Towards development of a malaria diagnostic: Generation, screening and validation of novel aptamers recognising Plasmodium falciparum lactate dehydrogenase
- Authors: Frith, Kelly-Anne
- Date: 2020
- Subjects: Plasmodium falciparum , Malaria -- Chemotherapy , Oligonucleotides , Lactate dehydrogenase , Biochemical markers , Systematic evolution of ligands through exponential enrichment (SELEX)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142247 , vital:38062
- Description: Malaria, caused by infection with the Plasmodium parasite, is one of the leading causes of death in under-developed countries. Early detection is crucial for the effective treatment of malaria, particularly in cases where infection is due to Plasmodium falciparum. There is, therefore, an enduring need for portable, sensitive, reliable, accurate, durable, self-validating and cost-effective techniques for the rapid detection of malaria. Moreover, there is a demand to distinguish between various infectious species causing malaria. Research in the area of malarial biomarkers has identified a unique, species-specific, epitope of P. falciparum lactate dehydrogenase (PfLDH), enhancing prospects for the development of diagnostics capable of identifying the species causing malarial infection. In recent years, improvements have been made towards the development of rapid diagnostic tests for detecting malarial biomarkers. Owing to their low cost, ease of labeling, and high thermal stability (relative to antibodies), the development and synthesis of aptamers that target the malarial lactate dehydrogenase represents one of the key innovations in the field of rapid diagnostics for malaria. This study explored the generation of aptamers that specifically target P. falciparum. Two sets of aptamers with diagnostically-supportive functions were generated independently, through parallel SELEX of recombinantly-expressed, full-length Plasmodium falciparum lactate dehydrogenase (rPfLDH), and an oligopeptide comprising the P. falciparum-specific epitope on lactate dehydrogenase (LDHp). The latter offers a promising solution for generating aptamers capable of binding with high specificity to P. falciparum. In this work, an rLDH class of aptamers was generated when SELEX was performed using the full-length rPfLDH protein as the target and the LDHp class of aptamers was generated when SELEX was performed using the oligopeptide LDHp as a target. Aptamers were successfully generated through the process of SELEX (systematic evolution of ligands through exponential enrichment) following the study and application of several optimisation steps, particularly during the amplification stage of SELEX. Optimisation steps included the study of improvements in PCR conditions; role of surfactants (Triton-X), modifying the PCR clean-up protocol; and agarose gel excision. Structurally-relevant moieties with particular consensus sequences (GGTAG and GGCG) were found in aptamers both reported here and previously published, confirming their importance in recognition of the target. Novel moieties particular to this work (ATTAT and poly-A stretches) were identified. Clades of consensus sequences were identified in both the rLDH and LDHp groups of aptamers, where sequences in the rLDH clade did not show preferential binding to rPfLDH while those in the LDHp clade (particularly LDHp 3 and 18) were able to recognise and bind only LDHp. Of the 19 sequences returned from the parallel SELEX procedures for rPfLDH (11 sequences) and LDHp (8 sequences), six rPfLDH and all eight LDHp sequences underwent preliminary screening and those with low responses eliminated. Of the eight LDHp-targeting aptamer sequences, five were preliminarily shown to bind to LDHp, whereas only two rPfLDH-targeting sequences were shown to bind to the target (rLDH 4 and 7). To this small selection of rPfLDH oligonucleotide sequences, two more (rLDH 1 and 15) were chosen for further study based on their sequences, secondary and predicted tertiary conformations. Sequences chosen for further study were therefore: rLDH 1, 4, 7 and 15 in the rLDH class, and LDHp 1, 3, 11, 14 and 18 in the LDHp class. Binding properties of the aptamers towards their targets were investigated using enzyme-linked oligonucleotide assays (ELONA), fluorophore-linked oligonucleotide assays (FLONA), electromobility shift assays (EMSA), surface plasmon resonance (SPR), and GelRed dissociation assays, while applications towards aptasensors were explored using electrochemical impedance spectroscopy (EIS) and fluorescent microscopy. Some inconsistencies were seen for specific aptamer to target binding interactions using specific techniques; however, generally, binding to the targets was observed across the techniques assessed. These varied responses demonstrate the need to screen and validate aptamers using a variety of techniques and platforms not necessarily specific for the proposed application. From the aptamer binding screening studies using ELONA, the most promising aptamers generated were identified as LDHp 11, rLDH 4, rLDH 7 and rLDH 15. Aptamer rLDH 4, which was generated against rPfLDH, exhibited preferential and specific binding to the lactate dehydrogenase from P. falciparum, over the recombinantly-expressed lactate dehydrogenase from Plasmodium vivax (rPvLDH), albeit with lowered responses compared to LDHp 11 in ELONA and EMSA studies. However, in kinetic ELONA studies rLDH 4 showed binding to both rPfLDH and rPvLDH. Aptamer rLDH 7 showed high affinity for rPfLDH and rPvLDH in kinetic studies using ELONA. However, screening studies with ELONA indicates that aptamer rLDH 7 may not be suitable for diagnostic tests in serum samples given its non-specific binding to human serum albumin (HSA). Aptamer rLDH 15 exhibited species specificity for rPfLDH in screening studies using ELONA but showed affinity towards rPvLDH (albeit lower relative to its affinity for rPfLDH) in kinetic studies using ELONA. LDHp 11, generated against the PfLDH peptide, showed a clear preference for rPfLDH when compared to rPvLDH and other control proteins, in both sets of ELONA studies conducted, as well as EMSA, thus possessing a strong ability to identify the presence of Plasmodium falciparum owing to its generation against the species-specific epitope. While LDHp 1 demonstrated binding to plasmodial LDH in a flow-through system (SPR), so reiterating ELONA responses, it did not perform well in the remaining methodologies. Aptamers rLDH 1 and 15 and LDHp 3, 14 and 18 exhibited a mixed set of results throughout the target protein screening analyses and were, thus, not considered for selective binding in P. falciparum parasite bodies. In studies aimed at exploring biosensor assemblies utilising the developed aptamers, both rLDH 4 and LDHp 11, along with rLDH 7, LDHp 1 and pL1, demonstrated in situ binding to the native PfLDH in fluorescent microscopy. LDHp 11 exhibited FITC-based fluorescence equivalent to the anti-rPfLDHp IgY antibody in confocal fluorescent microscopy indicating superior binding to the native PfLDH compared to the remaining aptamers. An examination of electrochemical impedance as a platform for a biosensor assembly did not, in these studies, exhibit the required sensitivity using physiologically relevant concentrations of analyte expected for pLDH following infection with Plasmodium spp. Malstat/LDH activity was explored for application in a colorimetric aptasensor. A decrease in both rPfLDH and rPvLDH activity was observed following incubation with the tested aptamers, but rLDH 1, rLDH 7 and LDHp 14 did not exhibit similar decreases in rPvLDH activity. Aptamers rLDH 1, 4 and 7 and LDHp 11 and 14 were, therefore, not selected as candidates for LDH capture in LDH activity-based diagnostic devices for P. falciparum. The decreases in pLDH activity in the presence of aptamers could hold promise as direct or antagonistic malaria therapeutic agents. Preliminary studies on the application of aptamers as malaria therapeutic agents, while of interest, should be viewed with due caution given the challenges of aptamers reaching the intracellular native plasmodial LDH hosted within the red blood cells. In conclusion, this work has shown the ability of the LDHp 11 aptamer, generated in these studies, to selectively bind rPfLDH over rPvLDH, and to bind to the native PfLDH in fluorescent microscopy, indicating that this aptamer holds promise as a biorecognition element in malaria biosensors and other diagnostic devices for the detection, and differentiation, of P. falciparum and P. vivax. The use of a species-specific epitope of P. falciparum as a target in aptamer generation paves the way for similar such studies aimed at generating aptamers with species selectivity for other Plasmodium species.
- Full Text:
- Date Issued: 2020
- Authors: Frith, Kelly-Anne
- Date: 2020
- Subjects: Plasmodium falciparum , Malaria -- Chemotherapy , Oligonucleotides , Lactate dehydrogenase , Biochemical markers , Systematic evolution of ligands through exponential enrichment (SELEX)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142247 , vital:38062
- Description: Malaria, caused by infection with the Plasmodium parasite, is one of the leading causes of death in under-developed countries. Early detection is crucial for the effective treatment of malaria, particularly in cases where infection is due to Plasmodium falciparum. There is, therefore, an enduring need for portable, sensitive, reliable, accurate, durable, self-validating and cost-effective techniques for the rapid detection of malaria. Moreover, there is a demand to distinguish between various infectious species causing malaria. Research in the area of malarial biomarkers has identified a unique, species-specific, epitope of P. falciparum lactate dehydrogenase (PfLDH), enhancing prospects for the development of diagnostics capable of identifying the species causing malarial infection. In recent years, improvements have been made towards the development of rapid diagnostic tests for detecting malarial biomarkers. Owing to their low cost, ease of labeling, and high thermal stability (relative to antibodies), the development and synthesis of aptamers that target the malarial lactate dehydrogenase represents one of the key innovations in the field of rapid diagnostics for malaria. This study explored the generation of aptamers that specifically target P. falciparum. Two sets of aptamers with diagnostically-supportive functions were generated independently, through parallel SELEX of recombinantly-expressed, full-length Plasmodium falciparum lactate dehydrogenase (rPfLDH), and an oligopeptide comprising the P. falciparum-specific epitope on lactate dehydrogenase (LDHp). The latter offers a promising solution for generating aptamers capable of binding with high specificity to P. falciparum. In this work, an rLDH class of aptamers was generated when SELEX was performed using the full-length rPfLDH protein as the target and the LDHp class of aptamers was generated when SELEX was performed using the oligopeptide LDHp as a target. Aptamers were successfully generated through the process of SELEX (systematic evolution of ligands through exponential enrichment) following the study and application of several optimisation steps, particularly during the amplification stage of SELEX. Optimisation steps included the study of improvements in PCR conditions; role of surfactants (Triton-X), modifying the PCR clean-up protocol; and agarose gel excision. Structurally-relevant moieties with particular consensus sequences (GGTAG and GGCG) were found in aptamers both reported here and previously published, confirming their importance in recognition of the target. Novel moieties particular to this work (ATTAT and poly-A stretches) were identified. Clades of consensus sequences were identified in both the rLDH and LDHp groups of aptamers, where sequences in the rLDH clade did not show preferential binding to rPfLDH while those in the LDHp clade (particularly LDHp 3 and 18) were able to recognise and bind only LDHp. Of the 19 sequences returned from the parallel SELEX procedures for rPfLDH (11 sequences) and LDHp (8 sequences), six rPfLDH and all eight LDHp sequences underwent preliminary screening and those with low responses eliminated. Of the eight LDHp-targeting aptamer sequences, five were preliminarily shown to bind to LDHp, whereas only two rPfLDH-targeting sequences were shown to bind to the target (rLDH 4 and 7). To this small selection of rPfLDH oligonucleotide sequences, two more (rLDH 1 and 15) were chosen for further study based on their sequences, secondary and predicted tertiary conformations. Sequences chosen for further study were therefore: rLDH 1, 4, 7 and 15 in the rLDH class, and LDHp 1, 3, 11, 14 and 18 in the LDHp class. Binding properties of the aptamers towards their targets were investigated using enzyme-linked oligonucleotide assays (ELONA), fluorophore-linked oligonucleotide assays (FLONA), electromobility shift assays (EMSA), surface plasmon resonance (SPR), and GelRed dissociation assays, while applications towards aptasensors were explored using electrochemical impedance spectroscopy (EIS) and fluorescent microscopy. Some inconsistencies were seen for specific aptamer to target binding interactions using