A central enrichment-based comparison of two alternative methods of generating transcription factor binding motifs from protein binding microarray data
- Authors: Mahaye, Ntombikayise
- Date: 2013 , 2013-03-13
- Subjects: Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3890 , http://hdl.handle.net/10962/d1003049 , Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Description: Characterising transcription factor binding sites (TFBS) is an important problem in bioinformatics, since predicting binding sites has many applications such as predicting gene regulation. ChIP-seq is a powerful in vivo method for generating genome-wide putative binding regions for transcription factors (TFs). CentriMo is an algorithm that measures central enrichment of a motif and has previously been used as motif enrichment analysis (MEA) tool. CentriMo uses the fact that ChIP-seq peak calling methods are likely to be biased towards the centre of the putative binding region, at least in cases where there is direct binding. CentriMo calculates a binomial p-value representing central enrichment, based on the central bias of the binding site with the highest likelihood ratio. In cases where binding is indirect or involves cofactors, a more complex distribution of preferred binding sites may occur but, in many cases, a low CentriMo p-value and low width of maximum enrichment (about 100bp) are strong evidence that the motif in question is the true binding motif. Several other MEA tools have been developed, but they do not consider motif central enrichment. The study investigates the claim made by Zhao and Stormo (2011) that they have identified a simpler method than that used to derive the UniPROBE motif database for creating motifs from protein binding microarray (PBM) data, which they call BEEML-PBM (Binding Energy Estimation by Maximum Likelihood-PBM). To accomplish this, CentriMo is employed on 13 motifs from both motif databases. The results indicate that there is no conclusive difference in the quality of motifs from the original PBM and BEEML-PBM approaches. CentriMo provides an understanding of the mechanisms by which TFs bind to DNA. Out of 13 TFs for which ChIP-seq data is used, BEEML-PBM reports five better motifs and twice it has not had any central enrichment when the best PBM motif does. PBM approach finds seven motifs with better central enrichment. On the other hand, across all variations, the number of examples where PBM is better is not high enough to conclude that it is overall the better approach. Some TFs bind directly to DNA, some indirect or in combination with other TFs. Some of the predicted mechanisms are supported by literature evidence. This study further revealed that the binding specificity of a TF is different in different cell types and development stages. A TF is up-regulated in a cell line where it performs its biological function. The discovery of cell line differences, which has not been done before in any CentriMo study, is interesting and provides reasons to study this further.
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- Date Issued: 2013
A Comparative study of two copper(II) based metal-organic frameworks : Cu2¼(OH)½B4C•8H2O and Cu2Na(OH)B4C•7H2O
- Authors: Coombes, Matthew
- Date: 2013
- Subjects: Copper , Organometallic compounds , Supramolecular organometallic chemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4533 , http://hdl.handle.net/10962/d1016245
- Description: This study focussed on two copper(II)-containing metal-organic frameworks (MOFs): Cu2Na(OH)B4C•7H2O and Cu2¼(OH)½B4C•8H2O (B4C = 1,2,4,5- benzenetetracarboxylate). They are both covalent, three-dimensional metalorganic framework polymers containing voids filled with water molecules. Both were characterised by elemental analysis, infrared spectroscopy, X-ray powder diffractometry (both in situ and regular), thermogravimetric analysis, differential scanning calorimetry and X-ray photoelectron spectroscopy. These two MOFs are essentially identical, with the only difference being the substitution of sodium by copper at every 4th site (disordered throughout the crystal). The guest inclusion properties of both MOFs were studied and compared. Although both structures collapse on dehydration, it was observed that Cu2Na(OH)B4C•7H2O is able to take up signifcant amounts of water, methanol and ethanol. All these processes are fully reversible. Car-Parrinello molecular dynamics studies suggest that it is a strong interaction between the oxygen atoms on these molecules with the sodium cation of the MOF that is responsible for this signifcant uptake. In contrast, Cu2¼ (OH)½ B4C•8H2O, the MOF without a sodium cation, did not demonstrate any methanol or ethanol uptake, but was able to take up some water. The uptake of water, however, is not a fully reversible process. The absence of sodium likely results in insuffcient energy to draw methanol and ethanol into the framework, while a subtle rotation of a carboxylate group on dehydration decreases the ability of the framework to form hydrogen bonds, thus reducing the ability to take up water. A series of hydrothermal syntheses were performed in order to develop a method of synthesis superior to the current gel-based synthesis that requires several months and has poor yields. The hydrothermal products were characterized by elemental analysis, infrared spectroscopy, X-ray powder diffractometry, thermogravimetric analysis and differential scanning calorimetry. It was shown that the MOF Cu2Na(OH)B4C•7H2O may be synthesised in almost 100% yield by using a temperature of 120°C over a period of 72 hours. It was not possible to synthesise Cu2¼ (OH)½ B4C•8H2O in a 100% yield - it was only obtained as a minor product.
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- Date Issued: 2013
A marine chemical ecology study of the sea hare, Bursatella leachii in South Africa
- Authors: D'Souza, Nicole
- Date: 2013 , 2013-03-22
- Subjects: Sea hares (Mollusks) -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Ecology -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Behavior -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Defenses -- Behavior -- South Africa -- Kenton-on-Sea
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4283 , http://hdl.handle.net/10962/d1002952 , Sea hares (Mollusks) -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Ecology -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Behavior -- South Africa -- Kenton-on-Sea , Sea hares (Mollusks) -- Defenses -- Behavior -- South Africa -- Kenton-on-Sea
- Description: The large cosmopolitan sea hare Bursatella leachii is a common resident in Eastern Cape river mouths during summer and late autumn where they congregate in beds of Zostera capensis to breed. In this thesis, the previously known toxic formamide marine secondary metabolite (-)-bursatellin (2.2), which may deter predators of South African specimens of the globally distributed sea hare Bursatella leachii, was isolated and identified (Chapter 2). There have been no previous chemical ecology studies of B. leachii and the latter half of this thesis is devoted to chemical ecology studies of this organism. Interestingly, the isolation of the (-)-diastereomer of 2.2 from specimens of B. leachii collected from the Kariega River mouth (near Kenton-on-Sea) suggests that the South African specimens of this species are similar to specimens collected from Puerto Rico and from the Mediterranean Sea. Two different chromatographic techniques for isolating 2.2 were compared in order to maximize the amount of 2.2 isolated from the Kariega River mouth sea hares. The doubling of selected resonances observed in both the ¹H and ¹³C NMR spectra of the bursatellin isolated in this study suggest one of three possibilities; either firstly, the presence of closely related compound(s), secondly, the presence of diastereomers or thirdly the presence of rotamers. Through NMR kinetic studies, we were able to establish that the presence of rotamers was very unlikely due to no change in the relative ratio (3:1) of the ¹H NMR signals with an increase in temperature. Although the attempted synthesis of the acetate derivative (2.28), as a means of separating a diastereomeric mixture was successful, the chromatographic separation of the proposed acetylated diastereomers was not successful. Preparation of the camphanate ester derivatives (e.g. 2.30) proved to be unsuccessful. Five B. leachii specimens were dissected, their organs separated and individually extracted with methanol. The methanol extracts were individually chromatographed on HP-20 media, and the distribution of bursatellin determined by isolation and NMR. It was evident from this investigation that the distribution of 2.2 within individual B. leachii specimens was found to be highest within the B. leachii ink gland. The lower amounts of 2.2 contained in the digestive system, relative to other organs, was hypothesized to occur because 2.2 is sequestered from the diet of the sea hare and efficiently moved from the gut to various organs around the