Hydrological proceses, chemical variability, and multiple isotopestracing of water flow paths in the Kudumela Wetland- Limpopo Province, South Africa
- Authors: Mekiso, Feleke Abiyo
- Date: 2011
- Subjects: Kudumela Wetland -- South Africa -- Limpopo , Wetland hydrology -- South Africa -- Limpopo , Wetlands -- South Africa -- Limpopo , Wetland conservation -- South Africa -- Limpopo , Wetland management -- South Africa -- Limpopo , Isotopes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6027 , http://hdl.handle.net/10962/d1006153 , Kudumela Wetland -- South Africa -- Limpopo , Wetland hydrology -- South Africa -- Limpopo , Wetlands -- South Africa -- Limpopo , Wetland conservation -- South Africa -- Limpopo , Wetland management -- South Africa -- Limpopo , Isotopes
- Description: The hydrology of the Kudumela Wetland, Limpopo Province of South Africa was studied from November 2005 to April 2007, involving both fieldwork and laboratory analyses. This study presents the results of an investigation of the hydrology of the Kudumela Wetland in South Africa, and its contribution to dry season flow in the Mohlapitsi and Olifants Rivers. Initially, 40 Piezometers were installed along seven transects and water levels monitored in order to understand water table level characteristics (fluctuations) with time. Water levels in transects one, three, the right bank portion of transect four and transect six showed fluctuations. Transect two, the left bank portion of transect four and transect five did not show significant temporal changes. The relationships between piezometer water levels, rainfall in the study area and stream flow observed at a river gauging station are not clear. The river within the wetland is a gaining stream because the water table level elevation is above that of the river. This indicates that the wetland is feeding the river. The northern part of the wetland (T1 and T2) is affected by artificial drains and most of the piezometers closest to the river channel showed the lowest variations. The relationships between rainfall, groundwater, and surface water at this site shows that stream flow did not respond quickly to precipitation as expected, even in months when rainfall increased (for example, 74 and 103mm during 08/02/06 and 18/02/06 respectively), and the groundwater levels did not show fluctuations, indicating that groundwater responds gradually to precipitation, and that the relationship between rainfall, groundwater and surface water is complex. The environmental stable isotopes (deuterium and oxygen-18) and the radioactive isotope (tritium) were analyzed, along with field observations of electrical conductivity (EC), pH, total alkalinity (Talka) and some major and minor dissolved ion analyses for tracing water dynamics in the study area. A total of 39 water samples was taken and analyzed from boreholes, auger holes, right bank and left bank drains, various points along the river and springs in four sampling visits to the wetland. The results did not clearly provide a temporal record of isotope and chemical variations in the various sources. Results from the most extensive sampling survey in April 2007 provide the most comprehensive overview of hydrological relationships. Clustering of the stable isotope data suggests that the water samples of upstream and downstream river, auger holes further south and most drains clustered together suggesting a common water source and almost all samples fall above the global (GMWL) and local (Pretoria MWL) meteoric water lines, while some fall between the global and Pretoria meteoric water lines. Six representative water samples were analyzed for major ion concentration. Both cation (Ca, Mg, K, and Na) and anion (HCO3, SO4, Cl, and NO3) analyses in November 2007 confirmed conclusions reached from field observations. The analysis shows that a single type of water (Ca, Mg-HCO3) is involved in the study area. In almost all major ion plots, the right bank drains, upstream river and downstream river samples grouped together in a single cluster. As the means for reliable river flow measurements were not available, except for the gauging station at the outlet of the valley, rough, semi-quantitative estimates were made during several field visits. These, suggest considerable losses of river flow into the gravel/boulder beds at and below a gabion dam at the head of the valley. Three major and several other left bank springs and right bank drains at transects T1 and T2 contributed to the river flow at all times. Along with the isotopic and chemical evidence, these observations have lead to a hypothesis that river water enters the wetland and flows back to the Mohlapitsi River through boulder beds underlying the wetland and through drains on the surface of the argillaceous aquitard covering the more conductive boulder beds. Deeper dolomitic groundwater does not appear to contribute to the water balance at least in the northern half of the wetland. Although environmental isotope and hydrochemistry results may not unequivocally prove this hypothesis they do not contradict it.
- Full Text:
- Date Issued: 2011
Improved tree species discrimination at leaf level with hyperspectral data combining binary classifiers
- Authors: Dastile, Xolani Collen
- Date: 2011
- Subjects: Mathematical statistics , Analysis of variance , Nearest neighbor analysis (Statistics) , Trees--Classification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5567 , http://hdl.handle.net/10962/d1002807 , Mathematical statistics , Analysis of variance , Nearest neighbor analysis (Statistics) , Trees--Classification
- Description: The purpose of the present thesis is to show that hyperspectral data can be used for discrimination between different tree species. The data set used in this study contains the hyperspectral measurements of leaves of seven savannah tree species. The data is high-dimensional and shows large within-class variability combined with small between-class variability which makes discrimination between the classes challenging. We employ two classification methods: G-nearest neighbour and feed-forward neural networks. For both methods, direct 7-class prediction results in high misclassification rates. However, binary classification works better. We constructed binary classifiers for all possible binary classification problems and combine them with Error Correcting Output Codes. We show especially that the use of 1-nearest neighbour binary classifiers results in no improvement compared to a direct 1-nearest neighbour 7-class predictor. In contrast to this negative result, the use of neural networks binary classifiers improves accuracy by 10% compared to a direct neural networks 7-class predictor, and error rates become acceptable. This can be further improved by choosing only suitable binary classifiers for combination.
- Full Text:
- Date Issued: 2011
Initial investigations into dynamics of mesozooplankton community structure in Algoa Bay, South Africa
- Authors: Dali, Luzuko O'Brian
- Date: 2011
- Subjects: Zooplankton -- Research -- Indian Ocean -- South Africa , Phytoplankton -- Research -- Indian Ocean -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5715 , http://hdl.handle.net/10962/d1005401 , Zooplankton -- Research -- Indian Ocean -- South Africa , Phytoplankton -- Research -- Indian Ocean -- South Africa
- Description: As part of a long-term monitoring programme initiated by the South African Environmental Observation Network (SAEON) Elwandle Node, the spatio-temporal dynamics of mesozooplankton (200–2000 μm) community structure in Algoa Bay, on the Eastern Cape coastline of southern Africa, was investigated in summer and winter of 2008. Physical-chemical and biological variables were measured at selected sites in the eastern and western sectors of the Bay. During summer, nutrient rich waters upwelling into the eastern sector of the Bay contributed to significant spatial variation in selected physical-chemical variables. During winter, virtually no significant spatial patterns in the physical-chemical variables were observed (P>0.05 in all cases). For the majority of physical-chemical variables, no significant seasonal patterns in values were detected (P>0.05 in all cases). Notable exceptions were water column stability and water temperatures which were highest during summer, and seston, turbidity and ammonium concentrations which attained the highest values in winter. The striking seasonal pattern observed in the water column stability, coupled with the upwelling event, coincided with a strong seasonal pattern in the total surface and integrated chlorophyll-a concentrations within the Bay. During summer, the total surface phytoplankton biomass ranged from 1.87–3.11 μg.L⁻¹ and the integrated biomass values between 44.6 and 89.1 mg chl-a m⁻². In winter, surface chl-a concentrations ranged from 0.49 to 0.55 μg.L⁻¹ and integrated biomass from 13.5 to 13.8 mg chl-a m⁻². During both seasons, the large microphytoplankton (>20 μm) fraction contributed the most (>80%) to the total phytoplankton biomass suggesting that phytoplankton growth is not nutrient limited within the Bay. The total mesozooplankton abundance and biomass values during summer varied between 10088.92 and 28283.21 ind.m⁻³ and between 76.59 and 161.94 mg.m⁻³, respectively. During winter, total abundance and biomass of mesozooplankton within the Bay were significantly lower, ranging from 2392.49 to 11145.29 ind.m⁻³, and from 34.49 to 42.49 mg.m⁻³, respectively (P<0.05). During both seasons, cosmopolitan copepod species 200–500μm in size dominated the total mesozooplankton counts, numerically and in biomass. Hierarchical cluster analyses identified distinct zooplankton groupings within the Bay during both the summer (three groupings) and winter (four groupings) surveys. The different groupings identified during the two seasons were not associated with any specific geographic region or hydrological feature. Nonetheless, a distinct seasonal pattern in the mesozooplankton community was evident, largely reflecting the increased abundance of mesozooplankton during the summer survey. Canonical Correspondence Analyses (CCA) indicated that the zooplankton community structure within Algoa Bay reflected a complex interaction between physical-chemical (e.g. temperature, water column stability, turbidity, and nitrate, dissolved oxygen and nitrite concentrations) and biological factors (e.g. microphytoplankton and picophytoplankton concentrations). These data provide baseline information towards long-term monitoring programs that will be conducted in Algoa Bay, as part of the South African Environmental Observation Network (SAEON), in the near future.
