Application of hidden Markov models and their extensions to animal movement data
- Authors: Van Niekerk, Bracken
- Date: 2018
- Subjects: Markov processes Animal locomotion Time-series analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/23835 , vital:30624
- Description: Hidden Markov Models (HMMs) have become increasingly popular in animal movement studies as they provide a flexible modelling approach and take the correlation between successive observations into account. They can segment the movement paths into latent states, which can be considered as rough proxies for the behaviours of the animals. This study comprises of two sections, both involving the application of HMMs to large terrestrial mammal movement data. Usually step lengths representing the displacement distances between successive observations, turning angles measuring the tortuosity, or a bivariate input of both variables are used as inputs in the models. It has been found in the literature that the turning angle is either included in the modelling process or it is excluded without much justification for doing so. The first part of this study investigates the nfluence of the turning angle on the model output and resultant interpretations of the HMMs when modelling the trajectories of large terrestrial mammals in southern Africa. Results revealed at different time scales, and for both predator and herbivore species in this study, that the turning angle does not influence the state allocation of the HMMs, which is the main output in terms of interpreting the behaviours of the animals. It is thought in most cases that the inclusion of the turning angle overcomplicates the models unnecessarily without contributing any additional information in terms of the behavioural interpretations or improving the overall fit of the models. This was found for the variety of movements of the species under observation in this study. The second part of this study attempts to validate the state allocation of the HMMs fitted to eland trajectories in the Greater Addo Elephant National Park in the Eastern Cape, with the use of camera trap data. This presented a unique opportunity as this type of data is mainly used for abundance or capture-recapture studies, and the HMMs are rarely validated as the true behaviours of the animals are seldom known. Results revealed that the same diel patterns were detected by the HMMs that were shown by the classified camera trap data. Direct comparisons of the observations where the dates and times matched for the telemetry and camera trap data could be done in several rare instances, which revealed many similarities. Although it was not an ideal comparison, the camera trap data provided a rough validation of the state allocation of the HMMs used in the study.
- Full Text:
- Date Issued: 2018
- Authors: Van Niekerk, Bracken
- Date: 2018
- Subjects: Markov processes Animal locomotion Time-series analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/23835 , vital:30624
- Description: Hidden Markov Models (HMMs) have become increasingly popular in animal movement studies as they provide a flexible modelling approach and take the correlation between successive observations into account. They can segment the movement paths into latent states, which can be considered as rough proxies for the behaviours of the animals. This study comprises of two sections, both involving the application of HMMs to large terrestrial mammal movement data. Usually step lengths representing the displacement distances between successive observations, turning angles measuring the tortuosity, or a bivariate input of both variables are used as inputs in the models. It has been found in the literature that the turning angle is either included in the modelling process or it is excluded without much justification for doing so. The first part of this study investigates the nfluence of the turning angle on the model output and resultant interpretations of the HMMs when modelling the trajectories of large terrestrial mammals in southern Africa. Results revealed at different time scales, and for both predator and herbivore species in this study, that the turning angle does not influence the state allocation of the HMMs, which is the main output in terms of interpreting the behaviours of the animals. It is thought in most cases that the inclusion of the turning angle overcomplicates the models unnecessarily without contributing any additional information in terms of the behavioural interpretations or improving the overall fit of the models. This was found for the variety of movements of the species under observation in this study. The second part of this study attempts to validate the state allocation of the HMMs fitted to eland trajectories in the Greater Addo Elephant National Park in the Eastern Cape, with the use of camera trap data. This presented a unique opportunity as this type of data is mainly used for abundance or capture-recapture studies, and the HMMs are rarely validated as the true behaviours of the animals are seldom known. Results revealed that the same diel patterns were detected by the HMMs that were shown by the classified camera trap data. Direct comparisons of the observations where the dates and times matched for the telemetry and camera trap data could be done in several rare instances, which revealed many similarities. Although it was not an ideal comparison, the camera trap data provided a rough validation of the state allocation of the HMMs used in the study.
- Full Text:
- Date Issued: 2018
Effects of production systems and canola meal supplementation on carcass and meat quality characteristics of spent laying hens
- Authors: Semwogerere, Farouk
- Date: 2018
- Subjects: Broilers (Chickens) -- Feeding and feeds Chickens -- Feeding and feeds Chicken industry -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/9242 , vital:34309
- Description: This study evaluated the carcass and meat quality traits of spent laying hens as influenced by production systems (conventional cages and free range) and the inclusion/exclusion of canola meal in their diets. A total of 30 free range and 60 battery cage reared Lohmann Brown-Elite spent laying hens were obtained from a commercial egg producer. The 30 free range hens (53 weeks of age) and 30 of the caged hens (40 weeks of age) were fed a conventional diet, while the remaining 30 caged hens (48 weeks of age) were fed a diet supplemented with canola meal (20 percent). Carcass, portion and organ weights were determined. Physical attributes and proximate composition were analyzed for, with additional fatty acids and sensory profiles being determined for the effects of canola meal inclusion in the diet. Caged hens had heavier (P ≤ 0.05) warm and cold carcasses, thigh, wing and feet compared to free range hens. The percentages of the breast (26.1 ± 0.51 vs. 28.3 ± 0.28), drum, breast bones, breast thaw and cooking losses and thigh cooking loss were lower (P ≤ 0.05) for caged hens than for free range hens. Free range hens had heavier (P ≤ 0.05) gizzards (33.9 ± 1.04 vs. 30.5 ± 0.73) and bones and a lower (P ≤ 0.05) breast meat percentage (47.3 ± 0.94 vs. 51.7 ± 1.35). Meat redness (a*) (0.54 ± 0.222 vs. 1.40 ± 0.135) and hue angle value, skin redness (a*), breast and thigh, Warner-Bratzler shear force (WBSF) values (breast: 12.37 ± 0.411 vs. 17.10 ± 0.751, thigh: 29.68 ± 0.306 vs. 39.75 ± 0.826), breast moisture and thigh ash content were lower (P ≤ 0.05) for caged hens than free range hens. Caged hens had higher (P ≤ 0.05) thigh thaw loss and breast ash content than free range hens. Canola-fed hens had higher (P ≤ 0.05) drum percentages, breast bone weights and percentages, with lower (P ≤ 0.05) thigh and breast meat percentages. Canola-fed hens had lower (P ≤ 0.05) thaw losses, skin yellowness (b*) and Chroma values, breast fat content with higher cooking losses, skin redness (a*) and hue angle value, as well as breast WBSF (12.37 ± 0.411 vs. 15.43 ± 0.600). Palmitic acid, stearic acid, heneicosanoic acid acid, palmitoleic acid, saturated fatty acids (SFA) (34.0 ± 0.56 vs. 38.7 ± 0.71), n-6:n-3 polyunsaturated fatty acids (PUFA) ratio (5.5 ± 0.13 vs. 7.2 ± 0.28), atherogenic index (IA), thrombogenic index (IT), delta-5 desaturase (D5D, elongase index and thiosterase index were lower (P ≤ 0.05) for canola-fed hen breast meat. Breast meat from conventionally fed hens had lower (P ≤ 0.05) myristic acid, lignoceric acid, nervonic acid, alpha-linolenic acid (ALA), docosahexaenoic acid (DHA), PUFA:SFA ratio (0.7 ± 0.05 vs. 0.9 ± 0.02), n-3 PUFA (3.4 ± 0.31 vs. 5.1 ± 0.17), hypocholesterolemic:Hypercholesterolaemic (h/H), stearoyl-CoA desaturase 16 (SCD16) and stearoyl-CoA desaturase 18 (SCD18). The breast meat from conventionally fed hens had lower (P ≤ 0.05) metallic flavor than that from canola-fed hens. Strong positive correlations were observed for overall aroma with chicken (r = 0.965, P < 0.001) and brothy aroma (r = 0.827, P < 0.001); overall aroma with overall flavor (r = 0.680, P < 0.001), chicken flavor (r = 0.668, P < 0.001) and brothy flavor (r = 0.548, P = 0.006); initial juiciness with sustained juiciness (r = 0.771, P < 0.001) and tenderness (r = 0.537, P = 0.007); sustained juiciness with tenderness (r = 0.790, P < 0.001) and chewiness with residue (r = 0.783, P < 0.001). Whilst strong negative correlations were observed for: sustained juiciness with chewiness (r = -0.655, P = 0.001) and residue (r = 0.783, P < 0.001) and for tenderness with chewiness (r = 0.845, P < 0.001) and residue (r = -0.855, P < 0.001). Results of this study highlight that a free range production system when compared to a conventional cage system increased undesirable carcass and physical meat traits of spent laying hens. On the other hand, canola meal inclusion incorporates beneficial health aspects without affecting the sensory profile of meat derived from spent laying hens, both groups of hens being reared in battery cage system. Spent laying hen breasts can be consumed as a functional food (especially canolafed) since the fat content and composition was observed to be close to that which is recommended for a healthy diet.
- Full Text:
- Date Issued: 2018
- Authors: Semwogerere, Farouk
- Date: 2018
- Subjects: Broilers (Chickens) -- Feeding and feeds Chickens -- Feeding and feeds Chicken industry -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/9242 , vital:34309
- Description: This study evaluated the carcass and meat quality traits of spent laying hens as influenced by production systems (conventional cages and free range) and the inclusion/exclusion of canola meal in their diets. A total of 30 free range and 60 battery cage reared Lohmann Brown-Elite spent laying hens were obtained from a commercial egg producer. The 30 free range hens (53 weeks of age) and 30 of the caged hens (40 weeks of age) were fed a conventional diet, while the remaining 30 caged hens (48 weeks of age) were fed a diet supplemented with canola meal (20 percent). Carcass, portion and organ weights were determined. Physical attributes and proximate composition were analyzed for, with additional fatty acids and sensory profiles being determined for the effects of canola meal inclusion in the diet. Caged hens had heavier (P ≤ 0.05) warm and cold carcasses, thigh, wing and feet compared to free range hens. The percentages of the breast (26.1 ± 0.51 vs. 28.3 ± 0.28), drum, breast bones, breast thaw and cooking losses and thigh cooking loss were lower (P ≤ 0.05) for caged hens than for free range hens. Free range hens had heavier (P ≤ 0.05) gizzards (33.9 ± 1.04 vs. 30.5 ± 0.73) and bones and a lower (P ≤ 0.05) breast meat percentage (47.3 ± 0.94 vs. 51.7 ± 1.35). Meat redness (a*) (0.54 ± 0.222 vs. 1.40 ± 0.135) and hue angle value, skin redness (a*), breast and thigh, Warner-Bratzler shear force (WBSF) values (breast: 12.37 ± 0.411 vs. 17.10 ± 0.751, thigh: 29.68 ± 0.306 vs. 39.75 ± 0.826), breast moisture and thigh ash content were lower (P ≤ 0.05) for caged hens than free range hens. Caged hens had higher (P ≤ 0.05) thigh thaw loss and breast ash content than free range hens. Canola-fed hens had higher (P ≤ 0.05) drum percentages, breast bone weights and percentages, with lower (P ≤ 0.05) thigh and breast meat percentages. Canola-fed hens had lower (P ≤ 0.05) thaw losses, skin yellowness (b*) and Chroma values, breast fat content with higher cooking losses, skin redness (a*) and hue angle value, as well as breast WBSF (12.37 ± 0.411 vs. 15.43 ± 0.600). Palmitic acid, stearic acid, heneicosanoic acid acid, palmitoleic acid, saturated fatty acids (SFA) (34.0 ± 0.56 vs. 38.7 ± 0.71), n-6:n-3 polyunsaturated fatty acids (PUFA) ratio (5.5 ± 0.13 vs. 7.2 ± 0.28), atherogenic index (IA), thrombogenic index (IT), delta-5 desaturase (D5D, elongase index and thiosterase index were lower (P ≤ 0.05) for canola-fed hen breast meat. Breast meat from conventionally fed hens had lower (P ≤ 0.05) myristic acid, lignoceric acid, nervonic acid, alpha-linolenic acid (ALA), docosahexaenoic acid (DHA), PUFA:SFA ratio (0.7 ± 0.05 vs. 0.9 ± 0.02), n-3 PUFA (3.4 ± 0.31 vs. 5.1 ± 0.17), hypocholesterolemic:Hypercholesterolaemic (h/H), stearoyl-CoA desaturase 16 (SCD16) and stearoyl-CoA desaturase 18 (SCD18). The breast meat from conventionally fed hens had lower (P ≤ 0.05) metallic flavor than that from canola-fed hens. Strong positive correlations were observed for overall aroma with chicken (r = 0.965, P < 0.001) and brothy aroma (r = 0.827, P < 0.001); overall aroma with overall flavor (r = 0.680, P < 0.001), chicken flavor (r = 0.668, P < 0.001) and brothy flavor (r = 0.548, P = 0.006); initial juiciness with sustained juiciness (r = 0.771, P < 0.001) and tenderness (r = 0.537, P = 0.007); sustained juiciness with tenderness (r = 0.790, P < 0.001) and chewiness with residue (r = 0.783, P < 0.001). Whilst strong negative correlations were observed for: sustained juiciness with chewiness (r = -0.655, P = 0.001) and residue (r = 0.783, P < 0.001) and for tenderness with chewiness (r = 0.845, P < 0.001) and residue (r = -0.855, P < 0.001). Results of this study highlight that a free range production system when compared to a conventional cage system increased undesirable carcass and physical meat traits of spent laying hens. On the other hand, canola meal inclusion incorporates beneficial health aspects without affecting the sensory profile of meat derived from spent laying hens, both groups of hens being reared in battery cage system. Spent laying hen breasts can be consumed as a functional food (especially canolafed) since the fat content and composition was observed to be close to that which is recommended for a healthy diet.
