Computer aided approaches against Human African Trypanosomiasis
- Authors: Kimuda, Magambo Phillip
- Date: 2020
- Subjects: African trypanosomiasis , African trypanosomiasis -- Chemotherapy , Genomics , Macrophage migration inhibitory factor , Trypanosoma brucei , Pteridines , Tetrahydrofolate dehydrogenase , Adenylic acid , Molecular dynamics , Principal components analysis , Bioinformatics , Single nucleotide polymorphisms , Single Nucleotide Variants , Candidate Gene Association Study (CGAS)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142542 , vital:38089
- Description: The thesis presented here is divided into two parts under a common theme that is the use of computer based tools, genomics, and in vitro experiments to develop innovative ways of tackling Human African Trypanosomiasis (HAT). Part I of this thesis focused on the human host genetic determinants while Part II focused on the discovery of novel chemotherapeutics against the parasite. Part I is further sub-divided into two parts: The first involves a Candidate Gene Association Study (CGAS) on an African population to identify genetic determinants associated with disease and/or susceptibility to HAT. The second involves studying the effects of missense Single Nucleotide Variants (SNVs) on protein structure, dynamics, and function using Macrophage Migration Inhibitory Factor (MIF) as a case study. Part II is also sub-divided into two parts: The first involves a computer based rational drug discovery of potential inhibitors against the Trypanosoma the folate pathway; particularly by targeting Trypanosoma brucei Pteridine Reductase (TbPTR1) which is an enzyme used by trypanosomes to overcome T. brucei Dihydrofolate Reductase (TbDHFR) inhibition. Lastly the derivation of CHARMM force-field parameters that can be used to accurately model the geometry and dynamics of the T. brucei Phosphodiesterase B1 enzyme (TbrPDEB1) bimetallic active site center. The derived parameters were then used in MD simulations to characterise protein-ligand residue interactions that are important in TbrPDEB1 inhibition with the goal of targeting the cyclic Adenosine Monophosphate (cAMP) signalling pathway. In the CGAS we were unable to detect any genetic associations in the Ugandan cohort analysed that passed correction for multiple testing in spite of the study being sufficiently powered. Additionally, our study found no association of the Apo lipoprotein 1 (APOL1) G2 allele association with protection against acute HAT that has been previously reported. Future investigations for example, Genome Wide Association Studies using larger samples sizes (>3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies
- Full Text:
- Date Issued: 2020
- Authors: Kimuda, Magambo Phillip
- Date: 2020
- Subjects: African trypanosomiasis , African trypanosomiasis -- Chemotherapy , Genomics , Macrophage migration inhibitory factor , Trypanosoma brucei , Pteridines , Tetrahydrofolate dehydrogenase , Adenylic acid , Molecular dynamics , Principal components analysis , Bioinformatics , Single nucleotide polymorphisms , Single Nucleotide Variants , Candidate Gene Association Study (CGAS)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142542 , vital:38089
- Description: The thesis presented here is divided into two parts under a common theme that is the use of computer based tools, genomics, and in vitro experiments to develop innovative ways of tackling Human African Trypanosomiasis (HAT). Part I of this thesis focused on the human host genetic determinants while Part II focused on the discovery of novel chemotherapeutics against the parasite. Part I is further sub-divided into two parts: The first involves a Candidate Gene Association Study (CGAS) on an African population to identify genetic determinants associated with disease and/or susceptibility to HAT. The second involves studying the effects of missense Single Nucleotide Variants (SNVs) on protein structure, dynamics, and function using Macrophage Migration Inhibitory Factor (MIF) as a case study. Part II is also sub-divided into two parts: The first involves a computer based rational drug discovery of potential inhibitors against the Trypanosoma the folate pathway; particularly by targeting Trypanosoma brucei Pteridine Reductase (TbPTR1) which is an enzyme used by trypanosomes to overcome T. brucei Dihydrofolate Reductase (TbDHFR) inhibition. Lastly the derivation of CHARMM force-field parameters that can be used to accurately model the geometry and dynamics of the T. brucei Phosphodiesterase B1 enzyme (TbrPDEB1) bimetallic active site center. The derived parameters were then used in MD simulations to characterise protein-ligand residue interactions that are important in TbrPDEB1 inhibition with the goal of targeting the cyclic Adenosine Monophosphate (cAMP) signalling pathway. In the CGAS we were unable to detect any genetic associations in the Ugandan cohort analysed that passed correction for multiple testing in spite of the study being sufficiently powered. Additionally, our study found no association of the Apo lipoprotein 1 (APOL1) G2 allele association with protection against acute HAT that has been previously reported. Future investigations for example, Genome Wide Association Studies using larger samples sizes (>3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies
- Full Text:
- Date Issued: 2020
Conceptualisations of and responses to plagiarism in the South African higher education system
- Mphahlele, Martha Matee (Amanda)
- Authors: Mphahlele, Martha Matee (Amanda)
- Date: 2020
- Subjects: Plagiarism , Plagiarism -- Prevention -- South Africa , Education, Higher -- Moral and ethical aspects , Education, Higher -- South Africa , Cheating (Education) -- South Africa , College students -- Legal status, laws, etc. -- South Africa , College discipline -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162642 , vital:40963
- Description: Violations of academic integrity are a cause for concern in universities around the world and plagiarism is one of the most significant examples of these academic integrity issues with which universities are grappling . The approach taken to managing plagiarism depends to a large extent on the understanding of the phenomenon within institutions. This study investigated how plagiarism is conceptualised and responded to in the South African Higher Education system and how this impacts on teaching and learning. Data was collected from 25 out of the 26 South African public universities; the missing university had just been established and did not yet have policies or processes in place. The data was primarily in the form of documents known in these institutions as ‘plagiarism policies’, along with a wealth of other related policies and reports. This was supplemented by interviews as a means of verifying the document analysis with seven plagiarism committee members from across the three institutional types in South Africa, namely: traditional universities, comprehensive universities, and universities of technology. Using Bhaskar’s (2008) critical realism as a metatheory and Archer’s (1995) social realism as both a substantive theory and analytical framework, the experiences and events of plagiarism management were critically examined. Critical realism consider s these experiences and events at the level of the e mpirical and the actual , in order to identify the mechanisms at the l evel of the r eal from which these emerge. Social realism argues that when undertaking such an analysis in the social world, this entails identifying the emergent properties of both the parts (structure and culture) and people (agents). Therefore, the data was analysed using Archer’s analytical dualism to identify structural, cultural and agential mechanisms shaping the understanding of plagiarism and the practices associated with managing the phenomenon. The study found that dominant in the sector was an un derstanding of plagiarism as always being an intentional act, with implications for teaching and learning practices, which then focused on identifying and punishing incidents of plagiarism in student writing. A legal discourse was found to permeate the universities’ plagiarism management systems, such that most procedures replicated the legal framework. This was seen to undermine the identity of universities as teaching and learning spaces and of students as novice members of the disciplinary fields. The study further highlighted that due to plagiarism being perceived as an intentional act, punishment in almost all universities is prioritised as the key means of attending to plagiarism in the se institutions. This emerged as a structural constraint to students’ acquisition of academic writing norms. Such understandings and approaches were seen to be complementary to the risk-aversion of many institutions in a globalised era of university rankings. As increased bureaucracy has been put in place to attend to incidents of plagiarism, including obligatory reporting thereof, an unintentional consequence emerged, where it was at times simpler for academics to ignore incidences of plagiarism than to act on them. Turnitin was frequently referred to across the data as the preferred text - matching tool, but Turnitin together with other text-matching tools , was often used in a way that complemented the understanding of plagiarism as always being an intentional act. The stu dy found that text - matching software was largely misunderstood to be plagiarism software, where the similarity index was perceived to be a measure of plagiarism. This led to an understanding that students needed to paraphrase texts in order to avoid detect ion by the program me, and this may inadvertently encourage plagiarism , as students are taught to write towards the software. The research found that in those instances where educational responses to plagiarism were in place, they often demonstrated a lack of understanding of academic literacies development and the extent to which norms of knowledge production are disciplinary specific. Most (but not all) of the data about educational responses focused on add-on workshops and the signing of a declaration form, indicating that the student has not plagiarised. The workshops were seen to emphasise technical skills, such as the punctuation norms of referencing, and were often offered in a generic format by people outside of the target disciplines. These workshops were found to ignore the connection between the technical skills of referencing and the norms of knowledge construction, with a potential deleterious effect on the development of authorial identity. Finally, the data showed a few instances where particular institutions acknowledged that plagiarism occurs along a continuum, where on one side is intentional plagiarism associated with cheating and requiring punishment, and on the other side is unintentional plagiarism, which is understood to require an educational response , and was seen to emerge from either a lack of understanding of academic literacy norms , or from negligence. Literacy development with regard to taking on the norms of knowledge-making in the academy was seen to be a complex and lengthy process that was fundamental to educational endeavours of facilitating epistemological access, while cases of negligence were seen to be mainly caused by technical oversight rather than a lack of access to the relevant knowledge production norms. The study concludes by arguing that cases of intentional plagiarism require quick and appropriate punishment, but that there also needs to be an institution-wide understanding that unintentional plagiarism often emerges from students failing to access the specific knowledge-making norms of the discipline. There is thus a need for academics to be aware of the complexities related to taking on literacy practices, and who also understand the role of feedback in this process. But it ought not to be assumed that academics would have such insights simply by virtue of their expertise in the discipline. These academics need to have carefully constructed staff development support, as they take on such pedagogical approaches. The study argues that the dominant conceptualisation of plagiarism in the domain of culture as an intentional act and the complementary policies and processes in the domain of structure as focusing on detecting and punishing incidents of plagiarism, fail to address plagiarism in appropriate educational ways.
- Full Text:
- Date Issued: 2020
- Authors: Mphahlele, Martha Matee (Amanda)
- Date: 2020
- Subjects: Plagiarism , Plagiarism -- Prevention -- South Africa , Education, Higher -- Moral and ethical aspects , Education, Higher -- South Africa , Cheating (Education) -- South Africa , College students -- Legal status, laws, etc. -- South Africa , College discipline -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162642 , vital:40963
- Description: Violations of academic integrity are a cause for concern in universities around the world and plagiarism is one of the most significant examples of these academic integrity issues with which universities are grappling . The approach taken to managing plagiarism depends to a large extent on the understanding of the phenomenon within institutions. This study investigated how plagiarism is conceptualised and responded to in the South African Higher Education system and how this impacts on teaching and learning. Data was collected from 25 out of the 26 South African public universities; the missing university had just been established and did not yet have policies or processes in place. The data was primarily in the form of documents known in these institutions as ‘plagiarism policies’, along with a wealth of other related policies and reports. This was supplemented by interviews as a means of verifying the document analysis with seven plagiarism committee members from across the three institutional types in South Africa, namely: traditional universities, comprehensive universities, and universities of technology. Using Bhaskar’s (2008) critical realism as a metatheory and Archer’s (1995) social realism as both a substantive theory and analytical framework, the experiences and events of plagiarism management were critically examined. Critical realism consider s these experiences and events at the level of the e mpirical and the actual , in order to identify the mechanisms at the l evel of the r eal from which these emerge. Social realism argues that when undertaking such an analysis in the social world, this entails identifying the emergent properties of both the parts (structure and culture) and people (agents). Therefore, the data was analysed using Archer’s analytical dualism to identify structural, cultural and agential mechanisms shaping the understanding of plagiarism and the practices associated with managing the phenomenon. The study found that dominant in the sector was an un derstanding of plagiarism as always being an intentional act, with implications for teaching and learning practices, which then focused on identifying and punishing incidents of plagiarism in student writing. A legal discourse was found to permeate the universities’ plagiarism management systems, such that most procedures replicated the legal framework. This was seen to undermine the identity of universities as teaching and learning spaces and of students as novice members of the disciplinary fields. The study further highlighted that due to plagiarism being perceived as an intentional act, punishment in almost all universities is prioritised as the key means of attending to plagiarism in the se institutions. This emerged as a structural constraint to students’ acquisition of academic writing norms. Such understandings and approaches were seen to be complementary to the risk-aversion of many institutions in a globalised era of university rankings. As increased bureaucracy has been put in place to attend to incidents of plagiarism, including obligatory reporting thereof, an unintentional consequence emerged, where it was at times simpler for academics to ignore incidences of plagiarism than to act on them. Turnitin was frequently referred to across the data as the preferred text - matching tool, but Turnitin together with other text-matching tools , was often used in a way that complemented the understanding of plagiarism as always being an intentional act. The stu dy found that text - matching software was largely misunderstood to be plagiarism software, where the similarity index was perceived to be a measure of plagiarism. This led to an understanding that students needed to paraphrase texts in order to avoid detect ion by the program me, and this may inadvertently encourage plagiarism , as students are taught to write towards the software. The research found that in those instances where educational responses to plagiarism were in place, they often demonstrated a lack of understanding of academic literacies development and the extent to which norms of knowledge production are disciplinary specific. Most (but not all) of the data about educational responses focused on add-on workshops and the signing of a declaration form, indicating that the student has not plagiarised. The workshops were seen to emphasise technical skills, such as the punctuation norms of referencing, and were often offered in a generic format by people outside of the target disciplines. These workshops were found to ignore the connection between the technical skills of referencing and the norms of knowledge construction, with a potential deleterious effect on the development of authorial identity. Finally, the data showed a few instances where particular institutions acknowledged that plagiarism occurs along a continuum, where on one side is intentional plagiarism associated with cheating and requiring punishment, and on the other side is unintentional plagiarism, which is understood to require an educational response , and was seen to emerge from either a lack of understanding of academic literacy norms , or from negligence. Literacy development with regard to taking on the norms of knowledge-making in the academy was seen to be a complex and lengthy process that was fundamental to educational endeavours of facilitating epistemological access, while cases of negligence were seen to be mainly caused by technical oversight rather than a lack of access to the relevant knowledge production norms. The study concludes by arguing that cases of intentional plagiarism require quick and appropriate punishment, but that there also needs to be an institution-wide understanding that unintentional plagiarism often emerges from students failing to access the specific knowledge-making norms of the discipline. There is thus a need for academics to be aware of the complexities related to taking on literacy practices, and who also understand the role of feedback in this process. But it ought not to be assumed that academics would have such insights simply by virtue of their expertise in the discipline. These academics need to have carefully constructed staff development support, as they take on such pedagogical approaches. The study argues that the dominant conceptualisation of plagiarism in the domain of culture as an intentional act and the complementary policies and processes in the domain of structure as focusing on detecting and punishing incidents of plagiarism, fail to address plagiarism in appropriate educational ways.
