A critical realist account of a mentoring programme in the Faculty of Pharmacy at Rhodes University
- Authors: Oltmann, Carmen
- Date: 2009
- Subjects: Rhodes University -- Academic Development Programme Pharmacy -- Study and teaching (Higher) -- South Africa Mentoring in education -- South Africa Mentoring in Science -- South Africa Critical realism Communities of practice
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3781 , http://hdl.handle.net/10962/d1003259
- Description: This study originates from experiences I had as supervisor of the mentoring programme for first year students in the Faculty of Pharmacy, at Rhodes University. Our mentoring programme is a strategy for first year students – specifically those from previously disadvantaged backgrounds – to succeed at Rhodes University. Using an ontological meta-theory - critical realism - as my analytical lens, discourse as my unit of analysis, and Invitational Learning Theory as a theoretical tool I developed a model of mentoring based on Bhaskar’s transformational model (1993). This model illustrates the relationship between structure, culture and agency. Whilst developing this model I focussed on determining how mentors construct mentoring, and how mentoring facilitates access to a Community of Practice (CoP). Mentoring involves providing a shared space that is safe, that the mentor and mentee feel comfortable in, and that supports and challenges both the mentor and the mentee. It is a reciprocal, developmental relationship for both the mentor and the mentee that deals with issues that the mentee deems as ‘real’. Mentoring is a process, not an outcome. The mentoring strategies that the mentors employed changed as the mentors mentored. Mentors help mentees by using structures and mechanisms that worked for them, and/or by helping mentees access these structures and mechanisms. Mentoring facilitates access to a CoP by providing opportunities for engagement. This involves sharing of experiences and knowledge, and promoting discussion. The mentor helps the mentee move from being a peripheral member of the CoP to becoming a main member, i.e., becoming active, learning with and from others within the CoP. CoPs develop social capital and knowledge management. My research suggests that the knowledge, skills and attitude developed by the mentors within this study may be transferable to other aspects in Pharmacy.
- Full Text:
- Date Issued: 2009
- Authors: Oltmann, Carmen
- Date: 2009
- Subjects: Rhodes University -- Academic Development Programme Pharmacy -- Study and teaching (Higher) -- South Africa Mentoring in education -- South Africa Mentoring in Science -- South Africa Critical realism Communities of practice
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3781 , http://hdl.handle.net/10962/d1003259
- Description: This study originates from experiences I had as supervisor of the mentoring programme for first year students in the Faculty of Pharmacy, at Rhodes University. Our mentoring programme is a strategy for first year students – specifically those from previously disadvantaged backgrounds – to succeed at Rhodes University. Using an ontological meta-theory - critical realism - as my analytical lens, discourse as my unit of analysis, and Invitational Learning Theory as a theoretical tool I developed a model of mentoring based on Bhaskar’s transformational model (1993). This model illustrates the relationship between structure, culture and agency. Whilst developing this model I focussed on determining how mentors construct mentoring, and how mentoring facilitates access to a Community of Practice (CoP). Mentoring involves providing a shared space that is safe, that the mentor and mentee feel comfortable in, and that supports and challenges both the mentor and the mentee. It is a reciprocal, developmental relationship for both the mentor and the mentee that deals with issues that the mentee deems as ‘real’. Mentoring is a process, not an outcome. The mentoring strategies that the mentors employed changed as the mentors mentored. Mentors help mentees by using structures and mechanisms that worked for them, and/or by helping mentees access these structures and mechanisms. Mentoring facilitates access to a CoP by providing opportunities for engagement. This involves sharing of experiences and knowledge, and promoting discussion. The mentor helps the mentee move from being a peripheral member of the CoP to becoming a main member, i.e., becoming active, learning with and from others within the CoP. CoPs develop social capital and knowledge management. My research suggests that the knowledge, skills and attitude developed by the mentors within this study may be transferable to other aspects in Pharmacy.
- Full Text:
- Date Issued: 2009
A knowledge-oriented, context-sensitive architectural framework for service deployment in marginalized rural communities
- Authors: Thinyane, Mamello P
- Date: 2009
- Subjects: Information technology Expert systems (Computer science) Software architecture User interfaces (Computer systems) Ethnoscience Social networks Rural development Technical assistance -- Developing countries Information networks -- Developing countries
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4599 , http://hdl.handle.net/10962/d1004843
- Description: The notion of a global knowledge society is somewhat of a misnomer due to the fact that large portions of the global community are not participants in this global knowledge society which is driven, shaped by and socio-technically biased towards a small fraction of the global population. Information and Communication Technology (ICT) is culture-sensitive and this is a dynamic that is largely ignored in the majority of ICT for Development (ICT4D) interventions, leading to the technological determinism flaw and ultimately a failure of the undertaken projects. The deployment of ICT solutions, in particular in the context of ICT4D, must be informed by the cultural and socio-technical profile of the deployment environments and solutions themselves must be developed with a focus towards context-sensitivity and ethnocentricity. In this thesis, we investigate the viability of a software architectural framework for the development of ICT solutions that are context-sensitive and ethnocentric1, and so aligned with the cultural and social dynamics within the environment of deployment. The conceptual framework, named PIASK, defines five tiers (presentation, interaction, access, social networking, and knowledge base) which allow for: behavioural completeness of the layer components; a modular and functionally decoupled architecture; and the flexibility to situate and contextualize the developed applications along the dimensions of the User Interface (UI), interaction modalities, usage metaphors, underlying Indigenous Knowledge (IK), and access protocols. We have developed a proof-of-concept service platform, called KnowNet, based on the PIASK architecture. KnowNet is built around the knowledge base layer, which consists of domain ontologies that encapsulate the knowledge in the platform, with an intrinsic flexibility to access secondary knowledge repositories. The domain ontologies constructed (as examples) are for the provisioning of eServices to support societal activities (e.g. commerce, health, agriculture, medicine) within a rural and marginalized area of Dwesa, in the Eastern Cape province of South Africa. The social networking layer allows for situating the platform within the local social systems. Heterogeneity of user profiles and multiplicity of end-user devices are handled through the access and the presentation components, and the service logic is implemented by the interaction components. This services platform validates the PIASK architecture for end-to-end provisioning of multi-modal, heterogeneous, ontology-based services. The development of KnowNet was informed on one hand by the latest trends within service architectures, semantic web technologies and social applications, and on the other hand by the context consideration based on the profile (IK systems dynamics, infrastructure, usability requirements) of the Dwesa community. The realization of the service platform is based on the JADE Multi-Agent System (MAS), and this shows the applicability and adequacy of MAS’s for service deployment in a rural context, at the same time providing key advantages such as platform fault-tolerance, robustness and flexibility. While the context of conceptualization of PIASK and the implementation of KnowNet is that of rurality and of ICT4D, the applicability of the architecture extends to other similarly heterogeneous and context-sensitive domains. KnowNet has been validated for functional and technical adequacy, and we have also undertaken an initial prevalidation for social context sensitivity. We observe that the five tier PIASK architecture provides an adequate framework for developing context-sensitive and ethnocentric software: by functionally separating and making explicit the social networking and access tier components, while still maintaining the traditional separation of presentation, business logic and data components.
- Full Text:
- Date Issued: 2009
- Authors: Thinyane, Mamello P
- Date: 2009
- Subjects: Information technology Expert systems (Computer science) Software architecture User interfaces (Computer systems) Ethnoscience Social networks Rural development Technical assistance -- Developing countries Information networks -- Developing countries
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4599 , http://hdl.handle.net/10962/d1004843
- Description: The notion of a global knowledge society is somewhat of a misnomer due to the fact that large portions of the global community are not participants in this global knowledge society which is driven, shaped by and socio-technically biased towards a small fraction of the global population. Information and Communication Technology (ICT) is culture-sensitive and this is a dynamic that is largely ignored in the majority of ICT for Development (ICT4D) interventions, leading to the technological determinism flaw and ultimately a failure of the undertaken projects. The deployment of ICT solutions, in particular in the context of ICT4D, must be informed by the cultural and socio-technical profile of the deployment environments and solutions themselves must be developed with a focus towards context-sensitivity and ethnocentricity. In this thesis, we investigate the viability of a software architectural framework for the development of ICT solutions that are context-sensitive and ethnocentric1, and so aligned with the cultural and social dynamics within the environment of deployment. The conceptual framework, named PIASK, defines five tiers (presentation, interaction, access, social networking, and knowledge base) which allow for: behavioural completeness of the layer components; a modular and functionally decoupled architecture; and the flexibility to situate and contextualize the developed applications along the dimensions of the User Interface (UI), interaction modalities, usage metaphors, underlying Indigenous Knowledge (IK), and access protocols. We have developed a proof-of-concept service platform, called KnowNet, based on the PIASK architecture. KnowNet is built around the knowledge base layer, which consists of domain ontologies that encapsulate the knowledge in the platform, with an intrinsic flexibility to access secondary knowledge repositories. The domain ontologies constructed (as examples) are for the provisioning of eServices to support societal activities (e.g. commerce, health, agriculture, medicine) within a rural and marginalized area of Dwesa, in the Eastern Cape province of South Africa. The social networking layer allows for situating the platform within the local social systems. Heterogeneity of user profiles and multiplicity of end-user devices are handled through the access and the presentation components, and the service logic is implemented by the interaction components. This services platform validates the PIASK architecture for end-to-end provisioning of multi-modal, heterogeneous, ontology-based services. The development of KnowNet was informed on one hand by the latest trends within service architectures, semantic web technologies and social applications, and on the other hand by the context consideration based on the profile (IK systems dynamics, infrastructure, usability requirements) of the Dwesa community. The realization of the service platform is based on the JADE Multi-Agent System (MAS), and this shows the applicability and adequacy of MAS’s for service deployment in a rural context, at the same time providing key advantages such as platform fault-tolerance, robustness and flexibility. While the context of conceptualization of PIASK and the implementation of KnowNet is that of rurality and of ICT4D, the applicability of the architecture extends to other similarly heterogeneous and context-sensitive domains. KnowNet has been validated for functional and technical adequacy, and we have also undertaken an initial prevalidation for social context sensitivity. We observe that the five tier PIASK architecture provides an adequate framework for developing context-sensitive and ethnocentric software: by functionally separating and making explicit the social networking and access tier components, while still maintaining the traditional separation of presentation, business logic and data components.
- Full Text:
- Date Issued: 2009
A systems approach to mainstreaming environment and sustainability in universities : the case of Rhodes University, South Africa
- Authors: Togo, Muchaiteyi
- Date: 2009
- Subjects: Rhodes University Education, Higher -- South Africa Universities and colleges -- South Africa Universities and colleges -- Environmental aspects -- South Africa -- Case studies Environmental education -- South Africa -- Case studies Sustainable development -- South Africa -- Case studies
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4768 , http://hdl.handle.net/10962/d1007175
- Description: This study is influenced by the objectives of the Mainstreaming Environment and Sustainability in African Universities Partnership which aims to enhance the quality and relevance of university education through implementation of Environmental Education and sustainability across university functions and operations. It contributes to Education for Sustainable Development through the development of tools to assess sustainability in higher education, investigating sustainability practices in universities and proposing strategies for improving mainstreaming of sustainability. It also contributes to systems approaches in mainstreaming contextual sustainability challenges in university functions and operations. The aim of the study was to investigate how universities can mainstream sustainability in their functions and operations in response to contextual sustainability challenges in a changing environment using a systems approach. The research was a case study of Rhodes University in South Africa, which is situated in the impoverished Eastern Cape Province. The study involved 12 teaching departments (representing all faculties at the university), four research units and institutes, five managements units, the Estates Division and the Student Representative Council. The theoretical framework of the study draws from a critical realist ontology and systems thinking epistemology. Systems thinking emphasises the interdependencies of phenomena, thus providing the methodology and tools for a systems view of relationships between education and the environmental context in which it is embedded. Critical realism was employed as an underlabourer to systems thinking as it provides for some of the dimensions absent in systems thinking including its depth ontology which facilitates isolating causal factors influencing empirical reality. It recognises that explanation of phenomena can be embedded in history and acknowledges the fallibility of knowledge. The data collection methods employed in the study include a sustainability assessment using a Unit-based Sustainability Assessment Tool developed as part of the study, interviews, content analyses and observations. Data analyses were performed through employing morphogenetic analysis, and inductive, abductive and retroductive modes of inference. The morphogenetic analysis of social transformation/reproduction was employed to trace the historical emergence of sustainability initiatives at Rhodes University. Induction facilitated reorganisation of the data into themes which particularly represent the main sustainability activities at Rhodes University. Abduction, through recontextualising data in a systems thinking framework, enabled further insights into the phenomena. In the study, it enabled use of systems lenses as a framework and led to identification of systemic issues affecting mainstreaming and later, the development of systems thinking approaches in mainstreaming sustainability. Retroduction enabled identification of causal mechanisms which influenced the emergence of sustainability initiatives at the university. The study established that the emergence of sustainability initiatives at Rhodes University followed the 1990 Talloires Declaration and paralleled international institutional developments in relation to environmental and sustainability challenges. Since then, sustainability initiatives have continuously been emerging in various operational dimensions of the university in line with emerging sustainability challenges which resulted in a morphogenetic cycle. The study revealed that Rhodes University has mainstreamed sustainability across the functions and operations of most of the departments/divisions/units forming part of the study, especially in functions like teaching, research, community engagement and operations. There were a few exceptions like the Human Resources Division and to an extent the Research Office/Management Division which are not yet considering sustainability in their operations. While most of the teaching departments had sustainability initiatives in teaching, research and community engagement, there was diversity in the dimension(s) of sustainable development that the departments addressed and this seemed to relate to the disciplinary content of their subjects. In the Estates Division sustainability initiatives included sustainable landscaping, campus environmental management, water and energy conservation initiatives, waste recycling, use of biodiesel, to mention a few. Students were also involved in various sustainability activities especially through voluntary community engagement initiatives. Sustainability initiatives at the university were also discovered to be embedded within and responding to sustainability challenges of the immediate university environment of Makana District. The study unearthed the causal mechanisms enabling and constraining mainstreaming activities at the university. These were found to be embedded in the history and context within which the university is operating, and other factors related to university structures and agency of lecturers, other employees and students. Examples of these factors are unsustainable patterns in society, policies and the need to redress past inequalities. The study noted the existence of systemic issues at the university which need to be addressed to enable and enhance the promotion of a systems approach to mainstreaming: notably, complexity owing to diversity of approaches employed in mainstreaming, the absence of clearly defined university sustainability goals, problems of institutional support and in some cases, disciplinary governing rules which do not leave room for mainstreaming sustainability. The study established the possibility of improving mainstreaming of sustainability through the adoption of more explicit systems approaches. It suggests use of systems models including the systems-environment model, the functions/structure model and the motion picture model in the process. It recommends making the goal of mainstreaming more upfront, developing a shared understanding of sustainability and mapping out/defining contextual sustainable development issues to grapple with. The study also recommends adopting a holistic approach in mainstreaming, making it a campus-wide initiative, involving all students and developing interdisciplinary curricula. It suggests setting up of supporting mechanisms to strengthen, extend and spearhead mainstreaming and enhancement of collaborative work in sustainable development issues.
