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Synthesis, properties and reactions of Novel Quinone Methides

  • Authors: Taljaard, Jana Heloïse
  • Date: 2007
  • Subjects: Quinone , Chemistry, Organic
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:10408 , http://hdl.handle.net/10948/616 , Quinone , Chemistry, Organic
  • Description: Novel p-quinone methides have been synthesized by the dealkylation of 5-(p-alkyloxyaryl)- 10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-ols and related compounds. Aspects of the dealkylation reaction were investigated using computational methods in order to identify possible intermediates and postulate reasons for the observed reactivity patterns. This included studying the effect of varying the size of the central B-ring, changing the alkyloxy group, and altering the substitution pattern on the parent alcohols. We have assessed the relative energies of reaction intermediates and have also evaluated the influence of factors such as charge delocalisation, LUMO properties of the carbocations and thermodynamic factors on the dealkylation reaction. The use of different dealkylating reagents was also briefly investigated. Demethylation of 1,3- dimethyl-11-(4-methoxyphenyl)-6,11-dihydrodibenzo[b,e]oxepin-11-ol with pyridine hydrochloride led to acid-catalyzed ring-contraction of the parent alcohol to form a novel substituted anthraquinone, 9-(4-hydroxyphenyl)-1,3-dimethyl-anthracen-10-(9H)-one, in good yield. The general reactivity of the p-quinone methides of interest to us was explored by subjecting these compounds to reaction with a range of nucleophiles (bases, Grignard reagents and alcohols). A range of aryl Grignard reagents were reacted with the p-quinone methides, with the main product isolated in almost all cases being the aryl-coupled 1,2-addition product. The nucleophilic addition reactions of alcohols were supported by a computational study and a probable reaction mechanism has been postulated. A base-catalyzed rearrangement is proposed to account for the formation of products in which dehydrogenation of the ethane bridge was observed. These studies showed that in these p-quinone methides, chemical reactivity is strongly influenced by steric crowding, resulting in reversal of the normal 1,2- vs. 1,6- selectivities expected for nucleophilic addition. The ketalization process was explored further using diols and thiols. Products analogous to those obtained with the monohydric alcohols resulted from the diols, along with a series of novel bis-ethers. A range of miscellaneous reactions of 4-(dibenzo[a,d]cycloheptan-5-ylidene)cyclohexa-2,5,- dienone and related systems were investigated. Functionalization by epoxidation, dichlorocarbenation and Diels-Alder reactions, photochemical and [2+2] cycloaddition were attempted and reduction and oxidation reactions were also explored. Photochemical demethylation of an ortho-methoxyl substituent on the p-quinone methide system was observed to occur in good yield. The p-quinone methides underwent reductive coupling in the presence of Zn/AlCl3. The electronic spectra of highly conjugated carbocations were obtained and their potential as novel dyes evaluated. A low-temperature Grignard exchange reaction followed by spontaneous cyclization upon workup, was successful in synthesizing the lactone, spiro[10,11- dihydro-5H-dibenzo[a,d]cyclohepten-(3’,4’H)-phenyl-5,2’(5’H)-furan-5’-one], in one step from the starting ketone. A novel seven-membered Malachite Green dye analogue, 11-(4- dimethylamino-phenyl)-3-morpholin-4-yl-6,11-dihydro-dibenzo[b,e]oxepin-11-ol, was also synthesized and its electronic spectra compared to that of the unannulated Malachite Green dye series. All novel compounds synthesized were characterized using NMR, IR and HRMS-analysis.
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  • Date Issued: 2007

The community structure and feeding ecology of the ichthyofauna in the Mngazana and Mngazi estuaries, Port St. Johns, South Africa

  • Authors: Grant, Walter Lawrence
  • Date: 2007
  • Subjects: Estuarine fishes -- South Africa -- Eastern Cape , Fish communities -- South Africa -- Eastern Cape , Estuaries -- South Africa -- Eastern Cape
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10713 , http://hdl.handle.net/10948/513 , http://hdl.handle.net/10948/d1012017 , Estuarine fishes -- South Africa -- Eastern Cape , Fish communities -- South Africa -- Eastern Cape , Estuaries -- South Africa -- Eastern Cape
  • Description: The Mngazana and Mngazi estuaries are situated just south of Port St. Johns close to the biogeographical boundary between the warm temperate and subtropical zones along the east coast of Southern Africa. The Mngazana estuary is a permanently open estuary with three species of mangrove. The Mngazi estuary is a temporarily open/closed system. The ichthyofauna was sampled with seine nets and gillnets during June 2005, August 2005, November 2005, February 2006 and April 2006. The fish community structure was significantly different between the two estuaries with the differences being especially noticeable in the larger fish sampled with gillnets. There were significant differences in the fish community sampled with the seine net on both spatial and temporal scales in both of the estuaries. Certain warm temperate species were less abundant and certain subtropical species were more abundant at the Mngazana estuary than they were during a study conducted in 1975. Stomach content analysis revealed that most species had similar diets in the two estuaries with the only differences occurring among benthic feeding species. The diet of sub-adult piscivores comprised of a large proportion of penaeid prawns while the juveniles feed mainly on mysids. The zooplanktivorous fish feed mainly on copepods and mysids with the proportions varying between the species. Benthic feeding fishes showed the greatest variability in diet with plant material, detritus, crabs and copepods being the main food sources. Stable isotopes revealed that particulate organic matter and microphytobenthos were the most important carbon sources to fish in the Mngazi estuary. In the Mngazana estuary a combination of mangrove material, detritus, particulate organic matter and Zostera material were the most important carbon sources. The importance of each of these sources did, however, vary greatly between the different trophic guilds of the fish in the Mngazana estuary. The distribution of certain fish species was investigated in relation to physical parameters (temperature, salinity, turbidity and depth) and biological parameters (prey and predators) in the environment. It was found that most small fish (< 100 mm SL) were strongly correlated with turbidity where-as they showed weak correlations with their prey. Sub-adult piscivores fell into two groups, i.e. those that could tolerate turbid water and those that were only found in clear water. The group that also occurred in turbid water showed very strong correlations with their prey but the clear water group did not. It would appear that the small and thus vulnerable fish seemed to occur in areas that offered them protection rather than areas where their food supply is most abundant, where-as the piscivores were more influenced by prey distribution, as long as the physical conditions were tolerable to them.
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  • Date Issued: 2007