- Full Text:
- Date Issued: 2020
Conceptualising community radio: from global histories to the Kenyan example
- Authors: Korir, Geoffrey Kiplimo
- Date: 2020
- Subjects: Community radio , Community radio -- Kenya , Community development -- Kenya , Social change -- Kenya , Radio broadcasting -- Kenya
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165766 , vital:41279
- Description: This study sets out to gain insight into the way that the establishment of community radio in Kenya is located within the global history of ideas about such radio. The first four chapters in this study provide terms of reference for this examination through a series of literature reviews. It sets out, firstly, to locate the internationally shared conceptualisaiton of community radio within an existing spectrum of approaches to social analysis. It proposes that community radio can be located at the critical, emancipatory end of this spectrum. It then maps out the global circulation of ideas about community radio and proposes that such circulation was informed by the broader history of critical, emancipatory social analysis. The final literature review then deals with community radio in Kenya and examines the way in which the establishment of this sector was shaped by the social and political history of this country. It is argued that the establishment of a community radio sector became possible only when support for emancipatory approaches to media became acceptable in Kenya, in context of the establishment of multiparty democracy. It is proposed, further, that the articulation of a vision for community radio in Kenya depended in part on the existence of international support for such radio and in part on the efforts of local actors in civil society. The empirical component then focuses on the way global ideas about community radio have become realised in Kenya. The study achieves this purpose by drawing on qualitative interviews with individuals from within civil society who have participated in the history of the establishment and growth of community radio in Kenya. These individuals demonstrate consciousness of the internationally shared set of principles that can facilitate a successful establishment of community radio. However, they are also sceptical of the assumption that guidelines for community radio are universally applicable. They point, in particular, to the challenges involved in the realisation of these guidelines in an environment in which economic resources are limited, and which is characterised by extreme social inequality and conflict. The study concludes that it is individuals such as these participants, who are embedded within the local context, who are best placed to articulate locally appropriate alternatives to these guidelines.
- Full Text:
- Date Issued: 2020
- Authors: Korir, Geoffrey Kiplimo
- Date: 2020
- Subjects: Community radio , Community radio -- Kenya , Community development -- Kenya , Social change -- Kenya , Radio broadcasting -- Kenya
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165766 , vital:41279
- Description: This study sets out to gain insight into the way that the establishment of community radio in Kenya is located within the global history of ideas about such radio. The first four chapters in this study provide terms of reference for this examination through a series of literature reviews. It sets out, firstly, to locate the internationally shared conceptualisaiton of community radio within an existing spectrum of approaches to social analysis. It proposes that community radio can be located at the critical, emancipatory end of this spectrum. It then maps out the global circulation of ideas about community radio and proposes that such circulation was informed by the broader history of critical, emancipatory social analysis. The final literature review then deals with community radio in Kenya and examines the way in which the establishment of this sector was shaped by the social and political history of this country. It is argued that the establishment of a community radio sector became possible only when support for emancipatory approaches to media became acceptable in Kenya, in context of the establishment of multiparty democracy. It is proposed, further, that the articulation of a vision for community radio in Kenya depended in part on the existence of international support for such radio and in part on the efforts of local actors in civil society. The empirical component then focuses on the way global ideas about community radio have become realised in Kenya. The study achieves this purpose by drawing on qualitative interviews with individuals from within civil society who have participated in the history of the establishment and growth of community radio in Kenya. These individuals demonstrate consciousness of the internationally shared set of principles that can facilitate a successful establishment of community radio. However, they are also sceptical of the assumption that guidelines for community radio are universally applicable. They point, in particular, to the challenges involved in the realisation of these guidelines in an environment in which economic resources are limited, and which is characterised by extreme social inequality and conflict. The study concludes that it is individuals such as these participants, who are embedded within the local context, who are best placed to articulate locally appropriate alternatives to these guidelines.
- Full Text:
- Date Issued: 2020
Conflict related sexual violence against males:recognition by and responses of humanitarian organizations in Africa
- Authors: Akurut, Catherine
- Date: 2020
- Subjects: Male rape victims -- Africa , Gender in conflict management --Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46648 , vital:39605
- Description: The study investigated the knowledge, attitudes, and experiences of humanitarian service providers concerning the recognition of and response to the phenomenon of male victims of conflict-related sexual violence against males. Sources of literature in respect to the awareness, understanding, and recognition of conflict-related sexual violence against males were explored. Perceptions about the recognition of male victims were discovered. Response strategies available to male victims were explored through the experiences of humanitarian organisation representatives, including, inter alia, programme managers, gender-based violence advisers, protection officers and activists. Mechanisms to augment any existing practices to allow for the care of and support for male victims were examined. A qualitative research approach was used to explore the topic of this study. Data was collected using semi-structured interview questions that were developed. And document review was also used as the second means of data collection. The research participants were recruited using purposive sampling, which was complemented by snowballing until data saturation. Triangulation was used by combining the two data collection methods to avoid relying on one source. A narrative literature review was aimed to obtain further information about the phenomenon of conflict-related sexual violence against males.
- Full Text:
- Date Issued: 2020
- Authors: Akurut, Catherine
- Date: 2020
- Subjects: Male rape victims -- Africa , Gender in conflict management --Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46648 , vital:39605
- Description: The study investigated the knowledge, attitudes, and experiences of humanitarian service providers concerning the recognition of and response to the phenomenon of male victims of conflict-related sexual violence against males. Sources of literature in respect to the awareness, understanding, and recognition of conflict-related sexual violence against males were explored. Perceptions about the recognition of male victims were discovered. Response strategies available to male victims were explored through the experiences of humanitarian organisation representatives, including, inter alia, programme managers, gender-based violence advisers, protection officers and activists. Mechanisms to augment any existing practices to allow for the care of and support for male victims were examined. A qualitative research approach was used to explore the topic of this study. Data was collected using semi-structured interview questions that were developed. And document review was also used as the second means of data collection. The research participants were recruited using purposive sampling, which was complemented by snowballing until data saturation. Triangulation was used by combining the two data collection methods to avoid relying on one source. A narrative literature review was aimed to obtain further information about the phenomenon of conflict-related sexual violence against males.
- Full Text:
- Date Issued: 2020
Conservation biology of an apex predator in the Anthropocene : poaching, pastoralism and lions in multi-use landscapes, South-Eastern Africa
- Authors: Everatt, Kristoffer T
- Date: 2020
- Subjects: Conservation biology -- Africa, Southern
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48290 , vital:40839
- Description: Many of the world’s apex predators are experiencing catastrophic declines as a result of competition with humans. Understanding the mechanisms and ecosystem impacts of apex predator declines is a fundamental ecological question crucial to conserving the Earth’s biodiversity and functioning ecosystems. In this thesis I used the African lion Panthera leo, as a model species to investigate the impacts of anthropogenic pressures on the conservation and ecology of an apex predator. Specifically, I investigated the relative and cumulative influences of pastoralism and poaching on lion occurrence, population connectivity, ecological role, space use, prey selection and viability across a 73 000 km2 multi-use landscape in southern Africa. Using landscape occupancy spoor surveys, I tested the hypotheses that lions were most limited by either interference or by exploitative competition with humans and identified thresholds of lion tolerance to human activities. My results showed that lions occupied only a fraction of the landscape and were limited by a combination of interference and exploitative competition with humans. Interference competition with pastoralism however was the biggest driver limiting lion occupancy, creating a clear disturbance threshold for lions cumulating in their near complete loss from the landscape. I employed call-up surveys, pride monitoring and mortality analysis to investigate the numerical impacts of anthropogenic pressures on the viability of a lion sub-population. I found that persecution by pastoralists was the greatest source of lion mortalities across the landscape. However, the targeted poaching of lions for body parts had emerged as the greatest threat to lions in a nominally protected National Park where I documented a steep population decline and collapse of lion prides. I used GPS tracking and diet analysis of lions at the human-wildlands interface to test if lions foraged optimally or were constrained by competition with humans. I fount that individual lions appeared to select for prey and habitat optimally, while also showing some level of risk avoidance towards anthropogenic pressures. I then considered landscape resistances to test if sink habitats may provide connectivity between sources or act as ecological traps. I found that potential connectivity for lions between the region’s two source populations was limited by a loss of habitat and prey. Furthermore, the impacts of by-catch in snares risked transforming the few remaining potential conservation corridors into ecological traps. Finally, I examined interactions between lions and syntopic mesopredators across gradients of anthropogenic pressures to test if the functional role of lions was affected by human pressures. I found that lions showed limited suppression of mesopredators, however, anthropogenic pressures increased lion’s interactions with syntopic predators. As an apex predator, lions have evolved limited capacity to mitigate top-down competitive pressures, however, like many of the world’s apex predators, they are becoming increasingly limited by anthropogenic pressures. This study provides a predictive understanding of an apex predator’s ecological responses to top-down anthropogenic pressures which can be applied globally to the question of conservation in the Anthropocene.
- Full Text:
- Date Issued: 2020
- Authors: Everatt, Kristoffer T
- Date: 2020
- Subjects: Conservation biology -- Africa, Southern
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48290 , vital:40839
- Description: Many of the world’s apex predators are experiencing catastrophic declines as a result of competition with humans. Understanding the mechanisms and ecosystem impacts of apex predator declines is a fundamental ecological question crucial to conserving the Earth’s biodiversity and functioning ecosystems. In this thesis I used the African lion Panthera leo, as a model species to investigate the impacts of anthropogenic pressures on the conservation and ecology of an apex predator. Specifically, I investigated the relative and cumulative influences of pastoralism and poaching on lion occurrence, population connectivity, ecological role, space use, prey selection and viability across a 73 000 km2 multi-use landscape in southern Africa. Using landscape occupancy spoor surveys, I tested the hypotheses that lions were most limited by either interference or by exploitative competition with humans and identified thresholds of lion tolerance to human activities. My results showed that lions occupied only a fraction of the landscape and were limited by a combination of interference and exploitative competition with humans. Interference competition with pastoralism however was the biggest driver limiting lion occupancy, creating a clear disturbance threshold for lions cumulating in their near complete loss from the landscape. I employed call-up surveys, pride monitoring and mortality analysis to investigate the numerical impacts of anthropogenic pressures on the viability of a lion sub-population. I found that persecution by pastoralists was the greatest source of lion mortalities across the landscape. However, the targeted poaching of lions for body parts had emerged as the greatest threat to lions in a nominally protected National Park where I documented a steep population decline and collapse of lion prides. I used GPS tracking and diet analysis of lions at the human-wildlands interface to test if lions foraged optimally or were constrained by competition with humans. I fount that individual lions appeared to select for prey and habitat optimally, while also showing some level of risk avoidance towards anthropogenic pressures. I then considered landscape resistances to test if sink habitats may provide connectivity between sources or act as ecological traps. I found that potential connectivity for lions between the region’s two source populations was limited by a loss of habitat and prey. Furthermore, the impacts of by-catch in snares risked transforming the few remaining potential conservation corridors into ecological traps. Finally, I examined interactions between lions and syntopic mesopredators across gradients of anthropogenic pressures to test if the functional role of lions was affected by human pressures. I found that lions showed limited suppression of mesopredators, however, anthropogenic pressures increased lion’s interactions with syntopic predators. As an apex predator, lions have evolved limited capacity to mitigate top-down competitive pressures, however, like many of the world’s apex predators, they are becoming increasingly limited by anthropogenic pressures. This study provides a predictive understanding of an apex predator’s ecological responses to top-down anthropogenic pressures which can be applied globally to the question of conservation in the Anthropocene.
