Technology in conservation: towards a system for in-field drone detection of invasive vegetation
- James, Katherine Margaret Frances
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
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
Livelihood implications of a possible Ramsar declaration of the Swartkops estuary, Eastern Cape, South Africa
- Authors: Vembo, Glen Muchengeti
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164715 , vital:41157
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Environmental Science, 2020
- Full Text:
- Date Issued: 2020
- Authors: Vembo, Glen Muchengeti
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164715 , vital:41157
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Environmental Science, 2020
- Full Text:
- Date Issued: 2020
An analysis of the use of DNS for malicious payload distribution
- Authors: Dube, Ishmael
- Date: 2019
- Subjects: Internet domain names , Computer networks -- Security measures , Computer security , Computer network protocols , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97531 , vital:31447
- Description: The Domain Name System (DNS) protocol is a fundamental part of Internet activities that can be abused by cybercriminals to conduct malicious activities. Previous research has shown that cybercriminals use different methods, including the DNS protocol, to distribute malicious content, remain hidden and avoid detection from various technologies that are put in place to detect anomalies. This allows botnets and certain malware families to establish covert communication channels that can be used to send or receive data and also distribute malicious payloads using the DNS queries and responses. Cybercriminals use the DNS to breach highly protected networks, distribute malicious content, and exfiltrate sensitive information without being detected by security controls put in place by embedding certain strings in DNS packets. This research undertaking broadens this research field and fills in the existing research gap by extending the analysis of DNS being used as a payload distribution channel to detection of domains that are used to distribute different malicious payloads. This research undertaking analysed the use of the DNS in detecting domains and channels that are used for distributing malicious payloads. Passive DNS data which replicate DNS queries on name servers to detect anomalies in DNS queries was evaluated and analysed in order to detect malicious payloads. The research characterises the malicious payload distribution channels by analysing passive DNS traffic and modelling the DNS query and response patterns. The research found that it is possible to detect malicious payload distribution channels through the analysis of DNS TXT resource records.
- Full Text:
- Date Issued: 2019
- Authors: Dube, Ishmael
- Date: 2019
- Subjects: Internet domain names , Computer networks -- Security measures , Computer security , Computer network protocols , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97531 , vital:31447
- Description: The Domain Name System (DNS) protocol is a fundamental part of Internet activities that can be abused by cybercriminals to conduct malicious activities. Previous research has shown that cybercriminals use different methods, including the DNS protocol, to distribute malicious content, remain hidden and avoid detection from various technologies that are put in place to detect anomalies. This allows botnets and certain malware families to establish covert communication channels that can be used to send or receive data and also distribute malicious payloads using the DNS queries and responses. Cybercriminals use the DNS to breach highly protected networks, distribute malicious content, and exfiltrate sensitive information without being detected by security controls put in place by embedding certain strings in DNS packets. This research undertaking broadens this research field and fills in the existing research gap by extending the analysis of DNS being used as a payload distribution channel to detection of domains that are used to distribute different malicious payloads. This research undertaking analysed the use of the DNS in detecting domains and channels that are used for distributing malicious payloads. Passive DNS data which replicate DNS queries on name servers to detect anomalies in DNS queries was evaluated and analysed in order to detect malicious payloads. The research characterises the malicious payload distribution channels by analysing passive DNS traffic and modelling the DNS query and response patterns. The research found that it is possible to detect malicious payload distribution channels through the analysis of DNS TXT resource records.