The electrochemical synthesis of 3-tert-Butyl-4-Methoxybenzaldehyde

  • Authors: Qusheka, Sivuyile Emmanuel
  • Date: 2007
  • Subjects: Oxidation
  • Language: English
  • Type: Thesis , Masters , MTech
  • Identifier: vital:10410 , http://hdl.handle.net/10948/595 , Oxidation
  • Description: This project was concerned with the evaluation of three potential synthetic routes for 3-tert-butyl-4-methoxybenzaldehyde, a useful fine chemical intermediate and ingredient in many sunscreen agents. The three synthetic routes all involved the selective oxidation of the 3-tert-butyl-4-methoxytoluene to the desired benzaldehyde by (a) catalytic air oxidation, (b) direct electrochemical oxidation, and (c) indirect electrochemical oxidation. In order to decide whether catalytic oxidation should precede the alkylation of 4-methoxytoluene, the selective oxidation using the well-known cobalt(II)- bromide catalyst system in acetic acid solutions were investigated with the view to determine whether increased electron density on the aromatic ring improves selectivity to the desired benzaldehyde or not. In addition, the effect of various important reaction variables was also investigated. These studies showed that increased electron density, hence increased substitution, increases the desired benzaldehyde selectivity. In addition, while reaction conditions such as reaction temperature, catalyst concentration, water concentration, etc. may be optimised for maximum 3-tert-butyl-4- methoxybenzaldehyde yields (~80 percent), such yields can only be achieved at relatively low (<40 percent) alkoxytoluene conversions. The direct electrochemical oxidation of 3-tert-butyl-4-methoxytoluene was investigated in methanol solutions containing various supporting electrolytes and using constant current electrolysis with the intention of optimizing the production of 3-tert-butyl-4-methoxybenzyl dimethyl acetal which can later be hydrolyzed using sulfuric acid to the 3-tert-butyl-4-methoxybenzaldehyde. In this study, various parameters such as supporting electrolyte and electrodes were studied. Previous studies showed undoubtedly that methanol as a solvent gave better results amongst the rest of the solvents. Indirect route was also studied as a method of synthesizing 3-tert-butyl-4- methoxybenzaldehyde and compared to the direct electro synthesis.
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  • Date Issued: 2007

The evaluation of a pedagogical-program development environment for Novice programmers : a comparative study

  • Authors: Vogts, Dieter
  • Date: 2007
  • Subjects: Computer programming -- Study and teaching , Programming languages (Electronic computers) , Web site development
  • Language: English
  • Type: Thesis , Doctoral , DPhil
  • Identifier: vital:10477 , http://hdl.handle.net/10948/638 , Computer programming -- Study and teaching , Programming languages (Electronic computers) , Web site development
  • Description: It is an acknowledged fact that many novice programmers experience difficulty in the process of learning to program. One of the contributing factors to this difficulty is the Program Development Environment (PDE). Professional-PDEs are those developed specifically for professional programmers, but are often used by educational institutions in the instruction of programming. It has long been accepted that such environments are inappropriate in the instruction of programming due to unnecessary complexity and lack of support for novice programmers in the learning process. Numerous pedagogical-PDEs supporting the mechanics of programming have been developed in response to this. A review of literature, however, indicates that very limited empirical studies comparing pedagogical-PDEs and professional-PDEs have been conducted. The current study investigates whether there are measurable benefits to using a pedagogical-PDE supporting the mechanics of programming in the instruction of programming instead of a professional-PDE. A comparative study of this nature requires a representative pedagogical-PDE and representative professional-PDE be compared with one another. The first part of the current study determines a set of requirements that a pedagogical- PDE should adhere to based on literature. A set of representative features for a pedagogical-PDE is derived by examining the features of existing PDEs in conjunction with the set of requirements. Based on these features, a pedagogical-PDE, known as SimplifIDE, is developed that implements the representative set of features and that meets are the requirements for a pedagogical-PDE. The second part of the current study is the specification and administration of an empirical experiment in which SimplifIDE and Borland© DelphiTM are compared with one another. A holistic approach in determining the differences between the PDEs is taken and three main areas are examined, namely academic performance, perceptions and programming behavior.
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  • Date Issued: 2007

The kinetics and associated equilibria of high oxidation state osmium complexes

  • Authors: McFadzean, Belinda Julie
  • Date: 2007
  • Subjects: Chemical equilibrium , Osmium , Chemical kinetics , Chemistry
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:10371 , http://hdl.handle.net/10948/732 , Chemical equilibrium , Osmium , Chemical kinetics , Chemistry
  • Description: The reduction of osmium tetroxide by a series of alcohols was studied spectrophotometrically. The reaction was observed to occur in two steps, unlike previously reported studies on this reaction. The identities of both reactants and products were established via a range of techniques. Equilibrium and kinetic data were gathered and reaction models were evaluated using equilibrium and kinetic modelling software. The following complexation reaction model emerged that simulates both the equilibrium and kinetic data. Os(VIII) + RCH2OHOs(VI) + RCHO2 Os(VIII) + Os(VI)k+2k1Complexk-2 Conditional rate constants and equilibrium constants were generated. Rate constants for the alcohol reactions were correlated with the Taft σ* constant. The ρ* value obtained (-1.4) is consistent with a hydride transfer mechanism coupled with synchronous removal of the hydroxyl proton. The identity of the osmium(VIII)-osmium(VI) complex has been suggested. Thermodynamic parameters were also reported. The rate constants for benzyl alcohol and 2-chloroethanol deviated from those predicted by the Taft plot. An explanation of enhanced resonance effects is offered for benzyl alcohol and an alternative reaction mechanism, involving proton abstraction, is offered for 2-chloroethanol. The reaction of the oxidation products of alcohols, namely ketones, with osmium tetroxide produced rate constants that were, perhaps surprisingly, far larger than those of the alcohols. A reaction mechanism for the oxidation of the ketones is suggested, which involves the enolate ion as the reactive starting reagent.
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  • Date Issued: 2007