- Full Text:
- Date Issued: 2020
Conserving land for people: transformative adaptive co-management of sustainable protected areas in the eastern Democratic Republic of Congo
- Authors: Kalyongo, Kujirakwinja Deo
- Date: 2020
- Subjects: Protected areas -- Congo (Democratic Republic) , Protected areas -- Government policy -- Congo (Democratic Republic) , Protected areas -- Management -- Congo (Democratic Republic) , Conservation of natural resources -- Congo (Democratic Republic)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165912 , vital:41296
- Description: Conservation practices and approaches in the Democratic Republic of Congo (DRC), as in other parts of the world, have evolved from traditional to fortress and collaborative contemporary approaches such as adaptive co-management. These approaches aim to include multiple decision-makers using diversified resources and, existing formal and informal governance structures. Collaborative approaches also consider conflict resolution and external factors that can influence conservation outputs and outcomes. In the DRC context, conflicts over resources are related not only to resource access and power but also to the ineffectiveness of collaborative approaches that exclude stakeholders such as local communities. These conflicts have negatively affected protected areas and weakened the management and governance of protected areas. Therefore, evolving approaches such as adaptive co-management that consider power relations, the multi-scaled involvement of actors and learning loops to adjust strategies are seen as better options to improve the governance of protected areas and minimise the degradation of key ecosystems. My research explored the gazettement processes of three protected areas in the eastern DRC (Itombwe, Kabobo and Okapi Reserves). I focused on the influence of social-political, historical and psychological factors on the management and governance of protected areas in the DRC. In addition, the research reveals the inclusive gazettement processes of protected areas is the foundation of successful co-management approaches. I found that values and good governance practices play a key role in influencing local perceptions and support to conservation interventions. Whilst some conservation practitioners believe that economic benefits to communities are the most predominant motivating factor, I found that good conservation management practices can motivate communities to support protected area management. Bad management practices were related not only to inadequate conservation approaches and practices but also to factors such as corruption, inadequate law enforcement and the inappropriate equipment of rangers. Therefore, I suggest that long term protected area management in DRC should consider how the value of resources for communities and protected areas have been changing throughout the history of conservation, and how to best share power and responsibilities with local resource users and stakeholders. This is only possible if conservation practices and approaches, governance process and institutions are transformed at multiple levels.
- Full Text:
- Date Issued: 2020
- Authors: Kalyongo, Kujirakwinja Deo
- Date: 2020
- Subjects: Protected areas -- Congo (Democratic Republic) , Protected areas -- Government policy -- Congo (Democratic Republic) , Protected areas -- Management -- Congo (Democratic Republic) , Conservation of natural resources -- Congo (Democratic Republic)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165912 , vital:41296
- Description: Conservation practices and approaches in the Democratic Republic of Congo (DRC), as in other parts of the world, have evolved from traditional to fortress and collaborative contemporary approaches such as adaptive co-management. These approaches aim to include multiple decision-makers using diversified resources and, existing formal and informal governance structures. Collaborative approaches also consider conflict resolution and external factors that can influence conservation outputs and outcomes. In the DRC context, conflicts over resources are related not only to resource access and power but also to the ineffectiveness of collaborative approaches that exclude stakeholders such as local communities. These conflicts have negatively affected protected areas and weakened the management and governance of protected areas. Therefore, evolving approaches such as adaptive co-management that consider power relations, the multi-scaled involvement of actors and learning loops to adjust strategies are seen as better options to improve the governance of protected areas and minimise the degradation of key ecosystems. My research explored the gazettement processes of three protected areas in the eastern DRC (Itombwe, Kabobo and Okapi Reserves). I focused on the influence of social-political, historical and psychological factors on the management and governance of protected areas in the DRC. In addition, the research reveals the inclusive gazettement processes of protected areas is the foundation of successful co-management approaches. I found that values and good governance practices play a key role in influencing local perceptions and support to conservation interventions. Whilst some conservation practitioners believe that economic benefits to communities are the most predominant motivating factor, I found that good conservation management practices can motivate communities to support protected area management. Bad management practices were related not only to inadequate conservation approaches and practices but also to factors such as corruption, inadequate law enforcement and the inappropriate equipment of rangers. Therefore, I suggest that long term protected area management in DRC should consider how the value of resources for communities and protected areas have been changing throughout the history of conservation, and how to best share power and responsibilities with local resource users and stakeholders. This is only possible if conservation practices and approaches, governance process and institutions are transformed at multiple levels.
- Full Text:
- Date Issued: 2020
Consumer behaviour regarding stock market participation in South Africa
- Authors: Mbewe, Wise
- Date: 2020
- Subjects: Financial Literacy -- South Africa , Stock ownership -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50328 , vital:42107
- Description: South Africa (SA) has a highly sophisticated financial services sector that contributes significantly to the economy. A stock market forms a significant component of the financial sector of any economy. While the Johannesburg Stock Exchange (JSE) has managed to arouse interest of many South Africans, there appears to be apathy and inertia when it comes to actual participation in the stock market by South African consumers. Stock market non-participation is considered a “puzzle” in microeconomics and finance literature because it is not easy to explain the reason why many consumers, in spite of high stock returns, do not own listed shares. Thus, the primary objective of this study was to investigate consumer behaviour regarding stock market participation in SA by considering the antecedents and outcomes of stock market participation in SA.The study presented a theoretical literature review on the factors influencing stock market participation in SA. From the literature review, three sets of variables classified as independent variables, an intervening variable and dependent variables were identified. The independent variables (Demographic characteristics; Financial literacy; Investment risk tolerance; Communication; and Consumer trust) were identified as possibly influencing the intervening variable (Stock market participation) and ultimately the dependent variables (Client satisfaction and loyalty, Financial sustainability and Repurchase intentions). These variables were used to construct a hypothesised model and research hypotheses. The study further presented the research methodology (following a positivistic paradigm and quantitative research method), and the results of this study. In order to establish the influence of the independent variables on stock market participation, as well as ultimate influences on the dependent variables, an empirical investigation was conducted. Since it was not possible to reach all members of the target population, the population of this study was South African consumers located in four of the nine provinces, namely, Eastern Cape, Western Cape, Kwa-Zulu Natal and Gauteng. A sample of 510 respondents participated in the study.
- Full Text:
- Date Issued: 2020
- Authors: Mbewe, Wise
- Date: 2020
- Subjects: Financial Literacy -- South Africa , Stock ownership -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50328 , vital:42107
- Description: South Africa (SA) has a highly sophisticated financial services sector that contributes significantly to the economy. A stock market forms a significant component of the financial sector of any economy. While the Johannesburg Stock Exchange (JSE) has managed to arouse interest of many South Africans, there appears to be apathy and inertia when it comes to actual participation in the stock market by South African consumers. Stock market non-participation is considered a “puzzle” in microeconomics and finance literature because it is not easy to explain the reason why many consumers, in spite of high stock returns, do not own listed shares. Thus, the primary objective of this study was to investigate consumer behaviour regarding stock market participation in SA by considering the antecedents and outcomes of stock market participation in SA.The study presented a theoretical literature review on the factors influencing stock market participation in SA. From the literature review, three sets of variables classified as independent variables, an intervening variable and dependent variables were identified. The independent variables (Demographic characteristics; Financial literacy; Investment risk tolerance; Communication; and Consumer trust) were identified as possibly influencing the intervening variable (Stock market participation) and ultimately the dependent variables (Client satisfaction and loyalty, Financial sustainability and Repurchase intentions). These variables were used to construct a hypothesised model and research hypotheses. The study further presented the research methodology (following a positivistic paradigm and quantitative research method), and the results of this study. In order to establish the influence of the independent variables on stock market participation, as well as ultimate influences on the dependent variables, an empirical investigation was conducted. Since it was not possible to reach all members of the target population, the population of this study was South African consumers located in four of the nine provinces, namely, Eastern Cape, Western Cape, Kwa-Zulu Natal and Gauteng. A sample of 510 respondents participated in the study.
- Full Text:
- Date Issued: 2020
Contesting boundaries: a case of municipal demarcation disputes in Vuwani Vhembe District
- Authors: Khowa, Thandeka Promise
- Date: 2020
- Subjects: Geographical boundaries
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50767 , vital:42670
- Description: The research study in Vuwani Vhembe district sought to investigate demarcation disputes, the relationship between service delivery and demarcation disputes. The study further investigates the role of municipal demarcation board and local government adherence to sound governance principles and the causes of the demarcation dispute in Vuwani. The study additionally examines the conceptions and misconceptions, their impact on the current demarcation disputes in Vuwani. It further intended to establish the role and involvement of Vuwani stakeholders such as traditional structures/ leaders, civil unions, community members etc. in the processes of demarcating Vuwani. “What is the cause of Vuwani community member’s rejection of the re-demarcation, which is said to correct the past spatial injustices and promote municipal sizing, thus enabling better performance in service provision by municipalities?” The study employed a mixed-method involving the use of both quantitative (mini-survey) and qualitative (use of in-depth, semi structures interviews and focus group discussions). Research findings suggest that re-demarcation is a sensitive aspect/process in South Africa, mainly due to the past Apartheid era. There was forceful removal of people from their land supported by Apartheid legislation such as the Native Land Act 1913, Group Act 1950, Native Resettlement Act 1954 etc. Thus, fears of the past Apartheid system cloud any attempt to correct spatial injustices of the country. The new democratic South African government, therefore, needs to be cautious in its acts to correct the spatial injustices, thus adhering to sound governance principles. Findings reveal that several misconceptions and lack of adherence of good governance principles by the Municipal Demarcation Board and Local government have, to some extent, fueled the demarcation disputes in Vuwani. Municipal performance in the rendering of service delivery has a major impact and contributes to the community’s acceptance or rejection of demarcation/ amalgamations. The study further reveals that in Vuwani municipal performance with the establishment of the new Collins Chabane municipality has been clouded by fear of the unknown as this form of “demarcation of establishing a new municipality” altogether is relatively new. Rural land authority, the role of traditional leaders, ethnicity ties have all been found to have contributed to the disputes in Vuwani. Limpopo Province is home to three ethnic groups, namely, vaVhenda, baPedi and xiTsonga. The study findings have presented traits of tribalism as contributing to on-going demarcation disputes in Vuwani.
- Full Text:
- Date Issued: 2020
- Authors: Khowa, Thandeka Promise
- Date: 2020
- Subjects: Geographical boundaries
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50767 , vital:42670
- Description: The research study in Vuwani Vhembe district sought to investigate demarcation disputes, the relationship between service delivery and demarcation disputes. The study further investigates the role of municipal demarcation board and local government adherence to sound governance principles and the causes of the demarcation dispute in Vuwani. The study additionally examines the conceptions and misconceptions, their impact on the current demarcation disputes in Vuwani. It further intended to establish the role and involvement of Vuwani stakeholders such as traditional structures/ leaders, civil unions, community members etc. in the processes of demarcating Vuwani. “What is the cause of Vuwani community member’s rejection of the re-demarcation, which is said to correct the past spatial injustices and promote municipal sizing, thus enabling better performance in service provision by municipalities?” The study employed a mixed-method involving the use of both quantitative (mini-survey) and qualitative (use of in-depth, semi structures interviews and focus group discussions). Research findings suggest that re-demarcation is a sensitive aspect/process in South Africa, mainly due to the past Apartheid era. There was forceful removal of people from their land supported by Apartheid legislation such as the Native Land Act 1913, Group Act 1950, Native Resettlement Act 1954 etc. Thus, fears of the past Apartheid system cloud any attempt to correct spatial injustices of the country. The new democratic South African government, therefore, needs to be cautious in its acts to correct the spatial injustices, thus adhering to sound governance principles. Findings reveal that several misconceptions and lack of adherence of good governance principles by the Municipal Demarcation Board and Local government have, to some extent, fueled the demarcation disputes in Vuwani. Municipal performance in the rendering of service delivery has a major impact and contributes to the community’s acceptance or rejection of demarcation/ amalgamations. The study further reveals that in Vuwani municipal performance with the establishment of the new Collins Chabane municipality has been clouded by fear of the unknown as this form of “demarcation of establishing a new municipality” altogether is relatively new. Rural land authority, the role of traditional leaders, ethnicity ties have all been found to have contributed to the disputes in Vuwani. Limpopo Province is home to three ethnic groups, namely, vaVhenda, baPedi and xiTsonga. The study findings have presented traits of tribalism as contributing to on-going demarcation disputes in Vuwani.
- Full Text:
- Date Issued: 2020
Creating Citizen-Science for Groundwater Monitoring prior to potential Shale Gas Development in Cradock (South-Eastern Karoo, South Africa)
- Authors: Dhliwayo, Nyaradzo
- Date: 2020
- Subjects: Natural gas -- Prospecting -- Environmental aspects -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48224 , vital:40526
- Description: Citizen Science is an integral tool for community engagement in scientific project design, implementation, data interpretation and reporting, in the quest to promote local capacity development as well as scientific knowledge. Based on the relevance of public engagement in aspects of the natural environment and associated scientific issues associated with the risks and opportunities of potential Shale Gas Development (SGD), a Citizen-Science (CS) study was designed in the Eastern Karoo region of South Africa linked to a Shale Gas Baseline Study initiated by the Africa Earth Observatory Network (AEON). As the pilot area of the baseline study, the town of Cradock was chosen to be the study area for this research; and CS was used to facilitate the identification of the Cradock community’s abilities to monitor the effects of potential SGD in this region. The development of new knowledge, skills and support, as well as a deeper understanding of the community’s role in Citizen Science studies, was also facilitated by this process. This study demonstrates the feasibility of integrating Citizen Science into existing community structures in Africa, thereby encouraging community engagement in the developmental programmes through participatory methods. Using a collaborative Action-Research Approach, consistent community roundtable meetings and key informant interviews served as invaluable platforms for the establishment of a 7-member community working group, that played the liaison role between the researcher and the Cradock community in the CS implementation process. Coupled with this was the recruitment and the training of eight young citizens in conducting a hydro-census and groundwater sampling for six boreholes within the identified Cradock commonage farms, as well as two boreholes on the farm of an identified emergent farmer. The engagements between the researcher, AEON scientists, the community working group and the community at large, enabled the successful implementation of CS training in two groundwater monitoring aspects and the testing of eleven water quality parameters. The training process was combined with the design and the development of a customised ‘Xoras’ Online Application, which was used to capture and share the hydro-census data recorded. Experiential learning in hydro-census and groundwater sampling resulted subsequently in an increased understanding and awareness of these aspects (Figure A). Even if SGD does not materialise in the South-Eastern Karoo, CS training will enable communities in the Shale-Gas Development precincts to participate in local decision-making forums on ground water, health, or on any related regional development projects. It is anticipated that the adoption of CS will ix promote future community engagements, especially about water across this water-scarce region, allowing for greater community-voice representation in resource-policy decisions related to potential Shale-Gas and related natural resource industries in the Karoo.
