Detecting derivative malware samples using deobfuscation-assisted similarity analysis
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
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Developing an attractant for monitoring fruit-feeding moths in citrus orchards
- Authors: Goddard, Mathew Keith
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2981 , vital:20349
- Description: Fruit-piercing moths are a sporadic pest of citrus, especially in the Eastern Cape Province of South Africa, where the adults can cause significant damage in outbreak years. Currently the only way in which to successfully control fruit-feeding moths within the orchards is the use of repellent lights. However, growers confuse fruit-piercing moths with fruit-sucking moths that don‘t cause primary damage, and there is no way of monitoring which moth species are attacking the fruit in the orchards during the night. In a previous study, banana was shown to be the most attractive bait for a variety of fruit-feeding moth species. Therefore the aim of this study was to determine the population dynamics of fruit-feeding moths develop a cost-effective alternative to the use of fresh banana as a bait for fruit-piercing moths. Fresh banana was compared to nine alternative synthetic attractants, frozen banana and a control under field conditions in several orchards in the Eastern Cape Province. Once again, banana was shown to be the most attractive bait. Some 23 species of fruit-feeding moth species were sampled in the traps, but there was only two fruit-piercing species, Serrodes partita (Fabricius) (Lepidoptera: Noctuidae) and Eudocima sp. Surprisingly S. partita, which was thought to be the main pest, comprised only 6.9% of trap catches. Serrodes partita, is a sporadic pest, only becoming problematic every five to 10 years after good rainfall in the Little Karoo region that causes flushes of their larval host, wild plum, Pappea capensis (Ecklon and Zeyher). During these outbreaks, damage to fruit can range from 70 to 90% and this is especially so for soft skinned citrus. A study on the morphology of the proboscis confirmed that only two species of fruit-piercing moths were present. Trap catches over three citrus growing seasons was linked to fruit damage found within several orchards. Once again fruit-piercing moth damage was relatively low in comparison to other types of damage such as mechanical and undefined damage. There was a very weak correlation between S. partita trap catches and damage, but generally damage was recorded two to three weeks after a peak in S. partita trap catches. Climatic conditions were also recorded and compared to weekly trap catches of S. partita, and while temperature and wind direction had no influence on moth populations, precipitation in the orchards was weakly correlated with trap catches. This study has shown that in non-outbreak seasons, the main fruit-piercing moth, S. partita comprises a small percentage of fruit-feeding moths in citrus orchards, but that growers are unable to determine the difference between fruit-piercing species and the harmless fruit-sucking species. Further fresh banana remains the best method for attracting fruit-piecing moths to traps, but this is not cost effective and thus a commercially viable protocol for monitoring these species remains elusive.
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Development of a high-throughput bioassay to determine the rate of antimalarial drug action using fluorescent vitality probes
- Authors: Laming, Dustin
- Date: 2016
- Subjects: Malaria -- Africa , Plasmodium falciparum , Drug development , Fluorescence
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64434 , vital:28542
- Description: Malaria is one of the most prevalent diseases in Africa and the Plasmodium falciparum species is widely accepted as the most virulent, with a fatality rate of 15 – 20 % of reported cases of infection. While various treatments have been accepted into early stage clinical trials there has been little progress towards a proven vaccine. Pending a long term solution, endemic countries rely heavily on the development of innovative drugs with acute efficacy coupled with rapids mode of action. Until recently the rate of drug action has been measured by light microscopic examination of parasite morphology using blood slides of drug treated parasite cultures at regular time intervals. This technique is tedious and, most importantly, subject to interpretation with regards to distinguishing between viable and comprised parasite cells, thus making it impossible to objectively quantitate the rate of drug action. This study aimed to develop a series of bioassays using the calcein-acetoxymethyl and propidium iodide vitality probes which would allow the rate of drug action on Plasmodium falciparum malaria parasites to be assessed and ranked in relation to each other. A novel bioassay using these fluorescent vitality probes coupled with fluorescence microscopy was developed and optimized and allowed the rate of drug action on malaria parasites to be assessed i) rapidly (in relation to current assay techniques) and ii) in a semi-quantitative manner. Extrapolation to flow cytometry for improved quantification provided favourable rankings of drug killing rates in the pilot study, however, requires further development to increase throughput and approach the ultimate goal of producing a medium-throughput assay for rapidly assessing the rate of action of antimalarial drugs. Attempts to adapt the assay for use in a multiwell plate reader, as well as using ATP measurements as an indication of parasite vitality after drug treatment, was met with erratic results. The viability probes assay as it stands represents an improvement on other assay formats in terms of rapidity and quantification of live/compromised parasites in cultures.
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Do differences in personality traits affect how drivers experience music at different intensities?
