Prediction of mass spectra using an ab initio approach
- Authors: Novokoza, Yolanda
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/${Handle} , vital:72818
- Description: Access restricted. Expected release date in 2025. , Thesis (PhD) -- Faculty of Science, Chemistry, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Novokoza, Yolanda
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/${Handle} , vital:72818
- Description: Access restricted. Expected release date in 2025. , Thesis (PhD) -- Faculty of Science, Chemistry, 2023
- Full Text:
- Date Issued: 2023-10-13
The heterologous expression and in vitro biochemical characterization of the Hsp70 escort protein 1 and mitochondrial Hsp70 partner proteins of the Trypanosoma brucei parasite and humans
- Authors: Mahlalela, Maduma Ernst
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431832 , vital:72807 , DOI 10.21504/10962/431832
- Description: The 70 kDa family of heat shock proteins (Hsp70) plays a central role in the maintenance of cellular proteostasis, with paralogues occurring in all the major compartments of the eukaryotic cell. Hsp70s act in conjunction with proteins known as co-chaperones, as part of the larger molecular chaperone network. In the mitochondrion, Hsp70 (mtHsp70) is responsible for the import of proteins synthesized in the cytosol, protein folding in the matrix and the maintenance of the iron-sulphur cluster. In human cells mtHsp70 (HSPA9) is also referred to as mortalin, as the knockdown of the protein leads to cell mortality. Trypanosoma brucei is the causative agent of sleeping sickness in humans and nagana in animals. In the T. brucei parasite there are three identical mtHsp70 (TbmtHsp70) proteins that are produced, forming part of the Hsp70 machinery that is essential for parasite survival. In humans, the levels of HSPA9 are often elevated in non-communicable diseases such as cancer and neurodegeneration. Despite their vital cellular roles, mtHsp70s are characteristically prone to self-aggregation. The binding of the Hsp70 escort protein (Hep1) is required to prevent the aggregation of mtHsp70 proteins, enabling the proteins to function. In many non-communicable diseases, mtHsp70 and other molecular chaperones such as heat shock protein 90 (Hsp90) are being investigated as potential drug targets. Existing anti-trypanosomal drugs for treating sleeping sickness are toxic, having adverse side effects that are potentially lethal. Investigations into Hsp70s, and other molecular chaperones, form part of the research into the discovery of novel and efficacious therapeutics. This is the first study to characterise Hep1 and investigate its partnership with mtHsp70 in T. brucei. The overall aim of this study was to comparatively assess the T. brucei and human mtHsp70/Hep1 partnerships. The putative T. brucei Hep1 (TbHep1) orthologue was analysed in silico, and it was found to possess a zinc finger domain consisting of anti-parallel β-sheets that are characteristic of canonical Hep1 proteins, whilst the N-terminal domain was unstructured. Based on sequence analysis, the regions outside of the zinc finger domains lacked conservation. Despite the lack of sequence conservation, the N- and C-terminal regions of TbHep1 shared segments of similarity with Hep1 orthologues of other kinetoplastid and trypanosomal orthologues. The same held true for the N- and C-termini of human Hep1 (HsHep1) when compared to other Hep1 orthologues of mammalian origin. Biochemical analysis revealed TbmtHsp70 and HSPA9 to be prone to self-aggregation, which was reduced by co-expression with TbHep1 and HsHep1, respectively. Recently Hep1 proteins have been determined to be present in the cytosol. In this study, TbHep1 and HsHep1 also interacted with the cytosolic Hsp70s, HSPA1A and TbHsp70, by preventing their thermally induced aggregation and stimulating their ATPase activities. TbHep1 and HsHep1 also suppressed the thermally induced aggregation of the model substrates malate dehydrogenase and citrate synthase, independently of Hsp70. To date, only two Hep1 orthologues, HsHep1 and LbHep1, have been found to function in a similar manner to a J-protein co-chaperone by stimulating the ATPase activities of their partner mtHsp70 proteins. In this study, TbHep1 stimulated the ATPase activity of TbmtHsp70. HsHep1 also stimulated the ATPase activity of TbmtHsp70. However, the mechanism of action still needs to be determined. This study also explored the potential of the Hep1 orthologues to be functionally activated by oxidative stress, which is prevalent in mitochondria. The abilities of TbHep1 and HsHep1 to reduce the thermally induced aggregation of malate dehydrogenase were enhanced under oxidative conditions. Disrupting the function of Hep1 has been found to eventually lead to cell death, and given the critical role played by mtHsp70 in the cell, this partnership could be exploited as a potential drug target. In conclusion, this study demonstrated that TbHep1 and HsHep1 functionally interact with mtHsp70s, whilst also possessing independent chaperone activities that are also potentially influenced by the environmental redox state. , Thesis (PhD) -- Faculty of Science, Biotechnology Innovation Centre, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Mahlalela, Maduma Ernst
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431832 , vital:72807 , DOI 10.21504/10962/431832