- Full Text:
- Date Issued: 2020
- Authors: Dhliwayo, Nyaradzo
- Date: 2020
- Subjects: Natural gas -- Prospecting -- Environmental aspects -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48224 , vital:40526
- Description: Citizen Science is an integral tool for community engagement in scientific project design, implementation, data interpretation and reporting, in the quest to promote local capacity development as well as scientific knowledge. Based on the relevance of public engagement in aspects of the natural environment and associated scientific issues associated with the risks and opportunities of potential Shale Gas Development (SGD), a Citizen-Science (CS) study was designed in the Eastern Karoo region of South Africa linked to a Shale Gas Baseline Study initiated by the Africa Earth Observatory Network (AEON). As the pilot area of the baseline study, the town of Cradock was chosen to be the study area for this research; and CS was used to facilitate the identification of the Cradock community’s abilities to monitor the effects of potential SGD in this region. The development of new knowledge, skills and support, as well as a deeper understanding of the community’s role in Citizen Science studies, was also facilitated by this process. This study demonstrates the feasibility of integrating Citizen Science into existing community structures in Africa, thereby encouraging community engagement in the developmental programmes through participatory methods. Using a collaborative Action-Research Approach, consistent community roundtable meetings and key informant interviews served as invaluable platforms for the establishment of a 7-member community working group, that played the liaison role between the researcher and the Cradock community in the CS implementation process. Coupled with this was the recruitment and the training of eight young citizens in conducting a hydro-census and groundwater sampling for six boreholes within the identified Cradock commonage farms, as well as two boreholes on the farm of an identified emergent farmer. The engagements between the researcher, AEON scientists, the community working group and the community at large, enabled the successful implementation of CS training in two groundwater monitoring aspects and the testing of eleven water quality parameters. The training process was combined with the design and the development of a customised ‘Xoras’ Online Application, which was used to capture and share the hydro-census data recorded. Experiential learning in hydro-census and groundwater sampling resulted subsequently in an increased understanding and awareness of these aspects (Figure A). Even if SGD does not materialise in the South-Eastern Karoo, CS training will enable communities in the Shale-Gas Development precincts to participate in local decision-making forums on ground water, health, or on any related regional development projects. It is anticipated that the adoption of CS will ix promote future community engagements, especially about water across this water-scarce region, allowing for greater community-voice representation in resource-policy decisions related to potential Shale-Gas and related natural resource industries in the Karoo.
- Full Text:
- Date Issued: 2020
Design ethnography: methodological considerations for rebalancing socio-technical phenomena in CMS performativity
- Authors: Jordaan, Leandra
- Date: 2020
- Subjects: Database management -- Social aspects , Information technology -- Social aspects , Management information systems -- Social aspects , Database management -- Philosophy , Information technology -- Philosophy , Management information systems -- Philosophy
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164781 , vital:41164
- Description: As a practitioner, I had been part of two Content Management System (CMS) Projects in a particular setting that did not deliver on the expected outcomes. The expected outcomes of the projects included streamlined processes, better access to information, functionalities to drive engagement, reduced time searching for information, and improved reusability of content. As I began to reflect on the projects, a certain discomfort developed when the social aspect was ignored in favour of the technological. I sought a better understanding, but I was unaware of the fact at first. The techno-centricity as a concept found in literature and my experience as content management (CM) practitioner – together informed my interest in rebalancing the social and the technological. Thus, I focused on conduct in performing of tasks and emphasised attention on the practices of experts who gave insight into context of CM and use. The research participants are communication practitioners who have the responsibility to communicate internally and externally on behalf of a publicly-funded university in South Africa. Guided by the abductive argument and literature, the key themes for the research focused on technology, individuals and the organisation. The focus on technology (CMS as a subfield of Information Systems) began with my involvement in two CMS Projects. What came to the fore was that the practitioner perspective, and thus their experiential knowledge are neglected in research and that it may be an over-emphasis on techno-centrism in CMS research. I sought to better balance the social and technological aspects. The second focus on individuals (communication practitioners) was to value the stakeholder who was considered representative of the worldviews of the community. I sought to support corporate communication practices in the task of relationship building with stakeholders. The findings showed that the culture of informatio sharing was low at the University. The third focus on the organisation (the University) was to prioritise the success of the communication undertaken by the University. I interrogated the role of power. I demonstrated how the role of power could be seen as productive and positive in the context of HE, the social reality of CUT, and this IS research itself. I positioned the research as interpretivistic. I used hermeneutics as a mode of analysis because as researcher-practitioner, I am part of the social reality of the research. A safeguard against my subjectivity was the use of Phronesis as an orientation to knowledge. An organisation with a shared understanding of ethics and values will balance instrumental rationality (scientific and technical reasoning) with value-rationality (moral reasoning about right and wrong actions). Phronesis is the virtue that should ensure ethical behaviour in actions, yet over time, social science research, in a quest to mimic the natural sciences, centred on episteme and techne. I constructed the lens by particularising the four value-rational questions of Flyvbjerg’s contemporary Phronesis to the performative perspective of the research. My interest in social reality, as well as socio-technical aspects, have led to design-ethnography (D-E) to emerge as the most suitable and most appropriate approach to the research. D-E asked the prescriptive ‘How’ and descriptive ‘What’ questions, whilst the Flyvbjergian Phronesis lens brought focus on the ‘Why’ question. D-E emphasised the betterment of the interaction and synergy between research conducted and practice. My status as an immersed researcher needed careful consideration, and D-E accepted that a certain level of immersion is necessary, D-E has short interventional fieldwork, and D-E has future-oriented engagement. The contemporary Phronesis used in the research is to enact D-E and not an all-encompassing guide for doing Phronesis research The key contributions to the research are predominantly methodological. The claims draw on evidence focused on the three themes technology, individuals and organisation, and the phenomena of interest which are to rebalance the social and the technological in CM practices. The first claim is that immersion in the context is possible and supported by the specific particularised approaches to the research. The second claim suggests a way to rebalance the socio-technical nature of Information Systems (IS). The third claim suggests that there is a viewpoint for power that is not focused on power’s oppressive nature which could see a diverging focus on power in IS research in future. In this viewpoint, the status quo of social reality is not questioned, nor are their emancipatory ambitions. The fourth and final claim suggests that Phronesis as a lens could enact D-E, which in turn is a method that assists in valuing the experience of the practitioner and the support of collaborative work. The research is recommended for IT/IS practitioners who prefer to value participants’ views in design. The approaches used could be of value for researchers who consider the context of their research to be of higher importance than the generalisation of outcomes. Researchers who find themselves in the position of being immersed in the context but question the correctness of active engagement in the field may discover some value from the research approaches and my experience. Also, researchers or practitioners who have an interest in the balance between social and the technological aspects of IS projects. Researchers or practitioners interested in Phronesis, and perhaps the viewpoint of a lens may also find value in this research.
- Full Text:
- Date Issued: 2020
- Authors: Jordaan, Leandra
- Date: 2020
- Subjects: Database management -- Social aspects , Information technology -- Social aspects , Management information systems -- Social aspects , Database management -- Philosophy , Information technology -- Philosophy , Management information systems -- Philosophy
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164781 , vital:41164
- Description: As a practitioner, I had been part of two Content Management System (CMS) Projects in a particular setting that did not deliver on the expected outcomes. The expected outcomes of the projects included streamlined processes, better access to information, functionalities to drive engagement, reduced time searching for information, and improved reusability of content. As I began to reflect on the projects, a certain discomfort developed when the social aspect was ignored in favour of the technological. I sought a better understanding, but I was unaware of the fact at first. The techno-centricity as a concept found in literature and my experience as content management (CM) practitioner – together informed my interest in rebalancing the social and the technological. Thus, I focused on conduct in performing of tasks and emphasised attention on the practices of experts who gave insight into context of CM and use. The research participants are communication practitioners who have the responsibility to communicate internally and externally on behalf of a publicly-funded university in South Africa. Guided by the abductive argument and literature, the key themes for the research focused on technology, individuals and the organisation. The focus on technology (CMS as a subfield of Information Systems) began with my involvement in two CMS Projects. What came to the fore was that the practitioner perspective, and thus their experiential knowledge are neglected in research and that it may be an over-emphasis on techno-centrism in CMS research. I sought to better balance the social and technological aspects. The second focus on individuals (communication practitioners) was to value the stakeholder who was considered representative of the worldviews of the community. I sought to support corporate communication practices in the task of relationship building with stakeholders. The findings showed that the culture of informatio sharing was low at the University. The third focus on the organisation (the University) was to prioritise the success of the communication undertaken by the University. I interrogated the role of power. I demonstrated how the role of power could be seen as productive and positive in the context of HE, the social reality of CUT, and this IS research itself. I positioned the research as interpretivistic. I used hermeneutics as a mode of analysis because as researcher-practitioner, I am part of the social reality of the research. A safeguard against my subjectivity was the use of Phronesis as an orientation to knowledge. An organisation with a shared understanding of ethics and values will balance instrumental rationality (scientific and technical reasoning) with value-rationality (moral reasoning about right and wrong actions). Phronesis is the virtue that should ensure ethical behaviour in actions, yet over time, social science research, in a quest to mimic the natural sciences, centred on episteme and techne. I constructed the lens by particularising the four value-rational questions of Flyvbjerg’s contemporary Phronesis to the performative perspective of the research. My interest in social reality, as well as socio-technical aspects, have led to design-ethnography (D-E) to emerge as the most suitable and most appropriate approach to the research. D-E asked the prescriptive ‘How’ and descriptive ‘What’ questions, whilst the Flyvbjergian Phronesis lens brought focus on the ‘Why’ question. D-E emphasised the betterment of the interaction and synergy between research conducted and practice. My status as an immersed researcher needed careful consideration, and D-E accepted that a certain level of immersion is necessary, D-E has short interventional fieldwork, and D-E has future-oriented engagement. The contemporary Phronesis used in the research is to enact D-E and not an all-encompassing guide for doing Phronesis research The key contributions to the research are predominantly methodological. The claims draw on evidence focused on the three themes technology, individuals and organisation, and the phenomena of interest which are to rebalance the social and the technological in CM practices. The first claim is that immersion in the context is possible and supported by the specific particularised approaches to the research. The second claim suggests a way to rebalance the socio-technical nature of Information Systems (IS). The third claim suggests that there is a viewpoint for power that is not focused on power’s oppressive nature which could see a diverging focus on power in IS research in future. In this viewpoint, the status quo of social reality is not questioned, nor are their emancipatory ambitions. The fourth and final claim suggests that Phronesis as a lens could enact D-E, which in turn is a method that assists in valuing the experience of the practitioner and the support of collaborative work. The research is recommended for IT/IS practitioners who prefer to value participants’ views in design. The approaches used could be of value for researchers who consider the context of their research to be of higher importance than the generalisation of outcomes. Researchers who find themselves in the position of being immersed in the context but question the correctness of active engagement in the field may discover some value from the research approaches and my experience. Also, researchers or practitioners who have an interest in the balance between social and the technological aspects of IS projects. Researchers or practitioners interested in Phronesis, and perhaps the viewpoint of a lens may also find value in this research.
