Navigating Blackness in the African Diaspora
- Authors: Yates, Sarah
- Date: 2020
- Subjects: Ellison, Ralph. Invisible man , Everett, Percival. Erasure , Wicomb, Zoe. Playing in the light , Bulawayo, NoViolet. We need new names , Africans in literature , Race in literature , African fiction (English) -- History and criticism
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145720 , vital:38461
- Description: This thesis offers a comparative reading of Ralph Ellison’s Invisible Man, Percival Everett’s Erasure, Zoë Wicomb’s Playing in the Light and NoViolet Bulawayo’s We Need New Names in order to explore the diversity of subjectivities included within the terms ‘African’ and ‘black’ and to argue for the necessity of renewed definitions of Africa(nness) and blackness which allow for diverse and fluid representations. The diverse historical and political contexts in which these novels are published, as well as the critical and theoretical discussions which surround them demonstrate an evolution in literary portrayals of identity politics. As the categories of race and nation become more fluid, so too do narrative forms. In particular, this thesis is interested in the textual strategies authors use to navigate the various ways in which depictions of blackness continue to be restricted by racism, stereotypes, and the dynamics of a global literary market. As portrayals and discussions of identity politics proliferate in popular culture, they become increasingly commodified, and therefore increasingly restricted by the market.
- Full Text:
- Date Issued: 2020
- Authors: Yates, Sarah
- Date: 2020
- Subjects: Ellison, Ralph. Invisible man , Everett, Percival. Erasure , Wicomb, Zoe. Playing in the light , Bulawayo, NoViolet. We need new names , Africans in literature , Race in literature , African fiction (English) -- History and criticism
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145720 , vital:38461
- Description: This thesis offers a comparative reading of Ralph Ellison’s Invisible Man, Percival Everett’s Erasure, Zoë Wicomb’s Playing in the Light and NoViolet Bulawayo’s We Need New Names in order to explore the diversity of subjectivities included within the terms ‘African’ and ‘black’ and to argue for the necessity of renewed definitions of Africa(nness) and blackness which allow for diverse and fluid representations. The diverse historical and political contexts in which these novels are published, as well as the critical and theoretical discussions which surround them demonstrate an evolution in literary portrayals of identity politics. As the categories of race and nation become more fluid, so too do narrative forms. In particular, this thesis is interested in the textual strategies authors use to navigate the various ways in which depictions of blackness continue to be restricted by racism, stereotypes, and the dynamics of a global literary market. As portrayals and discussions of identity politics proliferate in popular culture, they become increasingly commodified, and therefore increasingly restricted by the market.
- Full Text:
- Date Issued: 2020
A holistic approach in understanding the effects of dietary protein sources on the growth and reproductive development of farmed abalone, Haliotis midae
- Wu, Yu
- Authors: Wu, Yu
- Date: 2020
- Subjects: Abalones -- Nutrition , Abalones -- Reproduction , Abalones -- Growth , Abalone culture , Haliotis midae -- Nutrition , Haliotis midae -- Reproduction , Haliotis midae -- Growth , Haliotis midae fisheries
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167719 , vital:41506
- Description: The combination of fishmeal and soya in the formulated feed of farmed South African abalone, Haliotis midae, not only improved abalone growth, but also the sustainability of the compound diets by reducing the reliance on fishmeal. However, the presence of soya produced larger gonads compared to those of abalone fed kelp or single-source protein diets. There is an increasing drive to control sexual maturation and reduce undesirable spawning events in farmed abalone. However, the reasons for the reported effects of soya inclusion on the reproductive development of farmed H. midae remain unresolved. The aim of this research was to use a combination of techniques to contribute to the understanding of the relationship between growth, reproductive and nutritional physiology of farmed H. midae fed diets of varying protein sources. These techniques included stable isotope analysis (SIA), fatty acid analysis, gonad histological assessments and haemolymph sexsteroid hormone analysis. The objectives were to examine the allocation of protein and nutritional components to somatic and reproductive tissues. This study also included the first attempt to investigate the role that sex steroid hormones play during gametogenesis. Abalone (40 – 50 g abalone-1) were fed one of four diets: either a single-source protein-based diet, i.e., (1) fishmeal-only (FM) or (2) soya-only (S), or a combination diet of (3) fishmeal-soya (FM S) or (4) fishmeal-sunflower meal (FM SM). Sampling occurred in 45-day intervals over one year. Dietary protein source had an effect on the growth of abalone, with enhancements in growth linked to the combination of fishmeal and a plant-protein source. The fishmeal ingredient was the most utilised protein source throughout the temporal changes in protein allocation into somatic and reproductive tissue, followed by soya and then sunflower meal. The mean whole- body mass of abalone was significantly influenced by an interaction between time and dietary treatment, with average whole-body mass changing differently over time between treatments (RM-ANOVA, F(24, 96) = 2.13, p = 0.005). Overall, abalone that were fed FM S had higher mean whole-body mass values than abalone that were fed the single-protein based diets, while abalone that were fed FM SM were similar to animals from all dietary treatments (RMANOVA, F(3, 12) = 5.75, p = 0.01). Male abalone had significantly higher gonad bulk index (GBI) values compared to females (RM-ANOVA, F(1, 24) = 49.03, p < 0.001) and this was independent of dietary treatment. Within each sex, female abalone fed the FM S diet (15.92 ± 1.88 mm3 g-1) had significantly higher GBI values than abalone fed S (9.76 ± 1.08 mm3 g-1), while abalone fed FM (11.96 ± 1.71 mm3 g-1) and FM SM (11.90 ± 0.80 mm3 g-1) were similar to abalone from all other dietary treatments (Tukey’s HSD, p < 0.05). Male abalone fed the FM S (21.59 ± 2.10 mm3 g-1) and FM SM diet (19.30 ± 2.63 mm3 g-1) had similar GBI values and they were significantly higher than in abalone fed the S diet (14.74 ± 1.27 mm3 g-1), while abalone fed FM S had significantly higher GBI values than abalone that consumed the FM diet (15.08 ±1.63mm3 g-1) ( Tukey’s HSD, p < 0.05). Although sunflower meal was poorly utilised, it produced similar overall growth to abalone that were fed the FM S diets. Yet, feed conversion ratio values were significantly lower for abalone fed FM S (1.30 ± 0.13) compared to those in the other three treatments, with ratios ranging from 1.65 – 1.72 over the one-year. The fatty acid compositions of the somatic and gonadal tissues were similar between treatments (PERMANOVA, p = 0.21), while fatty acid composition was influenced by sampling day, tissue type and abalone sex (PERMANOVA, p < 0.05). The essential fatty acids (EFAs) eicosadienoic acid and a-linolenic acid were present in abalone tissue, but they were not detected in the diets, suggesting the important role that an alternate food source (e.g. farmed abalone also had access to diatoms) may have played and the ability that H. midae may have in converting long-chain polyunsaturated fatty acids from C18 precursors. A change in the abundance of EFAs in the gonad tissue during highest and lowest GBI values suggested that arachidonic, eicosapentaenoic, g-linolenic and linoleic acid were important in females, while eicosapentaenoic, eicosadienoic and a-linolenic acid were important for male reproductive development. Dietary protein sources had an effect on the frequency distribution of maturity stages, where females that were fed FM S produced more ripe gonads and more males that were fed FM SM contained testes that showed signs of ripeness over the one-year study. Although dietary protein influenced the sex steroid concentrations in females and males, exhibiting fluctuations throughout the one-year period, no distinct pattern linked to gametogenesis were observed. The results from this study illustrate: (1) the importance of conducting laboratory studies when implementing SIA and mixing models in aquaculture nutrition; (2) conducting nutritional studies on mature, grow-out abalone; and (3) assessing the importance of naturally occurring diatoms in their diet and their contribution to growth and reproduction. The novel contribution of this research towards abalone nutritional physiology, the implications of these findings to industry as well as potential considerations for future studies were addressed.
- Full Text:
- Date Issued: 2020
- Authors: Wu, Yu
- Date: 2020
- Subjects: Abalones -- Nutrition , Abalones -- Reproduction , Abalones -- Growth , Abalone culture , Haliotis midae -- Nutrition , Haliotis midae -- Reproduction , Haliotis midae -- Growth , Haliotis midae fisheries
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167719 , vital:41506
- Description: The combination of fishmeal and soya in the formulated feed of farmed South African abalone, Haliotis midae, not only improved abalone growth, but also the sustainability of the compound diets by reducing the reliance on fishmeal. However, the presence of soya produced larger gonads compared to those of abalone fed kelp or single-source protein diets. There is an increasing drive to control sexual maturation and reduce undesirable spawning events in farmed abalone. However, the reasons for the reported effects of soya inclusion on the reproductive development of farmed H. midae remain unresolved. The aim of this research was to use a combination of techniques to contribute to the understanding of the relationship between growth, reproductive and nutritional physiology of farmed H. midae fed diets of varying protein sources. These techniques included stable isotope analysis (SIA), fatty acid analysis, gonad histological assessments and haemolymph sexsteroid hormone analysis. The objectives were to examine the allocation of protein and nutritional components to somatic and reproductive tissues. This study also included the first attempt to investigate the role that sex steroid hormones play during gametogenesis. Abalone (40 – 50 g abalone-1) were fed one of four diets: either a single-source protein-based diet, i.e., (1) fishmeal-only (FM) or (2) soya-only (S), or a combination diet of (3) fishmeal-soya (FM S) or (4) fishmeal-sunflower meal (FM SM). Sampling occurred in 45-day intervals over one year. Dietary protein source had an effect on the growth of abalone, with enhancements in growth linked to the combination of fishmeal and a plant-protein source. The fishmeal ingredient was the most utilised protein source throughout the temporal changes in protein allocation into somatic and reproductive tissue, followed by soya and then sunflower meal. The mean whole- body mass of abalone was significantly influenced by an interaction between time and dietary treatment, with average whole-body mass changing differently over time between treatments (RM-ANOVA, F(24, 96) = 2.13, p = 0.005). Overall, abalone that were fed FM S had higher mean whole-body mass values than abalone that were fed the single-protein based diets, while abalone that were fed FM SM were similar to animals from all dietary treatments (RMANOVA, F(3, 12) = 5.75, p = 0.01). Male abalone had significantly higher gonad bulk index (GBI) values compared to females (RM-ANOVA, F(1, 24) = 49.03, p < 0.001) and this was independent of dietary treatment. Within each sex, female abalone fed the FM S diet (15.92 ± 1.88 mm3 g-1) had significantly higher GBI values than abalone fed S (9.76 ± 1.08 mm3 g-1), while abalone fed FM (11.96 ± 1.71 mm3 g-1) and FM SM (11.90 ± 0.80 mm3 g-1) were similar to abalone from all other dietary treatments (Tukey’s HSD, p < 0.05). Male abalone fed the FM S (21.59 ± 2.10 mm3 g-1) and FM SM diet (19.30 ± 2.63 mm3 g-1) had similar GBI values and they were significantly higher than in abalone fed the S diet (14.74 ± 1.27 mm3 g-1), while abalone fed FM S had significantly higher GBI values than abalone that consumed the FM diet (15.08 ±1.63mm3 g-1) ( Tukey’s HSD, p < 0.05). Although sunflower meal was poorly utilised, it produced similar overall growth to abalone that were fed the FM S diets. Yet, feed conversion ratio values were significantly lower for abalone fed FM S (1.30 ± 0.13) compared to those in the other three treatments, with ratios ranging from 1.65 – 1.72 over the one-year. The fatty acid compositions of the somatic and gonadal tissues were similar between treatments (PERMANOVA, p = 0.21), while fatty acid composition was influenced by sampling day, tissue type and abalone sex (PERMANOVA, p < 0.05). The essential fatty acids (EFAs) eicosadienoic acid and a-linolenic acid were present in abalone tissue, but they were not detected in the diets, suggesting the important role that an alternate food source (e.g. farmed abalone also had access to diatoms) may have played and the ability that H. midae may have in converting long-chain polyunsaturated fatty acids from C18 precursors. A change in the abundance of EFAs in the gonad tissue during highest and lowest GBI values suggested that arachidonic, eicosapentaenoic, g-linolenic and linoleic acid were important in females, while eicosapentaenoic, eicosadienoic and a-linolenic acid were important for male reproductive development. Dietary protein sources had an effect on the frequency distribution of maturity stages, where females that were fed FM S produced more ripe gonads and more males that were fed FM SM contained testes that showed signs of ripeness over the one-year study. Although dietary protein influenced the sex steroid concentrations in females and males, exhibiting fluctuations throughout the one-year period, no distinct pattern linked to gametogenesis were observed. The results from this study illustrate: (1) the importance of conducting laboratory studies when implementing SIA and mixing models in aquaculture nutrition; (2) conducting nutritional studies on mature, grow-out abalone; and (3) assessing the importance of naturally occurring diatoms in their diet and their contribution to growth and reproduction. The novel contribution of this research towards abalone nutritional physiology, the implications of these findings to industry as well as potential considerations for future studies were addressed.