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- Date Issued: 2011
Investigating the role of heat shock proteins (Hsps) 40, 70 and 90 in the life cycle of Theiler's murine encephalomyelitis virus (TMEV)
- Authors: Mutsvunguma, Lorraine Zvichapera
- Date: 2011
- Subjects: Heat shock proteins , Picornaviruses , Encephalomyelitis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3966 , http://hdl.handle.net/10962/d1004025 , Heat shock proteins , Picornaviruses , Encephalomyelitis
- Description: Introduction: Picornaviruses are a family of RNA viruses which are economically and clinically significant. Like many other viruses, picornaviruses utilise host cell machinery to facilitate their replication and assembly, including heat shock proteins (Hsps). The aim of this research was to investigate the role of Hsp40, Hsp70 and Hsp90 during picornavirus infection using the cardiovirus, Theiler’s murine encephalomyelitis virus (TMEV), as a study model. Methodology: Picornavirus VP1 capsid proteins were analysed by multiple sequence alignment and multiple structural comparisons. Protein domain architecture was used to analyse Hsp90 cellular and viral client proteins. Effects of Hsp90 inhibitors, novobiocin and geldanamycin, on TMEV growth in BHK-21 cells was observed over a 48hr period. Localisation of Hsp40, Hsp90 and Hsp70 in TMEV-infected BHK-21 cells was investigated by indirect immunofluorescence and confocal microscopy. Results and Discussion: VP1 proteins of picornaviruses are highly divergent within the family at the amino acid level, which might be linked to the protein’s function in determining virus tropism and antibody neutralisation. An eight-stranded anti-parallel beta-barrel structure was found conserved in the VP1 protein structures which might be linked to the highly conserved picornavirus capsid assembly process. Absence of a common protein domain between Hsp90 viral and cellular client proteins that might be functionally connected to Hsp90, suggests that Hsp90 most likely recognises surface features rather than sequence motifs/patterns. The Hsp90 inhibitors, novobiocin and geldanamycin, had a negative effect on virus growth as virus-induced cytopathic effect was not observed in treated cell after 48hrs. TMEV 2C protein was detected by Western analysis in infected cell lysates treated with geldanamycin but not novobiocin, suggesting novobiocin affects the translation or processing of TMEV 2C. Immunofluorescence analysis of TMEV-infected cells showed a relocalisation of Hsp40 into the nucleus during infection. Overlap of Hsp40 and TMEV P1 was observed in the perinuclear region, suggesting colocalisation between these proteins. Hsp70 converged around the replication complex during infection but did not overlap with TMEV 2C. Hsp90 concentrated in the region of the replication complex where it overlapped with TMEV 2C and this redistribution was found to be dependent on the stage of infection. The overlap between Hsp90 and TMEV 2C signals observed, suggested colocalisation between the two proteins. Conclusion: This study identified Hsp90, Hsp70 and Hsp40 as possible host factors required in TMEV replication.
- Full Text:
- Date Issued: 2011
Investigation into the extended capabilities of the new DPS-4D ionosonde
- Authors: Ssessanga, Nicholas
- Date: 2011
- Subjects: Ionosondes , Ionosphere , Ionosphere -- Observations -- South Africa -- Hermanus (Cape of Good Hope) , Ionosphere -- Research -- South Africa -- Hermanus (Cape of Good Hope)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5472 , http://hdl.handle.net/10962/d1005257 , Ionosondes , Ionosphere , Ionosphere -- Observations -- South Africa -- Hermanus (Cape of Good Hope) , Ionosphere -- Research -- South Africa -- Hermanus (Cape of Good Hope)
- Description: The DPS-4D is the latest version of digital ionosonde developed by the UMLCAR (University of Massachusetts in Lowell Center for Atmospheric Research) in 2008. This new ionosonde has advances in both the hardware and software which allows for the promised advanced capabilities. The aim of this thesis was to present results from an experiment undertaken using the Hermanus DPS-4D (34.4°S 19.2°E, South Africa), the first of this version to be installed globally, to answer a science question outside of the normally expected capabilities of an ionosonde. The science question posed focused on the ability of the DPS-4D to provide information on day-time Pc3 pulsations evident in the ionosphere. Day-time Pc3 ULF waves propagating down through the ionosphere cause oscillations in the Doppler shift of High Frequency (HF) radio transmissions that are correlated with the magnetic pulsations recorded on the ground. Evidence is presented which shows that no correlation exists between the ground magnetic pulsation data and DPS-4D ionospheric data. The conclusion was reached that although the DPS-4D is more advanced in its eld of technology than its predecessors it may not be used to observe Pc3 pulsations.
