An exposition of Hilbert C-modules
- Authors: Sokopo, Bulelani Joab
- Date: 2015
- Subjects: Mathematics Algebra , Functions, Continuous Mathematical analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50008 , vital:41974
- Description: In trying to prove that derivations of type I AW -algebras are inner, I. Kaplansky introduced and developed the basics of the concept of Hilbert C- modules. He sought to generalize the idea of a Hilbert space by replacing the field C of all complex numbers with a general (commutative and unital) C-algebra. Twenty years later, the concept was broadened and expanded to non-commutative C-algebras by W. L. Paschke and M. A. Rieffel in their papers on inner product modules over B-algebras and induced representations of C-algebras, respectively. Since then, the theory of Hilbert C-modules has grown rapidly. It was used by G. G. Kasparov as the framework for his bivariant K-theory. More recently, Hilbert C-modules have formed the technical basis for the C*-algebraic approach to quantum group theory. The aim of this dissertation is to provide as detailed an account as possible of the theory of Hilbert C-modules, as given in a book of E. C. Lance, up to and including the KSGNS construction. The KSGNS construction, named after Kasparov, Stinespring, Gelfand, Naimark and Segal, is a generalization to Hilbert C-modules of the familiar GNS construction for C-algebras. The result by Kaplansky that all derivations of a type I AW-algebra are inner is given as an application in the final chapter of the dissertation.
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- Date Issued: 2015
An in-silico investigation of Morita-Baylis-Hillman accessible heterocyclic analogues for applications as novel HIV-1 C protease inhibitors
- Authors: Sigauke, Lester Takunda
- Date: 2015
- Subjects: Protease inhibitors , Heterocyclic compounds , HIV (Viruses) , HIV infections , Drug resistance , Cheminformatics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4152 , http://hdl.handle.net/10962/d1017913
- Description: Cheminformatic approaches have been employed to optimize the bis-coumarin scaffold identified by Onywera et al. (2012) as a potential hit against the protease HIV-1 protein. The Open Babel library of commands was used to access functions that were incorporated into a markov chain recursive program that generated 17750 analogues of the bis-coumarin scaffold. The Morita-Baylis-Hillman accessible heterocycles were used to introduce structural diversity within the virtual library. In silico high through-put virtual screening using AutoDock Vina was used to rapidly screen the virtual library ligand set against 61 protease models built by Onywera et al. (2012). CheS-Mapper computed a principle component analysis of the compounds based on 13 selected chemical descriptors. The compounds were plotted against the principle component analysis within a 3 dimensional chemical space in order to inspect the diversity of the virtual library. The physicochemical properties and binding affinities were used to identify the top 3 performing ligands. ACPYPE was used to inspect the constitutional properties and eliminated virtual compounds that possessed open valences. Chromene based ligand 805 and ligand 6610 were selected as the lead candidates from the high-throughput virtual screening procedure we employed. Molecular dynamic simulations of the lead candidates performed for 5 ns allowed the stability of the ligand protein complexes with protease model 305152. The free energy of binding of the leads with protease model 305152 was computed over the first 50 ps of simulation using the molecular mechanics Poisson-Boltzmann method. Analysis structural features and energy profiles from molecular dynamic simulations of the protein–ligand complexes indicated that although ligand 805 had a weaker binding affinity in terms of docking, it outperformed ligand 6610 in terms of complex stability and free energy of binding. Medicinal chemistry approaches will be used to optimize the lead candidates before their analogues will be synthesized and assayed for in vivo protease activity.