- Full Text:
- Date Issued: 2020
Formulation development, manufacture and evaluation of a lamivudine-zidovudine nano co-crystal thermo-responsive suspension
- Authors: Witika, Bwalya Angel
- Date: 2020
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140546 , vital:37897 , http://dx.doi.org/10.21504/10962/140546
- Description: Expected release date-April 2021
- Full Text:
- Date Issued: 2020
- Authors: Witika, Bwalya Angel
- Date: 2020
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140546 , vital:37897 , http://dx.doi.org/10.21504/10962/140546
- Description: Expected release date-April 2021
- 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
Identifying a Successful Accounting Student: Profiling of Postgraduate Accounting Students in the Eastern Cape
- Authors: Weldon, Lana Joy
- Date: 2020
- Subjects: Personality -- South Africa -- Eastern Cape , Accounting -- Study and teaching (Higher) -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50699 , vital:42343
- Description: Throughput rates and transformation have long been considered major challenges to accounting departments in South Africa. While much research has been done on various aspects of study techniques in an attempt to assist students to succeed, little attention has been paid to profiling students to ascertain whether there are common traits in terms of personality, aptitude, values and motives, which distinguish successful students from others. This study looks at these factors and uses sub-tests of the Differential Aptitude Test (DAT), selected with reference to the South African Institute of Chartered Accountants (SAICA) Competency Framework, to determine the correlation between these aptitudes and the success of accounting students. In addition, the impact of biographical data, including gender, race and type of school attended, is considered on the success of the students and the individual sub-tests of aptitude. The study then considers the impact of various personality types, personality traits and values on the success or failure of accounting students, and finally seeks to ascertain whether there is a holistic profile of a student who has a statistically significant chance of succeeding in accounting studies. Results indicate that the sub-tests of aptitude for verbal reasoning and reading comprehension have the most significance in predicting student success and that gender and race have a medium effect. Furthermore, personality types, personality traits and values do not have a significant impact on student success. The only biographical factor to have an impact on success was race. Despite the findings in the individual factors considered, no distinct personality profile of a successful Results indicate that the sub-tests of aptitude for verbal reasoning and reading comprehension have the most significance in predicting student success and that gender and race have a medium effect. Furthermore, personality types, personality traits and values do not have a significant impact on student success. The only biographical factor to have an impact on success was race. Despite the findings in the individual factors considered, no distinct personality profile of a successful accounting student emerged. Future research on the use of literacy competency assessments in the admission requirements for chartered accounting programmes, or to inform student academic support initiatives is recommended. accounting student emerged. Future research on the use of literacy competency assessments in the admission requirements for chartered accounting programmes, or to inform student academic support initiatives is recommended.
- Full Text:
- Date Issued: 2020
- Authors: Weldon, Lana Joy
- Date: 2020
- Subjects: Personality -- South Africa -- Eastern Cape , Accounting -- Study and teaching (Higher) -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50699 , vital:42343
- Description: Throughput rates and transformation have long been considered major challenges to accounting departments in South Africa. While much research has been done on various aspects of study techniques in an attempt to assist students to succeed, little attention has been paid to profiling students to ascertain whether there are common traits in terms of personality, aptitude, values and motives, which distinguish successful students from others. This study looks at these factors and uses sub-tests of the Differential Aptitude Test (DAT), selected with reference to the South African Institute of Chartered Accountants (SAICA) Competency Framework, to determine the correlation between these aptitudes and the success of accounting students. In addition, the impact of biographical data, including gender, race and type of school attended, is considered on the success of the students and the individual sub-tests of aptitude. The study then considers the impact of various personality types, personality traits and values on the success or failure of accounting students, and finally seeks to ascertain whether there is a holistic profile of a student who has a statistically significant chance of succeeding in accounting studies. Results indicate that the sub-tests of aptitude for verbal reasoning and reading comprehension have the most significance in predicting student success and that gender and race have a medium effect. Furthermore, personality types, personality traits and values do not have a significant impact on student success. The only biographical factor to have an impact on success was race. Despite the findings in the individual factors considered, no distinct personality profile of a successful Results indicate that the sub-tests of aptitude for verbal reasoning and reading comprehension have the most significance in predicting student success and that gender and race have a medium effect. Furthermore, personality types, personality traits and values do not have a significant impact on student success. The only biographical factor to have an impact on success was race. Despite the findings in the individual factors considered, no distinct personality profile of a successful accounting student emerged. Future research on the use of literacy competency assessments in the admission requirements for chartered accounting programmes, or to inform student academic support initiatives is recommended. accounting student emerged. Future research on the use of literacy competency assessments in the admission requirements for chartered accounting programmes, or to inform student academic support initiatives is recommended.
- Full Text:
- Date Issued: 2020
The role of microhabitats within mangroves: an invertebrate and fish larval perspective
- Authors: Vorsatz, Lyle Dennis
- Date: 2020
- Subjects: Mangrove ecology -- South Africa , Mangrove forests -- South Africa , Niche (Ecology) , Rhizophora mucronata , Acanthaceae , Rhizophoraceae , Fishes -- Larvae -- South Africa , Aquatic ecology -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167644 , vital:41499
- Description: Microhabitats provided through structural complexity are central for the diversity, productivity, connectivity and niche differentiation within and among ecosystems. Mangrove forests afford juvenile fish and invertebrates with nursery and recruitment habitats, facilitated by the fine scale configuration of their specialised root systems. Although the importance of mangroves for resident and transient juveniles is well recognised, the roles that mangrove microhabitats play for larvae is not yet comprehensively understood. This study aimed to determine how microhabitats with varying degrees of complexity influence the composition, abundance and distribution of larval communities that inhabit mangrove forests and the physiological responses of larvae to acute temperature variations in relation to ontogenetic stage and microenvironment exposure. Two relatively pristine study sites were selected to represent a warm temperate and subtropical mangrove system in the Eastern Cape and KwaZulu-Natal on the east coast of South Africa, respectively. The differences in complexity among the root systems of Rhizophora mucronata, Avicennia marina and Bruguiera gymnorhiza were assessed using 3D scanning and the computed 3D models were then analysed using four complexity metrics. Results indicated that A. marina is the most complex in terms of surface-volume ratio, R. mucronata has the most interstitial space among its roots and B. gymnorhiza and R. mucronata differ in their fractal dimensions. Larvae collected in each microhabitat at each site using light traps showed that, despite temperature and salinity homogeneity across microenvironments, spatio-temporal differences occurred in both fish and invertebrate assemblages. This trend suggests that microhabitat structural complexity exerts an influence on larval community composition by acting as a microscape of available habitat, which ensures ecological linkages within and among the mangrove forest and adjacent ecosystems. In addition, the oxygen consumption rates of mangrove-associated brachyuran larvae varied according to mangrove microhabitat, whereby larvae collected at less complex environments had the highest metabolic rates at increased temperatures. Moreover, ontogenetic shifts in physiology were prevalent as older brachyuran larvae were more eurythermal than earlier stages, suggesting that thermally stressful events will have a greater impact on recently spawned larvae. Overall, the interstitial spaces within individual root systems are the most important complexity measure, as utilisation of these mangrove microhabitats is scale-dependent, and larvae will most likely occupy spaces inaccessible to large predators. Likewise, microscale variation in the environmental conditions and ontogenetic stage of brachyuran larvae within the mangrove microscape, can amplify the physiological responses to rapid temperature variations. Results suggest that early stage larvae are the most vulnerable to mass-mortality, and if thermally stressful events increase in frequency, duration and magnitude, the larval supply for the successful recruitment into adult populations could be under threat. Through linking how mangrove microhabitat complexity influences larvae in terms of community metrics and physiology, this study paves the way for further advancement of our understanding of how microscale processes emerge into meso- and macroscale patterns and influence the stability and functioning of highly productive ecosystems.
- Full Text:
- Date Issued: 2020
- Authors: Vorsatz, Lyle Dennis
- Date: 2020
- Subjects: Mangrove ecology -- South Africa , Mangrove forests -- South Africa , Niche (Ecology) , Rhizophora mucronata , Acanthaceae , Rhizophoraceae , Fishes -- Larvae -- South Africa , Aquatic ecology -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167644 , vital:41499
- Description: Microhabitats provided through structural complexity are central for the diversity, productivity, connectivity and niche differentiation within and among ecosystems. Mangrove forests afford juvenile fish and invertebrates with nursery and recruitment habitats, facilitated by the fine scale configuration of their specialised root systems. Although the importance of mangroves for resident and transient juveniles is well recognised, the roles that mangrove microhabitats play for larvae is not yet comprehensively understood. This study aimed to determine how microhabitats with varying degrees of complexity influence the composition, abundance and distribution of larval communities that inhabit mangrove forests and the physiological responses of larvae to acute temperature variations in relation to ontogenetic stage and microenvironment exposure. Two relatively pristine study sites were selected to represent a warm temperate and subtropical mangrove system in the Eastern Cape and KwaZulu-Natal on the east coast of South Africa, respectively. The differences in complexity among the root systems of Rhizophora mucronata, Avicennia marina and Bruguiera gymnorhiza were assessed using 3D scanning and the computed 3D models were then analysed using four complexity metrics. Results indicated that A. marina is the most complex in terms of surface-volume ratio, R. mucronata has the most interstitial space among its roots and B. gymnorhiza and R. mucronata differ in their fractal dimensions. Larvae collected in each microhabitat at each site using light traps showed that, despite temperature and salinity homogeneity across microenvironments, spatio-temporal differences occurred in both fish and invertebrate assemblages. This trend suggests that microhabitat structural complexity exerts an influence on larval community composition by acting as a microscape of available habitat, which ensures ecological linkages within and among the mangrove forest and adjacent ecosystems. In addition, the oxygen consumption rates of mangrove-associated brachyuran larvae varied according to mangrove microhabitat, whereby larvae collected at less complex environments had the highest metabolic rates at increased temperatures. Moreover, ontogenetic shifts in physiology were prevalent as older brachyuran larvae were more eurythermal than earlier stages, suggesting that thermally stressful events will have a greater impact on recently spawned larvae. Overall, the interstitial spaces within individual root systems are the most important complexity measure, as utilisation of these mangrove microhabitats is scale-dependent, and larvae will most likely occupy spaces inaccessible to large predators. Likewise, microscale variation in the environmental conditions and ontogenetic stage of brachyuran larvae within the mangrove microscape, can amplify the physiological responses to rapid temperature variations. Results suggest that early stage larvae are the most vulnerable to mass-mortality, and if thermally stressful events increase in frequency, duration and magnitude, the larval supply for the successful recruitment into adult populations could be under threat. Through linking how mangrove microhabitat complexity influences larvae in terms of community metrics and physiology, this study paves the way for further advancement of our understanding of how microscale processes emerge into meso- and macroscale patterns and influence the stability and functioning of highly productive ecosystems.