specific techniques; however, generally, binding to the targets was observed across the techniques assessed. These varied responses demonstrate the need to screen and validate aptamers using a variety of techniques and platforms not necessarily specific for the proposed application. From the aptamer binding screening studies using ELONA, the most promising aptamers generated were identified as LDHp 11, rLDH 4, rLDH 7 and rLDH 15. Aptamer rLDH 4, which was generated against rPfLDH, exhibited preferential and specific binding to the lactate dehydrogenase from P. falciparum, over the recombinantly-expressed lactate dehydrogenase from Plasmodium vivax (rPvLDH), albeit with lowered responses compared to LDHp 11 in ELONA and EMSA studies. However, in kinetic ELONA studies rLDH 4 showed binding to both rPfLDH and rPvLDH. Aptamer rLDH 7 showed high affinity for rPfLDH and rPvLDH in kinetic studies using ELONA. However, screening studies with ELONA indicates that aptamer rLDH 7 may not be suitable for diagnostic tests in serum samples given its non-specific binding to human serum albumin (HSA). Aptamer rLDH 15 exhibited species specificity for rPfLDH in screening studies using ELONA but showed affinity towards rPvLDH (albeit lower relative to its affinity for rPfLDH) in kinetic studies using ELONA. LDHp 11, generated against the PfLDH peptide, showed a clear preference for rPfLDH when compared to rPvLDH and other control proteins, in both sets of ELONA studies conducted, as well as EMSA, thus possessing a strong ability to identify the presence of Plasmodium falciparum owing to its generation against the species-specific epitope. While LDHp 1 demonstrated binding to plasmodial LDH in a flow-through system (SPR), so reiterating ELONA responses, it did not perform well in the remaining methodologies. Aptamers rLDH 1 and 15 and LDHp 3, 14 and 18 exhibited a mixed set of results throughout the target protein screening analyses and were, thus, not considered for selective binding in P. falciparum parasite bodies. In studies aimed at exploring biosensor assemblies utilising the developed aptamers, both rLDH 4 and LDHp 11, along with rLDH 7, LDHp 1 and pL1, demonstrated in situ binding to the native PfLDH in fluorescent microscopy. LDHp 11 exhibited FITC-based fluorescence equivalent to the anti-rPfLDHp IgY antibody in confocal fluorescent microscopy indicating superior binding to the native PfLDH compared to the remaining aptamers. An examination of electrochemical impedance as a platform for a biosensor assembly did not, in these studies, exhibit the required sensitivity using physiologically relevant concentrations of analyte expected for pLDH following infection with Plasmodium spp. Malstat/LDH activity was explored for application in a colorimetric aptasensor. A decrease in both rPfLDH and rPvLDH activity was observed following incubation with the tested aptamers, but rLDH 1, rLDH 7 and LDHp 14 did not exhibit similar decreases in rPvLDH activity. Aptamers rLDH 1, 4 and 7 and LDHp 11 and 14 were, therefore, not selected as candidates for LDH capture in LDH activity-based diagnostic devices for P. falciparum. The decreases in pLDH activity in the presence of aptamers could hold promise as direct or antagonistic malaria therapeutic agents. Preliminary studies on the application of aptamers as malaria therapeutic agents, while of interest, should be viewed with due caution given the challenges of aptamers reaching the intracellular native plasmodial LDH hosted within the red blood cells. In conclusion, this work has shown the ability of the LDHp 11 aptamer, generated in these studies, to selectively bind rPfLDH over rPvLDH, and to bind to the native PfLDH in fluorescent microscopy, indicating that this aptamer holds promise as a biorecognition element in malaria biosensors and other diagnostic devices for the detection, and differentiation, of P. falciparum and P. vivax. The use of a species-specific epitope of P. falciparum as a target in aptamer generation paves the way for similar such studies aimed at generating aptamers with species selectivity for other Plasmodium species.
- 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
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
Ecological assessment of a temperate river system using biomonitoring techniques: a case study of the Bloukrans River system, South Africa
- Authors: Magadze, Tinotenda
- Date: 2020
- Subjects: Bloukrans River , Ecological assessment (Biology) -- South Africa , Stream ecology -- South Africa , Rivers -- Environmental aspects -- South Africa , Benthic animals -- Effect of human beings on -- South Africa , Water quality biological assessment -- South Africa , Diatoms -- South Africa -- Data processing
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142933 , vital:38177
- Description: Escalating pressures from growing human populations and environmental impacts increasingly imperil freshwater ecosystems. The Bloukrans River, which drains an urbanised and agricultural catchment in the Eastern Cape province of South Africa, is no exception. Detailed knowledge of the structure and function of the aquatic ecosystems is required in order to create models and matrices that predict, guide assessment and direct intervention on ecological integrity and water quality management in these systems. The main objectives of this research were to: examine the effects of urbanization on the benthic macroinvertebrate functional feeding guild structure among different stream orders; determine if benthic diatoms can be used as effective and reliable indicators of ionic composition and conductivity in different stream order categories and finally; to evaluate the applicability of the South African Diatom Index (SADI) and other indices in the Eastern Cape region of South Africa. Field studies were carried out to explore temporal patterns in community structure (macroinvertebrates and diatoms) and ecosystem function related to land-use patterns, instream habitat availability, and water quality parameters in the Bloukrans River system across four study periods: February (summer) and July (winter) 2016 and February (summer) and May/July (winter) 2018. The study was conducted along a gradient of impacts from less impacted agricultural headwaters to highly impacted urban sites located immediately downstream of the city of Makhanda. Macroinvertebrates were separated into functional feeding groups (FFGs) (i.e. collector-gatherer, collector-filterer, scraper, shredder, and predator) which were then used to assess the effects of selected physico-chemical variables and riparian zone condition on FFG organization. Collector-gatherers were the most abundant in the Bloukrans River and represented 71.3 % of the macroinvertebrate assemblages. Stream order 1species such as Nitzschia palea, Gomphonema parvulum, Tryblionella apiculata, Diploneis vulgaris and Staurosira elliptica. Multivariate analysis (Canonical correspondence analysis (CCA)) indicated that differences in diatom community assemblages were best explained by calcium, magnesium, pH, phosphate, nitrate, dissolved oxygen, sediment nitrate, conductivity and salinity. These results indicate that diatoms can be used as bioindicators for monitoring highly impacted river systems and to also further examine pollution gradients and impacts of specific/point pollution sources. In order to further test the application of diatom indices, nine sites with contrasting water quality were sampled along the length river system in February, May and July 2018. Diatom-based indices incorporated in OMNIDIA software were applied to assess the integrity of the water quality as indicated by diatom communities. For comparative purposes, several foreign indices (e.g. the trophic diatom index (TDI), the percentage pollution-tolerant valves (%PTV), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. From the results, the Percentage Pollution-Tolerant Valves (%PTV) of most urban sites in the Bloukrans River was above the 20% limit indicating the presence of organic pollutants. Although the foreign diatom indices were applicable in the study, the SADI had significant correlations with most water quality variables (p < 0.05) compared to other indices such as Watanabe Index (WAT), Biological Index of Water Quality Trophic Index (BIWQ) and Trophic Index (TI)). These results support wider use of the SADI as an indicator of water quality conditions in South African river systems. Finally, the observed variations in diatom community structure and composition as a result of changes in water quality were broadly in agreement with the results of macroinvertebrate FFG structure indicating that the two biological indicators can, and should, be used as complementary techniques in the biomonitoring of rivers and streams in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Magadze, Tinotenda
- Date: 2020
- Subjects: Bloukrans River , Ecological assessment (Biology) -- South Africa , Stream ecology -- South Africa , Rivers -- Environmental aspects -- South Africa , Benthic animals -- Effect of human beings on -- South Africa , Water quality biological assessment -- South Africa , Diatoms -- South Africa -- Data processing
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142933 , vital:38177
- Description: Escalating pressures from growing human populations and environmental impacts increasingly imperil freshwater ecosystems. The Bloukrans River, which drains an urbanised and agricultural catchment in the Eastern Cape province of South Africa, is no exception. Detailed knowledge of the structure and function of the aquatic ecosystems is required in order to create models and matrices that predict, guide assessment and direct intervention on ecological integrity and water quality management in these systems. The main objectives of this research were to: examine the effects of urbanization on the benthic macroinvertebrate functional feeding guild structure among different stream orders; determine if benthic diatoms can be used as effective and reliable indicators of ionic composition and conductivity in different stream order categories and finally; to evaluate the applicability of the South African Diatom Index (SADI) and other indices in the Eastern Cape region of South Africa. Field studies were carried out to explore temporal patterns in community structure (macroinvertebrates and diatoms) and ecosystem function related to land-use patterns, instream habitat availability, and water quality parameters in the Bloukrans River system across four study periods: February (summer) and July (winter) 2016 and February (summer) and May/July (winter) 2018. The study was conducted along a gradient of impacts from less impacted agricultural headwaters to highly impacted urban sites located immediately downstream of the city of Makhanda. Macroinvertebrates were separated into functional feeding groups (FFGs) (i.e. collector-gatherer, collector-filterer, scraper, shredder, and predator) which were then used to assess the effects of selected physico-chemical variables and riparian zone condition on FFG organization. Collector-gatherers were the most abundant in the Bloukrans River and represented 71.3 % of the macroinvertebrate assemblages. Stream order 1species such as Nitzschia palea, Gomphonema parvulum, Tryblionella apiculata, Diploneis vulgaris and Staurosira elliptica. Multivariate analysis (Canonical correspondence analysis (CCA)) indicated that differences in diatom community assemblages were best explained by calcium, magnesium, pH, phosphate, nitrate, dissolved oxygen, sediment nitrate, conductivity and salinity. These results indicate that diatoms can be used as bioindicators for monitoring highly impacted river systems and to also further examine pollution gradients and impacts of specific/point pollution sources. In order to further test the application of diatom indices, nine sites with contrasting water quality were sampled along the length river system in February, May and July 2018. Diatom-based indices incorporated in OMNIDIA software were applied to assess the integrity of the water quality as indicated by diatom communities. For comparative purposes, several foreign indices (e.g. the trophic diatom index (TDI), the percentage pollution-tolerant valves (%PTV), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. From the results, the Percentage Pollution-Tolerant Valves (%PTV) of most urban sites in the Bloukrans River was above the 20% limit indicating the presence of organic pollutants. Although the foreign diatom indices were applicable in the study, the SADI had significant correlations with most water quality variables (p < 0.05) compared to other indices such as Watanabe Index (WAT), Biological Index of Water Quality Trophic Index (BIWQ) and Trophic Index (TI)). These results support wider use of the SADI as an indicator of water quality conditions in South African river systems. Finally, the observed variations in diatom community structure and composition as a result of changes in water quality were broadly in agreement with the results of macroinvertebrate FFG structure indicating that the two biological indicators can, and should, be used as complementary techniques in the biomonitoring of rivers and streams in South Africa.