body where it is stored. The absence of 2.2 from the skin was surprising and may be a result of a smaller mass of skin relative to other organs coupled with the limitations of the chromatographic separation techniques employed. Surprisingly, no bursatellin was found within juvenile sea hares. Chapter three discusses the isolation of ilimaquinone (3.1) and pelorol (3.19) from the sponge Hippospongia metachroma and the structure elucidation of each compound using computer modeling to illustrate the conformation. It was deemed necessary to isolate these well known and abundant bioactive marine natural products from a sponge as standard compounds in the bioassays given the paucity of 2.2 available for this study. Chapter four describes the assays used to test the biological activity of the bursatellin 2.2 compared to the generally bioactive ilimaquinone and the structurally related and commercially available broad spectrum antibiotic chloramphenicol. B. leachii, a shell-less marine mollusc inhabits a variety of intertidal habitats and, therefore, is exposed to several different predators, yet does not appear to have any specific predators. Potential predators of this sea hare in the Kariega Estuary could be fish and amphipods which are found in close proximity to these sea hares. Results of the assays showed that at roughly natural concentrations, (calculated from the isolated chromatographic yield) feeding was deterred by the fish and amphipods, which implied that 2.2 may confer a defensive role within the organism. The relatively high concentration present within the ink gland of B. leachii may support this hypothesis. Surprisingly, given its structural similarity to chloramphenicol, 2.3 did not show any antimicrobial action against five of the six bacterial strains against which it was screened [chloramphenicol inhibited the growth of all the bacterial strains at very low concentrations (0.25 mg/mL)]. Bursatellin was found to be only active against Staphylococus aureus at high concentrations ca. 2 mg/mL when compared to chloramphenicol. Neither bursatellin nor chloramphenicol showed anti-fungal activity. Although this study suggests that the sea hares may use chemical defences in addition to opaline ink to defend themselves, they also live within the seagrass Z. capensis, which possibly provides the sea hare with a cryptic form of physical defence against several predators that are unable to swim freely within the weed beds in the littoral zone of the estuary. , Adobe Acrobat 9.53 Paper Capture Plug-in
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- Date Issued: 2013
A mobile toolkit and customised location server for the creation of cross-referencing location-based services
- Authors: Ndakunda, Shange-Ishiwa Tangeni
- Date: 2013
- Subjects: Location-based services -- Security measures , Mobile communication systems -- Security measures , Digital communications , Java (Computer program language) , Application software -- Development -- Computer programs , User interfaces (Computer systems)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4703 , http://hdl.handle.net/10962/d1013604
- Description: Although there are several Software Development kits and Application Programming Interfaces for client-side location-based services development, they mostly involve the creation of self-referencing location-based services. Self-referencing location-based services include services such as geocoding, reverse geocoding, route management and navigation which focus on satisfying the location-based requirements of a single mobile device. There is a lack of open-source Software Development Kits for the development of client-side location-based services that are cross-referencing. Cross-referencing location-based services are designed for the sharing of location information amongst different entities on a given network. This project was undertaken to assemble, through incremental prototyping, a client-side Java Micro Edition location-based services Software Development Kit and a Mobicents location server to aid mobile network operators and developers alike in the quick creation of the transport and privacy protection of cross-referencing location-based applications on Session Initiation Protocol bearer networks. The privacy of the location information is protected using geolocation policies. Developers do not need to have an understanding of Session Initiation Protocol event signaling specifications or of the XML Configuration Access Protocol to use the tools that we put together. The developed tools are later consolidated using two sample applications, the friend-finder and child-tracker services. Developer guidelines are also provided, to aid in using the provided tools.
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- Date Issued: 2013
A process assessment framework for rural ICT projects in developing countries: an exploration of the Siyakhula Living Lab, South Africa
- Authors: Osah, Umeoniso Joshua
- Date: 2013
- Subjects: Siyakhula Living Lab Information technology -- South Africa -- Eastern Cape Rural development projects -- South Africa -- Eastern Cape Rural development projects -- Evaluation -- South Africa -- Eastern Cape Communication in economic development -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:1133 , http://hdl.handle.net/10962/d1001623
- Description: Rural development can be supported by information and knowledge which are key strategic resources for socio economic development. ICTs enable the facilitation and communication of information between remotely dispersed individuals or groups and more developed regions. While it has become common place that ICTs possess capabilities to potentially support rural development, the concept of ICT for development (ICT4D) is still fraught with challenges and barriers, which impede the success and sustainability of ICT4D projects. It is therefore essential to evaluate rural ICT projects, as such an analysis may aid in revealing information related to the need, effectiveness, impact, and sustainability of these projects. This research seeks to further the implementation and exploration of the Rural ICT Comprehensive Evaluation Framework (RICT-CEF), through the application of the Process Assessment domain in a real life rural ICT project environment. The RICT-CEF framework consisting of 7 evaluation domains has the primary objective of evaluating rural ICT projects from their inception stages to post implementation. A process assessment seeks to determine whether or not a rural ICT project is operating to implement its intended functions in the intended way specified in the projects plan. Such an assessment is invaluable to a comprehensive evaluation. Evaluation questions for a process assessment are centred around critical themes of project performance. Critical themes are aspects of a programme or projects implementation which must be enacted in order to achieve desired project outcomes. This research study is aimed at identifying critical themes of process assessment relevant to rural ICT4D projects. To identify critical themes, assessment approaches on social programme process assessments, evaluation of information systems in use, and rural ICT4D project evaluation case studies are comparatively analysed. Fourteen assessment approaches from these three categories are selected based on criteria. To analyse selected assessment approaches, a template is created based on the research questions, foundational literature on process assessment and identified challenges applicable to process assessments of rural ICT4D projects. Comparing and contrasting critical themes from these assessment approaches highlight critical themes essential to assess in the iterative implementation phase of rural ICT projects. Accentuated critical themes include, service utilization, organizational function and external project factors. These themes, along with suggested guiding principles from literature for conducting process assessments enable the creation of a framework for conducting process assessments of rural ICT projects. The framework is labelled "the Rural ICT Project Process Assessment Framework (RICTP-PAF)". The application of the RICTP-PAF in a real life rural ICT project through a design science case study provides lessons learned (suitability and shortcomings) from applying the framework. This essentially demonstrates the sensitivity of the RICTP-PAF to rural contexts in which it is implemented in. For instance, the implemented prototype of the RICTP-PAF reveals that the framework places a great deal of emphasis on rural beneficiary perspectives. A practice which has been lacking in such evaluation exercises. Furthermore, the guiding principles elucidated, bring to mind best practices to deal with issues such as stakeholder conflict, unreliable data elicitation and unethical assessment practices. The RICTP-PAF represents a fundamental tool for process assessments of rural ICT projects, and may be adopted and customized to various rural ICT project contexts in developing countries.