- Full Text:
- Date Issued: 2019
Initiating biological control for Nymphaea mexicana zuccarini (Nymphaeaceae) in South Africa
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
Stochastic models in finance
- Authors: Mazengera, Hassan
- Date: 2017
- Subjects: Finance -- Mathematical models , C++ (Computer program language) , GARCH model , Lebesgue-Radon-Nikodym theorems , Radon measures , Stochastic models , Stochastic processes , Stochastic processes -- Computer programs , Martingales (Mathematics) , Pricing -- Mathematical models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/162724 , vital:40976
- Description: Stochastic models for pricing financial securities are developed. First, we consider the Black Scholes model, which is a classic example of a complete market model and finally focus on Lévy driven models. Jumps may render the market incomplete and are induced in a model by inclusion of a Poisson process. Lévy driven models are more realistic in modelling of asset price dynamics than the Black Scholes model. Martingales are central in pricing, especially of derivatives and we give them the desired attention in the context of pricing. There are an increasing number of important pricing models where analytical solutions are not available hence computational methods come in handy, see Broadie and Glasserman (1997). It is also important to note that computational methods are also applicable to models with analytical solutions. We computationally value selected stochastic financial models using C++. Computational methods are also used to value or price complex financial instruments such as path dependent derivatives. This pricing procedure is applied in the computational valuation of a stochastic (revenue based) loan contract. Derivatives with simple pay of functions and models with analytical solutions are considered for illustrative purposes. The Black-Scholes P.D.E is complex to solve analytically and finite difference methods are widely used. Explicit finite difference scheme is considered in this thesis for computational valuation of derivatives that are modelled by the Black-Scholes P.D.E. Stochastic modelling of asset prices is important for the valuation of derivatives: Gaussian, exponential and gamma variates are simulated for the valuation purposes.
- Full Text:
- Date Issued: 2017
- Authors: Mazengera, Hassan
- Date: 2017
- Subjects: Finance -- Mathematical models , C++ (Computer program language) , GARCH model , Lebesgue-Radon-Nikodym theorems , Radon measures , Stochastic models , Stochastic processes , Stochastic processes -- Computer programs , Martingales (Mathematics) , Pricing -- Mathematical models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/162724 , vital:40976
- Description: Stochastic models for pricing financial securities are developed. First, we consider the Black Scholes model, which is a classic example of a complete market model and finally focus on Lévy driven models. Jumps may render the market incomplete and are induced in a model by inclusion of a Poisson process. Lévy driven models are more realistic in modelling of asset price dynamics than the Black Scholes model. Martingales are central in pricing, especially of derivatives and we give them the desired attention in the context of pricing. There are an increasing number of important pricing models where analytical solutions are not available hence computational methods come in handy, see Broadie and Glasserman (1997). It is also important to note that computational methods are also applicable to models with analytical solutions. We computationally value selected stochastic financial models using C++. Computational methods are also used to value or price complex financial instruments such as path dependent derivatives. This pricing procedure is applied in the computational valuation of a stochastic (revenue based) loan contract. Derivatives with simple pay of functions and models with analytical solutions are considered for illustrative purposes. The Black-Scholes P.D.E is complex to solve analytically and finite difference methods are widely used. Explicit finite difference scheme is considered in this thesis for computational valuation of derivatives that are modelled by the Black-Scholes P.D.E. Stochastic modelling of asset prices is important for the valuation of derivatives: Gaussian, exponential and gamma variates are simulated for the valuation purposes.
- Full Text:
- Date Issued: 2017
The impact of elephants on thicket vegetation and other mammals in the Eastern Cape Province, South Africa
- Authors: Nuttall-Smith, Gareth David
- Date: 2019
- Subjects: Albany Thicket -- Effect of browsing on , Elephants -- South Africa -- Eastern Cape , African elephant populations -- South Africa -- Eastern Cape , Woody plants -- Effect of browsing on -- South Africa -- Eastern Cape , Animal-plant relationships -- South Africa -- Eastern Cape , Vegetation monitoring -- South Africa -- Eastern Cape , African elephant populations -- Environmental aspects -- South Africa -- Eastern Cape , Biotic communities -- South Africa -- Eastern Cape , African elephant -- Food , Vegetation dynamics -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76365 , vital:30554
- Description: African elephants (Loxodonta africana) were absent from large portions of the Eastern Cape Province of South Africa for more than 100 years following widespread hunting for ivory. However, recent shifts in land use practices have resulted in the establishment of many private game reserves throughout the region. Some of these reserves have reintroduced elephants, raising management concerns because of the perceived impact that elephants can have on vegetation and the animals that rely on it for resources. My thesis aimed to assess the role of elephants in determining the structure and complexity of the locally important Thicket Biome and how medium and large mammals are affected. I quantified the woody and succulent components of Albany Thicket across nine reserves with elephants between May 2016 and November 2017 using a modified Point-Centre-Quarter method. Camera traps were deployed at each site for the duration of a calendar year to measure the relative abundances of all medium and large mammals at the sites. Across all study sites, climatic conditions (specifically rainfall and temperature) were the primary drivers of woody vegetation structure and diversity. Elephants appeared to have little influence since they were reintroduced at low densities 20 years ago. The associated mammal communities were mostly influenced by the height and basal area coverage of the thicket across the sites. I conclude that because elephant populations have been maintained at relatively low densities across my study sites, negative effects on the thicket vegetation and the associated mammal communities were not observed. In fact, the establishment of private game reserves, even with elephants, present may offer sustainable conservation for the threatened Albany Thicket. However, these elephant populations are still relatively new and changes to the vegetation are likely to be cumulative. Thus, future research should focus on how the vegetation is affected over time. To this end, I recommend the establishment of permanent sampling stations across all reserves with elephants in the Eastern Cape Province.