- Full Text:
- Date Issued: 2018
NetwIOC: a framework for the automated generation of network-based IOCS for malware information sharing and defence
- Authors: Rudman, Lauren Lynne
- Date: 2018
- Subjects: Malware (Computer software) , Computer networks Security measures , Computer security , Python (Computer program language)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60639 , vital:27809
- Description: With the substantial number of new malware variants found each day, it is useful to have an efficient way to retrieve Indicators of Compromise (IOCs) from the malware in a format suitable for sharing and detection. In the past, these indicators were manually created after inspection of binary samples and network traffic. The Cuckoo Sandbox, is an existing dynamic malware analysis system which meets the requirements for the proposed framework and was extended by adding a few custom modules. This research explored a way to automate the generation of detailed network-based IOCs in a popular format which can be used for sharing. This was done through careful filtering and analysis of the PCAP hie generated by the sandbox, and placing these values into the correct type of STIX objects using Python, Through several evaluations, analysis of what type of network traffic can be expected for the creation of IOCs was conducted, including a brief ease study that examined the effect of analysis time on the number of IOCs created. Using the automatically generated IOCs to create defence and detection mechanisms for the network was evaluated and proved successful, A proof of concept sharing platform developed for the STIX IOCs is showcased at the end of the research.
- Full Text:
- Date Issued: 2018
- Authors: Rudman, Lauren Lynne
- Date: 2018
- Subjects: Malware (Computer software) , Computer networks Security measures , Computer security , Python (Computer program language)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60639 , vital:27809
- Description: With the substantial number of new malware variants found each day, it is useful to have an efficient way to retrieve Indicators of Compromise (IOCs) from the malware in a format suitable for sharing and detection. In the past, these indicators were manually created after inspection of binary samples and network traffic. The Cuckoo Sandbox, is an existing dynamic malware analysis system which meets the requirements for the proposed framework and was extended by adding a few custom modules. This research explored a way to automate the generation of detailed network-based IOCs in a popular format which can be used for sharing. This was done through careful filtering and analysis of the PCAP hie generated by the sandbox, and placing these values into the correct type of STIX objects using Python, Through several evaluations, analysis of what type of network traffic can be expected for the creation of IOCs was conducted, including a brief ease study that examined the effect of analysis time on the number of IOCs created. Using the automatically generated IOCs to create defence and detection mechanisms for the network was evaluated and proved successful, A proof of concept sharing platform developed for the STIX IOCs is showcased at the end of the research.
- Full Text:
- Date Issued: 2018
Towards a collection of cost-effective technologies in support of the NIST cybersecurity framework
- Shackleton, Bruce Michael Stuart
- Authors: Shackleton, Bruce Michael Stuart
- Date: 2018
- Subjects: National Institute of Standards and Technology (U.S.) , Computer security , Computer networks Security measures , Small business Information technology Cost effectiveness , Open source software
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62494 , vital:28199
- Description: The NIST Cybersecurity Framework (CSF) is a specific risk and cybersecurity framework. It provides guidance on controls that can be implemented to help improve an organisation’s cybersecurity risk posture. The CSF Functions consist of Identify, Protect, Detect, Respond, and Recover. Like most Information Technology (IT) frameworks, there are elements of people, processes, and technology. The same elements are required to successfully implement the NIST CSF. This research specifically focuses on the technology element. While there are many commercial technologies available for a small to medium sized business, the costs can be prohibitively expensive. Therefore, this research investigates cost-effective technologies and assesses their alignment to the NIST CSF. The assessment was made against the NIST CSF subcategories. Each subcategory was analysed to identify where a technology would likely be required. The framework provides a list of Informative References. These Informative References were used to create high- level technology categories, as well as identify the technical controls against which the technologies were measured. The technologies tested were either open source or proprietary. All open source technologies tested were free to use, or have a free community edition. Proprietary technologies would be free to use, or considered generally available to most organisations, such as components contained within Microsoft platforms. The results from the experimentation demonstrated that there are multiple cost-effective technologies that can support the NIST CSF. Once all technologies were tested, the NIST CSF was extended. Two new columns were added, namely high-level technology category, and tested technology. The columns were populated with output from the research. This extended framework begins an initial collection of cost-effective technologies in support of the NIST CSF.
- Full Text:
- Date Issued: 2018
- Authors: Shackleton, Bruce Michael Stuart
- Date: 2018
- Subjects: National Institute of Standards and Technology (U.S.) , Computer security , Computer networks Security measures , Small business Information technology Cost effectiveness , Open source software
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62494 , vital:28199
- Description: The NIST Cybersecurity Framework (CSF) is a specific risk and cybersecurity framework. It provides guidance on controls that can be implemented to help improve an organisation’s cybersecurity risk posture. The CSF Functions consist of Identify, Protect, Detect, Respond, and Recover. Like most Information Technology (IT) frameworks, there are elements of people, processes, and technology. The same elements are required to successfully implement the NIST CSF. This research specifically focuses on the technology element. While there are many commercial technologies available for a small to medium sized business, the costs can be prohibitively expensive. Therefore, this research investigates cost-effective technologies and assesses their alignment to the NIST CSF. The assessment was made against the NIST CSF subcategories. Each subcategory was analysed to identify where a technology would likely be required. The framework provides a list of Informative References. These Informative References were used to create high- level technology categories, as well as identify the technical controls against which the technologies were measured. The technologies tested were either open source or proprietary. All open source technologies tested were free to use, or have a free community edition. Proprietary technologies would be free to use, or considered generally available to most organisations, such as components contained within Microsoft platforms. The results from the experimentation demonstrated that there are multiple cost-effective technologies that can support the NIST CSF. Once all technologies were tested, the NIST CSF was extended. Two new columns were added, namely high-level technology category, and tested technology. The columns were populated with output from the research. This extended framework begins an initial collection of cost-effective technologies in support of the NIST CSF.
- Full Text:
- Date Issued: 2018
Development and optimisation of a novel Plasmodium falciparum Hsp90-Hop interaction assay
- Authors: Wambua, Lynn
- Date: 2018
- Subjects: Plasmodium falciparum , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Antimalarials
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62626 , vital:28216
- Description: Protein-protein interactions are involved in a range of disease processes and thus have become the focus of many drug discovery programs. Widespread drug resistance to all currently used antimalarial drugs drives the search for alternative drug targets with novel mechanisms of action that offer new therapeutic options. Molecular chaperones such as heat shock proteins facilitate protein folding, play a role in protein trafficking and prevent protein misfolding in cells under stress. Heat shock protein 90 (Hsp90) is a well-studied chaperone that has been the focus of cancer drug development with moderate success. In Plasmodium falciparum (P. falciparum), heat shock proteins are thought to play a vital role in parasite survival of the physiologically diverse habitats of the parasite lifecycle and because Hsp90 is prominently expressed in P. falciparum, the chaperone is considered a potentially ideal drug target. Hsp90 function in cells is regulated by interactions with co-chaperones, which includes Heat shock protein 70-Heat shock protein 90 organising protein (Hop). As opposed to directly inhibiting Hsp90 activity, targeting Hsp90 interaction with Hop has recently been suggested as an alternative method of Hsp90 inhibition that has not been explored in P. falciparum. The aim of this research project was to demonstrate PfHsp90 and PfHop robustly interact in vitro and to facilitate high-throughput screening of PfHsp90-PfHop inhibitors by developing and optimising a novel plate capture Hsp90-Hop interaction assay. To establish the assay, the respective domains of the proteins that mediate Hsp90-Hop interaction were used (Hsp90 C- terminal domain and Hop TPR2A domain). The human Hsp90 C-terminal domain and glutathione-S-transferase (GST) coding sequences were cloned into pET-28a(+) and murine and P. falciparum TPR2A sequences into pGEX-4T-1 plasmids to enable expression of histidine-tagged and GST fusion proteins, respectively, in Escherichia coli. The P. falciparum Hsp90 C-terminal domain sequence cloned into pET-28a(+) was supplied by GenScript. The constructs were transformed into T7 Express lysYcompetent E. coli cells and subsequent small- scale expression studies showed the recombinant proteins were expressed in a soluble form allowing for subsequent protein purification. Purification of the recombinant proteins was achieved using nickel-NTA and glutathione affinity chromatography for the His-tagged (Hsp90 C-terminal domains and GST) and GST fusion proteins (TPR2A domains), respectively. The purified proteins were used to establish and optimise mammalian and P. falciparum Hsp90- Hop interaction assays on nickel-coated plates by immobilising the His-tagged C-terminal domains on the plates and detecting the binding of the GST-TPR2A domains using a colorimetric GST enzyme assay. Z’-factor values above 0.5 were observed for both assays indicating good separation between the protein interaction signals and negative control background signals, although relatively high background signals were observed for the mammalian interaction due to non-specific binding of murine TPR2A to the plate. Designed human and P. falciparum TPR peptides were observed to be effective inhibitors of the mammalian and P. falciparum interactions, demonstrating the assay’s ability to respond to inhibitor compounds. Comparison of assay performance using GST assay kit reagents and lab- prepared reagents showed the assay was more efficient using lab-prepared reagents, however, lower GST signals were observed when comparing assay performance using a custom prepared Ni-NTA plate to a purchased Ni-NTA plate. The Hsp90-Hop interaction assays were also performed using an alternative assay format in which the GST-TPR2A fusion proteins were immobilised on glutathione-coated plates and binding of the His-tagged C-terminal domains detected with a nickel-horseradish peroxidase (HRP) conjugate and a colorimetric HRP substrate. The assay showed higher interaction signals for the P. falciparum proteins but comparatively low signals for the mammalian proteins. Z’-factor values for the assay were above 0.8 for both protein sets, suggesting this assay format is superior to the GST assay. However, further optimisation of this assay format is required. This study demonstrated direct binding of PfHsp90-PfHop in vitro and established a novel and robust PfHsp90-PfHop interaction assay format that can be used in future screening campaigns.
- Full Text:
- Date Issued: 2018
- Authors: Wambua, Lynn
- Date: 2018
- Subjects: Plasmodium falciparum , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Antimalarials
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62626 , vital:28216
- Description: Protein-protein interactions are involved in a range of disease processes and thus have become the focus of many drug discovery programs. Widespread drug resistance to all currently used antimalarial drugs drives the search for alternative drug targets with novel mechanisms of action that offer new therapeutic options. Molecular chaperones such as heat shock proteins facilitate protein folding, play a role in protein trafficking and prevent protein misfolding in cells under stress. Heat shock protein 90 (Hsp90) is a well-studied chaperone that has been the focus of cancer drug development with moderate success. In Plasmodium falciparum (P. falciparum), heat shock proteins are thought to play a vital role in parasite survival of the physiologically diverse habitats of the parasite lifecycle and because Hsp90 is prominently expressed in P. falciparum, the chaperone is considered a potentially ideal drug target. Hsp90 function in cells is regulated by interactions with co-chaperones, which includes Heat shock protein 70-Heat shock protein 90 organising protein (Hop). As opposed to directly inhibiting Hsp90 activity, targeting Hsp90 interaction with Hop has recently been suggested as an alternative method of Hsp90 inhibition that has not been explored in P. falciparum. The aim of this research project was to demonstrate PfHsp90 and PfHop robustly interact in vitro and to facilitate high-throughput screening of PfHsp90-PfHop inhibitors by developing and optimising a novel plate capture Hsp90-Hop interaction assay. To establish the assay, the respective domains of the proteins that mediate Hsp90-Hop interaction were used (Hsp90 C- terminal domain and Hop TPR2A domain). The human Hsp90 C-terminal domain and glutathione-S-transferase (GST) coding sequences were cloned into pET-28a(+) and murine and P. falciparum TPR2A sequences into pGEX-4T-1 plasmids to enable expression of histidine-tagged and GST fusion proteins, respectively, in Escherichia coli. The P. falciparum Hsp90 C-terminal domain sequence cloned into pET-28a(+) was supplied by GenScript. The constructs were transformed into T7 Express lysYcompetent E. coli cells and subsequent small- scale expression studies showed the recombinant proteins were expressed in a soluble form allowing for subsequent protein purification. Purification of the recombinant proteins was achieved using nickel-NTA and glutathione affinity chromatography for the His-tagged (Hsp90 C-terminal domains and GST) and GST fusion proteins (TPR2A domains), respectively. The purified proteins were used to establish and optimise mammalian and P. falciparum Hsp90- Hop interaction assays on nickel-coated plates by immobilising the His-tagged C-terminal domains on the plates and detecting the binding of the GST-TPR2A domains using a colorimetric GST enzyme assay. Z’-factor values above 0.5 were observed for both assays indicating good separation between the protein interaction signals and negative control background signals, although relatively high background signals were observed for the mammalian interaction due to non-specific binding of murine TPR2A to the plate. Designed human and P. falciparum TPR peptides were observed to be effective inhibitors of the mammalian and P. falciparum interactions, demonstrating the assay’s ability to respond to inhibitor compounds. Comparison of assay performance using GST assay kit reagents and lab- prepared reagents showed the assay was more efficient using lab-prepared reagents, however, lower GST signals were observed when comparing assay performance using a custom prepared Ni-NTA plate to a purchased Ni-NTA plate. The Hsp90-Hop interaction assays were also performed using an alternative assay format in which the GST-TPR2A fusion proteins were immobilised on glutathione-coated plates and binding of the His-tagged C-terminal domains detected with a nickel-horseradish peroxidase (HRP) conjugate and a colorimetric HRP substrate. The assay showed higher interaction signals for the P. falciparum proteins but comparatively low signals for the mammalian proteins. Z’-factor values for the assay were above 0.8 for both protein sets, suggesting this assay format is superior to the GST assay. However, further optimisation of this assay format is required. This study demonstrated direct binding of PfHsp90-PfHop in vitro and established a novel and robust PfHsp90-PfHop interaction assay format that can be used in future screening campaigns.