- Full Text:
- Date Issued: 2009
- Authors: Togo, Muchaiteyi
- Date: 2009
- Subjects: Rhodes University Education, Higher -- South Africa Universities and colleges -- South Africa Universities and colleges -- Environmental aspects -- South Africa -- Case studies Environmental education -- South Africa -- Case studies Sustainable development -- South Africa -- Case studies
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4768 , http://hdl.handle.net/10962/d1007175
- Description: This study is influenced by the objectives of the Mainstreaming Environment and Sustainability in African Universities Partnership which aims to enhance the quality and relevance of university education through implementation of Environmental Education and sustainability across university functions and operations. It contributes to Education for Sustainable Development through the development of tools to assess sustainability in higher education, investigating sustainability practices in universities and proposing strategies for improving mainstreaming of sustainability. It also contributes to systems approaches in mainstreaming contextual sustainability challenges in university functions and operations. The aim of the study was to investigate how universities can mainstream sustainability in their functions and operations in response to contextual sustainability challenges in a changing environment using a systems approach. The research was a case study of Rhodes University in South Africa, which is situated in the impoverished Eastern Cape Province. The study involved 12 teaching departments (representing all faculties at the university), four research units and institutes, five managements units, the Estates Division and the Student Representative Council. The theoretical framework of the study draws from a critical realist ontology and systems thinking epistemology. Systems thinking emphasises the interdependencies of phenomena, thus providing the methodology and tools for a systems view of relationships between education and the environmental context in which it is embedded. Critical realism was employed as an underlabourer to systems thinking as it provides for some of the dimensions absent in systems thinking including its depth ontology which facilitates isolating causal factors influencing empirical reality. It recognises that explanation of phenomena can be embedded in history and acknowledges the fallibility of knowledge. The data collection methods employed in the study include a sustainability assessment using a Unit-based Sustainability Assessment Tool developed as part of the study, interviews, content analyses and observations. Data analyses were performed through employing morphogenetic analysis, and inductive, abductive and retroductive modes of inference. The morphogenetic analysis of social transformation/reproduction was employed to trace the historical emergence of sustainability initiatives at Rhodes University. Induction facilitated reorganisation of the data into themes which particularly represent the main sustainability activities at Rhodes University. Abduction, through recontextualising data in a systems thinking framework, enabled further insights into the phenomena. In the study, it enabled use of systems lenses as a framework and led to identification of systemic issues affecting mainstreaming and later, the development of systems thinking approaches in mainstreaming sustainability. Retroduction enabled identification of causal mechanisms which influenced the emergence of sustainability initiatives at the university. The study established that the emergence of sustainability initiatives at Rhodes University followed the 1990 Talloires Declaration and paralleled international institutional developments in relation to environmental and sustainability challenges. Since then, sustainability initiatives have continuously been emerging in various operational dimensions of the university in line with emerging sustainability challenges which resulted in a morphogenetic cycle. The study revealed that Rhodes University has mainstreamed sustainability across the functions and operations of most of the departments/divisions/units forming part of the study, especially in functions like teaching, research, community engagement and operations. There were a few exceptions like the Human Resources Division and to an extent the Research Office/Management Division which are not yet considering sustainability in their operations. While most of the teaching departments had sustainability initiatives in teaching, research and community engagement, there was diversity in the dimension(s) of sustainable development that the departments addressed and this seemed to relate to the disciplinary content of their subjects. In the Estates Division sustainability initiatives included sustainable landscaping, campus environmental management, water and energy conservation initiatives, waste recycling, use of biodiesel, to mention a few. Students were also involved in various sustainability activities especially through voluntary community engagement initiatives. Sustainability initiatives at the university were also discovered to be embedded within and responding to sustainability challenges of the immediate university environment of Makana District. The study unearthed the causal mechanisms enabling and constraining mainstreaming activities at the university. These were found to be embedded in the history and context within which the university is operating, and other factors related to university structures and agency of lecturers, other employees and students. Examples of these factors are unsustainable patterns in society, policies and the need to redress past inequalities. The study noted the existence of systemic issues at the university which need to be addressed to enable and enhance the promotion of a systems approach to mainstreaming: notably, complexity owing to diversity of approaches employed in mainstreaming, the absence of clearly defined university sustainability goals, problems of institutional support and in some cases, disciplinary governing rules which do not leave room for mainstreaming sustainability. The study established the possibility of improving mainstreaming of sustainability through the adoption of more explicit systems approaches. It suggests use of systems models including the systems-environment model, the functions/structure model and the motion picture model in the process. It recommends making the goal of mainstreaming more upfront, developing a shared understanding of sustainability and mapping out/defining contextual sustainable development issues to grapple with. The study also recommends adopting a holistic approach in mainstreaming, making it a campus-wide initiative, involving all students and developing interdisciplinary curricula. It suggests setting up of supporting mechanisms to strengthen, extend and spearhead mainstreaming and enhancement of collaborative work in sustainable development issues.
- Full Text:
- Date Issued: 2009
Advances in platinum-amine chemotherapeutic agents : their chemistry and applicationc
- Authors: Jaganath, Yatish
- Date: 2009
- Subjects: Coordination compounds , Antineoplastic antibiotics , Cancer -- Chemotherapy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10446 , http://hdl.handle.net/10948/d1021222
- Description: The research conducted in this study focussed on advancing the knowledge database of diamineplatinum complexes on two frontiers: 1) the development of novel anticancer complexes, and 2) improvements in their synthetic chemistry. Novel square-planar dichloro and oxalato platinum(II) complexes were synthesized as potential anticancer agents in accordance with a comprehensive set of factors identified as being significant in optimizing such action. The nonleaving ligands consisted of asymmetric chelating chiral diamines of the form 1- (1-R-imidazol-2yl)(R')methanamine (R representing methyl, butyl and R' methyl, phenyl). The complexes were characterized by a host of spectral, thermal and crystallographic techniques. In addition, the stabilities of the complexes were monitored in aqueous and saline solutions. Cytotoxicity screening on three cultured cancer cell lines (MCF-7, HeLa and HT29) indicated the compounds, present as their respective racemates, to have rather modest activities relative to cisplatin; with complexes having the smallest substituents, R,R' = methyl, being most active. In recognition of the limitations of traditional silver-based syntheses of oxalatoplatinum(II) complexes, innovative non-silver methods were developed using the well known cancer drug, oxaliplatin, (trans-R,R-1,2- diaminocyclohexane)oxalatoplatinum(II), as a prototype. These involved direct ligand exchange reactions of the dichloro precursor, (trans-R,R-1,2- diaminocyclohexane)dichloroplatinum(II), with tetrabutylammonium oxalate in essentially non-aqueous solvents. A 90:10 mixture of isoamyl alcohol (3-methyl- 1-butanol):water, proved to be a promising solvent, enabling the recovery of pure oxaliplatin (~98 percent) after 9 hours at 88 °C in yields of up to 86 percent. In light of the perceived unique mode of anticancer action available to mononitroplatinum(IV) complexes (i.e. their STAT3-binding potential), octahedral diamineoxalatoplatinum(IV) complexes containing axially-coordinated nitro and halo co-ligands were synthesized and extensively characterized. Electrochemical studies revealed trends in reduction potential which could be correlated to structural / chemical traits of the coordinated diamine and axial ligands. The similarities of the determined cytotoxicities of the platinum(IV) compounds and their respective platinum(II) analogues, implicated reduction as a means of activation of the platinum(IV) complexes.
- Full Text:
- Date Issued: 2009
- Authors: Jaganath, Yatish
- Date: 2009
- Subjects: Coordination compounds , Antineoplastic antibiotics , Cancer -- Chemotherapy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10446 , http://hdl.handle.net/10948/d1021222
- Description: The research conducted in this study focussed on advancing the knowledge database of diamineplatinum complexes on two frontiers: 1) the development of novel anticancer complexes, and 2) improvements in their synthetic chemistry. Novel square-planar dichloro and oxalato platinum(II) complexes were synthesized as potential anticancer agents in accordance with a comprehensive set of factors identified as being significant in optimizing such action. The nonleaving ligands consisted of asymmetric chelating chiral diamines of the form 1- (1-R-imidazol-2yl)(R')methanamine (R representing methyl, butyl and R' methyl, phenyl). The complexes were characterized by a host of spectral, thermal and crystallographic techniques. In addition, the stabilities of the complexes were monitored in aqueous and saline solutions. Cytotoxicity screening on three cultured cancer cell lines (MCF-7, HeLa and HT29) indicated the compounds, present as their respective racemates, to have rather modest activities relative to cisplatin; with complexes having the smallest substituents, R,R' = methyl, being most active. In recognition of the limitations of traditional silver-based syntheses of oxalatoplatinum(II) complexes, innovative non-silver methods were developed using the well known cancer drug, oxaliplatin, (trans-R,R-1,2- diaminocyclohexane)oxalatoplatinum(II), as a prototype. These involved direct ligand exchange reactions of the dichloro precursor, (trans-R,R-1,2- diaminocyclohexane)dichloroplatinum(II), with tetrabutylammonium oxalate in essentially non-aqueous solvents. A 90:10 mixture of isoamyl alcohol (3-methyl- 1-butanol):water, proved to be a promising solvent, enabling the recovery of pure oxaliplatin (~98 percent) after 9 hours at 88 °C in yields of up to 86 percent. In light of the perceived unique mode of anticancer action available to mononitroplatinum(IV) complexes (i.e. their STAT3-binding potential), octahedral diamineoxalatoplatinum(IV) complexes containing axially-coordinated nitro and halo co-ligands were synthesized and extensively characterized. Electrochemical studies revealed trends in reduction potential which could be correlated to structural / chemical traits of the coordinated diamine and axial ligands. The similarities of the determined cytotoxicities of the platinum(IV) compounds and their respective platinum(II) analogues, implicated reduction as a means of activation of the platinum(IV) complexes.
- Full Text:
- Date Issued: 2009
An institutional analysis of community and home based care and support for HIV/AIDS sufferers in rural households in Malawi
- Authors: Munthali, Spy Mbiriyawaka
- Date: 2009
- Subjects: AIDS (Disease) -- Patients -- Care -- Malawi HIV-positive persons -- Care -- Malawi HIV infections -- Malawi Home-based family services -- Malawi Community health services -- Malawi Community development -- Malawi Economic development -- Malawi
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:985 , http://hdl.handle.net/10962/d1002719
- Description: Standard economic models often emphasize inputs, outputs and an examination of the structures in order to conduct an economic performance evaluation. This study applies the Institutional and Development Framework (IAD) in the broader context of New Institutional Economics (NIE) in order to examine the transaction costs of delivering Community and Home Based Care and Support (CHBC) to HIV/AIDS sufferers. For purposes of unveiling the empirical reality guiding decision making processes in the CHBC service delivery, comparative qualitative research techniques of normative variable and concept formation have been adopted to draw out the relative institutional influences from the HIV/AIDS national response partnerships. The study identifies the conflict between the predominantly standardized and more rigid formal management techniques adopted by key members of the national response and the informal cultural techniques familiar to the rural communities, and a lack of motivational incentives in the CHBC structures as the key factors against CHBC capacities to draw external funding for service delivery. CHBCs are also weakened by incoherent governance structures at the district level for facilitation of funding and information flow exacerbating the community vulnerability. Rationalization of the institutional arrangements and a clarification of roles from district to community levels, a shift of focus to facilitation of informal techniques and an integration of performance enhancing incentives are the critical policy insights envisaged to spur CHBCs to work better.
- Full Text:
- Date Issued: 2009
- Authors: Munthali, Spy Mbiriyawaka
- Date: 2009
- Subjects: AIDS (Disease) -- Patients -- Care -- Malawi HIV-positive persons -- Care -- Malawi HIV infections -- Malawi Home-based family services -- Malawi Community health services -- Malawi Community development -- Malawi Economic development -- Malawi
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:985 , http://hdl.handle.net/10962/d1002719
- Description: Standard economic models often emphasize inputs, outputs and an examination of the structures in order to conduct an economic performance evaluation. This study applies the Institutional and Development Framework (IAD) in the broader context of New Institutional Economics (NIE) in order to examine the transaction costs of delivering Community and Home Based Care and Support (CHBC) to HIV/AIDS sufferers. For purposes of unveiling the empirical reality guiding decision making processes in the CHBC service delivery, comparative qualitative research techniques of normative variable and concept formation have been adopted to draw out the relative institutional influences from the HIV/AIDS national response partnerships. The study identifies the conflict between the predominantly standardized and more rigid formal management techniques adopted by key members of the national response and the informal cultural techniques familiar to the rural communities, and a lack of motivational incentives in the CHBC structures as the key factors against CHBC capacities to draw external funding for service delivery. CHBCs are also weakened by incoherent governance structures at the district level for facilitation of funding and information flow exacerbating the community vulnerability. Rationalization of the institutional arrangements and a clarification of roles from district to community levels, a shift of focus to facilitation of informal techniques and an integration of performance enhancing incentives are the critical policy insights envisaged to spur CHBCs to work better.