- Full Text:
- Date Issued: 2020
Understanding climate change and rural livelihoods in Zimbabwe: adaptation by communal farmers in Ngundu, Chivi District
- Authors: Nciizah, Elinah
- Date: 2020
- Subjects: Agriculture -- Zimbabwe , Agriculture -- Climatic factors -- Chivi District (Zimbabwe) , Chivi District (Zimbabwe) -- Rural conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/118765 , vital:34666
- Description: Climate change and variability is a global phenomenon which has deeply localised patterns, dynamics and effects. Amongst those people who are particularly vulnerable to climate change effects are small-scale farmers who are dependent in large part on rain-fed agriculture in pursuing their livelihoods. This is true of small-scale farmers in contemporary Zimbabwe and, more specifically, farmers in communal areas. At the same time, at international and national levels, there are attempts currently to minimise the effects of, and to adapt to, climate change. However, adaptation measures also exist at local levels amongst small-scale farmers, such as communal farmers in Zimbabwe. In this context, as its main objective, this thesis examines climate change and small-scale farmer livelihood adaptation to climate change with specific reference to communal farmers in Chivi District in Zimbabwe and, in particular, in Ward 25 which is popularly known as Ngundu. In pursuing this main objective, a number of subsidiary objectives are addressed, including a focus on the established livelihoods of Ngundu farmers, the perceptions and concerns of Ngundu farmers about climate change, the coping and adaptation measures of Ngundu farmers, and the enablements and constraints which affect attempts by Ngundu farmers to adopt such measures. The fieldwork for the thesis involved a diverse array of research methods, such as a questionnaire survey, life-history interviews, key informant interviews, focus group discussions and transect walks. In terms of theoretical framing, the thesis makes use of both middle-level theory (the Sustainable Livelihoods Framework) and macro-theory in the form of the sociological work of Margaret Archer. Combined, these two theories allow for a focus on both structure and agency when seeking to understand livelihood adaptations to climate change by communal farmers in Ngundu. The thesis concludes that there are massive constraints inhibiting adaptation measures by Ngundu farmers, but that this should not distract from the deep, often historically-embedded, concerns of Ngundu farmers about climate change and the multiple ways in which they express agency in and through adaptation and coping activities. It also highlights the need for more specifically sociological investigations of climate change and small-scale farmer adaptation, as well as the need for localised studies which are able to identify and analyse the specificities of adaptation.
- Full Text:
- Date Issued: 2020
- Authors: Nciizah, Elinah
- Date: 2020
- Subjects: Agriculture -- Zimbabwe , Agriculture -- Climatic factors -- Chivi District (Zimbabwe) , Chivi District (Zimbabwe) -- Rural conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/118765 , vital:34666
- Description: Climate change and variability is a global phenomenon which has deeply localised patterns, dynamics and effects. Amongst those people who are particularly vulnerable to climate change effects are small-scale farmers who are dependent in large part on rain-fed agriculture in pursuing their livelihoods. This is true of small-scale farmers in contemporary Zimbabwe and, more specifically, farmers in communal areas. At the same time, at international and national levels, there are attempts currently to minimise the effects of, and to adapt to, climate change. However, adaptation measures also exist at local levels amongst small-scale farmers, such as communal farmers in Zimbabwe. In this context, as its main objective, this thesis examines climate change and small-scale farmer livelihood adaptation to climate change with specific reference to communal farmers in Chivi District in Zimbabwe and, in particular, in Ward 25 which is popularly known as Ngundu. In pursuing this main objective, a number of subsidiary objectives are addressed, including a focus on the established livelihoods of Ngundu farmers, the perceptions and concerns of Ngundu farmers about climate change, the coping and adaptation measures of Ngundu farmers, and the enablements and constraints which affect attempts by Ngundu farmers to adopt such measures. The fieldwork for the thesis involved a diverse array of research methods, such as a questionnaire survey, life-history interviews, key informant interviews, focus group discussions and transect walks. In terms of theoretical framing, the thesis makes use of both middle-level theory (the Sustainable Livelihoods Framework) and macro-theory in the form of the sociological work of Margaret Archer. Combined, these two theories allow for a focus on both structure and agency when seeking to understand livelihood adaptations to climate change by communal farmers in Ngundu. The thesis concludes that there are massive constraints inhibiting adaptation measures by Ngundu farmers, but that this should not distract from the deep, often historically-embedded, concerns of Ngundu farmers about climate change and the multiple ways in which they express agency in and through adaptation and coping activities. It also highlights the need for more specifically sociological investigations of climate change and small-scale farmer adaptation, as well as the need for localised studies which are able to identify and analyse the specificities of adaptation.
- Full Text:
- Date Issued: 2020
Understanding biotic interactions in invaded pond communities in the Sundays River irrigation network, South Africa
- Authors: Mofu, Lubabalo
- Date: 2020
- Subjects: Mozambique tilapia -- South Africa -- Sundays River (Eastern Cape) , Western mosquitofish -- South Africa -- Sundays River (Eastern Cape) , Gobiidae -- South Africa -- Sundays River (Eastern Cape) , Clupeidae -- South Africa -- Sundays River (Eastern Cape) , Reservoirs -- South Africa -- Sundays River (Eastern Cape) , Zooplankton -- South Africa -- Sundays River (Eastern Cape) , Freshwater ecology -- South Africa -- Sundays River (Eastern Cape) , Biotic communities -- South Africa -- Sundays River (Eastern Cape) , Fishes -- Effect of temperature on -- South Africa -- Sundays River (Eastern Cape) , Stable isotopes , Relative Impact Potential
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167089 , vital:41436
- Description: The Sundays River valley irrigation ponds provide a unique opportunity to investigate biotic interactions within a biological invasions context, as they contain both native and non-native fish species. This study focusses on two native species (Glossogobius callidus and Gilchristella aestuaria) and two non-native species (Oreochromis mossambicus and Gambusia affinis). The ecology of the ponds was driven by physico-chemical variables, mainly temperature, but the interactions between fishes were a complex interplay between temperature, pond community ecology and food web structure. Seasonal changes in temperature and subsequent fluctuations in water levels resulted in changes in zooplankton community. Chlorophyll-a, temperature, G. callidus and G. affinis were the drivers of the seasonal changes in macroinvertebrate composition. Stable isotope analysis identified substantial ontogenetic dietary shifts in all species, corresponding to changes in body size. Stable isotope analysis revealed that the niche space occupied by G. affinis was broad and overlapped with that of the other three focal species. Stable isotope metrics showed that G. affinis and O. mossambicus utilised a wide range of resources compared to G. callidus and G. aestuaria. Stomach content analysis showed that G. callidus, O. mossambicus and G. affinis fed predominantly on benthic resources, while G. aestuaria fed mainly plankton resources. Functional response experiments revealed that G. callidus and G. affinis both displayed Type II functional responses. In single fish trials, G. affinis had significantly higher functional responses than G. callidus. In heterospecific G. callidus-G. affinis combinations the functional response of G. callidus was reduced by the presence of G. affinis, whereas, this combination greatly enhanced G. affinis functional response magnitudes. The functional response of G. callidus, O. mossambicus and G. affinis under two temperature treatments along with fish abundance data was used to determine temporal differences in the ecological impacts of each fish species between seasons. The relative impact potential of O. mossambicus was consistently higher than that of G. callidus and G. affinis. This study demonstrates how seasonal temperature fluctuations affect the relative impact capacities of introduced species. Overall, this thesis showed that high temperature along with life-history traits contributes to the biotic interactions between native and non-native species in novel environments.
- Full Text:
- Date Issued: 2020
- Authors: Mofu, Lubabalo
- Date: 2020
- Subjects: Mozambique tilapia -- South Africa -- Sundays River (Eastern Cape) , Western mosquitofish -- South Africa -- Sundays River (Eastern Cape) , Gobiidae -- South Africa -- Sundays River (Eastern Cape) , Clupeidae -- South Africa -- Sundays River (Eastern Cape) , Reservoirs -- South Africa -- Sundays River (Eastern Cape) , Zooplankton -- South Africa -- Sundays River (Eastern Cape) , Freshwater ecology -- South Africa -- Sundays River (Eastern Cape) , Biotic communities -- South Africa -- Sundays River (Eastern Cape) , Fishes -- Effect of temperature on -- South Africa -- Sundays River (Eastern Cape) , Stable isotopes , Relative Impact Potential
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167089 , vital:41436
- Description: The Sundays River valley irrigation ponds provide a unique opportunity to investigate biotic interactions within a biological invasions context, as they contain both native and non-native fish species. This study focusses on two native species (Glossogobius callidus and Gilchristella aestuaria) and two non-native species (Oreochromis mossambicus and Gambusia affinis). The ecology of the ponds was driven by physico-chemical variables, mainly temperature, but the interactions between fishes were a complex interplay between temperature, pond community ecology and food web structure. Seasonal changes in temperature and subsequent fluctuations in water levels resulted in changes in zooplankton community. Chlorophyll-a, temperature, G. callidus and G. affinis were the drivers of the seasonal changes in macroinvertebrate composition. Stable isotope analysis identified substantial ontogenetic dietary shifts in all species, corresponding to changes in body size. Stable isotope analysis revealed that the niche space occupied by G. affinis was broad and overlapped with that of the other three focal species. Stable isotope metrics showed that G. affinis and O. mossambicus utilised a wide range of resources compared to G. callidus and G. aestuaria. Stomach content analysis showed that G. callidus, O. mossambicus and G. affinis fed predominantly on benthic resources, while G. aestuaria fed mainly plankton resources. Functional response experiments revealed that G. callidus and G. affinis both displayed Type II functional responses. In single fish trials, G. affinis had significantly higher functional responses than G. callidus. In heterospecific G. callidus-G. affinis combinations the functional response of G. callidus was reduced by the presence of G. affinis, whereas, this combination greatly enhanced G. affinis functional response magnitudes. The functional response of G. callidus, O. mossambicus and G. affinis under two temperature treatments along with fish abundance data was used to determine temporal differences in the ecological impacts of each fish species between seasons. The relative impact potential of O. mossambicus was consistently higher than that of G. callidus and G. affinis. This study demonstrates how seasonal temperature fluctuations affect the relative impact capacities of introduced species. Overall, this thesis showed that high temperature along with life-history traits contributes to the biotic interactions between native and non-native species in novel environments.