- Full Text:
- Date Issued: 2018
Investigating the viability and performance of a pilot scale Fly Ash/Lime Filter Tower (FLFT) for greywater treatment and the fate of Triclosan post treatment
- Authors: Nondlazi, Sinoyolo
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63704 , vital:28473
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
- Authors: Nondlazi, Sinoyolo
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63704 , vital:28473
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
Quantification of pre-competitive sleep/wake behaviour in a sample of South African cyclists
- Authors: Steenekamp, Travis
- Date: 2018
- Subjects: Sleep deprivation , Cyclists Health and hygiene South Africa , Sleep Physiological aspects , Performance , Performance anxiety
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59015 , vital:27408
- Description: The quantification of athlete pre-competitive sleep behaviour is of interest owing to the possibility that sleep loss may have a negative effect on health and performance. The purpose of this study was to monitor and quantify the sleep/wake patterns of South African cyclists prior to competitive races. A total of 336 cyclists, male and female and of differing competition levels, cycling in either the 2015 Tsogo Sun Amashova or the 2016 Telkom 94.7 Cycle Challenge completed an altered version of the Competitive Sports and Sleep Questionnaire. The questionnaire asked cyclists to report on precompetitive sleep over the past year. A subset of 92 cyclists also recorded a Core Consensus Sleep Diary for the three nights leading up to the races. The questionnaire showed that 67% of the cyclists reported worsened sleep at least once prior to competition within the past 12 months. The sleep diary found that the cyclists’ average sleep duration the night before the races was 6h19min (±1h38min), which was significantly less than two and three nights prior to the races. Sleep quality was also shown to deteriorate significantly the night before the races. The contributing factors leading to worsened pre-competitive sleep were the time the cyclists had to wake-up as well as perceived increases in sleep latency and awakenings after sleep onset. Anxiety was found to be the major cause of sleep disturbances. While females were found to be significantly more likely to report having experienced poorer sleep before competition in the past year, the sleep diary showed no difference in sleep the night before the races between the sexes. Females were significantly more likely to report instances of unpleasant dreams and waking up during the night. Again, the sleep diary data did not corroborate these findings. Females were also found to report significantly more accounts of nervousness or thoughts about competition as being the cause of sleep problems. There was no difference in sleep loss the night before competition when comparing competition-level groups. The only significant difference was that recreational cyclists were more likely to report sleeping in foreign environments as a cause of sleep disturbances. Despite a large percentage of cyclists experiencing pre-competitive sleep loss, over half (55%) perceived sleep loss to have no impact on their performance. Analysis of pre-sleep behaviour also revealed that the cyclists engaged in several practices that may have a negative effect on subsequent sleep. The vast majority of the cyclists (61%) indicated having no specific strategy to help them sleep the night before competition. Fifteen percent of cyclists reporting using media devices to help them fall asleep, a practice that has been shown to disrupt sleep. In conclusion, most cyclists, regardless of sex and level of competition experience precompetitive sleep loss attributed largely to anxiety but with the perception that this loss in sleep does not negatively impact their performance.
- Full Text:
- Date Issued: 2018
- Authors: Steenekamp, Travis
- Date: 2018
- Subjects: Sleep deprivation , Cyclists Health and hygiene South Africa , Sleep Physiological aspects , Performance , Performance anxiety
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59015 , vital:27408
- Description: The quantification of athlete pre-competitive sleep behaviour is of interest owing to the possibility that sleep loss may have a negative effect on health and performance. The purpose of this study was to monitor and quantify the sleep/wake patterns of South African cyclists prior to competitive races. A total of 336 cyclists, male and female and of differing competition levels, cycling in either the 2015 Tsogo Sun Amashova or the 2016 Telkom 94.7 Cycle Challenge completed an altered version of the Competitive Sports and Sleep Questionnaire. The questionnaire asked cyclists to report on precompetitive sleep over the past year. A subset of 92 cyclists also recorded a Core Consensus Sleep Diary for the three nights leading up to the races. The questionnaire showed that 67% of the cyclists reported worsened sleep at least once prior to competition within the past 12 months. The sleep diary found that the cyclists’ average sleep duration the night before the races was 6h19min (±1h38min), which was significantly less than two and three nights prior to the races. Sleep quality was also shown to deteriorate significantly the night before the races. The contributing factors leading to worsened pre-competitive sleep were the time the cyclists had to wake-up as well as perceived increases in sleep latency and awakenings after sleep onset. Anxiety was found to be the major cause of sleep disturbances. While females were found to be significantly more likely to report having experienced poorer sleep before competition in the past year, the sleep diary showed no difference in sleep the night before the races between the sexes. Females were significantly more likely to report instances of unpleasant dreams and waking up during the night. Again, the sleep diary data did not corroborate these findings. Females were also found to report significantly more accounts of nervousness or thoughts about competition as being the cause of sleep problems. There was no difference in sleep loss the night before competition when comparing competition-level groups. The only significant difference was that recreational cyclists were more likely to report sleeping in foreign environments as a cause of sleep disturbances. Despite a large percentage of cyclists experiencing pre-competitive sleep loss, over half (55%) perceived sleep loss to have no impact on their performance. Analysis of pre-sleep behaviour also revealed that the cyclists engaged in several practices that may have a negative effect on subsequent sleep. The vast majority of the cyclists (61%) indicated having no specific strategy to help them sleep the night before competition. Fifteen percent of cyclists reporting using media devices to help them fall asleep, a practice that has been shown to disrupt sleep. In conclusion, most cyclists, regardless of sex and level of competition experience precompetitive sleep loss attributed largely to anxiety but with the perception that this loss in sleep does not negatively impact their performance.
- Full Text:
- Date Issued: 2018
Towards understanding the effect of size variation on the aggressive and feeding behaviours of juvenile dusky kob Argyrosomus japonicus (Pisces: Sciaenidae)
- Authors: Babane, Siviwe Elvis
- Date: 2018
- Subjects: Argyrosomus -- Feeding and feeds , Aquaculture , Fishes -- Cannibalism , Fishes -- Feeding and feeds
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59592 , vital:27629
- Description: Many studies have been conducted on the effect of size-grading in other fish species. However, there is a paucity of scientific information on the effects of size variation on cannibalism of juvenile dusky kob. Thus, a study focusing on the effect of size variation on juvenile dusky kob aggressive and feeding (browsing) behaviours was conducted. Three separate groups of hatchery-reared juvenile dusky kob of were obtained from Oceanwise (Pty) Ltd for use in a series of three experimental trials. In all trials, juvenile fish of the same age were size-graded and the COV-value was used to determine the size variation. The focal fish (largest fish) was exposed to groups of fish with different size variation for 30-min. behavioural observations before and after feeding in randomised trials. The first experimental trial (Chapter 2) quantified the effect of increasing size variation and observation time on the aggressive and browsing behaviours of juvenile dusky kob. On average, juvenile dusky kob weighed 3.60 ± 0.68 g fish-1 and measured 5.8 ± 0.41 mm. Each focal fish was observed (a) before feeding in the morning, (b) 2 h after feeding, (c) 6 h after feeding and (d) 12 h after feeding. Fish increased browsing behaviours (averaging 6.60 ± 0.56) and decreased intimidating aggressive behaviours (18.60 ± 1.39) 12 h after feeding. Other aggressive behaviours occurred but did not differ between observation times. Aggressive and browsing behaviours positively correlated with size variation variables, predominantly, 12 h after feeding. An average frequency of 19 chases were observed positively correlated with size variation, followed by average frequencies of 17 body bites and browses, and 11 tail bites per 30 min. Some behaviours including average frequencies of 0.2 chases, 4 tail bites, 2.4 intimidating and 0.3 browsing behaviours negatively correlated with the size variation, generally closer to the last meal. These preliminary observations thus showed that fish have become hungry approximately 6-12 h after feeding and substituted certain behaviours for others as time after feeding passed and as size variation increased. The second experimental trial (Chapter 3) consisted of the observations further testing the relationship between aggressive behaviours and size variation of juveniles of dusky kob averaging 0.43 ± 0.27 g fish-1. The focal fish was exposed to groups of fish of four size variation (COV) treatments for observations before and 12 h after feeding. Aggressive behaviours positively correlated with size variation both before and 12 h after feeding. An average frequency of 437 body bites positively correlated more often with COV, followed by average frequencies of 365 intimidating behaviours and 199 tail bites per 30 min., respectively, before and 12 h after feeding. The least often exhibited aggressive behaviours averaged 26 chases while positively correlating with size variation on the times specified. An average frequency of 311 intimidating behaviours before and after feeding including average of 28 tail bites after feeding negatively correlated with size variation. This may relate to shift of behaviours depending on the needs and capacity of the fish. Apparently, aggressive fish can change its behaviour as a function of COV-values rather than the mean size of the other fish. The third trial (Chapter 4) investigated the effect of the aggressor’s (focal fish) size in relation its aggressive and browsing behaviours to other fish (non-focal fish). Juvenile fish used for this trial, on average, weighed 30 ± 7.63 g fish-1. Aggressive and browsing behaviours were observed in four treatments of a) high COV and mean weight below, b) low COV and mean weight less, c) high COV and mean weight equivalent to and d) low COV and mean weight higher than that of the focal fish. Increased frequencies of aggressive and browsing behaviours per 30 min. occurred in treatment A, sharing similar frequencies in treatment C, compared to the other treatments (B and D) which shared certain frequencies. The intimidating behaviours predominated, followed by browsing, body bites, chases and tail bites, respectively. The results of the overall study suggest that the time passed after feeding and increasing size variation and differences facilitated aggressive and browsing behaviours in juvenile dusky kob. Dusky kob showed increasing aggressive behaviours as early as in the first two weeks after hatching, averaging 0.43 ± 0.27 g fish-1 with the frequency correlating with size differences. Consistent size-grading technique in the same-age fish should be used to manage size variation associated with aggressive behaviours. The period of about 4-6 h after feeding may explain the noticeable increased aggressive and browsing behaviours. Thus, fish should be fed immediately before or after evacuation of their guts to maintain less-aggressive behaviours of juvenile dusky kob. Fish generally increased aggressive and browsing acts before and long time after feeding than closer to after feeding. The study has provided the fundamental scientific groundwork for fish farmers and future researchers can further explore size variation, time after feeding and gut evacuation rate as critical components of aggressive behaviours. The scientific knowledge of aggressive and cannibalistic behaviours has essential application in farming management to achieve improved survival and growth rates in juvenile fish.
- Full Text:
- Date Issued: 2018
- Authors: Babane, Siviwe Elvis
- Date: 2018
- Subjects: Argyrosomus -- Feeding and feeds , Aquaculture , Fishes -- Cannibalism , Fishes -- Feeding and feeds
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59592 , vital:27629
- Description: Many studies have been conducted on the effect of size-grading in other fish species. However, there is a paucity of scientific information on the effects of size variation on cannibalism of juvenile dusky kob. Thus, a study focusing on the effect of size variation on juvenile dusky kob aggressive and feeding (browsing) behaviours was conducted. Three separate groups of hatchery-reared juvenile dusky kob of were obtained from Oceanwise (Pty) Ltd for use in a series of three experimental trials. In all trials, juvenile fish of the same age were size-graded and the COV-value was used to determine the size variation. The focal fish (largest fish) was exposed to groups of fish with different size variation for 30-min. behavioural observations before and after feeding in randomised trials. The first experimental trial (Chapter 2) quantified the effect of increasing size variation and observation time on the aggressive and browsing behaviours of juvenile dusky kob. On average, juvenile dusky kob weighed 3.60 ± 0.68 g fish-1 and measured 5.8 ± 0.41 mm. Each focal fish was observed (a) before feeding in the morning, (b) 2 h after feeding, (c) 6 h after feeding and (d) 12 h after feeding. Fish increased browsing behaviours (averaging 6.60 ± 0.56) and decreased intimidating aggressive behaviours (18.60 ± 1.39) 12 h after feeding. Other aggressive behaviours occurred but did not differ between observation times. Aggressive and browsing behaviours positively correlated with size variation variables, predominantly, 12 h after feeding. An average frequency of 19 chases were observed positively correlated with size variation, followed by average frequencies of 17 body bites and browses, and 11 tail bites per 30 min. Some behaviours including average frequencies of 0.2 chases, 4 tail bites, 2.4 intimidating and 0.3 browsing behaviours negatively correlated with the size variation, generally closer to the last meal. These preliminary observations thus showed that fish have become hungry approximately 6-12 h after feeding and substituted certain behaviours for others as time after feeding passed and as size variation increased. The second experimental trial (Chapter 3) consisted of the observations further testing the relationship between aggressive behaviours and size variation of juveniles of dusky kob averaging 0.43 ± 0.27 g fish-1. The focal fish was exposed to groups of fish of four size variation (COV) treatments for observations before and 12 h after feeding. Aggressive behaviours positively correlated with size variation both before and 12 h after feeding. An average frequency of 437 body bites positively correlated more often with COV, followed by average frequencies of 365 intimidating behaviours and 199 tail bites per 30 min., respectively, before and 12 h after feeding. The least often exhibited aggressive behaviours averaged 26 chases while positively correlating with size variation on the times specified. An average frequency of 311 intimidating behaviours before and after feeding including average of 28 tail bites after feeding negatively correlated with size variation. This may relate to shift of behaviours depending on the needs and capacity of the fish. Apparently, aggressive fish can change its behaviour as a function of COV-values rather than the mean size of the other fish. The third trial (Chapter 4) investigated the effect of the aggressor’s (focal fish) size in relation its aggressive and browsing behaviours to other fish (non-focal fish). Juvenile fish used for this trial, on average, weighed 30 ± 7.63 g fish-1. Aggressive and browsing behaviours were observed in four treatments of a) high COV and mean weight below, b) low COV and mean weight less, c) high COV and mean weight equivalent to and d) low COV and mean weight higher than that of the focal fish. Increased frequencies of aggressive and browsing behaviours per 30 min. occurred in treatment A, sharing similar frequencies in treatment C, compared to the other treatments (B and D) which shared certain frequencies. The intimidating behaviours predominated, followed by browsing, body bites, chases and tail bites, respectively. The results of the overall study suggest that the time passed after feeding and increasing size variation and differences facilitated aggressive and browsing behaviours in juvenile dusky kob. Dusky kob showed increasing aggressive behaviours as early as in the first two weeks after hatching, averaging 0.43 ± 0.27 g fish-1 with the frequency correlating with size differences. Consistent size-grading technique in the same-age fish should be used to manage size variation associated with aggressive behaviours. The period of about 4-6 h after feeding may explain the noticeable increased aggressive and browsing behaviours. Thus, fish should be fed immediately before or after evacuation of their guts to maintain less-aggressive behaviours of juvenile dusky kob. Fish generally increased aggressive and browsing acts before and long time after feeding than closer to after feeding. The study has provided the fundamental scientific groundwork for fish farmers and future researchers can further explore size variation, time after feeding and gut evacuation rate as critical components of aggressive behaviours. The scientific knowledge of aggressive and cannibalistic behaviours has essential application in farming management to achieve improved survival and growth rates in juvenile fish.