- Full Text:
- Date Issued: 2020
Design of Immunobiosensors for Detection of Tumor-Associated Anti-P53 Autoantibodies: Method Development
- Authors: Adeniyi, Omotayo Kayode
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162988 , vital:41002 , 10.21504/10962/162988
- Description: Introduction -- Experimental -- Label-Free Impedimetric Sensing of Anti-P53ab... -- Fluorescent detection of Anti-P53ab -- Peroxidase-like activity of Fe3O4@SiNP-APTES-Au@Pd... -- Colorimetric detection of Anti-P53ab , Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020. , Detection and profiling of circulating tumor-associated autoantibodies (TAAbs) are useful for screening and early-stage diagnosis of asymptomatic lung cancer. Immunobiosensor technologies aimed to accomplish the highly sensitive, rapid and low-cost detection of TAAbs can improve the early-stage detection of lung cancer. Immunobiosensors for the detection of anti-P53-tumour associated autoantibodies have been developed in this work. The design of sensing interfaces with immobilized P53 protein (P53ag) as a sensing element layer on a solid interface was investigated. Several methods of detecting anti-P53-antibodies (anti-P53ab) were investigated. These methods are label-free detection using electrochemical impedance spectroscopy (EIS) and two label techniques. The label-free electrochemical techniques utilize gold electrode pre-modified with a conducting layer of electrochemically grafted phenylethylamine for covalent immobilization of P53ag. The limit of anti-P53ab detection with the label-free EIS was 103.0 pg.ml-1. The labeled technique developed utilizes fluorescent, and peroxidase-like nanomaterial labeled antibody as a detection probe. For the fluorescence detection, fluorescent silica nanoparticles were synthesized by overloading FITC into the silica matrix and conjugated to detection antibody (anti-IgG). The detection of the anti-P53ab was based on the dissolution of the silica nanoparticles to release the loaded dye as a signal amplification strategy. The fluorescence detection was carried out on a microplate, and magnetic bead modified P53-antigen platforms and limit of detection (LoD) were 42.0 fg.ml-1 and 3.3 fg.ml-1 for anti-P53ab; respectively. Fe3O4@SiNP-APTES-Au@Pd hybrid nanoparticles were synthesized, and their peroxidase-like activity and colorimetric detection were evaluated. The Fe3O4@SiNP-APTES-Au@Pd exhibited comparable activity to HRP. The Fe3O4@SiNP-APTES-Au@Pd was conjugated to protein-G-anti-IgG for the detection of anti-P53ab on a microplate and cellulose paper platforms. The LoD was 20.0 fg.ml-1 and 63.0 fg.ml-1 for the microplate and cellulose paper platform; respectively. The potential application of the designed immunobiosensor was evaluated in simulated serum samples. The developed sensors showed higher detection sensitivity, stability and had a lower detection limit for anti-P53ab when compared with the ELISA based detection. The results have provided alternative and effective quantification approaches to ELISA and a promising future for multiplexed detection of tumor-associated autoantibodies. The developed methodologies in this thesis could be applied for the detection of other autoantibodies in other cancer types and auto-immune diseases.
- Full Text:
- Date Issued: 2020
- Authors: Adeniyi, Omotayo Kayode
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162988 , vital:41002 , 10.21504/10962/162988
- Description: Introduction -- Experimental -- Label-Free Impedimetric Sensing of Anti-P53ab... -- Fluorescent detection of Anti-P53ab -- Peroxidase-like activity of Fe3O4@SiNP-APTES-Au@Pd... -- Colorimetric detection of Anti-P53ab , Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020. , Detection and profiling of circulating tumor-associated autoantibodies (TAAbs) are useful for screening and early-stage diagnosis of asymptomatic lung cancer. Immunobiosensor technologies aimed to accomplish the highly sensitive, rapid and low-cost detection of TAAbs can improve the early-stage detection of lung cancer. Immunobiosensors for the detection of anti-P53-tumour associated autoantibodies have been developed in this work. The design of sensing interfaces with immobilized P53 protein (P53ag) as a sensing element layer on a solid interface was investigated. Several methods of detecting anti-P53-antibodies (anti-P53ab) were investigated. These methods are label-free detection using electrochemical impedance spectroscopy (EIS) and two label techniques. The label-free electrochemical techniques utilize gold electrode pre-modified with a conducting layer of electrochemically grafted phenylethylamine for covalent immobilization of P53ag. The limit of anti-P53ab detection with the label-free EIS was 103.0 pg.ml-1. The labeled technique developed utilizes fluorescent, and peroxidase-like nanomaterial labeled antibody as a detection probe. For the fluorescence detection, fluorescent silica nanoparticles were synthesized by overloading FITC into the silica matrix and conjugated to detection antibody (anti-IgG). The detection of the anti-P53ab was based on the dissolution of the silica nanoparticles to release the loaded dye as a signal amplification strategy. The fluorescence detection was carried out on a microplate, and magnetic bead modified P53-antigen platforms and limit of detection (LoD) were 42.0 fg.ml-1 and 3.3 fg.ml-1 for anti-P53ab; respectively. Fe3O4@SiNP-APTES-Au@Pd hybrid nanoparticles were synthesized, and their peroxidase-like activity and colorimetric detection were evaluated. The Fe3O4@SiNP-APTES-Au@Pd exhibited comparable activity to HRP. The Fe3O4@SiNP-APTES-Au@Pd was conjugated to protein-G-anti-IgG for the detection of anti-P53ab on a microplate and cellulose paper platforms. The LoD was 20.0 fg.ml-1 and 63.0 fg.ml-1 for the microplate and cellulose paper platform; respectively. The potential application of the designed immunobiosensor was evaluated in simulated serum samples. The developed sensors showed higher detection sensitivity, stability and had a lower detection limit for anti-P53ab when compared with the ELISA based detection. The results have provided alternative and effective quantification approaches to ELISA and a promising future for multiplexed detection of tumor-associated autoantibodies. The developed methodologies in this thesis could be applied for the detection of other autoantibodies in other cancer types and auto-immune diseases.
- Full Text:
- Date Issued: 2020
Design of immunosensor for the detection of C-reactive protein using oriented antibody immobilization
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
Designing a parental involvement programme to enhance parental engagement in the educational support programme at a disadvantaged primary school in the Nelson Mandela Bay Metropole, South Africa through participatory action research
- WIlliams, Pearl Juanita Cherrol
- Authors: WIlliams, Pearl Juanita Cherrol
- Date: 2020
- Subjects: Education -- Parent participation -- South Africa -- Nelson Mandela Bay Municipality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/47303 , vital:39841
- Description: Over the past decades parental involvement in education has increased rapidly within disadvantaged schools in South Africa. This transformation is evident in the legislation of the country which celebrates a spirit of Ubuntu in a democratised society, and, education at large. The ideal of effective school-home partnership across racial boundaries are, for example, emphasised and strengthened via parental involvement at all public schools. Parents, according to the Department of Education (DoE, 1996b:11; 2000c:29; 2001b:29; 2008:23; 2009:17; 2014b:27; n.d.:6), are considered key role-players in school governance and encouraged to support equal educational opportunities for all learners. It implies that the praxis of parental involvement – especially at disadvantaged schools – is a huge benefit to learners with existing backlogs in education. In relation to this view, Stofile and Green (2007:63) emphasise the significance of parental involvement in school life as it can assist greatly in addressing the divere needs of disadvantaged learners. The dynamics associated with parental involvement are investigated in this study through two cycles of participatory action research. Initially ten parents from one of the disadvantaged primary schools within the Nelson Mandela Bay Metropole were purposively selected to participate in an in-depth qualitative research study pertaining to the design of a suitable parental involvement programme for disadvantaged learners. All the relevant information was gathered during action learning sets, individual interviews, and observations to triangulate the data and fill in possible gaps. This data was coded and categorised throughout the cyclical process via inductive participatory data analysis, as described by Patton (2015:216 & 551). Three main themes with sub-themes emerged from the study, namely (1) deficits of the academic programme: remedial education, teacher-assistants, homeworksupport, technical abilities; (2) the neglect of social wellness programmes: need for parental guidance, necessary professional assistance, upgrading of safety measures, availability of clothing bank, sustainability of a nutritional programme; and (3) voids in communication and relationships: the home environment, community, school environment. These themes and sub-themes successfully answered all the research questions. An increasing number of learners at disadvataged primary schools are neglected and/or leave school at a very young age. This scenario is often linked to poor communication and/or a lack of adequate educational support programmes to enhance better learning outcomes. The design of a PIP aimed to address the diverse needs of learners at a specific disadvantaged primary school with the full cooperation of their parents. Nested within the Ecological Model of Bronfenbrenner, the participating parents were engaged in comprehensive discussions about educational support programmes that the school could embark on with them. Numerous programmes were identified as fundamental to transforming the quality of education for many disadvantaged learners. This research therefore encouraged greater parental involvement at disadvantaged primary schools in order to sustain better learning outcomes.
- Full Text:
- Date Issued: 2020
- Authors: WIlliams, Pearl Juanita Cherrol
- Date: 2020
- Subjects: Education -- Parent participation -- South Africa -- Nelson Mandela Bay Municipality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/47303 , vital:39841
- Description: Over the past decades parental involvement in education has increased rapidly within disadvantaged schools in South Africa. This transformation is evident in the legislation of the country which celebrates a spirit of Ubuntu in a democratised society, and, education at large. The ideal of effective school-home partnership across racial boundaries are, for example, emphasised and strengthened via parental involvement at all public schools. Parents, according to the Department of Education (DoE, 1996b:11; 2000c:29; 2001b:29; 2008:23; 2009:17; 2014b:27; n.d.:6), are considered key role-players in school governance and encouraged to support equal educational opportunities for all learners. It implies that the praxis of parental involvement – especially at disadvantaged schools – is a huge benefit to learners with existing backlogs in education. In relation to this view, Stofile and Green (2007:63) emphasise the significance of parental involvement in school life as it can assist greatly in addressing the divere needs of disadvantaged learners. The dynamics associated with parental involvement are investigated in this study through two cycles of participatory action research. Initially ten parents from one of the disadvantaged primary schools within the Nelson Mandela Bay Metropole were purposively selected to participate in an in-depth qualitative research study pertaining to the design of a suitable parental involvement programme for disadvantaged learners. All the relevant information was gathered during action learning sets, individual interviews, and observations to triangulate the data and fill in possible gaps. This data was coded and categorised throughout the cyclical process via inductive participatory data analysis, as described by Patton (2015:216 & 551). Three main themes with sub-themes emerged from the study, namely (1) deficits of the academic programme: remedial education, teacher-assistants, homeworksupport, technical abilities; (2) the neglect of social wellness programmes: need for parental guidance, necessary professional assistance, upgrading of safety measures, availability of clothing bank, sustainability of a nutritional programme; and (3) voids in communication and relationships: the home environment, community, school environment. These themes and sub-themes successfully answered all the research questions. An increasing number of learners at disadvataged primary schools are neglected and/or leave school at a very young age. This scenario is often linked to poor communication and/or a lack of adequate educational support programmes to enhance better learning outcomes. The design of a PIP aimed to address the diverse needs of learners at a specific disadvantaged primary school with the full cooperation of their parents. Nested within the Ecological Model of Bronfenbrenner, the participating parents were engaged in comprehensive discussions about educational support programmes that the school could embark on with them. Numerous programmes were identified as fundamental to transforming the quality of education for many disadvantaged learners. This research therefore encouraged greater parental involvement at disadvantaged primary schools in order to sustain better learning outcomes.
- Full Text:
- Date Issued: 2020
Determination of nonlinear optical properties of phthalocyanine regioisomers using computational models
- Date: 2020
- Subjects: Electrochemistry , Phthalocyanines , Nanoparticles , Nonlinear optics , Nonlinear optical spectroscopy , Refraction
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/166197 , vital:41337
- Description: This work investigates the effects of the nonlinear optical properties of four different constitutional isomers (C4h, C2v, Cs, and D2h) of a series of tetrasubstituted phthalocyanines (free-base 3-4-tert-butylphenoxyether phthalocyanines, free-base 4-4-tertbutylphenoxyether phthalocyanines, SnCl2 tetra substituted 3-4-tert-butylphenoxyether phthalocyanine, and SnCl2 tetra substituted 4-4-tert-butylphenoxyether phthalocyanine). The properties investigated were the real and imaginary components of the 3rd order hyperpolarizability, as well as the excited state absorption and refraction cross sections. The investigations were performed with a z-scan over a range of laser beam intensities. This work determined the imaginary component of the 3rd order hyperpolarizability for the free-base and SnCl2 3-4-tert-butylphenoxyether phthalocyanines and 4-4-tert-butylphenoxyether phthalocyanines to be highly dependent on the excited state cross sections. The refraction caused due to the real component of the 3rd order hyperpolarizability of the phthalocyanines was also investigated, however, the values found were strongly dependent on the laser beam intensity and the cause of this was investigated. A Five-level model was developed and run on GPGPU computing devices in order to isolate the absorption and refractive cross sections. Theeffects of the regio substitution on the excited state cross sections were also investigated, and the 1st singlet excited state and 1st triplet state absorption cross sections were calculated for all constitutional isomers. It was found that the symmetry of the constitutional isomers have a disproportionately large effect on the excited state absorption when compared to the ground state absorption. The nonlinear refractive properties of all constitutional isomers were also investigated, and the values of the parametric susceptibility are reported herein. The nonlinear refraction was found to have less effect than was seen in the nonlinear absorption. The 1st singlet excited state and 1st triplet state refractive cross sections of all constitutional isomer was determined. The results indicated that if more than one excited state was present and contributing to the nonlinear refraction, then more data than was collected here would be required. However, the 1st singlet excited state cross section were successfully determined for the free-base constitutional isomers. This work concluded that the region substitution affected the excited states more than the ground state.