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- Date Issued: 2015
An investigation into the role played by perceived security concerns in the adoption of mobile money services : a Zimbabwean case study
- Authors: Madebwe, Charles
- Date: 2015
- Subjects: Banks and banking, Mobile -- Zimbabwe , Global system for mobile communications , Cell phones -- Security measures
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4711 , http://hdl.handle.net/10962/d1017933
- Description: The ubiquitous nature of mobile phones and their popularity has led to opportunistic value added services (VAS), such as mobile money, riding on this phenomenon to be implemented. Several studies have been done to find factors that influence the adoption of mobile money and other information systems. The thesis looks at factors determining the uptake of mobile money over cellular networks with a special emphasis on aspects relating to perceived security even though other factors namely perceived usefulness, perceived ease of use, perceived trust and perceived cost were also looked at. The research further looks at the security threats introduced to mobile money by virtue of the nature, architecture, standards and protocols of Global System for Mobile Communications (GSM). The model employed for this research was the Technology Acceptance Model (TAM). Literature review was done on the security of GSM. Data was collected from a sample population around Harare, Zimbabwe using physical questionnaires. Statistical tests were performed on the collected data to find the significance of each construct to mobile money adoption. The research has found positive correlation between perceived security concerns and the adoption of money mobile money services over cellular networks. Perceived usefulness was found to be the most important factor in the adoption of mobile money. The research also found that customers need to trust the network service provider and the systems in use for them to adopt mobile money. Other factors driving consumer adoption were found to be perceived ease of use and perceived cost. The findings show that players who intend to introduce mobile money should strive to offer secure and useful systems that are trustworthy without making the service expensive or difficult to use. Literature review done showed that there is a possibility of compromising mobile money transactions done over GSM
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- Date Issued: 2015
An investigation into the synergistic action of cellulose-degrading enzymes on complex substrates
- Authors: Thoresen, Mariska
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Cellulosic ethanol , Saccharomyces cerevisiae , Cellulase , Enzymes -- Biotechnology , Hydrolases
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4154 , http://hdl.handle.net/10962/d1017915
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- Date Issued: 2015
An investigation of ISO/IEC 27001 adoption in South Africa
- Authors: Coetzer, Christo
- Date: 2015
- Subjects: ISO 27001 Standard , Information technology -- Security measures , Computer security , Data protection
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4720 , http://hdl.handle.net/10962/d1018669
- Description: The research objective of this study is to investigate the low adoption of the ISO/IEC 27001 standard in South African organisations. This study does not differentiate between the ISO/IEC 27001:2005 and ISO/IEC 27001:2013 versions, as the focus is on adoption of the ISO/IEC 27001 standard. A survey-based research design was selected as the data collection method. The research instruments used in this study include a web-based questionnaire and in-person interviews with the participants. Based on the findings of this research, the organisations that participated in this study have an understanding of the ISO/IEC 27001 standard; however, fewer than a quarter of these have fully adopted the ISO/IEC 27001 standard. Furthermore, the main business objectives for organisations that have adopted the ISO/IEC 27001 standard were to ensure legal and regulatory compliance, and to fulfil client requirements. An Information Security Management System management guide based on the ISO/IEC 27001 Plan-Do-Check-Act model is developed to help organisations interested in the standard move towards ISO/IEC 27001 compliance.
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- Date Issued: 2015
An overview of energy minerals in the Springbok Flatsbasin, South Africa : implications for geochemical and geophysical exploration
- Authors: Ledwaba, Lebogang John
- Date: 2015
- Subjects: Energy minerals -- South Africa -- Springbok Flats (Limpopo) , Geochemistry , Prospecting -- Geophysical methods , Coal -- South Africa -- Springbok Flats (Limpopo) , Uranium -- South Africa -- Springbok Flats (Limpopo) , Coalbed methane -- South Africa -- Springbok Flats (Limpopo)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5092 , http://hdl.handle.net/10962/d1019880
- Description: This study is informed by the rising demand for power needs in South Africa and aims at understanding the geophysical and geochemical characteristics of the energy minerals in the Springbok Flats Basin and relating them to the prevailing geological and structural setting for improved exploration targeting. The Springbok Flats Basin is part of the Karoo sediments and host to uranium, coal and coal bed methane (CBM) resources. The lithology sections in the basin indicate presence of basaltic lavas at the top, underlain by mudrocks, siltstones, sandstones, conglomerates and diamictite, with interbedded coal beds occasionally. The coals are uraniferous and shale bounded and of lower Beaufort age at 250 Ma. The regional radiometric data identifies the regional extent of the Springbok Flats Basin as a basin with low total count values. This information is useful in exploration as it gives an idea of the limits of the area where to focus application for prospecting licenses. The reduced to pole of the total magnetic field, residuals and first vertical derivative maps clearly show the high magnetic susceptibility nature of the surrounding Bushveld rocks as compared to the low Karoo sediment susceptibility within the basin. There are distinct ring shaped picks within the basin possibly due to known Karoo dolerite sills in particular to the central south western part of the grid. The regional geochemical mapping program is a cost-effective way of providing an overview of the relative abundance levels, regional trends and anomalous patterns in the underlying lithological units. Background values of elements in soils over different lithological units and the identification of anomalous values relative to these elements can easily be identified. The geochemical results show an excellent correlation between soil chemistry and underlying geological formations. A few distinct gravity highs are clearly shown within the basin. Assuming the effect of the Letaba basalt to the gravity readings is uniform across the basin; these distinct anomalies could be due to Karoo dolerite sills as they coincide with areas of distinct high magnetic signature. A conceptual model was generated assuming that the Karoo sediments’ layering is uniform across the gravity profile but changes in the residual are due to an increased thickness of the sill supported by the gentle changes on the surface topography. Satellite imagery has got its challenges especially in areas of vegetation but it does provide a very useful tool in exploration. A number of spectral analysis techniques and band rations can be used to differentiate the areas underlain by the Letaba basalts, the Karoo sandstones/shale and Bushveld granites for mapping purposes. The priority focus will be on the shallower Karoo sediments because of the potential for cheaper mining. Exploration targeting needs to be guided by observed geochemical and geophysical characteristics in order to prioritize areas taking into account the presence of Karoo intrusives such as the dolerite sills that tend to devolatize the coal hence affecting the quality/rank. Structures and gravity signatures are very important in delineating areas with thick sediments that have a potential for CBM. The same understanding in targeting goes a long way in planning drill holes, resource modelling and pre-feasibility stages for mine planning. A high resolution airborne geophysical survey is recommended over the basin to better resolve structures. Geophysical borehole logging is recommended to be part of the exploration drilling programs in the Springbok Flats Basin in order to define the in-situ geophysical characteristics. Geophysical logging is useful in particular for the uranium reserves that cannot be delineated from the surface due to deep intersection.