- Full Text:
- Date Issued: 2019
- Authors: Nuttall-Smith, Gareth David
- Date: 2019
- Subjects: Albany Thicket -- Effect of browsing on , Elephants -- South Africa -- Eastern Cape , African elephant populations -- South Africa -- Eastern Cape , Woody plants -- Effect of browsing on -- South Africa -- Eastern Cape , Animal-plant relationships -- South Africa -- Eastern Cape , Vegetation monitoring -- South Africa -- Eastern Cape , African elephant populations -- Environmental aspects -- South Africa -- Eastern Cape , Biotic communities -- South Africa -- Eastern Cape , African elephant -- Food , Vegetation dynamics -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76365 , vital:30554
- Description: African elephants (Loxodonta africana) were absent from large portions of the Eastern Cape Province of South Africa for more than 100 years following widespread hunting for ivory. However, recent shifts in land use practices have resulted in the establishment of many private game reserves throughout the region. Some of these reserves have reintroduced elephants, raising management concerns because of the perceived impact that elephants can have on vegetation and the animals that rely on it for resources. My thesis aimed to assess the role of elephants in determining the structure and complexity of the locally important Thicket Biome and how medium and large mammals are affected. I quantified the woody and succulent components of Albany Thicket across nine reserves with elephants between May 2016 and November 2017 using a modified Point-Centre-Quarter method. Camera traps were deployed at each site for the duration of a calendar year to measure the relative abundances of all medium and large mammals at the sites. Across all study sites, climatic conditions (specifically rainfall and temperature) were the primary drivers of woody vegetation structure and diversity. Elephants appeared to have little influence since they were reintroduced at low densities 20 years ago. The associated mammal communities were mostly influenced by the height and basal area coverage of the thicket across the sites. I conclude that because elephant populations have been maintained at relatively low densities across my study sites, negative effects on the thicket vegetation and the associated mammal communities were not observed. In fact, the establishment of private game reserves, even with elephants, present may offer sustainable conservation for the threatened Albany Thicket. However, these elephant populations are still relatively new and changes to the vegetation are likely to be cumulative. Thus, future research should focus on how the vegetation is affected over time. To this end, I recommend the establishment of permanent sampling stations across all reserves with elephants in the Eastern Cape Province.