- Full Text:
- Date Issued: 2018
The impact of the construction regulations 2014 on a water utility’s projects’ health and safety performance in South Africa
- Authors: Malindi, Rajandree Mandy
- Date: 2018
- Subjects: Construction industry -- Safety regulations -- South Africa , Construction industry -- Standards -- South Africa Construction industry -- Law and legislation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/31655 , vital:31645
- Description: The construction industry plays a major role in South Africa’s economic development. Since promulgation of the Construction Regulations, the expectation is that project stakeholders are placing more emphasis on H&S to contribute to project success. The study aimed to assess the impact of the involvement of clients and other project stakeholders on the overall project H&S performance on projects undertaken by a large water utility. The scope was limited to the organisation’s engineering and operations division and its internal project stakeholders, namely the designers, quantity surveyors, project managers, and construction H&S professionals. Local literature pointed out that poor construction H&S performance is attributable to a lack of management commitment, inadequate supervision, inadequate or lack of H&S training, lack of worker involvement, personal risk appreciation and work pressures (cidb, 2009: 37). International literature indicated that the total CoA exceeds the cost of H&S (cidb, 2009: 9). Quantitative methods were utilised in two phases to gather and analyse data. In Phase 1, a questionnaire was developed and distributed to a target population, and in Phase 2, data was obtained from existing records of historic and completed project files for projects undertaken by the water utility. A total of 67 responses were used to analyse data. All stakeholders somehow contributed to H&S however, most respondents regarded CHS professionals, contractors and PMs as the primary stakeholders. The study found that stakeholders perceived H&S to be influenced during the later rather than the initial stages of projects and that H&S actions were significantly undertaken during stage 5. The frequency of H&S actions varied with each stakeholder dependent on the stage in which they were involved in. Recommendations were for H&S to be integrated in the initial stages of projects and for a follow up research to be conducted to investigate if there are improvements during the six project stages after full implementation of the Construction Regulations 2014. This requirement will force industry to comply and most importantly to drive joint efforts by the various stakeholders.
- Full Text:
- Date Issued: 2018
- Authors: Malindi, Rajandree Mandy
- Date: 2018
- Subjects: Construction industry -- Safety regulations -- South Africa , Construction industry -- Standards -- South Africa Construction industry -- Law and legislation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/31655 , vital:31645
- Description: The construction industry plays a major role in South Africa’s economic development. Since promulgation of the Construction Regulations, the expectation is that project stakeholders are placing more emphasis on H&S to contribute to project success. The study aimed to assess the impact of the involvement of clients and other project stakeholders on the overall project H&S performance on projects undertaken by a large water utility. The scope was limited to the organisation’s engineering and operations division and its internal project stakeholders, namely the designers, quantity surveyors, project managers, and construction H&S professionals. Local literature pointed out that poor construction H&S performance is attributable to a lack of management commitment, inadequate supervision, inadequate or lack of H&S training, lack of worker involvement, personal risk appreciation and work pressures (cidb, 2009: 37). International literature indicated that the total CoA exceeds the cost of H&S (cidb, 2009: 9). Quantitative methods were utilised in two phases to gather and analyse data. In Phase 1, a questionnaire was developed and distributed to a target population, and in Phase 2, data was obtained from existing records of historic and completed project files for projects undertaken by the water utility. A total of 67 responses were used to analyse data. All stakeholders somehow contributed to H&S however, most respondents regarded CHS professionals, contractors and PMs as the primary stakeholders. The study found that stakeholders perceived H&S to be influenced during the later rather than the initial stages of projects and that H&S actions were significantly undertaken during stage 5. The frequency of H&S actions varied with each stakeholder dependent on the stage in which they were involved in. Recommendations were for H&S to be integrated in the initial stages of projects and for a follow up research to be conducted to investigate if there are improvements during the six project stages after full implementation of the Construction Regulations 2014. This requirement will force industry to comply and most importantly to drive joint efforts by the various stakeholders.
- Full Text:
- Date Issued: 2018
Predicting reintroduction outcomes: assessing the feasibility of reintroducing African wild dog to a small protected area
- Authors: Vogel, John Thomas
- Date: 2018
- Subjects: African wild dog , Wild dogs -- South Africa Wild dogs -- Conservation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/36464 , vital:33947
- Description: Large mammalian carnivores have experienced significant contractions in population sizes and geographical ranges. The conservation of large carnivores is crucially important, particularly due to their vulnerability to extinction and their functional significance and ability to structure ecosystems. Due to an expanding human footprint, large carnivores are increasingly subject to modified and spatially constrained habitats. A growing debate exists as to how to conserve and coexist with large carnivores in an anthropogenically induced environment. Reintroduction, as a conservation tool to restore locally extirpated large carnivores to portions of their former ranges is increasingly being applied. However, in South Africa, habitat to support large carnivores remain small and non-contiguous. Food is a fundamental ecological requirement to sustain reintroduced large carnivores. Therefore, an understanding of large predator foraging patterns can be informative in the context of how the predator species influences and utilises a novel ecosystem. We investigated the foraging behaviour of reintroduced African wild dog (Lycaon pictus) at five small protected areas in KwaZulu-Natal, South Africa. Wild dog utilised 16 prey species, albeit they primarily used nyala (Tragelaphus angasii) and impala (Aepyceros melampus) which collectively form 75 % of their diet. Only nyala was significantly preferred, suggesting that this prey species is used in greater proportion to their abundance. As wild dogs are social cooperative hunters, we tested whether wild dog pack size was correlated to prey mass selection. There was no evidence to suggest that larger packs use larger prey. However, the mean wild dog pack size in our sample sites, was relatively smaller than those encountered elsewhere. Furthermore, wild dog have been shown to modify their hunting behaviour in the presence of wildlife-proof fencing, by using fences to aid in the capture of larger prey species than would innately occur. We compared the prey mass of wild dog kills in relation to proximity of these hard boundaries. Despite the affinity towards kills occurring within 200 m of fences, the upward bias caused by fences on prey mass selection was inconsistent across sample sites. The relatively small size of wild dogs makes them particularly vulnerable to competition. As the energetic output of wild dog is high, interspecific competition can increase foraging costs. The reintroduction of large carnivores to small artificially induced systems may be a contentious issue as resources available to support large carnivores are expected to be relatively more finite. We compared both the potential inter- and intraspecific dietary niche dimensions of an intact large carnivore guild in context of a wild dog reintroduction. We determined cheetah (Acinonyx jubatus), leopard (Panthera pardus), and lion (Panthera leo) prey composition, diet breadth, overlap, prey preference and predicted the density of an intact large carnivore guild in a novel landscape. Further, we compared the foraging behaviour of these large carnivores to that of wild dog. Our findings suggest that large African carnivores in small protected areas are subject to a considerable dietary niche overlap. Wild dog and cheetah, particularly reproductive females with dependent offspring, displayed the greatest potential for dietary overlap and subsequent competition. Leopard and lion at the population species level exhibited greater degrees of foraging plasticity. Lion displayed a contrasting prey species preference to sympatric predators as they selected for prey items frequently avoided by cheetah, leopard and wild dog. The proposed wild dog reintroduction site is expected to sustain seven wild dog based on the availability of preferred prey biomass. However, the reintroduction of wild dog to the small protected area is expected to have negative lateral trophic influences on other species of conservation concern. This should be of vital importance to management of the protected area. As the influence of competition in food-web and population dynamics, particularly in resource poor environments may be profound, our research highlights the need to assess the influence of competitive forces in structuring and restoring large predators to portions of their historical range.
- Full Text:
- Date Issued: 2018
- Authors: Vogel, John Thomas
- Date: 2018
- Subjects: African wild dog , Wild dogs -- South Africa Wild dogs -- Conservation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/36464 , vital:33947
- Description: Large mammalian carnivores have experienced significant contractions in population sizes and geographical ranges. The conservation of large carnivores is crucially important, particularly due to their vulnerability to extinction and their functional significance and ability to structure ecosystems. Due to an expanding human footprint, large carnivores are increasingly subject to modified and spatially constrained habitats. A growing debate exists as to how to conserve and coexist with large carnivores in an anthropogenically induced environment. Reintroduction, as a conservation tool to restore locally extirpated large carnivores to portions of their former ranges is increasingly being applied. However, in South Africa, habitat to support large carnivores remain small and non-contiguous. Food is a fundamental ecological requirement to sustain reintroduced large carnivores. Therefore, an understanding of large predator foraging patterns can be informative in the context of how the predator species influences and utilises a novel ecosystem. We investigated the foraging behaviour of reintroduced African wild dog (Lycaon pictus) at five small protected areas in KwaZulu-Natal, South Africa. Wild dog utilised 16 prey species, albeit they primarily used nyala (Tragelaphus angasii) and impala (Aepyceros melampus) which collectively form 75 % of their diet. Only nyala was significantly preferred, suggesting that this prey species is used in greater proportion to their abundance. As wild dogs are social cooperative hunters, we tested whether wild dog pack size was correlated to prey mass selection. There was no evidence to suggest that larger packs use larger prey. However, the mean wild dog pack size in our sample sites, was relatively smaller than those encountered elsewhere. Furthermore, wild dog have been shown to modify their hunting behaviour in the presence of wildlife-proof fencing, by using fences to aid in the capture of larger prey species than would innately occur. We compared the prey mass of wild dog kills in relation to proximity of these hard boundaries. Despite the affinity towards kills occurring within 200 m of fences, the upward bias caused by fences on prey mass selection was inconsistent across sample sites. The relatively small size of wild dogs makes them particularly vulnerable to competition. As the energetic output of wild dog is high, interspecific competition can increase foraging costs. The reintroduction of large carnivores to small artificially induced systems may be a contentious issue as resources available to support large carnivores are expected to be relatively more finite. We compared both the potential inter- and intraspecific dietary niche dimensions of an intact large carnivore guild in context of a wild dog reintroduction. We determined cheetah (Acinonyx jubatus), leopard (Panthera pardus), and lion (Panthera leo) prey composition, diet breadth, overlap, prey preference and predicted the density of an intact large carnivore guild in a novel landscape. Further, we compared the foraging behaviour of these large carnivores to that of wild dog. Our findings suggest that large African carnivores in small protected areas are subject to a considerable dietary niche overlap. Wild dog and cheetah, particularly reproductive females with dependent offspring, displayed the greatest potential for dietary overlap and subsequent competition. Leopard and lion at the population species level exhibited greater degrees of foraging plasticity. Lion displayed a contrasting prey species preference to sympatric predators as they selected for prey items frequently avoided by cheetah, leopard and wild dog. The proposed wild dog reintroduction site is expected to sustain seven wild dog based on the availability of preferred prey biomass. However, the reintroduction of wild dog to the small protected area is expected to have negative lateral trophic influences on other species of conservation concern. This should be of vital importance to management of the protected area. As the influence of competition in food-web and population dynamics, particularly in resource poor environments may be profound, our research highlights the need to assess the influence of competitive forces in structuring and restoring large predators to portions of their historical range.
- Full Text:
- Date Issued: 2018
Construction management’s perceptions of health and safety
- Authors: Sigama, Takalani
- Date: 2018
- Subjects: Construction industry -- Management , Building -- Safety measures Construction industry -- Health aspects Construction industry -- Safety regulations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/35713 , vital:33784
- Description: Projects in the construction sector are reputed for poor health and safety (H&S) performance, compared to other industries. This can be attributed to, inter alia, a relatively uncontrolled working environment, inherent operational risks, workers' behaviour in relation to H&S commitment, cultural and religious beliefs, and uncertainties inherent in projects. Hazards and risk arising from poor H&S practices result in injuries, and in some cases, fatalities. The aim of this study is to explore the perceptions of construction management regarding H&S on construction sites. This study investigates the relationship between behaviours, attitudes, perceptions, and behaviours towards H&S, and compares cultural divergences among levels of construction personnel, namely construction management, construction supervision, construction H&S personnel, and H&S representatives. The construction industry has for many years developed and maintained a very bad reputation for coping with project cost, H&S, quality, and schedule. The industry often delivers projects late, and contributes to a disproportionate rate of work-related injuries, and fatalities. Project H&S management is acknowledged as one of the techniques that could be improved on construction projects to enhance performance of construction contractors in South Africa. To answer the research question: ‘Why construction management perceive H&S as a hindrance to production?” the mixed-method research approach was used. An indepth literature review with respect to project H&S was carried out, followed by qualitative and quantitative empirical research. The study established the need for H&S training and awareness of Construction Managers, Construction Supervisors, Construction Health and Safety Managers (CHSMs), Officers (CHSOs), and H&S Representatives. The study recommends that an H&S training needs analysis is critical for all employees, since it raises H&S awareness among all stakeholders in the construction industry, and enables the development of training plans, thereby supporting the reduction of accidents and related incident.