- Full Text:
- Date Issued: 2020
“A position of great trust and responsibility”: a social history of the Grahamstown Asylum, 1875 – c. 1905
- Authors: Van Zyl, Kylie
- Date: 2020
- Subjects: Mental health services -- South Africa -- Cape of Good Hope , Psychiatric hospitals -- South Africa -- History , South Africa -- Race relations -- Social aspects , Mentally ill -- Commitment and detention -- South Africa , Mentally ill -- Abuse of -- South Africa , Mental health policy -- South Africa , Asylums -- South Africa -- Grahamstown , Discrimination in mental health services -- South Africa , Health and race -- South Africa -- History
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/151031 , vital:39025
- Description: Much has been written about the inequalities inherent in the psychiatric care provided to mentally ill individuals in the Cape Colony, but to date few works have been produced that describe in detail the processes and care regimes at particular institutions. This thesis examines the history of care and custody provided by the Grahamstown Asylum in the Cape between the years of 1875 and 1905. The intention is to determine the means and methods by which the Asylum’s authorities developed, almost unchallenged, a system of unequal treatment and favouritism within that facility, and what this meant for the men and women committed to the Asylum’s custody. To this end, contemporaneous official reports from Asylum staff and Colonial authorities were consulted, in conjunction with the Asylum’s internal records such as registers and individual patient files. This thesis concludes that the evolution of the Colony’s psychiatric community’s beliefs around mental illness, philosophies of protective custody and moral treatment within the psychiatric community at the time, the region’s laws governing psychiatric institutionalisation, and the larger context of the Cape’s socio-political environment at the time converged to create an institution that practiced discrimination on both a macro- and micro-level. This discriminatory framework affected who was admitted, the diagnosis that each person received, the asylum facilities to which they had access, and further, to the odds against their recovery. The implications of this study are relevant in the present day, as the modern South African system of psychiatric institutionalisation, though embedded within a socio-political context of equality and non-discrimination nevertheless appears to suffer from a similarly undemocratic framework of operation.
- Full Text:
- Date Issued: 2020
- Authors: Van Zyl, Kylie
- Date: 2020
- Subjects: Mental health services -- South Africa -- Cape of Good Hope , Psychiatric hospitals -- South Africa -- History , South Africa -- Race relations -- Social aspects , Mentally ill -- Commitment and detention -- South Africa , Mentally ill -- Abuse of -- South Africa , Mental health policy -- South Africa , Asylums -- South Africa -- Grahamstown , Discrimination in mental health services -- South Africa , Health and race -- South Africa -- History
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/151031 , vital:39025
- Description: Much has been written about the inequalities inherent in the psychiatric care provided to mentally ill individuals in the Cape Colony, but to date few works have been produced that describe in detail the processes and care regimes at particular institutions. This thesis examines the history of care and custody provided by the Grahamstown Asylum in the Cape between the years of 1875 and 1905. The intention is to determine the means and methods by which the Asylum’s authorities developed, almost unchallenged, a system of unequal treatment and favouritism within that facility, and what this meant for the men and women committed to the Asylum’s custody. To this end, contemporaneous official reports from Asylum staff and Colonial authorities were consulted, in conjunction with the Asylum’s internal records such as registers and individual patient files. This thesis concludes that the evolution of the Colony’s psychiatric community’s beliefs around mental illness, philosophies of protective custody and moral treatment within the psychiatric community at the time, the region’s laws governing psychiatric institutionalisation, and the larger context of the Cape’s socio-political environment at the time converged to create an institution that practiced discrimination on both a macro- and micro-level. This discriminatory framework affected who was admitted, the diagnosis that each person received, the asylum facilities to which they had access, and further, to the odds against their recovery. The implications of this study are relevant in the present day, as the modern South African system of psychiatric institutionalisation, though embedded within a socio-political context of equality and non-discrimination nevertheless appears to suffer from a similarly undemocratic framework of operation.
- Full Text:
- Date Issued: 2020
Thermal tolerance and the potential effects of climate change on coastal intertidal and estuarine organisms in the Kariega Estuary and adjacent intertitdal coastline, Eastern Cape, South Africa
- Authors: Van der Walt, Kerry-Ann
- Date: 2020
- Subjects: Ectotherms -- Climatic factors , Ectotherms -- Effect of temperature on , Fishes -- Climatic factors , Fishes -- Effect of temperature on , Climatic changes -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/148459 , vital:38741
- Description: Temperature changes due to the effects of climate change are evident on all continents and oceans. As a result, there is a growing concern over how marine ectotherms will respond to extreme or fluctuating environmental temperatures. Temperature changes have strong direct and indirect effects on individual, population, and ecosystem functioning traits. A multi-scale approach determining the thermal tolerance and performance of several marine ectotherms belonging to different coastal habitats is rarely considered in thermal physiology studies but is effective for an integrated ecosystem assessment. As such, for this thesis, I aimed to quantify and compare the thermal tolerance and performance of a range of coastal marine ectotherms (fish and macro-invertebrates) with different biogeographical distributions from estuarine, subtidal and rocky intertidal habitats to available and projected in situ temperature data. This was also undertaken to gauge the local vulnerability of each species across summer and winter in a warm-temperate region of South Africa. This was done using a multi-method physiological approach, which included the dynamic method (CTmax and CTmin), static respirometry and maximum heart rate fHmax). Results of the dynamic method on several fish and macro-invertebrate species indicated that there are differences in thermal tolerance according to taxonomy, biogeography and habitat for both summer and winter. Macro-invertebrate species generally had higher CTmax endpoints, lower CTmin endpoints, higher upper and lower breadths in tolerance, higher upper and lower thermal safety margins and higher thermal scopes than the fish species. This could be a result of the macro-invertebrate species studied being less mobile compared with fish species (which are able to move to more favourable conditions) as well as having broader geographical distributions. In addition, macro-invertebrates from the intertidal rock pool habitat (Palaemon peringueyi; Pernaperna) were more tolerant of high and low temperatures compared with the macro-invertebrates from the estuarine habitat (Clibanarius virescens; Parasesarma catenatum; Upogebia africana). Overall, macro-invertebrates, with the exception of Parechinus angulosus, investigated in this study indicated that current temperatures and projected climate change scenarios across seasons would not have a significant impact on them and that they are highly adaptable to changing temperature regimes. This sign of high tolerance was further supported by the heart rates of P. perna and P. catenatum under an acute increase in temperature (1.0 °C.h-1) which showed individuals of each species physiologically depressing their metabolism until a final Arrhenius breakpoint temperature was reached (TAB). Among the fish species investigated in this study, tropical species (Chaetodon marleyi; Kuhlia mugil) had the highest CTmax and CTmin endpoints when compared with the temperate (Diplodus capensis; Sarpa salpa), warm-water endemic (Chelon dumerili; Rhabdosargus holubi) and cool-water endemic (Chelon richardsonii) fishes. This suggests that due to their lower breadths in tolerance and thermal safety margins being small, tropical species may be less tolerant of cold temperatures and thermal variability, especially in the form of summer upwelling events which are expected to increase in intensity and frequency in this region as a result of anthropogenic climate change effects. On the other hand, however, if a temperature increase of 2.0 - 4.0 °C takes place at the end of the century as predicted by the Intergovernmental Panel on Climate Change (IPCC), it is likely that tropical species such as C. marleyi will become more common. Temperate species such as D. capensis and S. salpa were able to tolerate a wide range of temperatures (wide thermal scope) compared with the other fish species. These findings may suggest that D. capensis and S. salpa are thermally resilient and may be the least vulnerable to climate change effects and temperature variability. When evaluating the different life stages of D. capensis, however, using the dynamic method (juveniles and adults), static respirometry (juveniles) and maximum heart rate (adults), results suggested that juveniles of this temperate species will be more resilient to increases in ocean temperatures compared with the adults because they have a higher thermal tolerance (CTmax/TCRIT) and a greater metabolic scope (TOPT) at higher temperatures. For both juveniles and adults, temperatures beyond 28.0 °C (upper Tpej; Tarr) will have a significant impact on their physiology. Using a multi-scale and multi-method approach thus helped to identify which species or community may be vulnerable to the effects of climate change within shallow coastal environments in this warm-temperate climate change hotspot. Adopting this type of approach will assist policy makers in developing comprehensive climate change management frameworks for coastal ecosystems globally and around South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Van der Walt, Kerry-Ann
- Date: 2020
- Subjects: Ectotherms -- Climatic factors , Ectotherms -- Effect of temperature on , Fishes -- Climatic factors , Fishes -- Effect of temperature on , Climatic changes -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/148459 , vital:38741
- Description: Temperature changes due to the effects of climate change are evident on all continents and oceans. As a result, there is a growing concern over how marine ectotherms will respond to extreme or fluctuating environmental temperatures. Temperature changes have strong direct and indirect effects on individual, population, and ecosystem functioning traits. A multi-scale approach determining the thermal tolerance and performance of several marine ectotherms belonging to different coastal habitats is rarely considered in thermal physiology studies but is effective for an integrated ecosystem assessment. As such, for this thesis, I aimed to quantify and compare the thermal tolerance and performance of a range of coastal marine ectotherms (fish and macro-invertebrates) with different biogeographical distributions from estuarine, subtidal and rocky intertidal habitats to available and projected in situ temperature data. This was also undertaken to gauge the local vulnerability of each species across summer and winter in a warm-temperate region of South Africa. This was done using a multi-method physiological approach, which included the dynamic method (CTmax and CTmin), static respirometry and maximum heart rate fHmax). Results of the dynamic method on several fish and macro-invertebrate species indicated that there are differences in thermal tolerance according to taxonomy, biogeography and habitat for both summer and winter. Macro-invertebrate species generally had higher CTmax endpoints, lower CTmin endpoints, higher upper and lower breadths in tolerance, higher upper and lower thermal safety margins and higher thermal scopes than the fish species. This could be a result of the macro-invertebrate species studied being less mobile compared with fish species (which are able to move to more favourable conditions) as well as having broader geographical distributions. In addition, macro-invertebrates from the intertidal rock pool habitat (Palaemon peringueyi; Pernaperna) were more tolerant of high and low temperatures compared with the macro-invertebrates from the estuarine habitat (Clibanarius virescens; Parasesarma catenatum; Upogebia africana). Overall, macro-invertebrates, with the exception of Parechinus angulosus, investigated in this study indicated that current temperatures and projected climate change scenarios across seasons would not have a significant impact on them and that they are highly adaptable to changing temperature regimes. This sign of high tolerance was further supported by the heart rates of P. perna and P. catenatum under an acute increase in temperature (1.0 °C.h-1) which showed individuals of each species physiologically depressing their metabolism until a final Arrhenius breakpoint temperature was reached (TAB). Among the fish species investigated in this study, tropical species (Chaetodon marleyi; Kuhlia mugil) had the highest CTmax and CTmin endpoints when compared with the temperate (Diplodus capensis; Sarpa salpa), warm-water endemic (Chelon dumerili; Rhabdosargus holubi) and cool-water endemic (Chelon richardsonii) fishes. This suggests that due to their lower breadths in tolerance and thermal safety margins being small, tropical species may be less tolerant of cold temperatures and thermal variability, especially in the form of summer upwelling events which are expected to increase in intensity and frequency in this region as a result of anthropogenic climate change effects. On the other hand, however, if a temperature increase of 2.0 - 4.0 °C takes place at the end of the century as predicted by the Intergovernmental Panel on Climate Change (IPCC), it is likely that tropical species such as C. marleyi will become more common. Temperate species such as D. capensis and S. salpa were able to tolerate a wide range of temperatures (wide thermal scope) compared with the other fish species. These findings may suggest that D. capensis and S. salpa are thermally resilient and may be the least vulnerable to climate change effects and temperature variability. When evaluating the different life stages of D. capensis, however, using the dynamic method (juveniles and adults), static respirometry (juveniles) and maximum heart rate (adults), results suggested that juveniles of this temperate species will be more resilient to increases in ocean temperatures compared with the adults because they have a higher thermal tolerance (CTmax/TCRIT) and a greater metabolic scope (TOPT) at higher temperatures. For both juveniles and adults, temperatures beyond 28.0 °C (upper Tpej; Tarr) will have a significant impact on their physiology. Using a multi-scale and multi-method approach thus helped to identify which species or community may be vulnerable to the effects of climate change within shallow coastal environments in this warm-temperate climate change hotspot. Adopting this type of approach will assist policy makers in developing comprehensive climate change management frameworks for coastal ecosystems globally and around South Africa.