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- Date Issued: 2015
Analysis of predictive power of binding affinity of PBM-derived sequences
- Authors: Matereke, Lavious Tapiwa
- Date: 2015
- Subjects: Transcription factors , Protein binding , DNA-binding proteins , Chromatin , Protein microarrays
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4161 , http://hdl.handle.net/10962/d1018666
- Description: A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.
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- Date Issued: 2015
Application of Baylis-Hillman methodology in the synthesis of HIV-1 enzyme inhibitors
- Authors: Manyeruke, Meloddy Hlatini
- Date: 2015
- Subjects: HIV infections , Enzyme inhibitors , AZT (Drug) , Bioconjugates
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4540 , http://hdl.handle.net/10962/d1017920
- Description: The application of Baylis-Hillman methodology has afforded access to a range of β-hydroxypropionate ester-AZT conjugates as potential dual-action HIV-1 IN/RT inhibitors. Two families comprising a total of nine β-hydroxypropionate ester-AZT conjugates were synthesised. The first family was accessed using O-benzylated salicylaldehydes and methyl acrylate and the second from unprotected salicylaldehydes using tert-butyl acrylate as the activated alkene. Spectroscopic methods were employed to fully characterize the compounds. Propargylation of the respective Baylis-Hillman adducts was achieved via conjugate addition of propargylamine. The resulting products were then employed in Cu(I)-catalysed “click” reactions with azidothymidine (AZT) to yield the desired β-hydroxypropionate ester-AZT conjugates. Exploratory studies were also conducted to access 4-hydroxycoumarins from Baylis-Hillman derived adducts and to construct customized chiral Baylis-Hillman reaction sites. Many 4- hydroxycoumarins are known to exhibit a wide range of biological activities, and extending Baylis-Hillman methodology to access these systems is an important challenge. Two approaches were investigated. The first involved the formation of a 4-phthalimidocoumarin, aromatisation and hydrolysis of which was expected to lead to the 4-hydroxycoumarin target. The second, a variation of the first, involved the use of 4-(chrolomethyl)coumarin intermediates. Unfortunately, while various intermediates were prepared and characterised, neither approach led ultimately to the desired targets. N-substituted borneol-10-sulfonamides were constructed from camphor-10- sulfonyl chloride as chiral Baylis-Hillman reaction sites. In a preliminary study, however, none of the N-substituted borneol-10-sulfonamides exhibited Baylis-Hillman catalytic activity.
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- Date Issued: 2015
Approaches in the prioritisation of areas for biodiversity conservation: a case study from the Western Cape pf South Africa
- Authors: Southey, Phillippa Kate
- Date: 2015
- Subjects: Biodiversity conservation -- South Africa -- Western Cape , Conservation of natural resources -- South Africa -- Western Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/4122 , vital:20548
- Description: Historical ad hoc allocations of land for biodiversity conservation have led to a biased representation of habitat within the Cape Floristic Region, with Protected Areas concentrated in upland areas at high altitudes and on steep slopes. The field of Conservation Planning developed to ensure that allocations of areas to Protected status no longer result in such bias and rather promotes the persistence of biodiversity. This study reviewed a recent allocation of land to biodiversity conservation within Western Cape of South Africa, using both a quantitative and qualitative approach, to determine their value to biodiversity conservation. The area was previously used for commercial forestry but now has been allocated to conservation land-uses. The allocation was based on the area’s value to the forestry industry. The qualitative approach in this study engaged with relevant stakeholder groups to map priority areas, while the quantitative approach used available data on biodiversity features to map priority areas. Neither approach determined that the area allocated is in its full extent a priority for biodiversity conservation. This indicated that in the current era of Conservation Planning, Protected Areas are still being allocated in an ad hoc manner, as a result of their limited perceived benefit to anthropocentric needs. The future allocation of land to biodiversity conservation should rather integrate expert knowledge and available quantifiable data to ensure that priority areas for biodiversity conservation are being protected.