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- Date Issued: 2013
A role for heat shock protein 90 (Hsp90) in fibronectin matrix dynamics
- Authors: O'Hagan, Kyle Leonard
- Date: 2013
- Subjects: Molecular chaperones , Heat shock proteins , Metastasis , Cancer -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4157 , http://hdl.handle.net/10962/d1018260
- Description: To date, a significant portion of research has been devoted to understanding the biological role of the molecular chaperone, heat shock protein 90 (Hsp90), in cancer development and metastasis. Studies have alluded to over 300 clients for intracellular Hsp90, many of which are involved in oncogenic signaling pathways, making Hsp90 a bone fide drug target with several inhibitors already in clinical trials. In recent years, a limited number of extracellular Hsp90 clients have been elucidated with roles in cancer cell migration and invasion. Examples of such clients include matrix metalloproteinase-2 (MMP-2), LRP-1/CD91 and HER-2. Inhibition of extracellular Hsp90 using cellimpermeable inhibitors has been shown to reduce cancer cell migration and metastasis by a hitherto undefined mechanism. Using surface biotinylation and an enzyme linked immunosorbent assay, we provided evidence to support that Hsp90 was found extracellularly in cancers of different origin, cell type and malignancy. Next, we isolated extracellular Hsp90-containing complexes from MDA-MB-231 breast cancer cells using a cell impermeable crosslinker followed by immunoprecipitation and identified by mass spectrometry that the extracellular matrix protein, fibronectin, co-precipitated with Hsp90β. This interaction between Hsp90β and fibronectin was confirmed using pull down assays and surface plasmon resonance spectroscopy with the purified proteins. The ability of exogenous Hsp90β to increase the insoluble fibronectin matrix in Hs578T breast cancer cells indicated a role for Hsp90 in fibronectin matrix stability or fibrillogenesis. Hsp90 knockdown by RNA interference or inhibition with the small molecule inhibitor, novobiocin, resulted in a dose and time-dependent reduction of the extracellular fibronectin matrix. Furthermore, novobiocin was shown to cause the internalization of a fluorescently-labeled exogenous fibronectin matrix incorporated into the extracellular matrix by Hs578T cells. This suggested endocytosis as a possible mechanism for fibronectin turnover. This was supported by the colocalization of fibronectin with key vesicular trafficking markers (Rab-5 and LAMP-1) in small, intracellular vesicles. Furthermore, treatment with the vesicular trafficking inhibitor, methyl-β-cyclodextrin, resulted in a dose-dependent recovery in the extracellular fibronectin matrix following treatment with novobiocin. Taken together, these data provided the first evidence to suggest fibronectin as a new client of Hsp90 and that Hsp90 was involved in regulating extracellular fibronectin matrix dynamics.
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- Date Issued: 2013
A standardised protocol for roadkill detection and the determinants of roadkill in the greater Mapungubwe Transfrontier Conservation Area, Limpopo Province, South Africa
- Authors: Collinson, Wendy Jane
- Date: 2013
- Subjects: Roadkill -- South Africa -- Mapungubwe Site , Traffic safety and wildlife -- South Africa -- Mapungubwe Site
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5606 , http://hdl.handle.net/10962/d1002056 , Roadkill -- South Africa -- Mapungubwe Site , Traffic safety and wildlife -- South Africa -- Mapungubwe Site
- Description: Despite evidence suggesting that road traffic is a major threat to biodiversity loss, very little is known about its actual impact on wildlife populations in South Africa. Globally, road density and traffic volumes are increasing, and although huge budgets are devoted to the construction and upgrading of roads, there is little or no allocation to mitigation measures for protecting fauna in most countries, particularly Africa. Further, no global standardised protocol exists for the rapid assessment of roadkill or the most economical and efficient approach for assessing roadkill rates. Using vehicle field trials, the reliability of detecting artificially deployed roadkill was assessed. Roadkill detection rates decreased significantly at speeds >50 km/h and were also significantly influenced by light conditions (i.e. detection success was greater when the sun was high) and the position of the roadkill on the road (i.e. smaller roadkill on verges were often missed). These results suggest that roadkill sampling was most effective between 1.5 hours after dawn and 1.5 hours before dusk and that driving at slower speeds (<50 km.h⁻ₑ) was required to detect roadkill. This protocol was implemented across three ecological seasons on a 100 km paved road and a 20 km unpaved road in the Greater Mapungubwe Transfrontier Conservation Area, Limpopo Province, South Africa. Driven daily over a 120-day period (three periods consisting each of 40 days), a total of 1,027 roadkill were recorded. These comprised 162 species from all terrestrial vertebrate groups with birds being the most commonly encountered roadkill (50% of all incidents). The high numbers of vertebrates identified as roadkill suggests that road traffic could have potentially unsustainable impacts on wildlife populations and hence the biodiversity of the area. Seventeen variables were identified as possible determinants of roadkill occurrence with season, rainfall, minimum and maximum temperature, habitat type, grass height, grass density, fence type and vehicle type significantly influencing roadkill numbers. Significantly more roadkill were detected on the paved road (9.91/100km) than on the unpaved road (1.8/100km) probably because of greater traffic volumes and the increased speed that vehicles travelled on the paved road. Warmer temperatures and increased rainfall in the preceding 24 hours also increased road mortality numbers as animals tended to become more active during these times. Interestingly, more roadkill was detected in open roadside habitats compared to dense roadside habitats on both the paved and unpaved roads and when grass on the roadside verge was of intermediate height. Open habitat possibly may provide a natural corridor for wildlife which ultimately end up on the road. Roadkill numbers increased when certain other physical barriers, such as cattle fences, were present, probably because these barriers were more penetrable than electric fencing. A series of mitigation measures are proposed to reduce the impacts of roads on wildlife in South Africa. These mitigation measures highlight the need to address the balance between the development of a country’s transport infrastructure and the conservation of its fauna. It is important that research on the impacts of roads becomes standardised to enable robust statistical comparisons which will provide a greater understanding of the potential threats to vertebrate biodiversity
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- Date Issued: 2013
A study of electrospun nanofibers and diatomaceous earth materials for the extraction of alkaloids, flavonoids and aromatic amines in various matrices
- Authors: Mothibedi, Kediemetse (Kedimetse)
- Date: 2013 , 2013-04-07
- Subjects: Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4288 , http://hdl.handle.net/10962/d1003052 , Nanofibers , Electrospinning , Sorbents , Extraction (Chemistry) , Alkaloids , Flavonoids , Amines , Matrices , Goldenseal , Ginkgo , Dyes and dyeing -- Chemistry
- Description: The thesis explored the use of different sorbent materials in solid phase extraction method development. The methods included the use of the polymeric Agilent Bond Elut Plexa solid phase extraction and electrospun polymer-silica composite sorbents for clean-up and preconcentration. Sample clean-up for alkaloids (hydrastine and berberine) in goldenseal, Hydrastis canadensis and flavonoids (quercetin, kaempferol and isorhamnetin) in Ginkgo biloba was achieved using Bond Elut Plexa SPE sorbent. Clean-up of flavonoids in Ginkgo biloba was also achieved using electrospun polymer-silica composite (polystyrene-silica, polyacrylonitrile-silica and nylon 6-silica) sorbents. All analysis of flavonoids and alkaloids was carried out using an Agilent 1200 Series HPLC coupled with a diode array detector. Good peak separation was achieved in less than 6 min employing an Agilent ZORBAX Eclipse Plus C18 column (4.6 x 75 mm, 3.5 μm) at 35⁰C. The mobile phases employed were 0.1% phosphoric acid/methanol gradient and 0.5% phosphoric acid/methanol (40:60) for alkaloids and flavonoids respectively. The calibration curves exhibited linearity up to 120 μg mL⁻¹ with correlation coefficients of more than 0.9980. The recoveries ranged from 73-109% with relative standard deviation of less than 5% for all analytes. Agilent Chem Elut supported liquid extraction was employed for the development of a sample preparation method for the determination of 24 banned aromatic amines from azo dyes in textile following the EU standard method EN 14362-1:2003 (E) and the Chinese standard method GB/T 17592-2006. The supported liquid extraction was effective in the extraction of the aromatic amines from textile (cotton, wool and polyester/cotton [80%:20%]). Most of the recoveries obtained were conforming to the minimum requirements set in the EN 14362-1:2003 (E) standard method and the relative standard deviations were less than 15%. Good peak separation was obtained within 70 min run time using the Agilent Zorbax SB-Phenyl column (4.6 mm x 250 mm, 5-micron) or the Agilent DB-35 MS (J & W) (30 m x 0.25 mm, 0.25 μm film thickness. It was demonstrated that the polymeric Agilent Bond Elut Plexa, electrospun nanofibers and diatomaceous earth were effective in extraction of alkaloids, flavonoids and aromatic amines in different matrices. The developed methods were simple, rapid and reproducible.
