A comparison of open source and proprietary digital forensic software
- Authors: Sonnekus, Michael Hendrik
- Date: 2015
- Subjects: Computer crimes , Computer crimes -- Investigation , Electronic evidence , Open source software
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4717 , http://hdl.handle.net/10962/d1017939
- Description: Scrutiny of the capabilities and accuracy of computer forensic tools is increasing as the number of incidents relying on digital evidence and the weight of that evidence increase. This thesis describes the capabilities of the leading proprietary and open source digital forensic tools. The capabilities of the tools were tested separately on digital media that had been formatted using Windows and Linux. Experiments were carried out with the intention of establishing whether the capabilities of open source computer forensics are similar to those of proprietary computer forensic tools, and whether these tools could complement one another. The tools were tested with regards to their capabilities to make and analyse digital forensic images in a forensically sound manner. The tests were carried out on each media type after deleting data from the media, and then repeated after formatting the media. The results of the experiments performed demonstrate that both proprietary and open source computer forensic tools have superior capabilities in different scenarios, and that the toolsets can be used to validate and complement one another. The implication of these findings is that investigators have an affordable means of validating their findings and are able to more effectively investigate digital media.
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A flight of fancy in the Chorister Robin-Chat (Cossypha dichroa) : an isotopic standpoint
- Authors: Wolmarans, Milena Helena Louise
- Date: 2015
- Subjects: Muscicapidae -- South Africa , Muscicapidae -- Food , Muscicapidae -- Habitat , Muscicapidae -- Habitat -- Conservation , Forest birds -- South Africa , Isotopes , Stable isotope tracers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5920 , http://hdl.handle.net/10962/d1017207
- Description: Forested areas have been cited for their highly diverse floral and faunal assemblages, which are currently under threat from anthropogenic activities that restrict their range and deplete the resources produced within these naturally fragmented patches. Historically, up to 67 percent of avifaunal species associated with well-treed areas have undergone localised extinctions, consequentially affecting biodiversity as a measure of species richness and ecosystem functionality. To date, more than 900 of the bird species affiliated with forests are under threat and despite the theory surrounding functional redundancy, the mass extinction that is currently underway poses considerable limitations on the ecological integrity of these biomes. In South Africa, indigenous forest (one of the rarest biomes), occurs predominantly in small isolated patches along the eastern escarpment. With mountainous terrain emphasised as ‘prominent hotspots of extinction’, the limited dispersal and habitat sensitivity of montane forest fauna renders these species more prone to localised extinctions. BirdLife International, the IUCN and SABAP2 all indicate reductions in the range and abundance of the Chorister Robin-Chat (Cossypha dichroa) - an endemic forest specialist that is reported to move seasonally between high-altitude forest patches where they breed in summer, and lowland coastal forests where they overwinter. Beyond diet, body morphology and vocalisations, much of the information available on the altitudinal movements of C. dichroa is based on secondary sources and the assumptions therein. This study aimed to investigate the potential utilisation of δ13C and δ15N stable isotopes in determining the dietary niche width and altitudinal movements of C. dichroa. Feathers obtained in forested patches of the Limpopo, KwaZulu-Natal and Eastern Cape provinces exhibited a wide trophic niche width and generalised diet. Strong regional separation is apparent in the isotopic signatures suggesting little movement between provinces. A comparison of 13C-isotopes showed minimal variation that point to a uniformity in the carbon-base utilised by C. dichroa across their range. The 15N-signatures obtained in Limpopo, however, revealed a distinct trophic segregation between the northern-most Chorister populations and their southern counterparts. No altitudinal movements were detected in the isotopic signatures of recaptured Choristers, but more research is needed to investigate the long-term accuracy of these results and the breeding potential of resident Choristers in lowland coastal forests; especially when considering the reduced range and abundance reported for this endemic species.
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A Framework for using Open Source intelligence as a Digital Forensic Investigative tool
- Authors: Rule, Samantha Elizabeth
- Date: 2015
- Subjects: Open source intelligence , Criminal investigation , Electronic evidence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4715 , http://hdl.handle.net/10962/d1017937
- Description: The proliferation of the Internet has amplified the use of social networking sites by creating a platform that encourages individuals to share information. As a result there is a wealth of information that is publically and easily accessible. This research explores whether open source intelligence (OSINT), which is freely available, could be used as a digital forensic investigative tool. A survey was created and sent to digital forensic investigators to establish whether they currently use OSINT when performing investigations. The survey results confirm that OSINT is being used by digital forensic investigators when performing investigations but there are currently no guidelines or frameworks available to support the use thereof. Additionally, the survey results showed a belief amongst those surveyed that evidence gleaned from OSINT sources is considered supplementary rather than evidentiary. The findings of this research led to the development of a framework that identifies and recommends key processes to follow when conducting OSINT investigations. The framework can assist digital forensic investigators to follow a structured and rigorous process, which may lead to the unanimous acceptance of information obtained via OSINT sources as evidentiary rather than supplementary in the near future.