- Full Text:
- Date Issued: 2019
Reproductive isolation mechanisms of two cryptic species of Eccritotarsus (Hemiptera: Miridae), biological control agents of water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae)
- Authors: Mnguni, Sandiso
- Date: 2019
- Subjects: Eccritotarsus , Meridae , Noxious weeds -- Biological control -- South Africa , Aquatic weeds -- Biological control -- South Africa , Water hyacinth -- Biological control -- South Africa , Biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68133 , vital:29202
- Description: Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae), is one of the world’s worst alien invasive plants. It is indigenous to the Amazon basin in South America but has become a problematic alien invasive in other parts of the world. As such, several host-specific biological control agents have been sourced from the native distributions in South America and have been released to control this plant where it has become problematic. Two of these agents include the geographically and reproductively isolated cryptic species of Eccritotarsus (Hemiptera: Miridae). One of these species was collected in the upper reaches of the Amazon River in Peru, while the other was collected over 3500km away from that site, in Florianopolis, southern Brazil. These cryptic species were thought to be a single species until recently, when DNA barcoding indicated that they were likely to be two species, and the species status has now been confirmed by interbreeding experiments and detailed morphological studies. The Brazilian population remains Eccritotarsus catarinensis (Carvalho), while the Peruvian population is now known as Eccritotarsus eichhorniae (Henry). The aim of this project was to investigate the mating behaviour and other behavioural traits of the two species that have resulted in reproductive isolation, and which could have led to speciation. In addition, investigations involving analysis of chemical compound compositions of the two species aimed to determine the extent to which the compounds played a role in the development and maintenance of reproductive isolation. To achieve the aims, behavioural-observation experiments were conducted in the form of no-choice, bi-choice and multi-choice tests in 1:1, 2:1 and 3:1 sex ratio assessments, both within and between species. Chemical compound compositions of E. catarinensis and E. eichhorniae were also assessed using Nuclear Magnetic Resonance (NMR), Solid-phase micro-extraction (SPME) and Gas-Chromatography Mass-Spectrometry (GC-MS) techniques. In no-choice experiments, the highest number of single and multiple copula incidences, and average total copula duration was found within species while copulation between species was much rarer. In bi-choice experiments, E. eichhorniae females and E. catarinensis males only chose to mate with their respective conspecifics, and within species copulations continued to have higher average total copula duration. In multi-choice experiments, the highest number of single and multiple copula incidences and average total copula duration was also found within species. GC-MS analysis suggested that E. catarinensis females and E. eichhorniae males have unique chemical compounds missing in their conspecifics and same sex of the other species. Further analysis suggested that E. catarinensis females and E. eichhorniae males have similar chemical compound compositions, whereas as E. eichhorniae females and E. catarinensis males have similar chemical compound compositions. These results suggest that there are behavioural differences that led to the development and maintenance of prezygotic reproductive isolation mechanisms, and that this is probably driven by pheromones in chemical compound compositions. These two species were geographically isolated in the native range and the populations have diverged to the point that they are now reproductively incompatible and therefore, distinct species. The main driver of the speciation is most likely mate recognition and attraction, as only reproductively important traits such as pheromones, genitalia, the scent glands and antennae have changed, while other traits, including host range and morphology, have remained remarkably stable. This provides evidence that differences in sexual selection in isolated populations may be important drivers of speciation and reproductive isolation in cryptic species.
- Full Text:
- Date Issued: 2019
- Authors: Mnguni, Sandiso
- Date: 2019
- Subjects: Eccritotarsus , Meridae , Noxious weeds -- Biological control -- South Africa , Aquatic weeds -- Biological control -- South Africa , Water hyacinth -- Biological control -- South Africa , Biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68133 , vital:29202
- Description: Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae), is one of the world’s worst alien invasive plants. It is indigenous to the Amazon basin in South America but has become a problematic alien invasive in other parts of the world. As such, several host-specific biological control agents have been sourced from the native distributions in South America and have been released to control this plant where it has become problematic. Two of these agents include the geographically and reproductively isolated cryptic species of Eccritotarsus (Hemiptera: Miridae). One of these species was collected in the upper reaches of the Amazon River in Peru, while the other was collected over 3500km away from that site, in Florianopolis, southern Brazil. These cryptic species were thought to be a single species until recently, when DNA barcoding indicated that they were likely to be two species, and the species status has now been confirmed by interbreeding experiments and detailed morphological studies. The Brazilian population remains Eccritotarsus catarinensis (Carvalho), while the Peruvian population is now known as Eccritotarsus eichhorniae (Henry). The aim of this project was to investigate the mating behaviour and other behavioural traits of the two species that have resulted in reproductive isolation, and which could have led to speciation. In addition, investigations involving analysis of chemical compound compositions of the two species aimed to determine the extent to which the compounds played a role in the development and maintenance of reproductive