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- Date Issued: 2013
A systematic study of Berkheya and allies (Compositae)
- Authors: Phaliso, Ntombifikile
- Date: 2013
- Subjects: Compositae -- Africa, Southern , Daisies -- Africa, Southern , Compositae -- Phylogeny -- Africa, Southern , Compositae -- Geographical distribution -- Africa, Southern , Compositae -- Classification -- Africa, Southern , Cladistic analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4179 , http://hdl.handle.net/10962/d1003054
- Description: Berkheya Ehrh. is a genus of daisies in the tribe Arctotideae, subtribe Gorteriinae with over 80 species, most of which occur in southern Africa. This genus has centres of diversity associated with the montane regions of South Africa, including the Drakensberg Alpine Centre and Mpumalanga escarpment regions. Previous molecular and morphological studies indicate that Berkheya is paraphyletic. I present phylogenies based on nrDNA (ITS; Internal Transcribed Spacer) and cpDNA (psbA-trnH) sequence data analysed with Bayesian Inference and Parsimony. A phylogeny of combined cp- and nrDNA is also presented. These phylogenies are used to assess generic limits and to investigate the biogeographic patterns of Berkheya and its allies. The ITS phylogeny shows five well supported clades of Berkheya, two of which (Clades I and 2) are monophyletic summer rainfall region clades. Clades 3 to 5 are all paraphyletic winter rainfall clades with Cullumia occurring in the third clade, Cuspida occurring in the fourth and Didelta in Clade 5. Both psbA-trnH and combined phylogenies show concordance with the clade distribution shown in the ITS phylogeny. The ITS phylogeny was used to analyse correspondence with Roessler’s (1959) Series. It was found that the phylogeny showed considerable agreement with Roessler’s series, but B. bipinnatifida and B. spinosa of Series Speciosae may require some revision as well as taxa of monotypic series Cruciatae and Angustae. It is suggested that the latter series be merged with Cullumia species to form a single series. Some consideration should be taken to include Didelta species into Series Fruticosae as Didelta occurs in subclade 5b of Clade 5 with other Series Fruticosae taxa. Achene morphology was examined from species from each of the five clades to investigate the relationships of Berkheya and its allies, as well as to determine if there were any consistent achene features for each clade. The structure of surface cells on the fruit, the presence, absence and morphology of twin hairs as well as the structure of the pappus scales were found to be most useful in reflecting phylogenetic relationships within the clades. When compared with the clades of the ITS phylogeny, achene morphology showed consistent characters between taxa occurring in the same clades. As the most comprehensive study involving Berkheya, this phylogenenetic investigation was able to confirm that Berkheya is a paraphyletic genus with Didelta, Cullumia and Cuspida needing to be subsumed into Berkheya. An alternative classification is that taxa of Clade 5 could possibly be erected as an expanded Didelta, separate and sister to Berkheya.
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- Date Issued: 2013
An analysis of regulatory mechanisms during sustained task execution in cognitive, motor and sensory tasks
- Authors: Tau, Sethunya Harriet Hlobisa
- Date: 2013 , 2013-10-11
- Subjects: Work -- Physiological aspects , Work -- Psychological aspects , Fatigue , Attention , Mental fatigue , Human information processing , Decision making , Labor productivity , Employees -- Workload , Performance
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5140 , http://hdl.handle.net/10962/d1006806 , Work -- Physiological aspects , Work -- Psychological aspects , Fatigue , Attention , Mental fatigue , Human information processing , Decision making , Labor productivity , Employees -- Workload , Performance
- Description: Fatigue is a state that, although researched for many years, is still not completely understood. Alongside this lack of a general understanding of fatigue is a lack of knowledge on the processes involved in the regulation of fatigue. The existing theories relating to regulation are focussed on mental effort regulation, suggesting that performance outcomes are co-ordinated by effort regulation that functions by making alterations to physiological processes and strategic adjustments at a cognitive level in response to cognitive demands and goals. Since fatigue is a multi-dimensional construct with psychological, physiological, and behavioural effects that respond to endogenous and exogenous variables, it follows then that fatigue assessment techniques ought to include multi-dimensional measures to acquire a holistic depiction of the fatigue symptom. This study aimed to assess whether or not a mechanism that regulated fatigue during sustained task execution could be identified and whether this mechanism resulted in regulation patterns that were distinct to a specific task. An additional aim of the study was on assessing whether the manner in which performance, psychophysical and subjective variables were modified over time followed a similar regulation pattern. The research design was aimed at inducing task-related fatigue twice on two different occasions in the same participants and evaluating the resultant changes in fatigue manifestation. This was done to assess the ability of participants to cope with fatigue as a result of previous experience. The research protocol included three tasks executed for an hour aimed at targeting and taxing the sensory, cognitive, motor resources, each task performed twice. 60 participants were recruited to participate in the current study, with 20 participants – 10 males and 10 females – randomly assigned to each of the three tasks. The cognitive resource task consisted of a memory recall task relying on working memory intended to evaluate the extent of reductions in memory and attention. The sensory resource task consisted of a reading task measuring visual scanning and perception designed to evaluate the extent of reduced vigilance. The motor resource task consisted of a modified Fitts’ stimulus response task targeted at monitoring the extent of movement timing disruption. Performance measures comprised of: response delay and the number of correctly identified digits during the cognitive resource task, the amount of correctly identified errors and reading speed during the sensory resource task, response time during the motor resource task, and responses to simple auditory reaction time tests (RTT) initiated at intervals during the task and then again at the end of each task. Physiological measures included ear temperature, eye blink frequency and duration, heart rate (HR), and heart rate variability (HRV). Subjective measures included the use of the Ratings of Perceived Exertion Category Ratio 10 scale (RPE CR 10) to measure cognitive exertion and the NASA-Task Load Index (NASA-TLX) to index mental workload. Eye blink frequency and duration, HR and HRV were sensitive to the type of task executed, showing differing response patterns both over the different tasks and over the two test sessions. The subjective measures indicated increasing RPE ratings over time in all tasks while the NASA-TLX indicated that each task elicited different workloads. Differing task performance responses were measured between the 1st test session and the 2nd test session during all tasks; while performance was found to improve during the 2nd test session for the motor and sensory tasks, it declined during the cognitive task. The findings of this research indicate that there was a regulatory mechanism for fatigue that altered the manner in which performance, psychophysical and subjective variables were modified over time, initiating a unique fatigue regulation pattern for each variable and each task. This regulation mechanism is understood to be a proactive and protective mechanism that functions through reducing a person’s ability to be vigilant, attentive, to exercise discernment, and to direct their level of responsiveness, essentially impacting how the body adapts to and copes with fatigue. The noted overall findings have industry implications; industries should consider accounting for the effects of this regulatory mechanism in their fatigue management interventions, specifically when designing job rotation and work/rest schedules because each cognitive task, having elicited a unique fatigue regulation pattern, ought to also have a different management program. , Microsoft� Office Word 2007 , Adobe Acrobat 9.54 Paper Capture Plug-in
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- Date Issued: 2013
An assessment of the Kenyan coastal artisanal fishery and implications for the introduction of fish aggregation devices
- Authors: Mbaru, Emmanuel Kakunde
- Date: 2013 , 2013-07-30
- Subjects: Fisheries -- Kenya , Fishery management -- Kenya , Fish aggregation devices , Small-scale fisheries -- Kenya , Small-scale fisheries -- Economic aspects -- Kenya
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5341 , http://hdl.handle.net/10962/d1006055 , Fisheries -- Kenya , Fishery management -- Kenya , Fish aggregation devices , Small-scale fisheries -- Kenya , Small-scale fisheries -- Economic aspects -- Kenya