The role of pacC in Aspergillus flavus

  • Authors: Suleman, Essa
  • Date: 2007
  • Subjects: Fungi -- Biotechnology , Pathogenic microorganisms
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10332 , http://hdl.handle.net/10948/612 , Fungi -- Biotechnology , Pathogenic microorganisms
  • Description: Many microorganisms, and in particular fungi, are able to grow over a wide pH range. Thus, these microorganisms must possess some regulatory mechanism or system that senses the environmental pH signal and ensures that gene expression of certain molecules is tailored to the pH of the environment (Penalva and Arst, 2002). In Aspergillus species and several other fungi, pH regulation is mediated by seven genes viz. palA, palB, palC, palF, palH, palI and the global pH regulatory gene, pacC (MacAbe et al, 1996; Negrete-Urtasun, 1999; Denison, 2000). The activated form of the PacC protein activates genes that are required at alkaline pH, e.g. genes coding for alkaline phosphatases, and represses certain genes that are functional at acidic pH, e.g. genes encoding acid phosphatases (Negrete-Urtasun, 1999). PacC (and its homologues) also positively regulates genes involved in penicillin biosynthesis, e.g. the isopenicillin N synthase gene, ipnA, in A. nidulans (Penalva and Arst, 2002). It has also been hypothesised that pacC may negatively regulate aflatoxin biosynthesis, a carcinogenic secondary metabolite in several species of Aspergillus (Keller et al, 1997). To elucidate the role of pacC a novel method of post-transcriptional gene silencing known as RNA interference was utilized. This method involved the cloning of a partial pacC gene fragment first in the forward and then the reverse orientations in a fungal expression cassette to create an RNA interference (RNAi) vector. The unique structure of this vector would allow the cloned fragments to be expressed and the resulting RNA to immediately form a double stranded stem-loop structure or short hairpin RNA (shRNA; McDonald et al, 2005). The formation of this shRNA, in turn, would be responsible for activating the endogenous RNA degradation complexes that would lead to mRNA degradation and subsequent gene silencing (Liu et al, 2003; Kadotoni et al, 2003; McDonald et al, 2005). The results presented here have shown that confirmed pacC RNAi mutants produced aflatoxins irrespective of environmental pH (i.e. the mutants produce aflatoxins under acidic and alkaline conditions). Thus, pacC is essential for pH regulation of aflatoxin production in A. flavus. There are numerous other biological (e.g. presence of oxylipins, lipooxygenases) and non-biological factors (pH, carbon source etc.) which affect maize colonisation and aflatoxin production by A. flavus (Burrow et al, 1996; Wilson et al, 2001; Calvo et al; 2002; Tsitsigiannis et al, 2006). However, all the genetic mechanisms involved have as yet not been identified. It has been shown by Caracuel et al (2003) that pacC acts as a negative virulence regulator in plants and these workers have hypothesised that PacC prevents expression of genes that are important for infection and virulence of the pathogen. Therefore the physiological effects that pacC silencing had on the growth, conidiation and pathogenicity of A. flavus mutants were also investigated. The results of this study showed that pacC does not play a significant role in primary growth and development but does affect conidial production. SEM results showed that mutants have many “open ended” phialides and poorly developed conidiophores. This would suggest that pacC activation of conidial production genes is also required. Furthermore, pacC RNAi silencing severely impaired the ability of the A. flavus mutants to infect and cause damage on maize. The results obtained here are similar to that of pacC null mutants in A. nidulans, C. albicans and F. oxysporum which also exhibited low pathogenicity (Davis et al, 2000; Fonzi, W.A, 2002; Caracuel et al, 2003; Bignell et al, 2005 and Cornet et al, 2005). This study indicates that pathogenicity of A. flavus on maize is directly related to the structural integrity of conidia, which in turn is greatly influenced by PacC. This gene is a global transcriptional regulator and may either repress or activate one or many genes in each of the above pathways (Penalva and Arst, 2002). Studies on the genetic mechanisms of pacC regulation on these pathways are needed to elucidate the mechanisms of activation or repression of these genes.
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  • Date Issued: 2007

The use of thermal modelling in improving rural subsistence aquaculture

  • Authors: Bailey, Dylan Francis
  • Date: 2007
  • Subjects: Sustainable aquaculture -- South Africa , Aquaculture industry -- South Africa
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10715 , http://hdl.handle.net/10948/473 , Sustainable aquaculture -- South Africa , Aquaculture industry -- South Africa
  • Description: There has been a long history of attempts to promote subsistence rural aquaculture within South Africa. Many of these attempts have failed due to inadequate support from government and support agencies. There has been a recent revived interest in promoting rural aquaculture development. Presented in this project are six scenarios demonstrating the potential application of thermal modelling techniques to improving subsistence rural aquaculture. These scenarios were based on a model validated against a real life system, and run with environmental data for the year 2005. Bovine manure, grass thatch, cereal straw and Typha spp. water reeds were tested for thermal performance. These results were then applied to the scenarios. The open and kraal enclosed pond scenarios yielded the widest deviation in temperatures throughout the year, with an average temperature of 3.8oC and 6.0oC above ambient and a temperature range of 10.6oC and 12.4oC for the year respectively. Eliminating solar radiation and reducing wind speed resulted in an average difference of 1.5oC below ambient and a temperature range of 7.5oC for the year. When completely enclosed in a well-sealed traditional Xhosa style hut, the pond had an average difference of 5.6oC below outside ambient temperature, with a range of 7.8oC for the year. A passive solar heating scenario added to the sealed hut scenario, which when run continuously maintained an average difference of 34.7oC above outside ambient temperatures, with a range of 56oC for the year. When a hypothetical 25oC temperature control was included in the model, the system maintained an average of 7.1oC above ambient outside temperatures, with a temperature range of 0.8oC throughout the year. The wider range of temperatures made available through the use of thermal modelling approaches provides a more diverse range of species available for subsistence rural aquaculture at any site, significantly improving its potential.
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  • Date Issued: 2007