isolation. To achieve the aims, behavioural-observation experiments were conducted in the form of no-choice, bi-choice and multi-choice tests in 1:1, 2:1 and 3:1 sex ratio assessments, both within and between species. Chemical compound compositions of E. catarinensis and E. eichhorniae were also assessed using Nuclear Magnetic Resonance (NMR), Solid-phase micro-extraction (SPME) and Gas-Chromatography Mass-Spectrometry (GC-MS) techniques. In no-choice experiments, the highest number of single and multiple copula incidences, and average total copula duration was found within species while copulation between species was much rarer. In bi-choice experiments, E. eichhorniae females and E. catarinensis males only chose to mate with their respective conspecifics, and within species copulations continued to have higher average total copula duration. In multi-choice experiments, the highest number of single and multiple copula incidences and average total copula duration was also found within species. GC-MS analysis suggested that E. catarinensis females and E. eichhorniae males have unique chemical compounds missing in their conspecifics and same sex of the other species. Further analysis suggested that E. catarinensis females and E. eichhorniae males have similar chemical compound compositions, whereas as E. eichhorniae females and E. catarinensis males have similar chemical compound compositions. These results suggest that there are behavioural differences that led to the development and maintenance of prezygotic reproductive isolation mechanisms, and that this is probably driven by pheromones in chemical compound compositions. These two species were geographically isolated in the native range and the populations have diverged to the point that they are now reproductively incompatible and therefore, distinct species. The main driver of the speciation is most likely mate recognition and attraction, as only reproductively important traits such as pheromones, genitalia, the scent glands and antennae have changed, while other traits, including host range and morphology, have remained remarkably stable. This provides evidence that differences in sexual selection in isolated populations may be important drivers of speciation and reproductive isolation in cryptic species.
- Full Text:
- Date Issued: 2019
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
Isolation and structure elucidation of halogenated metabolites from Portieria hornemannii and Portieria tripinnata
- Authors: Adam, Mohammed
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64674 , vital:28591
- Description: The red marine algal genus, Portieria, is known to produce a number of potent cytotoxic compounds with anticancer potential. The most important anticancer lead produced by this genus is the compound halomon. Unfortunately, the lack of sufficient quantities of this compound hampered its further development. Two Portieria species, Portieria hornemannii and Portieria tripinnata, are found along the South African coastline. Recent studies, based on DNA analysis, suggest that Portieria hornemannii may in fact be divided into several cryptic species. The current project is part of a larger study designed to investigate the use of secondary metabolites to identify new marine algal species. In this study 1H NMR profiles of the organic extracts of selected Portieria spp were compared in order to identify new species. Selected compounds were then isolated and characterised as potential chemotaxonomic markers. Four halogenated monoterpenes were isolated from Portieria hornemannii. Two of these were new compounds 4-(3-bromo-4-chloro-4-methylpentyl)-3-chlorofuran-2(5H)-one, which were isomers of each other. The two known compounds had been previously isolated from Portieria hornemannii samples off the Madagascar coast. These compounds could prove to be useful as chemotaxonomic marker compounds, as they have never been isolated from any other species of marine algae. Three known halogenated monoterpenes were isolated from Portieria tripinnata. These compounds had been previously isolated from different species of marine algae and therefore, could not serve as chemotaxonomic marker compounds for this species of marine alga. Further work needs to be done on Portieria tripinnata, with regards to its chemistry, as it is a species of marine algae that has not been previously researched.
- Full Text:
- Date Issued: 2015
- Authors: Adam, Mohammed
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64674 , vital:28591
- Description: The red marine algal genus, Portieria, is known to produce a number of potent cytotoxic compounds with anticancer potential. The most important anticancer lead produced by this genus is the compound halomon. Unfortunately, the lack of sufficient quantities of this compound hampered its further development. Two Portieria species, Portieria hornemannii and Portieria tripinnata, are found along the South African coastline. Recent studies, based on DNA analysis, suggest that Portieria hornemannii may in fact be divided into several cryptic species. The current project is part of a larger study designed to investigate the use of secondary metabolites to identify new marine algal species. In this study 1H NMR profiles of the organic extracts of selected Portieria spp were compared in order to identify new species. Selected compounds were then isolated and characterised as potential chemotaxonomic markers. Four halogenated monoterpenes were isolated from Portieria hornemannii. Two of these were new compounds 4-(3-bromo-4-chloro-4-methylpentyl)-3-chlorofuran-2(5H)-one, which were isomers of each other. The two known compounds had been previously isolated from Portieria hornemannii samples off the Madagascar coast. These compounds could prove to be useful as chemotaxonomic marker compounds, as they have never been isolated from any other species of marine algae. Three known halogenated monoterpenes were isolated from Portieria tripinnata. These compounds had been previously isolated from different species of marine algae and therefore, could not serve as chemotaxonomic marker compounds for this species of marine alga. Further work needs to be done on Portieria tripinnata, with regards to its chemistry, as it is a species of marine algae that has not been previously researched.