- Full Text:
- Date Issued: 2009
An investigation into the use of guidelines and patterns in the interaction design process
- Authors: Cowley, Niel Lester Orr
- Date: 2009
- Subjects: Human-computer interaction , Web sites -- Design , User interfaces (Computer systems) -- Design
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10466 , http://hdl.handle.net/10948/1062 , Human-computer interaction , Web sites -- Design , User interfaces (Computer systems) -- Design
- Description: Design guidelines are used in interaction design (IxD) for physical design and for evaluating the usability of designs and interactive products. Guidelines are widely used for physical design and evaluation, but have a number of problems. IxD patterns have been proposed as an alternative to guidelines, as they are claimed to have several advantages over guidelines. A small number of empirical studies provide evidence that patterns are beneficial when used in IxD. Additional research on the usefulness of IxD patterns is required. The primary research question investigated in this thesis was thus: How useful are IxD patterns as physical design and evaluation aids in IxD, as compared to design guidelines? The role of guidelines and patterns as design and evaluation aids in IxD was investigated and a comparison of guidelines and patterns, based on a set of guideline and pattern properties, was conducted. The concept of pattern and guideline usefulness was explored and a research agenda for guidelines and patterns was identified, together with a set of research questions for an empirical study. The empirical study of the use of patterns for evaluation, redesign and new design, as compared to guidelines, was conducted at the Nelson Mandela Metropolitan University in 2004. The participants were a purposive sample of post-graduate Computing students, who were regarded as novice interaction designers. Two equivalent groups were formed, one that used patterns and one that used guidelines. Patterns were found to be as useful as guidelines when used as evaluation aids. Guidelines and patterns were identified as effective tools for identifying and explaining usability issues and design features. Best-effort matched sets of guidelines and patterns produced substantially different result sets when used to identify issues and features, with fairly low overlap. A substantial evaluator effect was observed for the use of guidelines and patterns for evaluation, and the results obtained were similar to those obtained by Molich et al. in their Comparative Usability Evaluation (CUE) studies. There was no statistically significant difference between the effectiveness of guidelines and patterns for evaluation. There was also no statistically significant difference between the perceived efficiency, effectiveness and satisfaction in use of guidelines and patterns for evaluation. Guidelines and patterns were found to be used in similar ways for evaluation. Patterns were found to be more effective than guidelines for redesign. Patterns were found to be as useful as guidelines when used for new design. There was no statistically significant difference between the effectiveness of guidelines and patterns for new design. There was also no statistically significant difference between the perceived efficiency, effectiveness and satisfaction in use of guidelines and patterns for redesign and new design. Guidelines and patterns were found to be used in similar ways for design. There was no statistically significant difference between the perceived usefulness of the format, content, ease of learning, and usefulness as personal and shared design languages, of guidelines and patterns. Both participant groups were equally agreeable to using guidelines and patterns in the future. The perceived usefulness of pattern collections was found to depend on the usability of the collection interface and the content quality of the patterns. The results of the empirical study thus provided empirical evidence that patterns were as useful as guidelines for evaluation and new design, and were perceived as positively as guidelines were. Patterns were found to be superior to guidelines for redesign. Patterns can therefore be used with a measure of confidence as early stage design aids for physical design and evaluation in the future. In addition to these findings, a number of opportunities for further research were identified.
- Full Text:
- Date Issued: 2009
- Authors: Cowley, Niel Lester Orr
- Date: 2009
- Subjects: Human-computer interaction , Web sites -- Design , User interfaces (Computer systems) -- Design
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10466 , http://hdl.handle.net/10948/1062 , Human-computer interaction , Web sites -- Design , User interfaces (Computer systems) -- Design
- Description: Design guidelines are used in interaction design (IxD) for physical design and for evaluating the usability of designs and interactive products. Guidelines are widely used for physical design and evaluation, but have a number of problems. IxD patterns have been proposed as an alternative to guidelines, as they are claimed to have several advantages over guidelines. A small number of empirical studies provide evidence that patterns are beneficial when used in IxD. Additional research on the usefulness of IxD patterns is required. The primary research question investigated in this thesis was thus: How useful are IxD patterns as physical design and evaluation aids in IxD, as compared to design guidelines? The role of guidelines and patterns as design and evaluation aids in IxD was investigated and a comparison of guidelines and patterns, based on a set of guideline and pattern properties, was conducted. The concept of pattern and guideline usefulness was explored and a research agenda for guidelines and patterns was identified, together with a set of research questions for an empirical study. The empirical study of the use of patterns for evaluation, redesign and new design, as compared to guidelines, was conducted at the Nelson Mandela Metropolitan University in 2004. The participants were a purposive sample of post-graduate Computing students, who were regarded as novice interaction designers. Two equivalent groups were formed, one that used patterns and one that used guidelines. Patterns were found to be as useful as guidelines when used as evaluation aids. Guidelines and patterns were identified as effective tools for identifying and explaining usability issues and design features. Best-effort matched sets of guidelines and patterns produced substantially different result sets when used to identify issues and features, with fairly low overlap. A substantial evaluator effect was observed for the use of guidelines and patterns for evaluation, and the results obtained were similar to those obtained by Molich et al. in their Comparative Usability Evaluation (CUE) studies. There was no statistically significant difference between the effectiveness of guidelines and patterns for evaluation. There was also no statistically significant difference between the perceived efficiency, effectiveness and satisfaction in use of guidelines and patterns for evaluation. Guidelines and patterns were found to be used in similar ways for evaluation. Patterns were found to be more effective than guidelines for redesign. Patterns were found to be as useful as guidelines when used for new design. There was no statistically significant difference between the effectiveness of guidelines and patterns for new design. There was also no statistically significant difference between the perceived efficiency, effectiveness and satisfaction in use of guidelines and patterns for redesign and new design. Guidelines and patterns were found to be used in similar ways for design. There was no statistically significant difference between the perceived usefulness of the format, content, ease of learning, and usefulness as personal and shared design languages, of guidelines and patterns. Both participant groups were equally agreeable to using guidelines and patterns in the future. The perceived usefulness of pattern collections was found to depend on the usability of the collection interface and the content quality of the patterns. The results of the empirical study thus provided empirical evidence that patterns were as useful as guidelines for evaluation and new design, and were perceived as positively as guidelines were. Patterns were found to be superior to guidelines for redesign. Patterns can therefore be used with a measure of confidence as early stage design aids for physical design and evaluation in the future. In addition to these findings, a number of opportunities for further research were identified.
- Full Text:
- Date Issued: 2009
Application of Baylis-Hillman methodology in the construction of complex heterocyclic targets
- Ganto, Mlungiseleli MacDonald
- Authors: Ganto, Mlungiseleli MacDonald
- Date: 2009
- Subjects: Heterocyclic compounds -- Derivatives Heterocyclic chemistry
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4401 , http://hdl.handle.net/10962/d1006703
- Description: Baylis-Hillman reactions using various aromatic aldehydes, activated alkenes and catalysts have been used to: - access an extensive range of poly-heterocyclic products;explore chemoselectivity; and optimise reaction efficiency. Chromone-3-carbaldehydes and chromone-2-carbaldehydes, prepared via Vielsmeier-Haack and Kostanecki-Robinson methodology, respectively, have been used as Baylis-Hillman substrates with four different catalysts, viz., 1,4-diazabicyclo[2.2.2]octane (DABCO), 3-hydroxyquinuclidine (3-HQ), imidazole and N’,N’,N’,N’- tetramethylpropanediamine (TMPDA), and with methyl vinyl ketone (MVK), methyl acrylate, cyclic enones (2-cyclohexen-1-one, 2-cyclopenten-1-one and chromones) as activated alkenes. Reactions of the chromone- -carbaldehydes with MVK afforded dimeric Baylis-Hillman adducts when catalyzed by DABCO but when the same reactions were repeated using 3-HQ as catalyst, the dimeric products were accompanied by tricyclic Baylis-Hillman adducts. Use of excess MVK, however, led to mixtures of the normal Baylis-Hillman adducts and the tricyclic adducts – interestingly, with the apparent absence of the dimeric products. While reactions of chromone-3-carbaldehydes with methyl acrylate afforded the normal Baylis-Hillman adducts, the chromone-2- carbaldehydes produced, instead, rearrangement products, consistent with an earlier, single observation. Reactions of 2-nitrobenzaldehydes with cyclic enones using imidazole as catalyst afforded the normal Baylis-Hillman adducts, reductive cyclisation of the 2-cyclohexen-1- one and 2-cyclopenten-1-one adducts, using acetic acid and iron powder, afforded the corresponding quinoline erivatives. Treatment of cyclic enones with pyridine-2-carbaldehydes and quinoline-2-carbaldehydes using TMPDA as catalyst generally gave the expected Baylis-Hillman adducts. However, indolizine derivatives were isolated directly from Baylis-Hillman reactions involving pyridine-2-carbaldehydes and 2-cyclohexen-1-one. The remaining Baylis-Hillman adducts were cyclized to the corresponding indolizines by treatment with acetic anhydride both under reflux and under microwave-assisted conditions, the latter approach providing remarkably rapid and efficient access to the polycyclic products. Computer modelling studies have been conducted on selected polycyclic products at the Molecular Mechanics (MM), Quantum Mechanical (QM) and Density Functional (DFT) levels. The theoretical results have been used to calculate UV, IR and NMR absorption data, which have been compared, in turn, with the experimental spectroscopic data. Use has also been made of the estreNova NMR prediction programme and, generally, good agreement has been observed between the predicted and experimental spectroscopic data.
- Full Text:
- Date Issued: 2009
- Authors: Ganto, Mlungiseleli MacDonald
- Date: 2009
- Subjects: Heterocyclic compounds -- Derivatives Heterocyclic chemistry
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4401 , http://hdl.handle.net/10962/d1006703
- Description: Baylis-Hillman reactions using various aromatic aldehydes, activated alkenes and catalysts have been used to: - access an extensive range of poly-heterocyclic products;explore chemoselectivity; and optimise reaction efficiency. Chromone-3-carbaldehydes and chromone-2-carbaldehydes, prepared via Vielsmeier-Haack and Kostanecki-Robinson methodology, respectively, have been used as Baylis-Hillman substrates with four different catalysts, viz., 1,4-diazabicyclo[2.2.2]octane (DABCO), 3-hydroxyquinuclidine (3-HQ), imidazole and N’,N’,N’,N’- tetramethylpropanediamine (TMPDA), and with methyl vinyl ketone (MVK), methyl acrylate, cyclic enones (2-cyclohexen-1-one, 2-cyclopenten-1-one and chromones) as activated alkenes. Reactions of the chromone- -carbaldehydes with MVK afforded dimeric Baylis-Hillman adducts when catalyzed by DABCO but when the same reactions were repeated using 3-HQ as catalyst, the dimeric products were accompanied by tricyclic Baylis-Hillman adducts. Use of excess MVK, however, led to mixtures of the normal Baylis-Hillman adducts and the tricyclic adducts – interestingly, with the apparent absence of the dimeric products. While reactions of chromone-3-carbaldehydes with methyl acrylate afforded the normal Baylis-Hillman adducts, the chromone-2- carbaldehydes produced, instead, rearrangement products, consistent with an earlier, single observation. Reactions of 2-nitrobenzaldehydes with cyclic enones using imidazole as catalyst afforded the normal Baylis-Hillman adducts, reductive cyclisation of the 2-cyclohexen-1- one and 2-cyclopenten-1-one adducts, using acetic acid and iron powder, afforded the corresponding quinoline erivatives. Treatment of cyclic enones with pyridine-2-carbaldehydes and quinoline-2-carbaldehydes using TMPDA as catalyst generally gave the expected Baylis-Hillman adducts. However, indolizine derivatives were isolated directly from Baylis-Hillman reactions involving pyridine-2-carbaldehydes and 2-cyclohexen-1-one. The remaining Baylis-Hillman adducts were cyclized to the corresponding indolizines by treatment with acetic anhydride both under reflux and under microwave-assisted conditions, the latter approach providing remarkably rapid and efficient access to the polycyclic products. Computer modelling studies have been conducted on selected polycyclic products at the Molecular Mechanics (MM), Quantum Mechanical (QM) and Density Functional (DFT) levels. The theoretical results have been used to calculate UV, IR and NMR absorption data, which have been compared, in turn, with the experimental spectroscopic data. Use has also been made of the estreNova NMR prediction programme and, generally, good agreement has been observed between the predicted and experimental spectroscopic data.
- Full Text:
- Date Issued: 2009
Aspects of the ecology and biology of the isopod, Exosphaeroma hylocoetes, (Barnard, 1940) in three temporarily open/closed southern African estuaries
- Authors: Henninger, Tony Oskar
- Date: 2009
- Subjects: Estuaries -- South Africa -- Eastern Cape Estuarine ecology -- South Africa -- Eastern Cape Isopoda -- South Africa -- Eastern Cape Estuarine biology -- South Africa -- Eastern Cape Ruppia maritima
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5640 , http://hdl.handle.net/10962/d1005322
- Description: Temporarily open/closed estuaries (TOCE’s) are the numerically dominant type of estuary accounting for ≈ 70 % of all estuaries along the South African coastline. Despite their numerical dominance, aspects of the biology of organisms within these systems, particularly macrocrustacea remain poorly understood. This study firstly assessed the abundance and biomass of the most common isopod, Exosphaeroma hylocoetes, in three Eastern Cape TOCE’s, (the West Kleinemonde, East Kleinemonde and Kasouga Estuaries), and their response to mouth breaching events. This study was followed by aspects of the biology of the isopod including their utilisation of submerged macrophytes as a refuge from predation and/or possible food source, as well as the growth rates of the isopods in the laboratory under different environmental conditions. Mean isopod abundances and biomasses ranged between 0 and 4 791 ind. m⁻² and 0 and 9.65 mg dwt. m⁻² in the West Kleinemonde Estuary and between 0 and 108 ind. m⁻² and 0 and 0.318 mg dwt. m⁻² in the nearby East Kleinemonde Estuary. In the Kasouga Estuary, the values ranged between 0 and 3 650 ind. m⁻² and 0 and 5.105 mg dwt. m⁻². Temporal and spatial changes in the abundance and biomass of E. hylocoetes within the three systems was primarily linked to mouth phase, with populations declining when the mouth was open and to a lesser extent, seasonality. In all three estuaries maximum isopod abundances and biomasses were recorded in their middle and upper reaches, which could be ascribed to the presence of submerged macrophytes particularly Ruppia maritima, in two of the estuaries. Males (5.71 ± 0.41 mm) were significantly larger than females (3.99 ± 0.26 mm), but the sex ratios were skewed in favour of females, (a common feature in many isopod populations). Females were found carrying brood throughout the study, releasing offspring directly into the water column, to allow recruitment to the populations. The larger the female, the larger the brood carried (up to a maximum of 72 embryo/mancas). Results of laboratory experiments indicate that the close association of Exosphaeroma hylocoetes with submerged macrophytes is a result of the plant stands providing a refuge against predation by selected ichthyofauna. However stable carbon isotope and fatty acid analyses indicate that E. hylocoetes made use of ephiphytic algae and detritus on the stems of R. maritima, rather than the submerged macrophyte itself. There were no significant differences in the growth rates of male and female isopods at combinations of temperature (15 and 25 °C) and salinity (15 and 35 ‰). Laboratory growth studies revealed that males lived longer than females (25.77 ± 3.40 weeks vs 21.52 ± 3.00 weeks), and therefore achieved larger overall size. Females, however, reached sexual maturity (at 2.5 mm) at a faster rate (two to four weeks) than males (5.5 mm after 6.5 to 11 weeks), dependent on temperature. Exosphaeroma hylocoetes with its association with submerged macrophytes, early maturity, its growth rates and longevity, female-biased sex ratios and year-round breeding, all contribute to its success in temporary open/closed estuaries.