The zooplankton of Mngazana estuary

  • Authors: Louw, Liezel
  • Date: 2007
  • Subjects: Marine zooplankton -- South Africa -- Mngazana Estuary , Mngazana Estuary (Eastern Cape, South Africa) , Estuarine ecology -- South Africa -- Mngazana Estuary , Estuarine area conservation -- South Africa -- Mngazana Estuary
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10707 , http://hdl.handle.net/10948/702 , Marine zooplankton -- South Africa -- Mngazana Estuary , Mngazana Estuary (Eastern Cape, South Africa) , Estuarine ecology -- South Africa -- Mngazana Estuary , Estuarine area conservation -- South Africa -- Mngazana Estuary
  • Description: The zooplankton community of the main channel of the Mngazana estuary was investigated on six occasions over one year. Spatial and temporal variability in zooplankton abundance and distribution were sampled using two slightly modified WP2 plankton nets of 200 μm mesh and 57 cm mouth diameter. Nets were fitted with calibrated Kahlsico 005 WA 130 flow meters. A set of environmental variables were also measured at each site. The water column of the main channel of Mngazana estuary was stratified in summer but well mixed in winter. Temperature progressively increased from the lower stations to the upper reaches of the estuary. Maximum vertical temperature differences occurred in the middle estuarine reaches. Salinity progressively decreased from the lower reaches to the upper reaches, but was generally above 26 from Station 3 to Station 8. Only during November 2005, were salinity readings low due to heavy rains. Summer salinity values were always lower than the winter salinity values as a result of summer rainfall. A total of 76 zooplankton taxa were identified. The estuarine copepods Acartia natalensis and Pseudodiaptomus hessei dominated the assemblage, with maximum abundances in the middle to upper reaches. Acartia natalensis reached high densities in winter (> 50 000 m-3) although lowest abundances were recorded when maximum rainfall was received (November 2005). Wooldridge (1977) and Deyzel (2004) recorded maximum densities during summer. Pseudodiaptomus hessei reached high densities (> 17 000 m-3) during the highest rainfall month. Previous studies indicated that this pioneer species is able to recover quickly after a flood and subsequently increase rapidly in numbers. The mysid, Mesopodopsis africana reached high densities (> 5 000 m-3) in the middle estuarine reaches during summer. Ichtyofauna, brachyura and anomura were important contributors to the merozooplankton component of the community. The maximum number of species was recorded during winter in the lower estuarine reaches, when vertical differences in salinities were minimal.
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  • Date Issued: 2007

Towards knowing through doing : improving the societal relevance of systematic conservation assessments

  • Authors: Knight, Andrew Thomas
  • Date: 2007
  • Subjects: Conservation of natural resources -- Planning , Nature conservation -- South Africa
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:10598 , http://hdl.handle.net/10948/711 , Conservation of natural resources -- Planning , Nature conservation -- South Africa
  • Description: Systematic conservation assessments are spatially-explicit techniques for prioritising areas for the implementation of conservation action. There has been considerable reference in the peer-reviewed literature as to the usefulness of these tools, which appear to be primarily used by academics for theoretical research. A literature review and author survey reveals the peer-reviewed literature is largely theoretical, although conservation action results more frequently than reported. The effectiveness of these interventions is generally described as only ‘fairly effective’. This general trend, coupled with previous personal failures in translating systematic conservation assessments into effective conservation action triggered an explicit process of social learning implemented as action research. It examined the workings of the Subtropical Thicket Ecosystem Planning (STEP) project, which included development of a systematic conservation assessment. Systematic conservations assessments simply provide information on where action should be implemented, and so are only useful if situated within broader operational models for conservation planning. Most operational models presented in the peer-reviewed literature are primarily focused upon the testing ecological data, not upon the delivery of conservation action. A new operational model for conservation planning is presented which more accurately reflects the ‘real-world’ process of conservation planning. An implementation strategy is an essential complement to a systematic conservation assessment. It describes how specific, explicitly-stated goals will be achieved, who is accountable for undertaking these activities, and the resources required. As the Implementation Specialist for the STEP Project, I co-lead the collaborative development of an implementation strategy with stakeholders that aimed to mobilise resources towards achieving common goals. Whilst the development and initial uptake of the strategy was good, subsequent implementation has flounder. The reasons for this are explored. The ultimate pragmatic goal of a conservation planning process is the establishment of effective social learning institutions. These develop common visions, mobilise collective action, and adaptively learn and refine their conservation activities. Thicket Forum is one xi such institution established through the STEP Project. My involvement with Thicket Forum since 2004 in implementing an adaptive learning approach facilitates collaboration between land managers, government and research organisations. Systematic conservation assessments evolved in response to the ad hoc way in which protected areas were implemented, leaving unrepresentative, biased protected area networks. Most research is theoretical and without an intimate understanding of the social-ecological system of a planning region, notably opportunities and constraints for implementing conservation action. Highlighting the importance of an approach which is flexible, not only in space, but in time, which can capitalise upon implementation opportunities, is important for stemming the myth that opportunism is the nemesis of systematic conservation assessments. To this end, conservation planners have been slow to include factors influencing effective implementation in systematic conservation assessments. Many studies which identify candidate protected area networks, first, fail to identify the specific instrument(s) to be applied, and second, assume all intact land is available. Having mapped the willingness of land managers in the Albany District, South Africa, to sell their land, it is demonstrated the majority of targets fail to be achieved because land managers will not sell. Knowing this, the current focus of gathering ever-more ecological data is misplaced. Human, social and economic factors influence target achievement, efficiency and spatial configuration of priority areas. Selecting important areas for conservation, particularly at the local-scale, requires the mapping of factors which define opportunities for conservation. Land manager willingness to collaborate and participate, entrepreneurial orientation, conservation knowledge, social capital, and local champions were applied using a method of hierarchical clustering to identify land managers who represent conservation opportunities for private land conservation initiatives.
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  • Date Issued: 2007