- Full Text:
- Date Issued: 2020
A personality-based surveillance model for Facebook apps
- Authors: Van der Schyff, Karl Izak
- Date: 2020
- Subjects: Facebook (Electronic resource) , Electronic surveillance -- Psychological aspects , Online social networks -- Psychological aspects , Social media -- Psychological aspects , Personality
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145534 , vital:38447
- Description: The surveillance of data through the use of Facebook Apps is an ongoing and persistent problem that impacts millions of users. Nonetheless, limited research has been conducted investigating to what extent a Facebook user’s personality influences their awareness of such surveillance practices. Thus, to understand this situation better, the current study inductively developed four propositions from secondary data sources as part of a detailed content analysis. Spanning three search and analysis phases the content analysis led to the development of the research model. Guided by the propositions and research questions, a questionnaire was developed based on the relevant constructs prescribed by the Theory of Planned Behaviour. This questionnaire was used, and a total of 651 responses were collected from Facebook users over the age of 18 years old and residing in the United States of America. Primary data took place at both a univariate and multivariate level with a specific focus on the development of a structural model. Interpretation of the structural model revealed that out of all the Big Five personality traits, Conscientiousness exhibited the strongest relationship with information security awareness followed by Openness to Experience and Neuroticism, respectively. The results further indicated that the model constructs based on attitude, social norms and awareness significantly influenced the intended use of Facebook Apps. The study also contributes by indicating which personality traits are most vulnerable to Facebook App surveillance. For example, it was found that individuals high in Conscientiousness are the least vulnerable with individuals high in Extraversion being the most vulnerable. Since the results indicate that not all the personality traits are significantly related to the model constructs, additional factors may contribute to App surveillance in this context. Concerning this, factors such as user apathy, information privacy, privacy concerns, control and Facebook dependency are discussed as a means to argue why this might be the case.
- Full Text:
- Date Issued: 2020
- Authors: Van der Schyff, Karl Izak
- Date: 2020
- Subjects: Facebook (Electronic resource) , Electronic surveillance -- Psychological aspects , Online social networks -- Psychological aspects , Social media -- Psychological aspects , Personality
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145534 , vital:38447
- Description: The surveillance of data through the use of Facebook Apps is an ongoing and persistent problem that impacts millions of users. Nonetheless, limited research has been conducted investigating to what extent a Facebook user’s personality influences their awareness of such surveillance practices. Thus, to understand this situation better, the current study inductively developed four propositions from secondary data sources as part of a detailed content analysis. Spanning three search and analysis phases the content analysis led to the development of the research model. Guided by the propositions and research questions, a questionnaire was developed based on the relevant constructs prescribed by the Theory of Planned Behaviour. This questionnaire was used, and a total of 651 responses were collected from Facebook users over the age of 18 years old and residing in the United States of America. Primary data took place at both a univariate and multivariate level with a specific focus on the development of a structural model. Interpretation of the structural model revealed that out of all the Big Five personality traits, Conscientiousness exhibited the strongest relationship with information security awareness followed by Openness to Experience and Neuroticism, respectively. The results further indicated that the model constructs based on attitude, social norms and awareness significantly influenced the intended use of Facebook Apps. The study also contributes by indicating which personality traits are most vulnerable to Facebook App surveillance. For example, it was found that individuals high in Conscientiousness are the least vulnerable with individuals high in Extraversion being the most vulnerable. Since the results indicate that not all the personality traits are significantly related to the model constructs, additional factors may contribute to App surveillance in this context. Concerning this, factors such as user apathy, information privacy, privacy concerns, control and Facebook dependency are discussed as a means to argue why this might be the case.
- Full Text:
- Date Issued: 2020
“Don’t be alarmed. It’s to do with sex.” Sherlock Holmes fanfiction and freedom of the imaginary domain
- Authors: van der Nest, Megan
- Date: 2020
- Subjects: Fan fiction , Fans (Persons) -- Fiction , Holmes, Sherlock , Literature and the internet , Sex in literature
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/124208 , vital:35576
- Description: In this thesis I argue that, for the individual fan, reading and writing fanfiction texts, and engaging with the online fandom communities within which these texts are produced, is a potentially valuable experience. This is because the kind of social and creative spaces found in these communities allow for, and celebrate, the free imaginative play with romantic and sexual desires, identities, and relationships. To articulate the importance of these spaces, I draw on Drucilla Cornell’s concept of the imaginary domain, defined as the psychic space each individual uses to explore different sexual desires and personae, which exploration is necessary for the development of full personhood. I also argue that the growing visibility and influence of fandom in modern society means that it could serve as a mechanism for social change, particularly in the acceptance and support of multiple sexual identities and forms of love. Selected texts, drawn from the Sherlock fandom, are discussed as representative of the approach taken within fanfiction communities towards various aspects of sexuality and sexual ethics. This approach combines the enthusiastic exploration of sexual desires without shame or fear of judgment with an ongoing, critical interrogation of sexual ethics.
- Full Text:
- Date Issued: 2020
- Authors: van der Nest, Megan
- Date: 2020
- Subjects: Fan fiction , Fans (Persons) -- Fiction , Holmes, Sherlock , Literature and the internet , Sex in literature
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/124208 , vital:35576
- Description: In this thesis I argue that, for the individual fan, reading and writing fanfiction texts, and engaging with the online fandom communities within which these texts are produced, is a potentially valuable experience. This is because the kind of social and creative spaces found in these communities allow for, and celebrate, the free imaginative play with romantic and sexual desires, identities, and relationships. To articulate the importance of these spaces, I draw on Drucilla Cornell’s concept of the imaginary domain, defined as the psychic space each individual uses to explore different sexual desires and personae, which exploration is necessary for the development of full personhood. I also argue that the growing visibility and influence of fandom in modern society means that it could serve as a mechanism for social change, particularly in the acceptance and support of multiple sexual identities and forms of love. Selected texts, drawn from the Sherlock fandom, are discussed as representative of the approach taken within fanfiction communities towards various aspects of sexuality and sexual ethics. This approach combines the enthusiastic exploration of sexual desires without shame or fear of judgment with an ongoing, critical interrogation of sexual ethics.
- Full Text:
- Date Issued: 2020
Hop as an anti-cancer drug target
- Vaaltyn, Michaelone Chantelle
- Authors: Vaaltyn, Michaelone Chantelle
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164704 , vital:41156 , doi:10.21504/10962/164704
- Description: Thesis (PhD)--Rhodes University, Biochemistry and Microbiology, 2020
- Full Text:
- Date Issued: 2020
- Authors: Vaaltyn, Michaelone Chantelle
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164704 , vital:41156 , doi:10.21504/10962/164704
- Description: Thesis (PhD)--Rhodes University, Biochemistry and Microbiology, 2020
- Full Text:
- Date Issued: 2020
Multiplexed Mass Spectrometry: Single, On-Bead, Detection Analysis Using MALDI-TOF MS
- Authors: Twala, Busisiwe Victoria
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164693 , vital:41155 , doi:10.21504/10962/164693
- Description: Thesis (PhD)--Rhodes University, Biochemistry and Microbiology, 2020
- Full Text:
- Date Issued: 2020
- Authors: Twala, Busisiwe Victoria
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/164693 , vital:41155 , doi:10.21504/10962/164693
- Description: Thesis (PhD)--Rhodes University, Biochemistry and Microbiology, 2020
- Full Text:
- Date Issued: 2020
Resource recovery options in brewery effluent treatment using activated sludge and high rate algal ponds: assessing environmental impacts
- Authors: Taylor, Richard Peter
- Date: 2020
- Subjects: Sewage -- Purification -- Activated sludge process , Sewage disposal plants , Sewage -- Purification -- Biological treatament , Sewage -- Purification -- Nitrogen removal , Brewery waste , Breweries -- Waste disposal , Microalgae -- Biotechnology , Algal biofuels
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/153746 , vital:39507
- Description: Wastewater treatment plants (WWTPs) are designed to clean effluents, but they also consume resources and produce waste. Various treatment technologies allow for the recovery of energy, nutrients and water from effluents turning this waste into products, which increases their sustainability and decreases the impact of WWTPs on the environment. There is a lack of literature which comprehensively compares the treatment performances, environmental impacts and beneficial downstream uses of the biomass generated by high rate algal pond (HRAP) and activated sludge (AS) treatment systems. This thesis aimed to compare (1) effluent treatment performance, (2) emissions and (3) downstream use of algae cultured in HRAP to sludge produced in AS and to obtain data to conduct a life cycle analysis (LCA) to compare the systems. The focus was on adding value to the effluent treatment process, while identifying the associated environmental impacts and contributing to the first ever zero-waste brewery effluent treatment system. Furthermore, these data were used to provide a basis to critically review and contribute to improving the methods used in the LCA of effluent treatment systems; particularly since this was the first wastewater treatment LCA that compared AS and HRAP using data collected from the same temporal and geographic location and from a single effluent stream. The electrical consumption water emission and land application of waste biomass caused the major environmental impacts of both treatment systems. The HRAP had less than 50 % of the electrical energy consumption (0.11±0.01 kW/m3 of effluent treated) compared to the AS system (0.29±0.11 kW/m3) which resulted in the technology having a lower climate change, photochemical oxidant formation, freshwater and marine ecotoxicity and fossil fuel depletion impact. It is imperative to understand the method of electrical energy (fossil fuel vs renewable) generation when conducting a LCA and deciding which technologies to use, since they have a major influence on the aforementioned impacts. The biogas yield of algal and sludge substrates was similar with an average gas production of 241 ml/g volatile solids fed. Biogas from algae fed digesters had a significantly higher methane content (64.73±0.81 %) and lower carbon dioxide content (22.94±0.24 %) when compared to WAS fed digesters (60.08±0.18 % and 27.37±0.43 %) respectively due to it being a less oxidised substrate. Swiss chard plants (Beta vulgaris) fertilised with anaerobically digested (AD) algae or sludge had a significantly higher mean biweekly yield (5.08±0.73 kg/m2) when compared to the inorganic-fertiliser control (3.45±0.89 kg/m2; p<0.0001). No difference was observed in the soil’s physical fertility when algae or sludge were applied to the soil (p>0.05). The HRAP produced more biomass (317.18±27.76 g/m3) than the AS (83.12±64.91 g/m3), which resulted in a significantly greater downstream production of biogas and fertiliser per volume of effluent treated. According to the LCA, this also resulted in the HRAP system having a higher terrestrial ecotoxicity, due to the greater volume of solids and thus heavy metals applied to the soil. This interpretation can be misleading, because the mass of heavy metals released into the environment is the same for both systems, with a greater portion being applied to the land in the HRAP scenario and discharged into fresh water in the case of AS. Future LCA models should clarify if these biomasses are going to be applied to a single piece of land or multiple sites as this will influence the risk of contamination via pollutant build up in the soil. The application of sludge or algae on soil increased the soil’s sodium concentration and sodium absorption ratio from 774.80±13.66 mg/kg to 952.17±34.89 mg/kg and 2.91±0.04 to 3.53±0.13, respectively. Regulations on the application of algae or sludge on agricultural soils should be altered to consider the limit values for sodium and future LCA’s associated with effluent treatment facilities should incorporate the possibility of soil contamination through sodium build-up. This work also conceptualised the importance of reporting water emissions in wastewater treatment LCA in as much detail as possible, because this had a significant influence on the eutrophication impacts on water systems. Reporting water emissions as total nitrogen underestimated downstream eutrophication impacts compared with those using nitrogen-species concentration (ammonia, nitrite, nitrate etc). A marine eutrophication sensitivity co-efficient should be included in future LCA models which accounts for the probability of nitrogen and phosphorus emissions entering the coastal environment as well as the vulnerability of the marine environment to eutrophication. Activated sludge systems are favourable for situations where space is limited, were there are inadequate options for biomass disposal (biomass not be used in agriculture or AD) and were electricity is generated from a renewable source; whereas, HRAP are more suitable under circumstances where electricity production relies on fossil fuel that carries a high environmental impact and where options are available to use the biomass for economic gain such as biogas and fertiliser production. This thesis contributes towards a zero-waste brewery effluent treated process. The HRAP and AS treated effluent for reuse in the brewery or in agricultural irrigation. The solids were anaerobically digested, and the carbon was recovered as a biogas, while the digestate was applied as an agricultural fertiliser. This allowed for the recovery of water, nutrients and carbon.