- Full Text:
- Date Issued: 2018
- Authors: Sigama, Takalani
- Date: 2018
- Subjects: Construction industry -- Management , Building -- Safety measures Construction industry -- Health aspects Construction industry -- Safety regulations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/35713 , vital:33784
- Description: Projects in the construction sector are reputed for poor health and safety (H&S) performance, compared to other industries. This can be attributed to, inter alia, a relatively uncontrolled working environment, inherent operational risks, workers' behaviour in relation to H&S commitment, cultural and religious beliefs, and uncertainties inherent in projects. Hazards and risk arising from poor H&S practices result in injuries, and in some cases, fatalities. The aim of this study is to explore the perceptions of construction management regarding H&S on construction sites. This study investigates the relationship between behaviours, attitudes, perceptions, and behaviours towards H&S, and compares cultural divergences among levels of construction personnel, namely construction management, construction supervision, construction H&S personnel, and H&S representatives. The construction industry has for many years developed and maintained a very bad reputation for coping with project cost, H&S, quality, and schedule. The industry often delivers projects late, and contributes to a disproportionate rate of work-related injuries, and fatalities. Project H&S management is acknowledged as one of the techniques that could be improved on construction projects to enhance performance of construction contractors in South Africa. To answer the research question: ‘Why construction management perceive H&S as a hindrance to production?” the mixed-method research approach was used. An indepth literature review with respect to project H&S was carried out, followed by qualitative and quantitative empirical research. The study established the need for H&S training and awareness of Construction Managers, Construction Supervisors, Construction Health and Safety Managers (CHSMs), Officers (CHSOs), and H&S Representatives. The study recommends that an H&S training needs analysis is critical for all employees, since it raises H&S awareness among all stakeholders in the construction industry, and enables the development of training plans, thereby supporting the reduction of accidents and related incident.
- Full Text:
- Date Issued: 2018
Development of a low-cost bioprinting system for the fabrication of cell-laden sodium alginate hydrogels
- Authors: Honiball, John Robert
- Date: 2018
- Subjects: Regenerative medicine , Tissue engineering , Alginates , Colloids , Three-dimensional printing
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59204 , vital:27470
- Description: Bioprinting is a rapidly expanding technology with the ability to fabricate in vitro 3D tissues in a layer-by-layer manner to ultimately produce a living tissue which physiologically resembles native in vivo tissue functionality. Unfortunately, large costs associated with commercially available bioprinters severely limit the amount of people/research groups with access to the technology. Here, we investigated the potential for modifying a commercially available RepRap Prusa iteration 3 (i3) three-dimensional (3D) printer, by replacing the traditional plastic-based print-head with various open-source syringe-housed microextrusion print-head units, such that deposition of composite bioinks consisting of cells, biopolymer scaffolds and/or biomolecules may be achieved at a relatively low cost. Using adipose-derived human mesenchymal stromal stem cells (ad-HMSC) induced for adipogenic differentiation, as well as human umbilical vein endothelial cells (HUVEC), the potential for fabricating vascularised adipose tissue was investigated. The non-toxic, inexpensive algal polysaccharide, sodium alginate, was used to test the printability of the system, as well as for investigating the functionality unmodified sodium alginate has for use as a potential bioink in adipose tissue engineering. Cell viability assays, namely WST-1 and fluorescein diacetate (FDA)/propidium iodide (PI) live/dead cell staining, revealed that ad-HMSC were viable after 7 days of culture. However, viability of HUVEC encapsulated hydrogels revealed significantly lower cell viability. Live/dead cell staining revealed that the modified printing system was able to print ad-HMSC/HUVEC co-cocultures with a large degree of cell viability after 1 day of culture. However, after 7 days of culture, the majority of cells were revealed to be dead. Furthermore, due to the lack of mechanical integrity possessed by alginate in a liquid-like state, printing sodium alginate hydrogels in air consistently resulted in deformation of printed constructs. The newly developed 3D printing technique termed freeform reversible embedding of suspended hydrogels (FRESH) was therefore investigated as a means for achieving 3D spatial control of printed hydrogels using the modified system. Printing cell-free sodium alginate hydrogels within gelatin sacrificial support baths allowed for fabricating constructs in a spatially defined manner. However, overprinting and swelling of alginate hydrogels negatively affected the overall printing accuracy. The present study aimed to pave the way for further system modifications and refinements, such that the ultimate goal of low-cost bioprinting may be achieved. Further optimisation of printing parameters, hydrogel characteristics and sterilisation techniques may allow for fabricating viable, physiologically relevant tissues using the modified system developed.
- Full Text:
- Date Issued: 2018
- Authors: Honiball, John Robert
- Date: 2018
- Subjects: Regenerative medicine , Tissue engineering , Alginates , Colloids , Three-dimensional printing
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59204 , vital:27470
- Description: Bioprinting is a rapidly expanding technology with the ability to fabricate in vitro 3D tissues in a layer-by-layer manner to ultimately produce a living tissue which physiologically resembles native in vivo tissue functionality. Unfortunately, large costs associated with commercially available bioprinters severely limit the amount of people/research groups with access to the technology. Here, we investigated the potential for modifying a commercially available RepRap Prusa iteration 3 (i3) three-dimensional (3D) printer, by replacing the traditional plastic-based print-head with various open-source syringe-housed microextrusion print-head units, such that deposition of composite bioinks consisting of cells, biopolymer scaffolds and/or biomolecules may be achieved at a relatively low cost. Using adipose-derived human mesenchymal stromal stem cells (ad-HMSC) induced for adipogenic differentiation, as well as human umbilical vein endothelial cells (HUVEC), the potential for fabricating vascularised adipose tissue was investigated. The non-toxic, inexpensive algal polysaccharide, sodium alginate, was used to test the printability of the system, as well as for investigating the functionality unmodified sodium alginate has for use as a potential bioink in adipose tissue engineering. Cell viability assays, namely WST-1 and fluorescein diacetate (FDA)/propidium iodide (PI) live/dead cell staining, revealed that ad-HMSC were viable after 7 days of culture. However, viability of HUVEC encapsulated hydrogels revealed significantly lower cell viability. Live/dead cell staining revealed that the modified printing system was able to print ad-HMSC/HUVEC co-cocultures with a large degree of cell viability after 1 day of culture. However, after 7 days of culture, the majority of cells were revealed to be dead. Furthermore, due to the lack of mechanical integrity possessed by alginate in a liquid-like state, printing sodium alginate hydrogels in air consistently resulted in deformation of printed constructs. The newly developed 3D printing technique termed freeform reversible embedding of suspended hydrogels (FRESH) was therefore investigated as a means for achieving 3D spatial control of printed hydrogels using the modified system. Printing cell-free sodium alginate hydrogels within gelatin sacrificial support baths allowed for fabricating constructs in a spatially defined manner. However, overprinting and swelling of alginate hydrogels negatively affected the overall printing accuracy. The present study aimed to pave the way for further system modifications and refinements, such that the ultimate goal of low-cost bioprinting may be achieved. Further optimisation of printing parameters, hydrogel characteristics and sterilisation techniques may allow for fabricating viable, physiologically relevant tissues using the modified system developed.
- Full Text:
- Date Issued: 2018
Procurement challenges faced by Eskom contractors during the tender stage
- Authors: Hlalutye, Thandiwe
- Date: 2018
- Subjects: Management -- Procurement -- South Africa -- Northern Cape , Project management -- South Africa -- Northern Cape Contractors' operation -- South Africa -- Northern Cape -- Finance
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30260 , vital:30913
- Description: The procurement process within South Africa has become an increasing focus in open market access for local economic development. The government introduced Preferential Procurement Policy Frame Act 5 of 2000 (PPPFA) which must be followed by all government owned organisations, including parastatals. Eskom, therefore, has to abide to this regulation and, since it started utilising the Act in its tendering process, there has been a challenge to getting contractors who are commercially and technically approved to be able to execute work or projects. The aim of this study is to examine challenges faced by Eskom Northern Cape Operating Unit contractors during the tender stage in terms of tender requirements, whereby they fail to submit all required tender returnables and fail to meet a set threshold in order to be successful and being awarded with the contract. This study undertook an empirical study using a case study of Eskom after a literature review. A questionnaire was used to collect data from all the active contractors on the Eskom Northern Cape Operating Unit data base. The key findings included that; contractors agreed that they still lack understanding of a quality management system. However they disagreed that they are not complying with safety health and environment and that they lack knowledge of technical requirements which leads them to not submitting objective evidence. The study concluded that contracting firms still do not comply with procurement requirements during the tender stage.
- Full Text:
- Date Issued: 2018
- Authors: Hlalutye, Thandiwe
- Date: 2018
- Subjects: Management -- Procurement -- South Africa -- Northern Cape , Project management -- South Africa -- Northern Cape Contractors' operation -- South Africa -- Northern Cape -- Finance
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30260 , vital:30913
- Description: The procurement process within South Africa has become an increasing focus in open market access for local economic development. The government introduced Preferential Procurement Policy Frame Act 5 of 2000 (PPPFA) which must be followed by all government owned organisations, including parastatals. Eskom, therefore, has to abide to this regulation and, since it started utilising the Act in its tendering process, there has been a challenge to getting contractors who are commercially and technically approved to be able to execute work or projects. The aim of this study is to examine challenges faced by Eskom Northern Cape Operating Unit contractors during the tender stage in terms of tender requirements, whereby they fail to submit all required tender returnables and fail to meet a set threshold in order to be successful and being awarded with the contract. This study undertook an empirical study using a case study of Eskom after a literature review. A questionnaire was used to collect data from all the active contractors on the Eskom Northern Cape Operating Unit data base. The key findings included that; contractors agreed that they still lack understanding of a quality management system. However they disagreed that they are not complying with safety health and environment and that they lack knowledge of technical requirements which leads them to not submitting objective evidence. The study concluded that contracting firms still do not comply with procurement requirements during the tender stage.
- Full Text:
- Date Issued: 2018
Biophysical monitoring of unphosphorylated STAT3 homodimerization
- Mtwebana, Sinethemba Siphokazi
- Authors: Mtwebana, Sinethemba Siphokazi
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63957 , vital:28514
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
- Authors: Mtwebana, Sinethemba Siphokazi
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63957 , vital:28514
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
Isolation and characterization of E. coli and Campylobacter spp. from diarrhoeal samples collected from selected hospitals in Amathole District Municipality, Eastern Cape, South Africa
- Authors: Omolajaiye, Sunday Abraham
- Date: 2018
- Subjects: Escherichia coli infections Campylobacter infections Diarrhea
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/6213 , vital:29515
- Description: Approximately 2-4 billion cases of infectious diarrhoea occur every year, with the highest numbers recorded in sub-Saharan Africa. It remains the most common public health issue among children in developing nations. The purpose of this research was to unfold the prevalence of diarrhoeagenic E. coli and Campylobacter pathotypes as well as elucidate their antibiogram characteristics in diarrhoeal stool samples collected in some medical facilities in Eastern Cape Province, South Africa. Two hundred stool samples were collected from both inpatients and outpatients from male and females of all age groups attending selected medical facilities in the study area. Isolation and characterization of both organisms were done using culture based and molecular methods. Antibiotic susceptibility patterns of identified isolates were determined against a panel of 12 antimicrobial agents. One hundred and twenty presumptive E. coli isolates and 42 presumptive isolates of Campylobacter spp. Were isolated. Eighty-two percent (82 percent) of the presumptive E. coli isolates were confirmed as E. coli while 46.3 percent belonged to Campylobacter spp. Pathotyping of the diarrhoeagenic E. coli isolates by Polymerase chain reaction (PCR) showed the following prevalences: DAEC 43 (32 percent), EHEC 18 (17 percent), EIEC 11 (10 percent) and EPEC 18 (17 percent). EAEC and ETEC were not detected, while for Campylobacter spp. 37 (88 percent) were C. jejuni, and C. coli was not detected. A total of 12 (32.4 percent) of the confirmed Campylobacter jejuni isolates were found to possess the fliM gene, 9 (24.3 percent) possessed the flhA gene and only 6 (16.2 percent) harboured the gene flgE2. None were positive for the flaA, flab and flhB genes.The antibiotic resistance patterns observed among the E. coli isolates were high against ampicillin (98.1 percent), chloramphenicol (94.3 percent) and tetracycline (90.6 percent). For Campylobacter spp., resistance observed were: chloramphenicol (91.6 percent), tetracycline (25.2 percent), erythromycin (49.6 percent) and gentamycin (56.4 percent). A lesser resistance against imipenem (35.9 percent) and quinolone (ciprofloxacin) (45.5 percent) were exhibited by the E.coli isolates. 10.8 percent and 20.3 percent of the Campylobacter isolates were resistant to imipenem and ciprofloxacin respectively. The presence of chloramphenicol (CatA1) and tetracycline (tetA) resistance genes were detected in 94 percent and 89 percent of E. coli isolates respectively while 98 percent of Campylobacter spp. Harboured the catA1 resistance gene. It could be deduced from this study that E. coli and Campylobacter spp. are predomiant enteric pathogens as the etiologic agents of diarrhoea in the study community, and that their antimicrobial resistance is high in the study location. The need to develop strategies to prevent infection and control resistant organisms is evident.