- Authors: Tlhoaele, Kebaabetswe
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3695 , vital:20536
- Description: Various researchers have investigated contributing factors towards the number of acute traffic incidences in and around Southern Africa. Some of these contributing factors include: the skills component of the driver predominately attributed to driving experience as well as the behavioural component influenced by the driver’s natural predisposition, individual differences and personality traits. In order to manage these factors drivers have developed varying coping mechanisms. One of these coping mechanisms is listening to music while driving, which is readily available in most cars and extensively used predominately during long duration driving. Listening to music neither increases one’s driving duration (as opposed to taking several breaks), nor does it interfere with the physical movements of driving (in the manner that eating and drinking may), but it might impact the concentration and attention of some drivers. This is based on the notion that music is assumed to impact arousal and cognitive ability. While there are several studies on the effect of music on driving performance and personality traits very few studies have looked at whether music has a positive or negative effect on driving performance based on differences in personality traits; and whether the extent of this effect might differ for different intensities of music? Consequently, this study aims to understand and determine the extent to which different personality traits predict the effect that listening to different music intensities has on driving performance. The impact of differing music conditions on the different personality traits used a repeated measures design and a between group design with respect to the personality traits with a sample size of (n=25)-16 females and 9 males-and their ages ranged between 19-35 years of age. The average age and standard deviation for this sample size was 22 years±2. A low-fidelity driving simulator task was utilised in order to provide a controllable, repeatable and a safe environment as compared to a real road situation. Personality was assessed using an online Big-Five Inventory scale (extraversion, agreeableness, conscientiousness, neuroticism, openness). All the different personality groups completed three conditions (45 minutes each) in a randomised order (without music, moderately loud music and loud music). Psychophysiological parameters i.e. heart rate frequency (HRF), heart rate variability (HRV) and eye movements (pupil diameter, eye speeds, fixation duration, blink frequency and blink duration) and driving performance were measured continuously. Subjective performance Multidimensional Driving Style Inventory was measured once-off prior to completion of the testing sessions, whilst the NASA-Task Load Index scale and Perceived control of participants were assessed after each condition. The expected outcomes revealed that music had an effect on objective driving performance (tracking deviation and reaction time) and psychophysiological measures only for participants of certain personality types while other personality types were unaffected by music. The subjective performance measures did not follow the same trend as objective performance measures. The conditions did not reveal an effect on driving performance, for most of the psychophysiological parameters and subjective measures. There was mainly a significant time on task effect and interactional effects on the psychophysiological measures (physiological and oculomotor) parameters at (p<0.05), but not on the subjective measures as anticipated. The study illustrated that the there are differences between personality traits. There was difficulty in the interpretation of the results based on the complexity of the findings for which each hypothesis was partially accepted. The research may establish practical implications for traffic safety campaigns in South Africa, as well as influence driving education for citizens. Assessing the personality trait would help to form an understanding as to which of the personality traits might be affected negatively from listening to music while driving and those that might benefit. Moreover, this study may assist motorists in understanding the implications of listening to music while driving as this may sometimes elicit risky driving behaviour and possibly cause an accident that may result in death.
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Ecological engineering on rocky shores: grazing, predation, nutrient availability and their influence on epifaunal communities
- Authors: Ndhlovu, Aldwin
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3453 , vital:20500
- Description: “Ecosystem engineers modify, create/destroy habitat and directly/indirectly modulate availability of resources to other species by causing physical state changes to biotic and abiotic materials” (Jones et al, 1994, page 1). Previous studies have analysed top-down and bottom-up relationships to determine which form of regulation is key in controlling community composition. This study assessed the direct and indirect effects of top down and bottom up factors on the epifaunal communities of macro-algae. Epifauna are subject to the direct top-down effects of predation and bottom up effects of habitat availability. Habitat availability in turn experiences the direct top down effects of grazing and bottom up effects of nutrient availability due to upwelling. Grazing and upwelling may therefore have indirect effects on macro-algal epifauna. Four treatments (Procedural controls, Controls, Predator or Grazer exclusion) set out in a block design (n = 5) were monitored monthly for algal cover of the substratum for 12 months with the surface area of algal plants and epifaunal species composition and abundances assessed at the end of the experiment. The red alga Gelidium pristoides was selected as the ecosystem engineer as it is common, supports a diverse community of epiphytic animals and acts as a nursery for small epifaunal organisms. The experiment was run at two upwelling sites interspersed with two non-upwelling sites. Sites were separated on scales of 100km along approximately 500km of coastline. Dipping whole algae in dish washing liquid provided a strong relationship between their surface area and the weight of the film of dish washing liquid covering them. Surface area was strongly correlated to dry weight but neither surface area nor dry weight was correlated to algal cover of the substratum. Algal cover was influenced by the interactions of treatment with site (nested in upwelling) and upwelling. At all sites, treatments that allowed access to grazers, Grazer + and Control treatments, showed no significant differences and these two treatments had lower algal cover than Predator + and Closed treatments which did not differ from one another 3 [Grazer + = Control < Predator + = Closed]. A total of 44 epifaunal species were identified, with the predominant orders being Amphipoda and Isopoda. Primer results showed that only site had a significant effect on species composition, with sites that were further apart being more different. Site (nested in upwelling) had an effect on total epifaunal abundances when data were non-normalised. When total epifaunal abundances were normalised for algal cover of the substratum or algal surface area to provide density data, predation had no significant effect. Grazing did have a significant effect, but only when data were normalised to algal surface area, not cover, leading to the conclusion that indirect top-down factors through grazing of the sea weed are important in structuring epifaunal communities depending on how habitat availability is measured.
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Effect of lipid inclusion levels in aquafeed on carcass composition, quality change during storage and nutrient excretion in dusky kob (Argyrosomus japonicus)
- Authors: Ginindza, Nhlanhla Joseph
- Date: 2016
- Subjects: Aquaculture
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5387 , http://hdl.handle.net/10962/d1020854
- Description: Dusky kob, Argyrosomus japonicus, is an aquaculture species in South Africa that is in pilot commercial production. While the major nutrient requirements of the species are known, the advantages of incorporating formulated feeds into the diet of the species has yet to be fully explored. Research on formulated feed composition is required to: minimise input costs; improve the organoleptic properties and meat quality; and minimise nutrient loss, which contributes to environmental pollution. This study sought to test the impact of different lipid levels in aquafeeds fed to dusky kob juveniles by determining: (i) growth performance, feeding efficiency, proximate and fatty acid composition; (ii) chemical changes and shelf-life of refrigerated fish fillets; and (iii) metabolic rates and nitrogen excretion of juvenile dusky kob. And more...