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- Date Issued: 2015
Assessing symptoms of eutrophication in estuaries
- Authors: Lemley, Daniel Alan
- Date: 2015
- Subjects: Estuarine eutrophication -- South Africa , Water quality -- South Africa , Ecological integrity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/3427 , vital:20429
- Description: Water quality and ecological integrity of estuaries reflect activities within the entire upstream catchment. Much emphasis has been placed on the response of estuaries to anthropogenic stressors through the use of monitoring programmes. Key to the success of these programmes is the use of indicators as they transform data into useful information. The ultimate aim of this study was to identify eutrophic symptoms in selected estuaries in the Gouritz Water Management Area (WMA) using a multi-metric classification method. The study sites included the permanently open Duiwenhoks, Goukou, Gouritz, and Kaaimans estuaries, as well as the temporarily open/closed Hartenbos, Klein Brak, Great Brak, Gwaing, and Goukamma estuaries. Initially, the “pressure” associated with all the estuaries in the Gouritz WMA was determined (e.g. total daily nutrient loads and changes in river inflow affecting flushing time) using long-term flow and water quality monitoring data provided by the Department of Water Affairs (DWA). Subsequently, the “state” of the selected estuaries was assessed using a variety of indicators, including: inorganic nutrients (~ N and P), phytoplankton, epiphytes and microphytobenthos. Estuaries with longer flushing time suggested greater vulnerability to eutrophication. For example, the Gwaing (281.11 kg DIN d-1; 78.85 kg DIP d-1) and Hartenbos (38.33 kg DIN d-1; 21.51 kg DIP d-1) estuaries generally received the highest daily inorganic nutrient loads. However, at the time of sampling, the Hartenbos Estuary had a longer flushing time (i.e. weeks) compared to the Gwaing Estuary (i.e. couple of days). Field data confirmed the greater vulnerability to eutrophication associated with longer flushing times, as the indicators measured in the Hartenbos Estuary exceeded all the proposed ‘thresholds’ of a eutrophic system (~ overall ‘Poor’ condition). The Great Brak Estuary (~ overall ‘Fair’ condition) provided an interesting example where eutrophic symptoms were only detected when assessing the microalgal primary producers (i.e. high biomass and low diversity). Furthermore, the need to distinguish between naturally and anthropogenically induced symptoms was highlighted. One such scenario was noted in the Kaaimans Estuary, where its natural hydro-morphological characteristics (i.e. steep banks, low river inflow, and deep/narrow channel) led to the possible exaggeration of its overall eutrophic condition, i.e. received a ‘Fair’ rather than ‘Good’ rating, arising from ‘Poor’ ratings for dissolved oxygen and benthic diatom diversity. Overall, this study demonstrated the importance of adopting a holistic approach when assessing the condition and trophic status of estuaries. Studies such as these allow for the detection of vulnerable and degraded systems, which can provide important information with regards to the identification of management priorities.
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- Date Issued: 2015
Assignment of spin and parity to states in the nucleus ¹⁹⁶T1
- Authors: Uwitonze, Pierre Celestin
- Date: 2015
- Subjects: Nuclear spin , Particles (Nuclear physics) -- Chirality
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5558 , http://hdl.handle.net/10962/d1017903
- Description: This work presents a study of high-spin states in the nucleus ¹⁹⁶Tl via γ-spectroscopy. ¹⁹⁶Tl was produced via the ¹⁹⁷Au(⁴He,5n) ¹⁹⁶Tl reaction at a beam energy of 63 MeV. The γ-γ coincidence measurements were performed using the AFRODITE γ-spectrometer array at iThemba LABS. The previous level scheme of ¹⁹⁶Tl has been extended up to an excitation of 4071 keV including 24 new γ-ray transitions. The spin and parity assignment to levels was made from the directional correlation of oriented nuclei (DCO) and linear polarization anisotropy ratios. An analysis of the B(M1)/B(E2) ratios was found to be consistent with the configuration of πh₉/₂♁vi₁₃/₂ for the ground state band. Although no chiral band was found in ¹⁹⁶TI and ¹⁹⁸TI.