A comparison framework for server virtualisation systems a case study

  • Authors: Van Tonder, Martin Stephen
  • Date: 2006
  • Subjects: Virtual computer systems -- South Africa Case studies , Virtual storage (Computer science) -- South Africa Case studies
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10481 , http://hdl.handle.net/10948/439 , http://hdl.handle.net/10948/d1012009 , Virtual computer systems -- South Africa Case studies , Virtual storage (Computer science) -- South Africa Case studies
  • Description: Recent years have seen a revival of interest in virtualisation research. Although this term has been used to refer to various systems, the focus of this research is on systems which partition a single physical server into multiple virtual servers. It is difficult for researchers and practitioners to get a clear picture of the state of the art in server virtualisation. This is due in part to the large number of systems available. Another reason is that information about virtualisation systems lacks structure, and is dispersed among multiple sources. Practitioners, such as data centre managers and systems administrators, may be familiar with virtualisation systems from a specific vendor, but generally lack a broader view of the field. This makes it difficult to make informed decisions when selecting these systems. Researchers and vendors who are developing virtualisation systems also lack a standard framework for identifying the strengths and weaknesses of their systems, compared to competing systems. It is also time-consuming for researchers who are new to the field to learn about current virtualisation systems. The purpose of this research was to develop a framework to solve these problems. The objectives of the research correspond to the applications of the framework. These include conducting comparative evaluations of server virtualisation systems, identifying strengths and weaknesses of particular virtualisation systems, specifying virtualisation system requirements to facilitate system selection, and gathering information about current virtualisation systems in a structured form. These four objectives were satisfied. The design of this framework was also guided by six framework design principles. These principles, or secondary objectives, were also met. The framework was developed based on an extensive literature study of data centres, virtualisation and current virtualisation systems. Criteria were selected through an inductive process. The feasibility of conducting evaluations using the framework was demonstrated by means of literature-based evaluations, and a practical case study. The use of the framework to facilitate virtualisation system selection was also demonstrated by means of a case study featuring the NMMU Telkom CoE data centre. This framework has a number of practical applications, ranging from the facilitation of decision-making to identifying areas for improvement in current virtualisation systems. The information resulting from evaluations using the framework is also a valuable resource for researchers who are new to the field. The literature study which forms the theoretical foundation of this work is particularly useful in this regard. A future extension to this work would be to develop a decision support system based on the framework. Another possibility is to make the framework, and evaluations, available on-line as a resource for data center managers, vendors and researchers. This would also enable other researchers to provide additional feedback, enabling the framework to be further refined
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  • Date Issued: 2006

A Hall-effect study of as-grown and hydrogenerated n-type ZnO layers grown by MOCVD

  • Authors: Somhlahlo, Nomabali Nelisiwe
  • Date: 2006
  • Subjects: Hall effect , Electric currents
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10535 , http://hdl.handle.net/10948/444 , http://hdl.handle.net/10948/d1012014 , Hall effect , Electric currents
  • Description: A series of as-grown ZnO layers have been electrically characterised by the temperature dependent (20 – 300 K) Hall-effect technique. The ZnO layers were grown by metal organic chemical vapour deposition (MOCVD) on glass substrates under various growth conditions. The temperature dependent Hall-effect technique produced mobility and carrier concentration measurements. These measurements were found to be reproducible and reliable. The carrier concentration data for the layers was fitted by the charge balance equation to accurately determine the donor level and corresponding donor concentration as well as the acceptor concentration for each sample. The measured donor levels were found to vary from sample to sample and there is evidence from the results that the variations are related to the differing growth conditions of the layers. The mobility data was also fitted to establish the dominant electron scattering mechanisms in the layers. The dominant scattering mechanisms were found to vary from sample to sample. For most of the layers studied, the dominant scattering mechanism was found to be both the ionised impurity scattering at low temperatures (20 – 100 K) and grain boundary scattering at higher temperatures (100 – 300 K). The effects of exposing the ZnO layers to hydrogen plasma were also investigated by the temperature dependent Hall-effect technique. Findings indicate that hydrogen is readily incorporated in ZnO, leading always to an increased carrier concentration. It was further noted that incorporating hydrogen into ZnO in some layers increased the mobility while in other layers it caused a decrease in the mobility. The hydrogenated samples were subsequently annealed at 600 °C for 1 hour in argon ambient resulting in the carrier concentration reducing to its original value. This effect is attributed to hydrogen diffusing out of ZnO.
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  • Date Issued: 2006

A model for information architecture of government web sites in Southern Africa

  • Authors: Bernardo, Tomás
  • Date: 2006
  • Subjects: Information storage and retrieval systems , Web sites -- Design , Government information -- South Africa
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10479 , http://hdl.handle.net/10948/459 , Information storage and retrieval systems , Web sites -- Design , Government information -- South Africa
  • Description: The main purpose of this research is to investigate the Information Architecture (IA) of government web sites in Southern Africa. The government web sites of Mozambique and South Africa were selected for the purpose of this research. A further aim of this research was to derive a model for the IA of government web sites. The model was based on IA components and guidelines as well as on web site components and E-government requirements. The IA guidelines in the model were derived from general design guidelines and guidelines for government web sites. The IA guidelines in the proposed model were used to conduct an analytical and empirical evaluation of the selected sites. The selection of the sites was based on similarities in the Information and Communication Technology (ICT) strategies and policies, the annual Internet growth rates, the Internet user profiles and the Egovernment initiatives in both countries. Differences between the sites also contributed to their selection. Mozambique is one of the least developed countries in the world, while South Africa is one of the most developed countries in Africa. Heuristic evaluation was used for the analytical evaluation while questionnaires and user testing were used for the empirical evaluation. Some of the usability problems identified in the heuristic evaluation, such as incorrect organisation of information and navigation issues, were also identified in the empirical evaluation, confirming to the existence of these usability problems. The results of this research show that the IA of government web sites has an impact on user performance and satisfaction and that the proposed model can be used to design and evaluate the IA of government web sites in Southern Africa.
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  • Date Issued: 2006