- Full Text:
- Date Issued: 2020
- Date: 2020
- Subjects: Electrochemistry , Phthalocyanines , Nanoparticles , Nonlinear optics , Nonlinear optical spectroscopy , Refraction
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/166197 , vital:41337
- Description: This work investigates the effects of the nonlinear optical properties of four different constitutional isomers (C4h, C2v, Cs, and D2h) of a series of tetrasubstituted phthalocyanines (free-base 3-4-tert-butylphenoxyether phthalocyanines, free-base 4-4-tertbutylphenoxyether phthalocyanines, SnCl2 tetra substituted 3-4-tert-butylphenoxyether phthalocyanine, and SnCl2 tetra substituted 4-4-tert-butylphenoxyether phthalocyanine). The properties investigated were the real and imaginary components of the 3rd order hyperpolarizability, as well as the excited state absorption and refraction cross sections. The investigations were performed with a z-scan over a range of laser beam intensities. This work determined the imaginary component of the 3rd order hyperpolarizability for the free-base and SnCl2 3-4-tert-butylphenoxyether phthalocyanines and 4-4-tert-butylphenoxyether phthalocyanines to be highly dependent on the excited state cross sections. The refraction caused due to the real component of the 3rd order hyperpolarizability of the phthalocyanines was also investigated, however, the values found were strongly dependent on the laser beam intensity and the cause of this was investigated. A Five-level model was developed and run on GPGPU computing devices in order to isolate the absorption and refractive cross sections. Theeffects of the regio substitution on the excited state cross sections were also investigated, and the 1st singlet excited state and 1st triplet state absorption cross sections were calculated for all constitutional isomers. It was found that the symmetry of the constitutional isomers have a disproportionately large effect on the excited state absorption when compared to the ground state absorption. The nonlinear refractive properties of all constitutional isomers were also investigated, and the values of the parametric susceptibility are reported herein. The nonlinear refraction was found to have less effect than was seen in the nonlinear absorption. The 1st singlet excited state and 1st triplet state refractive cross sections of all constitutional isomer was determined. The results indicated that if more than one excited state was present and contributing to the nonlinear refraction, then more data than was collected here would be required. However, the 1st singlet excited state cross section were successfully determined for the free-base constitutional isomers. This work concluded that the region substitution affected the excited states more than the ground state.
- Full Text:
- Date Issued: 2020
Developing macroinvertebrate trait- and taxonomically-based approaches for biomonitoring wadeable riverine systems in the Niger delta, Nigeria
- Authors: Edegbene, Ovie Augustine
- Date: 2020
- Subjects: Water – Pollution -- Nigeria -- Niger River Delta , Stream health -- Nigeria -- Niger River Delta , Water -- Pollution -- Measurement , Environmental monitoring -- Nigeria -- Niger River Delta , Water quality -- Nigeria -- Niger River Delta , Water quality biological assessment -- Nigeria -- Niger River Delta , Aquatic invertebrates -- Nigeria -- Niger River Delta , Stream restoration -- Nigeria -- Niger River Delta , Urban agriculture -- Nigeria -- Niger River Delta , Stream ecology -- Nigeria -- Niger River Delta
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140660 , vital:37907
- Description: Riverine systems are increasingly subjected to pollution due to rapid urbanisation, industrialisation, and agricultural activities. Increasing pollution in freshwater systems impairs water quality, causes biodiversity loss and impairs aquatic ecosystem functionality and supply of ecosystem services. Rivers in the Niger Delta region of Nigeria are particularly vulnerable to urban pollution and agricultural activities as natural forests are increasingly replaced by urbanisation and agriculture. The differential effects of these pressures on the ecological processes of these river systems are poorly explored, as is the development of appropriate biomonitoring tools for routine monitoring of river health. In this study, a physico-chemically-based approach and macroinvertebrate trait- and taxonomic- approaches were developed to better understand the effects of multiple pressures on riverine systems, while developing multimetric indices to enable sustainable management of rivers within the region. Sixty-six stations in 20 river systems within the Edo and Delta States of the Niger Delta ecoregion were monitored seasonally for a period of five (2008–2012) years. The physico-chemically based approach makes apparent the extent of degradation of rivers and streams in the Niger Delta. For each dominant land use type, river stations were classified into least impacted stations (LIS), moderately impacted stations (MIS) or heavily impacted stations (HIS). Of 11 stations within urban catchments, only two were considered least impacted, suggesting that urgent measures are necessary to revise the current trajectories of urban rivers within the region. Most of the stations designated as MIS and HIS in the urban and urban-agriculture catchments were found to be significantly correlated with increased nutrients, EC and BOD5. Characteristics of most of the MIS and HIS within rivers in urban catchments evidenced the so-called urban stream syndrome, a state of persistent degradation of urban streams. The results of the traits and ecological preferences approach showed traits sensitive to urban and urban-agriculture pollution. Traits and ecological preferences that were associated with the LIS include the possession of hardshell, moderate and high sensitivities to oxygen depletion, very large body sized individuals (>20-40mm), swimmers, flattened body shape, a preference for temporary attachment, crawling, respiration with aerial/vegetation, possession of breathing tubes, possession of strap or other apparatus for respiration, streamlined body, and a high sensitivity to oxygen depletion. Permanent attachment as an ecological preference associated with LIS was also positively correlated with increasing dissolved oxygen (DO) and was deemed a pollution sensitive ecological preference. The possession of very small body size (<5mm), associated with HIS, was deemed a pollution-tolerant trait and was negatively correlated with DO, confirming the deteriorating state of the urban and urban-agricultural rivers. The impact of urban-forestry pollution on the distribution pattern of macroinvertebrate traits and ecological preferences was also explored in the selected rivers. Traits and ecological preferences such as possession of hard-shell, large body size, and grazing as a feeding preference which were significantly positively associated with the LIS, were also either significantly positively correlated with DO, or significantly negatively correlated with increasing any two of flow velocity, water temperature, BOD5 and nutrient. These traits and ecological preferences were deemed sensitive in forested rivers receiving urban pollution. Further, burrowing, the pupa aquatic stage, and predation which were significantly positively associated with HIS on the RLQ ordination, were also significantly negatively associated with DO. These traits were deemed tolerant of forested systems receiving urban pollution. Multimetric indices (MMI) were developed, validated and applied for urban, urban-agriculture and urban-forested (MMI-urban, MMI-urban-agric and urban-forest) areas. Of the 26 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban, only five metric were retained for integration into MMI-urban, they are log VeL, Hemiptera abundance, % Coleoptera + Hemiptera, % Chironomidae + Oligochaeta and Evenness index. Further, of the 18 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban-agric, only 12 metrics were retained and nine proved to be redundant. The nine metrics represent different measures; two of them were retained in addition to Chironomidae/Diptera abundance, % Odonata and Oligochaeta richness. The two metrics selected in addition to the hironomidae/Diptera abundance, % Odonata and Oligochaeta richness were the Margalef index and the logarithm of relative abundance of sprawler. For the MMI-urban-forest, 14 metrics satisfactorily discriminated between the LIS, the MIS, and the HIS, and 12 metrics were retained and 11 proved to be redundant. The non-redundant metric was Trichoptera abundance. Three metrics were further selected in addition to the Trichoptera abundance which include % Chironomidae + Oligochaeta, Coleoptera + Hemiptera richness and Shannon diversity. The MMI-urban and MMI-urban-agric indices performed better for LIS designated stations compared to the MIS and HIS deignated stations. The developed indices proved effective as biomonitoring tools for assessing the ecological health of rivers in the urban and urban-agriculture catchments within the Niger Delta. Overall, the results of the macroinvertebrate traits and ecological preferences, and taxonomic approaches showed the strength in the complementarity of both approaches in developing biomonitoring tools for assessing levels of deterioration in riverine systems. The study contributes significantly to understanding the ecology of riverine systems in the Niger Delta, particularly those subject to urban stresses, agricultural activities and urban pollution in forested systems, and thus makes an important contribution to the science and practice of biomonitoring in Nigeria where such studies are sparse.
- Full Text:
- Date Issued: 2020
- Authors: Edegbene, Ovie Augustine
- Date: 2020
- Subjects: Water – Pollution -- Nigeria -- Niger River Delta , Stream health -- Nigeria -- Niger River Delta , Water -- Pollution -- Measurement , Environmental monitoring -- Nigeria -- Niger River Delta , Water quality -- Nigeria -- Niger River Delta , Water quality biological assessment -- Nigeria -- Niger River Delta , Aquatic invertebrates -- Nigeria -- Niger River Delta , Stream restoration -- Nigeria -- Niger River Delta , Urban agriculture -- Nigeria -- Niger River Delta , Stream ecology -- Nigeria -- Niger River Delta
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140660 , vital:37907
- Description: Riverine systems are increasingly subjected to pollution due to rapid urbanisation, industrialisation, and agricultural activities. Increasing pollution in freshwater systems impairs water quality, causes biodiversity loss and impairs aquatic ecosystem functionality and supply of ecosystem services. Rivers in the Niger Delta region of Nigeria are particularly vulnerable to urban pollution and agricultural activities as natural forests are increasingly replaced by urbanisation and agriculture. The differential effects of these pressures on the ecological processes of these river systems are poorly explored, as is the development of appropriate biomonitoring tools for routine monitoring of river health. In this study, a physico-chemically-based approach and macroinvertebrate trait- and taxonomic- approaches were developed to better understand the effects of multiple pressures on riverine systems, while developing multimetric indices to enable sustainable management of rivers within the region. Sixty-six stations in 20 river systems within the Edo and Delta States of the Niger Delta ecoregion were monitored seasonally for a period of five (2008–2012) years. The physico-chemically based approach makes apparent the extent of degradation of rivers and streams in the Niger Delta. For each dominant land use type, river stations were classified into least impacted stations (LIS), moderately impacted stations (MIS) or heavily impacted stations (HIS). Of 11 stations within urban catchments, only two were considered least impacted, suggesting that urgent measures are necessary to revise the current trajectories of urban rivers within the region. Most of the stations designated as MIS and HIS in the urban and urban-agriculture catchments were found to be significantly correlated with increased nutrients, EC and BOD5. Characteristics of most of the MIS and HIS within rivers in urban catchments evidenced the so-called urban stream syndrome, a state of persistent degradation of urban streams. The results of the traits and ecological preferences approach showed traits sensitive to urban and urban-agriculture pollution. Traits and ecological preferences that were associated with the LIS include the possession of hardshell, moderate and high sensitivities to oxygen depletion, very large body sized individuals (>20-40mm), swimmers, flattened body shape, a preference for temporary attachment, crawling, respiration with aerial/vegetation, possession of breathing tubes, possession of strap or other apparatus for respiration, streamlined body, and a high sensitivity to oxygen depletion. Permanent attachment as an ecological preference associated with LIS was also positively correlated with increasing dissolved oxygen (DO) and was deemed a pollution sensitive ecological preference. The possession of very small body size (<5mm), associated with HIS, was deemed a pollution-tolerant trait and was negatively correlated with DO, confirming the deteriorating state of the urban and urban-agricultural rivers. The impact of urban-forestry pollution on the distribution pattern of macroinvertebrate traits and ecological preferences was also explored in the selected rivers. Traits and ecological preferences such as possession of hard-shell, large body size, and grazing as a feeding preference which were significantly positively associated with the LIS, were also either significantly positively correlated with DO, or significantly negatively correlated with increasing any two of flow velocity, water temperature, BOD5 and nutrient. These traits and ecological preferences were deemed sensitive in forested rivers receiving urban pollution. Further, burrowing, the pupa aquatic stage, and predation which were significantly positively associated with HIS on the RLQ ordination, were also significantly negatively associated with DO. These traits were deemed tolerant of forested systems receiving urban pollution. Multimetric indices (MMI) were developed, validated and applied for urban, urban-agriculture and urban-forested (MMI-urban, MMI-urban-agric and urban-forest) areas. Of the 26 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban, only five metric were retained for integration into MMI-urban, they are log VeL, Hemiptera abundance, % Coleoptera + Hemiptera, % Chironomidae + Oligochaeta and Evenness index. Further, of the 18 metrics that satisfactorily discriminated between the LIS, the MIS, and the HIS for MMI-urban-agric, only 12 metrics were retained and nine proved to be redundant. The nine metrics represent different measures; two of them were retained in addition to Chironomidae/Diptera abundance, % Odonata and Oligochaeta richness. The two metrics selected in addition to the hironomidae/Diptera abundance, % Odonata and Oligochaeta richness were the Margalef index and the logarithm of relative abundance of sprawler. For the MMI-urban-forest, 14 metrics satisfactorily discriminated between the LIS, the MIS, and the HIS, and 12 metrics were retained and 11 proved to be redundant. The non-redundant metric was Trichoptera abundance. Three metrics were further selected in addition to the Trichoptera abundance which include % Chironomidae + Oligochaeta, Coleoptera + Hemiptera richness and Shannon diversity. The MMI-urban and MMI-urban-agric indices performed better for LIS designated stations compared to the MIS and HIS deignated stations. The developed indices proved effective as biomonitoring tools for assessing the ecological health of rivers in the urban and urban-agriculture catchments within the Niger Delta. Overall, the results of the macroinvertebrate traits and ecological preferences, and taxonomic approaches showed the strength in the complementarity of both approaches in developing biomonitoring tools for assessing levels of deterioration in riverine systems. The study contributes significantly to understanding the ecology of riverine systems in the Niger Delta, particularly those subject to urban stresses, agricultural activities and urban pollution in forested systems, and thus makes an important contribution to the science and practice of biomonitoring in Nigeria where such studies are sparse.