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A geochemical and morphological investigation of placer gold grains from the southern Seward Peninsula, Alaska : implications for source and transport mechanisms
- Authors: Gauntlett, Ernest John Herbert
- Date: 2015
- Subjects: Placer deposits -- Alaska -- Seward Peninsula , Gold alloys , Gold mines and mining -- Alaska -- Seward Peninsula , Geochemical surveys -- Alaska -- Seward Peninsula , Trace elements -- Alaska -- Seward Peninsula , Drift -- Alaska -- Seward Peninsula , Gold -- Standards of fineness
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5085 , http://hdl.handle.net/10962/d1018202
- Description: [Partial abstract]: This study presents the first detailed geochemical and morphological characterisation of gold grains from the southern Seward Peninsula, Alaska, a region with significant historical and on-going placer gold mining. Quantitative Au, Ag, Hg, and Cu data are presented for gold grains from eleven sites. Additionally, quantitative Te, W, As, and Sb trace element data are presented for gold grains from ten of the eleven sites. Although it is acknowledged that quantitative trace element analysis of gold grains is a relatively new endeavour, the limited trace element data obtained in this study suggest that trace element analysis could be useful for characterising gold sources on the southern Seward Peninsula. Major and minor element geochemical profiling is sufficient at differentiating between sites from regional provenance systems but insufficient at differentiating between sites within a single system. Differentiating among sites within a single system will likely require microchemical analysis of mineral inclusions and analysis of trace element signatures.
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A light-emitting-diode pulsing system for measurement of time-resolved luminescence
- Authors: Uriri, Solomon Akpore
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20976 , http://hdl.handle.net/10962/5788
- Description: A new light-emitting-diode based pulsing system for measurement of time-resolved luminescence has been developed. The light-emitting-diodes are pulsed at various pulse-widths by a 555-timer operated as a monostable multivibrator. The light-emitting-diodes are arranged in a dural holder connected in parallel in sets of four, each containing four diodes in series. The output pulse from the 555-timer is fed into an 2N7000 MOSFET to produce a pulse-current of 500 mA to drive the set of 16 light-emitting-diodes. This size of current is sufficient to drive the diodes with each driven at a pulse-current of 90 mA with a possible maximum of 110 mA per diode. A multichannel scaler is used to trigger the pulsing system and to record data at selectable dwell times. The system is capable of generating pulse-widths in the range of microseconds upwards.
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A study of barred preferential arrangements with applications to numerical approximation in electric circuits
- Authors: Nkonkobe, Sithembele
- Date: 2015
- Subjects: Electric circuits , Numerical calculations , Sequences (Mathematics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5433 , http://hdl.handle.net/10962/d1020394
- Description: In 1854 Cayley proposed an interesting sequence 1,1,3,13,75,541,... in connection with analytical forms called trees. Since then there has been various combinatorial interpretations of the sequence. The sequence has been interpreted as the number of preferential arrangements of members of a set with n elements. Alternatively the sequence has been interpreted as the number of ordered partitions; the outcomes in races in which ties are allowed or geometrically the number of vertices, edges and faces of simplicial objects. An interesting application of the sequence is found in combination locks. The idea of a preferential arrangement has been extended to a wider combinatorial object called barred preferential arrangement with multiple bars. In this thesis we study barred preferential arrangements combinatorially with application to resistance of certain electrical circuits. In the process we derive some results on cyclic properties of the last digit of the number of barred preferential arrangements. An algorithm in python has been developed to find the number of barred preferential arrangements.