- Description: The marine fishery in Kenya is predominantly small-scale and artisanal with about 11,000 fishers intensely fishing near shore coastal reefs using minimally selective fishing gears. A large majority (88%) of fishers use outdated equipment such as basket traps, beach seines, hand lines (hook and lines), fence traps, gillnets, spearguns and cast nets. Handmade canoes propelled by paddles (kasia) or sail power are used to access offshore waters, while only a few fishers have motorized boats. Although fishers along this coast know and express the potential of offshore fishing, most of them are disempowered and unable to access any of the largely untapped offshore pelagic resources. Using a unique dataset from four distinct coastal areas: Funzi-Shirazi bay area, Diani-Chale area, Mombasa-Kilifi north coast area and the Malindi-Ungwana bay area, containing species level length frequency catch data from the multi-gear and multi-species fishery, abundance of specific species, gear use comparisons in various regions, catch per unit effort and total catch estimate over a nine year period (2001 – 2009) were evaluated. Despite high diversity in the fishery, five species (Lethrinus lentjan, Siganus sutor, Leptoscarus vaigiensis, Lethrinus harak and Parupeneus macronemus) represented over 75% of the catch. A total of 11 legitimate gears were observed in this coastal artisanal fishery with basket traps (42%) being the most popular. Fishers along the Mombasa-Kilifi area predominatly used beach seines while those in Diani-Chale, Malindi-Ungwana bay and Funzi-shirazi bay predominaltly used spearguns, gillnets and basket traps, respectively. Apart from gillnets, a general declining trend for most of the gear types was observed since 2004. Beach seines recorded the lowest (20.9±0.2 cm) mean length while gillnets recorded the highest (34.2±0.3 cm). The highest catch (~26,000 metric tons) came in 2001 and the lowest (~15,000 metric tons) in 2005. The highest number of fishers was observed in 2008 while 2009 recorded the highest (4.8±2.3) mean number of hours per outing. The mean annual CPUE per region ranged from (1.5 kg.fisher-1.hr-1) in Diani-Chale to (1.0 kg.fisher-1.hr-1) in Malindi-Ungwana bay. Making use of questionnaire data, the attitudes towards offshore fishing strategies, FADs in particular, were evaluated. Some communities (about 25% in every location) were not even aware of FAD fisheries. With the imminent introduction of a FAD fishery in Kenya, it was concluded that, for this fishery to realize its full potential, training on FAD fishing techniques has to be done. Finally, effective management is necessary if small-scale fisheries are to continue providing food security for many poor coastal communities. Gear-based management in Kenya, although under represented and under studied, has the potential to be adaptive, address multiple objectives, and be crafted to the socio-economic setting. Management effectiveness in near shore fisheries has generally been evaluated at the scale of the fish community. However, community level indicators can mask species-specific declines that provide significant portions of the fisheries yields and income. This thesis seeks to identify ways in which the Kenyan artisanal fishery can be sustained and managed from within coastal communities, giving them the resources and education to effectively improve their lives. The introduction of a offshore FAD fishery and hence access to offshore pelagic species provides an opportunity to not only alleviate pressure on coastal resources but also to empower coastal communities and contribute to the growth of Kenya’s national economy as a whole.
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- Date Issued: 2013
An assessment of urban residents' knowledge and appreciation of the intangible benefits of trees in two medium sized towns in South Africa
- Authors: Chinyimba, Abby
- Date: 2013
- Subjects: Trees in cities -- South Africa--Limpopo , Cities and towns -- South Africa -- Limpopo , Ecology -- South Africa -- Limpopo , Human-plant relationships -- South Africa -- Limpopo , Plants and civilization -- South Africa -- Limpopo , Willingness to pay -- South Africa -- Limpopo , Limpopo (South Africa) -- Environmental conditions , Cultural importance , Cultural and regulating services , Intangible benefits , Urban systems
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4730 , http://hdl.handle.net/10962/d1001957
- Description: In order to meet the different public needs and requirements of contemporary urban society, a better understanding of public perceptions, appreciation and knowledge of the assorted values derived from urban trees is beneficial for improved urban greening. Thus, this study carried out an assessment of urban residents’ knowledge and appreciation of the benefits of trees and the role they play in enhancing the quality of life in urban systems. The study primarily focused on the intangible benefits (also referred to as cultural and regulating services) of urban trees, because most research to date in South Africa on trees and the benefits derived from them is biased towards the provisioning services of trees in rural areas. The significance and contribution of the intangible benefits of trees in urban systems is often underestimated and not seriously taken into account by urban planners, policy makers and other key decision makers. The study was conducted in three different residential settlement types (formal townships, RDP settlements and informal settlements) in two towns in the Limpopo Province in South Africa, namely Bela-Bela and Tzaneen. Findings revealed that the intangible benefits of trees are seen to play a significant role in improving both residents’ quality of life and the environmental conditions in cities, including the preservation of biodiversity. Findings also showed that urban residents had strong spiritual connections with trees and placed considerable cultural and historical importance on specific tree species and individual trees. Urban residents in both towns had moderate knowledge of the intangible benefits of trees based on the knowledge score that was created for the purposes of this study. Fifty seven percent of the residents had ‘reasonable’ knowledge of some of the intangible benefits of trees, while 43% had low levels of knowledge. That said, the majority of residents demonstrated high appreciation (98%) of the intangible benefits of trees (especially social and cultural values), with few residents not recognising these, suggesting that knowledge does not necessarily lead to appreciation. Age and level of education were found to influence knowledge of the intangible benefits of trees. A large proportion (86%) of residents who possessed tertiary level qualifications had more knowledge of the intangible benefits of trees as compared to residents with no formal education. Findings also revealed that younger respondents (60%) had more knowledge of the intangible benefits of trees. Factors that influenced appreciation of the intangible benefits of trees included links to crime, peoples’ value systems (their pro-environmental and altruistic values) and residential settlement type. Sixty five percent of residents in both towns felt that urban street trees and trees in public spaces attract criminals and promote crime, while 67% of RDP and 96% of informal township residents did not use or appreciate the social and recreational benefits of trees mainly because of the absence or long distances to public parks. A Willingness To Pay (WTP) survey revealed that a high proportion of residents in Bela-Bela (86%) were WTP a small annual fee in order to sustain greening initiatives in their communities compared to the residents in Tzaneen (53%). In terms of the planting and retention of trees, it was found that 300 households in both study towns had planted and retained a total of 1 615 trees in spite of the various factors that negatively influenced planting and retention of trees such as residency time and tenure security. The majority (66%) of informal township residents said tenure security was an important factor to consider when making tree planting decisions, while this was not an issue for formal township and RDP residents. Policy implications and recommendations are presented to help municipalities and urban planners improve and develop effective policies and programmes that will enable implementation of sustainable urban greening programmes
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- Date Issued: 2013
An empirical investigation into task aversion
- Authors: Sunshine, Megan
- Date: 2013 , 2013-07-25
- Subjects: Work aversion , Mental fatigue , Labor productivity , Employees -- Workload , Industrial hygiene
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5138 , http://hdl.handle.net/10962/d1006085 , Work aversion , Mental fatigue , Labor productivity , Employees -- Workload , Industrial hygiene