- Full Text:
- Date Issued: 2015
The remote sensing of fires and their effects on soil properties in the uKhahlamba Drakensberg Park
- Authors: Moore, Natasha Jade
- Date: 2019
- Subjects: Remote sensing -- South Africa -- KwaZulu-Natal , Soil ecology -- South Africa -- KwaZulu-Natal , Grassland fires -- South Africa -- KwaZulu-Natal , Grassland fires -- Remote sensing -- South Africa -- KwaZulu-Natal , Soils -- Effect of fires on -- South Africa -- KwaZulu-Natal , uKhalamba Drakensberg Park (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94400 , vital:31042
- Description: Fires are a common and natural occurrence globally and specifically on the African continent. The Drakensberg Mountains are home to southern Africa’s high-altitude fire-climax grasslands, where fire is the dominant management tool. Fire is used to maintain the grasslands in the uKhahlamba Drakensberg Park (UDP) World Heritage Site, located on the eastern escarpment of the KwaZulu-Natal Drakensberg. This study aimed to investigate the spatial and temporal frequency of fires using remote sensing, and to investigate the effect of fire frequency on soil properties in the UDP. Remote sensing offers a set of supportive tools for the management of this sensitive vegetation and specifically to assess the frequency and spatial extent of fires. Field assessments can then be used to assess the impact of fires. Remotely sensed data were used to determine fire frequency and the spatial extent of fires in the UDP. The Moderate Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) active fire detection point data were processed to investigate the temporal resolution of fires. Landsat 5 and 8 imagery were utilised for conducting Normalised Burn Ratios (NBR) to determine the spatial extent of the burn scars of fires. The results from the remotely sensed data were used to select study sites for accessing the effects of fire frequency on soil properties. The remote sensing results showed the main fire season in the UDP was from May to October, and annual burn scars from the available Landsat data for 1998 to 2017 ranged from 22.5% to 57.67% of the UDP. Remote sensing was shown to be an effective tool for monitoring fires in the UDP, with a combination of satellite data producing the best results. Soil properties were highly varied across the UDP. Environmental factors were shown to have a more significant influence on soil properties than fire frequency. This study highlighted the complex nature and diversity of fires and soils across the UDP.
- Full Text:
- Date Issued: 2019
- Authors: Moore, Natasha Jade
- Date: 2019
- Subjects: Remote sensing -- South Africa -- KwaZulu-Natal , Soil ecology -- South Africa -- KwaZulu-Natal , Grassland fires -- South Africa -- KwaZulu-Natal , Grassland fires -- Remote sensing -- South Africa -- KwaZulu-Natal , Soils -- Effect of fires on -- South Africa -- KwaZulu-Natal , uKhalamba Drakensberg Park (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94400 , vital:31042
- Description: Fires are a common and natural occurrence globally and specifically on the African continent. The Drakensberg Mountains are home to southern Africa’s high-altitude fire-climax grasslands, where fire is the dominant management tool. Fire is used to maintain the grasslands in the uKhahlamba Drakensberg Park (UDP) World Heritage Site, located on the eastern escarpment of the KwaZulu-Natal Drakensberg. This study aimed to investigate the spatial and temporal frequency of fires using remote sensing, and to investigate the effect of fire frequency on soil properties in the UDP. Remote sensing offers a set of supportive tools for the management of this sensitive vegetation and specifically to assess the frequency and spatial extent of fires. Field assessments can then be used to assess the impact of fires. Remotely sensed data were used to determine fire frequency and the spatial extent of fires in the UDP. The Moderate Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) active fire detection point data were processed to investigate the temporal resolution of fires. Landsat 5 and 8 imagery were utilised for conducting Normalised Burn Ratios (NBR) to determine the spatial extent of the burn scars of fires. The results from the remotely sensed data were used to select study sites for accessing the effects of fire frequency on soil properties. The remote sensing results showed the main fire season in the UDP was from May to October, and annual burn scars from the available Landsat data for 1998 to 2017 ranged from 22.5% to 57.67% of the UDP. Remote sensing was shown to be an effective tool for monitoring fires in the UDP, with a combination of satellite data producing the best results. Soil properties were highly varied across the UDP. Environmental factors were shown to have a more significant influence on soil properties than fire frequency. This study highlighted the complex nature and diversity of fires and soils across the UDP.