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A water footprint assessment of primary citrus production in the Lower Sundays River Valley Citrus Farms, Eastern Cape, South Africa
- Authors: Munro, Samantha Alanna
- Date: 2015
- Subjects: Water efficiency -- South Africa -- Eastern Cape -- Evaluation , Water consumption -- Environmental aspects -- South Africa -- Eastern Cape , Citrus -- Water requirements -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:1120 , http://hdl.handle.net/10962/d1017558
- Description: With the current implementation of the South African National Water Act (NWA) underway, comprehensive tools to assist in the efficient, fair and sustainable management of water resources are needed. Water footprints (WFs) are increasingly being recognised as a meaningful way to represent human appropriation of water resources and provide a framework for assessing the sustainability of water use. The study calculated blue, green and grey WFs for the lower Sundays River Valley (LSRV) citrus sector across dry, humid and long-term average climates for a number of cultivars. The sustainability of both the LSRV and the production process of citrus were examined through the adoption of a number of environmental, social and economic indicators. The study revealed that there was no water scarcity in the area because of an inter-basin transfer and that water pollution levels attributed to citrus production required a more comprehensive indicator than the grey WF. Results showed that navels, despite being the dominant cultivar, had the highest WF and the lowest water productivity and technical efficiency. It also provided lower benefits of income and employment in terms of water use in comparison to other cultivars. Conversely, cultivars such as lemons, which required a greater amount of water and fertiliser, were the most productive cultivar with the lowest blue, green and grey WF. The study demonstrated the complexity of decisions regarding water management and the need to assess accurately the environmental, social and economic implications of strategies to increase efficiency of water. The importance of incorporating local data and verifying WFs was also illustrated. The analysis highlighted that WF assessments could be useful for the South African government and agricultural sectors to assist in future water management decisions and promote increased collaboration between stakeholders. The study found that the adoption of local benchmarks could be useful in aiding the promotion of more efficient water use and could factor in sensitive economic and social attributes. WFs in conjunction with other economic and social indicators could also be used to evaluate the sustainability of current and future allocations pertaining to the implementation of the NWA. It was however noted that this requires vast amounts of accurate data.
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Amber : a aero-interaction honeypot with distributed intelligence
- Authors: Schoeman, Adam
- Date: 2015
- Subjects: Security systems -- Security measures , Computer viruses , Intrusion detection systems (Computer security) , Computer security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4716 , http://hdl.handle.net/10962/d1017938
- Description: For the greater part, security controls are based on the principle of Decision through Detection (DtD). The exception to this is a honeypot, which analyses interactions between a third party and itself, while occupying a piece of unused information space. As honeypots are not located on productive information resources, any interaction with it can be assumed to be non-productive. This allows the honeypot to make decisions based simply on the presence of data, rather than on the behaviour of the data. But due to limited resources in human capital, honeypots’ uptake in the South African market has been underwhelming. Amber attempts to change this by offering a zero-interaction security system, which will use the honeypot approach of decision through Presence (DtP) to generate a blacklist of third parties, which can be passed on to a network enforcer. Empirical testing has proved the usefulness of this alternative and low cost approach in defending networks. The functionality of the system was also extended by installing nodes in different geographical locations, and streaming their detections into the central Amber hive.
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An analysis of malware evasion techniques against modern AV engines
- Authors: Haffejee, Jameel
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20979 , http://hdl.handle.net/10962/5821
- Description: This research empirically tested the response of antivirus applications to binaries that use virus-like evasion techniques. In order to achieve this, a number of binaries are processed using a number of evasion methods and are then deployed against several antivirus engines. The research also documents the process of setting up an environment for testing antivirus engines, including building the evasion techniques used in the tests. The results of the empirical tests illustrate that an attacker can evade multiple antivirus engines without much effort using well-known evasion techniques. Furthermore, some antivirus engines may respond to the occurrence of an evasion technique instead of the presence of any malicious code. In practical terms, this shows that while antivirus applications are useful for protecting against known threats, their effectiveness against unknown or modified threats is limited.
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An analysis of the risk exposure of adopting IPV6 in enterprise networks
- Authors: Berko, Istvan Sandor
- Date: 2015
- Subjects: International Workshop on Deploying the Future Infrastructure , Computer networks , Computer networks -- Security measures , Computer network protocols
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4722 , http://hdl.handle.net/10962/d1018918
- Description: The IPv6 increased address pool presents changes in resource impact to the Enterprise that, if not adequately addressed, can change risks that are locally significant in IPv4 to risks that can impact the Enterprise in its entirety. The expected conclusion is that the IPv6 environment will impose significant changes in the Enterprise environment - which may negatively impact organisational security if the IPv6 nuances are not adequately addressed. This thesis reviews the risks related to the operation of enterprise networks with the introduction of IPv6. The global trends are discussed to provide insight and background to the IPv6 research space. Analysing the current state of readiness in enterprise networks, quantifies the value of developing this thesis. The base controls that should be deployed in enterprise networks to prevent the abuse of IPv6 through tunnelling and the protection of the enterprise access layer are discussed. A series of case studies are presented which identify and analyse the impact of certain changes in the IPv6 protocol on the enterprise networks. The case studies also identify mitigation techniques to reduce risk.