- Description: Aversion is a complex phenomenon that arises over time through performance of cognitively demanding tasks and has been associated with the mechanisms of mental fatigue and compensatory control. However, little is known about this sensation to dissociate from the task at hand and the causation thereof. It is apparent that aversion is a negative state for the operator and could result in decreased performance and productivity. Through identification of factors that contribute to aversion when performing cognitively demanding tasks, recommendations to reduce design deficits may be employed to promote worker wellbeing and further advance performance and productivity. The current study examined possible factors that may influence aversion experienced through execution of cognitive tasks. A subsequent aim of this study was to assess a possible cause of aversion. The cause of aversion was hypothesized to be related to efficiency, namely the perception of efficiency when performing tasks and actual efficiency calculated through performance of tasks in relation to the expenditure of effort. Four investigations were undertaken with a non-repeated design between investigations and a repeated design within investigations. The first investigation was an analysis of the effect that stimulus cycling had on the aversion experienced. This consisted of a proof reading task with two conditions varying in the repetitiveness of the text, therefore, allowing an analysis as to how aversion is altered by the provision of a new stimulus to the participants. Investigation two investigated the effect that task difficulty imposed on aversion experienced. This comprised of two conditions with varied difficulty that were implemented through a driving simulator tracking task with difficulty altered by the width of the driving lane. The effect of performance feedback on the aversion experienced towards a task was the focus of the third investigation. The effect on aversion experienced was assessed through a driving simulator tracking task with a condition providing feedback of performance to participants and a condition with no knowledge of performance. The final experiment evaluated the effect of task alternations on aversion. This experiment was conducted through alternations between a driving simulator tracking task and a choice reaction task. The choice reaction tasks required participants to identify critical and non-critical stimulus. Four conditions were required for this experiment and were made up of two conditions where there was provision of alternation that varied in frequencies between the two tasks (medium alternation condition and fast alternation condition) and two conditions where no alternations were instated (driving simulator task condition and choice reaction task condition). Separations between all testing conditions were three or more days apart with sixty participants distributed between the investigations. Test duration of each condition was 30 minutes. Subjective data was recorded throughout investigations for all conditions in the form of aversion, subjectively perceived efficiency and rate of perceived exertion. Objective data was collected in the form of physiological responses and performance of tasks for the analysis of objective efficiency. For factors influencing aversion analysis, no differences in aversion experienced were found for the task difficulty and performance feedback investigations. Aversion was found to be less for the changes imposed through the task cycles and task alternation investigations. This concludes that aversion is aggravated through monotonous tasks and by a change of the stimulus or the structure of the cognitive tasks provided to operators; aversion can be alleviated. The results for the cause of aversion analysis found no difference in objective efficiency over time, with a subsequent decrease in perceived efficiency associated with the increasing aversion. Inference from these findings suggest that aversion cannot be attributed to objective inefficiency of task performance, however it can further be assumed that perception of actual efficiency is inaccurate. Perception of efficiency however had a large influence on the sensation of aversion. Aversion is seen to be more of a product of time on task, however whether this is mechanism of fatigue or compensatory control is still to be determined.
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- Date Issued: 2013
An experimental and theoretical investigation of unstable Fischer chromium carbene complexes
- Authors: Makanjee, Che Azad
- Date: 2013 , 2013-03-27
- Subjects: Chromium , Organolithium compounds , Carbenes (Methylene compounds) , Organometallic chemistry , Organometallic compounds , Organochromium compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4284 , http://hdl.handle.net/10962/d1002953 , Chromium , Organolithium compounds , Carbenes (Methylene compounds) , Organometallic chemistry , Organometallic compounds , Organochromium compounds
- Description: This organometallic study involves the use organostannanes and organolithiums as precursors to chromium Fischer carbene complexes. Fischer carbenes are typically electrophilic and are stabilized by a single π-donor substituent, and contain low oxidation state metals (often but not always from Group 6). They are highly reactive and can give access to a range of biologically active compounds through cyclopropanations, insertions, coupling and photochemical reactions. Synthesis and characterization of three MOM-protected α-alkoxy organostannanes was successfully carried out via a nucleophilic addition of tributylstannyllithium to suitable aldehydes, and immediate protection of the alcohol with MOM. Two N-BOC protected α-amino organostannanes were successfully synthesized and characterized via α-lithiation and tin-lithium exchange in the presence of TMEDA. Tin-lithium transmetallation of the organostannanes allowed access to the organolithiums required for the synthesis of novel Fischer carbenes. Addition of chromium hexacarbonyl to the organolithiums formed the acylpentacarbonyl chromate salt which was alkylated with Meerwein salt, resulting in the Fischer carbene and a by-product, tetrabutyltin, which proved difficult to remove. Several Fischer carbenes were synthesized and characterized, some simple and known and some novel. In silico work explored the reaction coordinate of the [2+2] cycloaddition towards the formation of β-lactams, and the photoactivation cycle that precedes this process. Computational work also showed the effect of the ligand on the stability and reactivity of the carbene. It was found that in some cases the oxygen on the ligand could negatively influence the stability of the carbene (when compared to a simple methyl carbene). A link between bond orders and back donation in Fischer carbenes was explored in an attempt to theoretically predict the stability of a range of carbenes. , Microsoft� Office Word 2007
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- Date Issued: 2013
An exploratory study of techniques in passive network telescope data analysis
- Authors: Cowie, Bradley
- Date: 2013
- Subjects: Web search engines Internet searching World Wide Web Malware (Computer software) Computer viruses Computer networks -- Monitoring Computer networks -- Security measures
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4573 , http://hdl.handle.net/10962/d1002038
- Description: Careful examination of the composition and concentration of malicious traffic in transit on the channels of the Internet provides network administrators with a means of understanding and predicting damaging attacks directed towards their networks. This allows for action to be taken to mitigate the effect that these attacks have on the performance of their networks and the Internet as a whole by readying network defences and providing early warning to Internet users. One approach to malicious traffic monitoring that has garnered some success in recent times, as exhibited by the study of fast spreading Internet worms, involves analysing data obtained from network telescopes. While some research has considered using measures derived from network telescope datasets to study large scale network incidents such as Code-Red, SQLSlammer and Conficker, there is very little documented discussion on the merits and weaknesses of approaches to analyzing network telescope data. This thesis is an introductory study in network telescope analysis and aims to consider the variables associated with the data received by network telescopes and how these variables may be analysed. The core research of this thesis considers both novel and previously explored analysis techniques from the fields of security metrics, baseline analysis, statistical analysis and technical analysis as applied to analysing network telescope datasets. These techniques were evaluated as approaches to recognize unusual behaviour by observing the ability of these techniques to identify notable incidents in network telescope datasets
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- Date Issued: 2013
An investigation into control mechanisms of driving performance : resource depletion and effort-regulation
- Authors: Louw, Tyron Linton
- Date: 2013
- Subjects: Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5101 , http://hdl.handle.net/10962/d1001842 , Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue
- Description: Driver fatigue is a complex phenomenon that has a range of causal factors including sleeprelated and task-related factors. These manifest as different safety and performance outcomes. Extensive research has been applied to linking these factors to performance impairment. However, little research focuses on the mechanisms by which this link exists. This research project therefore focuses on the processes underlying how driving performance is controlled and maintained during the development on non-sleep-related driver fatigue. The main aim was to establish whether progressive impairment of driving control over a prolonged drive could be attributed to a depletion of attentional resources, as proposed by Resource Theory, or to a withdrawal of effort, as proposed by Effort-Regulation Theory. As a multicomponent skill, driving requires perception, cognition and motor output. The secondary aim of this research was therefore to assess whether a prolonged drive impairs stage-specific information processing. Participants (n=24) in three experimental groups performed a 90-minute simulated drive wherein they were expected to keep the bonnet of a car on a lane (tracking task). The three groups differed in terms of lane width: small, medium and large, corresponding to low, medium, and high task-demand, respectively. To assess the impacts of this task on stagespecific information processing, participants performed a set of resource specific tests before and after the prolonged drive. Each task had two difficulty variations to ensure that performance decrement was due not only to the task-characteristic, but specifically to resource depletion. The tests probing information processing were: a modified Fitts' tapping task for motor programming, a digit recall task for perception, and an object recognition reading task for cognition. Performance was measured as lateral deviation of the car. Physiological measures included heart rate frequency (HR) and various time- and frequencydomain heart rate variability (HRV) parameters, eye blink frequency and duration. The Borg CR-10 scale was used to evaluate subjective effort and fatigue during the task. Driving control declined over time and was supplemented by HR, HRV, blink frequency and duration, indicating an increase in parasympathetic activity (or a reduction in arousal). An increase in blink frequency was considered as a sign of withdrawal of attentional resources over time. Driving control declined to a greater extent in the large road width group and reflected a lower parasympathetic activity, whereas the inverse was observed for the small road width group. Resource tests reveal a non-specific impairment of information processing following the prolonged drive. However, this was accompanied by an increase in parasympathetic activity. Overall, results indicate that Effort-Regulation Theory better accounts for the impairment of driving control in prolonged driving than does Resource Theory. This suggests that the impact of fatigue is guided more by task goals and intrinsic motivation than by the manner in which the fatigue state developed. Moreover, performance impairment by effort-regulation is dependant more on time on task than on task-demand
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- Date Issued: 2013
An investigation of online threat awareness and behaviour patterns amongst secondary school learners
- Authors: Irwin, Michael Padric
- Date: 2013 , 2013-04-29
- Subjects: Computer security -- South Africa -- Grahamstown , Risk perception -- South Africa -- Grahamstown , High school students -- South Africa -- Grahamstown , Communication -- Sex differences -- South Africa -- Grahamstown , Internet and teenagers -- South Africa -- Grahamstown , Internet and teenagers -- Risk assessment -- South Africa -- Grahamstown , Internet -- Safety measures -- South Africa -- Grahamstown , Online social networks -- Social aspects -- South Africa -- Grahamstown
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4576 , http://hdl.handle.net/10962/d1002965 , Computer security -- South Africa -- Grahamstown , Risk perception -- South Africa -- Grahamstown , High school students -- South Africa -- Grahamstown , Communication -- Sex differences -- South Africa -- Grahamstown , Internet and teenagers -- South Africa -- Grahamstown , Internet and teenagers -- Risk assessment -- South Africa -- Grahamstown , Internet -- Safety measures -- South Africa -- Grahamstown , Online social networks -- Social aspects -- South Africa -- Grahamstown
- Description: The research area of this work is online threat awareness within an information security context. The research was carried out on secondary school learners at boarding schools in Grahamstown. The participating learners were in Grades 8 to 12. The goals of the research included determining the actual levels of awareness, the difference between these and self-perceived levels of the participants, the assessment of risk in terms of online behaviour, and the determination of any gender differences in the answers provided by the respondents. A review of relevant literature and similar studies was carried out, and data was collected from the participating schools via an online questionnaire. This data was analysed and discussed within the frameworks of awareness of threats, online privacy social media, sexting, cyberbullying and password habits. The concepts of information security and online privacy are present throughout these discussion chapters, providing the themes for linking the discussion points together. The results of this research show that the respondents have a high level of risk. This is due to the gaps identified in actual awareness and perception, as well as the exhibition of online behaviour patterns that are considered high risk. A strong need for the construction and adoption of threat awareness programmes by these and other schools is identified, as are areas of particular need for inclusion in such programmes. Some gender differences are present, but not to the extent that, there is as significant difference between male and female respondents in terms of overall awareness, knowledge and behaviour.
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- Date Issued: 2013
Assessing household assets to understand vulnerability to HIV/Aids and climate change in the Eastern Cape, South Africa
- Authors: Stadler, Leigh Tessa
- Date: 2013
- Subjects: Climatic changes -- South Africa -- Eastern Cape Climatic changes -- Health aspects -- South Africa -- Eastern Cape Climatic changes -- Economic aspects -- South Africa -- Eastern Cape HIV infections -- Economic aspects -- South Africa -- Eastern Cape AIDS (Disease) -- Economic aspects -- South Africa -- Eastern Cape HIV infections -- Social aspects -- South Africa -- Eastern Cape AIDS (Disease) -- Social aspects -- South Africa -- Eastern Cape Poverty -- Social aspects -- South Africa -- Eastern Cape Income -- South Africa -- Eastern Cape Human capital -- South Africa -- Eastern Cape Sex role -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4726 , http://hdl.handle.net/10962/d1001655
- Description: Livelihood stressors in southern Africa, such as HIV/Aids and climate change, do not act in isolation but rather interact concurrently in complex socio-ecological systems with diverse, interrelated and compounded affects. Households experience differential vulnerability to such stressors based on contextual factors such as geographical location, income level and the gender and age of its members. Households’ differential experiences of vulnerability are further defined by the households’ use of their capital stocks: the human, social, natural, financial and physical capital available to the household to form livelihoods and resist the detrimental effects of a stressor. The capital stocks of 340 households were measured in two sites in the Eastern Cape, South Africa, using a household survey. These data were analysed to determine differences between the sites, households with heads of different gender and households of different income levels. Further data relating to the drivers and interactions of stressors over temporal and spatial scales, as well as the perceived value of various forms of capital by different social groups in the two sites, were collected via Participatory Learning and Action (PLA) methods including timelines, mental modelling and pair-wise ranking. Although the two sites have similar levels of income and fall within the same province, many significant differences emerged. The two sites showed different distributions of household head genders and different stressors and perceptions of vulnerability, perhaps owing to differences in their capital stocks, acting alongside the influence of culture and access on a shifting rural-urban continuum. These discrepancies further transpired to reflect crucial differential experiences along gender lines and income levels in each site. Vulnerability was often context specific, not only because of unique drivers of stress in different areas, but also because socio-economic groups and localities often had characteristics that could potentially exacerbate vulnerability, as well as characteristics that can potentially facilitate adaptive capacity. Stressors were found to have depleted multiple forms of capital over time, while new stressors were emerging, raising concerns over the most appropriate means of social protection within these contexts.