A raman spectroscopy study of semiconducting thin films

  • Authors: Goosen, William Edward
  • Date: 2006
  • Subjects: Raman spectroscopy , Semiconductor films , Thin films
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10514 , http://hdl.handle.net/10948/426 , Raman spectroscopy , Semiconductor films , Thin films
  • Description: A home-built Raman system, utilizing a pseudo-backscattering geometry, was built in the Physics Department at the Nelson Mandela Metropolitan University (NMMU). The system was then used to analyse a variety of bulk and thin film semiconducting materials currently being studied in the Physics Department. Silicon wafers were exposed to hydrogen plasma. Raman analysis of hydrogen induced platelets (HIPs), resulting from hydrogen plasma treatment of silicon, is reported. ZnO layers were deposited on glass, GaAs, Si, sapphire and SiC-Si substrates by metalorganic chemical vapour deposition (MOCVD) in the Physics Department at the NMMU. It was found that the ZnO layers grown by MOCVD all exhibited a strong E2 (high) phonon mode that dominated the Raman spectra. Furthermore, the spectra lacked the A1 (LO) phonon mode which is usually associated with the O-vacancy, the Zn-interstitial, or complexes of the two, indicating that the layers were all of good quality. The influence of depositing the ZnO thin film on a 3 mm thick SiC layer was also investigated and compared with the deposition of ZnO on Si substrate, in order to reduce the lattice mismatch between ZnO and the Si substrate. The possible shift of the Raman peaks due to the residual strain in the film, if present, could not be resolved. Characterization of GaN and AlxGa1-xN produced by MOCVD at the CRHEA laboratory of the CNRS in Valbonne, France is reported. A sharp peak at 567 cm-1 corresponding to the E2 (high) mode of GaN broadens and shifts to higher wavenumbers as the aluminium content of the AlxGa1-xN is increased. The shift is accompanied by a decrease in the intensity and a broadening of this peak. The broadening was attributed to a general decrease in the quality of the layers which accompanies increased aluminium content in AlxGa1-xN.
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  • Date Issued: 2006

A structural study of Witteberg group rocks (Cape supergroup) in the Cape fold belt, Steytlerville district, Eastern Cape

  • Authors: Brunsdon, Gideon
  • Date: 2006
  • Subjects: Geology, Structural|zSouth Africa|zEastern Cape , Faults (Geology)|zSouth Africa|zEastern Cape , Folds (Geology)|zSouth Africa|zEastern Cape
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10666 , http://hdl.handle.net/10948/d1019682
  • Description: A structural study of Witteberg Group Rocks was conducted along the Soutkloof River, approximately 14 km east of Steytlerville, Eastern Cape Province of South Africa. Here a north to south geotraverse was studied in an attempt at unravelling the structural geology of the rocks belonging to the Upper Devonian to Lower Carboniferous Witteberg Group (Upper Cape Supergroup). These rocks are mostly arenaceous and include quartzite, sandstone, siltstone and shale which have been folded, faulted and metamorphosed. Thrust, normal and strike-slip faulting occur in the area. Shallow south-dipping low-angle thrust fault planes are displaced by steep south-dipping thrust planes and subordinate north-dipping backthrusts. Displacement along thrust planes is predominantly northwards. Steeply dipping thrust fault planes are often reactivated as east-west striking normal faults. Strike-slip faulting postdates all observed structural features and displaces normal and thrust fault planes. Open to tight folds are present and are mostly northvergent and often steepened or truncated by steep south-dipping thrust fault planes. South-vergent folds are related to backthrusting and post-fold faulting. The study has revealed that the current geological map and the local stratigraphy were compiled without recognising major structural features such as thrust, normal and strike-slip faulting and their (the map and currently accepted stratigraphy) validity are therefore questioned. The presence of extensive faulting suggests that the conventional stratigraphic interpretation of the Witteberg Group should be revised.
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  • Date Issued: 2006

An investigation of the binding capacities of recombinant domain mutants of the human Polymeric Immunoglobulin Receptor (pIgR)