- Full Text:
- Date Issued: 2019
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
Chemical composition of leaf essential oils of Lantana camara varieties in South Africa and their effect on the behavioural preference of Falconia intermedia
- Authors: Ngxande-Koza, Samella W
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4877 , vital:20739
- Description: Lantana camara L. (Verbenaceae) is one the most problematic invaders in South Africa invading forest edges, sand dunes, and shorelines by forming impenetrable thickets. Lantana camara invasions degrade natural biodiversity, reduce the value of land and consequently it has been a target for biological control, over the last 50 years in South Africa. Studies that have reported on chemical profile of Lantana camara have been conducted around the world but not in South Africa. Hence, the first aim of the current study was to identify the chemical baseline of L. camara varieties in the Eastern Cape, South Africa. Recent studies have shown that feeding by one of the agents released against L. camara, Falconia intermedia (Distant) (Hemiptera: Miridae), induces anti-herbivory response through increased leaf toughness and trichome density. A preliminary study conducted also reported the production of volatile chemicals by one variety, Whitney Farm, due to feeding by the mirids. Therefore, the second aim was to determine the induced changes in chemical compounds of L. camara varieties after feeding by F. intermedia. A third aim was to determine the effect these chemical compounds have on the behaviour of F. intermedia. To identify the chemical baseline of L. camara varieties, the essential oils of four L. camara varieties (East London, Port Alfred, Whitney Farm and Heather Glen) were analysed using gas chromatography mass spectrometry (GC-MS) and that resulted to the identification of 163 constitutive and 75 induced chemicals across the varieties tested. Lantana camara varieties showed different chemical classes but were highly dominated by terpenes. A great variation in the number of constitutive chemical compounds was found in all the varieties. There were 56 constitutive chemical compounds in the Whitney Farm variety, 41 in the East London variety, 36 in the Heather Glen variety and 30 in the Port Alfred variety. The Whitney Farm variety had the highest number (22) of unique constitutive chemicals identified when compared with other varieties. This indicates the chemical distinctiveness of the Whitney Farm variety from the other varieties. In the varieties tested, there were common chemical compounds identified in constitutive and induced (discussed below) states of the plants such as caryophyllene, hexane, naphthalene, copaene and a-caryophyllene. Besides naphthalene, the majority of chemical compounds in South African L. camara varieties were similar to compounds that have been identified across the world, suggesting that they are closely related. The expression of naphthalene in these varieties may be due to changes in the chemicals expressed over evolutionary time as predicted by the Novel Weapons Hypothesis. Amongst the varieties, a great variation in chemical compounds and their concentrations was shown in the induced states of the plants. The concentration of constitutive caryophyllene ranged from (3.13 - 15.7) %, to (4.02 - 11.10) % after feeding. The concentration of constitutive hexane ranged from (6.13 - 71.19) %, to (33.3 - 75.8) % after feeding. The concentration of constitutive naphthalene ranged from (0.21 - 4.79) %, to (0.92 - 2.11) % after feeding. The concentration of constitutive copaene ranged from (0.57 - 1.57) %, to (1.20 - 2.72) %. Lastly, the concentration of constitutive a-caryophyllene ranged from (1.18 - 9.03) %, to (0.78 - 5.48) % after feeding. The changes in chemical concentrations in lantana varieties indicated that feeding by the mirid on L. camara varieties causes an induction by either reducing or increasing the chemical concentrations. To determine the effect of the identified compounds on the behaviour of F. intermedia adults, olfactometer bioassays were conducted using a Y-tube technique. A significantly higher proportion of F. intermedia were attracted to undamaged leaves over damaged leaves and purified air. Undamaged leaves attracted 52 % of F. intermedia from the East London variety, 62.5 % from the Port Alfred variety, 56 % from the Whitney Farm variety, 58 % from the Lyndhurst variety and 54.5 % from the Heather Glen variety in dual choice trials versus damaged leaves. Furthermore, a significantly higher proportion of F. intermedia were attracted to damaged leaves over purified air. Damaged leaves attracted 67 % of F. intermedia from the East London variety, 67 % from