- Full Text:
- Date Issued: 2020
The Influence of Clientelism on the Informal Sector in Zimbabwe : a Case Study of Glen View 8 Complex, Harare
- Authors: Tandire, Justin
- Date: 2021-04
- Subjects: Patron and client -- Zimbabwe -- Harare , Informal sector (Economics) -- Zimbabwe -- Harare , Informal sector (Economics) -- Political aspects -- Zimbabwe -- Harare , Patronage, Political -- Zimbabwe -- Harare , ZANU-PF (Organization : Zimbabwe) , Zimbabwe -- Social conditions , Glen View Complex 8 (Zimbabwe)
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/177986 , vital:42896 , 10.21504/10962/177986
- Description: This study focuses on the influence of clientelism in the informal sector of Zimbabwe in Glen View 8 (Complex). The study used the case of Glen view 8 (complex) in Harare Province. The study focused on political dynamics in the informal sector; livelihood strategies employed by informal sector operators; manifestation of “Big Men”, social networks in the informal sector; and different strategies employed by operators to overcome the problems of political manipulation, clientelism and patronage. It employs a qualitative research methodology to enable a nuanced comprehension of the clientelistic relationships that take place in the informal sector of Zimbabwe. Through in-depth interviews, focus group discussions, narratives and in-depth interviews with key informants, the study explored the clientelistic nature of the informal sector. The major findings of the study are that the informal sector in Zimbabwe is influenced by political patronage. It was established that patronage influences the informal sector in Zimbabwe in general and at Glen View Complex 8 in particular. Some of the operators revealed that patronage negatively affects their business as they are sometimes forced to attend political party meetings either at the complex or at ZANU-PF star rallies in town. The operators experience a plethora of problems such as lack of security, poor sanitation, stiff competition, poor infrastructure, lack of insurance and fire outbreaks. It has been revealed that most of the problems experienced at the complex are a result of the politicisation of the informal sector particularly by the ZANU-PF party. Operators at the complex have described the politicisation of the informal sector as a major drawback to their efforts of realising maximum benefits from their work. Therefore, the thrust of this thesis is premised on the de-politicisation of the informal sector as the starting point in the transformation of the activities of the operators. , Thesis (PhD) -- Faculty of Humanities, Sociology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Tandire, Justin
- Date: 2021-04
- Subjects: Patron and client -- Zimbabwe -- Harare , Informal sector (Economics) -- Zimbabwe -- Harare , Informal sector (Economics) -- Political aspects -- Zimbabwe -- Harare , Patronage, Political -- Zimbabwe -- Harare , ZANU-PF (Organization : Zimbabwe) , Zimbabwe -- Social conditions , Glen View Complex 8 (Zimbabwe)
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/177986 , vital:42896 , 10.21504/10962/177986
- Description: This study focuses on the influence of clientelism in the informal sector of Zimbabwe in Glen View 8 (Complex). The study used the case of Glen view 8 (complex) in Harare Province. The study focused on political dynamics in the informal sector; livelihood strategies employed by informal sector operators; manifestation of “Big Men”, social networks in the informal sector; and different strategies employed by operators to overcome the problems of political manipulation, clientelism and patronage. It employs a qualitative research methodology to enable a nuanced comprehension of the clientelistic relationships that take place in the informal sector of Zimbabwe. Through in-depth interviews, focus group discussions, narratives and in-depth interviews with key informants, the study explored the clientelistic nature of the informal sector. The major findings of the study are that the informal sector in Zimbabwe is influenced by political patronage. It was established that patronage influences the informal sector in Zimbabwe in general and at Glen View Complex 8 in particular. Some of the operators revealed that patronage negatively affects their business as they are sometimes forced to attend political party meetings either at the complex or at ZANU-PF star rallies in town. The operators experience a plethora of problems such as lack of security, poor sanitation, stiff competition, poor infrastructure, lack of insurance and fire outbreaks. It has been revealed that most of the problems experienced at the complex are a result of the politicisation of the informal sector particularly by the ZANU-PF party. Operators at the complex have described the politicisation of the informal sector as a major drawback to their efforts of realising maximum benefits from their work. Therefore, the thrust of this thesis is premised on the de-politicisation of the informal sector as the starting point in the transformation of the activities of the operators. , Thesis (PhD) -- Faculty of Humanities, Sociology, 2021
- Full Text:
- Date Issued: 2021-04
A combined modelling approach for simulating channel–wetland exchanges in large African river basins
- Authors: Makungu, Eunice J
- Date: 2020
- Subjects: Watersheds -- Africa , Watershed management -- Africa , Water resources development -- Africa -- International cooperation , Floodplain management -- Africa , Wetland ecology -- Simulation methods -- Africa , Wetland management -- Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/123288 , vital:35424
- Description: In Africa, many large and extensive wetlands are hydrologically connected to rivers, and their environmental integrity, as well as their influence on downstream flow regimes, depends on the prevailing channel–wetland exchange processes. These processes are inherently complex and vary spatially and temporally. Understanding channel–wetland exchanges is therefore, indispensable for the effective management of wetlands and the associated river basins. However, this information is limited in most of the river basins containing large wetlands in Africa. Furthermore, it is important to understand the links between upstream and downstream flow regimes and the wetland dynamics themselves, specifically where there are water resource developments that may affect these links (upstream developments), or be affected by them (downstream developments). Hydrological modelling of the entire basin using basin-scale models that include wetland components in their structures can be used to provide the information required to manage water resources in such basins. However, the level of detail of wetland processes included in many basin-scale models is typically very low and the lack of understanding of the wetland dynamics makes it difficult to quantify the relevant parameters. Detailed hydraulic models represent the channel-wetland exchanges in a much more explicit manner, but require relatively more data and time resources to establish than coarser scale hydrological models. The main objective of this study was, therefore, to investigate the use of a detailed hydraulic wetland model to provide a better understanding of channel–wetland exchanges and wetland dynamics, and to use the results to improve the parameterisation of a basin-scale model. The study focused on improving the water resource assessments modelling of three data-scarce African river basins that contain large wetlands: the floodplains of the Luangwa and Upper Zambezi River basins and the Usangu wetland in the Upper Great Ruaha River basin. The overall objective was achieved through a combined modelling approach that uses a detailed high-resolution LISFLOOD-FP hydraulic model to inform the structure and parameters of the GW Pitman monthly hydrological model. The results from the LISFLOOD-FP were used to improve the understanding of the channel–wetland exchange dynamics and to establish the wetland parameters required in the GW Pitman model. While some wetland parameters were directly quantified from the LISFLOOD-FP model results, others, which are highly empirical, were estimated by manually calibrating the GW Pitman wetland sub-model implemented in excel spreadsheets containing the LISFLOOD-FP model results. Finally, the GW Pitman model with the inclusion of the estimated wetland parameters was applied for each basin and the results compared to the available downstream observed flow data. The two models have been successfully applied in southern Africa, with the GW Pitman model being one of the most widely applied hydrological models in this region. To address the issue of data scarcity, during setup of these models, the study mainly relied on the global datasets which clearly adds to the overall uncertainty of the modelling approach. However, this is a typical situation for most of the data scarce regions of the continent. A number of challenges were, however, faced during the setup of the LISFLOOD-FP, mainly due to the limitations of the data inputs. Some of the LISFLOOD-FP data inputs include boundary conditions (upstream and downstream), channel cross-sections and wetland topography. In the absence of observed daily flows to quantify the wetland upstream boundary conditions, monthly flow volumes simulated using the GW Pitman monthly model (without including the wetland sub-model) were disaggregated into daily flows using a disaggregation sub-model. The simulated wetland inflows were evaluated using the observed flow data for downstream gauging stations that include the wetland effects. The results highlighted that it is important to understand the possible impacts of each wetland on the downstream flow regime during the evaluations of the model simulation results. Although the disaggregation approach cannot be validated due to a lack of observed data, it at least enables the simulated monthly flows to be used in the daily time step hydraulic model. One of the recommendations is that improvements are required in gauging station networks to provide more observed information for the main river and the larger tributary inflows into these large and important wetland systems. Even a limited amount of newly observed data would be helpful to reduce some of the uncertainties in the combined modelling approach. The SRTM 90 m DEM (used to represent wetland topography) was filtered to reduce local variations and noise effects (mainly vegetation bias), but there were some pixels that falsely affect the inundation results, and the recently released vegetation-corrected DEMs are suggested to improve the simulation results. Channel cross-section values derived from global datasets should be examined because some widths estimated from the Andreadis et al. (2013) dataset were found to be over-generalised and did not reflect widths measured using high-resolution Google Earth in many places. There is an indication that channel cross-sections digitised from Google Earth images can be successfully used in the model setup except in densely vegetated swamps where the values are difficult to estimate, and in such situations, field measured cross-section data are required. Small channels such as those found in the Usangu wetland could play major role in the exchange dynamics, but digitising them all was not straightforward and only key ones were included in the model setup. Clearly, this inevitably introduced uncertainties in the simulated results, and future studies should consider applying methods that simplify extractions of most of these channels from high-resolution images to improve the simulated results. The study demonstrated that the wetland and channel physical characteristics, as well as the seasonal flow magnitude, largely influence the channel–wetland exchanges and wetland dynamics. The inundation results indicated that the area–storage and storage–inflow relationships form hysteretic curves, but the shape of these curves vary with flood magnitude and wetland type. Anticlockwise hysteresis curves were observed in both relationships for the floodplains (Luangwa and Barotse), whereas there appears to be no dominant curve type for the Usangu wetlands. The lack of well-defined hysteretic relationships in the Usangu could be related to some of the difficulties (and resulting uncertainties) that were experienced in setting up the model for this wetland. The storage–inflow relationships in all wetlands have quite complex rising limbs due to multiple flow peaks during the main wet season. The largest inundation area and storage volume for the Barotse and Usangu wetlands occurred after the peak discharge of the wet season, a result that is clearly related to the degree of connectivity between the main channel and those areas of the wetlands that are furthest away from the channel. Hysteresis effects were found to increase with an increase in flood magnitudes and temporal variations in the wetland inflows. Overall, hysteresis behaviour is common in large wetlands and it is recommended that hysteresis curves should be reflected in basin-scale modelling of large river basins with substantial wetland areas. At a daily time scale, inflow–outflow relationships showed a significant peak reduction and a delayed time to peak of several weeks in the Barotse and Usangu wetlands, whereas the attenuation effects of the Luangwa floodplain are minimal. To a large extent, the LISFLOOD-FP results provided useful information to establish wetland parameters and assess the structure of Pitman wetland sub-model. The simple spreadsheet used to estimate wetland parameters did not account for the wetland water transfers from the upstream to the next section downstream (the condition that is included in the LISFLOOD-FP model) for the case when the wetlands were distributed across more than one sub-basin. It is recommended that a method that allows for the upstream wetland inflows and the channel inflows should be included in the spreadsheet. The same is true to the Pitman model structure, and a downstream transfer of water can be modelled through return flows to the channel. The structure of the wetland sub-model was modified to allow an option for the return flows to occur at any time during the simulation period to provide for types of wetlands (e.g. the Luangwa) where spills from the channel and drainage back to the channel occur simultaneously. The setup of the GW Pitman model with the inclusion of wetland parameters improved the simulation results. However, the results for the Usangu wetlands were not very satisfactory and the collection of additional field data related to exchange dynamics is recommended to achieve improvements. The impacts of the Luangwa floodplain on the flow regime of the Luangwa River are very small at the monthly time scale, whereas the Barotse floodplain system and the Usangu wetlands extensively regulate flows of the Zambezi River and the Great Ruaha River, respectively. The results highlighted the possibilities of regionalising some wetland parameters using an understanding of wetland physical characteristics and their water exchange dynamics. However, some parameters remain difficult to quantify in the absence of site-specific information about the water exchange dynamics. The overall conclusion is that the approach implemented in this study presents an important step towards the improvements of water resource assessments modelling for research and practical purposes in data-scarce river basins. This approach is not restricted to the two used models, as it can be applied using different model combinations to achieve similar study purpose.