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An ergonomics intervention study into the physiological, perceptual and productivity effects of three citrus harvesting bag designs in the Eastern Cape of South Africa : a combined laboratory and field approach
- Authors: Bassey-Duke, Elizabeth Misan
- Date: 2015
- Subjects: Citrus -- Harvesting -- South Africa -- Eastern Cape , Lifting and carrying -- South Africa -- Eastern Cape , Manual work -- South Africa -- Eastern Cape , Blue collar workers -- South Africa -- Eastern Cape , Work -- Physiological aspects , Human mechanics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5176 , http://hdl.handle.net/10962/d1018908
- Description: Background: Agriculture plays a vital role in the economy of any industrially developing country, including South Africa. In the Eastern Cape of South Africa citrus farming is a significant contributor to the local economy (Johnson et al., 2005). The harvesting phase of citrus farming is performed manually and exposes workers to physical risks, which can lead to the development of musculoskeletal disorders. In particular, the standard harvesting bag comprises of a single shoulder strap and promotes asymmetrical load carriage which results in shoulder and lower back pain complaints. The current study compared the physiological (EMG), perceptual (RPE), usability (PUEU) and productivity effects of two new harvesting bag designs (a hip belt and a backpack bag design) to the standard harvesting bag design. This was performed in a laboratory as well as a field setting. Methods (Laboratory phase): 36 participants (12 males and 24 females) were assigned to one worker group. The “tall ladder worker” group was comprised of only males and the “step ladder worker” and “ground worker” group of females. Each participant was required to simulate a citrus harvesting task while utilizing each of the bag designs on different days. On each day/test session, participants performed three harvesting cycles. Muscle activity was measured throughout the entire testing session and RPE were recorded at the end of each cycle. Results (Laboratory phase): The EMG and RPE results indicate that the backpack design was the most ideal design to reduce asymmetry, while the standard harvesting bag design was the worst. Although not significant, there was greater muscle asymmetry (p=0.109) and a significantly higher perceived exertion when using the standard bag (p=0.0004), in comparison to using the backpack. Methods (Field phase): 17 Xhosa-speaking citrus harvesters (6 females and 11 males) participated in this study. Each harvester worked with one of the three bag designs on a different day. Productivity of each worker was assessed every hour by recording the number of bags filled with fruit and at the end of the shift. A Perceived Usefulness & Ease of Use questionnaire was presented to each participant to obtain feedback on worker acceptance to the new bag designs. Results (Field phase): A general trend in support of the hip belt bag design over the other two bag designs were found, even within the different worker demographic groups (age, sex and worker experience). The workers perceived less exertion (7.98 ± 1.86) and were more productive (9.90 ± 2.11 bags/hour) when using the hip belt design; they also found this bag the most useful (1.02 ± 0.09) and easy to use (1.07 ± 0.25). In contrast, the backpack bag design had significantly poorer responses when compared to the other two bag designs and this was evident in all the dependent variables assessed (RPE, productivity and PUEU). Conclusion: The results from the laboratory phase supported the expectation that the backpack bag design reduces asymmetry and hence, is more suitable than the standard harvesting bag. However, results from the field show that the hip belt bag design was the most preferred and the backpack was the least preferred. Bao & Shahnavaz (1989) highlight the need for ergonomics researcher to convey laboratory findings into the field context. However, as shown by the current study, there are numerous challenges associated with field work, making it difficult for laboratory findings to be successfully conveyed to the field. Limitations and Recommendations: For the laboratory phase of the project, no biomechanical and cardiovascular responses were assessed. However, for a holistic approach, these variables should be considered in future studies. Due to high variability from one harvesting cycle to another, more than three harvesting cycles should also be performed to accurately replicate the harvesting process as done in the field over extended durations of time. For the field phase, data should be collected from more than one citrus farm and thus a larger sample size could be obtained. This would improve the validity of the study. In addition to this, data should be collected for a full working day, especially if environmental conditions are not a hindrance, as well as for a whole season, since workloads vary, depending on the time of the harvesting season. , Name on Graduation Programme: Bassey-Duke, Elizabeth Missan
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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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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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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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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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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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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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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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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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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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