  • Authors: Prinsloo, Earl Adin Gerard
  • Date: 2006
  • Subjects: Immunoglobulins
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:10307 , http://hdl.handle.net/10948/403 , Immunoglobulins
  • Description: The membrane bound glycoprotein, polymeric immunoglobulin receptor (pIgR) is the primary transport molecule of the polymeric immunoglobulins, dimeric IgA and pentameric IgM, across epithelial cells. This process, known as transcytosis, is essential in order to establish immunity at mucosal surfaces. Typically, pIgR binds to the polymeric immunoglobulin at the basolateral surface of the epithelial cell, via five homologous immunoglobulin-like domains of the ectodomain. Binding is covalent to IgA and non-covalent to IgM; the IgM binding varying among species. The pIgR-bound complex is released at the apical surface of the cell after cleavage of pIgR at Arg585, thereafter referred to as secretory component (SC). SC confers protective and immunologic functions to the polymeric immunoglobulin. Free SC, i.e. not complexed with polymeric immunoglobulins, is also known to be released into mucosal secretions; and binds to pathogenic bacteria and bacterial products. It is known that domain I of the ectodomain is the primary domain in the interaction with polymeric immunoglobulins, while domain V is involved in a covalent linkage with IgA. However, little is known of domains II-IV and their role in immunoglobulin binding, particularly to IgM. This study aimed to characterize the binding of recombinant human pIgR domain mutants to polymeric IgM using immunological, biophysical and cell based techniques; thereby allowing greater insight into the contribution of each of the five domains. The unique domain structure allowed for selective amplification of single and multiple domain mutants from cloned human PIGR ectodomain cDNA. Mutants were cloned and expressed in Esherichia coli BL21 (DE3) as inclusion bodies. Recombinant mutant proteins were refolded in vitro by equilibrium gradient dialysis and purified to homogeneity. Equilibrium binding data show significant contributions to specific binding as a factor of domain presence. Binding kinetics determined by biophysical surface plasmon resonance measurements show the interplay between association and dissociation rates as defined by individual domains. In vitro competitive binding studies using the human intestinal carcinoma, HT29, known to constitutively express pIgR, show that the constructed recombinant domain mutants outcompete native pIgR. The level of competition is shown to be dependant on the domains downstream of domain I. The data also confirm the biological activity of the first in vitro refolded recombinant human SC.
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  • Date Issued: 2006

An investigation of the in vitro anticancer properties of selected platinum compounds

  • Authors: Du Plessis-Stoman, Debbie
  • Date: 2006
  • Subjects: Antineoplastic agents , Platinum compounds , Cancer -- Immunological aspects , Cancer -- Chemotherapy
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10334 , http://hdl.handle.net/10948/498 , http://hdl.handle.net/10948/d1012002 , Antineoplastic agents , Platinum compounds , Cancer -- Immunological aspects , Cancer -- Chemotherapy
  • Description: This dissertation mainly deals with some biochemical aspects regarding the efficacy of novel platinum anticancer compounds, as part of a broader study in which both chemistry and biochemistry are involved. Various novel diamine and N-S donor chelate compounds of platinum II and IV have been developed in which factors such as stereochemistry, ligand exchange rate and biocompatibility were considered as additional parameters. In the first order testing, each of these compounds was tested with reference to their “killing” potential by comparing their rate of killing, over a period of 48 hours with those of cisplatin and oxaliplatin. Some 80 compounds were tested in this way. Although only a few could be regarded as equal to or even better than cisplatin and oxaliplatin, the testing of these compounds on cancer cells provided useful knowledge for the further development of novel compounds. Four of the better compounds, namely Y9, Y14, Y16 and Lt16.2 were selected for further studies to obtain more detailed knowledge of their anticancer action, including some flow cytometric studies. In addition to the above, cisplatin resistant cells were produced for each of the three different cell lines tested, namely, HeLa, HT29 and MCF7 cancer cell lines, by intermittent and incremental exposure to cisplatin (all the cell lines tested became resistant to cisplatin). Each of the selected compounds were exposed to the cells in the same manner, in order to attempt the induction of resistance against these compounds in the three cell lines tested (i.e. whether these cells will become resistant to the various compounds). Each of these selected platinum containing compounds were subsequently tested against the “cisplatin resistant” cell lines in order to determine their efficacy against such cells. One such compound could be singled out, since cervical cancer cells (HeLa cells) do not become resistant to it. This behaviour is similar to that of oxaliplatin against cervical cancer and colon cancer (HT29) cells (oxaliplatin is the number one treatment for colon cancer at present). This compound also proved to be more active against cisplatin resistant cell lines. It was found that all the compounds induced apoptosis in the cell lines tested as well as inhibit the DNA cycle at one or more phase. Finally, an effort was made to evaluate the different compounds by comparing them with respect to their properties relating to anticancer action.
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  • Date Issued: 2006

Cytokine signalling functions of human soluble IgE receptors in peripheral blood mononuclear cells from normal and hyper-allergic individuals and in B-lymphoblastoid and monocytic cell lines

  • Authors: Askew, Sandra Lyn
  • Date: 2006
  • Subjects: Ligands , Cell receptors , Cellular signal transduction
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10305 , http://hdl.handle.net/10948/455 , Ligands , Cell receptors , Cellular signal transduction
  • Description: CD23 is a multifunctional receptor/ligand, found in a variety of cell types, such as human peripheral blood mononuclear cells (PBMCs), B-lymphoblastoid cell lines, mast cells and basophils. It is also found on a variety of haematopoietic cell lines. As the low-affinity receptor for immunoglobulin E (IgE), CD23 plays a role in antigen-presentation and macrophage activation. As a surface molecule cleaved from the cell membrane, soluble CD23 (sCD23) can act as an adhesion molecule and a cytokine. Perturbances of such molecular interactions may lead to various diseases such as allergies and other inflammatory diseases. It has been speculated that elevated levels of sCD23 may be used to bind secreted IgE, thus preventing it from binding to membrane CD23 on haematopoietic cells, preventing B cells from being activated into IgE producing cells. Signal transduction by sCD23 is dependent on cell subsets, ligands and co-factors required for its function. sCD23 plays a direct role in inducing tumour necrosis factor alpha (TNFα), interleukin-1 alpha (IL-1α) and interleukin-1 beta (IL-1β) and soluble IL-1 receptor from activated human monocytes and PBMCs in vitro. Recombinant forms of 25 and 37 kDa human sCD23 were produced by polymerase chain reaction (PCR)-cloning into pET23a, a bacterial expression vector. The proteins were expressed and refolded, followed by purification by gel filtration chromatography. The purified proteins were biochemically characterized to ensure purity and biological activity, by observing the binding to human IgE both in enzyme-linked immunosorbant assay (ELISA) and surface plasmon resonance (SPR) spectroscopy. ELISA showed KD values of 7.23 x 10-9M and 8.12 x 10-9M for the 25 and 37 kDa proteins, respectively. These values were significantly lower than that of Hibbert et al., (2005). SPR data obtained for the 25 kDa CD23 was not of reliable quality but SPR for the 33kDa sCD23 showed a KD of 1.18 x 10-7M, close to that of Hibbert et al., (2005), J. Exp. Med, 202: 751-760. To test the therapeutic potential of the recombinant molecule, a B-lymphoblastoid cell line (Raji), a pre-monocytic cell line (U937), and PBMCs from normal and hyper-allergic individuals were used. All cells showed no change in production of cytokines. It is essential to investigate further cytokine functions and production implicated by recombinant forms of sCD23, as well as binding of sCD23 to CD21 and CD11b/c, and in vivo IgE regulation before a conclusion can be drawn as to whether recombinant sCD23 is a potential therapeutic target against allergic disease.
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  • Date Issued: 2006