- Full Text:
- Date Issued: 2018
- Authors: Omolajaiye, Sunday Abraham
- Date: 2018
- Subjects: Escherichia coli infections Campylobacter infections Diarrhea
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/6213 , vital:29515
- Description: Approximately 2-4 billion cases of infectious diarrhoea occur every year, with the highest numbers recorded in sub-Saharan Africa. It remains the most common public health issue among children in developing nations. The purpose of this research was to unfold the prevalence of diarrhoeagenic E. coli and Campylobacter pathotypes as well as elucidate their antibiogram characteristics in diarrhoeal stool samples collected in some medical facilities in Eastern Cape Province, South Africa. Two hundred stool samples were collected from both inpatients and outpatients from male and females of all age groups attending selected medical facilities in the study area. Isolation and characterization of both organisms were done using culture based and molecular methods. Antibiotic susceptibility patterns of identified isolates were determined against a panel of 12 antimicrobial agents. One hundred and twenty presumptive E. coli isolates and 42 presumptive isolates of Campylobacter spp. Were isolated. Eighty-two percent (82 percent) of the presumptive E. coli isolates were confirmed as E. coli while 46.3 percent belonged to Campylobacter spp. Pathotyping of the diarrhoeagenic E. coli isolates by Polymerase chain reaction (PCR) showed the following prevalences: DAEC 43 (32 percent), EHEC 18 (17 percent), EIEC 11 (10 percent) and EPEC 18 (17 percent). EAEC and ETEC were not detected, while for Campylobacter spp. 37 (88 percent) were C. jejuni, and C. coli was not detected. A total of 12 (32.4 percent) of the confirmed Campylobacter jejuni isolates were found to possess the fliM gene, 9 (24.3 percent) possessed the flhA gene and only 6 (16.2 percent) harboured the gene flgE2. None were positive for the flaA, flab and flhB genes.The antibiotic resistance patterns observed among the E. coli isolates were high against ampicillin (98.1 percent), chloramphenicol (94.3 percent) and tetracycline (90.6 percent). For Campylobacter spp., resistance observed were: chloramphenicol (91.6 percent), tetracycline (25.2 percent), erythromycin (49.6 percent) and gentamycin (56.4 percent). A lesser resistance against imipenem (35.9 percent) and quinolone (ciprofloxacin) (45.5 percent) were exhibited by the E.coli isolates. 10.8 percent and 20.3 percent of the Campylobacter isolates were resistant to imipenem and ciprofloxacin respectively. The presence of chloramphenicol (CatA1) and tetracycline (tetA) resistance genes were detected in 94 percent and 89 percent of E. coli isolates respectively while 98 percent of Campylobacter spp. Harboured the catA1 resistance gene. It could be deduced from this study that E. coli and Campylobacter spp. are predomiant enteric pathogens as the etiologic agents of diarrhoea in the study community, and that their antimicrobial resistance is high in the study location. The need to develop strategies to prevent infection and control resistant organisms is evident.
- Full Text:
- Date Issued: 2018
The implementation of a push-pull programme for the control of Eldana saccharina (Lepidoptera: Pyralidae) in sugarcane in the coastal regions of Kwazulu-Natal, South Africa
- Authors: Mulcahy, Megan Marie
- Date: 2018
- Subjects: Pyralidae -- South Africa -- KwaZulu-Natal , Pests -- Integrated control , Sugarcane -- Diseases and pests -- South Africa -- KwaZulu-Natal , Stem borers -- Effect of habitat modification on -- South Africa -- KwaZulu-Natal , Insect-plant relationships -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63290 , vital:28390
- Description: Eldana saccharina, an indigenous lepidopteran stemborer, is considered the most damaging pest of sugarcane in South Africa. Researchers have advocated the use of an area-wide integrated pest management (AW-IPM) programme as a means of improving the control of this pest. A push-pull strategy was developed as a component of this AW-IPM approach. The push-pull strategy in sugarcane is a habitat management method of pest control that uses plants that are both repellent (Melinis Minutiflora) and attractive (Cyperus dives, Cyperus papyrus and Bt-maize) to E. saccharina. Previous research into push-pull has shown that this strategy is an effective tool for the control of E. saccharina. Push-pull has been implemented successfully in the Midlands North sugarcane growing region of KwaZulu-Natal (KZN), South Africa. Despite the proven efficacy of push-pull, very little push-pull research has been conducted in the coastal sugarcane growing regions of KZN, and adoption of this technology has been poor in these regions. Therefore, the aim of this research was to facilitate the implementation of push-pull for the management of E. saccharina in sugarcane in the coastal regions of KZN. This was done by focussing on on-farm field trials and farmer participatory research. On-farm push-pull field trials were conducted on five model farms in the North and South Coast sugarcane growing regions of KZN. High levels of E. saccharina were recorded during this study. The push-pull treatment sites showed a significant reduction of E. saccharina damage on four of the five farms used in the study. Mean percentage of stalks damaged decreased by up to 50 % in the presence of the repellent grass species, M. minutiflora. The number of E. saccharina found per 100 stalks also decreased significantly at these farms. The farm which did not show a significant reduction in E. saccharina populations or damage had low numbers of this pest in the sugarcane throughout the experiment. This demonstrates that push-pull is more effective in areas that have high levels of E. saccharina. Stem borer surveys in wetlands on sugarcane farms revealed that high numbers of E. saccharina were found within the pull plants, C. papyrus and C. dives, in comparison to the push-pull sites. This verifies that the pull plants do work efficiently to attract E. saccharina away from sugarcane. Additionally, eight parasitoids emerged from E. saccharina larvae collected in wetland sedges. The beneficial roles that push-pull plants play in attracting and maintaining natural enemies in the agroecosystem are discussed, and these findings further demonstrate the important ecosystem, and pest management services that wetlands provide on sugarcane farms. The success of the push-pull trials in this study show that this technology can be an effective tool for controlling E. saccharina in the coastal sugarcane growing regions. The timing of the planting of push-pull plants was shown to play a role in the efficacy of this technology. The study also confirmed that push-pull should be used as a component of AW-IPM in conjunction with good crop management practices. Surveys were undertaken to determine large-scale sugarcane growers' (LSGs) knowledge and perceptions of E. saccharina and other pests. Research regarding the farmers' perceptions of push- pull was also conducted to better understand the drivers and barriers to adoption of push-pull, and other new technologies. The surveys found that large-scale farmers in the coastal regions suffer from high infestations of E. saccharina. As such there is scope for the introduction of new pest management practices such as push-pull in this area. Farmers also demonstrated a good basic knowledge of E. saccharina and IPM. However, LSGs had a poor understanding of push-pull and how it works, as well as the plants that make up the push-pull system that is being implemented against E. saccharina in South Africa. A dearth in practical knowledge regarding the implementation of push-pull was seen as a major barrier to the adoption of this strategy, as was financial instability, farmer attitudes and poor institutional support. Farmers recommended collaboration amongst stakeholders, improved education, proof of the efficacy of push-pull and incentives as tools to improve the implementation of this strategy in the coastal sugarcane growing regions of KZN. Farmers preferred direct contact with extension personnel and experiential learning opportunities when acquiring information about push- pull and other new pest management practices. If opportunities for push-pull education are increased through direct contact with extension personnel, and through on-farm demonstrations, and if inputs are provided in the form of push-pull plants, it is likely that push-pull will succeed amongst coastal LSGs, especially since farmers had an overall positive attitude towards the technology. Surveys amongst small-scale sugarcane growers (SSGs) showed that sugarcane is important in the lives of these farmers. The SSGs perceive pests to be a major constraint to their farming systems, and they identified E. saccharina as a major pest of sugarcane. The farmers also demonstrated good knowledge of sugarcane pests and vegetable pests. However, SSGs lacked knowledge regarding pest management practices and beneficial insects. Extension and advisory services should to continue concentrating on pest management practices to educate SSGs on the variety and application of pest control strategies. SSGs were found to employ complex, diverse and integrated agricultural systems that are well-suited to the implementation of IPM technologies such as push-pull. Since insect pests act were found to be a major constraint to SSG sugarcane production, push-pull was deemed a feasible pest management strategy for coastal farmers and its implementation by SSGs should be further explored. SSGs in this study were also concerned about vegetable pests, therefore if push-pull can be adapted to help protect additional crops, adoption of this technology by small-scale growers will improve.
- Full Text:
- Date Issued: 2018
- Authors: Mulcahy, Megan Marie
- Date: 2018
- Subjects: Pyralidae -- South Africa -- KwaZulu-Natal , Pests -- Integrated control , Sugarcane -- Diseases and pests -- South Africa -- KwaZulu-Natal , Stem borers -- Effect of habitat modification on -- South Africa -- KwaZulu-Natal , Insect-plant relationships -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63290 , vital:28390
- Description: Eldana saccharina, an indigenous lepidopteran stemborer, is considered the most damaging pest of sugarcane in South Africa. Researchers have advocated the use of an area-wide integrated pest management (AW-IPM) programme as a means of improving the control of this pest. A push-pull strategy was developed as a component of this AW-IPM approach. The push-pull strategy in sugarcane is a habitat management method of pest control that uses plants that are both repellent (Melinis Minutiflora) and attractive (Cyperus dives, Cyperus papyrus and Bt-maize) to E. saccharina. Previous research into push-pull has shown that this strategy is an effective tool for the control of E. saccharina. Push-pull has been implemented successfully in the Midlands North sugarcane growing region of KwaZulu-Natal (KZN), South Africa. Despite the proven efficacy of push-pull, very little push-pull research has been conducted in the coastal sugarcane growing regions of KZN, and adoption of this technology has been poor in these regions. Therefore, the aim of this research was to facilitate the implementation of push-pull for the management of E. saccharina in sugarcane in the coastal regions of KZN. This was done by focussing on on-farm field trials and farmer participatory research. On-farm push-pull field trials were conducted on five model farms in the North and South Coast sugarcane growing regions of KZN. High levels of E. saccharina were recorded during this study. The push-pull treatment sites showed a significant reduction of E. saccharina damage on four of the five farms used in the study. Mean percentage of stalks damaged decreased by up to 50 % in the presence of the repellent grass species, M. minutiflora. The number of E. saccharina found per 100 stalks also decreased significantly at these farms. The farm which did not show a significant reduction in E. saccharina populations or damage had low numbers of this pest in the sugarcane throughout the experiment. This demonstrates that push-pull is more effective in areas that have high levels of E. saccharina. Stem borer surveys in wetlands on sugarcane farms revealed that high numbers of E. saccharina were found within the pull plants, C. papyrus and C. dives, in comparison to the push-pull sites. This verifies that the pull plants do work efficiently to attract E. saccharina away from sugarcane. Additionally, eight parasitoids emerged from E. saccharina larvae collected in wetland sedges. The beneficial roles that push-pull plants play in attracting and maintaining natural enemies in the agroecosystem are discussed, and these findings further demonstrate the important ecosystem, and pest management services that wetlands provide on sugarcane farms. The success of the push-pull trials in this study show that this technology can be an effective tool for controlling E. saccharina in the coastal sugarcane growing regions. The timing of the planting of push-pull plants was shown to play a role in the efficacy of this technology. The study also confirmed that push-pull should be used as a component of AW-IPM in conjunction with good crop management practices. Surveys were undertaken to determine large-scale sugarcane growers' (LSGs) knowledge and perceptions of E. saccharina and other pests. Research regarding the farmers' perceptions of push- pull was also conducted to better understand the drivers and barriers to adoption of push-pull, and other new technologies. The surveys found that large-scale farmers in the coastal regions suffer from high infestations of E. saccharina. As such there is scope for the introduction of new pest management practices such as push-pull in this area. Farmers also demonstrated a good basic knowledge of E. saccharina and IPM. However, LSGs had a poor understanding of push-pull and how it works, as well as the plants that make up the push-pull system that is being implemented against E. saccharina in South Africa. A dearth in practical knowledge regarding the implementation of push-pull was seen as a major barrier to the adoption of this strategy, as was financial instability, farmer attitudes and poor institutional support. Farmers recommended collaboration amongst stakeholders, improved education, proof of the efficacy of push-pull and incentives as tools to improve the implementation of this strategy in the coastal sugarcane growing regions of KZN. Farmers preferred direct contact with extension personnel and experiential learning opportunities when acquiring information about push- pull and other new pest management practices. If opportunities for push-pull education are increased through direct contact with extension personnel, and through on-farm demonstrations, and if inputs are provided in the form of push-pull plants, it is likely that push-pull will succeed amongst coastal LSGs, especially since farmers had an overall positive attitude towards the technology. Surveys amongst small-scale sugarcane growers (SSGs) showed that sugarcane is important in the lives of these farmers. The SSGs perceive pests to be a major constraint to their farming systems, and they identified E. saccharina as a major pest of sugarcane. The farmers also demonstrated good knowledge of sugarcane pests and vegetable pests. However, SSGs lacked knowledge regarding pest management practices and beneficial insects. Extension and advisory services should to continue concentrating on pest management practices to educate SSGs on the variety and application of pest control strategies. SSGs were found to employ complex, diverse and integrated agricultural systems that are well-suited to the implementation of IPM technologies such as push-pull. Since insect pests act were found to be a major constraint to SSG sugarcane production, push-pull was deemed a feasible pest management strategy for coastal farmers and its implementation by SSGs should be further explored. SSGs in this study were also concerned about vegetable pests, therefore if push-pull can be adapted to help protect additional crops, adoption of this technology by small-scale growers will improve.