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Effects of the biocontrol agent, coelocephalapion camarae kissinger, galling on petiole tissues, plant growth and stored reserves in plant parts of two lantana camara L.(verbenaceae) varieties
- Authors: Kistensamy, Yoganambal
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3126 , vital:20372
- Description: The agent evaluated in this study, Coelocephalapion camarae Kissinger (Brentidae), a petiole galling apionid, was released against Lantana camara L. (Verbenaceae) in South Africa and has the potential to significantly contribute to the control of this noxious weed. An important aspect of evaluating the effectiveness of a biocontrol agent; include the understanding of the mechanism in which the biocontrol agent causes damage to the plant and the plant’s response to this damage. Another aspect that was considered in evaluating the effects of the apionid was the varietal differences that exist within the weedy L. camara complex. Larval feeding of C. camarae damaged the tissue in the petioles causing gall formation and this was quantified on two common South African L. camara varieties (017 and 018). Up to 100% of the vascular tissue (xylem and phloem) of effected petioles was eaten by larvae, 25 days after ovipostion in both the L. camara varieties, effectively severing the vascular connection from the leaves. The effect of feeding and galling by different population densities of C. camarae, on biomass and total soluble sugar and starch concentrations of different plant parts was measured on these two varieties during autumn, and compared to a similar study, done during summer. Relatively low galling percentages were achieved in the experiments of this study. Plant growth was less affected by apionid feeding at similar galling levels, as higher galling densities in these trials were similar to those at low exposures in trials by Baars (2002). The dry weights of all individual and combined plant parts for lantana variety 017 was less for both adult density exposures after 70 days compared to the weights of its controls, although not statistically significant at P>0.05 The opposite effect, though barely noticeable was recorded for lantana variety 018; here, the dry weights of individual plant parts and as whole plants weighed more in the plants exposed to both densities of weevil feeding and galling after 70 days, compared to its controls. Coelocephalapion camarae herbivory may thus be more effective in inflicting damage on some L. camara varieties compared to others. The effects of late season carbohydrate storage revealed that, from early- to mid-autumn starch concentrations increased significantly in stems of both L. camara varieties and L. camara var. 018 had larger starch reserves for winter. In L. camara var. 018 stems, starch increased 52 times and concentrations doubled in stems of L. camara var 017. The increase in the sugar and decrease in starch concentrations in leaves of plants of both varieties exposed to apionids in this study was attributed to a possible reduction of available nitrogen and phosphorus, due to apionid feeding, whilst starch was reallocated within the plants to stems and roots. The increase in starch concentrations in stems of plants that were exposed to apionids may have been expected, as compensation for herbivory has been associated with, increases in photosynthetic rates and the mobilization of stored resources. Herbivory by the apionid early in the growing season may be easily compensated for by L. camara as there are nutrient flushes experienced by plants that allows the maximum uptake of nutrients facilitating recovery, whereas later in the season plants suffer lower nutrient availability and don’t recover so readily. Both early and late in the season the accumulated effects of C. camarae feeding over time will undoubtedly decrease fitness of most lantana varieties.
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Electrode surface modification using iron(II) phthalocyanine immobilized via electrografting and click chemistry and clicked onto azide-functionalized quantum dots: applications in electrocatalysis
- Authors: Nxele, Siphesihle Robin
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3464 , vital:20501
- Description: Tetrakis(5-hexynoxy)Fe(II) phthalocyanine was used alone and in combination with quantum dots (QDs) in order to test the electrocatalytic ability with hydrazine and paraquat as the analytes of interest. This novel phthalocaynine was successfully synthesised and characterized using various characterisation techniques. The QDs used were the well-known core-shell CdSe/ZnS nanostructures. The fabrication of glassy carbon electrodes involved covalent attachment by electrochemical grafting and click chemistry for the first part of the work and the second part involved the conjugation of the synthesised QDs and the phthalocyanine by click chemistry. This approach of conjugating these nanostructures introduced another aspect of novelty to the work reported in this thesis. The immobilisation of this conjugate on a glassy carbon electrode (GCE) was achieved by adsorption. Characterisation techniques such as infrared spectroscopy, x-ray diffractometry, UV/vis spectroscopy, transmission electron microscopy and x-ray photoelectron spectroscopy were used to characterise the molecules and conjugates of interest. With respect to the electrocatalytic part of the work, electrode surface characterisation involved scanning electrochemical microscopy and cyclic voltammetry to determine changes in the nature of the surface as well as reactivity of the surface at different modification steps. Detection limits and the sensitivity determined for the electrocatalysts fabricated here proved to be an improvement compared to other reported work involving phthalocyanines and the test analytes chosen for application. With respect to the conjugate, the electrocatalytic ability was improved when the QDs and phthalocyanine were combined using click chemistry compared to using the phthalocyanine alone.
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FRAME: frame routing and manipulation engine
- Authors: Pennefather, Sean Niel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3608 , vital:20529
- Description: This research reports on the design and implementation of FRAME: an embedded hardware network processing platform designed to perform network frame manipulation and monitoring. This is possible at line speeds compliant with the IEEE 802.3 Ethernet standard. The system provides frame manipulation functionality to aid in the development and implementation of network testing environments. Platform cost and ease of use are both considered during design resulting in fabrication of hardware and the development of Link, a Domain Specific Language used to create custom applications that are compatible with the platform. Functionality of the resulting platform is shown through conformance testing of designed modules and application examples. Throughput testing showed that the peak throughput achievable by the platform is limited to 86.4 Mbit/s, comparable to commodity 100 Mbit hardware and the total cost of the prototype platform ranged between $220 and $254.