- Full Text:
- Date Issued: 2009
- Authors: Henninger, Tony Oskar
- Date: 2009
- Subjects: Estuaries -- South Africa -- Eastern Cape Estuarine ecology -- South Africa -- Eastern Cape Isopoda -- South Africa -- Eastern Cape Estuarine biology -- South Africa -- Eastern Cape Ruppia maritima
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5640 , http://hdl.handle.net/10962/d1005322
- Description: Temporarily open/closed estuaries (TOCE’s) are the numerically dominant type of estuary accounting for ≈ 70 % of all estuaries along the South African coastline. Despite their numerical dominance, aspects of the biology of organisms within these systems, particularly macrocrustacea remain poorly understood. This study firstly assessed the abundance and biomass of the most common isopod, Exosphaeroma hylocoetes, in three Eastern Cape TOCE’s, (the West Kleinemonde, East Kleinemonde and Kasouga Estuaries), and their response to mouth breaching events. This study was followed by aspects of the biology of the isopod including their utilisation of submerged macrophytes as a refuge from predation and/or possible food source, as well as the growth rates of the isopods in the laboratory under different environmental conditions. Mean isopod abundances and biomasses ranged between 0 and 4 791 ind. m⁻² and 0 and 9.65 mg dwt. m⁻² in the West Kleinemonde Estuary and between 0 and 108 ind. m⁻² and 0 and 0.318 mg dwt. m⁻² in the nearby East Kleinemonde Estuary. In the Kasouga Estuary, the values ranged between 0 and 3 650 ind. m⁻² and 0 and 5.105 mg dwt. m⁻². Temporal and spatial changes in the abundance and biomass of E. hylocoetes within the three systems was primarily linked to mouth phase, with populations declining when the mouth was open and to a lesser extent, seasonality. In all three estuaries maximum isopod abundances and biomasses were recorded in their middle and upper reaches, which could be ascribed to the presence of submerged macrophytes particularly Ruppia maritima, in two of the estuaries. Males (5.71 ± 0.41 mm) were significantly larger than females (3.99 ± 0.26 mm), but the sex ratios were skewed in favour of females, (a common feature in many isopod populations). Females were found carrying brood throughout the study, releasing offspring directly into the water column, to allow recruitment to the populations. The larger the female, the larger the brood carried (up to a maximum of 72 embryo/mancas). Results of laboratory experiments indicate that the close association of Exosphaeroma hylocoetes with submerged macrophytes is a result of the plant stands providing a refuge against predation by selected ichthyofauna. However stable carbon isotope and fatty acid analyses indicate that E. hylocoetes made use of ephiphytic algae and detritus on the stems of R. maritima, rather than the submerged macrophyte itself. There were no significant differences in the growth rates of male and female isopods at combinations of temperature (15 and 25 °C) and salinity (15 and 35 ‰). Laboratory growth studies revealed that males lived longer than females (25.77 ± 3.40 weeks vs 21.52 ± 3.00 weeks), and therefore achieved larger overall size. Females, however, reached sexual maturity (at 2.5 mm) at a faster rate (two to four weeks) than males (5.5 mm after 6.5 to 11 weeks), dependent on temperature. Exosphaeroma hylocoetes with its association with submerged macrophytes, early maturity, its growth rates and longevity, female-biased sex ratios and year-round breeding, all contribute to its success in temporary open/closed estuaries.
- Full Text:
- Date Issued: 2009
Automating the conversion of natural language fiction to multi-modal 3D animated virtual environments
- Authors: Glass, Kevin Robert
- Date: 2009
- Subjects: Virtual computer systems , Virtual storage (Computer science) , Virtual reality , Computer animation , Fiction -- Computer programs , Narration (Rhetoric) -- Computer simulation , Animation (Cinematography) , Natural language processing (Computer Science)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4632 , http://hdl.handle.net/10962/d1006518
- Description: Popular fiction books describe rich visual environments that contain characters, objects, and behaviour. This research develops automated processes for converting text sourced from fiction books into animated virtual environments and multi-modal films. This involves the analysis of unrestricted natural language fiction to identify appropriate visual descriptions, and the interpretation of the identified descriptions for constructing animated 3D virtual environments. The goal of the text analysis stage is the creation of annotated fiction text, which identifies visual descriptions in a structured manner. A hierarchical rule-based learning system is created that induces patterns from example annotations provided by a human, and uses these for the creation of additional annotations. Patterns are expressed as tree structures that abstract the input text on different levels according to structural (token, sentence) and syntactic (parts-of-speech, syntactic function) categories. Patterns are generalized using pair-wise merging, where dissimilar sub-trees are replaced with wild-cards. The result is a small set of generalized patterns that are able to create correct annotations. A set of generalized patterns represents a model of an annotator's mental process regarding a particular annotation category. Annotated text is interpreted automatically for constructing detailed scene descriptions. This includes identifying which scenes to visualize, and identifying the contents and behaviour in each scene. Entity behaviour in a 3D virtual environment is formulated using time-based constraints that are automatically derived from annotations. Constraints are expressed as non-linear symbolic functions that restrict the trajectories of a pair of entities over a continuous interval of time. Solutions to these constraints specify precise behaviour. We create an innovative quantified constraint optimizer for locating sound solutions, which uses interval arithmetic for treating time and space as contiguous quantities. This optimization method uses a technique of constraint relaxation and tightening that allows solution approximations to be located where constraint systems are inconsistent (an ability not previously explored in interval-based quantified constraint solving). 3D virtual environments are populated by automatically selecting geometric models or procedural geometry-creation methods from a library. 3D models are animated according to trajectories derived from constraint solutions. The final animated film is sequenced using a range of modalities including animated 3D graphics, textual subtitles, audio narrations, and foleys. Hierarchical rule-based learning is evaluated over a range of annotation categories. Models are induced for different categories of annotation without modifying the core learning algorithms, and these models are shown to be applicable to different types of books. Models are induced automatically with accuracies ranging between 51.4% and 90.4%, depending on the category. We show that models are refined if further examples are provided, and this supports a boot-strapping process for training the learning mechanism. The task of interpreting annotated fiction text and populating 3D virtual environments is successfully automated using our described techniques. Detailed scene descriptions are created accurately, where between 83% and 96% of the automatically generated descriptions require no manual modification (depending on the type of description). The interval-based quantified constraint optimizer fully automates the behaviour specification process. Sample animated multi-modal 3D films are created using extracts from fiction books that are unrestricted in terms of complexity or subject matter (unlike existing text-to-graphics systems). These examples demonstrate that: behaviour is visualized that corresponds to the descriptions in the original text; appropriate geometry is selected (or created) for visualizing entities in each scene; sequences of scenes are created for a film-like presentation of the story; and that multiple modalities are combined to create a coherent multi-modal representation of the fiction text. This research demonstrates that visual descriptions in fiction text can be automatically identified, and that these descriptions can be converted into corresponding animated virtual environments. Unlike existing text-to-graphics systems, we describe techniques that function over unrestricted natural language text and perform the conversion process without the need for manually constructed repositories of world knowledge. This enables the rapid production of animated 3D virtual environments, allowing the human designer to focus on creative aspects.
- Full Text:
- Date Issued: 2009
- Authors: Glass, Kevin Robert
- Date: 2009
- Subjects: Virtual computer systems , Virtual storage (Computer science) , Virtual reality , Computer animation , Fiction -- Computer programs , Narration (Rhetoric) -- Computer simulation , Animation (Cinematography) , Natural language processing (Computer Science)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4632 , http://hdl.handle.net/10962/d1006518
- Description: Popular fiction books describe rich visual environments that contain characters, objects, and behaviour. This research develops automated processes for converting text sourced from fiction books into animated virtual environments and multi-modal films. This involves the analysis of unrestricted natural language fiction to identify appropriate visual descriptions, and the interpretation of the identified descriptions for constructing animated 3D virtual environments. The goal of the text analysis stage is the creation of annotated fiction text, which identifies visual descriptions in a structured manner. A hierarchical rule-based learning system is created that induces patterns from example annotations provided by a human, and uses these for the creation of additional annotations. Patterns are expressed as tree structures that abstract the input text on different levels according to structural (token, sentence) and syntactic (parts-of-speech, syntactic function) categories. Patterns are generalized using pair-wise merging, where dissimilar sub-trees are replaced with wild-cards. The result is a small set of generalized patterns that are able to create correct annotations. A set of generalized patterns represents a model of an annotator's mental process regarding a particular annotation category. Annotated text is interpreted automatically for constructing detailed scene descriptions. This includes identifying which scenes to visualize, and identifying the contents and behaviour in each scene. Entity behaviour in a 3D virtual environment is formulated using time-based constraints that are automatically derived from annotations. Constraints are expressed as non-linear symbolic functions that restrict the trajectories of a pair of entities over a continuous interval of time. Solutions to these constraints specify precise behaviour. We create an innovative quantified constraint optimizer for locating sound solutions, which uses interval arithmetic for treating time and space as contiguous quantities. This optimization method uses a technique of constraint relaxation and tightening that allows solution approximations to be located where constraint systems are inconsistent (an ability not previously explored in interval-based quantified constraint solving). 3D virtual environments are populated by automatically selecting geometric models or procedural geometry-creation methods from a library. 3D models are animated according to trajectories derived from constraint solutions. The final animated film is sequenced using a range of modalities including animated 3D graphics, textual subtitles, audio narrations, and foleys. Hierarchical rule-based learning is evaluated over a range of annotation categories. Models are induced for different categories of annotation without modifying the core learning algorithms, and these models are shown to be applicable to different types of books. Models are induced automatically with accuracies ranging between 51.4% and 90.4%, depending on the category. We show that models are refined if further examples are provided, and this supports a boot-strapping process for training the learning mechanism. The task of interpreting annotated fiction text and populating 3D virtual environments is successfully automated using our described techniques. Detailed scene descriptions are created accurately, where between 83% and 96% of the automatically generated descriptions require no manual modification (depending on the type of description). The interval-based quantified constraint optimizer fully automates the behaviour specification process. Sample animated multi-modal 3D films are created using extracts from fiction books that are unrestricted in terms of complexity or subject matter (unlike existing text-to-graphics systems). These examples demonstrate that: behaviour is visualized that corresponds to the descriptions in the original text; appropriate geometry is selected (or created) for visualizing entities in each scene; sequences of scenes are created for a film-like presentation of the story; and that multiple modalities are combined to create a coherent multi-modal representation of the fiction text. This research demonstrates that visual descriptions in fiction text can be automatically identified, and that these descriptions can be converted into corresponding animated virtual environments. Unlike existing text-to-graphics systems, we describe techniques that function over unrestricted natural language text and perform the conversion process without the need for manually constructed repositories of world knowledge. This enables the rapid production of animated 3D virtual environments, allowing the human designer to focus on creative aspects.
- Full Text:
- Date Issued: 2009
Chang liver cell line as a model for Type II Diabetes in the liver and possible reversal of this condition by an indigenous medicinal plant
- Authors: Williams, Saralene Iona
- Date: 2009
- Subjects: Diabetes -- Alternative treatment , Medicinal plants , Traditional medicine , Liver -- Diseases
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10339 , http://hdl.handle.net/10948/d1016179
- Description: The incidence of Type 2 Diabetes Mellittus (T2DM) is increasing world wide. In Africa the limited access to health care and the insidious course of the disease lead to more severe illness and diabetic complications. There is a need to find alternative approaches to treatment and prevention that address the problems and needs of Africa. Sutherlandia frutescens (S.frutescens) is a traditional herbal plant with known anti-diabetic properties, the precise mechanism of action of S.frutescens is not known. In order to develop new approaches for treatment and prevention of T2DM the pathophysiology of T2DM must be understood. T2DM is the final outcome of a multi-organ disease characterized by early defects in muscle, adipocytes, hepatocytes and pancreatic β-cells. In this study the role of the liver was investigated because of its central role in glucose and lipid metabolism. It is hard to differentiate between all the influences in an in vivo model, so the aim of this study was to develop an in vitro model of T2DM in Chang liver cells and to determine if S.frutescens can reverse the state of insulin resistance in this model. Different culture media conditions were screened to identify a method that can be used as the T2DM model in Chang liver cells. Serum free medium (MCBD-201) supplemented with human diabetic serum, (2.5%-10%), high insulin concentrations (0.1μM-1μM), high fructose concentrations (1-10mM). and a combination of high insulin and high fructose was used for this screening. Chang liver cells cultured in MCBD-201 medium supplemented with 1mM fructose and 0.1μM insulin showed reduced glucose uptake and increased lipid accumulation. The effect of two S.frutescens extracts, two anti-diabetic drugs, metformin and ciglitazone, and a hypolipidemic drug ciprofibrate were determined and shown to increase glucose uptake and reduce lipid accumulation. It was postulated that exposing the cells to excess nutrients in the form of high fructose would stimulate the cells to become adipogenic and accumulate lipids, which would interfere with the glucose uptake and induce insulin resistance. Gene expression of PPARγ, PPARα, and SREBP-1 transcription factors regulating lipid metabolism was determined in Chang liver cells cultured in insulin resistance inducing medium over a 48 hour time course. The expression of PPARγ, known to stimulate adipogenesis was increased after 6, 24 and 48 hours of exposure (P(H1)<0.0001). The expression of PPARα, known to stimulate β-oxidation expression, was significantly decreased after 24 hours of exposure (P(H1)<0.0001). The presence of the plant extracts in the insulin resistance inducing media protect against this increase in adipogenesis and decrease in β-oxidation after 48 hours of exposure by increasing PPARα expression and decreasing PPARγ expression. A PCR Array was performed which identified 32 more potential molecular targets of S.frutescens. Five of the 32 targets identified with the PCR Array were validated using qRT-PCR. These genes play a role in lipid and glucose metabolism and protection against oxidative stress and inflammation. In summary a cellular model of insulin resistace in hepatocytes has been established and the capacity of S.frutescens to reverse this process has been demonstrated by acting as a dual PPARγ/α agonist. New genes have been identified in the development of insulin resistance and as targets of S.frutescens.
