Building an E-health system for health awareness campaigns in poor areas
- Authors: Gremu, Chikumbutso David
- Date: 2015
- Subjects: National health services -- South Africa , Medical informatics , Public health -- Information services
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4708 , http://hdl.handle.net/10962/d1017930
- Description: Appropriate e-services as well as revenue generation capabilities are key to the deployment and the sustainability for ICT installations in poor areas, particularly common in developing country. The area of e-Health is a promising area for e-services that are both important to the population in those areas and potentially of direct interest to National Health Organizations, which already spend money for Health campaigns there. This thesis focuses on the design, implementation, and full functional testing of HealthAware, an application that allows health organization to set up targeted awareness campaigns for poor areas. Requirements for such application are very specific, starting from the fact that the preparation of the campaign and its execution/consumption happen in two different environments from a technological and social point of view. Part of the research work done for this thesis was to make the above requirements explicit and then use them in the design. This phase of the research was facilitated by the fact that the thesis' work was executed within the context of the Siyakhula Living Lab (SLL; www.siyakhulaLL.org), which has accumulated multi-year experience of ICT deployment in such areas. As a result of the found requirements, HealthAware comprises two components, which are web-based, Java applications that run in a peer-to-peer fashion. The first component, the Dashboard, is used to create, manage, and publish information for conducting awareness campaigns or surveys. The second component, HealthMessenger, facilitates users' access to the campaigns or surveys that were created using the Dashboard. The HealthMessenger was designed to be hosted on TeleWeaver while the Dashboard is hosted independently of TeleWeaver and simply communicates with the HealthMessenger through webservices. TeleWeaver is an application integration platform developed within the SLL to host software applications for poor areas. Using a core service of TeleWeaver, the profile service, where all the users' defining elements are contained, campaigns and surveys can be easily and effectively targeted, for example to match specific demographics or geographic locations. Revenue generation is attained via the logging of the interactions of the target users in the communities with the applications in TeleWeaver, from which billing data is generated according to the specific contractual agreements with the National Health Organization. From a general point of view, HealthAware contributes to the concrete realizations of a bidirectional access channel between Health Organizations and users in poor communities, which not only allows the communication of appropriate content in both directions, but get 'monetized' and in so doing becomes a revenue generator.
- Full Text:
- Authors: Gremu, Chikumbutso David
- Date: 2015
- Subjects: National health services -- South Africa , Medical informatics , Public health -- Information services
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4708 , http://hdl.handle.net/10962/d1017930
- Description: Appropriate e-services as well as revenue generation capabilities are key to the deployment and the sustainability for ICT installations in poor areas, particularly common in developing country. The area of e-Health is a promising area for e-services that are both important to the population in those areas and potentially of direct interest to National Health Organizations, which already spend money for Health campaigns there. This thesis focuses on the design, implementation, and full functional testing of HealthAware, an application that allows health organization to set up targeted awareness campaigns for poor areas. Requirements for such application are very specific, starting from the fact that the preparation of the campaign and its execution/consumption happen in two different environments from a technological and social point of view. Part of the research work done for this thesis was to make the above requirements explicit and then use them in the design. This phase of the research was facilitated by the fact that the thesis' work was executed within the context of the Siyakhula Living Lab (SLL; www.siyakhulaLL.org), which has accumulated multi-year experience of ICT deployment in such areas. As a result of the found requirements, HealthAware comprises two components, which are web-based, Java applications that run in a peer-to-peer fashion. The first component, the Dashboard, is used to create, manage, and publish information for conducting awareness campaigns or surveys. The second component, HealthMessenger, facilitates users' access to the campaigns or surveys that were created using the Dashboard. The HealthMessenger was designed to be hosted on TeleWeaver while the Dashboard is hosted independently of TeleWeaver and simply communicates with the HealthMessenger through webservices. TeleWeaver is an application integration platform developed within the SLL to host software applications for poor areas. Using a core service of TeleWeaver, the profile service, where all the users' defining elements are contained, campaigns and surveys can be easily and effectively targeted, for example to match specific demographics or geographic locations. Revenue generation is attained via the logging of the interactions of the target users in the communities with the applications in TeleWeaver, from which billing data is generated according to the specific contractual agreements with the National Health Organization. From a general point of view, HealthAware contributes to the concrete realizations of a bidirectional access channel between Health Organizations and users in poor communities, which not only allows the communication of appropriate content in both directions, but get 'monetized' and in so doing becomes a revenue generator.
- Full Text:
Carbonate petrography and geochemistry of BIF of the Transvaal supergroup : evaluating the potential of iron carbonates as proxies for palaeoproterozoic ocean chemistry
- Authors: Rafuza, Sipesihle
- Date: 2015
- Subjects: Carbonate rocks -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Transvaal Supergroup , Geochemistry -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Kuruman , Petrology -- South Africa -- Griekwastad , Geology, Stratigraphic -- Proterozoic , Chemical oceanography , Iron
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5089 , http://hdl.handle.net/10962/d1018611
- Description: The subject of BIF genesis, particularly their environmental conditions and ocean chemistry at the time of deposition and their evolution through time, has been a subject of much contentiousness, generating a wealth of proposed genetic models and constant refinements thereof over the years. The prevailing paradigm within the various schools of thought, is the widespread and generally agreed upon depositional and diagenetic model(s) which advocate for BIF deposition under anoxic marine conditions. According to the prevailing models, the primary depositional environment would have involved a seawater column whereby soluble Fe²⁺ expelled by hydrothermal activity mixed with free O₂ from the shallow photic zone produced by eukaryotes, forming a high valence iron oxy-hydroxide precursor such as FeOOH or Fe(OH)₃. An alternative biological mechanism producing similar ferric precursors would have been in the form of photo-ferrotrophy, whereby oxidation of ferrous iron to the ferric form took place in the absence of biological O₂ production. Irrespective of the exact mode of primary iron precipitation (which remains contentious to date), the precipitated ferric oxy-hydroxide precursor would have reacted with co-precipitated organic matter, thus acting as a suitable electron acceptor for organic carbon remineralisation through Dissimilatory Iron Reduction (DIR), as also observed in many modern anoxic diagenetic environments. DIR-dominated diagenetic models imply a predominantly diagenetic influence in BIF mineralogy and genesis, and use as key evidence the low δ¹³C values relative to the seawater bicarbonate value of ~0 ‰, which is also thought to have been the dissolved bicarbonate isotope composition in the early Precambrian oceans. The carbon for diagenetic carbonate formation would thus have been sourced through a combination of two end-member sources: pore-fluid bicarbonate at ~0 ‰ and particulate organic carbon at circa -28 ‰, resulting in the intermediate δ¹³C values observed in BIFs today. This study targets 65 drillcore samples of the upper Kuruman and Griquatown BIF from the lower Transvaal Supergroup in the Hotazel area, Northern Cape, South Africa, and sets out to explore key aspects in BIF carbonate petrography and geochemistry that are pertinent to current debates surrounding their interpretation with regard to primary versus diagenetic processes. The focus here rests on applications of carbonate (mainly siderite and ankerite) petrography, mineral chemistry, bulk and mineral-specific carbon isotopes and speciation analyses, with a view to obtaining valuable new insights into BIF carbonates as potential records of ocean chemistry for their bulk carbonate-carbon isotope signature. Evaluation of the present results is done in light of pre-existing, widely accepted diagenetic models against a proposed water-column model for the origin of the carbonate species in BIF. The latter utilises a combination of geochemical attributes of the studied carbonates, including the conspicuous Mn enrichment and stratigraphic variability in Mn/Fe ratio of the Griquatown BIF recorded solely in the carbonate fraction of the rocks. Additionally, the carbon isotope signatures of the Griquatown BIF samples are brought into the discussion and provide insights into the potential causes and mechanisms that may have controlled these signatures in a diagenetic versus primary sedimentary environment. Ultimately, implications of the combined observations, findings and arguments presented in this thesis are presented and discussed with particular respect to the redox evolution and carbon cycle of the ocean system prior to the Great Oxidation Event (GOE). A crucial conclusion reached is that, by contrast to previously-proposed models, diagenesis cannot singularly be the major contributing factor in BIF genesis at least with respect to the carbonate fraction in BIF, as it does not readily explain the carbon isotope and mineral-chemical signatures of carbonates in the Griquatown and uppermost Kuruman BIFs. It is proposed instead that these signatures may well record water-column processes of carbon, manganese and iron cycling, and that carbonate formation in the water column and its subsequent transfer to the precursor BIF sediment constitutes a faithful record of such processes. Corollary to that interpretation is the suggestion that the evidently increasing Mn abundance in the carbonate fraction of the Griquatown BIF up-section would point to a chemically evolving depositional basin with time, from being mainly ferruginous as expressed by Mn-poor BIFs in the lower stratigraphic sections (i.e. Kuruman BF) to more manganiferous as recorded in the upper Griquatown BIF, culminating in the deposition of the abnormally enriched in Mn Hotazel BIF at the stratigraphic top of the Transvaal Supergroup. The Paleoproterozoic ocean must therefore have been characterised by long-term active cycling of organic carbon in the water column in the form of an ancient biological pump, albeit with Fe(III) and subsequently Mn(III,IV) oxy-hydroxides being the key electron acceptors within the water column. The highly reproducible stratigraphic isotope profiles for bulk δ¹³C from similar sections further afield over distances up to 20 km, further corroborate unabatedly that bulk carbonate carbon isotope signatures record water column carbon cycling processes rather than widely-proposed anaerobic diagenetic processes.