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Genetic and biological characterisation of a novel South African Cydia pomonella granulovirus (CpGV-SA) isolate
- Authors: Motsoeneng, Boitumelo Madika
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20503 , http://hdl.handle.net/10962/d1021266
- Description: The codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is the primary pest of pome fruit cultivated worldwide. The control of this insect pest has been dependent on the frequent use of broad-spectrum chemical pesticides, which has led to the development of resistance in pest populations and negative effects on human health and the environment. The Betabaculovirus of C. pomonella has successfully been applied as a biological control agent in integrated pest management (IPM) programmes for the suppression of pest populations worldwide. Previously, all Cydia pomonella granulovirus (CpGV) biopesticides were based on a Mexican isolate (CpGV-M) and although these products are highly efficient at controlling C. pomonella, resistance cases have been reported across Europe. The identification of novel CpGV isolates as additional or alternative control agents to manage resistance is therefore necessary. This study aimed to genetically and biologically characterise a novel South African C. pomonella granulovirus isolate and to test its virulence against neonate larvae. Based on the morphology of the occlusion bodies observed using transmission electron microscopy, granuloviruses were recovered from diseased and dead larvae collected from an orchard in South Africa where no virus applications had been made. DNA was extracted and the identification of the isolated granulovirus was achieved through the PCR amplification and sequencing of the lef-8, lef-9, granulin and egt genes. Submission of the gene sequences to BLAST revealed high percentage identities to sequences from various CpGV isolates, resulting in the naming of the isolate in this study as the South African Cydia pomonella granulovirus (CpGV-SA) isolate. Phylogenetic analysis based on the single nucleotide polymorphisms (SNPs) detected in the lef-8, lef-9 and granulin nucleotide sequences grouped the South African isolate with CpGV-E2 (genome type B) and CpGV-S (genome type E). The CpGV-SA isolate was further genetically characterised by restriction endonuclease analysis and complete sequencing of the genomic DNA. Differences were observed for the BamHI, EcoRI, PstI and XhoI profiles of CpGV-SA in comparison to the respective profiles generated for CpGV-M extracted from a biopesticide, Carpovirusine® (Arysta Lifescience, France). Several genetic variations between the complete genome sequence of CpGV-SA and the reference isolate, CpGV-M1, as well as a recent genome submission of CpGV-M, both representing genome type A were observed. The complete genome analysis confirmed that CpGV-SA is genetically different from the Mexican CpGV isolate, used in thedevelopment of most biopesticides. In silico restriction profiles of the genome sequence obtained for CpGV-SA and genome sequences of genetically different CpGV isolates originating from Mexico (M1 and M), England (E2), Canada (S) and Iran (I12 and I07), available on the NCBI’s GenBank database confirmed that CpGV-SA is of mixed genotypes. Furthermore, the South African isolate shared the single common difference found in the pe38 gene of resistance overcoming isolates, which was the absence of an internal 24 nucleotide repeat present in CpGV-M1. In addition to the common difference, SNPs detected in the pe38 gene grouped the isolate with the CpGV-S isolate, suggesting that the CpGV-SA isolate is predominantly of genome type E. To determine the biological activity of CpGV-SA against neonate C. pomonella larvae, surface bioassays were conducted alongside CpGV-M (Carpovirusine®) bioassays. The LC50 and LC90 values for the South African isolate were 1.6 × 103 and 1.2 × 105 OBs/ml respectively. The LT50 was determined to be 135 hours. These values were similar to the values obtained for CpGV-M (Carpovirusine®). The results in this study suggest that a novel South African CpGV isolate of mixed genotypes, potentially able to overcome resistance in C. pomonella, with biological activity similar to CpGV-M (Carpovirusine®) and important for the control of C. pomonella was recovered. The CpGV-SA isolate could therefore potentially be developed into a biopesticide for use in resistance management strategies against C. pomonella populations in South Africa.