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- Date Issued: 2011
Investigations of the assessment of bioequivalence of topical clotrimazole products using a dermatopharmacokinetic approach
- Authors: Parfitt, Natalie Rae
- Date: 2011 , 2010-07-05
- Subjects: Dermatopharmacology , Drugs -- Therapeutic equivalency , Antifungal agents , Therapeutics, Cutaneous and external
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3840 , http://hdl.handle.net/10962/d1007659 , Dermatopharmacology , Drugs -- Therapeutic equivalency , Antifungal agents , Therapeutics, Cutaneous and external
- Description: The specialised nature of the stratum corneum makes it an efficient barrier to foreign substances, including drug molecules. Therefore, cutaneous drug absorption is a slow and complex process of which stratum corneum penetration is the rate limiting step. The rate and extent of stratum corneum penetration by a drug compound depends greatly on the presence of penetration enhancing/retarding excipients and therefore the clinical outcomes of a product rely greatly on the components and quality of the formulation. Hence, establishing bioequivalence between topical products is crucial to ensure that patients receiving multisource drug products are assured of the same efficacy and safety as the brand product. Since locally acting topical formulations do not target the systemic circulation, conventional methods of assessing bioequivalence using plasma levels are not appropriate. Consequently, the current regulatory guidelines require comparative clinical trials to be carried out to show bioequivalence between topical products. As these studies are very expensive and time consuming, the development of a more direct and relatively rapid and inexpensive method for determining bioequivalence between topical products is required. Clotrimazole is an anti-fungal agent where the target site of action is in the stratum corneum. In this work, tape stripping, which involves the sampling of stratum corneum, was investigated as a tool for the determination of bioequivalence between topical clotrimazole products. The tape stripping method involved the analysis of each tape strip individually and standardization of stratum corneum thickness between subjects was carried out using TEWL measurements. This approach provided detailed information regarding the amount of clotrimazole present in the stratum corneum as well as the extent of drug penetration. Prior to the tape stripping studies an HPLC method was developed for the quantitative analysis of clotrimazole from the tape strip samples. This method was shown to be accurate and reproducible across the required range. It was also shown to be selective for clotrimazole in the presence of possible interfering substances such as those present in the tape adhesive and also skin components. The bioequivalence studies were conducted using a single “uptake” time point. In order to determine an appropriate dose duration for these studies a novel approach was employed, involving a preliminary dose duration study. For the bioequivalence investigations, Canesten® Topical cream was used as both test and reference products to determine if the method was capable of showing bioequivalence. Subsequently, Canesten® Topical cream was also compared to a 1% gel formulation to determine if the method could detect formulation differences. The conventional BE limits of 0.8 – 1.25 were used for the assessment of BE, however, the clinical relevance of using these limits for dermal studies is debatable since they are derived from oral pharmacokinetic studies. Therefore, the data from the tape stripping investigations were also assessed using more realistic limits of 0.75 – 1.33 and even 0.7 – 1.44. In addition to the tape stripping studies a novel method of determining the amount of drug present in the stratum corneum, the “Residual Method”, was investigated. This method involved assaying the amount of clotrimazole found in the residual formulation after a specified dose duration had elapsed and subtracting that amount from the amount of clotrimazole initially applied. The results of tape stripping investigations showed that, if the study is sufficiently powered, tape stripping may be used to determine bioequivalence according to the conventional limits, as well as possibly detect formulation differences between different clotrimazole products. Bioequivalence assessment using the widened intervals showed that fewer subjects were required to achieve a sufficient statistical power. The variability associated with this method was acceptable and tape stripping may therefore have the potential to be used as a BE tool in a regulatory setting for clotrimazole or other antifungal topical formulations. The “Residual Method” also showed promising results as a bioequivalence tool, but further investigation and extensive validation of this method is required before it can be suggested as a regulatory method. The results of these studies have clearly indicated that tape stripping has the potential to be used as an alternative to comparative clinical trails for the assessment of bioequivalence between clotrimazole formulations and also to assess bioequivalence between other antifungal products.
- Full Text:
- Date Issued: 2011
Male and female cardiovascular risk in an urban, black working population
- Authors: Jackson, Lindsay May
- Date: 2011
- Subjects: Cardiovascular system -- Diseases -- South Africa -- Grahamstown , Obesity -- South Africa -- Grahamstown , Hypertension -- South Africa -- Grahamstown , Hypercholesteremia -- South Africa -- Grahamstown , Diabetes -- South Africa -- Grahamstown , Lifestyles -- Health aspects -- South Africa -- Grahamstown , Health behavior -- South Africa -- Grahamstown , Health attitudes -- South Africa -- Grahamstown , Black people -- South Africa -- Grahamstown -- Health and hygiene
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5127 , http://hdl.handle.net/10962/d1005205 , Cardiovascular system -- Diseases -- South Africa -- Grahamstown , Obesity -- South Africa -- Grahamstown , Hypertension -- South Africa -- Grahamstown , Hypercholesteremia -- South Africa -- Grahamstown , Diabetes -- South Africa -- Grahamstown , Lifestyles -- Health aspects -- South Africa -- Grahamstown , Health behavior -- South Africa -- Grahamstown , Health attitudes -- South Africa -- Grahamstown , Black people -- South Africa -- Grahamstown -- Health and hygiene
- Description: The aim of this research project was to assess and compare cardiovascular disease (CVD) risk in black males and females from an urban, working population in the Makana (Grahamstown) region of the Eastern Cape, South Africa. Two-hundred and ninety one individuals (males: n = 143, females: n = 148) with a mean age of 42.6 (±8.1) years were voluntarily recruited from the greater urban Makana (Grahamstown) area. Eight Cardiovascular disease (CVD) risks were assessed: stature and mass were obtained in order to calculate body mass index (BMI) (mass/stature2). Obesity, defined as a morphological risk, was classified according to the World Health Organisation (WHO) BMI criteria (BMI>30kg.m-2), as well as according to measures of waist circumference (WC) and body composition. Hypertension, hypercholesterolemia and type II diabetes, were grouped as cardiovascular (CV) risks. Hypertension was defined as a blood pressure greater than 140/90mmHg (JNC-7); hypercholesterolemia, as total cholesterol greater than 6.2mmol.L-1 (NCEP); and type II diabetes, as total glucose greater than 12mmol.L-1 (WHO). Physical activity, diet, tobacco use, and alcohol consumption and dependence were grouped as lifestyle-related risks. These were assessed by means of self-reporting through the use of various validated questionnaires. Finally, self-reporting of obesity, hypertension, hypercholesterolemia and type II diabetes was assessed, in addition to perception questions on individuals’ perceived body shape and size (Ziebland figures). Self-reported and perceived responses were then compared to actual measures. Females were significantly (p<0.001) heavier than the males (92.7kg compared to 72.1kg) and had significantly (p<0.001) higher BMIs than their male counterparts (37.6kg.m-2 compared to 25.7 kg.-2). They also recorded significantly (p<0.001) higher waist circumference (WC) values and had significantly (p<0.001) higher percentage and total body fat. Significantly (p<0.001) more females were obese (81%) compared to males (17%). While a higher percentage of males (25 % compared to 22%) presented with stage I hypertension (≥140/90mmHg, <160/95mmHg), significantly (p<0.05) more females (14% compared to 8%) presented with stage II hypertension (>160/95mmHg). The prevalence of hypercholesterolemia at a high level of risk (>6.2mmol.L-1) was relatively low (2.1 % of males, 3.4% of females), but notably more participants (22% of males and 26% of females) presented with the condition at a moderate level of risk (>5mmol.L-1). Type II diabetes was the least prevalent CV risk factor, with no males and only 3% of females presenting with the condition. Males consumed significantly (p<0.05) more in terms of total energy intake (9024 vs. 7234 kJ) and were significantly (p<0.05) more active (3315 compared to 2660 MET-mins.week). A significantly (p<0.05) higher percentage of males smoked (51.1% compared to 3.4%), consumed alcohol (73.4% compared to 46.6%) and were alcohol dependent (40% compared to 33.5%). Both males and females tended to be ignorant of their health status, with both samples under-reporting obesity, hypertension and hypercholesterolemia, while over-reporting type II diabetes. Furthermore, obesity was significantly (p<0.05) underestimated, with both male and female individuals perceiving themselves to be notably smaller than they actually were. Physical activity and diet were important determinants of CVD risk in this black urban sample of individuals. Obesity, in particular central adiposity, was the most notable risk (particularly in females), followed by hypertension (particularly in males). Although some risks presented at a moderate level of risk, a clustering of risk factors was evident in both samples, with 12.6% and 41.2% of males and females presenting with two risk factors, and 2.8% and 8.1% of males and females respectively presenting with three risks.