- Full Text:
- Date Issued: 2020
- Authors: Taylor, Richard Peter
- Date: 2020
- Subjects: Sewage -- Purification -- Activated sludge process , Sewage disposal plants , Sewage -- Purification -- Biological treatament , Sewage -- Purification -- Nitrogen removal , Brewery waste , Breweries -- Waste disposal , Microalgae -- Biotechnology , Algal biofuels
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/153746 , vital:39507
- Description: Wastewater treatment plants (WWTPs) are designed to clean effluents, but they also consume resources and produce waste. Various treatment technologies allow for the recovery of energy, nutrients and water from effluents turning this waste into products, which increases their sustainability and decreases the impact of WWTPs on the environment. There is a lack of literature which comprehensively compares the treatment performances, environmental impacts and beneficial downstream uses of the biomass generated by high rate algal pond (HRAP) and activated sludge (AS) treatment systems. This thesis aimed to compare (1) effluent treatment performance, (2) emissions and (3) downstream use of algae cultured in HRAP to sludge produced in AS and to obtain data to conduct a life cycle analysis (LCA) to compare the systems. The focus was on adding value to the effluent treatment process, while identifying the associated environmental impacts and contributing to the first ever zero-waste brewery effluent treatment system. Furthermore, these data were used to provide a basis to critically review and contribute to improving the methods used in the LCA of effluent treatment systems; particularly since this was the first wastewater treatment LCA that compared AS and HRAP using data collected from the same temporal and geographic location and from a single effluent stream. The electrical consumption water emission and land application of waste biomass caused the major environmental impacts of both treatment systems. The HRAP had less than 50 % of the electrical energy consumption (0.11±0.01 kW/m3 of effluent treated) compared to the AS system (0.29±0.11 kW/m3) which resulted in the technology having a lower climate change, photochemical oxidant formation, freshwater and marine ecotoxicity and fossil fuel depletion impact. It is imperative to understand the method of electrical energy (fossil fuel vs renewable) generation when conducting a LCA and deciding which technologies to use, since they have a major influence on the aforementioned impacts. The biogas yield of algal and sludge substrates was similar with an average gas production of 241 ml/g volatile solids fed. Biogas from algae fed digesters had a significantly higher methane content (64.73±0.81 %) and lower carbon dioxide content (22.94±0.24 %) when compared to WAS fed digesters (60.08±0.18 % and 27.37±0.43 %) respectively due to it being a less oxidised substrate. Swiss chard plants (Beta vulgaris) fertilised with anaerobically digested (AD) algae or sludge had a significantly higher mean biweekly yield (5.08±0.73 kg/m2) when compared to the inorganic-fertiliser control (3.45±0.89 kg/m2; p<0.0001). No difference was observed in the soil’s physical fertility when algae or sludge were applied to the soil (p>0.05). The HRAP produced more biomass (317.18±27.76 g/m3) than the AS (83.12±64.91 g/m3), which resulted in a significantly greater downstream production of biogas and fertiliser per volume of effluent treated. According to the LCA, this also resulted in the HRAP system having a higher terrestrial ecotoxicity, due to the greater volume of solids and thus heavy metals applied to the soil. This interpretation can be misleading, because the mass of heavy metals released into the environment is the same for both systems, with a greater portion being applied to the land in the HRAP scenario and discharged into fresh water in the case of AS. Future LCA models should clarify if these biomasses are going to be applied to a single piece of land or multiple sites as this will influence the risk of contamination via pollutant build up in the soil. The application of sludge or algae on soil increased the soil’s sodium concentration and sodium absorption ratio from 774.80±13.66 mg/kg to 952.17±34.89 mg/kg and 2.91±0.04 to 3.53±0.13, respectively. Regulations on the application of algae or sludge on agricultural soils should be altered to consider the limit values for sodium and future LCA’s associated with effluent treatment facilities should incorporate the possibility of soil contamination through sodium build-up. This work also conceptualised the importance of reporting water emissions in wastewater treatment LCA in as much detail as possible, because this had a significant influence on the eutrophication impacts on water systems. Reporting water emissions as total nitrogen underestimated downstream eutrophication impacts compared with those using nitrogen-species concentration (ammonia, nitrite, nitrate etc). A marine eutrophication sensitivity co-efficient should be included in future LCA models which accounts for the probability of nitrogen and phosphorus emissions entering the coastal environment as well as the vulnerability of the marine environment to eutrophication. Activated sludge systems are favourable for situations where space is limited, were there are inadequate options for biomass disposal (biomass not be used in agriculture or AD) and were electricity is generated from a renewable source; whereas, HRAP are more suitable under circumstances where electricity production relies on fossil fuel that carries a high environmental impact and where options are available to use the biomass for economic gain such as biogas and fertiliser production. This thesis contributes towards a zero-waste brewery effluent treated process. The HRAP and AS treated effluent for reuse in the brewery or in agricultural irrigation. The solids were anaerobically digested, and the carbon was recovered as a biogas, while the digestate was applied as an agricultural fertiliser. This allowed for the recovery of water, nutrients and carbon.
- Full Text:
- Date Issued: 2020
Phytoplankton of the Southern Agulhas Large Marine Ecosystem (sACLME)
- Authors: Sonnekus, Martinus Jakobus
- Date: 2020
- Subjects: Botanical chemistry
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/47646 , vital:40261
- Description: The southern Agulhas Large Marine Ecosystem (sACLME) consists of the greater Agulhas Current system, including the areas influenced by the Agulhas Current, the Agulhas Shelf, Agulhas Bank, Agulhas Retroflection as well as the Agulhas Return Current. Four biogeographical regions were identified within the sACLME and the composition of the phytoplankton communities and the associated physico-chemical variables in each were investigated. Water temperature and nitrate concentration were found to be the main drivers of the sACLME phytoplankton community. A total of 215 phytoplankton taxa were identified that were separated into two groups: the Agulhas Current group and the Southwest Indian Ocean Ridge group. The structure of the phytoplankton community was consistently homogeneous throughout the sACLME. Nutrient concentrations of the water varied, but nitrate was the most abundant source of nitrogen, especially in regions that were subjected to the upwelling of cold nutrient-rich water. The phytoplankton communities were significantly influenced by the availability and stoichiometry of the macronutrients nitrogen; phosphorus and silicon. The low mean N:P ratio of 5.5 is an indication that the waters of the sACLME are generally nitrogen limited, as is typical of oceanic systems. There is a change in phytoplankton cell size and functional groups within in the various water masses that are specific to certain biogeographical regions within the Agulhas Current system. It is clear that frontal systems may form barriers between phytoplankton communities.
- Full Text:
- Date Issued: 2020
- Authors: Sonnekus, Martinus Jakobus
- Date: 2020
- Subjects: Botanical chemistry
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/47646 , vital:40261
- Description: The southern Agulhas Large Marine Ecosystem (sACLME) consists of the greater Agulhas Current system, including the areas influenced by the Agulhas Current, the Agulhas Shelf, Agulhas Bank, Agulhas Retroflection as well as the Agulhas Return Current. Four biogeographical regions were identified within the sACLME and the composition of the phytoplankton communities and the associated physico-chemical variables in each were investigated. Water temperature and nitrate concentration were found to be the main drivers of the sACLME phytoplankton community. A total of 215 phytoplankton taxa were identified that were separated into two groups: the Agulhas Current group and the Southwest Indian Ocean Ridge group. The structure of the phytoplankton community was consistently homogeneous throughout the sACLME. Nutrient concentrations of the water varied, but nitrate was the most abundant source of nitrogen, especially in regions that were subjected to the upwelling of cold nutrient-rich water. The phytoplankton communities were significantly influenced by the availability and stoichiometry of the macronutrients nitrogen; phosphorus and silicon. The low mean N:P ratio of 5.5 is an indication that the waters of the sACLME are generally nitrogen limited, as is typical of oceanic systems. There is a change in phytoplankton cell size and functional groups within in the various water masses that are specific to certain biogeographical regions within the Agulhas Current system. It is clear that frontal systems may form barriers between phytoplankton communities.
- Full Text:
- Date Issued: 2020
A theory-based approach to evaluating a Continuing Teacher Professional Development Programme aimed at strengthening environment and sustainability education
- Authors: Songqwaru, Nonyameko Zintle
- Date: 2020
- Subjects: Fundisa for Change , Environmental education -- South Africa , Teachers -- Training of -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145267 , vital:38423
- Description: This study uses a theory-based approach to evaluate the Fundisa for Change training programme, a continuing teacher professional development programme aimed at strengthening environment and sustainability education. The aim of the study was to surface assumptions that underpin the design and implementation of the Fundisa for Change training programme. The Fundisa for Change Teacher Education programme is a national collaborative programme that is implemented in all the nine provinces of South Africa. The study reports on the implementation of the programme in five provinces. The study aimed to surface the Fundisa for Change training programme’s implementation theory and programme theory as these affect programme delivery. The Fundisa for Change training programme was implemented in diverse contexts by different facilitators to different participants. To determine how training programme outcomes were achieved, use was made of context-mechanism-outcome (CMO) configurations for each site where the programme was implemented. Data used to construct CMO configurations was generated through document analysis of Fundisa for Change documents, interviews with stakeholders and participants, as well as observations of programme implementation at five sites. There were three phases to data analysis: content analysis of Fundisa for Change documents, content analysis of observation transcripts and use of the CMO configuration, an analytical tool used in realist evaluation. An initial CMO configuration was constructed prior to observing implementation of the programme and a refined CMO configuration for the Fundisa for Change training programme was constructed based on similarities between the CMO configurations constructed for each of the five sites under study. The partnership model of the Fundisa for Change training programme brought diverse expertise and resources (material, cognitive, social and emotional) which were conducive to the achievement of programme outcomes. The programme’s action context (structure, culture, agency and relations) contributed to the achievement of programme outcomes by participants. Participants’ subject content knowledge, teaching practice and assessment practice was enhanced through attending the Fundisa for Change training. On-course tasks were mediated during training and this created opportunities for participants to discuss and reflect on current practice in ways that could lead to a change in practice. In evaluating professional development programmes, an elaborated definition of context in terms of structure, culture, agency and relations enables a comprehensive exploration of potential programme mechanisms that can be activated when programmes are implemented. It is also important to disaggregate resources and reasons when identifying mechanisms as this assists with differentiating between context and mechanisms. The study offers insights into the professional learning of teachers grappling with new content and pedagogical content knowledges related to environment in the context of recent curriculum changes where the South African national school curriculum has come into focus. Environmental education programmes in South Africa have implicitly used a realist approach. This study offers the first substantive professional learning evaluation that develops this approach explicitly using Theory of Change and Realist Evaluation in combination.