- Full Text:
- Date Issued: 2020
Development of a UV-tolerant strain of the South African isolate of Cryptophlebia leucotreta granulovirus for use as an enhanced biopesticide for Thaumatotibia leucotreta control on citrus
- Authors: Mwanza, Patrick
- Date: 2020
- Subjects: Baculoviruses -- South Africa , Ultraviolet astronomy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48533 , vital:40885
- Description: Baculoviruses are pathogenic to insects in the orders Diptera, Hymenoptera, and Lepidoptera. As a result of this natural relationship with insects they provide an environmentally friendly method to combat crop and forest pests. As such, a number of baculoviruses have been formulated into biopesticides. The use of baculovirus biopesticides is gaining popularity as the use of chemical pesticides has come under stringent regulatory conditions imposed by governments and continental blocks such as the European Union. Baculoviruses have a narrow host range and therefore do not harm non-pests or humans who consume the crops. One such baculovirus is Cryptophlebia leucotreta granulovirus (CrleGV), which is pathogenic to the citrus pest Thaumatotibia leucotreta, commonly referred to as the false codling moth (FCM). CrleGV has an occlusion body (OB) that encloses a single virion. Several CrleGV biopesticides have been registered in South Africa for use on citrus, avocadoes, macadamias, grapes and other crops by two commercial producers, River Bioscience (SA) and Andermatt (Switzerland). These biopesticides are used as part of the FCM integrated pest management (IPM) programme, a multifacetted approach to controlling FCM. However, baculoviruses are susceptible to the ultraviolet (UV) radiation component of sunlight and lose their activity within hours to a few days, after exposure to UV. Several substances have been tested as UV protectants to improve the persistence of baculovirus biopesticides in the field. These include optical brighteners, UV absorbers and anti-oxidants. While very promising in the laboratory, UV-protectants have not been as successful in the field. A few published reports have reported, that UV-tolerant baculoviruses could be isolated from a population by repeatedly exposing and re-exposing the virus to UV irradiation with a propagation step in insect host fourth or fifth instars between each exposure cycle. In this study, the South African isolate of Cryptophlebia leucotreta (CrleGV-SA) was exposed to UV irradiation for 5 exposure cycles in a Q-Sun Xe-3 HC test chamber (Qlab, USA) with parameters set to mimic a typical summer day in the Sundays River Valley, Eastern Cape Province, in South Africa. In between exposures the virus survivors were allowed to multiply in FCM fifth instars. Surface dose bioassays were also conducted to determine the LC50 of the virus after each exposure cycle. Samples from exposure cycle 1 and cycle 5 (UV-tolerant) irradiated for 72 h were prepared for Next Generation Sequencing (NGS) of DNA. The resultant sequence data were analysed using the Geneious R11 software (New Zealand) and compared with the unexposed CrleGV-SA sequence. In-silico restriction enzyme analsysis (REN) with several enzymes was also carried on both the cycle 1 and cycle 5 exposed samples and the resulting digestion patterns were compared with the original CrleGV-SA digestion patterns. The same samples were also analysed by transmission electron microscopy (TEM) and Attenuated Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) to evaluate the effect of UV irradiation on the structure of the CrleGV-SA OB. In addition, three UV protectants, lignin sulphate (Sappi, SA), BREAK-THRU®OE446 (OE446) (Evonik Industries, Germany) and Uvinul Easy (BASF, Germany) were prepared with CrleGV-SA to give final protectant concentrations of 0.09 %, 0.9 % and 9 %. The protectant-virus suspensions were exposed to UV for 24 h in the Q-Sun test chamber and bioassays conducted to determine the protective effect of each protectant concentration. The most successful protectants were then combined with the UV-tolerant CrleGV-SA and exposed to UV for 24 h in the Q-Sun test chamber and surface dose bioassays conducted afterwards. Samples exposed to UV in cycle 5 had lower LC50 values compared to samples in the early cycles. With each re-exposure cycle the LC50 values moved closer to that of the unexposed control. The LC50 of virus samples decreased from 2.89 x 108 OBs/ml after 24 h UV-exposure in cycle 1 to 2.16 x 105 OBs/ml after the same duration of exposure in cycle 5; and from 2.11 x 109 OBs/ml in cycle 1 after 72 h UV-exposure to 1.73 x 106 OBs/ml after the same duration of exposure. This represented a 1338-fold difference and a 1220-fold difference, respectively. When the UV-tolerant samples were sequenced seven SNPs were identified in cycle 1, which were thought to help establish UV tolerance, while a further seven SNPs were identified in cycle 5 samples; these were thought to further establish and maintain the UV-tolerance. Additionally, REN analysis with EcoR1 for both test samples yielded digestion patterns that were different from those of the original CrleGV-SA. TEM data showed that UV damages the virion as well as the crystalline structure of the OB. This is the first time visual evidence for UV damage to baculoviruses has been published. Comparison of cycle 1 and cycle 5 UV exposed OBs revealed that the cycle 5 OBs were significantly larger than the cycle 1 OBs (P<0.05). In addition, several peaks in the fingerprint region were shown to have either appeared or disapeered from the ATR-FTIR spectra after UV irradiation. However, there was no difference in the spectra of the Cycle 1 and Cycle 5 virus samples. The tests with potential UV-protectants revealed that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy were the most effective in protecting the virus from UV. However, there was no significant difference in their protection of UV tolerant CrleGV-SA and wild type CrleGV-SA. Going forward, it is recommended that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy combinations be explored further in future studies, particulary in the field. This study therefore forms an important foundation for the development of UV-tolerant baculovirus that will last longer in the field.
- Full Text:
- Date Issued: 2020
- Authors: Mwanza, Patrick
- Date: 2020
- Subjects: Baculoviruses -- South Africa , Ultraviolet astronomy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48533 , vital:40885
- Description: Baculoviruses are pathogenic to insects in the orders Diptera, Hymenoptera, and Lepidoptera. As a result of this natural relationship with insects they provide an environmentally friendly method to combat crop and forest pests. As such, a number of baculoviruses have been formulated into biopesticides. The use of baculovirus biopesticides is gaining popularity as the use of chemical pesticides has come under stringent regulatory conditions imposed by governments and continental blocks such as the European Union. Baculoviruses have a narrow host range and therefore do not harm non-pests or humans who consume the crops. One such baculovirus is Cryptophlebia leucotreta granulovirus (CrleGV), which is pathogenic to the citrus pest Thaumatotibia leucotreta, commonly referred to as the false codling moth (FCM). CrleGV has an occlusion body (OB) that encloses a single virion. Several CrleGV biopesticides have been registered in South Africa for use on citrus, avocadoes, macadamias, grapes and other crops by two commercial producers, River Bioscience (SA) and Andermatt (Switzerland). These biopesticides are used as part of the FCM integrated pest management (IPM) programme, a multifacetted approach to controlling FCM. However, baculoviruses are susceptible to the ultraviolet (UV) radiation component of sunlight and lose their activity within hours to a few days, after exposure to UV. Several substances have been tested as UV protectants to improve the persistence of baculovirus biopesticides in the field. These include optical brighteners, UV absorbers and anti-oxidants. While very promising in the laboratory, UV-protectants have not been as successful in the field. A few published reports have reported, that UV-tolerant baculoviruses could be isolated from a population by repeatedly exposing and re-exposing the virus to UV irradiation with a propagation step in insect host fourth or fifth instars between each exposure cycle. In this study, the South African isolate of Cryptophlebia leucotreta (CrleGV-SA) was exposed to UV irradiation for 5 exposure cycles in a Q-Sun Xe-3 HC test chamber (Qlab, USA) with parameters set to mimic a typical summer day in the Sundays River Valley, Eastern Cape Province, in South Africa. In between exposures the virus survivors were allowed to multiply in FCM fifth instars. Surface dose bioassays were also conducted to determine the LC50 of the virus after each exposure cycle. Samples from exposure cycle 1 and cycle 5 (UV-tolerant) irradiated for 72 h were prepared for Next Generation Sequencing (NGS) of DNA. The resultant sequence data were analysed using the Geneious R11 software (New Zealand) and compared with the unexposed CrleGV-SA sequence. In-silico restriction enzyme analsysis (REN) with several enzymes was also carried on both the cycle 1 and cycle 5 exposed samples and the resulting digestion patterns were compared with the original CrleGV-SA digestion patterns. The same samples were also analysed by transmission electron microscopy (TEM) and Attenuated Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) to evaluate the effect of UV irradiation on the structure of the CrleGV-SA OB. In addition, three UV protectants, lignin sulphate (Sappi, SA), BREAK-THRU®OE446 (OE446) (Evonik Industries, Germany) and Uvinul Easy (BASF, Germany) were prepared with CrleGV-SA to give final protectant concentrations of 0.09 %, 0.9 % and 9 %. The protectant-virus suspensions were exposed to UV for 24 h in the Q-Sun test chamber and bioassays conducted to determine the protective effect of each protectant concentration. The most successful protectants were then combined with the UV-tolerant CrleGV-SA and exposed to UV for 24 h in the Q-Sun test chamber and surface dose bioassays conducted afterwards. Samples exposed to UV in cycle 5 had lower LC50 values compared to samples in the early cycles. With each re-exposure cycle the LC50 values moved closer to that of the unexposed control. The LC50 of virus samples decreased from 2.89 x 108 OBs/ml after 24 h UV-exposure in cycle 1 to 2.16 x 105 OBs/ml after the same duration of exposure in cycle 5; and from 2.11 x 109 OBs/ml in cycle 1 after 72 h UV-exposure to 1.73 x 106 OBs/ml after the same duration of exposure. This represented a 1338-fold difference and a 1220-fold difference, respectively. When the UV-tolerant samples were sequenced seven SNPs were identified in cycle 1, which were thought to help establish UV tolerance, while a further seven SNPs were identified in cycle 5 samples; these were thought to further establish and maintain the UV-tolerance. Additionally, REN analysis with EcoR1 for both test samples yielded digestion patterns that were different from those of the original CrleGV-SA. TEM data showed that UV damages the virion as well as the crystalline structure of the OB. This is the first time visual evidence for UV damage to baculoviruses has been published. Comparison of cycle 1 and cycle 5 UV exposed OBs revealed that the cycle 5 OBs were significantly larger than the cycle 1 OBs (P<0.05). In addition, several peaks in the fingerprint region were shown to have either appeared or disapeered from the ATR-FTIR spectra after UV irradiation. However, there was no difference in the spectra of the Cycle 1 and Cycle 5 virus samples. The tests with potential UV-protectants revealed that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy were the most effective in protecting the virus from UV. However, there was no significant difference in their protection of UV tolerant CrleGV-SA and wild type CrleGV-SA. Going forward, it is recommended that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy combinations be explored further in future studies, particulary in the field. This study therefore forms an important foundation for the development of UV-tolerant baculovirus that will last longer in the field.