- Full Text:
- Date Issued: 2020
A combined modelling approach for simulating channel–wetland exchanges in large African river basins
- Authors: Makungu, Eunice J
- Date: 2020
- Subjects: Watersheds -- Africa , Watershed management -- Africa , Water resources development -- Africa -- International cooperation , Floodplain management -- Africa , Wetland ecology -- Simulation methods -- Africa , Wetland management -- Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/123288 , vital:35424
- Description: In Africa, many large and extensive wetlands are hydrologically connected to rivers, and their environmental integrity, as well as their influence on downstream flow regimes, depends on the prevailing channel–wetland exchange processes. These processes are inherently complex and vary spatially and temporally. Understanding channel–wetland exchanges is therefore, indispensable for the effective management of wetlands and the associated river basins. However, this information is limited in most of the river basins containing large wetlands in Africa. Furthermore, it is important to understand the links between upstream and downstream flow regimes and the wetland dynamics themselves, specifically where there are water resource developments that may affect these links (upstream developments), or be affected by them (downstream developments). Hydrological modelling of the entire basin using basin-scale models that include wetland components in their structures can be used to provide the information required to manage water resources in such basins. However, the level of detail of wetland processes included in many basin-scale models is typically very low and the lack of understanding of the wetland dynamics makes it difficult to quantify the relevant parameters. Detailed hydraulic models represent the channel-wetland exchanges in a much more explicit manner, but require relatively more data and time resources to establish than coarser scale hydrological models. The main objective of this study was, therefore, to investigate the use of a detailed hydraulic wetland model to provide a better understanding of channel–wetland exchanges and wetland dynamics, and to use the results to improve the parameterisation of a basin-scale model. The study focused on improving the water resource assessments modelling of three data-scarce African river basins that contain large wetlands: the floodplains of the Luangwa and Upper Zambezi River basins and the Usangu wetland in the Upper Great Ruaha River basin. The overall objective was achieved through a combined modelling approach that uses a detailed high-resolution LISFLOOD-FP hydraulic model to inform the structure and parameters of the GW Pitman monthly hydrological model. The results from the LISFLOOD-FP were used to improve the understanding of the channel–wetland exchange dynamics and to establish the wetland parameters required in the GW Pitman model. While some wetland parameters were directly quantified from the LISFLOOD-FP model results, others, which are highly empirical, were estimated by manually calibrating the GW Pitman wetland sub-model implemented in excel spreadsheets containing the LISFLOOD-FP model results. Finally, the GW Pitman model with the inclusion of the estimated wetland parameters was applied for each basin and the results compared to the available downstream observed flow data. The two models have been successfully applied in southern Africa, with the GW Pitman model being one of the most widely applied hydrological models in this region. To address the issue of data scarcity, during setup of these models, the study mainly relied on the global datasets which clearly adds to the overall uncertainty of the modelling approach. However, this is a typical situation for most of the data scarce regions of the continent. A number of challenges were, however, faced during the setup of the LISFLOOD-FP, mainly due to the limitations of the data inputs. Some of the LISFLOOD-FP data inputs include boundary conditions (upstream and downstream), channel cross-sections and wetland topography. In the absence of observed daily flows to quantify the wetland upstream boundary conditions, monthly flow volumes simulated using the GW Pitman monthly model (without including the wetland sub-model) were disaggregated into daily flows using a disaggregation sub-model. The simulated wetland inflows were evaluated using the observed flow data for downstream gauging stations that include the wetland effects. The results highlighted that it is important to understand the possible impacts of each wetland on the downstream flow regime during the evaluations of the model simulation results. Although the disaggregation approach cannot be validated due to a lack of observed data, it at least enables the simulated monthly flows to be used in the daily time step hydraulic model. One of the recommendations is that improvements are required in gauging station networks to provide more observed information for the main river and the larger tributary inflows into these large and important wetland systems. Even a limited amount of newly observed data would be helpful to reduce some of the uncertainties in the combined modelling approach. The SRTM 90 m DEM (used to represent wetland topography) was filtered to reduce local variations and noise effects (mainly vegetation bias), but there were some pixels that falsely affect the inundation results, and the recently released vegetation-corrected DEMs are suggested to improve the simulation results. Channel cross-section values derived from global datasets should be examined because some widths estimated from the Andreadis et al. (2013) dataset were found to be over-generalised and did not reflect widths measured using high-resolution Google Earth in many places. There is an indication that channel cross-sections digitised from Google Earth images can be successfully used in the model setup except in densely vegetated swamps where the values are difficult to estimate, and in such situations, field measured cross-section data are required. Small channels such as those found in the Usangu wetland could play major role in the exchange dynamics, but digitising them all was not straightforward and only key ones were included in the model setup. Clearly, this inevitably introduced uncertainties in the simulated results, and future studies should consider applying methods that simplify extractions of most of these channels from high-resolution images to improve the simulated results. The study demonstrated that the wetland and channel physical characteristics, as well as the seasonal flow magnitude, largely influence the channel–wetland exchanges and wetland dynamics. The inundation results indicated that the area–storage and storage–inflow relationships form hysteretic curves, but the shape of these curves vary with flood magnitude and wetland type. Anticlockwise hysteresis curves were observed in both relationships for the floodplains (Luangwa and Barotse), whereas there appears to be no dominant curve type for the Usangu wetlands. The lack of well-defined hysteretic relationships in the Usangu could be related to some of the difficulties (and resulting uncertainties) that were experienced in setting up the model for this wetland. The storage–inflow relationships in all wetlands have quite complex rising limbs due to multiple flow peaks during the main wet season. The largest inundation area and storage volume for the Barotse and Usangu wetlands occurred after the peak discharge of the wet season, a result that is clearly related to the degree of connectivity between the main channel and those areas of the wetlands that are furthest away from the channel. Hysteresis effects were found to increase with an increase in flood magnitudes and temporal variations in the wetland inflows. Overall, hysteresis behaviour is common in large wetlands and it is recommended that hysteresis curves should be reflected in basin-scale modelling of large river basins with substantial wetland areas. At a daily time scale, inflow–outflow relationships showed a significant peak reduction and a delayed time to peak of several weeks in the Barotse and Usangu wetlands, whereas the attenuation effects of the Luangwa floodplain are minimal. To a large extent, the LISFLOOD-FP results provided useful information to establish wetland parameters and assess the structure of Pitman wetland sub-model. The simple spreadsheet used to estimate wetland parameters did not account for the wetland water transfers from the upstream to the next section downstream (the condition that is included in the LISFLOOD-FP model) for the case when the wetlands were distributed across more than one sub-basin. It is recommended that a method that allows for the upstream wetland inflows and the channel inflows should be included in the spreadsheet. The same is true to the Pitman model structure, and a downstream transfer of water can be modelled through return flows to the channel. The structure of the wetland sub-model was modified to allow an option for the return flows to occur at any time during the simulation period to provide for types of wetlands (e.g. the Luangwa) where spills from the channel and drainage back to the channel occur simultaneously. The setup of the GW Pitman model with the inclusion of wetland parameters improved the simulation results. However, the results for the Usangu wetlands were not very satisfactory and the collection of additional field data related to exchange dynamics is recommended to achieve improvements. The impacts of the Luangwa floodplain on the flow regime of the Luangwa River are very small at the monthly time scale, whereas the Barotse floodplain system and the Usangu wetlands extensively regulate flows of the Zambezi River and the Great Ruaha River, respectively. The results highlighted the possibilities of regionalising some wetland parameters using an understanding of wetland physical characteristics and their water exchange dynamics. However, some parameters remain difficult to quantify in the absence of site-specific information about the water exchange dynamics. The overall conclusion is that the approach implemented in this study presents an important step towards the improvements of water resource assessments modelling for research and practical purposes in data-scarce river basins. This approach is not restricted to the two used models, as it can be applied using different model combinations to achieve similar study purpose.
- Full Text:
- Date Issued: 2020
Performance, functionalism and form in Ịzọn oral poety
- Authors: Armstrong, Imomotimi
- Date: 2020
- Subjects: Ijo (African people , Ijo language , Folk poetry, Ijo , Folk poetry -- Nigeria
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140641 , vital:37906
- Description: Since the publication of Ruth Finnegan’s influential Oral Literature in Africa, way back in 1970, scholars have been paying earnest attention to oral traditions on the African continent. That seminal book pointed out to Africanist scholars the need to urgently collect and document the oral literatures of their various ethnic groups before they die out. However, it is the verbal arts of the major ethnic groups on the continent that very often benefit from this collection and documentation, as it were. Therefore, this study sought to examine the oral poetry of the Ịzọn, a minority ethnic nationality, located in the oil-rich Niger Delta region of Nigeria. The study employed unstructured interviews and participant observations to collect the data for the research. The transcribed and translated data was examined through three eclectic theories to the study of folklore: Russian formalism, performance and functionalism. The study found out that Ịzọn oral poetry is a combination of songs and one person’s praise chants. Moreover, it revealed that praise chanting is a recent practice amongst the Ịzọn that was introduced into Ịzọnland by Chief Adolphus Munamuna from the Yoruba of southwestern Nigeria. Furthermore, the study established that oral poetry plays important roles amongst the people. Besides, it ascertained that the performance of some sub-categories of the poetry is highly dramatic and theatrical. It also discovered that stylistic techniques such as formula, parallelism, proverb, ideophone, praise title, metaphor, repetition, alliteration, assonance, vowel lengthening, amongst others, give the poetry the quality of “literariness.” In addition, the study found out that the poetry, like oral poetry in other ethnic groups, demonstrates the three qualities of change, adaptability and survival. The study has contributed to existing scholarship on African oral traditions in the sense of collecting, documenting and generating awareness on Ịzọn oral poetry, most importantly pointing out the existence of praise chanting amongst a people who had no such culture and the conditions that gave rise to that practice.
- Full Text:
- Date Issued: 2020
- Authors: Armstrong, Imomotimi
- Date: 2020
- Subjects: Ijo (African people , Ijo language , Folk poetry, Ijo , Folk poetry -- Nigeria
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140641 , vital:37906
- Description: Since the publication of Ruth Finnegan’s influential Oral Literature in Africa, way back in 1970, scholars have been paying earnest attention to oral traditions on the African continent. That seminal book pointed out to Africanist scholars the need to urgently collect and document the oral literatures of their various ethnic groups before they die out. However, it is the verbal arts of the major ethnic groups on the continent that very often benefit from this collection and documentation, as it were. Therefore, this study sought to examine the oral poetry of the Ịzọn, a minority ethnic nationality, located in the oil-rich Niger Delta region of Nigeria. The study employed unstructured interviews and participant observations to collect the data for the research. The transcribed and translated data was examined through three eclectic theories to the study of folklore: Russian formalism, performance and functionalism. The study found out that Ịzọn oral poetry is a combination of songs and one person’s praise chants. Moreover, it revealed that praise chanting is a recent practice amongst the Ịzọn that was introduced into Ịzọnland by Chief Adolphus Munamuna from the Yoruba of southwestern Nigeria. Furthermore, the study established that oral poetry plays important roles amongst the people. Besides, it ascertained that the performance of some sub-categories of the poetry is highly dramatic and theatrical. It also discovered that stylistic techniques such as formula, parallelism, proverb, ideophone, praise title, metaphor, repetition, alliteration, assonance, vowel lengthening, amongst others, give the poetry the quality of “literariness.” In addition, the study found out that the poetry, like oral poetry in other ethnic groups, demonstrates the three qualities of change, adaptability and survival. The study has contributed to existing scholarship on African oral traditions in the sense of collecting, documenting and generating awareness on Ịzọn oral poetry, most importantly pointing out the existence of praise chanting amongst a people who had no such culture and the conditions that gave rise to that practice.
- Full Text:
- Date Issued: 2020
The precarious ‘good mother’ position: a psychosocial reading of maternal subjectivity of working mothers in scarcely-resourced South African communities
- Authors: Kinahan-Sweeney, Siobhan
- Date: 2020
- Subjects: Motherhood -- Psychological aspects -- South Africa , Working mothers -- South Africa -- Attitudes , Working mothers -- South Africa -- Psychology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142464 , vital:38082
- Description: This psychosocial study investigates the maternal subjectivities of mothers returning to work after maternity leave, who are living in scarcely-resourced Cape Town communities in South Africa. Engaging with interview texts and listening to mothers’ talk, I explore how and why maternal subjectivity is constructed discursively and defensively in our talk. This thesis claims that these particular mothers predominately employ instrumental mothering discourse. The traditional subject position of the intensive mother – which is typically assumed to be the ‘good mother’ – is not a position available to these mothers due to their social circumstances and working role. Subsequently, material provision, the baby’s thriving and surviving body, finding substitute carers and maternal preoccupation are constructed as qualities of ‘good mothering’ in their talk. This ‘good mother’ position, however, is a precarious position that both these mothers and I invest in to defend against feelings towards their babies and themselves as well as to deny (maternal) ambivalence in a problematic social system. In a combined analysis drawing on discursive theory and psychoanalysis, more specifically contemporary attachment theory and intersubjectivity theory, I illustrate how both these mothers and I – as emotional, social and political subjects – co-construct maternal subjectivity. Based on the findings, recommendations for parent-infant interventions are discussed. Arguing that a purely psychoanalytic reading of investment perpetuates notions of individual blame and pathology, I advocate for a psychosocial reading that does not neglect failing social systems but rather pursues an open and reflective, yet critical, mindfulness when listening to talk.