- Full Text:
- Date Issued: 2009
- Authors: Williams, Saralene Iona
- Date: 2009
- Subjects: Diabetes -- Alternative treatment , Medicinal plants , Traditional medicine , Liver -- Diseases
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10339 , http://hdl.handle.net/10948/d1016179
- Description: The incidence of Type 2 Diabetes Mellittus (T2DM) is increasing world wide. In Africa the limited access to health care and the insidious course of the disease lead to more severe illness and diabetic complications. There is a need to find alternative approaches to treatment and prevention that address the problems and needs of Africa. Sutherlandia frutescens (S.frutescens) is a traditional herbal plant with known anti-diabetic properties, the precise mechanism of action of S.frutescens is not known. In order to develop new approaches for treatment and prevention of T2DM the pathophysiology of T2DM must be understood. T2DM is the final outcome of a multi-organ disease characterized by early defects in muscle, adipocytes, hepatocytes and pancreatic β-cells. In this study the role of the liver was investigated because of its central role in glucose and lipid metabolism. It is hard to differentiate between all the influences in an in vivo model, so the aim of this study was to develop an in vitro model of T2DM in Chang liver cells and to determine if S.frutescens can reverse the state of insulin resistance in this model. Different culture media conditions were screened to identify a method that can be used as the T2DM model in Chang liver cells. Serum free medium (MCBD-201) supplemented with human diabetic serum, (2.5%-10%), high insulin concentrations (0.1μM-1μM), high fructose concentrations (1-10mM). and a combination of high insulin and high fructose was used for this screening. Chang liver cells cultured in MCBD-201 medium supplemented with 1mM fructose and 0.1μM insulin showed reduced glucose uptake and increased lipid accumulation. The effect of two S.frutescens extracts, two anti-diabetic drugs, metformin and ciglitazone, and a hypolipidemic drug ciprofibrate were determined and shown to increase glucose uptake and reduce lipid accumulation. It was postulated that exposing the cells to excess nutrients in the form of high fructose would stimulate the cells to become adipogenic and accumulate lipids, which would interfere with the glucose uptake and induce insulin resistance. Gene expression of PPARγ, PPARα, and SREBP-1 transcription factors regulating lipid metabolism was determined in Chang liver cells cultured in insulin resistance inducing medium over a 48 hour time course. The expression of PPARγ, known to stimulate adipogenesis was increased after 6, 24 and 48 hours of exposure (P(H1)<0.0001). The expression of PPARα, known to stimulate β-oxidation expression, was significantly decreased after 24 hours of exposure (P(H1)<0.0001). The presence of the plant extracts in the insulin resistance inducing media protect against this increase in adipogenesis and decrease in β-oxidation after 48 hours of exposure by increasing PPARα expression and decreasing PPARγ expression. A PCR Array was performed which identified 32 more potential molecular targets of S.frutescens. Five of the 32 targets identified with the PCR Array were validated using qRT-PCR. These genes play a role in lipid and glucose metabolism and protection against oxidative stress and inflammation. In summary a cellular model of insulin resistace in hepatocytes has been established and the capacity of S.frutescens to reverse this process has been demonstrated by acting as a dual PPARγ/α agonist. New genes have been identified in the development of insulin resistance and as targets of S.frutescens.
- Full Text:
- Date Issued: 2009
Characterisation of the cellulolytic and hemicellulolytic system of Bacillus Licheniformis SVD1 and the isolation and characterisation of a multi-enzyme complex
- Authors: Van Dyk, Jacoba Susanna
- Date: 2009
- Subjects: Lignocellulose Lignocellulose -- Biotechnology Lignocellulose -- Biodegradation Plant biotechnology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3936 , http://hdl.handle.net/10962/d1003995
- Description: The biological degradation of lignocellulose into fermentable sugars for the production of liquid transportation fuels is feasible and sustainable, but equires a variety of enzymes working in synergy as lignocellulose is a complex and recalcitrant substrate. The cellulosome is a multi-enzyme complex (MEC) with a variety of cellulolytic and hemicellulolytic enzymes that appears to facilitate an enhanced synergy and efficiency, as compared to free enzymes, for the degradation of recalcitrant substrates such as lignocellulose and plant cell walls. Most of the studies on cellulosomes have focused on a few organisms; C. thermocellum, C. cellulovorans and C. cellulolyticum, and there is only limited knowledge vailable on similar complexes in other organisms. Some MECs have been identified in aerobic bacteria such as Bacillus circulans and Paenibacillus curdlanolyticus, but the nature of these MECs have not been fully elucidated. This study investigated the cellulolytic and emi-cellulolytic system of Bacillus licheniformis SVD1 with specific reference to the presence of a MEC, which has never been reported in the literature for B. licheniformis. A MEC of approximately 2,000 kDa in size, based on size exclusion chromatography using Sepharose 4B, was purified from a culture of B. licheniformis. When investigating the presence of enzyme activity in the total crude fraction as well as the MEC of a birchwood xylan culture, B. licheniformis was found to display a variety of enzyme activities on a range of substrates, although xylanases were by far the predominant enzyme activity present in both the crude and MEC fractions. Based on zymogram analysis there were three CMCases, seven xylanases, three mannanases and two pectinases in the crude fraction, while the MEC had two CMCases, seven xylanases, two mannanases and one pectinase. The pectinases in the crude could be identified as a pectin methyl esterase and a lyase, while the methyl esterase was absent in the MEC. Seventeen protein species could be detected in the MEC but only nine of these displayed activity on the substrates tested. The possible presence of a β-xylosidase in the crude fraction was deduced from thin layer chromatography (TLC) which demonstrated the production of xylose by the crude fraction. It was furthermore established that B. licheniformis SVD1 was able to regulate levels of enzyme expression based on the substrate the organism was cultured on. It was found that complexed xylanase activity had a pH optimum of between pH 6.0 and 7.0 and a temperature optimum of 55oC. Complexed xylanase activity was found to be slightly inhibited by CaCl2 and inhibited to a greater extent by EDTA. Complexed xylanase activity was further shown to be activated in the presence of xylose and xylobiose, both compounds which are products of enzymatic degradation. Ethanol was found to inhibit complexed xylanase activity. The kinetic parameters for complexed xylanase activity were measured and the Km value was calculated as 2.84 mg/ml while the maximal velocity (Vmax) was calculated as 0.146 U (μmol/min/ml). Binding studies, transmission electron microscopy (TEM) and a bioinformatic analysis was conducted to investigate whether the MEC in B. licheniformis SVD1 was a putative cellulosome. The MEC was found to be unable to bind to Avicel, but was able to bind to insoluble birchwood xylan, indicating the absence of a CBM3a domain common to cellulosomal scaffoldin proteins. TEM micrographs revealed the presence of cell surface structures on cells of B. licheniformis SVD1 cultured on cellobiose and birchwood xylan. However, it could not be established whether these cell surface structures could be ascribed to the presence of the MECs on the cell surface. Bioinformatic analysis was conducted on the available genome sequence of a different strain of B. licheniformis, namely DSM 13 and ATCC 14580. No sequence homology was found with cohesin and dockerin sequences from various cellulosomal species, indicating that these strains most likely do not encode for a cellulosome. This study described and characterised a MEC that was a functional enzyme complex and did not appear to be a mere aggregation of proteins. It displayed a variety of hemi-cellulolytic activities and the available evidence suggests that it is not a cellulosome, but should rather be termed a xylanosome. Further investigation should be carried out to determine the structural basis of this MEC.
- Full Text:
- Date Issued: 2009
- Authors: Van Dyk, Jacoba Susanna
- Date: 2009
- Subjects: Lignocellulose Lignocellulose -- Biotechnology Lignocellulose -- Biodegradation Plant biotechnology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3936 , http://hdl.handle.net/10962/d1003995
- Description: The biological degradation of lignocellulose into fermentable sugars for the production of liquid transportation fuels is feasible and sustainable, but equires a variety of enzymes working in synergy as lignocellulose is a complex and recalcitrant substrate. The cellulosome is a multi-enzyme complex (MEC) with a variety of cellulolytic and hemicellulolytic enzymes that appears to facilitate an enhanced synergy and efficiency, as compared to free enzymes, for the degradation of recalcitrant substrates such as lignocellulose and plant cell walls. Most of the studies on cellulosomes have focused on a few organisms; C. thermocellum, C. cellulovorans and C. cellulolyticum, and there is only limited knowledge vailable on similar complexes in other organisms. Some MECs have been identified in aerobic bacteria such as Bacillus circulans and Paenibacillus curdlanolyticus, but the nature of these MECs have not been fully elucidated. This study investigated the cellulolytic and emi-cellulolytic system of Bacillus licheniformis SVD1 with specific reference to the presence of a MEC, which has never been reported in the literature for B. licheniformis. A MEC of approximately 2,000 kDa in size, based on size exclusion chromatography using Sepharose 4B, was purified from a culture of B. licheniformis. When investigating the presence of enzyme activity in the total crude fraction as well as the MEC of a birchwood xylan culture, B. licheniformis was found to display a variety of enzyme activities on a range of substrates, although xylanases were by far the predominant enzyme activity present in both the crude and MEC fractions. Based on zymogram analysis there were three CMCases, seven xylanases, three mannanases and two pectinases in the crude fraction, while the MEC had two CMCases, seven xylanases, two mannanases and one pectinase. The pectinases in the crude could be identified as a pectin methyl esterase and a lyase, while the methyl esterase was absent in the MEC. Seventeen protein species could be detected in the MEC but only nine of these displayed activity on the substrates tested. The possible presence of a β-xylosidase in the crude fraction was deduced from thin layer chromatography (TLC) which demonstrated the production of xylose by the crude fraction. It was furthermore established that B. licheniformis SVD1 was able to regulate levels of enzyme expression based on the substrate the organism was cultured on. It was found that complexed xylanase activity had a pH optimum of between pH 6.0 and 7.0 and a temperature optimum of 55oC. Complexed xylanase activity was found to be slightly inhibited by CaCl2 and inhibited to a greater extent by EDTA. Complexed xylanase activity was further shown to be activated in the presence of xylose and xylobiose, both compounds which are products of enzymatic degradation. Ethanol was found to inhibit complexed xylanase activity. The kinetic parameters for complexed xylanase activity were measured and the Km value was calculated as 2.84 mg/ml while the maximal velocity (Vmax) was calculated as 0.146 U (μmol/min/ml). Binding studies, transmission electron microscopy (TEM) and a bioinformatic analysis was conducted to investigate whether the MEC in B. licheniformis SVD1 was a putative cellulosome. The MEC was found to be unable to bind to Avicel, but was able to bind to insoluble birchwood xylan, indicating the absence of a CBM3a domain common to cellulosomal scaffoldin proteins. TEM micrographs revealed the presence of cell surface structures on cells of B. licheniformis SVD1 cultured on cellobiose and birchwood xylan. However, it could not be established whether these cell surface structures could be ascribed to the presence of the MECs on the cell surface. Bioinformatic analysis was conducted on the available genome sequence of a different strain of B. licheniformis, namely DSM 13 and ATCC 14580. No sequence homology was found with cohesin and dockerin sequences from various cellulosomal species, indicating that these strains most likely do not encode for a cellulosome. This study described and characterised a MEC that was a functional enzyme complex and did not appear to be a mere aggregation of proteins. It displayed a variety of hemi-cellulolytic activities and the available evidence suggests that it is not a cellulosome, but should rather be termed a xylanosome. Further investigation should be carried out to determine the structural basis of this MEC.
- Full Text:
- Date Issued: 2009
Characterisation of the plasmodium falciparum Hsp40 chaperones and their partnerships with Hsp70
- Authors: Botha, Melissa
- Date: 2009
- Subjects: Heat shock proteins Plasmodium falciparum Protein folding Molecular chaperones Malaria
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3938 , http://hdl.handle.net/10962/d1003997
- Description: Central to this research, 40 kDa Heat shock proteins (Hsp40s) are known to partner (or cochaperone) 70 kDa Heat shock proteins (Hsp70s), facilitating the selection and transfer of protein substrate to Hsp70 and the stimulation of the protein folding ability of Hsp70. Members of the diverse Hsp70-Hsp40 protein complement of Plasmodium falciparum have been implicated in the cytoprotection of this malaria parasite, and are thought to facilitate the protein folding, assembly and translocation tasks required by the parasite to commandeer the infected human erythrocyte subsequent to invasion. In particular, the parasite has evolved an expanded and specialised 43- member suite of Hsp40 proteins, 19 of which bear an identifiable export motif for secretion into the infected erythrocyte cytoplasm where they potentially interact with human Hsp70. Although type I Hsp40 proteins are representative of typical regulators of Hsp70 activity, only two of these proteins are apparent in the parasite’s Hsp40 complement. These include a characteristic type I Hsp40 termed PfHsp40, and a larger, atypical type I Hsp40 termed Pfj1. Both Hsp40 proteins are predicted to be parasite-resident and are most likely to facilitate the co-chaperone regulation of the highly abundant and stress-inducible Hsp70 homolog, PfHsp70-I. In this work, the co-chaperone functionality of PfHsp40 and Pfj1 was elucidated using in vivo and in vitro assays. Purified recombinant PfHsp40 was shown to stimulate the ATPase activity of PfHsp70-I in in vitro single turnover and steady state ATPase assays, and co-operate with PfHsp70-I in in vitro aggregation suppression assays. In these in vitro assays, heterologous partnerships could be demonstrated between PfHsp70-I and the human Hsp40, Hsj1a, and human Hsp70 and PfHsp40, suggesting a common mode of Hsp70-Hsp40 interaction in the parasite and host organism. The functionality of the signature Hsp40 domain, the Jdomain, of Pfj1 was demonstrated by its ability to replace the equivalent domain of the A. tumefaciens Hsp40, Agt DnaJ, in interactions with the prokaryotic Hsp70, DnaK, in the thermosensitive dnaJ cbpA E. coli OD259 deletion strain. An H33Q mutation introduced into the invariant and crucial HPD tripeptide motif abrogated the functionality of the J-domain in the in vivo complementation system. These findings provide the first evidence for the conservation of the prototypical mode of J-domain based interaction of Hsp40 with Hsp70 in P. falciparum. Immunofluorescence staining revealed the localisation of PfHsp40 to the parasite cytoplasm, and Pfj1 to the parasite cytoplasm and nucleus in cultured intraerythrocytic stage P. falciparum parasites. PfHsp70-I was also shown to localise to the parasite cytoplasm and nucleus in these stages, consistent with the literature. Overall we propose that PfHsp40 and Pfj1 co-localise with and regulate the chaperone activity of PfHsp70-I in P. falciparum. This is the first study to identify and provide evidence for a functional Hsp70-Hsp40 partnership in P. falciparum, and provides a platform for future studies to elucidate the importance of these chaperone partnerships in the establishment and survival of the parasite in the intraerythrocytic-stages of development.