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- Date Issued: 2015
Biotechnology from bench to market: the design, scale-up and commercialisation strategy development of a disruptive bioprocess for potable ethanol production
- Authors: Dhanani, Karim Colin Hassan
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55863 , vital:26750
- Description: The capacity of research institutions to engage in technology transfer activities has important implications on both economic development and technological advancement. This thesis explores the developmental and commercialisation processes involved in the transfer of a potentially disruptive bioprocessing technology for beverage alcohol production. Ethanolic fermentation strategies are of interest due to their global economic importance and their potential to produce clean renewable fuels in the future. Currently used methods are both energetically wasteful and economically inefficient. To this end more effective bioprocessing methods and implementation strategies are required to enable commercially viable decentralised small-scale ethanol production. Perfusion reactors have a number of advantages over batch and other continuous fermentation strategies. This study aimed to develop and study the fermentative efficiency of a perfusion tower bioreactor system at the bench scale, and subsequently through a scale up process to a low level commercial capacity. An HPLC method was developed for the Simultaneous quantification of common fermentation analytes; this was used to determine bench scale fermentation efficacies over an operational period. At steady state the ethanol volumetric productivity of the bench scale bioreactor system was 3.40 g. L-1.h-1, the average yield of ethanol to consumed sugar was 0.467 g.g -1, with an average sugar conversion percentage of 96%. Results showed that the tower perfusion bioreactor was appropriate for high performance ethyl alcohol fermentations. This reactor design was then scaled up to pilot scale and then commercial scale ca pacity. Similar efficienCies were achieved with these larger systems. Based on the process performance data obtained, a commercialisation strategy was developed and market performance was projected. It was found that productivity rates per unit volume were favourable, and the bioreactor system was determined to be very cost effective for a decentralised ethanolic beverage manufacturing model.
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- Date Issued: 2015
Building an E-health system for health awareness campaigns in poor areas
- Authors: Gremu, Chikumbutso David
- Date: 2015
- Subjects: National health services -- South Africa , Medical informatics , Public health -- Information services
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4708 , http://hdl.handle.net/10962/d1017930
- Description: Appropriate e-services as well as revenue generation capabilities are key to the deployment and the sustainability for ICT installations in poor areas, particularly common in developing country. The area of e-Health is a promising area for e-services that are both important to the population in those areas and potentially of direct interest to National Health Organizations, which already spend money for Health campaigns there. This thesis focuses on the design, implementation, and full functional testing of HealthAware, an application that allows health organization to set up targeted awareness campaigns for poor areas. Requirements for such application are very specific, starting from the fact that the preparation of the campaign and its execution/consumption happen in two different environments from a technological and social point of view. Part of the research work done for this thesis was to make the above requirements explicit and then use them in the design. This phase of the research was facilitated by the fact that the thesis' work was executed within the context of the Siyakhula Living Lab (SLL; www.siyakhulaLL.org), which has accumulated multi-year experience of ICT deployment in such areas. As a result of the found requirements, HealthAware comprises two components, which are web-based, Java applications that run in a peer-to-peer fashion. The first component, the Dashboard, is used to create, manage, and publish information for conducting awareness campaigns or surveys. The second component, HealthMessenger, facilitates users' access to the campaigns or surveys that were created using the Dashboard. The HealthMessenger was designed to be hosted on TeleWeaver while the Dashboard is hosted independently of TeleWeaver and simply communicates with the HealthMessenger through webservices. TeleWeaver is an application integration platform developed within the SLL to host software applications for poor areas. Using a core service of TeleWeaver, the profile service, where all the users' defining elements are contained, campaigns and surveys can be easily and effectively targeted, for example to match specific demographics or geographic locations. Revenue generation is attained via the logging of the interactions of the target users in the communities with the applications in TeleWeaver, from which billing data is generated according to the specific contractual agreements with the National Health Organization. From a general point of view, HealthAware contributes to the concrete realizations of a bidirectional access channel between Health Organizations and users in poor communities, which not only allows the communication of appropriate content in both directions, but get 'monetized' and in so doing becomes a revenue generator.
