreta , Cryptophlebia leucotreta -- Control , Pests -- Biological control , Citrus -- Diseases and pests
- Description: False codling moth (FCM), Thaumatotibia (=Cryptophlebia) leucotreta (Meyr) (Lepidoptera: Tortricidae), is one of the most important pests on citrus. The Cryptophlebia leucotreta granulovirus (CrleGV) has been developed into a successful biological control agent, registered under the name Cryptogran, and is currently the preferred product for the control of FCM on citrus in South Africa. A prerequisite to the continued success of Cryptogran as a means of controlling false codling moth is to understand the factors affecting field persistence of the virus, and to find ways to improve it. The aim of this study was to gain a clearer understanding of the product and the abiotic and biotic factors affecting its persistence in the field, and to investigate methods to improve this persistence. The effect of UV-irradiation on the virus was determined, and various products were tested as UV protectants in laboratory bioassays. Lignin was the most effective additive, and was tested in several field trials, where it also enhanced the efficacy of Cryptogran. Laboratory trials indicated that Cryptogran is rainfast. Cryptogran applications early in the season had a longer period of residual activity than sprays applied closer to harvest. Daytime applications were less effective that evening sprays. Sprays applied coinciding with peaks in pheromone moth trap catches were more effective than those applied between peaks. Biotic factors influencing persistence were investigated. Residual efficacy was longer when treatments were applied to blocks than as single tree treatments. Attempts were made to quantify the effect of the navel end of a navel orange on the field persistence of Cryptogran. Cryptogran was shown to be compatible with many agricultural chemicals used on citrus. Economic thresholds and various cost-benefit analyses are discussed. A list of practical recommendations to growers was drawn up, and possibilities for future research are presented.
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Verification of Ionospheric tomography using MIDAS over Grahamstown, South Africa
- Authors: Katamzi, Zama Thobeka
- Date: 2008
- Subjects: Ionosphere -- Remote sensing -- South Africa , Atmosphere, Upper , Tomography -- Scientific applications -- South Africa , Global Positioning System
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5497 , http://hdl.handle.net/10962/d1005283 , Ionosphere -- Remote sensing -- South Africa , Atmosphere, Upper , Tomography -- Scientific applications -- South Africa , Global Positioning System
- Description: Global Positioning System (GPS) satellites and receivers are used to derive total electron content (TEC) from the time delay and phase advance of the radiowaves as they travels through the ionosphere. TEC is defined as the integralof the electron density along the satellite-receiver signal path. Electron densityprofiles can be determined from these TEC values using ionospheric tomographic inversion techniques such as Multi-Instrument Data Analysis System (MIDAS).This thesis reports on a study aimed at evaluating the suitability of ionospheric tomography as a tool to derive one-dimensional electron density profiles, using the MIDAS inversion algorithm over Grahamstown, South Africa (33.30◦S, 26.50◦E). The evaluation was done by using ionosonde data from the Louisvale (28.50◦S, 21.20◦E) and Madimbo (22.40◦S, 30.90◦E) stations to create empirical orthonormal functions (EOFs). These EOFs were used by MIDAS in the inversion process to describe the vertical variation of the electron density. Profiles derived from the MIDAS algorithm were compared with profiles obtained from the international Reference Ionosphere (IRI) 2001 model and with ionosonde profiles from the Grahamstown ionosonde station. The optimised MIDAS profiles show a good agreement with the Grahamstown ionosonde profiles. The South African Bottomside Ionospheric Model (SABIM) was used to set the limits within which MIDAS was producing accurate peak electron density (NmF2) values and to define accuracy in this project, with the understanding that the national model (SABIM) is currently the best model for the Grahamstown region. Analysis show that MIDAS produces accurate results during the winter season, which had the lowest root mean square (rms) error of 0.37×1011[e/m3] and an approximately 86% chance of producing NmF2 closer to the actual NmF2 value than the national model SABIM. MIDAS was found to also produce accurate NmF2 values at 12h00 UT, where an approximately 88% chance of producing an accurate NmF2 value, which may deviate from the measured value by 0.72×1011[e/m3], was determined. In conclusion, ionospheric tomographic inversion techniques show promise in the reconstruction of electron density profiles over South Africa, and are worth pursuing further in the future.