- Description: The 70 kDa family of heat shock proteins (Hsp70) plays a central role in the maintenance of cellular proteostasis, with paralogues occurring in all the major compartments of the eukaryotic cell. Hsp70s act in conjunction with proteins known as co-chaperones, as part of the larger molecular chaperone network. In the mitochondrion, Hsp70 (mtHsp70) is responsible for the import of proteins synthesized in the cytosol, protein folding in the matrix and the maintenance of the iron-sulphur cluster. In human cells mtHsp70 (HSPA9) is also referred to as mortalin, as the knockdown of the protein leads to cell mortality. Trypanosoma brucei is the causative agent of sleeping sickness in humans and nagana in animals. In the T. brucei parasite there are three identical mtHsp70 (TbmtHsp70) proteins that are produced, forming part of the Hsp70 machinery that is essential for parasite survival. In humans, the levels of HSPA9 are often elevated in non-communicable diseases such as cancer and neurodegeneration. Despite their vital cellular roles, mtHsp70s are characteristically prone to self-aggregation. The binding of the Hsp70 escort protein (Hep1) is required to prevent the aggregation of mtHsp70 proteins, enabling the proteins to function. In many non-communicable diseases, mtHsp70 and other molecular chaperones such as heat shock protein 90 (Hsp90) are being investigated as potential drug targets. Existing anti-trypanosomal drugs for treating sleeping sickness are toxic, having adverse side effects that are potentially lethal. Investigations into Hsp70s, and other molecular chaperones, form part of the research into the discovery of novel and efficacious therapeutics. This is the first study to characterise Hep1 and investigate its partnership with mtHsp70 in T. brucei. The overall aim of this study was to comparatively assess the T. brucei and human mtHsp70/Hep1 partnerships. The putative T. brucei Hep1 (TbHep1) orthologue was analysed in silico, and it was found to possess a zinc finger domain consisting of anti-parallel β-sheets that are characteristic of canonical Hep1 proteins, whilst the N-terminal domain was unstructured. Based on sequence analysis, the regions outside of the zinc finger domains lacked conservation. Despite the lack of sequence conservation, the N- and C-terminal regions of TbHep1 shared segments of similarity with Hep1 orthologues of other kinetoplastid and trypanosomal orthologues. The same held true for the N- and C-termini of human Hep1 (HsHep1) when compared to other Hep1 orthologues of mammalian origin. Biochemical analysis revealed TbmtHsp70 and HSPA9 to be prone to self-aggregation, which was reduced by co-expression with TbHep1 and HsHep1, respectively. Recently Hep1 proteins have been determined to be present in the cytosol. In this study, TbHep1 and HsHep1 also interacted with the cytosolic Hsp70s, HSPA1A and TbHsp70, by preventing their thermally induced aggregation and stimulating their ATPase activities. TbHep1 and HsHep1 also suppressed the thermally induced aggregation of the model substrates malate dehydrogenase and citrate synthase, independently of Hsp70. To date, only two Hep1 orthologues, HsHep1 and LbHep1, have been found to function in a similar manner to a J-protein co-chaperone by stimulating the ATPase activities of their partner mtHsp70 proteins. In this study, TbHep1 stimulated the ATPase activity of TbmtHsp70. HsHep1 also stimulated the ATPase activity of TbmtHsp70. However, the mechanism of action still needs to be determined. This study also explored the potential of the Hep1 orthologues to be functionally activated by oxidative stress, which is prevalent in mitochondria. The abilities of TbHep1 and HsHep1 to reduce the thermally induced aggregation of malate dehydrogenase were enhanced under oxidative conditions. Disrupting the function of Hep1 has been found to eventually lead to cell death, and given the critical role played by mtHsp70 in the cell, this partnership could be exploited as a potential drug target. In conclusion, this study demonstrated that TbHep1 and HsHep1 functionally interact with mtHsp70s, whilst also possessing independent chaperone activities that are also potentially influenced by the environmental redox state. , Thesis (PhD) -- Faculty of Science, Biotechnology Innovation Centre, 2023
- Full Text:
- Date Issued: 2023-10-13
The morphogenesis of higher education leadership: a social realist exploratory journey
- Authors: Andrews, Ruth
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/442897 , vital:74051 , DOI 10.21504/10962/442897
- Description: The purpose of the study underpinning this thesis was to explore the tensions experienced by university leaders as they balance politics, power and the academic project whilst pursuing their ultimate concerns in the world. Universities are undergoing constant change, particularly in the present time of hypercomplexity, where the discourses of globalisation and neoliberalism condition higher education institutions and their leaders. This predisposes universities to operate as a market economy rather than as a public good. University leaders are under immense pressure as they seek to reposition themselves and exercise their agency in steering their institutions in a landscape fraught with complexity and contestation about the very nature of the modern university. The study was located in a traditional university in South Africa, which added another layer of complexity given the history of Apartheid and, the use of education as a means of discriminating against the black majority population, and the subsequent attempts by the government to transform the system following the first democratic election of 1994. Bhaskar’s (1989) critical realism and Archer’s (1998, 2000) social realism were used to frame the study theoretically. Bhaskar argues for the understanding of the world as an ‘open system’ in which experiences and events emerge from the tendential interplay of mechanisms at a layer of reality not directly accessible to empirical observation. Archer’s (2000) social realism draws on critical realism to provide a set of tools that allows an exploration of the social world in more detail. This study draws on the