- Full Text:
- Date Issued: 2020
Development of bio-based xylan composites for food packaging applications
- Authors: Naidu, Darrel Sarvesh
- Date: 2020
- Subjects: Xylanases
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48544 , vital:40886
- Description: Currently a large number of chemicals and plastics are produced from petroleum-based resources. However, due to the concerns surrounding the depletion of petroleum resources and growing carbon emissions, there is a desire to produce chemicals and plastics from renewable and carbon natural sources. Lignocellulosic biomass (biomass consisting of cellulose, lignin and hemicellulose) is the most common biomass on earth and is renewable and carbon neutral. Of the three main constituents of lignocellulosic biomass, hemicellulose is composed of a mixture of sugars which can be converted into chemicals and plastics. The most common form of hemicellulose found in nature is xylan. This study is aimed at extracting xylan from maize stalk waste residues and the development of xylan films with properties that are suitable for food packaging applications. Xylan was extracted from maize stalk waste residues using an alkaline pre-treatment method. The effects of bleaching conditions (time, temperature and bleach concentration) prior to alkaline treatment on the yield and purity of xylan extracted was studied using a Box-Behnken experimental design. It was observed that the experimental conditions tested had no effect on the yield of the xylan extracted but the bleach concentration had a significant effect on the purity of the xylan extracted. The samples with the lowest lignin content were found to be the samples treated with 3wt% bleach prior to alkaline pre-treatment. One of the main disadvantages of xylan is that it has poor film forming properties, a method of overcoming this is to combine it with another abundantly available biopolymer that has good film forming properties, such as alginate. The effect of xylan, alginate and glycerol content on the mechanical, thermal, moisture uptake and water barrier properties of the films were investigated. It was observed that with an increase in the alginate content there was an increase in the tensile strength and Young’s modulus of the films, whereas the water vapour permeability (WVP) of the films decreased. This was attributed to the greater cohesion between alginate polymer chains compared to the cohesion between xylan polymer chains. The xylanalginate films exhibited better optical and water sorption properties at higher xylan content. In order to improve the inherently poor mechanical and barrier properties of the xylan-alginate films, bentonite and halloysite were incorporated into the films. It was found that 5wt% incorporation of either bentonite or halloysite resulted in a 49% decrease of the WVP, which was attributed to water vapour impermeable nature of the silicate layers that make up both clays. The incorporation of the clays into the xylan-alginate matrix resulted in a significant
- Full Text:
- Date Issued: 2020
- Authors: Naidu, Darrel Sarvesh
- Date: 2020
- Subjects: Xylanases
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48544 , vital:40886
- Description: Currently a large number of chemicals and plastics are produced from petroleum-based resources. However, due to the concerns surrounding the depletion of petroleum resources and growing carbon emissions, there is a desire to produce chemicals and plastics from renewable and carbon natural sources. Lignocellulosic biomass (biomass consisting of cellulose, lignin and hemicellulose) is the most common biomass on earth and is renewable and carbon neutral. Of the three main constituents of lignocellulosic biomass, hemicellulose is composed of a mixture of sugars which can be converted into chemicals and plastics. The most common form of hemicellulose found in nature is xylan. This study is aimed at extracting xylan from maize stalk waste residues and the development of xylan films with properties that are suitable for food packaging applications. Xylan was extracted from maize stalk waste residues using an alkaline pre-treatment method. The effects of bleaching conditions (time, temperature and bleach concentration) prior to alkaline treatment on the yield and purity of xylan extracted was studied using a Box-Behnken experimental design. It was observed that the experimental conditions tested had no effect on the yield of the xylan extracted but the bleach concentration had a significant effect on the purity of the xylan extracted. The samples with the lowest lignin content were found to be the samples treated with 3wt% bleach prior to alkaline pre-treatment. One of the main disadvantages of xylan is that it has poor film forming properties, a method of overcoming this is to combine it with another abundantly available biopolymer that has good film forming properties, such as alginate. The effect of xylan, alginate and glycerol content on the mechanical, thermal, moisture uptake and water barrier properties of the films were investigated. It was observed that with an increase in the alginate content there was an increase in the tensile strength and Young’s modulus of the films, whereas the water vapour permeability (WVP) of the films decreased. This was attributed to the greater cohesion between alginate polymer chains compared to the cohesion between xylan polymer chains. The xylanalginate films exhibited better optical and water sorption properties at higher xylan content. In order to improve the inherently poor mechanical and barrier properties of the xylan-alginate films, bentonite and halloysite were incorporated into the films. It was found that 5wt% incorporation of either bentonite or halloysite resulted in a 49% decrease of the WVP, which was attributed to water vapour impermeable nature of the silicate layers that make up both clays. The incorporation of the clays into the xylan-alginate matrix resulted in a significant
- Full Text:
- Date Issued: 2020
Development of paper-based aptasensors for detection of Plasmodium falciparum lactate dehydrogenase in malaria
- Ogunmolasuyi, Adewoyin Martin
- Authors: Ogunmolasuyi, Adewoyin Martin
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164601 , vital:41147 , doi:10.21504/10962/164601
- Description: Thesis (PhD)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre, 2020
- Full Text:
- Date Issued: 2020
- Authors: Ogunmolasuyi, Adewoyin Martin
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164601 , vital:41147 , doi:10.21504/10962/164601
- Description: Thesis (PhD)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre, 2020
- Full Text:
- Date Issued: 2020
Dynamics of stimulated luminescence in natural quartz: Thermoluminescence and phototransferred thermoluminescence
- Authors: Folley, Damilola Esther
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146255 , vital:38509
- Description: Natural quartz has remained an important mineral that is of topical interest in luminescence and dosimetry-related research. We investigate the dynamics of stimulated luminescence on this material through thermoluminescence (TL) and phototransferred thermoluminescence (PTTL). Measurements were made on unannealed natural quartz as well as quartz annealed at 800 and 1000̊C. The samples were annealed for 10 minutes and for 1 hour. The material, in its un- and annealed state has its main peak between 68 and 72̊C when measured at 1Cs ̃1 after a dose of 50 Gy. A study of dosimetric features and kinetic analysis was carried out on two prominent peaks, peak I and III for all the samples. The peaks show a sublinear dose response for irradiation doses between 10 and 300 Gy. Kinetic analysis shows that peak I is a first-order peak and peak III a general-order peak. Interestingly, we observe for peak I for the sample annealed at 800̊C for 1 hour an inverse thermal quenching behaviour. We demonstrate that a peak affected with an inverse thermal quenching-like behaviour can still show effect of thermal quenching when the dose the sample is irradiated to is significantly reduced. We ascribe the apparent dependence of thermal quenching on dose to competition between radiative and non-radiative transitions at the recombination centre. Peaks I, II, and III for all the samples were reproduced under phototransfer when the peaks, initially removed by preheating to a certain temperature are exposed to 470 and 525 nm light. The infuence of duration of illumination on the PTTL intensity of these peaks corresponding to various preheating temperatures is modelled using coupled first-order dfferential equations. The model is based on systems of acceptors and donors whose number and role depends on preheating temperature
- Full Text:
- Date Issued: 2020
- Authors: Folley, Damilola Esther
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146255 , vital:38509
- Description: Natural quartz has remained an important mineral that is of topical interest in luminescence and dosimetry-related research. We investigate the dynamics of stimulated luminescence on this material through thermoluminescence (TL) and phototransferred thermoluminescence (PTTL). Measurements were made on unannealed natural quartz as well as quartz annealed at 800 and 1000̊C. The samples were annealed for 10 minutes and for 1 hour. The material, in its un- and annealed state has its main peak between 68 and 72̊C when measured at 1Cs ̃1 after a dose of 50 Gy. A study of dosimetric features and kinetic analysis was carried out on two prominent peaks, peak I and III for all the samples. The peaks show a sublinear dose response for irradiation doses between 10 and 300 Gy. Kinetic analysis shows that peak I is a first-order peak and peak III a general-order peak. Interestingly, we observe for peak I for the sample annealed at 800̊C for 1 hour an inverse thermal quenching behaviour. We demonstrate that a peak affected with an inverse thermal quenching-like behaviour can still show effect of thermal quenching when the dose the sample is irradiated to is significantly reduced. We ascribe the apparent dependence of thermal quenching on dose to competition between radiative and non-radiative transitions at the recombination centre. Peaks I, II, and III for all the samples were reproduced under phototransfer when the peaks, initially removed by preheating to a certain temperature are exposed to 470 and 525 nm light. The infuence of duration of illumination on the PTTL intensity of these peaks corresponding to various preheating temperatures is modelled using coupled first-order dfferential equations. The model is based on systems of acceptors and donors whose number and role depends on preheating temperature
- Full Text:
- Date Issued: 2020
Ecological assessment of a temperate river system using biomonitoring techniques: a case study of the Bloukrans River system, South Africa
- Authors: Magadze, Tinotenda
- Date: 2020
- Subjects: Bloukrans River , Ecological assessment (Biology) -- South Africa , Stream ecology -- South Africa , Rivers -- Environmental aspects -- South Africa , Benthic animals -- Effect of human beings on -- South Africa , Water quality biological assessment -- South Africa , Diatoms -- South Africa -- Data processing
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142933 , vital:38177
- Description: Escalating pressures from growing human populations and environmental impacts increasingly imperil freshwater ecosystems. The Bloukrans River, which drains an urbanised and agricultural catchment in the Eastern Cape province of South Africa, is no exception. Detailed knowledge of the structure and function of the aquatic ecosystems is required in order to create models and matrices that predict, guide assessment and direct intervention on ecological integrity and water quality management in these systems. The main objectives of this research were to: examine the effects of urbanization on the benthic macroinvertebrate functional feeding guild structure among different stream orders; determine if benthic diatoms can be used as effective and reliable indicators of ionic composition and conductivity in different stream order categories and finally; to evaluate the applicability of the South African Diatom Index (SADI) and other indices in the Eastern Cape region of South Africa. Field studies were carried out to explore temporal patterns in community structure (macroinvertebrates and diatoms) and ecosystem function related to land-use patterns, instream habitat availability, and water quality parameters in the Bloukrans River system across four study periods: February (summer) and July (winter) 2016 and February (summer) and May/July (winter) 2018. The study was conducted along a gradient of impacts from less impacted agricultural headwaters to highly impacted urban sites located immediately downstream of the city of Makhanda. Macroinvertebrates were separated into functional feeding groups (FFGs) (i.e. collector-gatherer, collector-filterer, scraper, shredder, and predator) which were then used to assess the effects of selected physico-chemical variables and riparian zone condition on FFG organization. Collector-gatherers were the most abundant in the Bloukrans River and represented 71.3 % of the macroinvertebrate assemblages. Stream order 1species such as Nitzschia palea, Gomphonema parvulum, Tryblionella apiculata, Diploneis vulgaris and Staurosira elliptica. Multivariate analysis (Canonical correspondence analysis (CCA)) indicated that differences in diatom community assemblages were best explained by calcium, magnesium, pH, phosphate, nitrate, dissolved oxygen, sediment nitrate, conductivity and salinity. These results indicate that diatoms can be used as bioindicators for monitoring highly impacted river systems and to also further examine pollution gradients and impacts of specific/point pollution sources. In order to further test the application of diatom indices, nine sites with contrasting water quality were sampled along the length river system in February, May and July 2018. Diatom-based indices incorporated in OMNIDIA software were applied to assess the integrity of the water quality as indicated by diatom communities. For comparative purposes, several foreign indices (e.g. the trophic diatom index (TDI), the percentage pollution-tolerant valves (%PTV), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. From the results, the Percentage Pollution-Tolerant Valves (%PTV) of most urban sites in the Bloukrans River was above the 20% limit indicating the presence of organic pollutants. Although the foreign diatom indices were applicable in the study, the SADI had significant correlations with most water quality variables (p < 0.05) compared to other indices such as Watanabe Index (WAT), Biological Index of Water Quality Trophic Index (BIWQ) and Trophic Index (TI)). These results support wider use of the SADI as an indicator of water quality conditions in South African river systems. Finally, the observed variations in diatom community structure and composition as a result of changes in water quality were broadly in agreement with the results of macroinvertebrate FFG structure indicating that the two biological indicators can, and should, be used as complementary techniques in the biomonitoring of rivers and streams in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Magadze, Tinotenda
- Date: 2020
- Subjects: Bloukrans River , Ecological assessment (Biology) -- South Africa , Stream ecology -- South Africa , Rivers -- Environmental aspects -- South Africa , Benthic animals -- Effect of human beings on -- South Africa , Water quality biological assessment -- South Africa , Diatoms -- South Africa -- Data processing
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142933 , vital:38177
- Description: Escalating pressures from growing human populations and environmental impacts increasingly imperil freshwater ecosystems. The Bloukrans River, which drains an urbanised and agricultural catchment in the Eastern Cape province of South Africa, is no exception. Detailed knowledge of the structure and function of the aquatic ecosystems is required in order to create models and matrices that predict, guide assessment and direct intervention on ecological integrity and water quality management in these systems. The main objectives of this research were to: examine the effects of urbanization on the benthic macroinvertebrate functional feeding guild structure among different stream orders; determine if benthic diatoms can be used as effective and reliable indicators of ionic composition and conductivity in different stream order categories and finally; to evaluate the applicability of the South African Diatom Index (SADI) and other indices in the Eastern Cape region of South Africa. Field studies were carried out to explore temporal patterns in community structure (macroinvertebrates and diatoms) and ecosystem function related to land-use patterns, instream habitat availability, and water quality parameters in the Bloukrans River system across four study periods: February (summer) and July (winter) 2016 and February (summer) and May/July (winter) 2018. The study was conducted along a gradient of impacts from less impacted agricultural headwaters to highly impacted urban sites located immediately downstream of the city of Makhanda. Macroinvertebrates were separated into functional feeding groups (FFGs) (i.e. collector-gatherer, collector-filterer, scraper, shredder, and predator) which were then used to assess the effects of selected physico-chemical variables and riparian zone condition on FFG organization. Collector-gatherers were the most abundant in the Bloukrans River and represented 71.3 % of the macroinvertebrate assemblages. Stream order 1species such as Nitzschia palea, Gomphonema parvulum, Tryblionella apiculata, Diploneis vulgaris and Staurosira elliptica. Multivariate analysis (Canonical correspondence analysis (CCA)) indicated that differences in diatom community assemblages were best explained by calcium, magnesium, pH, phosphate, nitrate, dissolved oxygen, sediment nitrate, conductivity and salinity. These results indicate that diatoms can be used as bioindicators for monitoring highly impacted river systems and to also further examine pollution gradients and impacts of specific/point pollution sources. In order to further test the application of diatom indices, nine sites with contrasting water quality were sampled along the length river system in February, May and July 2018. Diatom-based indices incorporated in OMNIDIA software were applied to assess the integrity of the water quality as indicated by diatom communities. For comparative purposes, several foreign indices (e.g. the trophic diatom index (TDI), the percentage pollution-tolerant valves (%PTV), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. From the results, the Percentage Pollution-Tolerant Valves (%PTV) of most urban sites in the Bloukrans River was above the 20% limit indicating the presence of organic pollutants. Although the foreign diatom indices were applicable in the study, the SADI had significant correlations with most water quality variables (p < 0.05) compared to other indices such as Watanabe Index (WAT), Biological Index of Water Quality Trophic Index (BIWQ) and Trophic Index (TI)). These results support wider use of the SADI as an indicator of water quality conditions in South African river systems. Finally, the observed variations in diatom community structure and composition as a result of changes in water quality were broadly in agreement with the results of macroinvertebrate FFG structure indicating that the two biological indicators can, and should, be used as complementary techniques in the biomonitoring of rivers and streams in South Africa.
- Full Text:
- Date Issued: 2020