- Full Text:
- Date Issued: 2011
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.
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- Date Issued: 2011
Nanostructures and metallophthalocyanines : applications in microbial fuel cells
- Authors: Edwards, Sean
- Date: 2011
- Subjects: Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4107 , http://hdl.handle.net/10962/d1011742 , Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Description: Microbial fuel cells (MFCs) are a promising form of alternative energy capable of harnessing the potential energy stores in organic waste. The oxygen reduction reaction (ORR) forms an integral role in the generation of electricity in MFCs however it is also a potential obstacle in enhancing the performance of MFCs. Platinum, a commonly used catalyst for the ORR, is expensive and rare. Significant research has been conducted into developing alternative catalysts. Metallophthalocyanines (MPc) have garnered attention for use as catalysts. Iron phthalocyanine (FePc) has been shown to have catalytic activity towards the reduction of oxygen. Coupling of the catalyst to nanostructured carbon materials, such as multi-walled carbon nanotubes, has been observed to have several advantages as nanostructures have a high surface-to-volume ratio. In this study, we have attempted to assess the suitability of FePc, both its bulk and nanostructured form, as an oxygen reduction catalyst and acid functionalized multi-walled carbon nanotubes for use as a catalyst support using electrochemical techniques such as cyclic voltammetry and electrochemical impedance spectroscopy. We showed, for the first time, the catalytic nature of nanostructured FePc towards the ORR. Applying the data obtained from the electrochemical analyses, electrodes were modified using FePc and MWCNTs and applied to an Enterobacter cloacae-based MFC. Several operational parameters of the MFC, such as temperature and ionic strength, were optimized during the course of the study. We showed that optimized FePc:MWCNT-modified electrodes compared favourably to platinum-based electrodes in terms of power densities obtained in a microbial fuel cell.
- Full Text:
- Date Issued: 2011
Neogene fluvial deposits along the south-west coast of South Africa understanding the palaeoclimate through proxies
- Authors: Sciscio, Lara
- Date: 2011
- Subjects: Alluvium , Paleoclimatology -- South Africa , Paleoecology -- Miocene -- South Africa , Paleobotany -- Miocene -- South Africa , Paleogeography -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4981 , http://hdl.handle.net/10962/d1005593 , Alluvium , Paleoclimatology -- South Africa , Paleoecology -- Miocene -- South Africa , Paleobotany -- Miocene -- South Africa , Paleogeography -- South Africa
- Description: Branched glycerol dialkyl glycerol tetraether (GDGTs) membrane lipids have been used as a new proxy for the reconstruction of terrestrial palaeoclimates. These biomarkers (or molecular ‗fossils‘) in conjunction with palynology, have been effective in the novel analysis of Miocene organic-rich sediments from three South African west coast sites at Rondeberg, Noordhoek and Langebaanweg. Lastly, a Quaternary south coast site at Rietvlei, South Africa, was also studied to further elucidate the extent of use of this new proxy. The fluvial peat and organic-rich deposits of the Elandsfontyn Formation (Sandveld Group) were investigated at Noordhoek, Langebaanweg and Rondeberg to provide new evidence for the climate and vegetation patterns during Miocene in this region. Drill-core and quarry samples from all four sites were freeze-dried, powered, and prepared for biogeochemical and palynological analyses. The methylation index of branched tetraethers (MBT) and cyclisation ratio of branched tetraethers (CBT) proxies were used to calculate the mean annual air temperature (MAAT) and pH values of the organic-rich horizons at time of deposition. The Branched versus isoprenoid index of tetraethers (BIT) was used to assess the relative contributions of marine archaeal and terrestrial bacterial tetraethers, and thereby assess the validity of the MBT, CBT and calculated palaeoenvironmental factors. The results presented in this thesis suggest that the use of the MBT/CBT proxy has significant potential in southern Africa, and may complement previously attempted palaeoclimatic and palaeoecological studies of Neogene-aged South African sediments. This type of research has the capacity to provide palaeoenvironmental information where other proxies may be absent. Results indicate that all sites yielded branched tetraether membrane lipids with the exception of Rondeberg, where GDGTs were below detection as a result of poor preservation conditions. Palynological investigation confirmed proxy derived temperatures. Furthermore palynomorph analyses supplemented earlier studies of the Noordhoek site and were piloted for the Rondeberg site, reaffirming alternating sequences of tropical and subtropical palynofloras. The MAATs, likewise, show variability and pronounced trends through time at the Langebaanweg and Noordhoek sites, generally corresponding with the variation and diversity of the pollen population. The terrestrial MAAT results appear to compliment Southern Hemisphere sea level changes associated with Antarctic glaciations. Additionally, this data shows a pattern similar to the Southern and Northern Hemisphere marine isotope records of relative fluctuations in the global climate and sea level change from the early to middle Miocene. The application of these past climate change indicators have been proved to be useful in the reconstruction of South Africa Miocene palaeoclimates, and may aid in understanding the consequences of climate change in the Cape region.
- Full Text:
- Date Issued: 2011
Neuronal nitric oxide synthase : a biomarker for Alzheimers disease : interaction of neuronal nitric oxide synthase with beta-amyloid peptides in the brain
- Authors: Padayachee, Eden Rebecca
- Date: 2011 , 2013-07-19
- Subjects: Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4086 , http://hdl.handle.net/10962/d1007677 , Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Description: High levels of the amino acid arginine and low levels of the product citrulline in the cerebrospinal fluid of Alzheimer's patients could mean that there is a decrease in the enzymes that metabolize this amino acid. One such enzyme is neuronal nitric oxide synthase (nNOS). In this study, neuronal nitric oxide synthase (nNOS), sourced from bovine brain was extracted and concentrated using two methods of precipitation: poly (ethylene glycol) 20 000 (PEG) and ammonium sulphate [(NH₄)₂S0₄). These two techniques gave no increase in yield nor fold purification and hence were abandoned in favour of ion exchange chromatography by DEAE-Sepharose. The enzyme was then successfully purified by anion-exchange and after dialysis produced a 38% yield and three fold purification and yielded the highest specific activity of 2.27 U/mg. Neuronal nitric oxide synthase (nNOS) was a heterodimeric protein with a total molecular mass of ± 225 kDa (95 and 130 kDa monomers). The temperature and pH optima of the enzyme were 40⁰C and 6.5, respectively. The kinetic parameters (KM and Vmax) of nNOS were 70 μM and 0.332 μmol.min⁻¹, respectively. Moreover neuronal nitric oxide synthase (nNOS) was relatively stable at 40⁰C (t½ = 3 h). It was also confirmed that β-amyloid peptides inhibited nNOS when bound to the enzyme and that nNOS behaved as a catalyst in fibril formation through association-dissociation between enzyme and β-amyloid peptide. It was further shown that Aβ₁₇₋₂₈ inhibited nNOS the most with a Ki of 1.92 μM and also had the highest Stern-Volmer value (Ksv) of 0.11 μM⁻¹ indicating tight binding affinity to nNOS and easier accessibility to fluor molecules during binding. Congo red, turbidity, thioflavin-T assays and transmission electron microscopy were successfully used to detect and visualize the presence of fibrils by studying the process of fibrillogenesis. Computerized molecular modeling successfully studied protein dynamics and conformational changes of nNOS. These results correlated with resonance energy transfer (FRET) results which revealed the distance of tryptophan residues from the arginine bound at enzyme active site. Both the aforementioned techniques revealed that in the natural state of the enzyme with arginine bound at the active site, the tryptophan residues (TRP₆₂₅ and TRP₇₂₁) were positioned at the surface of the enzyme 28 Å away from the active site. When the amyloid peptide (Aβ₁₇₋₂₈) was bound to the active site, these same two amino acids moved 14 Å closer to the active site. A five residue hydrophobic fragment Aβ₁₇₋₂₁ [Leu₁₇ - Val₁₈ - Phe₁₉ - Phe₂₀ - Ala₁] within Aβ₁₇₋₂₈ was shown by computer modeling to be critical to the binding of the peptide to the active site of nNOS.