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- Date Issued: 2015
Carbonate petrography and geochemistry of BIF of the Transvaal supergroup : evaluating the potential of iron carbonates as proxies for palaeoproterozoic ocean chemistry
- Authors: Rafuza, Sipesihle
- Date: 2015
- Subjects: Carbonate rocks -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Transvaal Supergroup , Geochemistry -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Kuruman , Petrology -- South Africa -- Griekwastad , Geology, Stratigraphic -- Proterozoic , Chemical oceanography , Iron
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5089 , http://hdl.handle.net/10962/d1018611
- Description: The subject of BIF genesis, particularly their environmental conditions and ocean chemistry at the time of deposition and their evolution through time, has been a subject of much contentiousness, generating a wealth of proposed genetic models and constant refinements thereof over the years. The prevailing paradigm within the various schools of thought, is the widespread and generally agreed upon depositional and diagenetic model(s) which advocate for BIF deposition under anoxic marine conditions. According to the prevailing models, the primary depositional environment would have involved a seawater column whereby soluble Fe²⁺ expelled by hydrothermal activity mixed with free O₂ from the shallow photic zone produced by eukaryotes, forming a high valence iron oxy-hydroxide precursor such as FeOOH or Fe(OH)₃. An alternative biological mechanism producing similar ferric precursors would have been in the form of photo-ferrotrophy, whereby oxidation of ferrous iron to the ferric form took place in the absence of biological O₂ production. Irrespective of the exact mode of primary iron precipitation (which remains contentious to date), the precipitated ferric oxy-hydroxide precursor would have reacted with co-precipitated organic matter, thus acting as a suitable electron acceptor for organic carbon remineralisation through Dissimilatory Iron Reduction (DIR), as also observed in many modern anoxic diagenetic environments. DIR-dominated diagenetic models imply a predominantly diagenetic influence in BIF mineralogy and genesis, and use as key evidence the low δ¹³C values relative to the seawater bicarbonate value of ~0 ‰, which is also thought to have been the dissolved bicarbonate isotope composition in the early Precambrian oceans. The carbon for diagenetic carbonate formation would thus have been sourced through a combination of two end-member sources: pore-fluid bicarbonate at ~0 ‰ and particulate organic carbon at circa -28 ‰, resulting in the intermediate δ¹³C values observed in BIFs today. This study targets 65 drillcore samples of the upper Kuruman and Griquatown BIF from the lower Transvaal Supergroup in the Hotazel area, Northern Cape, South Africa, and sets out to explore key aspects in BIF carbonate petrography and geochemistry that are pertinent to current debates surrounding their interpretation with regard to primary versus diagenetic processes. The focus here rests on applications of carbonate (mainly siderite and ankerite) petrography, mineral chemistry, bulk and mineral-specific carbon isotopes and speciation analyses, with a view to obtaining valuable new insights into BIF carbonates as potential records of ocean chemistry for their bulk carbonate-carbon isotope signature. Evaluation of the present results is done in light of pre-existing, widely accepted diagenetic models against a proposed water-column model for the origin of the carbonate species in BIF. The latter utilises a combination of geochemical attributes of the studied carbonates, including the conspicuous Mn enrichment and stratigraphic variability in Mn/Fe ratio of the Griquatown BIF recorded solely in the carbonate fraction of the rocks. Additionally, the carbon isotope signatures of the Griquatown BIF samples are brought into the discussion and provide insights into the potential causes and mechanisms that may have controlled these signatures in a diagenetic versus primary sedimentary environment. Ultimately, implications of the combined observations, findings and arguments presented in this thesis are presented and discussed with particular respect to the redox evolution and carbon cycle of the ocean system prior to the Great Oxidation Event (GOE). A crucial conclusion reached is that, by contrast to previously-proposed models, diagenesis cannot singularly be the major contributing factor in BIF genesis at least with respect to the carbonate fraction in BIF, as it does not readily explain the carbon isotope and mineral-chemical signatures of carbonates in the Griquatown and uppermost Kuruman BIFs. It is proposed instead that these signatures may well record water-column processes of carbon, manganese and iron cycling, and that carbonate formation in the water column and its subsequent transfer to the precursor BIF sediment constitutes a faithful record of such processes. Corollary to that interpretation is the suggestion that the evidently increasing Mn abundance in the carbonate fraction of the Griquatown BIF up-section would point to a chemically evolving depositional basin with time, from being mainly ferruginous as expressed by Mn-poor BIFs in the lower stratigraphic sections (i.e. Kuruman BF) to more manganiferous as recorded in the upper Griquatown BIF, culminating in the deposition of the abnormally enriched in Mn Hotazel BIF at the stratigraphic top of the Transvaal Supergroup. The Paleoproterozoic ocean must therefore have been characterised by long-term active cycling of organic carbon in the water column in the form of an ancient biological pump, albeit with Fe(III) and subsequently Mn(III,IV) oxy-hydroxides being the key electron acceptors within the water column. The highly reproducible stratigraphic isotope profiles for bulk δ¹³C from similar sections further afield over distances up to 20 km, further corroborate unabatedly that bulk carbonate carbon isotope signatures record water column carbon cycling processes rather than widely-proposed anaerobic diagenetic processes.