- Full Text:
- Date Issued: 2020
- Authors: Songqwaru, Nonyameko Zintle
- Date: 2020
- Subjects: Fundisa for Change , Environmental education -- South Africa , Teachers -- Training of -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145267 , vital:38423
- Description: This study uses a theory-based approach to evaluate the Fundisa for Change training programme, a continuing teacher professional development programme aimed at strengthening environment and sustainability education. The aim of the study was to surface assumptions that underpin the design and implementation of the Fundisa for Change training programme. The Fundisa for Change Teacher Education programme is a national collaborative programme that is implemented in all the nine provinces of South Africa. The study reports on the implementation of the programme in five provinces. The study aimed to surface the Fundisa for Change training programme’s implementation theory and programme theory as these affect programme delivery. The Fundisa for Change training programme was implemented in diverse contexts by different facilitators to different participants. To determine how training programme outcomes were achieved, use was made of context-mechanism-outcome (CMO) configurations for each site where the programme was implemented. Data used to construct CMO configurations was generated through document analysis of Fundisa for Change documents, interviews with stakeholders and participants, as well as observations of programme implementation at five sites. There were three phases to data analysis: content analysis of Fundisa for Change documents, content analysis of observation transcripts and use of the CMO configuration, an analytical tool used in realist evaluation. An initial CMO configuration was constructed prior to observing implementation of the programme and a refined CMO configuration for the Fundisa for Change training programme was constructed based on similarities between the CMO configurations constructed for each of the five sites under study. The partnership model of the Fundisa for Change training programme brought diverse expertise and resources (material, cognitive, social and emotional) which were conducive to the achievement of programme outcomes. The programme’s action context (structure, culture, agency and relations) contributed to the achievement of programme outcomes by participants. Participants’ subject content knowledge, teaching practice and assessment practice was enhanced through attending the Fundisa for Change training. On-course tasks were mediated during training and this created opportunities for participants to discuss and reflect on current practice in ways that could lead to a change in practice. In evaluating professional development programmes, an elaborated definition of context in terms of structure, culture, agency and relations enables a comprehensive exploration of potential programme mechanisms that can be activated when programmes are implemented. It is also important to disaggregate resources and reasons when identifying mechanisms as this assists with differentiating between context and mechanisms. The study offers insights into the professional learning of teachers grappling with new content and pedagogical content knowledges related to environment in the context of recent curriculum changes where the South African national school curriculum has come into focus. Environmental education programmes in South Africa have implicitly used a realist approach. This study offers the first substantive professional learning evaluation that develops this approach explicitly using Theory of Change and Realist Evaluation in combination.
- Full Text:
- Date Issued: 2020
Addressing flux suppression, radio frequency interference, and selection of optimal solution intervals during radio interferometric calibration
- Authors: Sob, Ulrich Armel Mbou
- Date: 2020
- Subjects: CubiCal (Software) , Radio -- Interference , Imaging systems in astronomy , Algorithms , Astronomical instruments -- Calibration , Astronomy -- Data processing
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/147714 , vital:38663
- Description: The forthcoming Square Kilometre Array is expected to provide answers to some of the most intriguing questions about our Universe. However, as it is already noticeable from MeerKAT and other precursors, the amounts of data produced by these new instruments are significantly challenging to calibrate and image. Calibration of radio interferometric data is usually biased by incomplete sky models and radio frequency interference (RFI) resulting in calibration artefacts that limit the dynamic range and image fidelity of the resulting images. One of the most noticeable of these artefacts is the formation of spurious sources which causes suppression of real emissions. Fortunately, it has been shown that calibration algorithms employing heavy-tailed likelihood functions are less susceptible to this due to their robustness against outliers. Leveraging on recent developments in the field of complex optimisation, we implement a robust calibration algorithm using a Student’s t likelihood function and Wirtinger derivatives. The new algorithm, dubbed the robust solver, is incorporated as a subroutine into the newly released calibration software package CubiCal. We perform statistical analysis on the distribution of visibilities and provide an insight into the functioning of the robust solver and describe different scenarios where it will improve calibration. We use simulations to show that the robust solver effectively reduces the amount of flux suppressed from unmodelled sources both in direction independent and direction dependent calibration. Furthermore, the robust solver is shown to successfully mitigate the effects of low-level RFI when applied to a simulated and a real VLA dataset. Finally, we demonstrate that there are close links between the amount of flux suppressed from sources, the effects of the RFI and the employed solution interval during radio interferometric calibration. Hence, we investigate the effects of solution intervals and the different factors to consider in order to select adequate solution intervals. Furthermore, we propose a practical brute force method for selecting optimal solution intervals. The proposed method is successfully applied to a VLA dataset.
- Full Text:
- Date Issued: 2020
- Authors: Sob, Ulrich Armel Mbou
- Date: 2020
- Subjects: CubiCal (Software) , Radio -- Interference , Imaging systems in astronomy , Algorithms , Astronomical instruments -- Calibration , Astronomy -- Data processing
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/147714 , vital:38663
- Description: The forthcoming Square Kilometre Array is expected to provide answers to some of the most intriguing questions about our Universe. However, as it is already noticeable from MeerKAT and other precursors, the amounts of data produced by these new instruments are significantly challenging to calibrate and image. Calibration of radio interferometric data is usually biased by incomplete sky models and radio frequency interference (RFI) resulting in calibration artefacts that limit the dynamic range and image fidelity of the resulting images. One of the most noticeable of these artefacts is the formation of spurious sources which causes suppression of real emissions. Fortunately, it has been shown that calibration algorithms employing heavy-tailed likelihood functions are less susceptible to this due to their robustness against outliers. Leveraging on recent developments in the field of complex optimisation, we implement a robust calibration algorithm using a Student’s t likelihood function and Wirtinger derivatives. The new algorithm, dubbed the robust solver, is incorporated as a subroutine into the newly released calibration software package CubiCal. We perform statistical analysis on the distribution of visibilities and provide an insight into the functioning of the robust solver and describe different scenarios where it will improve calibration. We use simulations to show that the robust solver effectively reduces the amount of flux suppressed from unmodelled sources both in direction independent and direction dependent calibration. Furthermore, the robust solver is shown to successfully mitigate the effects of low-level RFI when applied to a simulated and a real VLA dataset. Finally, we demonstrate that there are close links between the amount of flux suppressed from sources, the effects of the RFI and the employed solution interval during radio interferometric calibration. Hence, we investigate the effects of solution intervals and the different factors to consider in order to select adequate solution intervals. Furthermore, we propose a practical brute force method for selecting optimal solution intervals. The proposed method is successfully applied to a VLA dataset.
- Full Text:
- Date Issued: 2020
Transformative ICT education practices in rural secondary schools for developmental needs and realities: the Eastern Cape Province, South Africa
- Authors: Simuja, Clement
- Date: 2020
- Subjects: Education, Secondary -- South Africa -- Data processing , Information technology -- Study and teaching (Secondary) --South Africa , Educational technology -- Developing countries , Rural development -- Developing countries , Computer-assisted instruction -- South Africa -- Eastern Cape , Internet in education -- South Africa , Rural schools -- South Africa -- Eastern Cape , Community and school -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/150631 , vital:38991
- Description: The perceived social development significance of Information and Communication Technology (ICT) has dramatically expanded the domains in which this cluster of ICTs is being discussed and acted upon. The action to promote community development in rural areas in South Africa has made its way into the introduction of ICT education in secondary schools. Since rural secondary schools form part of the framework for rural communities, they are being challenged to provide ICT education that makes a difference in learners’ lives. This requires engaging education practices that inspire learners to construct knowledge of ICT that does not only respond to examination purposes but rather, to the needs and development aspirations of the community. This research examines the experience of engaging learners and communities in socially informed ICT education in rural secondary schools. Specifically, it seeks to develop a critique of current practices involved in ICT education in rural secondary schools, and explores plausible alternatives to such practices that would make ICT education more transformative and structured towards the developmental concerns of communities. The main empirical focus for the research was five rural secondary schools in the Eastern Cape Province in South Africa. The research involved 53 participants that participated in a socially informed ICT training process. The training was designed to inspire participants to share their self-defined ICT education and ICT knowledge experiences. Critical Action Learning and Philosophical Inquiry provided the methodological framework, whilst the theoretical framework draws on Foucault’s philosophical ideas on power-knowledge relations. Through this theoretical analysis, the research examines the dynamic interplay of practices in ICT education with the values, ideals, and knowledge that form the core-life experiences of learners and rural communities. The research findings of this study indicate that current ICT education practices in rural secondary schools are endowed with ideologies that are affecting learners’ identity, social experiences, power, and ownership of the reflective meaning of using ICTs in community development. The contribution of this thesis lies in demonstrating ways that reframe ICT education transformatively, and more specifically its practices in the light of the way power, identity, ownership and social experience construct and offer learners a transformative view of self and the world. This could enable ICT education to fulfil the potential of contributing to social development in rural communities. The thesis culminates by presenting a theoretical framework that articulates the structural and authoritative components of ICT education practices – these relate to learners’ conscious understandings and represented thoughts, sensations and meanings embedded in the context, and actions and locations of using their knowledge of ICT.
- Full Text:
- Date Issued: 2020
- Authors: Simuja, Clement
- Date: 2020
- Subjects: Education, Secondary -- South Africa -- Data processing , Information technology -- Study and teaching (Secondary) --South Africa , Educational technology -- Developing countries , Rural development -- Developing countries , Computer-assisted instruction -- South Africa -- Eastern Cape , Internet in education -- South Africa , Rural schools -- South Africa -- Eastern Cape , Community and school -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/150631 , vital:38991
- Description: The perceived social development significance of Information and Communication Technology (ICT) has dramatically expanded the domains in which this cluster of ICTs is being discussed and acted upon. The action to promote community development in rural areas in South Africa has made its way into the introduction of ICT education in secondary schools. Since rural secondary schools form part of the framework for rural communities, they are being challenged to provide ICT education that makes a difference in learners’ lives. This requires engaging education practices that inspire learners to construct knowledge of ICT that does not only respond to examination purposes but rather, to the needs and development aspirations of the community. This research examines the experience of engaging learners and communities in socially informed ICT education in rural secondary schools. Specifically, it seeks to develop a critique of current practices involved in ICT education in rural secondary schools, and explores plausible alternatives to such practices that would make ICT education more transformative and structured towards the developmental concerns of communities. The main empirical focus for the research was five rural secondary schools in the Eastern Cape Province in South Africa. The research involved 53 participants that participated in a socially informed ICT training process. The training was designed to inspire participants to share their self-defined ICT education and ICT knowledge experiences. Critical Action Learning and Philosophical Inquiry provided the methodological framework, whilst the theoretical framework draws on Foucault’s philosophical ideas on power-knowledge relations. Through this theoretical analysis, the research examines the dynamic interplay of practices in ICT education with the values, ideals, and knowledge that form the core-life experiences of learners and rural communities. The research findings of this study indicate that current ICT education practices in rural secondary schools are endowed with ideologies that are affecting learners’ identity, social experiences, power, and ownership of the reflective meaning of using ICTs in community development. The contribution of this thesis lies in demonstrating ways that reframe ICT education transformatively, and more specifically its practices in the light of the way power, identity, ownership and social experience construct and offer learners a transformative view of self and the world. This could enable ICT education to fulfil the potential of contributing to social development in rural communities. The thesis culminates by presenting a theoretical framework that articulates the structural and authoritative components of ICT education practices – these relate to learners’ conscious understandings and represented thoughts, sensations and meanings embedded in the context, and actions and locations of using their knowledge of ICT.