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Genetic structure and biogeography of three wrasse species (Labridae) within the Western Indian Ocean
- Authors: Mayekiso, Sisanda
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1114 , vital:20021
- Description: The biogeography of wrasses within the Western Indian Ocean (WIO) is poorly understood, with regard to origins and genetic differentiation or connectivity among the regions of the WIO. This region is a good model for studying the influence of physical complexities and biogeographic breaks in shaping patterns of differentiation in wrasses. Three reef-associated fish species, Cheilio inermis, Thalassoma hebraicum and T. lunare, were selected to examine the factors that have influenced patterns of differentiation across the WIO. Each species was sampled from various localities of the WIO, the Red Sea and Indo-West Pacific Islands. Sequence data were generated from two mitochondrial gene fragments (cytochrome b and ATPase 6) and one nuclear locus (the first intron of the ribosomal protein S7 gene). Genetic analyses were used to calculate genetic diversity indices within species, which were then compared among species. The relationships among haplotypes and alleles were constructed using median-joining networks. Where necessary, neighbour-joining trees (NJ) were constructed to examine relationships among haplotypes and alleles for the Thalassoma species. Population structure was analysed using AMOVA and pairwise ФST to compare and calculate differentiation between the WIO localities. Mismatch distributions were used to examine population growth and decline or stability, and demographic parameters were used to calculate time of population expansion. There was high haplotype (h = 0.88 to 0.98) and low nucleotide diversities (π = 0.003 to 0.008) among all species for mitochondrial markers. For S7 intron I, high allelic (A = 0.95 to 0.98) and low nucleotide diversities (π = 0.002 to 0.014) were observed for all species. The pairwise ФST values revealed little to great (ФST = -0.02 to 0.67) genetic differentiation between localities, across all species for the three gene regions. The pairwise comparisons indicated the differentiation in C. inermis of Tanzania and Kenya from Mozambique and Nosy Be (Madagascar). The widespread C. inermis also revealed the differentiation of Kenya and Tanzania. For C. inermis, the AMOVAs of ATPase 6 and cytochrome b data indicated high differentiation among defined locality groups. The groups were defined according to geographic proximity. However, the AMOVA of the nuclear gene (S7 intron I) did not find variation among defined locality groups. Cheilio inermis revealed a sequence divergence of 0.4%. The divergence that was found in C. inermis was not enough to suggest a cryptic species within the WIO. Overall, the widespread and monotypic C. inermis revealed genetic differentiation within the WIO. Thalassoma hebraicum generally revealed little genetic differentiation across the WIO. The AMOVAs of the three gene regions showed no variation among specimens of the defined locality groups. However, some differentiation was found between localities. The pairwise comparisons of T. hebraicum revealed the differentiation of Seychelles from the African mainland and Madagascar. Southern Africa was observed to be differentiated from Nosy Be and Zanzibar. The observed differentiation could be caused by oceanic barriers such as the South Equatorial Current (SEQC), East African Coastal Current (EACC), and the Comoros Gyres and eddies in the Mozambique Channel, and Agulhas Current. Thalassoma lunare revealed genetic isolation between the WIO and the Red Sea as well as within the WIO. The genetic isolation between the WIO and the Red Sea is probably due to the historical isolation by the Bab al Mandab and contemporary barriers such as the cold upwelling cells in Somalia. The differentiation of Maldives from the African mainland and Seychelles could be due to distance and the upwelling cells created by monsoon winds. Mismatch distributions suggested that C. inermis and T. hebraicum had undergone demographic expansion during the Pleistocene (92 678 to 40 219 years ago). The results of the current study are similar to those from previous studies of WIO reef fish species, and the results of the present study could have potential implications for conservation and fisheries management. Single genetic markers and single species studies do not detect all barriers to dispersal in the WIO, thus they are insufficient to inform conservation management. Thus, the use of multispecies and genetic markers in the current study can be adopted by other studies of the marine taxa of the WIO.
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Geochemical exploration for copper - cobalt in the Democratic Republic of Congo, Central African Copperbelt: a case study on PR851
- Authors: Katombe-Kisumbule, Paul
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3035 , vital:20354
- Description: The PR851 licence area is located at about 80 km west from the town of Likasi in the district of Haut-Katanga and 175 km north-west of Lubumbashi, the capital city of Katanga Province in the Democratic Republic of Congo. The exploration licence was granted by the government of the Democratic Republic of Congo to First Quantum Minerals Ltd through its Congolese subsidiary Compagnie Minière de Sakania Sprl (CoMiSa Sprl) under certificate N˚ CAMI/CR/70/2003 on the 10th of October 2003 for a period of 5 years with a possibility of renewal for 3 years in respect to the new Congolese mining code. The PR851 area lies on fragments of Mines Subgroup rocks of the Roan Group in the Congolese Copperbelt where most of the Cu-Co and stratiform-stratabound deposits such as Kipushi, Ruashi-Etoile, Kinsevere, Kipoi, Luishya, Luswishi, Shituru, Kamoya, Kambove, Tenke- Fungurume, Shinkolobwe, Swambo, Mindingi and Kamoto among others are found. During the 20th century, the Union Minière du Haut Katanga (U.M.H.K.) undertook mineral exploration in the Congolese Copperbelt and numerous copper- and cobalt-occurrences were identified (for instance Kibamba copper occurrence in PR851 area). From 2003, the Compagnie Minière de Sakania Sprl initiated a grassroots exploration program in PR851 area and geochemical exploration survey as one of the mineral exploration tools was implemented to aim at detecting copper and cobalt concentration in soil. The B horizon of the thick tropical soil in the area was sampled and soil samples were sent to Genalysis laboratories in Johannesburg, Republic of South Africa for main chemical analysis of Cu and Co only, whereas 10% of analyzed samples were dispatched to Perth, Western Australia for quality control analysis. Thresholds for anomalies of copper and cobalt were defined by literature comparison, standard deviations and spatial analysis. The anomalies were tested at a later stage by reverse circulation / diamond drilling during the year of 2005 to 2008 and the Cu-Co resources were estimated by Digital Mining Services of Harare, Zimbabwe in the year of 2008. Geological logging of chips from reverse circulation and diamond drill cores revealed that copper mineralization is represented by malachite, chrysocolla, chalcopyrite and bornite whereas cobalt mineralization appeared in form of heterogenite. The source of supergene mineralization remains unknown. Recommendations have been made to undertake more geological exploration work in order to fully investigate the geological setting and structural architecture of the region, which may result in a better understanding of the Cu-Co mineralization system and ore genesis. The latter has been no consensus up-to-date and different theories have been proposed to discuss the ore genesis, including syn- and dia- genetic, synorogenic and sulphide remobilization to late-to-post- orogenic Cu-Zn-Pb Kipushi-type deposit. However, geological observations favored that the diagenetic and syngenetic models are applicable to numerous deposits in the Central African Copperbelt.