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- Date Issued: 2015
Changes in diet resource use by elephants, Loxodonta Africana, due to changes in resource availability in the Addo National Park
- Authors: Du Toit, Jana
- Date: 2015
- Subjects: Elephants -- Nutrition -- South Africa -- Eastern Cape , Elephants -- Habitat -- South Africa -- Eastern Cape , Wildlife conservation , Addo Elephant National Park (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10731 , ISSN http://hdl.handle.net/10948/d1021194
- Description: Animals are restricted in their diets by several factors, most notably the availability and quality of resources. Variation in resource availability causes herbivores to shift their diets seasonally and spatially. Elephants (Loxodonta africana), are known to have extensive impacts on plant communities, altering ecosystem functioning and causing a decline in biodiversity. In enclosed areas, these impacts are increased leading to a decline in resource availability and presumably resource quality. In the Addo Elephant National Park, the Main Camp section has a history of high elephant impacts and therefore reduced resource availability. Whereas, the recently added Colchester section has greater resource availability, due to the absence of elephants in this section since the fencing of the Park. This study investigated the changes in diet (diet breadth, preference and diet quality) of elephants due to an increase in resource availability. Three alternative hypotheses were contrasted: 1) elephants as generalist foragers, 2) elephants as optimal foragers, or 3) elephants learning foraging behaviour. Using microhistological analysis, the diets of elephants were described over five sampling periods (August 2010 – February 2014) in both sections. Forage availability was estimated using a modified line-intercept method, and was used to determine changes in preference by relating forage availability to use. In the Colchester section the diet breadth of elephants increased, and was coupled with a high initial variation between the diets of elephants, which decreased in subsequent sampling periods. This supported the elephants learning foraging behaviour hypothesis. However, there was no increase in diet preference by elephants in the Colchester section, which supported the elephants as generalist foragers hypothesis. There was also no difference in the diet quality of elephants in the Main Camp and Colchester sections, which did not support any of the three hypotheses. The elephants learning foraging behaviour hypothesis is proposed to be the link between the alternate two hypotheses, and given enough time, either of the two could be supported. The lack of difference in preference and diet quality between elephants in the Main Camp and Colchester sections is hypothesised to be due to the population level (not measured for individuals) at which these were measured. Microhistological analysis of faeces was used to describe the diet of elephants, which was compared to the diet described by DNA metabarcoding. Microhistological analysis is a traditional, favoured technique used in describing the diet of wild herbivores, whereas DNA metabarcoding is a relatively new and untested technique. These two techniques have not yet been compared in the diet of megaherbivores. Results indicated that microhistological analysis identified significantly more grass in the diet of elephants, than DNA metabarcoding did, which was expected as previous studies also found overestimation of grasses. Microhistological analysis identified more plant families in the diet of elephants, than DNA metabarcoding. Most of the differences between the two techniques can be attributed to the difference in taxonomic resolution, which was due to the lack of a complete reference collection for DNA metabarcoding. Although either of the two techniques can be used to describe the diet of elephants, the most reliable results would be obtained when using both techniques. The findings of this study suggest that due to the high initial variation between the diets of elephants, with an increase in resource availability, the impacts will also initially be highly varied. This suggests that identifying plant species to monitor elephants impacts initially will be difficult. However, important plant species, or those known to be vulnerable to elephants impacts should be carefully monitored initially and monitoring should not only occur annually, but also seasonally.