tools of analytical dualism, or the temporary separation of structure, culture and agency for analytical purposes, and Archer’s (1998) morphogenetic framework, which allows for the exploration of change, or non-change, over time. The overarching goal of the study was to explore how leaders at one South African university were enabled and constrained as they exercised their agency in the pursuit of projects they had identified to address their ultimate concerns about the world more generally and higher education in particular. However, the study also sought to explore the construct of leadership itself in a specific context by using Archer’s (2007, 2012) theoretical work on reflexivity. The study drew on in-depth interviews with senior leaders at the institution, including two vice-chancellors. The interviews were subjected to analysis, and the inferential tools of abduction and retroduction were used to identify the interplay of mechanisms located at the level of the Real, the deepest layer of reality posited by Bhaskar (1978), which led to the events and experiences reported by leaders. A literature review was used to identify additional theories that were used in the processes of abduction and retroduction. The study revealed that change, or rather non-change, is often concealed in cultural rhetoric veiled in leadership practices in acts assimilating past ideology and codified rules and practices with new codified rules and practices. Leaders often draw on powerful relational networks as they reflexively exercise their agency, and these networks can also work to constrain change. , Thesis (PhD) -- Faculty of Education, Education 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Andrews, Ruth
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/442897 , vital:74051 , DOI 10.21504/10962/442897
- Description: The purpose of the study underpinning this thesis was to explore the tensions experienced by university leaders as they balance politics, power and the academic project whilst pursuing their ultimate concerns in the world. Universities are undergoing constant change, particularly in the present time of hypercomplexity, where the discourses of globalisation and neoliberalism condition higher education institutions and their leaders. This predisposes universities to operate as a market economy rather than as a public good. University leaders are under immense pressure as they seek to reposition themselves and exercise their agency in steering their institutions in a landscape fraught with complexity and contestation about the very nature of the modern university. The study was located in a traditional university in South Africa, which added another layer of complexity given the history of Apartheid and, the use of education as a means of discriminating against the black majority population, and the subsequent attempts by the government to transform the system following the first democratic election of 1994. Bhaskar’s (1989) critical realism and Archer’s (1998, 2000) social realism were used to frame the study theoretically. Bhaskar argues for the understanding of the world as an ‘open system’ in which experiences and events emerge from the tendential interplay of mechanisms at a layer of reality not directly accessible to empirical observation. Archer’s (2000) social realism draws on critical realism to provide a set of tools that allows an exploration of the social world in more detail. This study draws on the tools of analytical dualism, or the temporary separation of structure, culture and agency for analytical purposes, and Archer’s (1998) morphogenetic framework, which allows for the exploration of change, or non-change, over time. The overarching goal of the study was to explore how leaders at one South African university were enabled and constrained as they exercised their agency in the pursuit of projects they had identified to address their ultimate concerns about the world more generally and higher education in particular. However, the study also sought to explore the construct of leadership itself in a specific context by using Archer’s (2007, 2012) theoretical work on reflexivity. The study drew on in-depth interviews with senior leaders at the institution, including two vice-chancellors. The interviews were subjected to analysis, and the inferential tools of abduction and retroduction were used to identify the interplay of mechanisms located at the level of the Real, the deepest layer of reality posited by Bhaskar (1978), which led to the events and experiences reported by leaders. A literature review was used to identify additional theories that were used in the processes of abduction and retroduction. The study revealed that change, or rather non-change, is often concealed in cultural rhetoric veiled in leadership practices in acts assimilating past ideology and codified rules and practices with new codified rules and practices. Leaders often draw on powerful relational networks as they reflexively exercise their agency, and these networks can also work to constrain change. , Thesis (PhD) -- Faculty of Education, Education 2023
- Full Text:
- Date Issued: 2023-10-13
Wildlife-vehicle collisions mitigation measures using road ecological data and deep learning
- Authors: Nandutu, Irene
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431907 , vital:72814
- Description: Access restricted. Expected release in 2025. , Thesis (PhD) -- Faculty of Science, Mathematics, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Nandutu, Irene
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431907 , vital:72814
- Description: Access restricted. Expected release in 2025. , Thesis (PhD) -- Faculty of Science, Mathematics, 2023
- Full Text:
- Date Issued: 2023-10-13
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