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Geology, regional diamond exploration and diamond provenance of the proterozoic diamondiferous Umkondo conglomerates, Umkondo group, eastern Zimbabwe
- Authors: Zhou, Takawira
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3598 , vital:20528
- Description: The Umkondo Sedimentary Basin in eastern Zimbabwe has been studied by various individuals and organizations since 1901. Their interest had been in finding limestone and beryl and base metal deposits, especially copper, iron and uranium, but these occurrences had proved to be of no economic value (Watson, 1969). The recent discovery of placer diamonds within the Proterozoic basal conglomerates of the Umkondo Sedimentary Basin has now attracted worldwide interest in the basin’s diamond economic potential, in understanding of the geology, and the diamond provenance of the Umkondo conglomerates. The Umkondo Sedimentary Basin basal conglomerate placer deposit might narrowly be defined as a mega-placer because of its sheer large size and high grades, especially on the 70,000 hectare western margin diamond dispersion halo where alluvial diamonds are being mined. Bluck, et al., (2005, pp 213) defines a diamond mega-placer as: . . . a number of linked deposits that are a result of one or a continuous process of transportation and deposition and holds or have held at least >= 50 million carats at >= 95% gem quality, for example, the Orange-Vaal dispersal, off the Kaapvaal craton in South Africa. On craton placers are residual, and transient placers are eroded and deposited into the exit drainage, while terminal placers, the final depositories of diamonds with the highest chances of being mega-placers are deposited into terminal basins like oceans and foreland basins. Though data is limited at the moment, the Umkondo conglomerates caratage is likely to run into hundreds of millions of carats, with a diamond gem content of between twenty and twenty-five percent, as is indicated from recent diamond production data. The greater part of the Umkondo diamonds are likely to be lodged beneath the deep gravels of the Middle and Lower Save River basin, because small remnant tilted mountain blocks and inselbergs forming the caps of hills are what remains of the host conglomerate on the western margin of the Umkondo Basin. Areas to be examined in this document will be the geology; the mode of formation of the Umkondo basin and its sedimentary system; the regional kimberlite exploration around the basin; and diamond production in the Marange diamond field, in order to come up with indications of the provenance of the diamonds within the Umkondo conglomerates. The kimberlite clusters in and around the Umkondo sedimentary basin have all proved to be barren or only nominally diamondiferous and that the kimberlites are between 200Ma and 500Ma and thus much younger than the greater than 1.1Ga Umkondo diamondiferous conglomerates. Studies so far undertaken have not managed to point to the origin, or provenance, of the Umkondo or Marange diamonds, which were discovered on the western edge of the Umkondo Basin and in the east of the basin below the Chimanimani Mountains along the Haroni River. This paper is an attempt to clear up some of the misconceptions surrounding the Marange diamond deposit and to raise interest in the urgent rquirement to study and understand the Umkondo Basin and the origin of its diamonds. The only meaningful studies on diamond occurrence and diamond exploration of the basin were undertaken from 1996 to 2006 by Kimberlitic Searches Zimbabwe (Pvt) Ltd, the then Zimbabwe kimberlite exploration arm of De Beers, Zimbabwe, in their quest to find kimberlites, which were thought to be related to the Umkondo alluvial diamond deposit. As will be shown in the following chapters, many of the discovered kimberlites range from very low grade to non-diamondiferous, and are much younger than the Umkondo conglomerates, whose diamonds are in turn a great deal older. Thus the basic question concerning the origin or provenance of the Umkondo placer diamonds still remains unresolved. Because of the sheer size of the basin, modern, wide-area-coverage, geophysical exploration methods become appropriate to effectively generate diamond potential targets for further examination. This document will attempt to collate various data available to paint a true picture of the state of exploration within the Umkondo Basin.
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Historical perspectives and future directions for access to land, water and related ecosystem services in the Lower Sundays River Valley, South Africa: implications for human well being
- Authors: Chadzingwa, Karabo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/442 , vital:19959
- Description: The legacy of South Africa’s history has facilitated unequal access to land and water resources. In the Lower Sundays River Valley (LSRV), a predominantly commercial farming area, differential access to land and water has impacted aspects of ecosystem service access and human well‐being for disenfranchised families over time. Despite the social, political and economic reform efforts in the past two decades, severe inertia towards efforts attempting to increase equitable access to land and water has been experienced. As a result, communities have mobilized and claimed their land from the government through the land restitution process. Based on a mixed‐methods approach, this research explores the ways in which access to land and water over time has influenced current levels of human well‐being among disenfranchised families. Provisioning and cultural ecosystem services were identified as key areas of loss as a result of forced evictions from land. Freedom of choice was a central and cross‐cutting theme regarding the ability to change levels of human well‐being. Although the loss of ecosystem services associated with land and water had an impact on households, the ecosystem services which are regarded as fundamental to human well‐being do not seem to have been lost. The study recommends the wide use of freedom of choice as an indicator for well‐being in the LSRV, as well as a consideration of subjective, objective and psychological measures of well‐being with regards to natural resources and ecosystem services access. Key agents in fostering desirable pathways toward equity and sustainability in the LSRV are identified with stakeholders as private businesses; inclusive governance; empowered and skilled individuals, as well as NGOs.
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How do social and personal identity, sense of place, connectedness to nature and environmental understanding influence the implementation of collective, large-scale biodiversity stewardship initiatives in South Africa?