- Full Text:
- Authors: Rafuza, Sipesihle
- Date: 2015
- Subjects: Carbonate rocks -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Transvaal Supergroup , Geochemistry -- South Africa -- Transvaal Supergroup , Petrology -- South Africa -- Kuruman , Petrology -- South Africa -- Griekwastad , Geology, Stratigraphic -- Proterozoic , Chemical oceanography , Iron
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5089 , http://hdl.handle.net/10962/d1018611
- Description: The subject of BIF genesis, particularly their environmental conditions and ocean chemistry at the time of deposition and their evolution through time, has been a subject of much contentiousness, generating a wealth of proposed genetic models and constant refinements thereof over the years. The prevailing paradigm within the various schools of thought, is the widespread and generally agreed upon depositional and diagenetic model(s) which advocate for BIF deposition under anoxic marine conditions. According to the prevailing models, the primary depositional environment would have involved a seawater column whereby soluble Fe²⁺ expelled by hydrothermal activity mixed with free O₂ from the shallow photic zone produced by eukaryotes, forming a high valence iron oxy-hydroxide precursor such as FeOOH or Fe(OH)₃. An alternative biological mechanism producing similar ferric precursors would have been in the form of photo-ferrotrophy, whereby oxidation of ferrous iron to the ferric form took place in the absence of biological O₂ production. Irrespective of the exact mode of primary iron precipitation (which remains contentious to date), the precipitated ferric oxy-hydroxide precursor would have reacted with co-precipitated organic matter, thus acting as a suitable electron acceptor for organic carbon remineralisation through Dissimilatory Iron Reduction (DIR), as also observed in many modern anoxic diagenetic environments. DIR-dominated diagenetic models imply a predominantly diagenetic influence in BIF mineralogy and genesis, and use as key evidence the low δ¹³C values relative to the seawater bicarbonate value of ~0 ‰, which is also thought to have been the dissolved bicarbonate isotope composition in the early Precambrian oceans. The carbon for diagenetic carbonate formation would thus have been sourced through a combination of two end-member sources: pore-fluid bicarbonate at ~0 ‰ and particulate organic carbon at circa -28 ‰, resulting in the intermediate δ¹³C values observed in BIFs today. This study targets 65 drillcore samples of the upper Kuruman and Griquatown BIF from the lower Transvaal Supergroup in the Hotazel area, Northern Cape, South Africa, and sets out to explore key aspects in BIF carbonate petrography and geochemistry that are pertinent to current debates surrounding their interpretation with regard to primary versus diagenetic processes. The focus here rests on applications of carbonate (mainly siderite and ankerite) petrography, mineral chemistry, bulk and mineral-specific carbon isotopes and speciation analyses, with a view to obtaining valuable new insights into BIF carbonates as potential records of ocean chemistry for their bulk carbonate-carbon isotope signature. Evaluation of the present results is done in light of pre-existing, widely accepted diagenetic models against a proposed water-column model for the origin of the carbonate species in BIF. The latter utilises a combination of geochemical attributes of the studied carbonates, including the conspicuous Mn enrichment and stratigraphic variability in Mn/Fe ratio of the Griquatown BIF recorded solely in the carbonate fraction of the rocks. Additionally, the carbon isotope signatures of the Griquatown BIF samples are brought into the discussion and provide insights into the potential causes and mechanisms that may have controlled these signatures in a diagenetic versus primary sedimentary environment. Ultimately, implications of the combined observations, findings and arguments presented in this thesis are presented and discussed with particular respect to the redox evolution and carbon cycle of the ocean system prior to the Great Oxidation Event (GOE). A crucial conclusion reached is that, by contrast to previously-proposed models, diagenesis cannot singularly be the major contributing factor in BIF genesis at least with respect to the carbonate fraction in BIF, as it does not readily explain the carbon isotope and mineral-chemical signatures of carbonates in the Griquatown and uppermost Kuruman BIFs. It is proposed instead that these signatures may well record water-column processes of carbon, manganese and iron cycling, and that carbonate formation in the water column and its subsequent transfer to the precursor BIF sediment constitutes a faithful record of such processes. Corollary to that interpretation is the suggestion that the evidently increasing Mn abundance in the carbonate fraction of the Griquatown BIF up-section would point to a chemically evolving depositional basin with time, from being mainly ferruginous as expressed by Mn-poor BIFs in the lower stratigraphic sections (i.e. Kuruman BF) to more manganiferous as recorded in the upper Griquatown BIF, culminating in the deposition of the abnormally enriched in Mn Hotazel BIF at the stratigraphic top of the Transvaal Supergroup. The Paleoproterozoic ocean must therefore have been characterised by long-term active cycling of organic carbon in the water column in the form of an ancient biological pump, albeit with Fe(III) and subsequently Mn(III,IV) oxy-hydroxides being the key electron acceptors within the water column. The highly reproducible stratigraphic isotope profiles for bulk δ¹³C from similar sections further afield over distances up to 20 km, further corroborate unabatedly that bulk carbonate carbon isotope signatures record water column carbon cycling processes rather than widely-proposed anaerobic diagenetic processes.
- Full Text:
Characterisation of the HSP70-HSP90 organising protein gene and its link to cancer
- Authors: Weeks, Stacey
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56006 , vital:26764
- Description: HOP (Heat shock protein 70/ Heat shock protein 90 organising protein) is a co-chaperone essential for client protein transfer from HSP70 to HSP90 within the HSP90 chaperone machine and has been found to be up-regulated in various cancers. However, minimal in vitro information can be found on the regulation of HOP expression. The aim of this study was to analyse the HOP gene structure across known orthologues, identify and characterise the HOP promoter, and identify the regulatory mechanisms influencing the expression of HOP in cancer. We hypothesized that the expression of HOP in cancer cells is likely regulated by oncogenic signalling pathways linked to cis-elements within the HOP promoter. An initial study of the evolution of the HOP gene speciation was performed across identified orthologues using Mega5.2. The evolutionary pathway of the HOP gene was traced from the unicellular organisms to fish, to amphibian and then to land mammal. The synteny across the orthologues was identified and the co-expression profile of HOP analysed. We identified the putative promoter region for HOP in silico and in vitro. Luciferase reporter assays were utilized to demonstrate promoter activity of the upstream region in vitro. Bioinformatic analysis of the active promoter region identified a large CpG island and a range of putative cis-elements. Many of the cis-elements interact with transcription factors which are activated by oncogenic pathways. We therefore tested the regulation of HOP levels by rat sarcoma viral oncogene homologue (RAS). Cancer cell lines were transfected with mutated RAS to observe the effect of constitutively active RAS expression on the production of HOP using qRT-PCR and Western Blot analyses. Additionally, inhibitors of the RAS signalling pathway were utilised to confirm the regulatory effect of mutated RAS on HOP expression. In cancer cell lines containing mutated RAS (Hs578T), HOP was up-regulated via a mechanism involving the MAPK signalling pathway and the ETS-1 and C/EBPβ cis-elements within the HOP promoter. These findings suggest for the first time that Hop expression in cancer may be regulated by RAS activation of the HOP promoter. Additionally, this study allowed us to determine the murine system to be the most suited genetic model organism with which to study the function of human HOP.
- Full Text:
- Authors: Weeks, Stacey
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56006 , vital:26764
- Description: HOP (Heat shock protein 70/ Heat shock protein 90 organising protein) is a co-chaperone essential for client protein transfer from HSP70 to HSP90 within the HSP90 chaperone machine and has been found to be up-regulated in various cancers. However, minimal in vitro information can be found on the regulation of HOP expression. The aim of this study was to analyse the HOP gene structure across known orthologues, identify and characterise the HOP promoter, and identify the regulatory mechanisms influencing the expression of HOP in cancer. We hypothesized that the expression of HOP in cancer cells is likely regulated by oncogenic signalling pathways linked to cis-elements within the HOP promoter. An initial study of the evolution of the HOP gene speciation was performed across identified orthologues using Mega5.2. The evolutionary pathway of the HOP gene was traced from the unicellular organisms to fish, to amphibian and then to land mammal. The synteny across the orthologues was identified and the co-expression profile of HOP analysed. We identified the putative promoter region for HOP in silico and in vitro. Luciferase reporter assays were utilized to demonstrate promoter activity of the upstream region in vitro. Bioinformatic analysis of the active promoter region identified a large CpG island and a range of putative cis-elements. Many of the cis-elements interact with transcription factors which are activated by oncogenic pathways. We therefore tested the regulation of HOP levels by rat sarcoma viral oncogene homologue (RAS). Cancer cell lines were transfected with mutated RAS to observe the effect of constitutively active RAS expression on the production of HOP using qRT-PCR and Western Blot analyses. Additionally, inhibitors of the RAS signalling pathway were utilised to confirm the regulatory effect of mutated RAS on HOP expression. In cancer cell lines containing mutated RAS (Hs578T), HOP was up-regulated via a mechanism involving the MAPK signalling pathway and the ETS-1 and C/EBPβ cis-elements within the HOP promoter. These findings suggest for the first time that Hop expression in cancer may be regulated by RAS activation of the HOP promoter. Additionally, this study allowed us to determine the murine system to be the most suited genetic model organism with which to study the function of human HOP.
- Full Text:
Coastal landscape change on the Cape St Francis/St Francis Bay peninsula from 1960 to 2014
- Authors: Schroeder, Daniel Heiko
- Date: 2015
- Subjects: Coast changes -- South Africa -- Saint Francis, Cape , Peninsulas -- South Africa -- Saint Francis, Cape , Human ecology -- South Africa -- Saint Francis, Cape , Geographic information systems -- South Africa -- Saint Francis, Cape , Surveying -- South Africa -- Saint Francis, Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5086 , http://hdl.handle.net/10962/d1018203
- Description: A large proportion of the human population, their settlements and socioeconomic activities occur on land directly adjacent to the coastline. The increased demand for coastal leisure and tourism has interfered with natural landscape features and their associated processes. The Cape St Francis/St Francis Bay peninsula located on the southeast coast of South Africa was rapidly developed and transformed from a little fishing village into an urban coastal developed area over a 50-year period (1961-2014). A system that once existed in a state of dynamic or non-equilibrium was interfered with through anthropogenic disturbances, resulting in more frequent and intense natural events, which ranged from floods to debris flows, decreased sand supply and resulting beach erosion. The aim of the project was to identify and map landscape features and changes on the peninsula using an interdisciplinary approach. The triangulated methods of a desktop study using Geographic Information Systems (GIS) and media reviews, a crowdsourcing/participatory approach based on interviews, and a one year land surveying period of measurable field based surveys of physical features gave a well balanced view. The research showed that the natural landscape has been altered dramatically by settlement and associated infrastructure development. In particular, the loss of dunefields and the artificial modification of river paths were major impact areas. Beach erosion is a continual issue for the peninsula residents, particularly in St Francis Bay.