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Water quality, abalone growth and the potential for integrated mariculture on a South African abalone Haliotis midae L. farm
- Authors: Yearsley, Rowan David
- Date: 2008
- Subjects: Abalones -- South Africa Abalone culture -- South Africa Abalones -- Growth Mariculture -- South Africa Water quality -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5334 , http://hdl.handle.net/10962/d1005180
- Description: Abalone Haliotis midae farming in South Africa is highly intensive, employing pump-ashore, flow-through systems. Despite the known sensitivity of abalone to water quality, there is only a rudimentary understanding of water quality dynamics on South African abalone farms and its effects on abalone production. Furthermore, the potential for reusing the relatively dilute abalone farm effluent to culture other animal species has not been investigated. This study investigated the dynamics of water quality and growth on a South African abalone farm and assessed the suitability of the effluent for the culture of silver kob Argyrosomus inodorus and bloodworm Arenicola loveni loveni. Monitoring of water quality and abalone growth in abalone tanks revealed that oxygen concentrations decreased, while H⁺ ion and free-ammonia (NH₃) concentration increased in a gradient between the inflow and outflow. Abalone growth was positively correlated with oxygen concentration and negatively correlated with free-ammonia and H⁺ ion concentration. The oxygen (O) concentration of the farm influent was dependent upon the influents’ temperature (T) and was described by the relationship O (mg L⁻¹) = 11.244 – 0.208T (r²=0.74). Linear regression analysis of data collected from abalone farm tanks revealed that the concentration of total ammonia at the outflow of abalone tanks (μg TAN L⁻¹) was dependant upon temperature (°C), flow-rate (L s⁻¹ kg⁻¹ H. midae), abalone size (g) and length of time since the tank was last cleaned (d) (n = 125, r² = 0.80). The production of total ammonia (μg TAN s⁻¹ kg⁻¹) was related to temperature, abalone size and days that the tanks remained un-cleaned (n = 125; r² = 0.81). A diurnal cycle of respiration was evident in abalone tanks with higher oxygen consumption and H+ ion production at night. The oxygen concentration of farm effluent was related to temperature, farm biomass and flow rate by means of a linear regression equation (n = 40; r² = 0.69). The results demonstrated the importance of optimising the flow-rate per unit of biomass for various temperatures and sizes of abalone. As abalone size and temperature cannot be controlled under farm conditions, the flow-rate per unit of biomass which the abalone culture system receives will determine the quality of the culture water. The specific growth rate (0.48 ± 0.01 % BW d⁻¹), mortality (1.8 ± 0.5 %), feed conversion ratio (3.0 ± 0.2) and protein efficiency ratio (1.0 ± 0.1) of silver kob kept in either abalone farm effluent or control seawater for 120 days did not differ significantly (t-test, P>0.05). A 90 day growth trial indicated that abalone farm effluent is a suitable culture medium for bloodworm. Bloodworm supplied with control seawater lost weight at 0.19 ± 0.04 % BW d-1, while those given abalone effluent grew at 0.39 ± 0.07 % BW d⁻¹. Mortality was 6 ± 3 % in effluent and 11 ± 8 % in seawater. The bloodworm were efficient at processing solid waste. Abalone farm effluent initially contained 7.7 ± 13 mg L⁻¹ more suspended solids than control seawater, which contained 3.5 ± 0.5 mg L⁻¹, but after passing through bloodworm systems the concentration in abalone effluent was reduced to only 1.4 ± 3.5 mg L⁻¹ above that in control seawater. Therefore, abalone farm effluent could be reused as a culture medium for both silver kob and bloodworm. Future work is needed to investigate aspects of the feasibility of such systems such as growth rates at different sizes and stocking densities.
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