- Authors: Potts, Tracey Ann
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3663 , vital:20534
- Description: Biodiversity stewardship is a mechanism that is used to conserve high value biodiversity assets. Biodiversity stewardship programmes focus on areas that are under immediate threat from development or under medium to long term threat from degradation or transformation that will result in habitat loss. Biodiversity stewardship provides a solution to the resource crisis being faced by many state and provincial conservation agencies, NGO’s (Non-Governmental Organisations) and PBO’s (Public Benefit Organisations) in that it facilitates the declaration, and the subsequent improved conservation management, of private or communally owned land whilst still retaining the existing tenure. The rate of habitat loss can often be slowed, or even reversed, by proactively securing these areas and facilitating management decision-making with a focus on biodiversity outcomes without the capital investment required by the State to purchase the land. In return for conservation management actions, certain land-use restrictions and the associated opportunity costs, the State offers a suite of incentives and benefits that are, where possible, tailored to meet the needs of the landowner. Particular regions of South Africa lend themselves well to the development of biodiversity stewardship initiatives which are designed to secure ecological processes and ecosystems across a landscape or an ecological feature at scales of tens of thousands of hectares. When developing landscape level biodiversity stewardship initiatives, negotiations tend to be focussed on groups of landowners. This requires collaboration and the collective alignment of natural resource management decision-making and conservation actions amongst neighbours. Gaining a better understanding of how the social constructs of ecological understanding, place attachment, connectedness to nature, occupational identity and social and personal identity influence decision-making, behaviour and group structure is a critically important factor when developing a tool to predict the likelihood of landowners to collectively commit to long-term, legally binding biodiversity stewardship programmes. The overarching hypothesis was that the social constructs listed above influence group dynamics within the context of collective pro-conservation behaviour. Social dynamics associated with large-scale biodiversity stewardship initiatives become complex when multiple landowners are involved. Could social cohesion and group culture be influenced by aspects of identity and do these in turn develop into barriers or motivators to coordinated and sustained conservation efforts? Further influences on the successful implementation of landscape scale biodiversity stewardship initiatives could include ecological understanding, connectedness to nature and place attachment. Structured interviews were held with the landowners engaged in two separate large-scale biodiversity stewardship sites, the Compassberg Protected Environment and the Baviaanskloof Hartland, in the Eastern Cape Province of South Africa. The interviews were followed up with surveys containing psychometric scales related to the influence of ecological understanding, place attachment, connectedness to nature and aspects of identity on commitment to collective long-term, large-scale biodiversity stewardship initiatives. The results from a set of non-parametric (exact) Wilcoxon rank-sum tests showed that scores on the new ecological paradigm scale and the place attachment scale latent variables were significantly different at the two study sites, at the 10% level of significance. Demographic differences between the two study sites influenced group dynamics, collective decision-making and commitment. The relationship between the latent variables (the five psychometric scales measured) and the ancillary variables (the demographic data describing the respondents) cannot be considered conclusive; however they do provide relatively useful insights into the development of a scale or tool to measure conservation opportunity. The thesis concludes with a proposed conservation opportunity assessment tool that can be utilised alongside the existing, well refined, conservation priority assessment tools to assist in decision-making when planning large, landscape scale biodiversity stewardship initiatives in South Africa.
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Identification of potential novel roles for Hsp70/Hsp90 organising protein (Hop) using proteomic analysis in human cells
- Authors: Wingate, Ianthe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64758 , vital:28598
- Description: Expected release date-May 2018
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Improved singlet oxygen generation by a novel bodipy dye and a study of upconverison nanoparticles mixed with a functionalized bodipy compound
- Authors: Wildervanck, Martijn Johannes
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3718 , vital:20538
- Description: This research explores the use of the versatile 4,4-difluoro-4-boro-3a,4a-diaza-s-indacene (BODIPY) dyes and the modification of their spectroscopic properties. The synthesis of a tetramethyl-BODIPY bearing a sterically hindered meso-phenyl ring with an ethynyl functional group at the para-position was compared to that of its freely rotating counterpart with no methyl substituents on the BODIPY core, with the fluorescence properties in particular proving to be markedly different. These phenyl-ethynyl-substituted BODIPYs were used as the starting materials for the synthesis of novel BODIPY dyes for sensor applications via Sonogashira coupling reactions at the ethynyl position, but this resulted instead in the serendipitous synthesis of a novel BODIPY dimer in which the para-positions of the meso-phenyl rings are linked by a diethynyl bridge. Following iodination at the 2, 6-positions, the dimer was found to have a singlet oxygen quantum yield of 0.88, compared to the value of 0.86 that was obtained for the analogous monomer. Since the εmax values for the main spectral bands of the dimers are significantly higher, the compounds may be of interest for singlet oxygen generation applications. A second study was carried out on the interaction between methyl ester functionalized BODIPY dyes and upconversion nanoparticles (UCNPs) to explore the possible use of BODIPY-UCNP conjugates in biomedical applications. The singlet oxygen generation properties of the BODIPY were tested following iodination at the 2, 6-positions, a singlet oxygen quantum yield value of 0.86 was obtained. Three sets of oleate capped UCNPs were synthesized with different diameters and were rendered water dispersible with the addition of a silica shell. The necessary scaffolding for conjugation to the BODIPY was provided by amine groups following functionalization of this shell. All of the sets of oleate capped and silica coated UCNPs were characterized by transmission electron microscopy (TEM) and X-ray diffractometry (XRD) and their emission properties were studied upon excitation at 978 nm with a diode laser with a Picoquant Fluotime 300 spectrophotometer that enables the measurement of anti-Stokes emission. The potential utility of UCNP-BODIPY conjugates for singlet oxygen applications, such as PDT, was then assessed.