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- Date Issued: 2011
Opportunity and connectivity : selecting land managers for involvement in a conservation corridor linking two protected areas in the Langkloof Valley, South Africa
- Authors: McClure, Alice
- Date: 2011
- Subjects: Corridors (Ecology) -- South Africa -- Eastern Cape , National parks and reserves -- South Africa , Landscape ecology -- South Africa , Wildlife conservation -- South Africa , Conservation of natural resources -- South Africa , Land use -- South Africa -- Planning
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4770 , http://hdl.handle.net/10962/d1007590 , Corridors (Ecology) -- South Africa -- Eastern Cape , National parks and reserves -- South Africa , Landscape ecology -- South Africa , Wildlife conservation -- South Africa , Conservation of natural resources -- South Africa , Land use -- South Africa -- Planning
- Description: The Eden To Addo Corridor Initiative aims to connect formally protected areas in a conservation corridor from the coastal area of the Eden District near Plettenberg Bay, Western Cape, South Africa to the Addo National Elephant Park, Eastern Cape, South Africa. The corridor will incorporate government and privately owned land, and will be an attempt to maintain ecological processes at a range of spatial and temporal scales. The Langkloof Valley lies between the Baviaanskloof World Heritage Area and the Tstitsikamma National Park; two formally protected areas that will be incorporated into the Eden To Addo Corridor. Spatial prioritization analyses allow conservation planners to select areas that should be targeted for conservation action based on a range of criteria. Historically, ecological criteria have been included mostly alone in spatial prioritization. Recently, the idea of ‘conservation opportunity’ has emerged in the field of conservation planning; the notion suggests that a range of different types of data should be included in processes to spatially prioritise for conservation. By including those data defined as ‘human’ and ‘social’ data into prioritising activities, the feasibility of conservation plans can be accounted for, but historically conservation planners have failed to do so. I conducted a literature review that demonstrated that although the importance of human and social data are acknowledged in the conservation planning literature, these data that define opportunity are rarely actually included in spatial prioritisation analyses. I then carried out a social assessment that allowed me to define the social and human context of our study area and, specifically, what stewardship instruments land managers in the Langkloof would be prepared to engage. We found that land managers were generally willing to engage, but lacked the financial capacity to adopt conservation methods. Using a subset of the social and human data that were collected in the social assessment, I trialled a new Decision Support Software to fuse those data with ecological data in a novel attempt to identify priority areas for conservation action based on ecological integrity and feasibility. We also scheduled (ranked) land managers to approach for conservation action with a focus on local champions and clusters of land managers displaying strong conservation characteristics. Two corridors were identified; a major corridor in the western region of the valley and a secondary corridor closer to the middle. The members of the Initiative have been briefed on the outcomes, which provided them an opportunity to provide feedback; it is hoped that the framework of this study can be used for planning future connections. The Eden To Addo Corridor Initiative sent out a stewardship extension officer in February 2011 to approach those land managers areas that were identified. This planning exercise is a good demonstration of how, by collaborating effectively, academic conservation planners can contribute to supporting decision making by organizations that are implementing conservation action.
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- Date Issued: 2011
OVR : a novel architecture for voice-based applications
- Authors: Maema, Mathe
- Date: 2011 , 2011-04-01
- Subjects: Telephone systems -- Research , User interfaces (Computer systems) -- Research , Expert systems (Computer science) , Artificial intelligence , VoiceXML (Document markup language) , Application software -- Development
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4671 , http://hdl.handle.net/10962/d1006694 , Telephone systems -- Research , User interfaces (Computer systems) -- Research , Expert systems (Computer science) , Artificial intelligence , VoiceXML (Document markup language) , Application software -- Development
- Description: Despite the inherent limitation of accessing information serially, voice applications are increasingly growing in popularity as computing technologies advance. This is a positive development, because voice communication offers a number of benefits over other forms of communication. For example, voice may be better for delivering services to users whose eyes and hands may be engaged in other activities (e.g. driving) or to semi-literate or illiterate users. This thesis proposes a knowledge based architecture for building voice applications to help reduce the limitations of serial access to information. The proposed architecture, called OVR (Ontologies, VoiceXML and Reasoners), uses a rich backend that represents knowledge via ontologies and utilises reasoning engines to reason with it, in order to generate intelligent behaviour. Ontologies were chosen over other knowledge representation formalisms because of their expressivity and executable format, and because current trends suggest a general shift towards the use of ontologies in many systems used for information storing and sharing. For the frontend, this architecture uses VoiceXML, the emerging, and de facto standard for voice automated applications. A functional prototype was built for an initial validation of the architecture. The system is a simple voice application to help locate information about service providers that offer HIV (Human Immunodeficiency Virus) testing. We called this implementation HTLS (HIV Testing Locator System). The functional prototype was implemented using a number of technologies. OWL API, a Java interface designed to facilitate manipulation of ontologies authored in OWL was used to build a customised query interface for HTLS. Pellet reasoner was used for supporting queries to the knowledge base and Drools (JBoss rule engine) was used for processing dialog rules. VXI was used as the VoiceXML browser and an experimental softswitch called iLanga as the bridge to the telephony system. (At the heart of iLanga is Asterisk, a well known PBX-in-a-box.) HTLS behaved properly under system testing, providing the sought initial validation of OVR. , LaTeX with hyperref package
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- Date Issued: 2011
Population assessments of priority plant species used by local communities in and around three Wild Coast reserves, Eastern Cape, South Africa
- Authors: Fearon, Joclyn Joe
- Date: 2011
- Subjects: Plant diversity conservation -- South Africa -- Eastern Cape , Rare plants -- South Africa -- Eastern Cape -- Population viability analysis , Biodiversity -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Conservation of natural resources -- South Africa -- Eastern Cape , Human-plant relationships -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4751 , http://hdl.handle.net/10962/d1007059 , Plant diversity conservation -- South Africa -- Eastern Cape , Rare plants -- South Africa -- Eastern Cape -- Population viability analysis , Biodiversity -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Conservation of natural resources -- South Africa -- Eastern Cape , Human-plant relationships -- South Africa -- Eastern Cape