- Full Text:
- Date Issued: 2020
Application of machine learning, molecular modelling and structural data mining against antiretroviral drug resistance in HIV-1
- Sheik Amamuddy, Olivier Serge André
- Authors: Sheik Amamuddy, Olivier Serge André
- Date: 2020
- Subjects: Machine learning , Molecules -- Models , Data mining , Neural networks (Computer science) , Antiretroviral agents , Protease inhibitors , Drug resistance , Multidrug resistance , Molecular dynamics , Renin-angiotensin system , HIV (Viruses) -- South Africa , HIV (Viruses) -- Social aspects -- South Africa , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115964 , vital:34282
- Description: Millions are affected with the Human Immunodeficiency Virus (HIV) world wide, even though the death toll is on the decline. Antiretrovirals (ARVs), more specifically protease inhibitors have shown tremendous success since their introduction into therapy since the mid 1990’s by slowing down progression to the Acquired Immune Deficiency Syndrome (AIDS). However, Drug Resistance Mutations (DRMs) are constantly selected for due to viral adaptation, making drugs less effective over time. The current challenge is to manage the infection optimally with a limited set of drugs, with differing associated levels of toxicities in the face of a virus that (1) exists as a quasispecies, (2) may transmit acquired DRMs to drug-naive individuals and (3) that can manifest class-wide resistance due to similarities in design. The presence of latent reservoirs, unawareness of infection status, education and various socio-economic factors make the problem even more complex. Adequate timing and choice of drug prescription together with treatment adherence are very important as drug toxicities, drug failure and sub-optimal treatment regimens leave room for further development of drug resistance. While CD4 cell count and the determination of viral load from patients in resource-limited settings are very helpful to track how well a patient’s immune system is able to keep the virus in check, they can be lengthy in determining whether an ARV is effective. Phenosense assay kits answer this problem using viruses engineered to contain the patient sequences and evaluating their growth in the presence of different ARVs, but this can be expensive and too involved for routine checks. As a cheaper and faster alternative, genotypic assays provide similar information from HIV pol sequences obtained from blood samples, inferring ARV efficacy on the basis of drug resistance mutation patterns. However, these are inherently complex and the various methods of in silico prediction, such as Geno2pheno, REGA and Stanford HIVdb do not always agree in every case, even though this gap decreases as the list of resistance mutations is updated. A major gap in HIV treatment is that the information used for predicting drug resistance is mainly computed from data containing an overwhelming majority of B subtype HIV, when these only comprise about 12% of the worldwide HIV infections. In addition to growing evidence that drug resistance is subtype-related, it is intuitive to hypothesize that as subtyping is a phylogenetic classification, the more divergent a subtype is from the strains used in training prediction models, the less their resistance profiles would correlate. For the aforementioned reasons, we used a multi-faceted approach to attack the virus in multiple ways. This research aimed to (1) improve resistance prediction methods by focusing solely on the available subtype, (2) mine structural information pertaining to resistance in order to find any exploitable weak points and increase knowledge of the mechanistic processes of drug resistance in HIV protease. Finally, (3) we screen for protease inhibitors amongst a database of natural compounds [the South African natural compound database (SANCDB)] to find molecules or molecular properties usable to come up with improved inhibition against the drug target. In this work, structural information was mined using the Anisotropic Network Model, Dynamics Cross-Correlation, Perturbation Response Scanning, residue contact network analysis and the radius of gyration. These methods failed to give any resistance-associated patterns in terms of natural movement, internal correlated motions, residue perturbation response, relational behaviour and global compaction respectively. Applications of drug docking, homology-modelling and energy minimization for generating features suitable for machine-learning were not very promising, and rather suggest that the value of binding energies by themselves from Vina may not be very reliable quantitatively. All these failures lead to a refinement that resulted in a highly sensitive statistically-guided network construction and analysis, which leads to key findings in the early dynamics associated with resistance across all PI drugs. The latter experiment unravelled a conserved lateral expansion motion occurring at the flap elbows, and an associated contraction that drives the base of the dimerization domain towards the catalytic site’s floor in the case of drug resistance. Interestingly, we found that despite the conserved movement, bond angles were degenerate. Alongside, 16 Artificial Neural Network models were optimised for HIV proteases and reverse transcriptase inhibitors, with performances on par with Stanford HIVdb. Finally, we prioritised 9 compounds with potential protease inhibitory activity using virtual screening and molecular dynamics (MD) to additionally suggest a promising modification to one of the compounds. This yielded another molecule inhibiting equally well both opened and closed receptor target conformations, whereby each of the compounds had been selected against an array of multi-drug-resistant receptor variants. While a main hurdle was a lack of non-B subtype data, our findings, especially from the statistically-guided network analysis, may extrapolate to a certain extent to them as the level of conservation was very high within subtype B, despite all the present variations. This network construction method lays down a sensitive approach for analysing a pair of alternate phenotypes for which complex patterns prevail, given a sufficient number of experimental units. During the course of research a weighted contact mapping tool was developed to compare renin-angiotensinogen variants and packaged as part of the MD-TASK tool suite. Finally the functionality, compatibility and performance of the MODE-TASK tool were evaluated and confirmed for both Python2.7.x and Python3.x, for the analysis of normals modes from single protein structures and essential modes from MD trajectories. These techniques and tools collectively add onto the conventional means of MD analysis.
- Full Text:
- Date Issued: 2020
- Authors: Sheik Amamuddy, Olivier Serge André
- Date: 2020
- Subjects: Machine learning , Molecules -- Models , Data mining , Neural networks (Computer science) , Antiretroviral agents , Protease inhibitors , Drug resistance , Multidrug resistance , Molecular dynamics , Renin-angiotensin system , HIV (Viruses) -- South Africa , HIV (Viruses) -- Social aspects -- South Africa , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115964 , vital:34282
- Description: Millions are affected with the Human Immunodeficiency Virus (HIV) world wide, even though the death toll is on the decline. Antiretrovirals (ARVs), more specifically protease inhibitors have shown tremendous success since their introduction into therapy since the mid 1990’s by slowing down progression to the Acquired Immune Deficiency Syndrome (AIDS). However, Drug Resistance Mutations (DRMs) are constantly selected for due to viral adaptation, making drugs less effective over time. The current challenge is to manage the infection optimally with a limited set of drugs, with differing associated levels of toxicities in the face of a virus that (1) exists as a quasispecies, (2) may transmit acquired DRMs to drug-naive individuals and (3) that can manifest class-wide resistance due to similarities in design. The presence of latent reservoirs, unawareness of infection status, education and various socio-economic factors make the problem even more complex. Adequate timing and choice of drug prescription together with treatment adherence are very important as drug toxicities, drug failure and sub-optimal treatment regimens leave room for further development of drug resistance. While CD4 cell count and the determination of viral load from patients in resource-limited settings are very helpful to track how well a patient’s immune system is able to keep the virus in check, they can be lengthy in determining whether an ARV is effective. Phenosense assay kits answer this problem using viruses engineered to contain the patient sequences and evaluating their growth in the presence of different ARVs, but this can be expensive and too involved for routine checks. As a cheaper and faster alternative, genotypic assays provide similar information from HIV pol sequences obtained from blood samples, inferring ARV efficacy on the basis of drug resistance mutation patterns. However, these are inherently complex and the various methods of in silico prediction, such as Geno2pheno, REGA and Stanford HIVdb do not always agree in every case, even though this gap decreases as the list of resistance mutations is updated. A major gap in HIV treatment is that the information used for predicting drug resistance is mainly computed from data containing an overwhelming majority of B subtype HIV, when these only comprise about 12% of the worldwide HIV infections. In addition to growing evidence that drug resistance is subtype-related, it is intuitive to hypothesize that as subtyping is a phylogenetic classification, the more divergent a subtype is from the strains used in training prediction models, the less their resistance profiles would correlate. For the aforementioned reasons, we used a multi-faceted approach to attack the virus in multiple ways. This research aimed to (1) improve resistance prediction methods by focusing solely on the available subtype, (2) mine structural information pertaining to resistance in order to find any exploitable weak points and increase knowledge of the mechanistic processes of drug resistance in HIV protease. Finally, (3) we screen for protease inhibitors amongst a database of natural compounds [the South African natural compound database (SANCDB)] to find molecules or molecular properties usable to come up with improved inhibition against the drug target. In this work, structural information was mined using the Anisotropic Network Model, Dynamics Cross-Correlation, Perturbation Response Scanning, residue contact network analysis and the radius of gyration. These methods failed to give any resistance-associated patterns in terms of natural movement, internal correlated motions, residue perturbation response, relational behaviour and global compaction respectively. Applications of drug docking, homology-modelling and energy minimization for generating features suitable for machine-learning were not very promising, and rather suggest that the value of binding energies by themselves from Vina may not be very reliable quantitatively. All these failures lead to a refinement that resulted in a highly sensitive statistically-guided network construction and analysis, which leads to key findings in the early dynamics associated with resistance across all PI drugs. The latter experiment unravelled a conserved lateral expansion motion occurring at the flap elbows, and an associated contraction that drives the base of the dimerization domain towards the catalytic site’s floor in the case of drug resistance. Interestingly, we found that despite the conserved movement, bond angles were degenerate. Alongside, 16 Artificial Neural Network models were optimised for HIV proteases and reverse transcriptase inhibitors, with performances on par with Stanford HIVdb. Finally, we prioritised 9 compounds with potential protease inhibitory activity using virtual screening and molecular dynamics (MD) to additionally suggest a promising modification to one of the compounds. This yielded another molecule inhibiting equally well both opened and closed receptor target conformations, whereby each of the compounds had been selected against an array of multi-drug-resistant receptor variants. While a main hurdle was a lack of non-B subtype data, our findings, especially from the statistically-guided network analysis, may extrapolate to a certain extent to them as the level of conservation was very high within subtype B, despite all the present variations. This network construction method lays down a sensitive approach for analysing a pair of alternate phenotypes for which complex patterns prevail, given a sufficient number of experimental units. During the course of research a weighted contact mapping tool was developed to compare renin-angiotensinogen variants and packaged as part of the MD-TASK tool suite. Finally the functionality, compatibility and performance of the MODE-TASK tool were evaluated and confirmed for both Python2.7.x and Python3.x, for the analysis of normals modes from single protein structures and essential modes from MD trajectories. These techniques and tools collectively add onto the conventional means of MD analysis.