- Full Text:
- Authors: Schroeder, Daniel Heiko
- Date: 2015
- Subjects: Coast changes -- South Africa -- Saint Francis, Cape , Peninsulas -- South Africa -- Saint Francis, Cape , Human ecology -- South Africa -- Saint Francis, Cape , Geographic information systems -- South Africa -- Saint Francis, Cape , Surveying -- South Africa -- Saint Francis, Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5086 , http://hdl.handle.net/10962/d1018203
- Description: A large proportion of the human population, their settlements and socioeconomic activities occur on land directly adjacent to the coastline. The increased demand for coastal leisure and tourism has interfered with natural landscape features and their associated processes. The Cape St Francis/St Francis Bay peninsula located on the southeast coast of South Africa was rapidly developed and transformed from a little fishing village into an urban coastal developed area over a 50-year period (1961-2014). A system that once existed in a state of dynamic or non-equilibrium was interfered with through anthropogenic disturbances, resulting in more frequent and intense natural events, which ranged from floods to debris flows, decreased sand supply and resulting beach erosion. The aim of the project was to identify and map landscape features and changes on the peninsula using an interdisciplinary approach. The triangulated methods of a desktop study using Geographic Information Systems (GIS) and media reviews, a crowdsourcing/participatory approach based on interviews, and a one year land surveying period of measurable field based surveys of physical features gave a well balanced view. The research showed that the natural landscape has been altered dramatically by settlement and associated infrastructure development. In particular, the loss of dunefields and the artificial modification of river paths were major impact areas. Beach erosion is a continual issue for the peninsula residents, particularly in St Francis Bay.
- Full Text:
Comparative study of clan CA cysteine proteases: an insight into the protozoan parasites
- Authors: Moyo, Sipho Dugunye
- Date: 2015
- Subjects: Cysteine proteinases , Proteolytic enzymes , Protozoan diseases , Parasites , Protozoan diseases -- Chemotherapy , Bioinformatics , Plasmodium , Antiprotozoal agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4165 , http://hdl.handle.net/10962/d1020309
- Description: Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.
- Full Text:
- Authors: Moyo, Sipho Dugunye
- Date: 2015
- Subjects: Cysteine proteinases , Proteolytic enzymes , Protozoan diseases , Parasites , Protozoan diseases -- Chemotherapy , Bioinformatics , Plasmodium , Antiprotozoal agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4165 , http://hdl.handle.net/10962/d1020309
- Description: Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.
- Full Text:
Comparative study of the effect of silver nanoparticles on the hexokinase activity from human and Trypanosoma brucei
- Authors: Mlozen, Madalitso Martin
- Date: 2015
- Subjects: Nanoparticles , Silver , Glucokinase , Trypanosoma brucei , Drug resistance , African trypanosomiasis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4149 , http://hdl.handle.net/10962/d1017910
- Full Text:
- Authors: Mlozen, Madalitso Martin
- Date: 2015
- Subjects: Nanoparticles , Silver , Glucokinase , Trypanosoma brucei , Drug resistance , African trypanosomiasis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4149 , http://hdl.handle.net/10962/d1017910
- Full Text:
Comparison of protein binding microarray derived and ChIP-seq derived transcription factor binding DNA motifs
- Hlatshwayo, Nkosikhona Rejoyce
- Authors: Hlatshwayo, Nkosikhona Rejoyce
- Date: 2015
- Subjects: Protein binding , DNA , DNA microarrays , Transcription factors , DNA-protein interactions , Gene regulatory networks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4146 , http://hdl.handle.net/10962/d1017907
- Description: Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .
- Full Text:
- Authors: Hlatshwayo, Nkosikhona Rejoyce
- Date: 2015
- Subjects: Protein binding , DNA , DNA microarrays , Transcription factors , DNA-protein interactions , Gene regulatory networks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4146 , http://hdl.handle.net/10962/d1017907
- Description: Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .
- Full Text:
Design, development and evaluation of novel lead compounds as HIV-1 enzyme inhibitors
- Authors: Sekgota, Khethobole Cassius
- Date: 2015
- Subjects: Enzyme inhibitors , Viruses -- Reproduction , HIV (Viruses)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4546 , http://hdl.handle.net/10962/d1017926
- Description: This project has been concerned with the application of the Baylis-Hillman methodology to the synthesis of medicinally important diketo acid analogues (cinnamate ester-AZT conjugates and 3-hydroxy ester-AZT conjugates) as dual-action HIV-1 IN/RT inhibitors; and on exploratory studies in the preparation of 3-(amidomethyl)-(1H)-2-quinolones as PR inhibitors; and (1H)-2- quinolone-AZT conjugates as dual action IN/RT inhibitors. A series of Baylis-Hillman adducts has been prepared, typically in moderate to excellent yield, by reacting 2-nitrobenzaldehyde with methyl acrylate, ethyl acrylate and methyl vinyl ketone in the presence of 1,4- diazabicyclo[2.2.2]octane (DABCO). Subsequently, various transformations that include conjugate addition of primary and secondary amines to the α,ß-unsaturated moiety to obtain 2- (aminomethyl)-3-hydroxy-3-(2-nitrophenyl)propanoate derivatives, effective SN2´ substitution of the BH ß-hydroxy by a Vilsmeier-Haack in situ-generated chloride to afford Baylis-Hillman allyl chlorides, iron in acetic acid-catalyzed cyclisation to 3-acetoxymethyl-(1H)-2-quinolone derivatives were achieved. Thus, using the Baylis-Hillman methodology, two nuanced classes of diketo acid analogues were constructed. These involved conjugating appropriate propargylamine derivatives with AZT using the „click‟ reaction. In an exploratory study, the quinolone derivative, precisely 3-acetoxymethyl- (1H)-quinol-2-one, was transformed into 3-hydroxymethyl-(1H)-quinol-2-one using potassium carbonate in a mixture of methanol and water (1:1). Following successful hydrolysis, the resulting alcohol was transformed to the corresponding chloride, 3-chloromethyl-(1H)-quinol-2- one, using thionyl chloride. Subsequent nucleophilic substitution afforded 3-(aminomethyl)- (1H)-2-quinolone derivatives which were subsequently transformed to 3-(amidomethyl)-(1H)-2- quinolones; and 3-[(propargylamino)-methyl]-(1H)-quinol-2-one as precursors to quinolone- AZT derivatives. All compounds were characterized by NMR, IR, and where appropriate, high resolution MS
- Full Text:
- Authors: Sekgota, Khethobole Cassius
- Date: 2015
- Subjects: Enzyme inhibitors , Viruses -- Reproduction , HIV (Viruses)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4546 , http://hdl.handle.net/10962/d1017926
- Description: This project has been concerned with the application of the Baylis-Hillman methodology to the synthesis of medicinally important diketo acid analogues (cinnamate ester-AZT conjugates and 3-hydroxy ester-AZT conjugates) as dual-action HIV-1 IN/RT inhibitors; and on exploratory studies in the preparation of 3-(amidomethyl)-(1H)-2-quinolones as PR inhibitors; and (1H)-2- quinolone-AZT conjugates as dual action IN/RT inhibitors. A series of Baylis-Hillman adducts has been prepared, typically in moderate to excellent yield, by reacting 2-nitrobenzaldehyde with methyl acrylate, ethyl acrylate and methyl vinyl ketone in the presence of 1,4- diazabicyclo[2.2.2]octane (DABCO). Subsequently, various transformations that include conjugate addition of primary and secondary amines to the α,ß-unsaturated moiety to obtain 2- (aminomethyl)-3-hydroxy-3-(2-nitrophenyl)propanoate derivatives, effective SN2´ substitution of the BH ß-hydroxy by a Vilsmeier-Haack in situ-generated chloride to afford Baylis-Hillman allyl chlorides, iron in acetic acid-catalyzed cyclisation to 3-acetoxymethyl-(1H)-2-quinolone derivatives were achieved. Thus, using the Baylis-Hillman methodology, two nuanced classes of diketo acid analogues were constructed. These involved conjugating appropriate propargylamine derivatives with AZT using the „click‟ reaction. In an exploratory study, the quinolone derivative, precisely 3-acetoxymethyl- (1H)-quinol-2-one, was transformed into 3-hydroxymethyl-(1H)-quinol-2-one using potassium carbonate in a mixture of methanol and water (1:1). Following successful hydrolysis, the resulting alcohol was transformed to the corresponding chloride, 3-chloromethyl-(1H)-quinol-2- one, using thionyl chloride. Subsequent nucleophilic substitution afforded 3-(aminomethyl)- (1H)-2-quinolone derivatives which were subsequently transformed to 3-(amidomethyl)-(1H)-2- quinolones; and 3-[(propargylamino)-methyl]-(1H)-quinol-2-one as precursors to quinolone- AZT derivatives. All compounds were characterized by NMR, IR, and where appropriate, high resolution MS
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Developing a cross platform IMS client using the JAIN SIP applet phone
- Authors: Muswera, Walter Tawanda
- Date: 2015
- Subjects: Internet Protocol multimedia subsystem , Java (Computer program language)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4712 , http://hdl.handle.net/10962/d1017934
- Description: Since the introduction of the IP Multimedia Subsystem (IMS) by the Third Generation Partnership Project (3GPP) in 2002, a lot of research has been conducted aimed at designing and implementing IMS capable clients and network elements. Though considerable work has been done in the development of IMS clients, there is no single, free and open source IMS client that provides researchers with all the required functionality needed to test the applications they are developing. For example, several open and closed source SIP/IMS clients are used within the Rhodes University Conver- gence Research Group (RUCRG) to test applications under development, as a result of the fact that the various SIP/IMS clients support different subsets of SIP/IMS features. The lack of a single client and the subsequent use of various clients comes with several problems. Researchers have to know how to deploy, configure, use and at times adapt the various clients to suit their needs. This can be very time consuming and, in fact, contradicts the IMS philosophy (the IMS was proposed to support rapid service creation). This thesis outlines the development of a Java-based, IMS compliant client called RUCRG IMS client, that uses the JAIN SIP Applet Phone (JSAP) as its foundation. JSAP, which originally offered only basic voice calling and instant messaging (IM) capabilities, was modified to be IMS compliant and support video calls, IM and presence using XML Configuration Access Protocol (XCAP).