- Description: The project was initiated by Eastern Cape Parks (ECP) as a request for the construction of inventories of priority species and their population levels inside three nature reserves on the Eastern Cape Wild Coast, South Africa, and to develop a strategic management plan to manage these natural resources in each reserve. Thirty key species were identified by local communities in and around Dwesa-Cwebe, Silaka and Mkambati Nature Reserves through community workshops. For forested areas belt transects of 100 m x 6 m where used. The basal circumference of key tree species within the belt transect was measured as well as the height of saplings (height < 150 m). Tree species were categorized based on densities, size class distribution (SCD) curves and values, and spatial grain. For grassland areas straight transects of 200 m long were used, along which ten 3 m x 3 m quadrates were placed at 20 m intervals. Within each grassland transect the height of herbs or tuft diameter of grasses was recorded and percentage cover estimated. Grassland species were categorized based on density, SCD curves and percentage cover. All species were placed into harvesting categories based on analysed ecological data that was collected in the field. Category 1 species were very rare or not found in the reserve and it was recommended that species be conserved and monitored. Category 2 species had low densities in the reserve indicating declining populations and was suggested that these be monitored and not harvested. Category 3 species had high densities and have potential for harvesting with strict limitations. Category 4 species were most abundant with very high densities and can be harvested within management guidelines. These categories were grouped further using social and ecological data such as harvesting risk, frequency of collection, use value and number of uses. This highlighted which species have conservation priority within each category and a decision can be made as to how intense or limited extraction should be. By incorporating GIS the distribution of each species was looked at and harvesting and non-harvesting zones established to determine where species can be extracted. Monitoring plans must consider the quantity of plant material collected, fire regimes, optimal harvesting rates and harvesting zones, and be able to pick up changes in populations. Also, it is important that the community be involved in conserving and monitoring these species. Adaptive monitoring and management must be used to steer harvesting practices in the Wild Coast reserves. This allows for the development of harvesting practices through ‘learning by doing’, and the evolution of good questions to guide monitoring decisions
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- Date Issued: 2011
Probing the biocompatibility of biomedical interfaces using the Quartz Crystal Microbalance with Dissipation
- Authors: Cromhout, Mary
- Date: 2011
- Subjects: Biomedical materials , Nanostructured materials , Biomedical engineering , Quartz crystal microbalances , Blood proteins , Nanoparticles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4102 , http://hdl.handle.net/10962/d1010660
- Description: The biomedical application of nanotechnology has come into the spotlight, with the promise of ‘personalised’ therapeutics that couple early diagnosis with targeted therapeutic activity. Due to the rapid growth of the biomedical applications of nanoparticles, along with the lack of understanding concerning their interactions with biomolecules, there is a pressing need for the development of standard methods directed at investigating the effect of introducing these unique particles into the human body. The central aim of this research is to establish a platform directed at assessing the biological fate of pioneering therapeutic particulate agents, such as metallophthalocyanines (MPcs) and multi-walled carbon nanotubes (FMWCNTs). In particular, we proposed, that Quartz Crystal Microbalance with Dissipation (QCM-D) technology may be employed to assess the composition of blood protein corona deposited on the therapeutic surface, and subsequently assess the biocompatibility of such particles. The proposed method of protein detection utilises the nanogram sensitivity of QCM-D technology to monitor highly specific antibody-antigen interactions. In particular those interactions which occur when probe antibodies are used to detect adsorbed blood proteins deposited on target particle-modified sensor surfaces. Protein detection analysis was directed toward identification of surface bound human serum albumin, complement factor C3c, and human plasma fibrinogen. Preliminary analysis of generic biomedical surfaces indicated human serum albumin demonstrates a higher binding affinity towards positively charged surfaces (i.e. cysteamine self-assembled monolayer), followed by hydrophobic surfaces. Detection of complement C3c, corresponded with literature, where lower levels were detected on negatively charged surfaces (i.e. mercapto undecanoic acid self-assembled monolayer), and higher levels of more hydrophobic surfaces (i.e. 11-amino undecane thiol self-assembled monolayer). Human plasma fibrinogen was observed to favour hydrophilic over hydrophobic self-assembled monolayer surfaces, which was in accordance with literature. Application of the proposed protein detection method for biocompatibility analysis of target therapeutic molecules, namely metallophthalocyanines and acid functionalised multi-walled carbon nanotubes, demonstrated a dependence on modified-surface film characteristics, such as surface charge and topography with regards to human serum albumin and human plasma fibrinogen analysis representing new insights into their potential biomolecular interactions The highest levels of detected human serum albumin and complement C3c were detected on the GePcSmix-modified surfaces. AlPcSmix-modified surfaces analysis suggested the highest levels of human plasma fibrinogen. Two methods of acid functionalisation were employed, using both nitric and sulphuric acid, and pure nitric acid. A general increase in detected human serum albumin, corresponding with an increase in functionalisation time, was observed. Complement C3c detection suggested an increase in deposited complement C3c, with increasing functionalisation time, when assessing nitric acid functionalised multi-walled carbon nanotubes, and a decrease, with increasing functionalisation time, when assessing nitric and sulphuric acid functionalised multi-walled carbon nanotubes. Analysis of human plasma fibrinogen was inconclusive, as were cytotoxicity experiments utilising MCF-7 cells in the presence of metallophthalocyanine complexes, raising simultaneously important considerations for their application and study. In the first such detailed examination of its kind it was concluded that the proposed method of protein detection, using QCM-D, allows for the rudimentary but rapid means of analysis of select protein corona deposited on particulate biomedical surfaces.
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- Date Issued: 2011
Quantifying crop damage by Grey crowned crane balearica regulorum regulorum and evaluating changes in crane distribution in the North Eastern Cape, South Africa
- Authors: Van Niekerk, Mark Harry
- Date: 2011
- Subjects: Cranes (Birds) -- South Africa -- Eastern Cape , Cranes (Birds) -- Geographical distribution -- South Africa -- Eastern Cape , Cranes (Birds) -- Behavior -- South Africa -- Eastern Cape , Cranes (Birds) -- Food -- South Africa -- Eastern Cape , Corn -- Effect of grazing on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5749 , http://hdl.handle.net/10962/d1005436 , Cranes (Birds) -- South Africa -- Eastern Cape , Cranes (Birds) -- Geographical distribution -- South Africa -- Eastern Cape , Cranes (Birds) -- Behavior -- South Africa -- Eastern Cape , Cranes (Birds) -- Food -- South Africa -- Eastern Cape , Corn -- Effect of grazing on -- South Africa -- Eastern Cape
- Description: Complaints of crop damage by cranes on planted maize in the North Eastern Cape, South Africa, have been increasing since the mid-1990‘s, and in some instances severe losses have been reported. Crop damage by the Grey Crowned Crane Balearica regulorum regulorum near the town of Maclear (31º04´S 28º22´E), has been quantified over two growing seasons, and assessed relative to losses caused by foraging Cape Crows Corvus capensis and other feeding damage assumed to be caused by insects. Twelve fields were selected based on previous patterns of crop depredation. Maize seed in seven of the fields was treated with the chemical ‗Gaucho‘ and five fields were planted with untreated maize. In order to determine the source of losses, twenty quadrats (4 m x 4 m) randomly distributed within each field were visited on average every second day, for a period of up to twenty eight days. Results indicate that seed treatments do act as a deterrent to feeding by both cranes and crows, however crane damage is generally insignificant compared to other sources of damage. My study also reviewed past sightings data of the Grey Crowned Crane in an effort to determine if the conversion of former grassland to plantations in this region may have increased foraging activity in maize fields. The data did not allow for clear-cut conclusions regarding changes in distribution or population trends. Conclusions provide direct input into the management of agricultural areas by enabling landowners to take steps to mitigate crop damage. These mitigation measures may either involve the application of seed treatments, or the planting of low risk crops in high risk areas. Future studies should consider the ppossible detrimental effects of chemical seed treatments on crane biology.