- Full Text:
- Date Issued: 2009
- Authors: Botha, Melissa
- Date: 2009
- Subjects: Heat shock proteins Plasmodium falciparum Protein folding Molecular chaperones Malaria
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3938 , http://hdl.handle.net/10962/d1003997
- Description: Central to this research, 40 kDa Heat shock proteins (Hsp40s) are known to partner (or cochaperone) 70 kDa Heat shock proteins (Hsp70s), facilitating the selection and transfer of protein substrate to Hsp70 and the stimulation of the protein folding ability of Hsp70. Members of the diverse Hsp70-Hsp40 protein complement of Plasmodium falciparum have been implicated in the cytoprotection of this malaria parasite, and are thought to facilitate the protein folding, assembly and translocation tasks required by the parasite to commandeer the infected human erythrocyte subsequent to invasion. In particular, the parasite has evolved an expanded and specialised 43- member suite of Hsp40 proteins, 19 of which bear an identifiable export motif for secretion into the infected erythrocyte cytoplasm where they potentially interact with human Hsp70. Although type I Hsp40 proteins are representative of typical regulators of Hsp70 activity, only two of these proteins are apparent in the parasite’s Hsp40 complement. These include a characteristic type I Hsp40 termed PfHsp40, and a larger, atypical type I Hsp40 termed Pfj1. Both Hsp40 proteins are predicted to be parasite-resident and are most likely to facilitate the co-chaperone regulation of the highly abundant and stress-inducible Hsp70 homolog, PfHsp70-I. In this work, the co-chaperone functionality of PfHsp40 and Pfj1 was elucidated using in vivo and in vitro assays. Purified recombinant PfHsp40 was shown to stimulate the ATPase activity of PfHsp70-I in in vitro single turnover and steady state ATPase assays, and co-operate with PfHsp70-I in in vitro aggregation suppression assays. In these in vitro assays, heterologous partnerships could be demonstrated between PfHsp70-I and the human Hsp40, Hsj1a, and human Hsp70 and PfHsp40, suggesting a common mode of Hsp70-Hsp40 interaction in the parasite and host organism. The functionality of the signature Hsp40 domain, the Jdomain, of Pfj1 was demonstrated by its ability to replace the equivalent domain of the A. tumefaciens Hsp40, Agt DnaJ, in interactions with the prokaryotic Hsp70, DnaK, in the thermosensitive dnaJ cbpA E. coli OD259 deletion strain. An H33Q mutation introduced into the invariant and crucial HPD tripeptide motif abrogated the functionality of the J-domain in the in vivo complementation system. These findings provide the first evidence for the conservation of the prototypical mode of J-domain based interaction of Hsp40 with Hsp70 in P. falciparum. Immunofluorescence staining revealed the localisation of PfHsp40 to the parasite cytoplasm, and Pfj1 to the parasite cytoplasm and nucleus in cultured intraerythrocytic stage P. falciparum parasites. PfHsp70-I was also shown to localise to the parasite cytoplasm and nucleus in these stages, consistent with the literature. Overall we propose that PfHsp40 and Pfj1 co-localise with and regulate the chaperone activity of PfHsp70-I in P. falciparum. This is the first study to identify and provide evidence for a functional Hsp70-Hsp40 partnership in P. falciparum, and provides a platform for future studies to elucidate the importance of these chaperone partnerships in the establishment and survival of the parasite in the intraerythrocytic-stages of development.
- Full Text:
- Date Issued: 2009
Characterisation of Trypanosomal Type III and Type IV Hsp40 proteins
- Louw, Cassandra Alexandrovna
- Authors: Louw, Cassandra Alexandrovna
- Date: 2009
- Subjects: Trypanosoma Heat shock proteins African trypanosomiasis Epidemic encephalitis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3926 , http://hdl.handle.net/10962/d1003985
- Description: The heat shock protein-70 (Hsp70) family of molecular chaperones are ubiquitous highly conserved proteins that are critical for the viability of cellular homeostasis. The ATPase activity of Hsp70 proteins is critical to their function as the affinity of a given Hsp70 for non-native substrate is modulated by ATP binding and hydrolysis. When bound to ATP, Hsp70s possess a low affinity for a given substrate protein, while the hydrolysis of ATP to ADP causes a conformational change that results in a high affinity for substrate proteins. The basal ATPase activity of Hsp70s is too low to facilitate their function in vivo, and co-chaperones are essential to modulate the efficient protein folding by Hsp70. Heat shock protein-40 (Hsp40) heat shock proteins are essential for the in vivo function of Hsp70s by stimulating the ATPase activity of these proteins and facilitating transfer of substrates. The Type III class of Hsp40 proteins have not been well characterised due to their poor levels of conservation at the primary sequence level. This is due to the fact that Type III Hsp40s only contain a J-domain and a poorly conserved C-terminal region. The newly identified Type IV class of Hsp40s, contain an abrogated HPD tripeptide motif in the J-domain and have also not been extensively studied. Trypanosoma brucei (T. brucei) is a unicellular flagellated protozoan parasite. It is the causative agent of Human African Trypansomiasis (HAT) which results in thousands of deaths and devastating agricultural losses in many parts of Africa. T. brucei undergoes a complex lifecycle that is characterised by the transition from an insect vector to a mammalian host in markedly different conditions of temperature, pH, nutrient availability and respiratory requirements. It has been proposed that molecular chaperones may enhance the survival of these parasites due to their cytoprotective effect in combating cellular stress. Due to the fact that T. brucei infection is invariably fatal if left untreated, and that no novel treatment regimens have been developed recently, the identification of potential novel drug targets among proteins essential to the parasite’s survival in the host organism is an attractive aspect of T. brucei research. Because Type III Hsp40s are poorly conserved with respect to Hsp40s found in the human host, the identification of any of these proteins found to be essential to T. brucei survival in humans could potentially make attractive novel drug targets. An in depth in silico investigation into the Type III Hsp40 complement as well as partner Hsp70 proteins in T.brucei was performed. T. brucei possesses 65 Hsp40 proteins, of which 47 were classed as Type III and 6 of which were identified as being putative Type IV Hsp40s. A small but significant number (5) of Type III TbHsp40s contained tetratricopeptide (TPR) domains in addition to the J-domain. The J-domains of the Type III TbHsp40 complement were found to be conserved with respect to those of canonical Hsp40 proteins, although the mutation of certain residues that play a key role in Hsp40-Hsp70 interaction was noted. Potential partnerships of these proteins in the parasite was also investigated. The coding regions of three previously uncharacterised TbHsp40s were successfully amplified from T. brucei TREU927 genomic DNA and cloned into an expression vector. Tbj1, a Tcj1 ortholog, was selected for further study and successfully expressed and biochemically characterised. Tbj1 expressed in E. coli was found to be insoluble, but large amounts were recovered with the aid of a denaturing purification followed by refolding elution strategies, and the bulk of the protein recovered was in compact monomeric form as determined by size-exclusion chromatography fast protein liquid chromatography (SEC-FPLC). The addition of Tbj1 to a thermally aggregated substrate resulted in increased levels of aggregation, although Tbj1 was able to assist two Hsp70 proteins in the suppression of aggregation. Tbj1 proved unable to stimulate the ATPase activity of these same Hsp70s, and could not rescue temperature sensitive cells when replacing E.coli DnaJ and CbpA. It was concluded that Tbj1 does not possess independent chaperone activity, but could display Hsp40 co-chaperone properties under certain circumstances. This could allude to a specialised function in the T. brucei parasite. The lack of human orthologues to Tbj1 could result in the attractiveness of this protein as a novel drug target.
- Full Text:
- Date Issued: 2009
- Authors: Louw, Cassandra Alexandrovna
- Date: 2009
- Subjects: Trypanosoma Heat shock proteins African trypanosomiasis Epidemic encephalitis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3926 , http://hdl.handle.net/10962/d1003985
- Description: The heat shock protein-70 (Hsp70) family of molecular chaperones are ubiquitous highly conserved proteins that are critical for the viability of cellular homeostasis. The ATPase activity of Hsp70 proteins is critical to their function as the affinity of a given Hsp70 for non-native substrate is modulated by ATP binding and hydrolysis. When bound to ATP, Hsp70s possess a low affinity for a given substrate protein, while the hydrolysis of ATP to ADP causes a conformational change that results in a high affinity for substrate proteins. The basal ATPase activity of Hsp70s is too low to facilitate their function in vivo, and co-chaperones are essential to modulate the efficient protein folding by Hsp70. Heat shock protein-40 (Hsp40) heat shock proteins are essential for the in vivo function of Hsp70s by stimulating the ATPase activity of these proteins and facilitating transfer of substrates. The Type III class of Hsp40 proteins have not been well characterised due to their poor levels of conservation at the primary sequence level. This is due to the fact that Type III Hsp40s only contain a J-domain and a poorly conserved C-terminal region. The newly identified Type IV class of Hsp40s, contain an abrogated HPD tripeptide motif in the J-domain and have also not been extensively studied. Trypanosoma brucei (T. brucei) is a unicellular flagellated protozoan parasite. It is the causative agent of Human African Trypansomiasis (HAT) which results in thousands of deaths and devastating agricultural losses in many parts of Africa. T. brucei undergoes a complex lifecycle that is characterised by the transition from an insect vector to a mammalian host in markedly different conditions of temperature, pH, nutrient availability and respiratory requirements. It has been proposed that molecular chaperones may enhance the survival of these parasites due to their cytoprotective effect in combating cellular stress. Due to the fact that T. brucei infection is invariably fatal if left untreated, and that no novel treatment regimens have been developed recently, the identification of potential novel drug targets among proteins essential to the parasite’s survival in the host organism is an attractive aspect of T. brucei research. Because Type III Hsp40s are poorly conserved with respect to Hsp40s found in the human host, the identification of any of these proteins found to be essential to T. brucei survival in humans could potentially make attractive novel drug targets. An in depth in silico investigation into the Type III Hsp40 complement as well as partner Hsp70 proteins in T.brucei was performed. T. brucei possesses 65 Hsp40 proteins, of which 47 were classed as Type III and 6 of which were identified as being putative Type IV Hsp40s. A small but significant number (5) of Type III TbHsp40s contained tetratricopeptide (TPR) domains in addition to the J-domain. The J-domains of the Type III TbHsp40 complement were found to be conserved with respect to those of canonical Hsp40 proteins, although the mutation of certain residues that play a key role in Hsp40-Hsp70 interaction was noted. Potential partnerships of these proteins in the parasite was also investigated. The coding regions of three previously uncharacterised TbHsp40s were successfully amplified from T. brucei TREU927 genomic DNA and cloned into an expression vector. Tbj1, a Tcj1 ortholog, was selected for further study and successfully expressed and biochemically characterised. Tbj1 expressed in E. coli was found to be insoluble, but large amounts were recovered with the aid of a denaturing purification followed by refolding elution strategies, and the bulk of the protein recovered was in compact monomeric form as determined by size-exclusion chromatography fast protein liquid chromatography (SEC-FPLC). The addition of Tbj1 to a thermally aggregated substrate resulted in increased levels of aggregation, although Tbj1 was able to assist two Hsp70 proteins in the suppression of aggregation. Tbj1 proved unable to stimulate the ATPase activity of these same Hsp70s, and could not rescue temperature sensitive cells when replacing E.coli DnaJ and CbpA. It was concluded that Tbj1 does not possess independent chaperone activity, but could display Hsp40 co-chaperone properties under certain circumstances. This could allude to a specialised function in the T. brucei parasite. The lack of human orthologues to Tbj1 could result in the attractiveness of this protein as a novel drug target.
- Full Text:
- Date Issued: 2009
Civil society's quest for democracy in Zimbabwe: origins,barriers and prospects, 1900-2008
- Authors: Magure, Booker
- Date: 2009
- Subjects: Civil Society -- Zimbabwe Zimbabwe -- Politics and government -- 1980 Zimbabwe -- Economic conditions Zimbabwe -- History
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:2798 , http://hdl.handle.net/10962/d1003008
- Description: This thesis is a critical examination of the origins, barriers and prospects for a working class-led civil society as it sought to democratise Zimbabwe’s post-colonial state. It is an interdisciplinary but historically informed analysis of how advanced capitalist development promoted the emergence of social movement unionism with a potentiality to advance democracy in Zimbabwe. Despite occurring on a much smaller and thinner scale, the evolution of civil society in colonial Zimbabwe was akin to what happened in 19th century Britain where capitalist expansion presented a foundation for democratisation. However, big underlying barriers exist in Zimbabwe, resulting from various forms of authoritarian structures and forcible mobilisation strategies emanating from colonialism and the protracted war of liberation. ZANU PF’s violent reaction to memory contests by non-participants in the war of liberation seeking an alternative political agenda attest to the controversial and polemical nature of struggles over memory and forgetting in contemporary Zimbabwean politics. These structural impediments forestalled the organic growth of civil society in Zimbabwe, thereby explaining its inchoate status and the failure to significantly determine the course of public policy. While recognising the democratic aspirations and capacities of the working class in precipitating political change, this thesis takes into consideration the impact of other factors on state-society relations. These include deepening state barbarism, globalisation, and technological advances in communication, transnational civil society, a dysfunctional economy, migration and remittances. Finally this thesis presents an optimistic scenario about the prospects for civil society and democratisation in Zimbabwe. I argue that the revival of the productive sectors of the economy can possibly strengthen the labour movement and revive its capacities for ushering in a democracy.
- Full Text:
- Date Issued: 2009
- Authors: Magure, Booker
- Date: 2009
- Subjects: Civil Society -- Zimbabwe Zimbabwe -- Politics and government -- 1980 Zimbabwe -- Economic conditions Zimbabwe -- History
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:2798 , http://hdl.handle.net/10962/d1003008
- Description: This thesis is a critical examination of the origins, barriers and prospects for a working class-led civil society as it sought to democratise Zimbabwe’s post-colonial state. It is an interdisciplinary but historically informed analysis of how advanced capitalist development promoted the emergence of social movement unionism with a potentiality to advance democracy in Zimbabwe. Despite occurring on a much smaller and thinner scale, the evolution of civil society in colonial Zimbabwe was akin to what happened in 19th century Britain where capitalist expansion presented a foundation for democratisation. However, big underlying barriers exist in Zimbabwe, resulting from various forms of authoritarian structures and forcible mobilisation strategies emanating from colonialism and the protracted war of liberation. ZANU PF’s violent reaction to memory contests by non-participants in the war of liberation seeking an alternative political agenda attest to the controversial and polemical nature of struggles over memory and forgetting in contemporary Zimbabwean politics. These structural impediments forestalled the organic growth of civil society in Zimbabwe, thereby explaining its inchoate status and the failure to significantly determine the course of public policy. While recognising the democratic aspirations and capacities of the working class in precipitating political change, this thesis takes into consideration the impact of other factors on state-society relations. These include deepening state barbarism, globalisation, and technological advances in communication, transnational civil society, a dysfunctional economy, migration and remittances. Finally this thesis presents an optimistic scenario about the prospects for civil society and democratisation in Zimbabwe. I argue that the revival of the productive sectors of the economy can possibly strengthen the labour movement and revive its capacities for ushering in a democracy.