- Full Text:
- Authors: Muswera, Walter Tawanda
- Date: 2015
- Subjects: Internet Protocol multimedia subsystem , Java (Computer program language)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4712 , http://hdl.handle.net/10962/d1017934
- Description: Since the introduction of the IP Multimedia Subsystem (IMS) by the Third Generation Partnership Project (3GPP) in 2002, a lot of research has been conducted aimed at designing and implementing IMS capable clients and network elements. Though considerable work has been done in the development of IMS clients, there is no single, free and open source IMS client that provides researchers with all the required functionality needed to test the applications they are developing. For example, several open and closed source SIP/IMS clients are used within the Rhodes University Conver- gence Research Group (RUCRG) to test applications under development, as a result of the fact that the various SIP/IMS clients support different subsets of SIP/IMS features. The lack of a single client and the subsequent use of various clients comes with several problems. Researchers have to know how to deploy, configure, use and at times adapt the various clients to suit their needs. This can be very time consuming and, in fact, contradicts the IMS philosophy (the IMS was proposed to support rapid service creation). This thesis outlines the development of a Java-based, IMS compliant client called RUCRG IMS client, that uses the JAIN SIP Applet Phone (JSAP) as its foundation. JSAP, which originally offered only basic voice calling and instant messaging (IM) capabilities, was modified to be IMS compliant and support video calls, IM and presence using XML Configuration Access Protocol (XCAP).
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Developing a GIS based method for school site identification in the rural Eastern Cape
- Authors: Swart, Conrad Dirk
- Date: 2015
- Subjects: Geographic information systems -- South Africa -- Eastern Cape , School sites -- South Africa -- Eastern Cape , School sites -- South Africa -- Eastern Cape -- Planning , Rural schools -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4891 , http://hdl.handle.net/10962/d1018939
- Description: Historically, South Africa has not had equal education in terms of funding, curriculum or physical resources and structures. These issues are still present in contemporary South Africa and none more so than the issues surrounding “mud schools”. Recently the Department of Basic Education (DBE) implemented a plan to eradicate inappropriate school structures using the Accelerated Schools Infrastructure Delivery Initiative program (ASIDI). Questions around effective placement of schools are now being asked. Using interviews and analysis of literature, this research developed criteria needed to determine how rural school sites are selected. Geographical Information Systems (GIS) was used to determine if current sites are in the most appropriate areas. The results of the research included a unique set of Eastern Cape criteria as well as an analysis of the current site selection methods used by the DBE. It also revealed that most of the schools are being constructed in acceptable areas. The main result that emerged from the research was that schools will be placed in areas where they are needed. Developing site selection criteria is still needed as South Africa seeks to reduce the education gap between rich and poor schools.
- Full Text:
- Authors: Swart, Conrad Dirk
- Date: 2015
- Subjects: Geographic information systems -- South Africa -- Eastern Cape , School sites -- South Africa -- Eastern Cape , School sites -- South Africa -- Eastern Cape -- Planning , Rural schools -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4891 , http://hdl.handle.net/10962/d1018939
- Description: Historically, South Africa has not had equal education in terms of funding, curriculum or physical resources and structures. These issues are still present in contemporary South Africa and none more so than the issues surrounding “mud schools”. Recently the Department of Basic Education (DBE) implemented a plan to eradicate inappropriate school structures using the Accelerated Schools Infrastructure Delivery Initiative program (ASIDI). Questions around effective placement of schools are now being asked. Using interviews and analysis of literature, this research developed criteria needed to determine how rural school sites are selected. Geographical Information Systems (GIS) was used to determine if current sites are in the most appropriate areas. The results of the research included a unique set of Eastern Cape criteria as well as an analysis of the current site selection methods used by the DBE. It also revealed that most of the schools are being constructed in acceptable areas. The main result that emerged from the research was that schools will be placed in areas where they are needed. Developing site selection criteria is still needed as South Africa seeks to reduce the education gap between rich and poor schools.
- Full Text:
Developing high-fidelity mental models of programming concepts using manipulatives and interactive metaphors
- Authors: Funcke, Matthew
- Date: 2015
- Subjects: Computer programming -- Study and teaching (Higher) , Computer programmers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4707 , http://hdl.handle.net/10962/d1017929
- Description: It is well established that both learning and teaching programming are difficult tasks. Difficulties often occur due to weak mental models and common misconceptions. This study proposes a method of teaching programming that both encourages high-fidelity mental models and attempts to minimise misconceptions in novice programmers, through the use of metaphors and manipulatives. The elements in ActionWorld with which the students interact are realizations of metaphors. By simple example, a variable has a metaphorical representation as a labelled box that can hold a value. The dissertation develops a set of metaphors which have several core requirements: metaphors should avoid causing misconceptions, they need to be high-fidelity so as to avoid failing when used with a new concept, students must be able to relate to them, and finally, they should be usable across multiple educational media. The learning style that ActionWorld supports is one which requires active participation from the student - the system acts as a foundation upon which students are encouraged to build their mental models. This teaching style is achieved by placing the student in the role of code interpreter, the code they need to interpret will not advance until they have demonstrated its meaning via use of the aforementioned metaphors. ActionWorld was developed using an iterative developmental process that consistently improved upon various aspects of the project through a continual evaluation-enhancement cycle. The primary outputs of this project include a unified set of high-fidelity metaphors, a virtual-machine API for use in similar future projects, and two metaphor-testing games. All of the aforementioned deliverables were tested using multiple quality-evaluation criteria, the results of which were consistently positive. ActionWorld and its constituent components contribute to the wide assortment of methods one might use to teach novice programmers.
- Full Text:
- Authors: Funcke, Matthew
- Date: 2015
- Subjects: Computer programming -- Study and teaching (Higher) , Computer programmers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4707 , http://hdl.handle.net/10962/d1017929
- Description: It is well established that both learning and teaching programming are difficult tasks. Difficulties often occur due to weak mental models and common misconceptions. This study proposes a method of teaching programming that both encourages high-fidelity mental models and attempts to minimise misconceptions in novice programmers, through the use of metaphors and manipulatives. The elements in ActionWorld with which the students interact are realizations of metaphors. By simple example, a variable has a metaphorical representation as a labelled box that can hold a value. The dissertation develops a set of metaphors which have several core requirements: metaphors should avoid causing misconceptions, they need to be high-fidelity so as to avoid failing when used with a new concept, students must be able to relate to them, and finally, they should be usable across multiple educational media. The learning style that ActionWorld supports is one which requires active participation from the student - the system acts as a foundation upon which students are encouraged to build their mental models. This teaching style is achieved by placing the student in the role of code interpreter, the code they need to interpret will not advance until they have demonstrated its meaning via use of the aforementioned metaphors. ActionWorld was developed using an iterative developmental process that consistently improved upon various aspects of the project through a continual evaluation-enhancement cycle. The primary outputs of this project include a unified set of high-fidelity metaphors, a virtual-machine API for use in similar future projects, and two metaphor-testing games. All of the aforementioned deliverables were tested using multiple quality-evaluation criteria, the results of which were consistently positive. ActionWorld and its constituent components contribute to the wide assortment of methods one might use to teach novice programmers.
- Full Text:
DNA-based identification of forensically significant beetles from Southern Africa
- Authors: Collett, Isabel Judith
- Date: 2015
- Subjects: Carrion insects , Forensic entomology , Cleridae , Dermestidae , Silphidae , Staphylinidae , Scarabaeidae , Histeridae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5923 , http://hdl.handle.net/10962/d1017801
- Description: Necrophilous insects, if correctly identified, can provide useful forensic information. Research in this area has focussed on flies and beetles remain comparatively under-studied, partly because some adult carrion beetles are difficult to identify morphologically, as are their juvenile stages, often requiring specialist expertise in both cases. Molecular taxonomy has been proposed as a solution to these problems. DNA “barcodes" are short fragments of mitochondrial cytochrome oxidase I (COI) DNA that are anticipated to delineate species. This approach is becoming increasingly popular, but has been met with varying enthusiasm from taxonomists. This thesis examines their use in identifying forensically significant beetles.The DNA barcodes of 234 specimens of 25 forensically significant southern African beetle species from seven families (Cleridae, Dermestidae, Silphidae, Staphylinidae, Scarabaeidae, Trogidae and Histeridae) were obtained. Thirty-three initial barcode amplification failures were overcome by using primers other than the standard Folmer pair, undermining the barcode concept’s hope of universal primers that would allow even non-specialists to produce barcodes. Another 150 specimens (64%) entirely failed to yield barcodes, including 18 fresh specimens of three species of Trogidae, implying another lack of universality of the barcoding protocol. The majority of the beetles clustered with confamilials on neighbour-joining and maximum likelihood trees, but 1.3% of the barcodes failed to cluster with their respective families, raising questions concerning the associating power of barcodes. The identification tools of the GenBank and BOLD on-line DNA sequence databases identified 21% of the specimens to the species level, 6% of them correctly. There was evidence of a paralogous sequence in the Cleridae that, while supporting identification now that it has been associated with a morphological identification, would hamper attempts at identification by clustering or phylogenetic analysis.Distance and haplotype network analyses of the barcodes of six widespread species showed that they are not geographically structured. Barcodes are thus unlikely to be indicators of the region of origin of a species and will not determine whether a corpse has been relocated after death. To assess whether a different mitochondrial DNA fragment might address (some of) these problems, a 2.2 kb fragment extending from the 5’ end of the COI gene to the 3’ end of the Cytochrome Oxidase II (COII) gene was analysed for nine species. It was found that, for Dermestidae, Scarabaeidae and Histeridae, higher degrees of diversity occurred downstreamof the barcode region, but the region of highest diversity in the Cleridae was in the barcode region. Thus, finding a more reliable fragment along the COI-COII region for each family may make robust and guaranteed DNA-based identification of these beetles more likely. The possibility of a forensic specimen being incorrectly or not identified based on its barcode alone exists in about 40% of cases, even with the new barcodes reported here. Forensic science sets a very high bar in assessing the performance of its techniques, and it is concluded that barcodes currently have unsettling failure rates as court-worthy evidence.