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- Date Issued: 2011
Responses of intertidal macroalgae and associated fauna to interactive processes acting over multiple spatial scales
- Authors: Mostert, Bruce Petrus
- Date: 2011 , 2010-12-01
- Subjects: Biodiversity -- South Africa , Spatial ecology , Marine algae -- South Africa , Marine organisms -- Effect of water pollution on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5890 , http://hdl.handle.net/10962/d1013370
- Description: The decrease of biological diversity from low latitudes near the equator towards high latitudes is one of the most fundamental patterns noted in ecology. These trends have been the subject of numerous terrestrial and marine studies and have caused the proposal of several explanatory hypotheses. No single hypothesis has adequately accounted for these observed trends. Furthermore, large-scale patterns are frequently modified by processes acting at meso- to small-scales. It is imperative to understand the interaction of these processes to elucidate the mechanisms controlling the structure of intertidal assemblages. The main aim of this thesis was to test the influence of multiple processes at a range of spatial scales on biogenic engineers. Biogenic engineers, such as macroalgae, have been reported to be strongly influenced by processes such as grazing, biogeography and upwelling and subsequent effects are expected to be linked to their associated assemblages. I used infaunal assemblages associated with macroalgae as a model system to understand the interactive effects of meso-scale upwelling in conjunction with large-scale factors (regional and biogeographic). Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis, inhabiting different but overlapping home ranges were used in this study. Smaller scale, physical attributes and the associated fauna of these algal species were compared. The effects of meso- to large-scale physical gradients on marine organisms have been investigated in many instances and resultant gradients in physical variables observed. This study was undertaken to investigate morphological trends exhibited by Hypnea spicifera and Champia lumbricalis to compare possible similarities between coastlines and to determine if inferred meso- to large-scale processes influence physical trends in a similar manner despite the coastlines being affected by different hydrodynamic processes. The macroalgae were located in two distinctly different upwelling regimes, Hypnea spicifera on the east and south coasts and Champia lumbricalis on the west coast. Upwelling (delivery of nutrients and primary production) was not found to be an important factor in determining the physical characteristics of macroalgae but there were clear patterns linked to latitude. Mean percentage cover of Hypnea spicifera was positively correlated with distance along the east and south coasts. Mean mass and mean surface area of H. spicifera were, however, negatively correlated with distance from Port St Johns. Mean frond length showed a negative trend but this relationship was not statistically significant. On the west coast, there was a significant increase in mean frond length from north to south for Champia lumbricalis. Mean surface area and mean mass of C. lumbricalis exhibited non-significant negative trends from north to south while there was a non-significant positive trend for mean percentage cover. Following the “Productivity Hypothesis”, these patterns from north to south along the coastlines of South Africa could have important implications for biodiversity associated with these algae. Many previous studies have focussed on the effects of upwelling on species (i.e. effects of nutrients and temperature) but have failed to separate this effect from large scale effects such as biogeography and latitudinal gradients. I tested the influence meso-scale upwelling, large-scale biogeographic processes and latitudinal gradients with two different species of macroalgae one on the east and south coasts of South Africa and the other on the west coast. Hypnea spicifera inhabits the east and south coasts of South Africa spanning two biogeographic provinces and is generally affected by relatively weak upwelling, whereas Champia lumbricalis inhabits the west coast spanning one biogeographic province which is subjected to intense persistent upwelling year round. Within the east and west coast biogeographic provinces there are, however, regions with both upwelling and non-upwelling. On the east and south coasts, entire assemblages differed significantly among the three Regions (St Lucia, Port Alfred and Knysna, while assemblages between upwelling/non-upwelling areas were not different. Assemblages on the different shores differed significantly from each other. There were no significant effects of region or upwelling for the number of individuals of Crustacea or Polychaeta, while Mollusca showed a significant effect of region. The number of individuals of other taxa showed a significant interaction of region and upwelling. Region had a significant effect on number of species of molluscs and other taxa, while there was no effect for either region or upwelling for the Crustacea or Polychaeta. In general different factors were shown to be important (region and shore) while upwelling was rarely important. On the west coast assemblages associated with C. lumbricalis were not influenced by region or upwelling but there were significant differences between shores. Region, upwelling ad shore did not affect number of individuals. There was a significant interaction of region and upwelling for the number of species of crustaceans, while numbers of species of Mollusca, Polychaeta and other taxa showed no effects. In general, regional factors strongly influenced most organisms, while upwelling played a minor role. Hypotheses about differences between upwelling and non-upwelling regions in terms of species abundances and composition due to the input of cold nutrient rich water were not supported. A link between the effects of larger-scale biogeographic factors and their influence on habitat forming taxa and the resultant effects on associated infauna would be a likely explanation for the patterns observed in this study. Diversity of assemblages is known to be influenced by the structural complexity of a habitat, increasing complexity increases the amount of available niches therefore potentially increasing the number of species found within that habitat. Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis were selected on the basis of being structurally similar and having their distributional ranges overlap in order to elucidate the effects of structure and macroalgal species on associated assemblages. Hypnea spicifera is different in terms of surface area and biomass from Champia lumbricalis and Bifurcaria brassicaeformis. Assemblages of species found on the three rhodophytes showed both shore and the species of alga had significant effects on composition. Only numbers of individuals of molluscs were affected by the species of alga. Crustacea and Polychaeta showed an interaction of the species of alga with shore. In the case of this study, it is likely that the three species of macroalgae mitigate biological stressors such as predation and physical stressors such as wave exposure and desiccation. In general, meso-scale upwelling is suggested to be marginalised when considering the structuring of assemblages associated with macroalgae, while large scale biogeography has more of an influence. Within shores, assemblages were also strongly influenced by smaller-scale factors such as differences in the structure and species of alga. This study indicates the importance of investigating patterns across a range of spatial scales to gain a comprehensive understanding of factors influencing intertidal organisms.
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- Date Issued: 2011
Solid-phase extraction based sample preparation for the determination of drug and organic pollutant residue
- Authors: Pule, Bellah Oreeditse
- Date: 2011 , 2011-02-08
- Subjects: Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4406 , http://hdl.handle.net/10962/d1006711 , Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Description: This thesis presents solid phase extraction (SPE) methodologies based on mixed-mode polymeric sorbents; a mixed mode strong anion exchanger (Agilent SampliQ SAX) and a mixed mode strong cation exchanger (Agilent SampliQ SCX). Furthermore, dispersive-SPE based on a quick, easy, cheap, effective, rugged and safe (QuEChERS) method was assessed for applicability in the determination of drug residues. The mixed-mode polymeric sorbents were evaluated for the simultaneous fractionation of drugs that exhibit diverse polarities with acidic, basic and neutral functionalities in biological matrices (plasma and urine). The polymeric skeleton of these sorbents entails an exchanger group and therefore provides two retention mechanisms, strong cation or anion exchange retention mechanisms with hydrophobic interactions. It was demonstrated that with a sequential elution protocol for sample clean-up analytes were fractionated into acidic, basic and neutral classes. The SAX was employed for analysis of ketoprofen, naproxen (acidic drugs), nortriptyline (basic) and secobarbital (neutral) from urine sample. The SCX was used for fractionating phenobarbital, p-toluamide (acidic), amphetamine, m-toluidine (basic) and acetaminophen (neutral drug) from plasma sample. QuEChERS method was employed for quantitative determination of 16 polycyclic aromatic hydrocarbons (PAHs) from fish fillets and soil; 9 sulfonamides (SAs) from chicken muscles and acrylamide (AA) in cooking oil. The analyte recoveries ranged from 79.6 - 109% with RSDs ranging from 0.06 - 1.9% at three different fortification levels. Good linearity (r2 > 0.9990) was attained for most analytes. The limits of detection and quantification ranged from 0.03 - 0.84 μg/ml and 0.81 - 1.89 μg/ml respectively for analytes in biological samples. LODs and LOQs for analytes in food and environmental samples ranged from 0.02 to 0.39 and 0.25 to 1.30 ng/g respectively.