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- Date Issued: 2013
Biochemical characterisation of Pfj2, a Plasmodium falciparum heat shock protein 40 chaperone potentially involved in protein quality control in the endoplasmic reticulum
- Authors: Afolayan, Omolola Folasade
- Date: 2013
- Subjects: Plasmodium falciparum Endoplasmic reticulum Heat shock proteins Malaria , Mosquito-borne infectious disease
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3883 , http://hdl.handle.net/10962/d1001617
- Description: Plasmodium falciparum is a protozoan parasite that causes a severe form of malaria, a mosquito-borne infectious disease in humans. P. falciparum encodes a number of proteins to facilitate its life-cycle, including a type II heat shock protein 40 (Hsp40), Pfj2. Pfj2 shows a degree of homology to human ERdj5, a resident protein of the endoplasmic reticulum (ER) that promotes protein quality control by facilitating the degradation of misfolded proteins. The overall aim of this study was to further understand the function of Pfj2 in the P. falciparum cell by characterising it biochemically. A bioinformatic analysis of Pfj2 was carried out to enable the identification of a potential ER signal sequence and cleavage site. Furthermore, an analysis of Pfj2 protein sequence was performed to compare domain similarities and identities with typical type II Hsp40s namely, human ERdj5, S. cerevisiae Sis1, human Hsj1a and human DnaJB4. The method used included the insertion of the codon-optimised coding sequence for the processed ER form of Pfj2 into the prokaryotic expression vector, pQE30, to enable overproduction of a histidine-tagged protein. A 62 kDa His₆-Pfj2 was successfully expressed in Escherichia coli and purified using denaturing nickel affinity chromatography. ATPase assays were performed to determine the ability of His₆- Pfj2 to stimulate the chaperone activity of the ER Hsp70, also called immunoglobulin binding protein (BiP). Initial studies were conducted on readily available mammalian His₆-BiP as a control, which was shown to have an intrinsic activity of 12.07±3.92 nmolPi/min/mg. His₆- Pfj2 did not stimulate the ATPase activity of mammalian His₆-BiP, suggesting that it either could not act as a co-chaperone of mammalian His₆-BiP (specificity), or it required a misfolded substrate in the system. Therefore, ongoing studies are addressing the interaction of Pfj2 and misfolded substrates with P. falciparum BiP. The results of these studies will further our understanding of a poorly-studied parasite chaperone that represents a potential drug target for development of novel strategies for the control of a serious human disease
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- Date Issued: 2013
Biology and ecology of largemouth bass Micropterus salmoides in two temperate South African impoundments
- Authors: Taylor, Geraldine Claire
- Date: 2013 , 2013-03-19
- Subjects: Largemouth bass -- Ecology -- South Africa -- Eastern Cape , Largemouth bass -- Behavior -- South Africa -- Eastern Cape , Largemouth bass -- Growth -- South Africa -- Eastern Cape , Largemouth bass -- Reproduction -- South Africa -- Eastern Cape , Largemouth bass -- Food -- South Africa -- Eastern Cape , Largemouth bass -- Age determination -- South Africa -- Eastern Cape , Introduced fishes -- South Africa -- Eastern Cape , Fish populations -- South Africa -- Eastern Cape , Otoliths , Largemouth bass -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5181 , http://hdl.handle.net/10962/d1001668 , Largemouth bass -- Ecology -- South Africa -- Eastern Cape , Largemouth bass -- Behavior -- South Africa -- Eastern Cape , Largemouth bass -- Growth -- South Africa -- Eastern Cape , Largemouth bass -- Reproduction -- South Africa -- Eastern Cape , Largemouth bass -- Food -- South Africa -- Eastern Cape , Largemouth bass -- Age determination -- South Africa -- Eastern Cape , Introduced fishes -- South Africa -- Eastern Cape , Fish populations -- South Africa -- Eastern Cape , Otoliths
- Description: Globally largemouth bass Micropterus salmoides is one of the most widely introduced game fish species which has now become invasive in many countries. Well researched in its native North America, there are few studies on this species in its introduced range. This study aims to improve the understanding of the biology and ecology of M. salmoides in temperate southern Africa, where it threatens native biota and supports a popular recreational fishery. This aim was addressed by assessing the age, growth, maturity, reproductive seasonality, feeding, mortality and movement, of two M. salmoides populations from Wriggleswade (1000 ha, 723 m amsl, 32º35'S; 27º33'E) and Mankazana (35 ha, 66 m amsl, 33º09'S; 26º57'E) Dams in the Eastern Cape of South Africa. The most suitable structure for ageing M. salmoides was determined by comparing the accuracy and precision of otoliths and scales. Scales tended to underestimate the age of fish older than five years. Sectioned sagittal otoliths were the more precise structures for ageing (otoliths CV = 15.8 vs. scales CV = 21.9). The periodicity of growth zone formation was validated as annual for otoliths using both edge analysis (EA), and mark recapture of chemically tagged fish (MRCT). EA indicated one annual peak in the frequency of opaque margins between September and January using a periodic logistic regression and a binomial model linked with a von Mises distribution for circular data. MRCT showed the linear relationship between time at liberty and number of growth zones distal to the fluorescent band was not significantly different from one (slope = 0.89). Reproduction was similar to that in native and non-native populations with fish reaching age at 50% maturity at ca. two years, and length at 50% maturity at 259-290 mm FL depending on growth rate. Spawning season occurred in the spring months of August to October. The Wriggleswade Dam population reached similar ages (14 yrs) to populations in temperate North America. Growth was described using the von Bertalanffy growth equations of (Lt = 420(1-ᵉ⁻°·³³⁽ᵗ⁺°·²¹⁾) mm FL in Wriggleswade and (Lt = 641(1-ᵉ⁻°·²²⁽ᵗ⁺°·⁷⁶⁾) mm FL in Mankazana. Growth performance of both populations, described using the phi prime index, seemed to be correlated with temperature and the Wriggleswade Dam population (Φ’ = 2.8) grew similarly to those native temperate North American populations and the non-native populations of Japan and Italy. The Mankazana population had a higher growth performance (Φ’ = 2.9) compared to Wriggleswade and growth was comparable to other nonnative African populations. Both populations utilised all available food resources, with the Mankazana population being in better condition than the Wriggleswade population as a result of a more diverse diet, highly abundant food sources throughout the year, and potentially the adoption of a more conservative ambush feeding strategy. The Wriggleswade population, which was utilised by competitive anglers, showed low mortality rates (Z = 0.43 yr⁻¹), and translocated fish dispersed from the common release site, travelling an average distance of 4km over the study time of 494 days. These results indicated that M. salmoides are successful in these environments, growing at expected temperature dependant rates, maturing at two years, using all available food groups, and suffering from low mortality. It is therefore likely that they will persist in South Africa and establish where introduced.
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- Date Issued: 2013