- Full Text:
- Authors: Collett, Isabel Judith
- Date: 2015
- Subjects: Carrion insects , Forensic entomology , Cleridae , Dermestidae , Silphidae , Staphylinidae , Scarabaeidae , Histeridae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5923 , http://hdl.handle.net/10962/d1017801
- Description: Necrophilous insects, if correctly identified, can provide useful forensic information. Research in this area has focussed on flies and beetles remain comparatively under-studied, partly because some adult carrion beetles are difficult to identify morphologically, as are their juvenile stages, often requiring specialist expertise in both cases. Molecular taxonomy has been proposed as a solution to these problems. DNA “barcodes" are short fragments of mitochondrial cytochrome oxidase I (COI) DNA that are anticipated to delineate species. This approach is becoming increasingly popular, but has been met with varying enthusiasm from taxonomists. This thesis examines their use in identifying forensically significant beetles.The DNA barcodes of 234 specimens of 25 forensically significant southern African beetle species from seven families (Cleridae, Dermestidae, Silphidae, Staphylinidae, Scarabaeidae, Trogidae and Histeridae) were obtained. Thirty-three initial barcode amplification failures were overcome by using primers other than the standard Folmer pair, undermining the barcode concept’s hope of universal primers that would allow even non-specialists to produce barcodes. Another 150 specimens (64%) entirely failed to yield barcodes, including 18 fresh specimens of three species of Trogidae, implying another lack of universality of the barcoding protocol. The majority of the beetles clustered with confamilials on neighbour-joining and maximum likelihood trees, but 1.3% of the barcodes failed to cluster with their respective families, raising questions concerning the associating power of barcodes. The identification tools of the GenBank and BOLD on-line DNA sequence databases identified 21% of the specimens to the species level, 6% of them correctly. There was evidence of a paralogous sequence in the Cleridae that, while supporting identification now that it has been associated with a morphological identification, would hamper attempts at identification by clustering or phylogenetic analysis.Distance and haplotype network analyses of the barcodes of six widespread species showed that they are not geographically structured. Barcodes are thus unlikely to be indicators of the region of origin of a species and will not determine whether a corpse has been relocated after death. To assess whether a different mitochondrial DNA fragment might address (some of) these problems, a 2.2 kb fragment extending from the 5’ end of the COI gene to the 3’ end of the Cytochrome Oxidase II (COII) gene was analysed for nine species. It was found that, for Dermestidae, Scarabaeidae and Histeridae, higher degrees of diversity occurred downstreamof the barcode region, but the region of highest diversity in the Cleridae was in the barcode region. Thus, finding a more reliable fragment along the COI-COII region for each family may make robust and guaranteed DNA-based identification of these beetles more likely. The possibility of a forensic specimen being incorrectly or not identified based on its barcode alone exists in about 40% of cases, even with the new barcodes reported here. Forensic science sets a very high bar in assessing the performance of its techniques, and it is concluded that barcodes currently have unsettling failure rates as court-worthy evidence.
- Full Text:
Drought responses of selected C₄ photosynthetic NADP-Me and NAD-Me Panicoideae and Aristidoideae grasses
- Authors: Venter, Nicolaas
- Date: 2015
- Subjects: Aristida , Panicum , Switchgrass , Grasses -- Effect of drought on , Grasses -- Phylogeny , Photosynthesis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4272 , http://hdl.handle.net/10962/d1018549
- Description: Grass species within South Africa show a photosynthetic subtype and phylogenetic response to rainfall gradients, with Panicoideae species (NADP-Me and NAD-Me) inhabiting mesic environments, while Aristidoideae species (NADP-Me) inhabit more arid environments. It is predicted that climate change will alter rainfall patterns within southern Africa, which could have implications for grassland distributions and functional composition. Globally, and in South Africa, species distributions indicates that NAD-Me species have a preference for more arid environments, but this may be complicated by phylogeny as most NAD-Me species belong to the Chloridoideae subfamily. Additionally, differences in the metabolism and energetic requirements of different carboxylation types are expected to confer different ecological advantages, such as drought tolerance, but the role of these different pathways is not well understood. Based on natural distribution and photosynthetic subtype differences, it was hypothesised that Panicoideae NADP-Me species would be less drought tolerant than Panicoideae NAD-Me and Aristidoideae NADP-Me species and that subtypes and lineages would show different drought recovery rates. Furthermore, drought sensitivity would be of a metabolic and not a stomatal origin and plants that maintained favourable leaf water status would be more drought tolerant and recover faster. This was tested experimentally by comparing Panicoideae species (NADP-Me and NAD-Me) and NADP-Me species (Panicoideae and Aristidoideae). Plants were subjected to a progressive 58 day drought period and a recovery phase where gas exchange, chlorophyll fluorescence and leaf water relations were measured at select intervals. In conjunction with this, a rapid drought experiment was performed on Zea mays (NADP-Me: Panicoideae) plants where similar parameters were measured. Photosynthetic drought and recovery responses showed both a subtype and phylogenetic response. Panicoideae species were less drought tolerant than Aristidoideae species, although Panicoideae NAD-Me showed better recovery rates than Panicoideae NADP-Me species, while Aristidoideae species recovered the quickest. Panicoideae NAD-Me and Aristidoideae species maintained higher leaf water status during drought which contributed to the maintenance of PSII integrity and thus facilitated rapid photosynthetic recovery. During drought Panicoideae species showed greater metabolic limitations over Aristidoideae species and for the first time, lower metabolic limitations were associated with osmotic adjustment. This is a novel finding whereby osmotic adjustment and the subsequent maintenance of leaf water are key to preventing metabolic limitations of photosynthesis in C₄ grasses. Results from the Z. mays rapid drought study showed the limitations to photosynthesis were exclusively metabolic and unlikely to be a direct consequence of turgor loss. It was apparent that the response to drought was stronger amongst lineages, as NADP-Me species from different subfamilies showed a significant difference in drought tolerances. Aristidoideae species’ exceptional drought tolerance and predicted increased aridification could favour these species over Panicoideae species under future climates.
- Full Text:
- Authors: Venter, Nicolaas
- Date: 2015
- Subjects: Aristida , Panicum , Switchgrass , Grasses -- Effect of drought on , Grasses -- Phylogeny , Photosynthesis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4272 , http://hdl.handle.net/10962/d1018549
- Description: Grass species within South Africa show a photosynthetic subtype and phylogenetic response to rainfall gradients, with Panicoideae species (NADP-Me and NAD-Me) inhabiting mesic environments, while Aristidoideae species (NADP-Me) inhabit more arid environments. It is predicted that climate change will alter rainfall patterns within southern Africa, which could have implications for grassland distributions and functional composition. Globally, and in South Africa, species distributions indicates that NAD-Me species have a preference for more arid environments, but this may be complicated by phylogeny as most NAD-Me species belong to the Chloridoideae subfamily. Additionally, differences in the metabolism and energetic requirements of different carboxylation types are expected to confer different ecological advantages, such as drought tolerance, but the role of these different pathways is not well understood. Based on natural distribution and photosynthetic subtype differences, it was hypothesised that Panicoideae NADP-Me species would be less drought tolerant than Panicoideae NAD-Me and Aristidoideae NADP-Me species and that subtypes and lineages would show different drought recovery rates. Furthermore, drought sensitivity would be of a metabolic and not a stomatal origin and plants that maintained favourable leaf water status would be more drought tolerant and recover faster. This was tested experimentally by comparing Panicoideae species (NADP-Me and NAD-Me) and NADP-Me species (Panicoideae and Aristidoideae). Plants were subjected to a progressive 58 day drought period and a recovery phase where gas exchange, chlorophyll fluorescence and leaf water relations were measured at select intervals. In conjunction with this, a rapid drought experiment was performed on Zea mays (NADP-Me: Panicoideae) plants where similar parameters were measured. Photosynthetic drought and recovery responses showed both a subtype and phylogenetic response. Panicoideae species were less drought tolerant than Aristidoideae species, although Panicoideae NAD-Me showed better recovery rates than Panicoideae NADP-Me species, while Aristidoideae species recovered the quickest. Panicoideae NAD-Me and Aristidoideae species maintained higher leaf water status during drought which contributed to the maintenance of PSII integrity and thus facilitated rapid photosynthetic recovery. During drought Panicoideae species showed greater metabolic limitations over Aristidoideae species and for the first time, lower metabolic limitations were associated with osmotic adjustment. This is a novel finding whereby osmotic adjustment and the subsequent maintenance of leaf water are key to preventing metabolic limitations of photosynthesis in C₄ grasses. Results from the Z. mays rapid drought study showed the limitations to photosynthesis were exclusively metabolic and unlikely to be a direct consequence of turgor loss. It was apparent that the response to drought was stronger amongst lineages, as NADP-Me species from different subfamilies showed a significant difference in drought tolerances. Aristidoideae species’ exceptional drought tolerance and predicted increased aridification could favour these species over Panicoideae species under future climates.