- Full Text:
- Date Issued: 2009
Compensation for polarization mode dispersion and nonlinear birefringence in a multichannel optical fibre system
- Authors: Waswa, David Wafula
- Date: 2009
- Subjects: Fiber optics , Nonlinear optics , Polarization (Light)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10375 , http://hdl.handle.net/10948/885 , Fiber optics , Nonlinear optics , Polarization (Light)
- Description: Polarization mode dispersion (PMD) is stochastic in nature and continues evolving in an unpredictable manner according to the changing environment. Nonlinear birefringence in multichannel systems alters the polarization states of the bits, so that they vary from one bit to the next in a way that is difficult to predict. These are the two major signal-impairment effects that are inherent in optical fibre transmission links which can seriously degrade network performance. It is therefore extremely challenging to compensate for both linear and nonlinear birefringence in multichannel systems. The purpose of this thesis is to investigate the interaction between PMD and nonlinear induced birefringence in a fibre with consideration of mode coupling. A sound knowledge of this interaction is necessary in designing a linear and nonlinear polarization mode dispersion compensator for WDM systems, as was successfully carried out in this study. The investigation shows that the effect of nonlinear birefringence alone depolarizes the signal, while in high PMD links where polarization mode coupling is high, the nonlinear birefringence effect couples with second-order PMD such that it may reduce the penalty and improve the signal DOP. Further investigation shows that when nonlinear birefringence becomes significant, asymmetry arises between the two principal axes of the fibre, such that it is only one axis which experiences the effect of nonlinear birefringence. It is found out that along this vii axis, there exists a critical point in pump power where the nonlinear birefringence cancels PMD in the link and improves the signal. An adaptive compensator to cancel PMD and nonlinear birefringence was designed based on feedforward DOP-monitoring signal. The compensator was tested both at laboratory level and on the Telkom buried fibre link and found to be functioning as intended. It was able to adaptively track and compensate PMD in the link in less than a second. The compensator was able to cancel PMD in the link up to a maximum of 30 ps. The compensator improved the DOP of the worst signal by more than 100 percent.
- Full Text:
- Date Issued: 2009
- Authors: Waswa, David Wafula
- Date: 2009
- Subjects: Fiber optics , Nonlinear optics , Polarization (Light)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10375 , http://hdl.handle.net/10948/885 , Fiber optics , Nonlinear optics , Polarization (Light)
- Description: Polarization mode dispersion (PMD) is stochastic in nature and continues evolving in an unpredictable manner according to the changing environment. Nonlinear birefringence in multichannel systems alters the polarization states of the bits, so that they vary from one bit to the next in a way that is difficult to predict. These are the two major signal-impairment effects that are inherent in optical fibre transmission links which can seriously degrade network performance. It is therefore extremely challenging to compensate for both linear and nonlinear birefringence in multichannel systems. The purpose of this thesis is to investigate the interaction between PMD and nonlinear induced birefringence in a fibre with consideration of mode coupling. A sound knowledge of this interaction is necessary in designing a linear and nonlinear polarization mode dispersion compensator for WDM systems, as was successfully carried out in this study. The investigation shows that the effect of nonlinear birefringence alone depolarizes the signal, while in high PMD links where polarization mode coupling is high, the nonlinear birefringence effect couples with second-order PMD such that it may reduce the penalty and improve the signal DOP. Further investigation shows that when nonlinear birefringence becomes significant, asymmetry arises between the two principal axes of the fibre, such that it is only one axis which experiences the effect of nonlinear birefringence. It is found out that along this vii axis, there exists a critical point in pump power where the nonlinear birefringence cancels PMD in the link and improves the signal. An adaptive compensator to cancel PMD and nonlinear birefringence was designed based on feedforward DOP-monitoring signal. The compensator was tested both at laboratory level and on the Telkom buried fibre link and found to be functioning as intended. It was able to adaptively track and compensate PMD in the link in less than a second. The compensator was able to cancel PMD in the link up to a maximum of 30 ps. The compensator improved the DOP of the worst signal by more than 100 percent.
- Full Text:
- Date Issued: 2009
Constructing the intellectually disabled person as a subject of education: a discourse analysis using Q-methodology
- Authors: McKenzie, Judith Anne
- Date: 2009
- Subjects: Foucault, Michel, 1926-1984 Learning disabled -- Education -- South Africa Discourse analysis -- Methodology Discourse analysis Children with mental disabilities -- Education -- South Africa Q technique Special education -- South Africa Children with disabilities -- Education -- South Africa Right to education Intelligence tests -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3017 , http://hdl.handle.net/10962/d1002526
- Description: The education of intellectually disabled (ID) people is constructed within mass education systems as a problem requiring specialised intervention, separation from “normal” school contexts and the application of professional expertise. A social model of disability resists these practices from a human rights perspective and underpins an inclusive education approach. In this study, a post-structuralist disability studies theoretical framework, drawing particularly on the work of Foucault, was used to examine discourses that construct the intellectually disabled person as a subject of education. The study was conducted in Buffalo City, South Africa at a time when an inclusive education policy is being implemented in the country. The research questions were: What discourses are deployed in the representation and educational practices of those identified as ID? What are the effects of these discourses in constructing the ID subject and associated educational practice? The study utilises Q-methodology, a factor analytic method that yields whole patterns of responses for analysis. A process of sorting selected statements along the dimension of agree to disagree was completed by three groups of participants, namely adults with ID, parents of people with ID and professionals working with ID. Discourses of representation and of educational practice were identified through statistical and interpretive analysis, following the discourse analysis school of Q-methodology. The findings of this study reveal the operation of power in a medico-psychological gaze that makes ID visible and supervises disability expertise within education. Representations of ID suffused with religious notions support the exercise of pastoral power by disability experts. Human rights discourses in education can marginalise ID people if applied uncritically. Fixed notions of impairment constrain an intellectually disabled subject who is vulnerable and incompetent. This study argues instead for a theory of (poss)ability, underpinned by an understanding of the situational and shared nature of competence and a fluid conception of impairment. Human rights should be supplemented by an ethics of care and belonging in the community (ubuntu). A research agenda supporting this effort would examine the ways in which ID people work on themselves as subjects (subjectivisation) and explore the potential for resistance in this process.
- Full Text:
- Date Issued: 2009
- Authors: McKenzie, Judith Anne
- Date: 2009
- Subjects: Foucault, Michel, 1926-1984 Learning disabled -- Education -- South Africa Discourse analysis -- Methodology Discourse analysis Children with mental disabilities -- Education -- South Africa Q technique Special education -- South Africa Children with disabilities -- Education -- South Africa Right to education Intelligence tests -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3017 , http://hdl.handle.net/10962/d1002526
- Description: The education of intellectually disabled (ID) people is constructed within mass education systems as a problem requiring specialised intervention, separation from “normal” school contexts and the application of professional expertise. A social model of disability resists these practices from a human rights perspective and underpins an inclusive education approach. In this study, a post-structuralist disability studies theoretical framework, drawing particularly on the work of Foucault, was used to examine discourses that construct the intellectually disabled person as a subject of education. The study was conducted in Buffalo City, South Africa at a time when an inclusive education policy is being implemented in the country. The research questions were: What discourses are deployed in the representation and educational practices of those identified as ID? What are the effects of these discourses in constructing the ID subject and associated educational practice? The study utilises Q-methodology, a factor analytic method that yields whole patterns of responses for analysis. A process of sorting selected statements along the dimension of agree to disagree was completed by three groups of participants, namely adults with ID, parents of people with ID and professionals working with ID. Discourses of representation and of educational practice were identified through statistical and interpretive analysis, following the discourse analysis school of Q-methodology. The findings of this study reveal the operation of power in a medico-psychological gaze that makes ID visible and supervises disability expertise within education. Representations of ID suffused with religious notions support the exercise of pastoral power by disability experts. Human rights discourses in education can marginalise ID people if applied uncritically. Fixed notions of impairment constrain an intellectually disabled subject who is vulnerable and incompetent. This study argues instead for a theory of (poss)ability, underpinned by an understanding of the situational and shared nature of competence and a fluid conception of impairment. Human rights should be supplemented by an ethics of care and belonging in the community (ubuntu). A research agenda supporting this effort would examine the ways in which ID people work on themselves as subjects (subjectivisation) and explore the potential for resistance in this process.
- Full Text:
- Date Issued: 2009
Discourse and the oppression of nonhuman animals: a critical realist account
- Authors: Mitchell, Leslie Roy
- Date: 2009
- Subjects: Animal rights Animal welfare -- Moral and ethical aspects Critical realism Critical discourse analysis Animal industry -- Moral and ethical aspects Livestock -- Social aspects Human-animal relationships Agriculture -- Moral and ethical aspects
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:1318 , http://hdl.handle.net/10962/d1003951
- Description: This work examines the use of nonhuman animals in the farming industry and seeks to understand why this practice takes place and what supports its continuation. The research is approached from a critical realist perspective and after a description of past and current practices in the industry, it uses abduction and retroduction to determine the essential conditions for the continuation of the phenomenon of nonhuman animal farming. One essential condition is found to be the existence of negative discourses relating to nonhuman animals and this aspect is examined in more detail by analyzing a corpus of texts from a farming magazine using Critical Discourse Analysis. Major discourses which were found to be present were those of production, science and slavery which construct the nonhumans respectively as objects of scientific investigation, as production machines and as slaves. A minor discourse of achievement relating to the nonhumans was also present. Further analysis of linguistic features examined the way in which the nonhumans are socially constructed in the discourses. Drawing on work in experimental psychology by Millgram, Zimbardo and Bandura it was found that the effects of these discourses fulfil many of the conditions for bringing about moral disengagement in people thus explaining why billions of people are able to support animal farming in various ways even though what happens in the phenomenon is contrary to their basic ethical and moral beliefs.
- Full Text:
- Date Issued: 2009
- Authors: Mitchell, Leslie Roy
- Date: 2009
- Subjects: Animal rights Animal welfare -- Moral and ethical aspects Critical realism Critical discourse analysis Animal industry -- Moral and ethical aspects Livestock -- Social aspects Human-animal relationships Agriculture -- Moral and ethical aspects
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:1318 , http://hdl.handle.net/10962/d1003951
- Description: This work examines the use of nonhuman animals in the farming industry and seeks to understand why this practice takes place and what supports its continuation. The research is approached from a critical realist perspective and after a description of past and current practices in the industry, it uses abduction and retroduction to determine the essential conditions for the continuation of the phenomenon of nonhuman animal farming. One essential condition is found to be the existence of negative discourses relating to nonhuman animals and this aspect is examined in more detail by analyzing a corpus of texts from a farming magazine using Critical Discourse Analysis. Major discourses which were found to be present were those of production, science and slavery which construct the nonhumans respectively as objects of scientific investigation, as production machines and as slaves. A minor discourse of achievement relating to the nonhumans was also present. Further analysis of linguistic features examined the way in which the nonhumans are socially constructed in the discourses. Drawing on work in experimental psychology by Millgram, Zimbardo and Bandura it was found that the effects of these discourses fulfil many of the conditions for bringing about moral disengagement in people thus explaining why billions of people are able to support animal farming in various ways even though what happens in the phenomenon is contrary to their basic ethical and moral beliefs.
- Full Text:
- Date Issued: 2009
Ecological role of estuarine brachyuran crabs in mangrove and salt marsh estuaries, Eastern Cape, South Africa
- Authors: Vorsatz, Jeanne Pauline
- Date: 2009
- Subjects: Crabs -- South Africa -- Mangrove Estuary , Crabs -- South Africa -- Salt Marsh Estuary , Salt marsh ecology , Mangrove ecology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10698 , http://hdl.handle.net/10948/1108 , Crabs -- South Africa -- Mangrove Estuary , Crabs -- South Africa -- Salt Marsh Estuary , Salt marsh ecology , Mangrove ecology
- Description: Crabs are conspicuous inhabitants of temperate salt marshes and tropical mangroves and interact with their environment through several processes. However, detailed information on crab community processes is absent for most South African estuaries and nearshore coastal regions. This study evaluated the primary producers supporting crab species in the salt marsh dominated Swartkops estuary and the mangrove Mngazana estuary. Various methods estimating crab abundances were also assessed in different microhabitats and the larval distribution of crabs in the coastal zone was also investigated. Various methods for estimating crab abundance have been employed in the past, each with its inherent biases. The microhabitat of a mangrove forest in Australia was structurally altered by the manipulation of the litter, pneumatophores and the associated algae. These alterations did not affect the behavioural activity or the numbers of crabs recorded in any of the experimental treatments by either visual counts or pitfall traps. However, the number of crabs caught in the pitfall traps differed between the sites. Species-specific behaviour which was not investigated in this study may bias crab abundance estimates when using pitfall traps and therefore requires further investigation. Benthic consumers inhabiting shallow coastal environments may ultimately have the origin of their nutrition in a number of possible sources. Isotopic and gut content analysis of Thalamita crenata and juvenile Scylla serrata in the Mngazana estuary in South Africa revealed that these two portunids are able to share a habitat by resource partitioning. Differences were noted for species-specific utilization of primary producers not only between seasons within a site, but also between sites. This highlighted the use of locally produced primary producers sustaining food webs in estuaries. Mangrove production in the Mngazana estuary is very important and contributes to most of the carbon in the underlying sediments in the mangrove forest. However, the relatively large number of species and biomass encountered in this estuary may also be attributed to the fact that the different species are able to exploit of a number of different resources. The variation in stable isotope analysis of the different crab species throughout the estuary indicated that these crabs able to occupy the same habitat by feeding on a number of different resources and may preferentially select for a specific primary producer. A stable isotope of crabs in the salt marsh Swartkops estuary indicated that the dominant primary producer sustaining crab communities may even take place on a relatively smallscale. Sesarma catenata found at the inner marsh site recorded more depleted carbon signatures than those encountered in the other sites approximately 100 m away, and reflected signatures similar to the locally-encountered inner marsh plants. The relatively enriched nitrogen signatures of the anthropogenically-impacted Swartkops estuary is an indication of extensive inputs due to urbanization and industrialization, in contrast to the relatively pristine Mngazana estuary which exhibited low nitrogen signatures. Emphasis has been placed on the abiotic component of the exchange of nutrients and energy, although living organisms may also be transported, both actively and passively, between ecosystems. Little variation in either species composition or abundance was found between seasons for the larval distribution of brachyuran crabs on the east coast of South Africa. Due to the lack of published larval descriptions, larvae could not be identified to species level and it was therefore not possible to identify whether the larvae were hatched or spawned in an estuary or in a marine environment, or whether the larvae originated in the northern tropical regions. Frequent wind-reversals which are common in this region may retain larvae close inshore and supply the southern temperate locations with larvae from the northern locations. In conclusion, this study has shown that in highly productive systems with a number of potential primary producers, the crabs that inhabit the estuary show a marked diversity in resource utilization which could potentially allow a number of closely related species to occupy different trophic levels. This study also highlights the importance of locally produced sources in an estuary, which may occur on very small scales and this needs to be factored in with the design of any future stable isotope studies of this nature.