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- Date Issued: 2011
SphereZyme (TM) technology for enhanced enzyme immobilisation application in biosensors
- Authors: Molawa, Letshego Gloria
- Date: 2011
- Subjects: Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3989 , http://hdl.handle.net/10962/d1004048 , Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Description: Self-immobilisation enzyme technologies, such as SphereZyme™, suffer from the lack of applicability to hydrolyse large substrates. Solid support immobilisation is usually a method of choice, to produce a stable biocatalyst for large substrates hydrolysis in the industry. In order to investigate this limitation, a commercial protease called Alcalase® was chosen as a model enzyme due to its natural activity (hydrolysis of large substrates-proteins). Prior to immobilising through the SphereZyme™ technology, Alcalase® was partially purified through dialysis followed by CM Sepharose™ FF cation exchanger. Sample contaminants, such as salts and stabilisers can inhibit protein crosslinking by reacting with glutaraldehyde. Alcalase® was successfully separated into 3 proteases with the major peak correlating to a positive control run on native PAGE, indicating that it was likely subtilisin Carlsberg. A 16% alkaline protease activity for azo-casein hydrolysis was retained when 5% v/v PEI: 25% v/v glutaraldehyde solution was used as a crosslinking agent in Alcalase® SphereZyme™ production. An increase in activity was also observed for monomeric substrates (PNPA) where the highest was 55%. The highest % activities maintained when 0.33 M EDA: 25% v/v glutaraldehyde solution was initially used as crosslinking agent were 4.5% and 1.6% for monomeric and polymeric substrates, respectively. PEI is a hydrophilic branched polymer with an abundance of amine groups compared to EDA. A comparison study of immobilisation efficiencies of SphereZyme™, Eupergit® and Dendrispheres was also performed for large substrate biocatalysis. The two latter technologies are solid-support immobilisation methods. Dendrispheres reached its maximum loading capacity in the first 5 minute of the one hour binding time. Twenty minutes was chosen as a maximum binding time since there was constant protein maintained on the solid support and no enzyme loss was observed during the 1 hour binding time. PEI at pH 11.5, its native pH, gave the highest immobilisation yield and specific activity over the PEI pH range of 11.5 to 7. SphereZyme™ had the highest ratio for azocasein hydrolysis followed by Dendrispheres and Eupergit®. The SphereZyme™ was also shown to be applicable to biosensors for phenol detection. Different modifications of glassy carbon electrode (GCE) were evaluated as a benchmark for the fabrication of SphereZyme™ modified phenol biosensor. GCE modified with laccase SphereZyme™ entrapped in cellulose membrane was the best modification due to the broad catechol range (<0.950 mM), high correlation coefficient (R2, 0.995) and relative high sensitivity factor (0.305 μA.mM-1). This type of biosensor was also shown to be electroactive at pH 7.0 for which its control, free laccase, lacked electroactivity. From the catalytic constants calculated, GCE modified with laccase SphereZyme™ entrapped in cellulose membrane also gave the highest effectiveness factor (Imax/Km app) of 1.84 μA.mM-1. The modified GCE with Alcalase® SphereZyme™ was relatively more sensitive than GCE modified with free Alcalase®.
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- Date Issued: 2011
Studies in South African marine molluscan chemistry
- Authors: Bromley, Candice Leigh
- Date: 2011
- Subjects: Mollusks -- South Africa , Marine invertebrates -- South Africa , Marine metabolites -- South Africa , Chemical oceanography -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4356 , http://hdl.handle.net/10962/d1005021
- Description: This thesis investigates the variability occurring in the secondary metabolites produced by three South African marine molluscs. Chapter Two discusses the isolation and spectroscopic structure elucidation of the metabolites isolated from two Siphonaria species. The re-investigation of Siphonaria capensis yielded siphonarienfuranone (2.2) as the only common polypropionate isolated from both the 1998 and 2009 collections of S. capensis from the same areas suggesting possible seasonal or genetic variation in polypropionate production. The sterol cholest-7-en-3,5,7- triol (2.33) was also isolated form the 2009 collection of S. capensis and this is the first time this compound has been isolated from a Siphonaria species. The second species, Siphonaria oculus is closely related to S. capensis and the investigation into the former’s secondary metaboliteproduction revealed 2.2 as a major metabolite suggesting an inter-species overlap in polypropionate production. Three new polypropionate metabolites, 2.35, 2.36 and 2.37 were also isolated from S. oculus. An unsuccessful attempt was made to establish the absolute configuration of 2.37 using the modified Mosher’s method and the limited amount of 2.37 available prevented any further attempts at resolving the absolute configuration of this compound. The 1H NMR analysis of the defensive mucus collected directly from S. oculus revealed the presence of the acyclic polypropionate 2.37 as a minor metabolite. The absence of characteristic signals for the furanone containing compounds 2.2, 2.35 and 2.36, might suggest that these compounds cyclise from a hypothetical acyclic precursor (2.38) during standard work up of bulk acetone extracts of Siphonaria species. Chapter Three discusses the re-isolation and spectroscopic structure elucidation of the metabolites isolated from the nudibranch, Leminda millecra. Three known natural products, millecrone A (3.1), 8-hydroxycalamenene (3.6) and cubebenone (3.8) were re-isolated from our 2010 collection of L. millecra, as well as the new minor metabolite 8-acetoxycalamenene (3.16). The cytotoxic prenylated toluquinones and toluhydroquinones (3.9-3.15) initially isolated from the 1998 collection of L. millecra were not found in the 2010 collection supporting the hypothesis that these compounds may be of fungal origin. L. millecra clearly shows variability in the compounds sequestered by this species with millecrone A (3.1) being the only common metabolite in the three investigations of L. millecra to date. An unsuccessful attempt was made to establish the absolute configuration of 3.1, 3.6 and 3.8 through initial LAH reduction of the ketone moiety contained in 3.1 and 3.8 and esterification of the resultant diastereomeric alcohol mixtures and the phenol functionality in 3.6 with (1S)-camphanic chloride. Crystallisation of the (S)- camphanate esters of 3.6 and 3.8 for X-ray analysis were unsuccessful, while the unexpected conjugate addition of a hydride in 3.1 resulted in complex diastereomeric mixtures which could not be separated by HPLC.
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- Date Issued: 2011