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In silico analysis of the effects of non-synonymous single nucleotide polymorphisms on the human macrophage migration inhibitory factor gene and their possible role in human African trypanosomiasis susceptibility
- Authors: Kimuda, Magambo Philip
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3047 , vital:20355
- Description: Human African trypanosomiasis (HAT) is a public health problem in sub-Saharan Africa, with approximately 10,000 cases being reported per year. The Macrophage Migration Inhibitory Factor (MIF) which is encoded by a functionally polymorphic gene is important in both innate andadaptive immune responses, and has been implicated in affecting the outcome and processes of several inflammatory conditions. A recent study in mice to that effect showed that MIF deficient and anti-MIF antibody treated mice showed lowered inflammatory responses, liver damage and anaemia than the wild type mice when experimentally challenged with Trypanosomes. These findings could mean that the transcript levels and/or polymorphisms in this gene can possibly affect individual risk to trypanosomiasis. This is especially of interest because there have been reports of spontaneous recovery i.e self-cure/resistance in some HAT cases in West Africa. Prior to this discovery the general paradigm was that trypanosomiasis is fatal if left untreated. The aim of this study was to gain insights into how human genetic variation in forms of nonsynonymous SNPs affects the MIF structure and function and possibly HAT susceptibility. NsSNPs in the mif gene were obtained from dbSNP. Through homology modeling, SNP prediction tools, protein interface analysis, alanine scanning, changes in free energy of folding, protein interactions calculator (PIC), and molecular dynamics simulations, SNP effects on the protein structure and function were studied. The study cohort comprised of human genome sequence data from 50 North Western Uganda Lugbara endemic individuals of whom 20 were cases (previous HAT patients) and 30 were controls (HAT free individuals). None of the 26 nsSNPs retrieved from dbSNP (July 2015) were present in the mif gene region in the study cohort. Out of the eight variants called in the mif coding region there was only one missense variant rs36065127 whose clinical significance is unknown. It was not possible to test for association of this variant with HAT due to its low global MAF that was less than 0.05. Alanine scanning provided a fast and computationally cheap means of quickly assessing nsSNPs of importance. NsSNPs that were interface residues were more likely to be hotspots (important in protein stability). Assessment of possible compensatory mutations using PIC analysis showed that some nsSNP sites were interacting with others, but this requires further experimentation. Analysis of changes in free energy using FOLDX was not enough to predict which nsSNPs would adversely affect protein structure, function and kinetics. The MD simulations were unfortunately too short to glean any meaningful inferences. This was the first genetic study carried out on the people of Lugbara ethnicity from North Western Uganda.
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Information security concerns around enterprise bring your own device adoption in South African higher education institutions
- Authors: Sauls, Gershwin Ashton
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3619 , vital:20530
- Description: The research carried out in this thesis is an investigation into the information security concerns around the use of personally-owned mobile devices within South African universities. This concept, which is more commonly known as Bring Your Own Device or BYOD has raised many data loss concerns for organizational IT Departments across various industries worldwide. Universities as institutions are designed to facilitate research and learning and as such, have a strong culture toward the sharing of information which complicates management of these data loss concerns even further. As such, the objectives of the research were to determine the acceptance levels of BYOD within South African universities in relation to the perceived security risks. Thereafter, an investigation into which security practices, if any, that South African universities are using to minimize the information security concerns was carried out by means of a targeted online questionnaire. An extensive literature review was first carried out to evaluate the motivation for the research and to assess advantages of using Smartphone and Tablet PC’s for work related purposes. Thereafter, to determine security concerns, other surveys and related work was consulted to determine the relevant questions needed by the online questionnaire. The quantity of comprehensive academic studies concerning the security aspects of BYOD within organizations was very limited and because of this reason, the research took on a highly exploratory design. Finally, the research deliberated on the results of the online questionnaire and concluded with a strategy for the implementation of a mobile device security strategy for using personally-owned devices in a work-related environment.
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Internal fingerprint extraction
- Authors: Darlow, Luke Nicholas
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2959 , vital:20347
- Description: Fingerprints are a non-invasive biometric that possess significant advantages. However, they are subject to surface erosion and damage; distortion upon scanning; and are vulnerable to fingerprint spoofing. The internal fingerprint exists as the undulations of the papillary junction - an intermediary layer of skin - and provides a solution to these disadvantages. Optical coherence tomography is used to capture the internal fingerprint. A depth profile of the papillary junction throughout the OCT scans is first constructed using fuzzy c-means clustering and a fine-tuning procedure. This information is then used to define localised regions over which to average pixels for the resultant internal fingerprint. When compared to a ground-truth internal fingerprint zone, the internal fingerprint zone detected automatically is within the measured bounds of human error. With a mean- squared-error of 21.3 and structural similarity of 96.4%, the internal fingerprint zone was successfully found and described. The extracted fingerprints exceed their surface counterparts with respect to orientation certainty and NFIQ scores (both of which are respected fingerprint quality assessment criteria). Internal to surface fingerprint correspondence and internal fingerprint cross correspondence were also measured. A larger scanned region is shown to be advantageous as internal fingerprints extracted from these scans have good surface correspondence (75% had at least one true match with a surface counterpart). It is also evidenced that internal fingerprints can constitute a fingerprint database. 96% of the internal fingerprints extracted had at least one corresponding match with another internal fingerprint. When compared to surface fingerprints cropped to match the internal fingerprints’ representative area and locality, the internal fingerprints outperformed these cropped surface counterparts. The internal fingerprint is an attractive biometric solution. This research develops a novel approach to extracting the internal fingerprint and is an asset to the further development of technologies surrounding fingerprint extraction from OCT scans. No earlier work has extracted or tested the internal fingerprint to the degree that this research has.
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