- Full Text:
Eliciting and combining expert opinion : an overview and comparison of methods
- Authors: Chinyamakobvu, Mutsa Carole
- Date: 2015
- Subjects: Decision making -- Statistical methods , Expertise , Bayesian statistical decision theory , Statistical decision , Delphi method , Paired comparisons (Statistics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5579 , http://hdl.handle.net/10962/d1017827
- Description: Decision makers have long relied on experts to inform their decision making. Expert judgment analysis is a way to elicit and combine the opinions of a group of experts to facilitate decision making. The use of expert judgment is most appropriate when there is a lack of data for obtaining reasonable statistical results. The experts are asked for advice by one or more decision makers who face a specific real decision problem. The decision makers are outside the group of experts and are jointly responsible and accountable for the decision and committed to finding solutions that everyone can live with. The emphasis is on the decision makers learning from the experts. The focus of this thesis is an overview and comparison of the various elicitation and combination methods available. These include the traditional committee method, the Delphi method, the paired comparisons method, the negative exponential model, Cooke’s classical model, the histogram technique, using the Dirichlet distribution in the case of a set of uncertain proportions which must sum to one, and the employment of overfitting. The supra Bayes approach, the determination of weights for the experts, and combining the opinions of experts where each opinion is associated with a confidence level that represents the expert’s conviction of his own judgment are also considered.
- Full Text:
- Authors: Chinyamakobvu, Mutsa Carole
- Date: 2015
- Subjects: Decision making -- Statistical methods , Expertise , Bayesian statistical decision theory , Statistical decision , Delphi method , Paired comparisons (Statistics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5579 , http://hdl.handle.net/10962/d1017827
- Description: Decision makers have long relied on experts to inform their decision making. Expert judgment analysis is a way to elicit and combine the opinions of a group of experts to facilitate decision making. The use of expert judgment is most appropriate when there is a lack of data for obtaining reasonable statistical results. The experts are asked for advice by one or more decision makers who face a specific real decision problem. The decision makers are outside the group of experts and are jointly responsible and accountable for the decision and committed to finding solutions that everyone can live with. The emphasis is on the decision makers learning from the experts. The focus of this thesis is an overview and comparison of the various elicitation and combination methods available. These include the traditional committee method, the Delphi method, the paired comparisons method, the negative exponential model, Cooke’s classical model, the histogram technique, using the Dirichlet distribution in the case of a set of uncertain proportions which must sum to one, and the employment of overfitting. The supra Bayes approach, the determination of weights for the experts, and combining the opinions of experts where each opinion is associated with a confidence level that represents the expert’s conviction of his own judgment are also considered.
- Full Text:
Exploration status for oxide and sulphide zinc ores at Skorpion Zinc Mine, Namibia
- Authors: Sitoka, Stefanus
- Date: 2015
- Subjects: Scorpion Zinc Mine (Namibia) , Zinc ores , Oxide minerals , Sulfide minerals , Zinc mines and mining -- Namibia , Prospecting -- Namibia
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5087 , http://hdl.handle.net/10962/d1018204
- Description: The thesis is inspired by recent interests in oxide zinc ores caused by new developments in the technology of hydrometallurgy. The improved techniques turned the non-sulphide zinc ores in to attractive exploration targets due to a number of advantages such as low metal recovery costs and favorable environmental aspects such as the obvious absence of sulfur (Large, 2001). Historically extraction of zinc metal from oxide ores was not possible until recently. The metallurgical complexity resulted in a lack of interest and hence some economic oxide zinc ores might have been missed by conventional exploration techniques. The study presents a review of exploration status at Skorpion mine based on different exploration techniques and their application to sulphide and oxide zinc ore exploration. The challenge facing the mineral exploration industry today is the inability to detect mineral deposits under cover. Therefore a key to successful exploration program lies in the selection of the right exploration technique. Important parameters that should be highlighted in the exploration methodology are the geological situation of an area, equipment applicability and effectiveness, survey limitation, equipment mobilization and the safety aspects involved. The aim of this thesis is to provide a general guideline for sulphide and non-sulphide zinc ore exploration on the Skorpion area and other similar geological environments. Geochemical surveys appears to be more complimentary in exploration of non-sulphide zinc exploration. Although geochemical techniques are preferred, it is equally important to choose the right soil horizon. Furthermore, sample media may mean the difference between success and failure in geochemical exploration of non-sulphide zinc mineralization, due to high mobility of zinc in the surficial environment. On cost comparison, surface geochemical surveys programs are more cost effective except for litho-geochemical sampling which are commonly carried out through subsurface drilling. Geophysical techniques have limited application in exploration of non-sulphide zinc mineralization due to a lack of major physical properties (e.g., magnetic and electrical properties) in non-sulphides unlike their sulphide counterparts. However geophysical methods are commendable in delineating massive and disseminated sulphides mainly if they are associated with major Fe minerals (pyrrhotite or magnetite). In addition, geophysical techniques may be effective in mapping of subsurface primary and secondary structures such as basin faults which might have acted as pathways for metal-rich fluids. Terms non-sulphide and oxide zinc mineralization are used interchangeably throughout the thesis. Recommendations on regional and local target generation are presented in the thesis to give some basic guide lines on target generation strategies. The most important conclusion reached in this study is that, success in exploration for non-sulphide or sulphide zinc mineralization might be enhanced through the integrated exploration methodology.
- Full Text:
- Authors: Sitoka, Stefanus
- Date: 2015
- Subjects: Scorpion Zinc Mine (Namibia) , Zinc ores , Oxide minerals , Sulfide minerals , Zinc mines and mining -- Namibia , Prospecting -- Namibia
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5087 , http://hdl.handle.net/10962/d1018204
- Description: The thesis is inspired by recent interests in oxide zinc ores caused by new developments in the technology of hydrometallurgy. The improved techniques turned the non-sulphide zinc ores in to attractive exploration targets due to a number of advantages such as low metal recovery costs and favorable environmental aspects such as the obvious absence of sulfur (Large, 2001). Historically extraction of zinc metal from oxide ores was not possible until recently. The metallurgical complexity resulted in a lack of interest and hence some economic oxide zinc ores might have been missed by conventional exploration techniques. The study presents a review of exploration status at Skorpion mine based on different exploration techniques and their application to sulphide and oxide zinc ore exploration. The challenge facing the mineral exploration industry today is the inability to detect mineral deposits under cover. Therefore a key to successful exploration program lies in the selection of the right exploration technique. Important parameters that should be highlighted in the exploration methodology are the geological situation of an area, equipment applicability and effectiveness, survey limitation, equipment mobilization and the safety aspects involved. The aim of this thesis is to provide a general guideline for sulphide and non-sulphide zinc ore exploration on the Skorpion area and other similar geological environments. Geochemical surveys appears to be more complimentary in exploration of non-sulphide zinc exploration. Although geochemical techniques are preferred, it is equally important to choose the right soil horizon. Furthermore, sample media may mean the difference between success and failure in geochemical exploration of non-sulphide zinc mineralization, due to high mobility of zinc in the surficial environment. On cost comparison, surface geochemical surveys programs are more cost effective except for litho-geochemical sampling which are commonly carried out through subsurface drilling. Geophysical techniques have limited application in exploration of non-sulphide zinc mineralization due to a lack of major physical properties (e.g., magnetic and electrical properties) in non-sulphides unlike their sulphide counterparts. However geophysical methods are commendable in delineating massive and disseminated sulphides mainly if they are associated with major Fe minerals (pyrrhotite or magnetite). In addition, geophysical techniques may be effective in mapping of subsurface primary and secondary structures such as basin faults which might have acted as pathways for metal-rich fluids. Terms non-sulphide and oxide zinc mineralization are used interchangeably throughout the thesis. Recommendations on regional and local target generation are presented in the thesis to give some basic guide lines on target generation strategies. The most important conclusion reached in this study is that, success in exploration for non-sulphide or sulphide zinc mineralization might be enhanced through the integrated exploration methodology.