- Full Text:
- Date Issued: 2020
Synthesis of novel heterocyclic systems as potential inhibitors of HIV-1 enzymes
- Authors: Sekgota, Khethobole Cassius
- Date: 2020
- Subjects: Protease inhibitors , Heterocyclic compounds , HIV (Viruses) , Quinoline , Amides , Nuclear magnetic resonance , Antiretroviral agents , AIDS vaccines , Nitrobenzaldehyde , Propylphosphonic acid anhydride
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146502 , vital:38531
- Description: This study has focussed on the application of Baylis-Hillman methodology in the development of efficient synthetic pathways to libraries of novel 3-[(N-cycloalkylbenzamido)methyl]-2-quinolones and indolizine-2-carboxamides and on an exploration of their medicinal potential. The approach to 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones involved a six-step pathway comprising: Baylis-Hillman reaction of 2-nitrobenzaldehyde derivatives and methyl acrylate to afford nitro-Baylis-Hillman adducts; thermal cyclisation of the adducts to give a range of 3-(acetoxymethyl)-2(1H)-quinolones in good to excellent yields; hydrolysis of the acetates; conversion of the resulting alcohols to the 3-chloromethyl analogues; amination; and, finally, acylation to afford the target amides. Variable temperature NMR methods were used to facilitate analysis of the ¹H and ¹³C NMR spectra which were complicated by internal rotation and cycloalkyl ring-flipping effects. On the other hand, the indolizine-2-carboxamides were obtained in several steps commencing with the Baylis-Hillman reaction of pyridine-2-carboxaldehyde and methyl acrylate. Thermal cyclisation of the Baylis-Hillman adduct afforded indolizine esters, hydrolysis of which gave the corresponding acids which served as precursors to the target indolizine-2-carboxamides. The final amidation step, however, proved to be particularly challenging. Various coupling strategies were explored to access indolizine-2-carboxamides. These included the use of 2,2,2-trifluoroethyl borate which showed limited promise, but propylphosphonic acid anhydride (T3P) proved to be the most effective coupling agent, permitting the formation of 24 novel indolizine-2-carboxamides from hydrazines, aliphatic amines and a range of heterocyclic amines. A high-field NMR-based kinetic study of the mechanism of the Baylis-Hillman reaction of pyridine-4-carboxaldehyde and methyl acrylate in the presence of 3-hydroxyquinuclidine in deuterated chloroform was initiated, reaction progress being followed by the automated collection of ¹H and DEPT 135 NMR spectra over ca. 24 hours using a high-field (600 MHz) NMR instrument. The results have provided critical new insights into the mechanism. NMR analysis has also been used to elucidate the multiplicity of signals associated with rotameric equilibria observed at ambient probe temperature. Variable temperature 1D- and 2D-NMR spectra were used to facilitate the unambiguous characterisation of the 2-quinolone benzamides and some of the indolizine-2-carboxamides. The 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones, together with selected precursors, and a number of the indolizine-2-carboxamides have been screened in vitro as potential HIV-1 enzyme inhibitors. A survey of the activity of the 2-quinolones against HIV-1 integrase, protease and reverse transcriptase revealed selective inhibition of HIV-1 integrase with the most active IN inhibitor, 3-[(cyclopentylamino)methyl-6-methoxy-2(1H)-quinolone 115e, producing residual enzyme activity of 40% at a concentration of 20 μM. Many of the 2-quinolones exhibited no significant cytotoxicity against HEK 293 cells at 20 μM concentrations. 3-[(N-Cyclohexylamino)methyl]-6-methoxy-2(1H)-quinolone 114e was the only compound to exhibit ant-plasmodial activity (55% pfLDH activity). The survey of indolizine-2-carboxamides also revealed encouraging inhibition against HIV-1 integrase. None of these compounds exhibited cytotoxicity at 20 μM against HEK 293 cells, while a number of them exhibited some activity against Plasmodium falciparum (3D7 strain) and Trypanosoma brucei. Selected indolizine-2-carboxamides exhibited significant anti-tubercular activity in the 7H9 CAS GLU Tx and 7H9 ADC GLU Tw media. In view of the inherent fluorescent character and biological potential of the synthesised indolizine-2-carboxamides, their photophysical properties were explored to establish their possible dual use as bio-imaging and therapeutic agents. The major absorption and corresponding emission bands, and the associated molar absorption coefficients (Ɛ) expressed in the form of log Ɛ were determined. Their high extinction coefficients, large Stokes shift and red-shifted emissions in the visible region indicate their potential for use as fluorophores.
- Full Text:
- Date Issued: 2020
- Authors: Sekgota, Khethobole Cassius
- Date: 2020
- Subjects: Protease inhibitors , Heterocyclic compounds , HIV (Viruses) , Quinoline , Amides , Nuclear magnetic resonance , Antiretroviral agents , AIDS vaccines , Nitrobenzaldehyde , Propylphosphonic acid anhydride
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146502 , vital:38531
- Description: This study has focussed on the application of Baylis-Hillman methodology in the development of efficient synthetic pathways to libraries of novel 3-[(N-cycloalkylbenzamido)methyl]-2-quinolones and indolizine-2-carboxamides and on an exploration of their medicinal potential. The approach to 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones involved a six-step pathway comprising: Baylis-Hillman reaction of 2-nitrobenzaldehyde derivatives and methyl acrylate to afford nitro-Baylis-Hillman adducts; thermal cyclisation of the adducts to give a range of 3-(acetoxymethyl)-2(1H)-quinolones in good to excellent yields; hydrolysis of the acetates; conversion of the resulting alcohols to the 3-chloromethyl analogues; amination; and, finally, acylation to afford the target amides. Variable temperature NMR methods were used to facilitate analysis of the ¹H and ¹³C NMR spectra which were complicated by internal rotation and cycloalkyl ring-flipping effects. On the other hand, the indolizine-2-carboxamides were obtained in several steps commencing with the Baylis-Hillman reaction of pyridine-2-carboxaldehyde and methyl acrylate. Thermal cyclisation of the Baylis-Hillman adduct afforded indolizine esters, hydrolysis of which gave the corresponding acids which served as precursors to the target indolizine-2-carboxamides. The final amidation step, however, proved to be particularly challenging. Various coupling strategies were explored to access indolizine-2-carboxamides. These included the use of 2,2,2-trifluoroethyl borate which showed limited promise, but propylphosphonic acid anhydride (T3P) proved to be the most effective coupling agent, permitting the formation of 24 novel indolizine-2-carboxamides from hydrazines, aliphatic amines and a range of heterocyclic amines. A high-field NMR-based kinetic study of the mechanism of the Baylis-Hillman reaction of pyridine-4-carboxaldehyde and methyl acrylate in the presence of 3-hydroxyquinuclidine in deuterated chloroform was initiated, reaction progress being followed by the automated collection of ¹H and DEPT 135 NMR spectra over ca. 24 hours using a high-field (600 MHz) NMR instrument. The results have provided critical new insights into the mechanism. NMR analysis has also been used to elucidate the multiplicity of signals associated with rotameric equilibria observed at ambient probe temperature. Variable temperature 1D- and 2D-NMR spectra were used to facilitate the unambiguous characterisation of the 2-quinolone benzamides and some of the indolizine-2-carboxamides. The 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones, together with selected precursors, and a number of the indolizine-2-carboxamides have been screened in vitro as potential HIV-1 enzyme inhibitors. A survey of the activity of the 2-quinolones against HIV-1 integrase, protease and reverse transcriptase revealed selective inhibition of HIV-1 integrase with the most active IN inhibitor, 3-[(cyclopentylamino)methyl-6-methoxy-2(1H)-quinolone 115e, producing residual enzyme activity of 40% at a concentration of 20 μM. Many of the 2-quinolones exhibited no significant cytotoxicity against HEK 293 cells at 20 μM concentrations. 3-[(N-Cyclohexylamino)methyl]-6-methoxy-2(1H)-quinolone 114e was the only compound to exhibit ant-plasmodial activity (55% pfLDH activity). The survey of indolizine-2-carboxamides also revealed encouraging inhibition against HIV-1 integrase. None of these compounds exhibited cytotoxicity at 20 μM against HEK 293 cells, while a number of them exhibited some activity against Plasmodium falciparum (3D7 strain) and Trypanosoma brucei. Selected indolizine-2-carboxamides exhibited significant anti-tubercular activity in the 7H9 CAS GLU Tx and 7H9 ADC GLU Tw media. In view of the inherent fluorescent character and biological potential of the synthesised indolizine-2-carboxamides, their photophysical properties were explored to establish their possible dual use as bio-imaging and therapeutic agents. The major absorption and corresponding emission bands, and the associated molar absorption coefficients (Ɛ) expressed in the form of log Ɛ were determined. Their high extinction coefficients, large Stokes shift and red-shifted emissions in the visible region indicate their potential for use as fluorophores.
- Full Text:
- Date Issued: 2020
Activity of diverse chalcones against several targets: statistical analysis of a high-throughput virtual screen of a custom chalcone library
- Authors: Sarron, Arthur F D
- Date: 2020
- Subjects: Acetophenone , Benzaldehyde , Ketones , Pyruvate kinase , Drug development , Aromatic compounds , Heat shock proteins
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/116028 , vital:34291
- Description: Chalcone family molecules are well known to have therapeutic proprieties (anti-inflammatory, anti-microbial or anti-cancer, etc). However the mechanism of action in some cases is not well known. A virtual library of this family of compounds was constructed using custom scripts, based on the aldol condensation, and this library was modified further to analogues by expansion of the α,β-unsaturated ketone linker. Acetophenone and benzaldehyde derivatives which are available and purchasable were used as a base to design the chalcone virtual library. 8063 chalcones were constructed and geometrically optimized with Gaussian 09. Their physicochemical characteristics linked to the Lipinski rules were analyzed with Knime and CDK. The entire library was after docked against several targets including HIV-1 integrase, MRSA pyruvate kinase, HSP90, COX-1, COX-2, ALR2, MAOA, MAOB, acetylcholinesterase, butyrylcholinesterase and PLA2. With the exception of MAOA, which does not have a crystal structure ligand, all dockings were validated by redocking the original ligand provided by the literature. These targets are known in the literature to be inhibited by chalcone-derivatives. However, specificity of the particular known chalcone inhibitors to the particular targets is not known. To this end the performance of the generated chalcone library against the list of targets was of interest. The binding energy of ligand-protein complexes was generally good across the library. Statistical analysis including principal component analysis and hierarchical clustering analysis were made in order to investigate for any physical/chemical characteristics which might explain what chalcone features affect the binding energy of the ligand-protein complexes. The spherical polar coordinates defining the orientation of the binding poses were also calculated and used in the statistical analysis. The statistical analysis has allowed us to hypothesize the importance of these radial distances and the polar angles of key atoms in the chalcones in binding to the pyruvate kinase crystal structure. This was validated by the docking of another small library of compound models in which the α,β-unsaturated ketone chain of the chalcone was replaced by incrementally longer conjugated chains. Further studies on the chalcones themselves reveal rotameric systems in both cis and trans-configurations (which may impact binding), and also studied was the effect of Topliss-based modification and its impact of binding to HSP90. Molecular dynamics confirmed good binding of identified chalcone hits.
- Full Text:
- Date Issued: 2020
- Authors: Sarron, Arthur F D
- Date: 2020
- Subjects: Acetophenone , Benzaldehyde , Ketones , Pyruvate kinase , Drug development , Aromatic compounds , Heat shock proteins
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/116028 , vital:34291
- Description: Chalcone family molecules are well known to have therapeutic proprieties (anti-inflammatory, anti-microbial or anti-cancer, etc). However the mechanism of action in some cases is not well known. A virtual library of this family of compounds was constructed using custom scripts, based on the aldol condensation, and this library was modified further to analogues by expansion of the α,β-unsaturated ketone linker. Acetophenone and benzaldehyde derivatives which are available and purchasable were used as a base to design the chalcone virtual library. 8063 chalcones were constructed and geometrically optimized with Gaussian 09. Their physicochemical characteristics linked to the Lipinski rules were analyzed with Knime and CDK. The entire library was after docked against several targets including HIV-1 integrase, MRSA pyruvate kinase, HSP90, COX-1, COX-2, ALR2, MAOA, MAOB, acetylcholinesterase, butyrylcholinesterase and PLA2. With the exception of MAOA, which does not have a crystal structure ligand, all dockings were validated by redocking the original ligand provided by the literature. These targets are known in the literature to be inhibited by chalcone-derivatives. However, specificity of the particular known chalcone inhibitors to the particular targets is not known. To this end the performance of the generated chalcone library against the list of targets was of interest. The binding energy of ligand-protein complexes was generally good across the library. Statistical analysis including principal component analysis and hierarchical clustering analysis were made in order to investigate for any physical/chemical characteristics which might explain what chalcone features affect the binding energy of the ligand-protein complexes. The spherical polar coordinates defining the orientation of the binding poses were also calculated and used in the statistical analysis. The statistical analysis has allowed us to hypothesize the importance of these radial distances and the polar angles of key atoms in the chalcones in binding to the pyruvate kinase crystal structure. This was validated by the docking of another small library of compound models in which the α,β-unsaturated ketone chain of the chalcone was replaced by incrementally longer conjugated chains. Further studies on the chalcones themselves reveal rotameric systems in both cis and trans-configurations (which may impact binding), and also studied was the effect of Topliss-based modification and its impact of binding to HSP90. Molecular dynamics confirmed good binding of identified chalcone hits.
- Full Text:
- Date Issued: 2020