- Full Text:
- Date Issued: 2015
Characterisation of the HSP70-HSP90 organising protein gene and its link to cancer
- Authors: Weeks, Stacey
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56006 , vital:26764
- Description: HOP (Heat shock protein 70/ Heat shock protein 90 organising protein) is a co-chaperone essential for client protein transfer from HSP70 to HSP90 within the HSP90 chaperone machine and has been found to be up-regulated in various cancers. However, minimal in vitro information can be found on the regulation of HOP expression. The aim of this study was to analyse the HOP gene structure across known orthologues, identify and characterise the HOP promoter, and identify the regulatory mechanisms influencing the expression of HOP in cancer. We hypothesized that the expression of HOP in cancer cells is likely regulated by oncogenic signalling pathways linked to cis-elements within the HOP promoter. An initial study of the evolution of the HOP gene speciation was performed across identified orthologues using Mega5.2. The evolutionary pathway of the HOP gene was traced from the unicellular organisms to fish, to amphibian and then to land mammal. The synteny across the orthologues was identified and the co-expression profile of HOP analysed. We identified the putative promoter region for HOP in silico and in vitro. Luciferase reporter assays were utilized to demonstrate promoter activity of the upstream region in vitro. Bioinformatic analysis of the active promoter region identified a large CpG island and a range of putative cis-elements. Many of the cis-elements interact with transcription factors which are activated by oncogenic pathways. We therefore tested the regulation of HOP levels by rat sarcoma viral oncogene homologue (RAS). Cancer cell lines were transfected with mutated RAS to observe the effect of constitutively active RAS expression on the production of HOP using qRT-PCR and Western Blot analyses. Additionally, inhibitors of the RAS signalling pathway were utilised to confirm the regulatory effect of mutated RAS on HOP expression. In cancer cell lines containing mutated RAS (Hs578T), HOP was up-regulated via a mechanism involving the MAPK signalling pathway and the ETS-1 and C/EBPβ cis-elements within the HOP promoter. These findings suggest for the first time that Hop expression in cancer may be regulated by RAS activation of the HOP promoter. Additionally, this study allowed us to determine the murine system to be the most suited genetic model organism with which to study the function of human HOP.
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- Date Issued: 2015
Coastal landscape change on the Cape St Francis/St Francis Bay peninsula from 1960 to 2014
- Authors: Schroeder, Daniel Heiko
- Date: 2015
- Subjects: Coast changes -- South Africa -- Saint Francis, Cape , Peninsulas -- South Africa -- Saint Francis, Cape , Human ecology -- South Africa -- Saint Francis, Cape , Geographic information systems -- South Africa -- Saint Francis, Cape , Surveying -- South Africa -- Saint Francis, Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5086 , http://hdl.handle.net/10962/d1018203
- Description: A large proportion of the human population, their settlements and socioeconomic activities occur on land directly adjacent to the coastline. The increased demand for coastal leisure and tourism has interfered with natural landscape features and their associated processes. The Cape St Francis/St Francis Bay peninsula located on the southeast coast of South Africa was rapidly developed and transformed from a little fishing village into an urban coastal developed area over a 50-year period (1961-2014). A system that once existed in a state of dynamic or non-equilibrium was interfered with through anthropogenic disturbances, resulting in more frequent and intense natural events, which ranged from floods to debris flows, decreased sand supply and resulting beach erosion. The aim of the project was to identify and map landscape features and changes on the peninsula using an interdisciplinary approach. The triangulated methods of a desktop study using Geographic Information Systems (GIS) and media reviews, a crowdsourcing/participatory approach based on interviews, and a one year land surveying period of measurable field based surveys of physical features gave a well balanced view. The research showed that the natural landscape has been altered dramatically by settlement and associated infrastructure development. In particular, the loss of dunefields and the artificial modification of river paths were major impact areas. Beach erosion is a continual issue for the peninsula residents, particularly in St Francis Bay.
- Full Text:
- Date Issued: 2015
Comparative study of clan CA cysteine proteases: an insight into the protozoan parasites
- Authors: Moyo, Sipho Dugunye
- Date: 2015
- Subjects: Cysteine proteinases , Proteolytic enzymes , Protozoan diseases , Parasites , Protozoan diseases -- Chemotherapy , Bioinformatics , Plasmodium , Antiprotozoal agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4165 , http://hdl.handle.net/10962/d1020309
- Description: Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.
- Full Text:
- Date Issued: 2015
Comparative study of the effect of silver nanoparticles on the hexokinase activity from human and Trypanosoma brucei
- Authors: Mlozen, Madalitso Martin
- Date: 2015
- Subjects: Nanoparticles , Silver , Glucokinase , Trypanosoma brucei , Drug resistance , African trypanosomiasis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4149 , http://hdl.handle.net/10962/d1017910
- Full Text:
- Date Issued: 2015
Comparison of protein binding microarray derived and ChIP-seq derived transcription factor binding DNA motifs
- Authors: Hlatshwayo, Nkosikhona Rejoyce
- Date: 2015
- Subjects: Protein binding , DNA , DNA microarrays , Transcription factors , DNA-protein interactions , Gene regulatory networks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4146 , http://hdl.handle.net/10962/d1017907
- Description: Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .
- Full Text:
- Date Issued: 2015