Epitaxial growth and characterisation of CuGaS2

  • Authors: Branch, Matthew Stewart
  • Date: 2006
  • Subjects: Epitaxy , Chalcopyrite , Semiconductors
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:10541 , http://hdl.handle.net/10948/438 , http://hdl.handle.net/10948/d1012893 , Epitaxy , Chalcopyrite , Semiconductors
  • Description: In this work, the growth and characterisation of the chalcopyrite semiconductor CuGaS2 is presented. The purpose of this study is to gain a better understanding of the defect chemistry of this class of materials through a systematic study relating the structural and optical properties to the composition of thin films grown by metalorganic vapour phase epitaxy. Details associated with the optimisation of the growth process are presented in a format relating the changes in the composition and morphology to variations in the growth process. The structural properties of thin films grown on GaAs(001) substrates are described. A dominance of polycrystalline growth is found to occur for Cu-rich material, whereas near-stoichiometric to Ga-rich material is typified by epitaxial growth. Secondary phases are identified by X-ray diffractometry and Raman spectroscopy for severely non-stoichiometric material. In some cases, the formation of the cubic zincblende and CuPt polytype of CuGaS2 are identified by transmission electron microscopy. It will be shown that changes in the Cu/Ga ratio of the solid strongly influence the photoluminescence response of the layers. Weak excitonic luminescence is observed for both slightly Ga-rich and Cu-rich material. Near stoichiometric layers exhibit luminescence centered at ~2.4 eV. Cu-rich layers are dominated by a line occurring at ~2.1 eV, whereas a different line at ~2.25 eV dominates for Ga-rich layers. A clear picture emerges of the radiative mechanisms dominating for Cu-rich and Ga-rich layers.
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  • Date Issued: 2006

Factors influencing species richness, cover and composition of vegetation on Namaqualand quartz fields

  • Authors: Van Tonder, Carlo
  • Date: 2006
  • Subjects: Plant diversity -- South Africa -- Namaqualand , Soil biology -- South Africa -- Namaqualand
  • Language: English
  • Type: Thesis , Masters , MTech
  • Identifier: vital:10752 , http://hdl.handle.net/10948/630 , Plant diversity -- South Africa -- Namaqualand , Soil biology -- South Africa -- Namaqualand
  • Description: Quartz fields contribute significantly to plant diversity in the Succulent Karoo biome. They are distinctly different from surrounding habitats and have high levels of plant endemism. Biological soil crusts are features of quartz field soils and fulfill a vital function in that they stabilize soils. It is important for managers of nature reserves and agricultural rangelands to know what factors influence quartz field soils and vegetation. Both stakeholders could benefit from new information that would allow for informed decision-making regarding land-use on quartz fields. The present study took place in the Namaqua National Park that contains a significant proportion of the Riethuis-Wallekraal quartz fields phytochorion. The first part of the study aimed to understand whether certain land-use activities potentially destabilize quartz field soils, which might have possible ramifications for associated biological soil crusts and vegetation. It was followed by relating variation in soil stability with species richness, cover and species composition of quartz field vegetation. Overall, positions assumed to be impacted by land-use activities had less stable soils compared to positions assumed not be impacted. Soil stability had a significant influence on species richness and cover but to a lesser degree on species composition. Quartz field vegetation was significantly influenced by soil physical and chemical properties as well as location in the quartz fields landscape. The second part of the study aimed at understanding how species richness of isolated quartz outcrops is related to their size compared to that of a mainland body of quartz outcrops. No clear species-area relationships emerged from the study. There were significant differences between isolated outcrops and mainland outcrops in substrate and vegetation composition. Findings are discussed in relation to Island Biogeography Theory.
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  • Date Issued: 2006

Horticultural propagation of the threatened species, Syncarpha revurvata (L.f.)B. Nord

  • Authors: Swart, Pierre André
  • Date: 2006
  • Subjects: Horticultural crops -- Propagation , Plant propagation , Horticulture
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10624 , http://hdl.handle.net/10948/613 , Horticultural crops -- Propagation , Plant propagation , Horticulture
  • Description: Syncarpha recurvata (L.f.) B. Nord. (Asteraceae, Gnaphalieae) is listed as a vulnerable (intermediate priority) species. The propagation methods of achene germination, stem cuttings, air layering and micropropagation were investigated to obtain an efficient propagation method. Smoke water dilutions of 1:100, 1:50 and 1:10 significantly increased germination, with the 1:100 smoke water dilutions showing the highest germination percentage (22.4 percent). Achenes collected between August and October 2005 showed higher germination and viability than achenes collected between May and July 2006. Fifty percent of the stem cuttings and 32 percent of the airlayered branches rooted. Embryo culture was the only successful culture type out of the four attempted. Two embryos germinated and four became photosynthetic. Two of the germinated embryos also produced callus cells, a medium supplemented with 5 μM IAA may be used to test for a suitable plant regulator for organogenesis or embryogenesis. Syncarpha recurvata plants were also transplanted into pots and 60 percent survived. A growth rate of 1.466 mm y-1 was obtained from total shoot length measurements. In this study, it was found that air-layering branches of transplanted Syncarpha recurvata plants is the most efficient propagation method.
  • Full Text:
  • Date Issued: 2006
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