- Full Text:
- Date Issued: 2020
- Authors: Kinahan-Sweeney, Siobhan
- Date: 2020
- Subjects: Motherhood -- Psychological aspects -- South Africa , Working mothers -- South Africa -- Attitudes , Working mothers -- South Africa -- Psychology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142464 , vital:38082
- Description: This psychosocial study investigates the maternal subjectivities of mothers returning to work after maternity leave, who are living in scarcely-resourced Cape Town communities in South Africa. Engaging with interview texts and listening to mothers’ talk, I explore how and why maternal subjectivity is constructed discursively and defensively in our talk. This thesis claims that these particular mothers predominately employ instrumental mothering discourse. The traditional subject position of the intensive mother – which is typically assumed to be the ‘good mother’ – is not a position available to these mothers due to their social circumstances and working role. Subsequently, material provision, the baby’s thriving and surviving body, finding substitute carers and maternal preoccupation are constructed as qualities of ‘good mothering’ in their talk. This ‘good mother’ position, however, is a precarious position that both these mothers and I invest in to defend against feelings towards their babies and themselves as well as to deny (maternal) ambivalence in a problematic social system. In a combined analysis drawing on discursive theory and psychoanalysis, more specifically contemporary attachment theory and intersubjectivity theory, I illustrate how both these mothers and I – as emotional, social and political subjects – co-construct maternal subjectivity. Based on the findings, recommendations for parent-infant interventions are discussed. Arguing that a purely psychoanalytic reading of investment perpetuates notions of individual blame and pathology, I advocate for a psychosocial reading that does not neglect failing social systems but rather pursues an open and reflective, yet critical, mindfulness when listening to talk.
- 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
Carnivore intra-guild competition in Selati Game Reserve, Limpopo Province, South Africa
- Authors: Comley, Jessica
- Date: 2020
- Subjects: Hyenas -- Behavior -- South Africa , Hyenas -- South Africa , Hyenas -- Ecology -- South Africa , Top predators -- South Africa , Top predators -- Ecology -- South Africa , Animal communities -- South Africa , Animal behavior -- South Africa , Mutualism (Biology) -- South Africa , Coexistence of species -- South Africa , Game farms -- South Africa , Selati Game Reserve (South Africa)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115558 , vital:34163
- Description: Carnivore intra-guild interactions can be important drivers of carnivore community composition and ecosystem functioning. Large carnivores are particularly important since they occupy the highest trophic levels and can exert extensive influences on subordinate carnivores and prey species. Given Africa’s rapidly expanding human population, enclosed reserves such as those found in South Africa, may become increasingly important for carnivore conservation. A major concern, however, is that the interactions and co-existence of multiple carnivores in these systems is poorly understood. Additionally, the majority of reserves in South Africa are small ( 400km²), potentially increasing the likelihood of competition. My research aimed to provide insight into the interactions and co-existence of a multi-carnivore community within a small, enclosed reserve in South Africa (Selati Game Reserve). I tackled this task by using a combination of field techniques including camera trap surveys, ungulate transect surveys, aerial count surveys, location data collected from collared large carnivores and scat and kill site analyses. I found that carnivore-carnivore interactions, and their associated impacts, varied within the carnivore guild and that co-existence may be due to trade-offs between various risks (i.e. interference and exploitative competition) and benefits (i.e. resources such as food and space). My findings also revealed that large carnivores, such as lions (Panthera leo), spotted hyaenas (Crocuta crocuta) and leopards (Panthera pardus) do not have homogenous effects and that site-specific research on multiple-carnivores is integral for conserving biodiversity and ecosystem dynamics. Lions were the dominant large carnivore (in terms of intra-guild predation, space use and resource use) despite being outnumbered seven to one by spotted hyaenas. Leopard occupancy was negatively influenced by lions and leopard diet overlapped almost completely (91%) with spotted hyaenas, suggesting increased kleptoparasitism of leopard kills by spotted hyaenas. While my study provides valuable insight into the complexity of carnivore intra-guild competition in a small, enclosed reserve it also highlights major research gaps and emphasises the need for ecosystem-based research throughout southern Africa to fully understand how multiple sympatric carnivores co-exist in these systems.
- Full Text:
- Date Issued: 2020
- Authors: Comley, Jessica
- Date: 2020
- Subjects: Hyenas -- Behavior -- South Africa , Hyenas -- South Africa , Hyenas -- Ecology -- South Africa , Top predators -- South Africa , Top predators -- Ecology -- South Africa , Animal communities -- South Africa , Animal behavior -- South Africa , Mutualism (Biology) -- South Africa , Coexistence of species -- South Africa , Game farms -- South Africa , Selati Game Reserve (South Africa)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115558 , vital:34163
- Description: Carnivore intra-guild interactions can be important drivers of carnivore community composition and ecosystem functioning. Large carnivores are particularly important since they occupy the highest trophic levels and can exert extensive influences on subordinate carnivores and prey species. Given Africa’s rapidly expanding human population, enclosed reserves such as those found in South Africa, may become increasingly important for carnivore conservation. A major concern, however, is that the interactions and co-existence of multiple carnivores in these systems is poorly understood. Additionally, the majority of reserves in South Africa are small ( 400km²), potentially increasing the likelihood of competition. My research aimed to provide insight into the interactions and co-existence of a multi-carnivore community within a small, enclosed reserve in South Africa (Selati Game Reserve). I tackled this task by using a combination of field techniques including camera trap surveys, ungulate transect surveys, aerial count surveys, location data collected from collared large carnivores and scat and kill site analyses. I found that carnivore-carnivore interactions, and their associated impacts, varied within the carnivore guild and that co-existence may be due to trade-offs between various risks (i.e. interference and exploitative competition) and benefits (i.e. resources such as food and space). My findings also revealed that large carnivores, such as lions (Panthera leo), spotted hyaenas (Crocuta crocuta) and leopards (Panthera pardus) do not have homogenous effects and that site-specific research on multiple-carnivores is integral for conserving biodiversity and ecosystem dynamics. Lions were the dominant large carnivore (in terms of intra-guild predation, space use and resource use) despite being outnumbered seven to one by spotted hyaenas. Leopard occupancy was negatively influenced by lions and leopard diet overlapped almost completely (91%) with spotted hyaenas, suggesting increased kleptoparasitism of leopard kills by spotted hyaenas. While my study provides valuable insight into the complexity of carnivore intra-guild competition in a small, enclosed reserve it also highlights major research gaps and emphasises the need for ecosystem-based research throughout southern Africa to fully understand how multiple sympatric carnivores co-exist in these systems.
- Full Text:
- Date Issued: 2020
The lived experiences of women with human immunodeficiency virus (HIV) in Malawi: an interpretative phenomenological analysis (IPA)
- Authors: Nkhalamba, Mathero Michelle
- Date: 2020
- Subjects: HIV-positive women -- Malawi , HIV infections -- Sex factors -- Malawi , HIV infections -- Social aspects -- Malawi , HIV-positive women -- Malawi -- Social conditions , HIV-positive women -- Malawi -- Economic conditions , Poverty -- Malawi , Antiretroviral agents -- Malawi , Phenomenological psychology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145291 , vital:38425
- Description: Research on African women and HIV, particularly research that investigates their experiences of living with the virus, has been relatively peripheral. As a response to the apparent knowledge and research gaps, this project is a qualitative study involving women living with human immunodeficiency virus (WLHIV) and attending an anti-retroviral treatment (ART) clinic at Zomba Central Hospital in Southern Malawi. The study utilised an interpretative phenomenological analysis (IPA) approach, which informed all aspects of the data-collection and data-analysis processes. Using purposive sampling, 12 women were recruited and interviewed on three occasions over a period of six months. The interviews were conducted in Chichewa and audio recorded and later transcribed into English. Fourteen superordinate themes emerged from the analysis representing the women’s prominent life experiences, how they received their diagnosis, and how they contained the trauma of their diagnosis. The analysis also developed themes regarding how they coped with the challenges of living with the human immunodeficiency virus (HIV) and made sense of their experiences. The results showed that the women struggled with multiple challenges experienced through their various identities as WLHIV. The findings also pointed to interlocking disadvantages that put the women at risk of infection, and which were present from childhood. This has implications for more structural and multidisciplinary interventions for WLHIV.
- Full Text:
- Date Issued: 2020
- Authors: Nkhalamba, Mathero Michelle
- Date: 2020
- Subjects: HIV-positive women -- Malawi , HIV infections -- Sex factors -- Malawi , HIV infections -- Social aspects -- Malawi , HIV-positive women -- Malawi -- Social conditions , HIV-positive women -- Malawi -- Economic conditions , Poverty -- Malawi , Antiretroviral agents -- Malawi , Phenomenological psychology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145291 , vital:38425
- Description: Research on African women and HIV, particularly research that investigates their experiences of living with the virus, has been relatively peripheral. As a response to the apparent knowledge and research gaps, this project is a qualitative study involving women living with human immunodeficiency virus (WLHIV) and attending an anti-retroviral treatment (ART) clinic at Zomba Central Hospital in Southern Malawi. The study utilised an interpretative phenomenological analysis (IPA) approach, which informed all aspects of the data-collection and data-analysis processes. Using purposive sampling, 12 women were recruited and interviewed on three occasions over a period of six months. The interviews were conducted in Chichewa and audio recorded and later transcribed into English. Fourteen superordinate themes emerged from the analysis representing the women’s prominent life experiences, how they received their diagnosis, and how they contained the trauma of their diagnosis. The analysis also developed themes regarding how they coped with the challenges of living with the human immunodeficiency virus (HIV) and made sense of their experiences. The results showed that the women struggled with multiple challenges experienced through their various identities as WLHIV. The findings also pointed to interlocking disadvantages that put the women at risk of infection, and which were present from childhood. This has implications for more structural and multidisciplinary interventions for WLHIV.