- Full Text:
- Date Issued: 2009
- Authors: Vorsatz, Jeanne Pauline
- Date: 2009
- Subjects: Crabs -- South Africa -- Mangrove Estuary , Crabs -- South Africa -- Salt Marsh Estuary , Salt marsh ecology , Mangrove ecology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10698 , http://hdl.handle.net/10948/1108 , Crabs -- South Africa -- Mangrove Estuary , Crabs -- South Africa -- Salt Marsh Estuary , Salt marsh ecology , Mangrove ecology
- Description: Crabs are conspicuous inhabitants of temperate salt marshes and tropical mangroves and interact with their environment through several processes. However, detailed information on crab community processes is absent for most South African estuaries and nearshore coastal regions. This study evaluated the primary producers supporting crab species in the salt marsh dominated Swartkops estuary and the mangrove Mngazana estuary. Various methods estimating crab abundances were also assessed in different microhabitats and the larval distribution of crabs in the coastal zone was also investigated. Various methods for estimating crab abundance have been employed in the past, each with its inherent biases. The microhabitat of a mangrove forest in Australia was structurally altered by the manipulation of the litter, pneumatophores and the associated algae. These alterations did not affect the behavioural activity or the numbers of crabs recorded in any of the experimental treatments by either visual counts or pitfall traps. However, the number of crabs caught in the pitfall traps differed between the sites. Species-specific behaviour which was not investigated in this study may bias crab abundance estimates when using pitfall traps and therefore requires further investigation. Benthic consumers inhabiting shallow coastal environments may ultimately have the origin of their nutrition in a number of possible sources. Isotopic and gut content analysis of Thalamita crenata and juvenile Scylla serrata in the Mngazana estuary in South Africa revealed that these two portunids are able to share a habitat by resource partitioning. Differences were noted for species-specific utilization of primary producers not only between seasons within a site, but also between sites. This highlighted the use of locally produced primary producers sustaining food webs in estuaries. Mangrove production in the Mngazana estuary is very important and contributes to most of the carbon in the underlying sediments in the mangrove forest. However, the relatively large number of species and biomass encountered in this estuary may also be attributed to the fact that the different species are able to exploit of a number of different resources. The variation in stable isotope analysis of the different crab species throughout the estuary indicated that these crabs able to occupy the same habitat by feeding on a number of different resources and may preferentially select for a specific primary producer. A stable isotope of crabs in the salt marsh Swartkops estuary indicated that the dominant primary producer sustaining crab communities may even take place on a relatively smallscale. Sesarma catenata found at the inner marsh site recorded more depleted carbon signatures than those encountered in the other sites approximately 100 m away, and reflected signatures similar to the locally-encountered inner marsh plants. The relatively enriched nitrogen signatures of the anthropogenically-impacted Swartkops estuary is an indication of extensive inputs due to urbanization and industrialization, in contrast to the relatively pristine Mngazana estuary which exhibited low nitrogen signatures. Emphasis has been placed on the abiotic component of the exchange of nutrients and energy, although living organisms may also be transported, both actively and passively, between ecosystems. Little variation in either species composition or abundance was found between seasons for the larval distribution of brachyuran crabs on the east coast of South Africa. Due to the lack of published larval descriptions, larvae could not be identified to species level and it was therefore not possible to identify whether the larvae were hatched or spawned in an estuary or in a marine environment, or whether the larvae originated in the northern tropical regions. Frequent wind-reversals which are common in this region may retain larvae close inshore and supply the southern temperate locations with larvae from the northern locations. In conclusion, this study has shown that in highly productive systems with a number of potential primary producers, the crabs that inhabit the estuary show a marked diversity in resource utilization which could potentially allow a number of closely related species to occupy different trophic levels. This study also highlights the importance of locally produced sources in an estuary, which may occur on very small scales and this needs to be factored in with the design of any future stable isotope studies of this nature.
- Full Text:
- Date Issued: 2009
Effects of marine reserves on the biology of rocky intertidal limpets along the southern coast of South Africa
- Nakin, Motebang Dominic Vincent
- Authors: Nakin, Motebang Dominic Vincent
- Date: 2009
- Subjects: Limpets Marine parks and reserves -- South Africa Marine biology -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5680 , http://hdl.handle.net/10962/d1005365
- Description: Limpets are harvested by people in South Africa, but are selected in terms of species and size. The effects of marine reserves on the biology of commonly exploited (Helcion concolor and Scutellastra longicosta) and rarely exploited species (Cellana capensis and Scutellastra granularis) were investigated on the southeast coast of South Africa at two reserve and two non-reserve sites. For each species, a 4-way nested ANOVA was used to test the effects of month, reserve, site (nested within reserve) and area (nested within site and reserve) on population density, size structure and recruitment of these limpets. The data were collected monthly over 20 months. The overall results indicated a gradient of exploitation among species, S. longicosta was the most heavily exploited species and S. granularis the least exploited species. However, there was also a gradient of exploitation between reserves and non-reserves. Xhora was the most heavily exploited site while Nqabara was less heavily exploited. Of the two reserve sites, Cwebe had more poachers than Dwesa. In most analyses, the month x area (reserve (site)) interaction was significant. However, this was largely an artifact due to comparisons of areas in different sites and significant differences between areas within sites occurred in relatively few months. Densities were greater inside reserves for all species except C. capensis. For S. longicosta and H. concolor this was expected but not for S. granularis and the result possibly reflects its opportunistic exploitation in the absence of the preferred species or indirect effects of reserves. Commonly exploited species and the rarely exploited C. capensis clearly showed greater mean and maximum sizes in reserves but there were month/site (reserve) interactions. Months with significant differences between reserves and nonreserves in both mean and maximum sizes generally occurred more often for commonly exploited than rarely exploited species, but C. capensis showed the strongest reserve effect on maximum size. Interview surveys showed that, although not normally exploited, C. capensis is sometimes mistaken for H. concolor and this suggests that large individuals are unintentionally harvested outside reserves. There were no significant reserve effects on recruitment for any species. Although Xhora had the lowest densities and limpet sizes, it showed the highest recruitment especially for S. longicosta, suggesting that larvae can be transported far from where they are released and settle in non-reserve sites regardless of adult densities. Reserve as a main factor was not significant for the rarely exploited species, but there was a significant month x reserve interaction, with non-reserves having greater GSI values than reserves in most months. Growth rates were examined using individual tagging and cohort analysis. The two techniques gave different results, with individual tagging giving higher growth estimates than cohort analysis. Except for the territorial species S. longicosta, growth was higher in non-reserves and inversely correlated with population density. Mortality estimates using the Cormack-Jolly-Seber model indicated that the rarely exploited species had significantly greater capture probabilities in reserves while no significant reserve effects were observed for the commonly exploited species. Reserve effects on survival probability were significant only for S. longicosta, with reserves being greater than nonreserves and no significant effects for any other species. Enhanced survival in reserves was attributed to the effects of human exploitation. In theory, marine protected areas show increases in densities, sizes and reproductive output of exploited species, but the present results revealed that the efficacy of reserves depends on the status of the species, not only whether it is exploited or non-exploited, but also whether it is territorial.
- Full Text:
- Date Issued: 2009
- Authors: Nakin, Motebang Dominic Vincent
- Date: 2009
- Subjects: Limpets Marine parks and reserves -- South Africa Marine biology -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5680 , http://hdl.handle.net/10962/d1005365
- Description: Limpets are harvested by people in South Africa, but are selected in terms of species and size. The effects of marine reserves on the biology of commonly exploited (Helcion concolor and Scutellastra longicosta) and rarely exploited species (Cellana capensis and Scutellastra granularis) were investigated on the southeast coast of South Africa at two reserve and two non-reserve sites. For each species, a 4-way nested ANOVA was used to test the effects of month, reserve, site (nested within reserve) and area (nested within site and reserve) on population density, size structure and recruitment of these limpets. The data were collected monthly over 20 months. The overall results indicated a gradient of exploitation among species, S. longicosta was the most heavily exploited species and S. granularis the least exploited species. However, there was also a gradient of exploitation between reserves and non-reserves. Xhora was the most heavily exploited site while Nqabara was less heavily exploited. Of the two reserve sites, Cwebe had more poachers than Dwesa. In most analyses, the month x area (reserve (site)) interaction was significant. However, this was largely an artifact due to comparisons of areas in different sites and significant differences between areas within sites occurred in relatively few months. Densities were greater inside reserves for all species except C. capensis. For S. longicosta and H. concolor this was expected but not for S. granularis and the result possibly reflects its opportunistic exploitation in the absence of the preferred species or indirect effects of reserves. Commonly exploited species and the rarely exploited C. capensis clearly showed greater mean and maximum sizes in reserves but there were month/site (reserve) interactions. Months with significant differences between reserves and nonreserves in both mean and maximum sizes generally occurred more often for commonly exploited than rarely exploited species, but C. capensis showed the strongest reserve effect on maximum size. Interview surveys showed that, although not normally exploited, C. capensis is sometimes mistaken for H. concolor and this suggests that large individuals are unintentionally harvested outside reserves. There were no significant reserve effects on recruitment for any species. Although Xhora had the lowest densities and limpet sizes, it showed the highest recruitment especially for S. longicosta, suggesting that larvae can be transported far from where they are released and settle in non-reserve sites regardless of adult densities. Reserve as a main factor was not significant for the rarely exploited species, but there was a significant month x reserve interaction, with non-reserves having greater GSI values than reserves in most months. Growth rates were examined using individual tagging and cohort analysis. The two techniques gave different results, with individual tagging giving higher growth estimates than cohort analysis. Except for the territorial species S. longicosta, growth was higher in non-reserves and inversely correlated with population density. Mortality estimates using the Cormack-Jolly-Seber model indicated that the rarely exploited species had significantly greater capture probabilities in reserves while no significant reserve effects were observed for the commonly exploited species. Reserve effects on survival probability were significant only for S. longicosta, with reserves being greater than nonreserves and no significant effects for any other species. Enhanced survival in reserves was attributed to the effects of human exploitation. In theory, marine protected areas show increases in densities, sizes and reproductive output of exploited species, but the present results revealed that the efficacy of reserves depends on the status of the species, not only whether it is exploited or non-exploited, but also whether it is territorial.
- Full Text:
- Date Issued: 2009
Establishing experimental systems for studying the replication biology of Providence virus
- Authors: Walter, Cheryl Tracy
- Date: 2009
- Subjects: Insects -- Viruses Insects -- Diseases Insects -- Parasites Host-virus relationships RNA viruses DNA Insects as carriers of disease
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3928 , http://hdl.handle.net/10962/d1003987
- Description: Providence virus (PrV) is a member of the Tetraviridae, a family of small, positive sense, single-stranded RNA viruses, which characteristically infect the midgut tissue of heliothine larvae. PrV is the only known tetravirus that replicates in cultured insect cells. The virus comprises a monopartite genome resembling members of the genus Betatetravirus with the capsid precursor protein undergoing autoproteolytic cleavage at its C-terminus consistent with other tetravirus capsid precursor proteins. Analysis of viral cDNA predicted the presence of three potential overlapping gene products (from 5` to 3`): (1) p130, a protein of unrecognized nucleotide or amino acid homology with a 2A-like processing site at its N-terminus; (2) p104, the replicase ORF, which was found to be phylogenetically related to tombus-and umbraviruses replicases. The presence of a read-through stop signal in the p104 ORF was proposed to produce and amino terminal product with a predicted MW of 40 kDa (p40) and (3) the capsid protein precursor (81 kDa) which has two 2A-like processing sites at its N-terminus. Metabolic radiolabelling of viral translation products in persistently infected MG8 cells and in vitro translation of the individual ORFs were performed in order to analyse the expression of PrV gene products. p130 was translated with no evidence of 2A-like processing. Two products of 40 kDa and 104 kDa were translated from the p104 ORF, indicating that the read-through stop signal was likely to be functional. Finally, the capsid protein precursor ORF produced a major translation product of 68 kDa corresponding to the capsid protein precursor as well a peptide of 15 kDa that was attributed to the activity of the second 2A-like site at the N-terminus of the p81 ORF. The subcellular distribution of viral RNA (vRNA) and p40 in MG8 cells was investigated using immunofluorescence and biochemical fractionation. The results showed that p40/p104 and vRNA accumulated in polarized, punctate structures in some but not all MG8 cells and in some cases, co-localization was observed. This thesis concludes that PrV is a novel tetravirus with significant similarities plant carmolike viruses that should be re-classified at the family level.
- Full Text:
- Date Issued: 2009
- Authors: Walter, Cheryl Tracy
- Date: 2009
- Subjects: Insects -- Viruses Insects -- Diseases Insects -- Parasites Host-virus relationships RNA viruses DNA Insects as carriers of disease
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3928 , http://hdl.handle.net/10962/d1003987
- Description: Providence virus (PrV) is a member of the Tetraviridae, a family of small, positive sense, single-stranded RNA viruses, which characteristically infect the midgut tissue of heliothine larvae. PrV is the only known tetravirus that replicates in cultured insect cells. The virus comprises a monopartite genome resembling members of the genus Betatetravirus with the capsid precursor protein undergoing autoproteolytic cleavage at its C-terminus consistent with other tetravirus capsid precursor proteins. Analysis of viral cDNA predicted the presence of three potential overlapping gene products (from 5` to 3`): (1) p130, a protein of unrecognized nucleotide or amino acid homology with a 2A-like processing site at its N-terminus; (2) p104, the replicase ORF, which was found to be phylogenetically related to tombus-and umbraviruses replicases. The presence of a read-through stop signal in the p104 ORF was proposed to produce and amino terminal product with a predicted MW of 40 kDa (p40) and (3) the capsid protein precursor (81 kDa) which has two 2A-like processing sites at its N-terminus. Metabolic radiolabelling of viral translation products in persistently infected MG8 cells and in vitro translation of the individual ORFs were performed in order to analyse the expression of PrV gene products. p130 was translated with no evidence of 2A-like processing. Two products of 40 kDa and 104 kDa were translated from the p104 ORF, indicating that the read-through stop signal was likely to be functional. Finally, the capsid protein precursor ORF produced a major translation product of 68 kDa corresponding to the capsid protein precursor as well a peptide of 15 kDa that was attributed to the activity of the second 2A-like site at the N-terminus of the p81 ORF. The subcellular distribution of viral RNA (vRNA) and p40 in MG8 cells was investigated using immunofluorescence and biochemical fractionation. The results showed that p40/p104 and vRNA accumulated in polarized, punctate structures in some but not all MG8 cells and in some cases, co-localization was observed. This thesis concludes that PrV is a novel tetravirus with significant similarities plant carmolike viruses that should be re-classified at the family level.
- Full Text:
- Date Issued: 2009