- Full Text:
Exploring the development of an integrated, participative, water quality management process for the Crocodile River catchment, focusing on the sugar industry
- Authors: Sahula, Asiphe
- Date: 2015
- Subjects: Water quality management -- South Africa -- Krokodilrivier (Mpumalanga) , Watersheds -- South Africa -- Krokodilrivier (Mpumalanga) , Integrated water development -- South Africa -- Krokodilrivier (Mpumalanga) , Water quality management -- Social aspects -- South Africa -- Krokodilrivier (Mpumalanga) , Social responsibility of business -- South Africa -- Krokodilrivier (Mpumalanga) , Water quality -- South Africa -- Krokodilrivier (Mpumalanga)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6051 , http://hdl.handle.net/10962/d1017876
- Description: Water quality deterioration is reaching crisis proportions in South Africa. Many South African catchments are over-allocated, and decreasing volumes of source water mean increasing concentrations of pollutants. The Crocodile River Catchment in the Mpumalanga province in South Africa was identified through previous research, as a catchment faced with deteriorating source water quality for water users in the catchment. Poor source water quality has become a sufficiently acute concern for the stakeholders in this catchment to co-operate in developing a process that assists with compliance control of their water use and waste disposal to reduce costs, decrease industrial risks as water quality compliance increases, and improve source water quality. The sugar industry is downstream within the Crocodile River Catchment, and is affected by the activities of all upstream water users; the industry is thus dependent on the stakeholders upstream participating in the effective management of the resource. However, the sugar industry is also located just before the confluence of the Crocodile River and Komati River upstream of the Mozambique border, and thus the water quality of the sugar industry effluent will affect the quality of the water that flows into Mozambique. The sugar industry is on the opposite river bank to the Kruger National Park, which has high water resource protection goals. Therefore, the sugar industry has a national role to play in the management of water resources in the Crocodile River Catchment. This study provides a focused view of the role of the sugar industry in the development of a co-operative, integrated water quality management process (IWQMP) in the Crocodile River Catchment. In order to address the objectives of this study, this research drew from an understanding of the social processes that influence water management practices within the sugar industry as well as social processes that influence the role of the Inkomati-Usuthu Catchment Management Agency as the main governing institution in water resource management in the Inkomati Water Management Area. The study also drew from an understanding of scientific knowledge in terms of a water chemistry which describes the upstream and downstream water quality impacts related to the sugar industry. The water quality analysis for the Lower Crocodile River Catchment shows a decline in water quality in terms of Total Dissolved Solids (TDS) loads when moving from below Mbombela to the Mozambique border. The major sources of TDS in the Lower Crocodile River are point source dominated, which may be attributed to the extensive mining, industrial and municipal activities that occur across the catchment. When observing Total Alkalinity (TAL) and pH values from below Mbombela to the furthest monitoring point, there is deterioration in the quality of the water in the Lower Crocodile River, with the Kaap River contributing a negative effect that is diluted by the Crocodile main stem. The Hectorspruit Waste Water Treatment Works (WWTWs) (located in the Lower Crocodile River Catchment) contributes high concentrations of TDS and TAL into the Crocodile River. Total Inorganic Nitrogen and Soluble Reactive Phosphorus concentrations decrease in the lower reaches of the Crocodile River compared with the river below Mbombela, which can be attributed to the extensive sugar cane plantations located in the Lower Crocodile River Catchment acting as an “agricultural wetland” that serves a function of bioremediation resulting in large scale absorption of nutrients. This is an interesting result as earlier assumptions were that fertiliser application would result in an overall increase in nutrient loads and concentrations. Biomonitoring data show no substantial change in aquatic health in the LowerCrocodile River Catchment. For a catchment that has an extensive agricultural land use in terms of sugarcane and citrus production, the Crocodile River is unexpectedly not in a toxic state in terms of aquatic health. This is a positive result and it suggests that pesticide use is strictly controlled in the sugar and citrus industry in the Crocodile River Catchment. For long term sustainability, it is essential for the sugar industry to maintain (and possibly improve) this pesticide management. The social component of this study aimed to provide an analysis of the management practices of the sugar mill as well as examining agricultural practices in the sugar cane fields in relation to water quality management through the use of Cultural Historical Activity System Theory (CHAT). This component showed that there are contradictions within the sugar industry activity system that are considered to be areas of “tension” that can be loosened or focused on to improve the contribution the sugar industry can make to the IWQMP. Surfacing contradictions within the sugar industry activity system and the Inkomati-Usuthu Catchment Management Agency activity systems highlighted areas of potential for learning and change. While an understanding of biophysical processes through scientific knowledge is critical in water management decision making, it is evident that an understanding of other actors, institutions and networks that inform water quality management decision-making also plays a significant role. The notion of improving the role of scientific or biophysical knowledge in contributing to socio-ecologically robust knowledge co-creation, decisions and actions towards resolving water quality problems is emphasised. Specifically, moving towards improving interactions between scientists and other actors (water users in the Crocodile Catchment in this case), so that scientific practices become more orientated towards societal platforms where water quality management is tackled to enable improved water quality management practices. Therefore, linking the social and biophysical components in this study provides a holistic understanding of how the sugar industry can contribute to the development of an IWQMP for the Crocodile River catchment.
- Full Text:
- Authors: Sahula, Asiphe
- Date: 2015
- Subjects: Water quality management -- South Africa -- Krokodilrivier (Mpumalanga) , Watersheds -- South Africa -- Krokodilrivier (Mpumalanga) , Integrated water development -- South Africa -- Krokodilrivier (Mpumalanga) , Water quality management -- Social aspects -- South Africa -- Krokodilrivier (Mpumalanga) , Social responsibility of business -- South Africa -- Krokodilrivier (Mpumalanga) , Water quality -- South Africa -- Krokodilrivier (Mpumalanga)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6051 , http://hdl.handle.net/10962/d1017876
- Description: Water quality deterioration is reaching crisis proportions in South Africa. Many South African catchments are over-allocated, and decreasing volumes of source water mean increasing concentrations of pollutants. The Crocodile River Catchment in the Mpumalanga province in South Africa was identified through previous research, as a catchment faced with deteriorating source water quality for water users in the catchment. Poor source water quality has become a sufficiently acute concern for the stakeholders in this catchment to co-operate in developing a process that assists with compliance control of their water use and waste disposal to reduce costs, decrease industrial risks as water quality compliance increases, and improve source water quality. The sugar industry is downstream within the Crocodile River Catchment, and is affected by the activities of all upstream water users; the industry is thus dependent on the stakeholders upstream participating in the effective management of the resource. However, the sugar industry is also located just before the confluence of the Crocodile River and Komati River upstream of the Mozambique border, and thus the water quality of the sugar industry effluent will affect the quality of the water that flows into Mozambique. The sugar industry is on the opposite river bank to the Kruger National Park, which has high water resource protection goals. Therefore, the sugar industry has a national role to play in the management of water resources in the Crocodile River Catchment. This study provides a focused view of the role of the sugar industry in the development of a co-operative, integrated water quality management process (IWQMP) in the Crocodile River Catchment. In order to address the objectives of this study, this research drew from an understanding of the social processes that influence water management practices within the sugar industry as well as social processes that influence the role of the Inkomati-Usuthu Catchment Management Agency as the main governing institution in water resource management in the Inkomati Water Management Area. The study also drew from an understanding of scientific knowledge in terms of a water chemistry which describes the upstream and downstream water quality impacts related to the sugar industry. The water quality analysis for the Lower Crocodile River Catchment shows a decline in water quality in terms of Total Dissolved Solids (TDS) loads when moving from below Mbombela to the Mozambique border. The major sources of TDS in the Lower Crocodile River are point source dominated, which may be attributed to the extensive mining, industrial and municipal activities that occur across the catchment. When observing Total Alkalinity (TAL) and pH values from below Mbombela to the furthest monitoring point, there is deterioration in the quality of the water in the Lower Crocodile River, with the Kaap River contributing a negative effect that is diluted by the Crocodile main stem. The Hectorspruit Waste Water Treatment Works (WWTWs) (located in the Lower Crocodile River Catchment) contributes high concentrations of TDS and TAL into the Crocodile River. Total Inorganic Nitrogen and Soluble Reactive Phosphorus concentrations decrease in the lower reaches of the Crocodile River compared with the river below Mbombela, which can be attributed to the extensive sugar cane plantations located in the Lower Crocodile River Catchment acting as an “agricultural wetland” that serves a function of bioremediation resulting in large scale absorption of nutrients. This is an interesting result as earlier assumptions were that fertiliser application would result in an overall increase in nutrient loads and concentrations. Biomonitoring data show no substantial change in aquatic health in the LowerCrocodile River Catchment. For a catchment that has an extensive agricultural land use in terms of sugarcane and citrus production, the Crocodile River is unexpectedly not in a toxic state in terms of aquatic health. This is a positive result and it suggests that pesticide use is strictly controlled in the sugar and citrus industry in the Crocodile River Catchment. For long term sustainability, it is essential for the sugar industry to maintain (and possibly improve) this pesticide management. The social component of this study aimed to provide an analysis of the management practices of the sugar mill as well as examining agricultural practices in the sugar cane fields in relation to water quality management through the use of Cultural Historical Activity System Theory (CHAT). This component showed that there are contradictions within the sugar industry activity system that are considered to be areas of “tension” that can be loosened or focused on to improve the contribution the sugar industry can make to the IWQMP. Surfacing contradictions within the sugar industry activity system and the Inkomati-Usuthu Catchment Management Agency activity systems highlighted areas of potential for learning and change. While an understanding of biophysical processes through scientific knowledge is critical in water management decision making, it is evident that an understanding of other actors, institutions and networks that inform water quality management decision-making also plays a significant role. The notion of improving the role of scientific or biophysical knowledge in contributing to socio-ecologically robust knowledge co-creation, decisions and actions towards resolving water quality problems is emphasised. Specifically, moving towards improving interactions between scientists and other actors (water users in the Crocodile Catchment in this case), so that scientific practices become more orientated towards societal platforms where water quality management is tackled to enable improved water quality management practices. Therefore, linking the social and biophysical components in this study provides a holistic understanding of how the sugar industry can contribute to the development of an IWQMP for the Crocodile River catchment.
- Full Text:
Gene expression analysis of Thaumatotibia leucotreta in response to the Cryptophlebia leucotreta granulovirus
- Authors: Ridgeway, Jaryd Antony
- Date: 2015
- Subjects: Gene expression , Insects -- Viruses , Tortricidae -- Viruses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5931 , http://hdl.handle.net/10962/d1017809
- Description: Gene expression studies provide baseline information on the interactions of insects with their environment. Despite the importance of this information, limited gene expression data are available for most insect pests, including the family Tortricidae (Lepidoptera), which includes Thaumatotibia leucotreta (Meyr), an important agricultural pest in Africa. Because T. leucotreta can be controlled successfully by a granulovirus, this system is a good model for exploring insect-virus susceptibility. The main aim of this study was to investigate gene expression of T. leucotreta in responce to virus infection. However, before pursuing this aim, two objectives required completion. First, the most suitable RNA extraction method for insects needed to be determined and second, the most suitable reference genes for qPCR for Tortricidae pests needed to be identified. Once these objectives were accomplished, the response of T. leucotreta to its granulovirus was evaluated at different temperatures and points after infection.Four RNA extraction methods, the RNeasy® Mini Kit, SV Total RNA isolation system, TRIzol® reagent, and a CTAB-based method, were compared using two beetle and two moth species, including T. leucotreta. The quality of extracted RNA was similar for all four species for all extraction methods. Based on several criteria, the best RNA extraction method was the SV Total RNA isolation system. Six candidate reference genes were evaluated for qPCR using different tissue types of T. leucotreta and two other Tortricidae pests. Additionally, reference genes were evaluated for T. leucotreta with and without its granulovirus at different temperatures. Reference gene stability was found to be dependent on species and tissue type. Overall the most suitable combination of reference genes for T. leucotreta were α-actin, arginine kinase and elongation factor 1-α.Gene expression of T. leucotreta in response to granulovirus infection at different temperatures and intervals after infection was evaluated by qPCR using 13 target genes associated with the infection process. Most genes were down-regulated after 24 and 48 h.p.i. However, after 72 h.p.i most genes were up-regulated. The same trend was observed at different temperatures, where most genes were down-regulated at 15°C and 25°C but up-regulated at 35°C. These results show that there is a dynamic gene expression response in T. leucotreta due to granulovirus infection under different conditions. Not only do these findings provide insight into the control of this tortricid pest, they also contribute further to our knowledge of insect-virus interactions.