- 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
A gendered analysis of conditional cash based transfers: a case study of Puntland Technical Vocational Skills Training Programme, Somalia
- Authors: Chitombi, Rumbidzai
- Date: 2020
- Subjects: Puntland Technical Vocational Skills Training Programme , Transfer payments -- Somalia -- Case studies , Economic assistance, Domestic -- Somalia , Economic development -- Social aspects -- Somalia , Women -- Somalia -- Social conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167335 , vital:41469
- Description: As part of the worldwide development system, conditional cash transfer (CCT) programmes have become an increasingly popular policy and development approach in seeking to address poverty, especially in developing countries. Under the CCT programmes, beneficiaries are given assistance in the form of either cash or cash vouchers after fulfilling certain obligations of the development programme, such as attending training, enacting proper health care, or ensuring regular school attendance of children. The programmes have been described as a ‘double-edged sword’ since they aim to address poverty and, at the same time, reduce reliance on government largesse. In this regard, they are seen as potentially effective, and more empowering, alternatives to more traditional social assistance programmes whereby poor people receive welfare assistance in the form of ‘in kind’ and ‘unconditional’ assistance, receiving this as either food or shelter commodities, and without having to meet any conditions in doing so. This ‘traditional’ way of assisting poor people has largely been criticised for creating a dependency syndrome amongst the beneficiaries. In certain cases, CCT programmes focus specifically on women, either in receiving the cash transfer or in meeting the conditions attached to the programme, or both. In this context, considerable debate exists in the scholarly literature about the effects of such CCT programmes on the situation and status of women, specifically in terms of possibly empowering women. While some scholars claim that these programmes enhance the human and financial assets of women, others argue that focusing specifically on women, and as care-givers within households, tends to reproduce gender-based inequalities and subordination. Since gender equality and female empowerment are now key issues in global development spheres, and at national levels, this thesis aims to contribute to literature on the effects of CCTs on gender and women’s empowerment. This is pursued by way of a gendered perspective on CCTs as a development methodology for empowering women with reference to Somalia, using the Puntland Technical Vocational Skills Training programme as a case study. This programme focused, in the main, on internally-displaced people in Somalia, with a particular emphasis on women in meeting the programme conditions (i.e. participating in a training programme) and in being the cash recipients. The study used both quantitative and qualitative approaches for data collection and analysis, focusing on sixty selected beneficiaries who participated in the Puntland Technical Vocational skills training programme in Somalia from 2013. The thesis examines the prevailing structures (including cultural dynamics and socio-economic factors) in Somalia which lead to women’s subordination, notably in the light of significant internal displacement because of war and conflict and the emergence of internally-displaced camps. On this basis, from a gendered perspective, there is a critical appraisal of the manner in which the Puntland CCT programme affected women’s subordinate status, including how it may have led to the restructuring of gendered relations at both household and community levels. In offering this appraisal with reference to the Puntland programme, the thesis argues that women’s subordination and, by extension, women’s empowerment, is multi-faceted, and that continuity and change along the dimensions of subordination is often uneven and contradictory. Further, as also demonstrated in the Puntland case study, women’s subordination (as a social totality) is not a totalising system, such that women regularly make use of gaps in the system as opportunities to enhance their well-being without confronting the totality of the system.
- Full Text:
- Date Issued: 2020
- Authors: Chitombi, Rumbidzai
- Date: 2020
- Subjects: Puntland Technical Vocational Skills Training Programme , Transfer payments -- Somalia -- Case studies , Economic assistance, Domestic -- Somalia , Economic development -- Social aspects -- Somalia , Women -- Somalia -- Social conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167335 , vital:41469
- Description: As part of the worldwide development system, conditional cash transfer (CCT) programmes have become an increasingly popular policy and development approach in seeking to address poverty, especially in developing countries. Under the CCT programmes, beneficiaries are given assistance in the form of either cash or cash vouchers after fulfilling certain obligations of the development programme, such as attending training, enacting proper health care, or ensuring regular school attendance of children. The programmes have been described as a ‘double-edged sword’ since they aim to address poverty and, at the same time, reduce reliance on government largesse. In this regard, they are seen as potentially effective, and more empowering, alternatives to more traditional social assistance programmes whereby poor people receive welfare assistance in the form of ‘in kind’ and ‘unconditional’ assistance, receiving this as either food or shelter commodities, and without having to meet any conditions in doing so. This ‘traditional’ way of assisting poor people has largely been criticised for creating a dependency syndrome amongst the beneficiaries. In certain cases, CCT programmes focus specifically on women, either in receiving the cash transfer or in meeting the conditions attached to the programme, or both. In this context, considerable debate exists in the scholarly literature about the effects of such CCT programmes on the situation and status of women, specifically in terms of possibly empowering women. While some scholars claim that these programmes enhance the human and financial assets of women, others argue that focusing specifically on women, and as care-givers within households, tends to reproduce gender-based inequalities and subordination. Since gender equality and female empowerment are now key issues in global development spheres, and at national levels, this thesis aims to contribute to literature on the effects of CCTs on gender and women’s empowerment. This is pursued by way of a gendered perspective on CCTs as a development methodology for empowering women with reference to Somalia, using the Puntland Technical Vocational Skills Training programme as a case study. This programme focused, in the main, on internally-displaced people in Somalia, with a particular emphasis on women in meeting the programme conditions (i.e. participating in a training programme) and in being the cash recipients. The study used both quantitative and qualitative approaches for data collection and analysis, focusing on sixty selected beneficiaries who participated in the Puntland Technical Vocational skills training programme in Somalia from 2013. The thesis examines the prevailing structures (including cultural dynamics and socio-economic factors) in Somalia which lead to women’s subordination, notably in the light of significant internal displacement because of war and conflict and the emergence of internally-displaced camps. On this basis, from a gendered perspective, there is a critical appraisal of the manner in which the Puntland CCT programme affected women’s subordinate status, including how it may have led to the restructuring of gendered relations at both household and community levels. In offering this appraisal with reference to the Puntland programme, the thesis argues that women’s subordination and, by extension, women’s empowerment, is multi-faceted, and that continuity and change along the dimensions of subordination is often uneven and contradictory. Further, as also demonstrated in the Puntland case study, women’s subordination (as a social totality) is not a totalising system, such that women regularly make use of gaps in the system as opportunities to enhance their well-being without confronting the totality of the system.
- Full Text:
- Date Issued: 2020
Design of immunosensor for the detection of C-reactive protein using oriented antibody immobilization
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
- Authors: Adesina, Abiola Olanike
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/163080 , vital:41010 , https://dx.doi.org/10.21504/10962/163080
- Description: Thesis (PhD)--Rhodes University, Science Faculty, Department of Chemistry, 2020.
- Full Text:
- Date Issued: 2020
Walking at the intersection of Seamon’s place ballet and Relph’s insideness: understanding how students experience the university as a place through their everyday habitual walking
- Mtolo, Siyathokoza Monwabisi
- Authors: Mtolo, Siyathokoza Monwabisi
- Date: 2020
- Subjects: Seamon, David , Relph, EC , College students -- South Africa -- Makhanda -- Attitudes , Walking -- Sociological aspects , College students -- South Africa -- Makhanda -- Political activity , Rhodes University -- Students -- Attitudes , Student movements -- South Africa -- Makhanda
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162901 , vital:40995
- Description: Walking as a way to experience a place is a relatively understudied area of phenomenological study. Furthermore, globally (the world) and locally (South Africa) the study of the experience of tertiary education institutions as walked environments is minimal (see Puig-Ribera et al., 2008; Speck et al., 2010; Mtolo, 2017). However, the events of the South African #MustFall moment – especially the #RhodesMustFall part of the moment and how it began with the desecration of a statue that was walked past and found to be a misplaced artefact in a society that is in postcolonial/post-Apartheid times and space – highlighted the pressing need to study the experience of the university as a place through which habitual walking takes the student through moments of movement, rest, and encounter that are a highly consequential way in which placeness is experienced. This study is a way to document how students at Rhodes University experience the university’s placeness quality, through habitual walking, in an example of the way in which a place is experienced through moments of movement, rest, and encounter. For this study in-depth mobile interviews were conducted with 12 student participants from Rhodes University. The interviews were video-recorded as the participants talked while traversing through habitually walked areas of the campus that are the meaning-infused spaces which make up the Rhodes University that they traverse through on a daily basis. The dissertation found that in the experience of Rhodes University, through habitually walking its placeness, people experience moments of movement, rest, and encounter that are highly targeted and personalised. The experience of the Rhodes University campus is an experience of people and the built-up and decorated environment along similar lines. People bring to the experience of their walked space past experiences which inform consequentially how any space that is walked is experienced. People further employ strategies to ensure that the experience of walking a space is more to their desired quality as an experience, which ends up being meaningful and most likely to affect future instances of walking through meaning-infusing and meaning-infused space. Ultimately, the habitual walking of Rhodes University consequentially informs the relationship between students and Rhodes University’s placeness, as the walking is a way of learning how to be within a placeness that is engaged through alternating moments of movement, rest, and encounter that incrementally ‘open’ for experience Rhodes University in such a targeted manner that every student eventually has their personal and customised Rhodes University by virtue of it being just those sites and situations which have been engaged through habitual walking.
- Full Text:
- Date Issued: 2020
- Authors: Mtolo, Siyathokoza Monwabisi
- Date: 2020
- Subjects: Seamon, David , Relph, EC , College students -- South Africa -- Makhanda -- Attitudes , Walking -- Sociological aspects , College students -- South Africa -- Makhanda -- Political activity , Rhodes University -- Students -- Attitudes , Student movements -- South Africa -- Makhanda
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162901 , vital:40995
- Description: Walking as a way to experience a place is a relatively understudied area of phenomenological study. Furthermore, globally (the world) and locally (South Africa) the study of the experience of tertiary education institutions as walked environments is minimal (see Puig-Ribera et al., 2008; Speck et al., 2010; Mtolo, 2017). However, the events of the South African #MustFall moment – especially the #RhodesMustFall part of the moment and how it began with the desecration of a statue that was walked past and found to be a misplaced artefact in a society that is in postcolonial/post-Apartheid times and space – highlighted the pressing need to study the experience of the university as a place through which habitual walking takes the student through moments of movement, rest, and encounter that are a highly consequential way in which placeness is experienced. This study is a way to document how students at Rhodes University experience the university’s placeness quality, through habitual walking, in an example of the way in which a place is experienced through moments of movement, rest, and encounter. For this study in-depth mobile interviews were conducted with 12 student participants from Rhodes University. The interviews were video-recorded as the participants talked while traversing through habitually walked areas of the campus that are the meaning-infused spaces which make up the Rhodes University that they traverse through on a daily basis. The dissertation found that in the experience of Rhodes University, through habitually walking its placeness, people experience moments of movement, rest, and encounter that are highly targeted and personalised. The experience of the Rhodes University campus is an experience of people and the built-up and decorated environment along similar lines. People bring to the experience of their walked space past experiences which inform consequentially how any space that is walked is experienced. People further employ strategies to ensure that the experience of walking a space is more to their desired quality as an experience, which ends up being meaningful and most likely to affect future instances of walking through meaning-infusing and meaning-infused space. Ultimately, the habitual walking of Rhodes University consequentially informs the relationship between students and Rhodes University’s placeness, as the walking is a way of learning how to be within a placeness that is engaged through alternating moments of movement, rest, and encounter that incrementally ‘open’ for experience Rhodes University in such a targeted manner that every student eventually has their personal and customised Rhodes University by virtue of it being just those sites and situations which have been engaged through habitual walking.
- Full Text:
- Date Issued: 2020
Analysing emergent time within an isolated Universe through the application of interactions in the conditional probability approach
- Authors: Bryan, Kate Louise Halse
- Date: 2020
- Subjects: Space and time , Quantum gravity , Quantum theory , Relativity (Physics)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146676 , vital:38547
- Description: Time remains a frequently discussed issue in physics and philosophy. One interpretation of growing popularity is the ‘timeless’ view which states that our experience of time is only an illusion. The isolated Universe model, provided by the Wheeler-DeWitt equation, supports this interpretation by describing time using clocks in the conditional probability interpretation (CPI). However, the CPI customarily dismisses interaction effects as negligible creating a potential blind spot which overlooks the potential influence of interaction effects. Accounting for interactions opens up a new avenue of analysis and a potential challenge to the interpretation of time. In aid of our assessment of the impact interaction effects have on the CPI, we present rudimentary definitions of time and its associated concepts. Defined in a minimalist manner, time is argued to require a postulate of causality as a means of accounting for temporal ordering in physical theories. Several of these theories are discussed here in terms of their respective approaches to time and, despite their differences, there are indications that the accounts of time are unified in a more fundamental theory. An analytic analysis of the CPI, incorporating two different clock choices, and a qualitative analysis both confirm that interactions have a necessary role within the CPI. The consequence of removing interactions is a maximised uncertainty in any measurement of the clock and a restriction to a two-state system, as indicated by the results of the toy models and qualitative argument respectively. The philosophical implication is that we are not restricted to the timeless view since including interactions as agents of causal interventions between systems provides an account of time as a real phenomenon. This result highlights the reliance on a postulate of causality which forms a pressing problem in explaining our experience of time.