- Full Text:
- Date Issued: 2018
The role of ecological processes in structuring reef fish communities in the Agulhas Ecoregion, South Africa
- Authors: Dyer, Alexander
- Date: 2018
- Subjects: Reef fishes -- South Africa -- Agulhas, Cape (Cape) , Reef fishes -- Ecology -- South Africa -- Agulhas, Cape (Cape) , Marine biodiversity -- South Africa -- Agulhas, Cape (Cape) , Biotic communities -- South Africa -- Agulhas, Cape (Cape) , Sparidae -- South Africa -- Agulhas, Cape (Cape) , Reef fishes -- Size -- South Africa -- Agulhas, Cape (Cape) , Baited remote underwater stereo-video systems (stereo-BRUVs)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63899 , vital:28504
- Description: Local, niche-based processes, which arise from the interplay between biotic interactions and abiotic constraints are considered to be important regulators of community structure. However, it is increasingly recognised that patterns of diversity can also be strongly influenced by dispersal-driven processes. While empirical research on the diversity of coral reef fishes on shallow tropical reefs has contributed greatly to the development of general concepts in ecology, there have been considerably fewer studies on the processes which shape the diversity of fish communities on shallow (10 - 30 m) and deep (30 - 75 m) rocky reefs. Consequently, it is less clear at which spatial scales niche partitioning and dispersal limitation contribute most strongly to the structure of reef-associated fish communities within rocky reef ecosystems. To address this caveat, research was conducted at four rocky reef complexes within the warm-temperate Agulhas Ecoregion, South Africa. The diversity of reef-associated fishes was sampled by baited remote underwater stereo-video systems (stereo-BRUVs) to incorporate the range of heterogeneous reef habitat in Tsitsikamma National Park Marine Protected Area (TNP MPA) and Algoa Bay (AB). To examine how niche-based and dispersal-driven processes influence patterns of diversity among species within the dominant family of resident fishes, the sparids (Sparidae), components of diversity were quantified at several spatial scales. Turnover in the number of species which locally co-occurred was found to be largely driven by the limited dispersal of species over hundreds of kilometres. When relative species abundances were taken into account, sparid communities were characterised by higher than expected rates of compositional turnover among local habitat patches separated by hundreds to thousands of metres of contiguous reef. Patterns of compositional turnover were associated with the spatial aggregation of conspecifics, particularly at scales which facilitate the post-settlement dispersal of fishes. Niche-based segregation of species along the depth gradient was found to be the primary driver of compositional turnover among both protected and exploited communities. However, spatial structuring within reefs, which was independent of variation in the environment, suggests that compositional differences among communities are also influenced by the limited post-settlement dispersal of resident fishes to adjacent areas during their ontogeny. Together, the results suggest that the diversity of reef-associated sparids is likely to depend both on an adequate diversity of suitable reef habitat and a sufficient degree of spatial connectivity to facilitate ontogenetic habitat shifts. Taxon-based descriptors of diversity do not adequately account for ecological difference among conspecifics within size-structured populations. To test whether differences in body size facilitated coexistence among sparid fishes, the number of species which coexisted at the local scale was related to variation in the size structure of communities. In communities which have been historically protected from fishing, local coexistence between a greater number of species was promoted by reduced levels of intraspecific variation in size of fishes. This suggests that, among species with similar trophic requirements, further niche segregation along a prey-size and body-size gradient is likely to mitigate the direct impacts of competition for shared food resources. Among exploited communities, size structure did not influence the number of species which coexisted at the local scale. This finding suggests that fishing-induced mortality of larger-bodied fishes is likely to remove some of the constraints to colonisation which arise from asymmetries in competitive fitness between small and large-bodied fishes. Together, these results highlight the importance of post-settlement processes and population size structure to the maintenance of reef-associated fish diversity within contiguous rocky reef habitats.
- Full Text:
- Date Issued: 2018
- Authors: Dyer, Alexander
- Date: 2018
- Subjects: Reef fishes -- South Africa -- Agulhas, Cape (Cape) , Reef fishes -- Ecology -- South Africa -- Agulhas, Cape (Cape) , Marine biodiversity -- South Africa -- Agulhas, Cape (Cape) , Biotic communities -- South Africa -- Agulhas, Cape (Cape) , Sparidae -- South Africa -- Agulhas, Cape (Cape) , Reef fishes -- Size -- South Africa -- Agulhas, Cape (Cape) , Baited remote underwater stereo-video systems (stereo-BRUVs)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63899 , vital:28504
- Description: Local, niche-based processes, which arise from the interplay between biotic interactions and abiotic constraints are considered to be important regulators of community structure. However, it is increasingly recognised that patterns of diversity can also be strongly influenced by dispersal-driven processes. While empirical research on the diversity of coral reef fishes on shallow tropical reefs has contributed greatly to the development of general concepts in ecology, there have been considerably fewer studies on the processes which shape the diversity of fish communities on shallow (10 - 30 m) and deep (30 - 75 m) rocky reefs. Consequently, it is less clear at which spatial scales niche partitioning and dispersal limitation contribute most strongly to the structure of reef-associated fish communities within rocky reef ecosystems. To address this caveat, research was conducted at four rocky reef complexes within the warm-temperate Agulhas Ecoregion, South Africa. The diversity of reef-associated fishes was sampled by baited remote underwater stereo-video systems (stereo-BRUVs) to incorporate the range of heterogeneous reef habitat in Tsitsikamma National Park Marine Protected Area (TNP MPA) and Algoa Bay (AB). To examine how niche-based and dispersal-driven processes influence patterns of diversity among species within the dominant family of resident fishes, the sparids (Sparidae), components of diversity were quantified at several spatial scales. Turnover in the number of species which locally co-occurred was found to be largely driven by the limited dispersal of species over hundreds of kilometres. When relative species abundances were taken into account, sparid communities were characterised by higher than expected rates of compositional turnover among local habitat patches separated by hundreds to thousands of metres of contiguous reef. Patterns of compositional turnover were associated with the spatial aggregation of conspecifics, particularly at scales which facilitate the post-settlement dispersal of fishes. Niche-based segregation of species along the depth gradient was found to be the primary driver of compositional turnover among both protected and exploited communities. However, spatial structuring within reefs, which was independent of variation in the environment, suggests that compositional differences among communities are also influenced by the limited post-settlement dispersal of resident fishes to adjacent areas during their ontogeny. Together, the results suggest that the diversity of reef-associated sparids is likely to depend both on an adequate diversity of suitable reef habitat and a sufficient degree of spatial connectivity to facilitate ontogenetic habitat shifts. Taxon-based descriptors of diversity do not adequately account for ecological difference among conspecifics within size-structured populations. To test whether differences in body size facilitated coexistence among sparid fishes, the number of species which coexisted at the local scale was related to variation in the size structure of communities. In communities which have been historically protected from fishing, local coexistence between a greater number of species was promoted by reduced levels of intraspecific variation in size of fishes. This suggests that, among species with similar trophic requirements, further niche segregation along a prey-size and body-size gradient is likely to mitigate the direct impacts of competition for shared food resources. Among exploited communities, size structure did not influence the number of species which coexisted at the local scale. This finding suggests that fishing-induced mortality of larger-bodied fishes is likely to remove some of the constraints to colonisation which arise from asymmetries in competitive fitness between small and large-bodied fishes. Together, these results highlight the importance of post-settlement processes and population size structure to the maintenance of reef-associated fish diversity within contiguous rocky reef habitats.
- Full Text:
- Date Issued: 2018
Assessment of indigenous forest degradation and deforestation along the wild coast, near Port St John’s, Eastern Cape Province, South Africa
- Katende, Lukyamuzi Lucky Fulgentius
- Authors: Katende, Lukyamuzi Lucky Fulgentius
- Date: 2018
- Subjects: Deforestation -- South Africa -- Eastern Cape , Forest degradation -- South Africa -- Eastern Cape Forest management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30649 , vital:31006
- Description: Indigenous forests along the Wild Coast of the Eastern Cape Province have experienced both degradation and deforestation over the past decades. In early 2000, steps were taken to rehabilitate some of the degraded areas. Nevertheless, there is no monitoring mechanism in place, so little is known about the extent of degradation and impact of the rehabilitation efforts. The present study assesses the extent to which deforestation and degradation of the indigenous forests have occurred, and evaluates rehabilitation efforts in the study area around Port Saint John’s. Forest degradation was defined as the decrease in forest cover density while deforestation was defined as an increase in the trend of light forests and/ or a decrease in dense forests. The details for this study were obtained from multi – temporal remotely sensed data for a period between 1982 and 2013 (31 years). Multi-temporal Landsat satellite imagery for 1982, 1986, 1989, 2002, 2009 and 2013 was acquired and analysed. On the basis of prior knowledge of the area, the supervised classification approach was used. The Maximum likelihood supervised classification technique was used to extract information from satellite data. The classified images were filtered using a majority filtering procedure to reduce noise. Google Earth (Astrium) ancillary images were used to refine the classification based on expert rules. The derived changes in the degraded and rehabilitated areas were further validated through field visits. The overall image classification accuracy generated from Landsat image data ranged from 80% to 90%. It was noted that the area of dense forest almost doubled between 1986 and 1989, coinciding with a 59% decrease in the light forest. Subsequently, dense forests increased by 14,820 ha while light forests decreased by 16,690 ha between 1989 and 2002. The subsequent reduction in light forest coverage is explained by the establishment of the Participatory Forest Management (PFMA) approach by Department of Water Affairs and Forestry (DWAF) which reversed the degradation trend. However, specific degradation hotspots were identified, particularly where new settlements have been established. The emergence of the non-vegetated area increased gradually from 7% in 1986 to 23.4% in 2013. Notably, dense forest was observed to have experienced higher rates of forest degradation and deforestation than the light forest. The highest number patches were 4 recorded between 2002 and 1998, followed by between 2010 and 2013 and lastly 1986. Based on spatial connectedness of patches, the year 1986 had the highest landscape connectedness of forest vegetation (CONAT = 35.3) followed by 2002 and 1996 while the year 2010 and 2013 had the lowest landscape contiguity. Over the study period, the distribution of patches clearly shows that forest degradation and deforestation rates were lower in the years 1986, 1998 and tremendously increased in the later period of between 2010 and 2013. However, as a result of rehabilitation efforts, dense forest was seen to steadily gain more land than light forest. Finer details of degradation trends could not be easily picked from the images used in the study, given their spatial resolution limitations. That notwithstanding, the trends identified are good for overview decisions. The study has also established that de-agraianisation, forest restoration and rehabilitation greatly contributed to increased forest cover. Therefore, with more use of GIS by forest managers, and imagery of the high resolution being readily available, forests will in future be easily monitored using remote sensing.
- Full Text:
- Date Issued: 2018
- Authors: Katende, Lukyamuzi Lucky Fulgentius
- Date: 2018
- Subjects: Deforestation -- South Africa -- Eastern Cape , Forest degradation -- South Africa -- Eastern Cape Forest management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30649 , vital:31006
- Description: Indigenous forests along the Wild Coast of the Eastern Cape Province have experienced both degradation and deforestation over the past decades. In early 2000, steps were taken to rehabilitate some of the degraded areas. Nevertheless, there is no monitoring mechanism in place, so little is known about the extent of degradation and impact of the rehabilitation efforts. The present study assesses the extent to which deforestation and degradation of the indigenous forests have occurred, and evaluates rehabilitation efforts in the study area around Port Saint John’s. Forest degradation was defined as the decrease in forest cover density while deforestation was defined as an increase in the trend of light forests and/ or a decrease in dense forests. The details for this study were obtained from multi – temporal remotely sensed data for a period between 1982 and 2013 (31 years). Multi-temporal Landsat satellite imagery for 1982, 1986, 1989, 2002, 2009 and 2013 was acquired and analysed. On the basis of prior knowledge of the area, the supervised classification approach was used. The Maximum likelihood supervised classification technique was used to extract information from satellite data. The classified images were filtered using a majority filtering procedure to reduce noise. Google Earth (Astrium) ancillary images were used to refine the classification based on expert rules. The derived changes in the degraded and rehabilitated areas were further validated through field visits. The overall image classification accuracy generated from Landsat image data ranged from 80% to 90%. It was noted that the area of dense forest almost doubled between 1986 and 1989, coinciding with a 59% decrease in the light forest. Subsequently, dense forests increased by 14,820 ha while light forests decreased by 16,690 ha between 1989 and 2002. The subsequent reduction in light forest coverage is explained by the establishment of the Participatory Forest Management (PFMA) approach by Department of Water Affairs and Forestry (DWAF) which reversed the degradation trend. However, specific degradation hotspots were identified, particularly where new settlements have been established. The emergence of the non-vegetated area increased gradually from 7% in 1986 to 23.4% in 2013. Notably, dense forest was observed to have experienced higher rates of forest degradation and deforestation than the light forest. The highest number patches were 4 recorded between 2002 and 1998, followed by between 2010 and 2013 and lastly 1986. Based on spatial connectedness of patches, the year 1986 had the highest landscape connectedness of forest vegetation (CONAT = 35.3) followed by 2002 and 1996 while the year 2010 and 2013 had the lowest landscape contiguity. Over the study period, the distribution of patches clearly shows that forest degradation and deforestation rates were lower in the years 1986, 1998 and tremendously increased in the later period of between 2010 and 2013. However, as a result of rehabilitation efforts, dense forest was seen to steadily gain more land than light forest. Finer details of degradation trends could not be easily picked from the images used in the study, given their spatial resolution limitations. That notwithstanding, the trends identified are good for overview decisions. The study has also established that de-agraianisation, forest restoration and rehabilitation greatly contributed to increased forest cover. Therefore, with more use of GIS by forest managers, and imagery of the high resolution being readily available, forests will in future be easily monitored using remote sensing.