- Full Text:
- Authors: Ridgeway, Jaryd Antony
- Date: 2015
- Subjects: Gene expression , Insects -- Viruses , Tortricidae -- Viruses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5931 , http://hdl.handle.net/10962/d1017809
- Description: Gene expression studies provide baseline information on the interactions of insects with their environment. Despite the importance of this information, limited gene expression data are available for most insect pests, including the family Tortricidae (Lepidoptera), which includes Thaumatotibia leucotreta (Meyr), an important agricultural pest in Africa. Because T. leucotreta can be controlled successfully by a granulovirus, this system is a good model for exploring insect-virus susceptibility. The main aim of this study was to investigate gene expression of T. leucotreta in responce to virus infection. However, before pursuing this aim, two objectives required completion. First, the most suitable RNA extraction method for insects needed to be determined and second, the most suitable reference genes for qPCR for Tortricidae pests needed to be identified. Once these objectives were accomplished, the response of T. leucotreta to its granulovirus was evaluated at different temperatures and points after infection.Four RNA extraction methods, the RNeasy® Mini Kit, SV Total RNA isolation system, TRIzol® reagent, and a CTAB-based method, were compared using two beetle and two moth species, including T. leucotreta. The quality of extracted RNA was similar for all four species for all extraction methods. Based on several criteria, the best RNA extraction method was the SV Total RNA isolation system. Six candidate reference genes were evaluated for qPCR using different tissue types of T. leucotreta and two other Tortricidae pests. Additionally, reference genes were evaluated for T. leucotreta with and without its granulovirus at different temperatures. Reference gene stability was found to be dependent on species and tissue type. Overall the most suitable combination of reference genes for T. leucotreta were α-actin, arginine kinase and elongation factor 1-α.Gene expression of T. leucotreta in response to granulovirus infection at different temperatures and intervals after infection was evaluated by qPCR using 13 target genes associated with the infection process. Most genes were down-regulated after 24 and 48 h.p.i. However, after 72 h.p.i most genes were up-regulated. The same trend was observed at different temperatures, where most genes were down-regulated at 15°C and 25°C but up-regulated at 35°C. These results show that there is a dynamic gene expression response in T. leucotreta due to granulovirus infection under different conditions. Not only do these findings provide insight into the control of this tortricid pest, they also contribute further to our knowledge of insect-virus interactions.
- Full Text:
Geomorphic and ambient environmental impacts on lichen distribution on two inland Nunataks in western Dronning Maud Land, Antarctica
- Authors: Dwight, Rosemary Anne
- Date: 2015
- Subjects: Lichens -- Antarctica -- Queen Maud Land , Lichen communities -- Antarctica -- Queen Maud Land , Lichens -- Climatic factors -- Antarctica -- Queen Maud Land , Lichens -- Effect of environment on -- Antarctica -- Queen Maud Land , Biotic communities -- Antarctica -- Queen Maud Land , Biotic communities -- Climatic factors -- Antarctica -- Queen Maud Land , Biodiversity -- Climatic factors -- Antarctica -- Queen Maud Land
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4889 , http://hdl.handle.net/10962/d1018189
- Description: Feedbacks between abiotic variables and community structure in Antarctica are poorly understood. Research is, therefore, required to elucidate the patterns of biodiversity that exist and the factors that influence them, particularly under changing climates. Landscape processes affect environmental heterogeneity, which in turn affect patterns of biodiversity. Two inland Antarctic nunataks, Robertskollen and the Northern Buttress of Vesleskarvet, were selected for investigation to determine the potential impact of selected environmental factors on lichen distribution and abundance, at the intra- and inter-nunatak scales. Lichens were found to prefer rock faces with dips between 1° and 45°, and northern/southern aspects. Lichen colonisation was mostly in microtopographical features that result from rock weathering. The distribution of lichens was found to be regular at the intra- and inter-nunatak scale, whereas lichen abundance was found to be mostly influenced by temperature. On the Northern Buttress, rock hardness displays a similar pattern to lichen abundance, both of which are suggested to be a function of exposure time, which is dependent on deglaciation. The two nunataks serve as excellent laboratories that can potentially be used as proxies for investigating the possible impacts of climate change
- Full Text:
- Authors: Dwight, Rosemary Anne
- Date: 2015
- Subjects: Lichens -- Antarctica -- Queen Maud Land , Lichen communities -- Antarctica -- Queen Maud Land , Lichens -- Climatic factors -- Antarctica -- Queen Maud Land , Lichens -- Effect of environment on -- Antarctica -- Queen Maud Land , Biotic communities -- Antarctica -- Queen Maud Land , Biotic communities -- Climatic factors -- Antarctica -- Queen Maud Land , Biodiversity -- Climatic factors -- Antarctica -- Queen Maud Land
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4889 , http://hdl.handle.net/10962/d1018189
- Description: Feedbacks between abiotic variables and community structure in Antarctica are poorly understood. Research is, therefore, required to elucidate the patterns of biodiversity that exist and the factors that influence them, particularly under changing climates. Landscape processes affect environmental heterogeneity, which in turn affect patterns of biodiversity. Two inland Antarctic nunataks, Robertskollen and the Northern Buttress of Vesleskarvet, were selected for investigation to determine the potential impact of selected environmental factors on lichen distribution and abundance, at the intra- and inter-nunatak scales. Lichens were found to prefer rock faces with dips between 1° and 45°, and northern/southern aspects. Lichen colonisation was mostly in microtopographical features that result from rock weathering. The distribution of lichens was found to be regular at the intra- and inter-nunatak scale, whereas lichen abundance was found to be mostly influenced by temperature. On the Northern Buttress, rock hardness displays a similar pattern to lichen abundance, both of which are suggested to be a function of exposure time, which is dependent on deglaciation. The two nunataks serve as excellent laboratories that can potentially be used as proxies for investigating the possible impacts of climate change
- Full Text:
Identification of novel SNPSTRs by 454 sequencing in Nguni and Sotho-Tswana populations
- Authors: Laurence, Jo-Anne Elizabeth
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55885 , vital:26752
- Description: DNA profiling is currently performed by analysis of the electropherogram that results following the amplification of a panel of Short Tandem Repeat (STR) loci. A need has arisen, however, for the development of a typing method that generates results which are compatible and comparable with existing databases, but that have a higher discrimination power by supplying sequence data as well as repeat-number data. Recent studies that explore these alternative typing methodologies have revealed the existence of a number of STR variants. There is, however, little information about the exact nature and prevalence of these sub-alleles. There have also been limited population studies of the genetic profiles of sub-Saharan African populations, despite the fact that evidence suggests that there is greater genetic structure and genetic diversity in these populations. In this study, a processing protocol for the generation of 454 sequencing-ready amplicons of vWA, D2S441, D3S1358, D13S317, D21S11 and D7S820 loci was developed. This protocol was applied to buccal swabs collected from 144 individuals of the Nguni and Sotho-Tswana population groups. A total of 145 485 reads were obtained from the sequencing of these amplicons, of which 97 400 and 48 085 reads were obtained for the Nguni and Sotho-Tswana populations respectively. The proportional representation for each locus ranged from 8-20%, and the allele calls and observed frequencies of these alleles suggested a high degree of relatedness between population groups. The sequencing results, furthermore, enabled the identification of a number of previously undescribed STR variants and SNPSTRs; with allele 13´ for D13S317 representing a SNP that may be predictive of Nguni-ancestry. The results also demonstrated the usefulness of next generation sequencing for increasing the number of discernible alleles for STR profiling.
- Full Text:
- Authors: Laurence, Jo-Anne Elizabeth
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55885 , vital:26752
- Description: DNA profiling is currently performed by analysis of the electropherogram that results following the amplification of a panel of Short Tandem Repeat (STR) loci. A need has arisen, however, for the development of a typing method that generates results which are compatible and comparable with existing databases, but that have a higher discrimination power by supplying sequence data as well as repeat-number data. Recent studies that explore these alternative typing methodologies have revealed the existence of a number of STR variants. There is, however, little information about the exact nature and prevalence of these sub-alleles. There have also been limited population studies of the genetic profiles of sub-Saharan African populations, despite the fact that evidence suggests that there is greater genetic structure and genetic diversity in these populations. In this study, a processing protocol for the generation of 454 sequencing-ready amplicons of vWA, D2S441, D3S1358, D13S317, D21S11 and D7S820 loci was developed. This protocol was applied to buccal swabs collected from 144 individuals of the Nguni and Sotho-Tswana population groups. A total of 145 485 reads were obtained from the sequencing of these amplicons, of which 97 400 and 48 085 reads were obtained for the Nguni and Sotho-Tswana populations respectively. The proportional representation for each locus ranged from 8-20%, and the allele calls and observed frequencies of these alleles suggested a high degree of relatedness between population groups. The sequencing results, furthermore, enabled the identification of a number of previously undescribed STR variants and SNPSTRs; with allele 13´ for D13S317 representing a SNP that may be predictive of Nguni-ancestry. The results also demonstrated the usefulness of next generation sequencing for increasing the number of discernible alleles for STR profiling.
- Full Text:
In silico analysis of human Hsp90 for the identification of novel anti-cancer drug target sites and natural compound inhibitors
- Authors: Penkler, David Lawrence
- Date: 2015
- Subjects: Heat shock proteins , Cancer -- Treatment , Molecular chaperones , Homeostasis , Carcinogenesis , Chemotherapy , Ligand binding (Biochemistry) , Protein-protein interactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4162 , http://hdl.handle.net/10962/d1018938
- Description: The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.
- Full Text:
- Authors: Penkler, David Lawrence
- Date: 2015
- Subjects: Heat shock proteins , Cancer -- Treatment , Molecular chaperones , Homeostasis , Carcinogenesis , Chemotherapy , Ligand binding (Biochemistry) , Protein-protein interactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4162 , http://hdl.handle.net/10962/d1018938
- Description: The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.
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