- Full Text:
- Date Issued: 2020
- Authors: Bryan, Kate Louise Halse
- Date: 2020
- Subjects: Space and time , Quantum gravity , Quantum theory , Relativity (Physics)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146676 , vital:38547
- Description: Time remains a frequently discussed issue in physics and philosophy. One interpretation of growing popularity is the ‘timeless’ view which states that our experience of time is only an illusion. The isolated Universe model, provided by the Wheeler-DeWitt equation, supports this interpretation by describing time using clocks in the conditional probability interpretation (CPI). However, the CPI customarily dismisses interaction effects as negligible creating a potential blind spot which overlooks the potential influence of interaction effects. Accounting for interactions opens up a new avenue of analysis and a potential challenge to the interpretation of time. In aid of our assessment of the impact interaction effects have on the CPI, we present rudimentary definitions of time and its associated concepts. Defined in a minimalist manner, time is argued to require a postulate of causality as a means of accounting for temporal ordering in physical theories. Several of these theories are discussed here in terms of their respective approaches to time and, despite their differences, there are indications that the accounts of time are unified in a more fundamental theory. An analytic analysis of the CPI, incorporating two different clock choices, and a qualitative analysis both confirm that interactions have a necessary role within the CPI. The consequence of removing interactions is a maximised uncertainty in any measurement of the clock and a restriction to a two-state system, as indicated by the results of the toy models and qualitative argument respectively. The philosophical implication is that we are not restricted to the timeless view since including interactions as agents of causal interventions between systems provides an account of time as a real phenomenon. This result highlights the reliance on a postulate of causality which forms a pressing problem in explaining our experience of time.
- Full Text:
- Date Issued: 2020
Synthesis, characterisation and electrocatalytic behaviour of three series of Metal Organic Frameworks
- Authors: Murinzi, Tafadzwa Wendy
- Date: 2020
- Subjects: Electrochemistry , Metal-organic frameworks , Polyoxometalates , Fourier transform infrared spectroscopy , Electrocatalysis , Cysteine
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167598 , vital:41495
- Description: Metal organic frameworks (MOFs) have received a lot of attention over the past few years due to their vast range of interesting properties and applications, such as catalysis, environmental sensing and storage. This wide range of potential applications is afforded by careful selection and manipulation of the components chosen in assembling of MOFs. In this study, three series of MOFs were synthesized from Co(II), Cu(II) and Mo(VI) polyoxometallates with either 1,3,5-benzenetricarboxylic acid, 1,2,4,5-benzenetetracarboxylic acid or 2,6- pyridinedicarboxylic acid as the ligands. In series 1, the common 1,3,5- benzenetricarboxylic acid MOF, HKUST-1, and POM modified HKUST-1 compounds involving encapsulation and encorporation of the POM were utilised. In series 2, flexible cobalt(II) benzenepolycarboxylate MOFs which investigated the effect of varying the degree of carboxylate substituent were utilised. In series 3, flexibly reduced heterocyclic polycarboxylate MOFs using 2,6-pyridine dicarboxylate were utilised. Solvothermal and slow evaporation synthesis conditions were employed. Where single crystals of good quality were produced, single crystal X-ray diffraction (SC-XRD) was employed for structural elucidation. In the absence of such crystals, a combination of elemental analysis, inductively coupled plasma optical emission spectrometry (ICP-OES) and powder X-ray diffraction (PXRD) was used. Characterization of the MOFs was done by Fourier transform infrared spectrometry (FTIR) and thermal methods, namely thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The electrocatalytic potential of the compounds in the oxidation of L-cysteine was then investigated using a variety of techniques. Cyclic voltammetry was used for L-cysteine detection whilst chronoamperometry and differential pulse voltammetry were used to determine the nanoprobes’ sensitivity, rate constants and detection limits. Electrochemical impedence spectroscopy was used to investigate the charge transfer resistance (RCT) and electron transfer kinetics. Of the three, series 3 gave the best signals and sensitivities for electrocatalysis of L-cysteine followed by series 2 and lastly series 1. Series 2 showed the highest stability and series 1 required the least overpotential. The results highlight the effects of different metal centres and ligands on electrocatalysis. The application of MOFs in electrochemistry is a relatively new field making the findings of this study a significant addition to the body of knowledge.
- Full Text:
- Date Issued: 2020
- Authors: Murinzi, Tafadzwa Wendy
- Date: 2020
- Subjects: Electrochemistry , Metal-organic frameworks , Polyoxometalates , Fourier transform infrared spectroscopy , Electrocatalysis , Cysteine
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167598 , vital:41495
- Description: Metal organic frameworks (MOFs) have received a lot of attention over the past few years due to their vast range of interesting properties and applications, such as catalysis, environmental sensing and storage. This wide range of potential applications is afforded by careful selection and manipulation of the components chosen in assembling of MOFs. In this study, three series of MOFs were synthesized from Co(II), Cu(II) and Mo(VI) polyoxometallates with either 1,3,5-benzenetricarboxylic acid, 1,2,4,5-benzenetetracarboxylic acid or 2,6- pyridinedicarboxylic acid as the ligands. In series 1, the common 1,3,5- benzenetricarboxylic acid MOF, HKUST-1, and POM modified HKUST-1 compounds involving encapsulation and encorporation of the POM were utilised. In series 2, flexible cobalt(II) benzenepolycarboxylate MOFs which investigated the effect of varying the degree of carboxylate substituent were utilised. In series 3, flexibly reduced heterocyclic polycarboxylate MOFs using 2,6-pyridine dicarboxylate were utilised. Solvothermal and slow evaporation synthesis conditions were employed. Where single crystals of good quality were produced, single crystal X-ray diffraction (SC-XRD) was employed for structural elucidation. In the absence of such crystals, a combination of elemental analysis, inductively coupled plasma optical emission spectrometry (ICP-OES) and powder X-ray diffraction (PXRD) was used. Characterization of the MOFs was done by Fourier transform infrared spectrometry (FTIR) and thermal methods, namely thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The electrocatalytic potential of the compounds in the oxidation of L-cysteine was then investigated using a variety of techniques. Cyclic voltammetry was used for L-cysteine detection whilst chronoamperometry and differential pulse voltammetry were used to determine the nanoprobes’ sensitivity, rate constants and detection limits. Electrochemical impedence spectroscopy was used to investigate the charge transfer resistance (RCT) and electron transfer kinetics. Of the three, series 3 gave the best signals and sensitivities for electrocatalysis of L-cysteine followed by series 2 and lastly series 1. Series 2 showed the highest stability and series 1 required the least overpotential. The results highlight the effects of different metal centres and ligands on electrocatalysis. The application of MOFs in electrochemistry is a relatively new field making the findings of this study a significant addition to the body of knowledge.
- Full Text:
- Date Issued: 2020
Computer aided approaches against Human African Trypanosomiasis
- Authors: Kimuda, Magambo Phillip
- Date: 2020
- Subjects: African trypanosomiasis , African trypanosomiasis -- Chemotherapy , Genomics , Macrophage migration inhibitory factor , Trypanosoma brucei , Pteridines , Tetrahydrofolate dehydrogenase , Adenylic acid , Molecular dynamics , Principal components analysis , Bioinformatics , Single nucleotide polymorphisms , Single Nucleotide Variants , Candidate Gene Association Study (CGAS)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142542 , vital:38089
- Description: The thesis presented here is divided into two parts under a common theme that is the use of computer based tools, genomics, and in vitro experiments to develop innovative ways of tackling Human African Trypanosomiasis (HAT). Part I of this thesis focused on the human host genetic determinants while Part II focused on the discovery of novel chemotherapeutics against the parasite. Part I is further sub-divided into two parts: The first involves a Candidate Gene Association Study (CGAS) on an African population to identify genetic determinants associated with disease and/or susceptibility to HAT. The second involves studying the effects of missense Single Nucleotide Variants (SNVs) on protein structure, dynamics, and function using Macrophage Migration Inhibitory Factor (MIF) as a case study. Part II is also sub-divided into two parts: The first involves a computer based rational drug discovery of potential inhibitors against the Trypanosoma the folate pathway; particularly by targeting Trypanosoma brucei Pteridine Reductase (TbPTR1) which is an enzyme used by trypanosomes to overcome T. brucei Dihydrofolate Reductase (TbDHFR) inhibition. Lastly the derivation of CHARMM force-field parameters that can be used to accurately model the geometry and dynamics of the T. brucei Phosphodiesterase B1 enzyme (TbrPDEB1) bimetallic active site center. The derived parameters were then used in MD simulations to characterise protein-ligand residue interactions that are important in TbrPDEB1 inhibition with the goal of targeting the cyclic Adenosine Monophosphate (cAMP) signalling pathway. In the CGAS we were unable to detect any genetic associations in the Ugandan cohort analysed that passed correction for multiple testing in spite of the study being sufficiently powered. Additionally, our study found no association of the Apo lipoprotein 1 (APOL1) G2 allele association with protection against acute HAT that has been previously reported. Future investigations for example, Genome Wide Association Studies using larger samples sizes (>3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies
- Full Text:
- Date Issued: 2020
- Authors: Kimuda, Magambo Phillip
- Date: 2020
- Subjects: African trypanosomiasis , African trypanosomiasis -- Chemotherapy , Genomics , Macrophage migration inhibitory factor , Trypanosoma brucei , Pteridines , Tetrahydrofolate dehydrogenase , Adenylic acid , Molecular dynamics , Principal components analysis , Bioinformatics , Single nucleotide polymorphisms , Single Nucleotide Variants , Candidate Gene Association Study (CGAS)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142542 , vital:38089
- Description: The thesis presented here is divided into two parts under a common theme that is the use of computer based tools, genomics, and in vitro experiments to develop innovative ways of tackling Human African Trypanosomiasis (HAT). Part I of this thesis focused on the human host genetic determinants while Part II focused on the discovery of novel chemotherapeutics against the parasite. Part I is further sub-divided into two parts: The first involves a Candidate Gene Association Study (CGAS) on an African population to identify genetic determinants associated with disease and/or susceptibility to HAT. The second involves studying the effects of missense Single Nucleotide Variants (SNVs) on protein structure, dynamics, and function using Macrophage Migration Inhibitory Factor (MIF) as a case study. Part II is also sub-divided into two parts: The first involves a computer based rational drug discovery of potential inhibitors against the Trypanosoma the folate pathway; particularly by targeting Trypanosoma brucei Pteridine Reductase (TbPTR1) which is an enzyme used by trypanosomes to overcome T. brucei Dihydrofolate Reductase (TbDHFR) inhibition. Lastly the derivation of CHARMM force-field parameters that can be used to accurately model the geometry and dynamics of the T. brucei Phosphodiesterase B1 enzyme (TbrPDEB1) bimetallic active site center. The derived parameters were then used in MD simulations to characterise protein-ligand residue interactions that are important in TbrPDEB1 inhibition with the goal of targeting the cyclic Adenosine Monophosphate (cAMP) signalling pathway. In the CGAS we were unable to detect any genetic associations in the Ugandan cohort analysed that passed correction for multiple testing in spite of the study being sufficiently powered. Additionally, our study found no association of the Apo lipoprotein 1 (APOL1) G2 allele association with protection against acute HAT that has been previously reported. Future investigations for example, Genome Wide Association Studies using larger samples sizes (>3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies
- Full Text:
- Date Issued: 2020