- Full Text:
- Date Issued: 2018
Assessing growth response patterns of microalgae to varying environmental conditions using sediments from ephemeral wetlands
- Authors: Mazwane, Sixolile
- Date: 2018
- Subjects: Microalgae -- South Africa , Wetland conservation -- South Africa Landscape ecology -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/22398 , vital:29966
- Description: Ephemeral wetlands serve as habitats for different fauna and flora. Microalgae make up a bulk of primary production in newly inundated wetlands and have a big influence on the aquatic community structure. As ephemeral wetlands have cyclical drying and wetting phases, algal species found in these habitats have evolved adaptations (i.e. dormancy and cysts) to survive during dry periods and become productive upon inundation. Algae have been used as ecological indicators in many aquatic ecosystems including wetlands, particularly associated with water quality and with varying inundation states. Whilst temperature and water level have been shown to affect microalgal biomass independently, this study aims to assess the effects of these two factors simultaneously on microalgal biomass, species diversity and community changes. The aim of the study was to investigate microalgal dynamics using two ephemeral wetlands in the Nelson Mandela Bay Municipality. The growth response patterns of microalgal communities to varying temperatures and inundation levels through experiments using dry temporary wetland sediments was also assessed. Dry sediments were collected from two depression wetlands with different sediment characteristics (1592 and Elephant Wallow (EW)). The study consisted of replicated treatments with three different surface area: volume ratios (SA:V) (Low surface area: volume (LSAV), Medium (MSAV) and High (HSAV)), inundated with distilled water. The microcosms were placed inside a Conviron environmental growth chamber and illuminated at between 106 to 138 μmol.m-2s-1, with a 12:12 light-dark cycle at constant temperatures of 12 °C (mean winter) and 22 °C (mean summer). Physicochemical data were recorded, and biological samples were collected every 4 days over a 28-day inundation period. In the field, Electrical conductivity (EC) and pH showed a gradual increase over the inundation period. The systems were well oxygenated (6-10 mg L-1). Overall, phytoplankton biomass in the field was ~10 μg L-1 whereas benthic biomass (MPB) was significantly higher 10 – 300 mg L-1. Within the experiments, the phytoplankton biomass showed a pattern while MPB biomass increased gradually for both experiments. There were no significant (p>0.05) differences between the 1592 and EW phytoplankton biomass. However, the MPB biomass showed significant (p<0.05) differences between the two sediments (EW high, 1592 low) and the experiments, respectively. In the winter experiment, the 1592 sediment had high phytoplankton biomass compared to EW, the reverse was observed for the MPB biomass. In summer experiment, similar results were observed in terms of phytoplankton biomass. For the MPBs, 1592 had greater biomass for all treatments compared to EW. The phytoplankton community for both field samples and experiments was dominated by chlorophytes (>50 %), followed by cyanophytes and euglenophytes (with cryptophytes in summer experiment) for both field and experiments. The MPB community was dominated by bacillariophytes (55 %) and chlorophytes (25 %) in the 1592 sediments and this was also the case with EW sediments bacillariophytes (70 %), although cyanophytes (15 %) made up the remainder of the MPB community. The 1592 sediments supported higher diatom abundances under the HSAV compared to the same treatment from the EW wetland suggesting that possibly grain size or texture might be responsible. In contrast, sediments from EW under LSAV conditions showed higher diatom cell numbers possibly indicating that increased water depth has the propensity to support greater diatom assemblages compared with the same water level for sediments from 1592. The results indicate that microalgae community is influenced by sediment type more than it is by water level. From this study it was also established that microalgae were able to reemerge from their dormancy state upon inundation and that tank experiments were successful in simulating natural ephemeral wetland conditions. The findings from this study will add to the available baseline data on microalgal dynamics in the ephemeral wetlands in South Africa, especially in semi-arid areas. This information can be valuable in enhancing our understanding regarding the role of microalgae in ephemeral wetlands in order to conserve them.
- Full Text:
- Date Issued: 2018
- Authors: Mazwane, Sixolile
- Date: 2018
- Subjects: Microalgae -- South Africa , Wetland conservation -- South Africa Landscape ecology -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/22398 , vital:29966
- Description: Ephemeral wetlands serve as habitats for different fauna and flora. Microalgae make up a bulk of primary production in newly inundated wetlands and have a big influence on the aquatic community structure. As ephemeral wetlands have cyclical drying and wetting phases, algal species found in these habitats have evolved adaptations (i.e. dormancy and cysts) to survive during dry periods and become productive upon inundation. Algae have been used as ecological indicators in many aquatic ecosystems including wetlands, particularly associated with water quality and with varying inundation states. Whilst temperature and water level have been shown to affect microalgal biomass independently, this study aims to assess the effects of these two factors simultaneously on microalgal biomass, species diversity and community changes. The aim of the study was to investigate microalgal dynamics using two ephemeral wetlands in the Nelson Mandela Bay Municipality. The growth response patterns of microalgal communities to varying temperatures and inundation levels through experiments using dry temporary wetland sediments was also assessed. Dry sediments were collected from two depression wetlands with different sediment characteristics (1592 and Elephant Wallow (EW)). The study consisted of replicated treatments with three different surface area: volume ratios (SA:V) (Low surface area: volume (LSAV), Medium (MSAV) and High (HSAV)), inundated with distilled water. The microcosms were placed inside a Conviron environmental growth chamber and illuminated at between 106 to 138 μmol.m-2s-1, with a 12:12 light-dark cycle at constant temperatures of 12 °C (mean winter) and 22 °C (mean summer). Physicochemical data were recorded, and biological samples were collected every 4 days over a 28-day inundation period. In the field, Electrical conductivity (EC) and pH showed a gradual increase over the inundation period. The systems were well oxygenated (6-10 mg L-1). Overall, phytoplankton biomass in the field was ~10 μg L-1 whereas benthic biomass (MPB) was significantly higher 10 – 300 mg L-1. Within the experiments, the phytoplankton biomass showed a pattern while MPB biomass increased gradually for both experiments. There were no significant (p>0.05) differences between the 1592 and EW phytoplankton biomass. However, the MPB biomass showed significant (p<0.05) differences between the two sediments (EW high, 1592 low) and the experiments, respectively. In the winter experiment, the 1592 sediment had high phytoplankton biomass compared to EW, the reverse was observed for the MPB biomass. In summer experiment, similar results were observed in terms of phytoplankton biomass. For the MPBs, 1592 had greater biomass for all treatments compared to EW. The phytoplankton community for both field samples and experiments was dominated by chlorophytes (>50 %), followed by cyanophytes and euglenophytes (with cryptophytes in summer experiment) for both field and experiments. The MPB community was dominated by bacillariophytes (55 %) and chlorophytes (25 %) in the 1592 sediments and this was also the case with EW sediments bacillariophytes (70 %), although cyanophytes (15 %) made up the remainder of the MPB community. The 1592 sediments supported higher diatom abundances under the HSAV compared to the same treatment from the EW wetland suggesting that possibly grain size or texture might be responsible. In contrast, sediments from EW under LSAV conditions showed higher diatom cell numbers possibly indicating that increased water depth has the propensity to support greater diatom assemblages compared with the same water level for sediments from 1592. The results indicate that microalgae community is influenced by sediment type more than it is by water level. From this study it was also established that microalgae were able to reemerge from their dormancy state upon inundation and that tank experiments were successful in simulating natural ephemeral wetland conditions. The findings from this study will add to the available baseline data on microalgal dynamics in the ephemeral wetlands in South Africa, especially in semi-arid areas. This information can be valuable in enhancing our understanding regarding the role of microalgae in ephemeral wetlands in order to conserve them.
- Full Text:
- Date Issued: 2018
Incidence of bacterial infections and colonisation in patients admitted to a tuberculosis hospital
- Authors: Annear, Dale John
- Date: 2018
- Subjects: Medical microbiology , Microbiology Bacteriology Tuberculosis -- Hospitals -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/21482 , vital:29526
- Description: Patients with drug resistant tuberculosis (TB) are treated with multiple antibiotics including moxifloxacin, linezolid, and meropenem, which puts them at greater risk for colonisation by multi-drug resistant (MDR) bacteria. The objectives of this study were to: (i) assess the antimicrobial prescribing patterns practiced within the hospital by retrospective patient file review; (ii) determine the spectrum of bacterial colonisation in TB patients upon admission and during hospitalisation; (iii) identify bacterial isolates and evaluate antimicrobial susceptibility profiles; (iv) detect antimicrobial resistance genes in the bacterial isolates by PCR and DNA sequencing; and (v) investigate genetic relatedness of Klebsiella pneumoniae isolates using Multi Locus Sequence Typing. Nasal, groin and rectal swabs [for the detection of extended spectrum beta lactamases (EBSLs), carbapenem-resistant Enterobacteriaceae (CRE), vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA)] were analysed from a cohort of patients (n=37) admitted either from the community (n = 28) or from other healthcare facilities (n=9) to a TB hospital. Swab samples were collected at admission and at four week intervals thereafter during hospitalization. Identification and antimicrobial susceptibility testing of bacterial isolates (n=62) were determined at the National Health Laboratory Services (NHLS) by the VITEK-MS and Vitek 2 systems respectively. Additional antimicrobial susceptibility testing was conducted by Sensititre Gram Negative Xtra (GNFX2) MIC plates. PCR and DNA sequencing were used for detection of resistance genes. Patients (n=13/37; 35%) were colonized by MDR bacteria (ESBLs [n=11], MRSA [n=2]) on admission. Colonization rates were lower in patients admitted from the community (9/28; 32%) compared to those transferred from other healthcare facilities (4/9; 44%). All admitted patients who did not exhibit colonization at baseline and who were resident within the hospital for longer than 4 weeks (17/37; 46% of total patients) became colonised by an ESBL-producing Enterobacteriaceae species. No patients acquired MRSA during hospitalisation. Among ESBL Enterobacteriaceae, Escherichia coli (41/62; 66%) and K. pneumoniae [14/62; 23%]) predominated. Nineteen percent (7/37) of patients demised during their hospitalization. Both the Vitek system and Sensititre Gram Negative Xtra (GNFX2) MIC plates susceptibilities were similar for most antimicrobials, however there were discrepancies for tigecycline susceptibility profiles. A high number of isolates exhibited resistance to aminoglycosides and fluoroquinolones. Genes encoding for ESBLs (CTX-M-14, CTX-M-15, SHV-28, OXA-1, and OXY-2-9) were detected among ESBL Enterobacteriaceae. Two Enterobacteriaceae isolates with reduced carbapenem susceptibility did not contain carbapenemase-encoding genes. MLST revealed unique sequence types and genetic diversity among the K. pneumoniae isolates from hospitalised patients. However, the source and colonization routes of these isolates could not be determined, which requires further investigation. This study provides insight into the spectrum of bacterial pathogen colonisation in hospitalised TB patients and suggests a review of infection control programs and practices at the TB hospital.
- Full Text:
- Date Issued: 2018
- Authors: Annear, Dale John
- Date: 2018
- Subjects: Medical microbiology , Microbiology Bacteriology Tuberculosis -- Hospitals -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/21482 , vital:29526
- Description: Patients with drug resistant tuberculosis (TB) are treated with multiple antibiotics including moxifloxacin, linezolid, and meropenem, which puts them at greater risk for colonisation by multi-drug resistant (MDR) bacteria. The objectives of this study were to: (i) assess the antimicrobial prescribing patterns practiced within the hospital by retrospective patient file review; (ii) determine the spectrum of bacterial colonisation in TB patients upon admission and during hospitalisation; (iii) identify bacterial isolates and evaluate antimicrobial susceptibility profiles; (iv) detect antimicrobial resistance genes in the bacterial isolates by PCR and DNA sequencing; and (v) investigate genetic relatedness of Klebsiella pneumoniae isolates using Multi Locus Sequence Typing. Nasal, groin and rectal swabs [for the detection of extended spectrum beta lactamases (EBSLs), carbapenem-resistant Enterobacteriaceae (CRE), vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA)] were analysed from a cohort of patients (n=37) admitted either from the community (n = 28) or from other healthcare facilities (n=9) to a TB hospital. Swab samples were collected at admission and at four week intervals thereafter during hospitalization. Identification and antimicrobial susceptibility testing of bacterial isolates (n=62) were determined at the National Health Laboratory Services (NHLS) by the VITEK-MS and Vitek 2 systems respectively. Additional antimicrobial susceptibility testing was conducted by Sensititre Gram Negative Xtra (GNFX2) MIC plates. PCR and DNA sequencing were used for detection of resistance genes. Patients (n=13/37; 35%) were colonized by MDR bacteria (ESBLs [n=11], MRSA [n=2]) on admission. Colonization rates were lower in patients admitted from the community (9/28; 32%) compared to those transferred from other healthcare facilities (4/9; 44%). All admitted patients who did not exhibit colonization at baseline and who were resident within the hospital for longer than 4 weeks (17/37; 46% of total patients) became colonised by an ESBL-producing Enterobacteriaceae species. No patients acquired MRSA during hospitalisation. Among ESBL Enterobacteriaceae, Escherichia coli (41/62; 66%) and K. pneumoniae [14/62; 23%]) predominated. Nineteen percent (7/37) of patients demised during their hospitalization. Both the Vitek system and Sensititre Gram Negative Xtra (GNFX2) MIC plates susceptibilities were similar for most antimicrobials, however there were discrepancies for tigecycline susceptibility profiles. A high number of isolates exhibited resistance to aminoglycosides and fluoroquinolones. Genes encoding for ESBLs (CTX-M-14, CTX-M-15, SHV-28, OXA-1, and OXY-2-9) were detected among ESBL Enterobacteriaceae. Two Enterobacteriaceae isolates with reduced carbapenem susceptibility did not contain carbapenemase-encoding genes. MLST revealed unique sequence types and genetic diversity among the K. pneumoniae isolates from hospitalised patients. However, the source and colonization routes of these isolates could not be determined, which requires further investigation. This study provides insight into the spectrum of bacterial pathogen colonisation in hospitalised TB patients and suggests a review of infection control programs and practices at the TB hospital.
- Full Text:
- Date Issued: 2018