the Port Alfred variety, 65.9 % from the Whitney Farm variety, 65.3 % from the Heather Glen variety and 64.5 % from the Lyndhurst variety. Olfactometer bioassays were also conducted using purified standard compounds of four chemical compounds identified from essential oils, hexane was used as a positive control as it is reported to be an insect attractant in literature. Hexane was highly attractive to the mirids compared to three standard compounds caryophyllene, caryophyllene oxide and naphthalene at the rate of 80 %, 73 % and 80 %, respectively. The standard compounds tested against F. intermedia are major compounds contained by L. camara varieties and they have proven to have a repellent effect. This may indicate that after feeding by F. intermedia, the major compounds expressed by the plant varieties repel F. intermedia contributing to the invasiveness of this weed. The increased expression of hexane and caryophyllene after feeding may also indicate increased attraction to some insects, opening up the potential for third trophic level interactions in varieties where this is the case. This is the first study on the chemical composition of essential oils of L. camara in South Africa. Therefore, we recommend that where appropriate chemical profile studies of the invasive alien plants should be considered during host specificity testing, and the vital role of chemical compounds on agent-weed interactions must be taken into consideration with other factors before and after the biological control agents are released.
- Full Text:
- Date Issued: 2017
- Authors: Ngxande-Koza, Samella W
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4877 , vital:20739
- Description: Lantana camara L. (Verbenaceae) is one the most problematic invaders in South Africa invading forest edges, sand dunes, and shorelines by forming impenetrable thickets. Lantana camara invasions degrade natural biodiversity, reduce the value of land and consequently it has been a target for biological control, over the last 50 years in South Africa. Studies that have reported on chemical profile of Lantana camara have been conducted around the world but not in South Africa. Hence, the first aim of the current study was to identify the chemical baseline of L. camara varieties in the Eastern Cape, South Africa. Recent studies have shown that feeding by one of the agents released against L. camara, Falconia intermedia (Distant) (Hemiptera: Miridae), induces anti-herbivory response through increased leaf toughness and trichome density. A preliminary study conducted also reported the production of volatile chemicals by one variety, Whitney Farm, due to feeding by the mirids. Therefore, the second aim was to determine the induced changes in chemical compounds of L. camara varieties after feeding by F. intermedia. A third aim was to determine the effect these chemical compounds have on the behaviour of F. intermedia. To identify the chemical baseline of L. camara varieties, the essential oils of four L. camara varieties (East London, Port Alfred, Whitney Farm and Heather Glen) were analysed using gas chromatography mass spectrometry (GC-MS) and that resulted to the identification of 163 constitutive and 75 induced chemicals across the varieties tested. Lantana camara varieties showed different chemical classes but were highly dominated by terpenes. A great variation in the number of constitutive chemical compounds was found in all the varieties. There were 56 constitutive chemical compounds in the Whitney Farm variety, 41 in the East London variety, 36 in the Heather Glen variety and 30 in the Port Alfred variety. The Whitney Farm variety had the highest number (22) of unique constitutive chemicals identified when compared with other varieties. This indicates the chemical distinctiveness of the Whitney Farm variety from the other varieties. In the varieties tested, there were common chemical compounds identified in constitutive and induced (discussed below) states of the plants such as caryophyllene, hexane, naphthalene, copaene and a-caryophyllene. Besides naphthalene, the majority of chemical compounds in South African L. camara varieties were similar to compounds that have been identified across the world, suggesting that they are closely related. The expression of naphthalene in these varieties may be due to changes in the chemicals expressed over evolutionary time as predicted by the Novel Weapons Hypothesis. Amongst the varieties, a great variation in chemical compounds and their concentrations was shown in the induced states of the plants. The concentration of constitutive caryophyllene ranged from (3.13 - 15.7) %, to (4.02 - 11.10) % after feeding. The concentration of constitutive hexane ranged from (6.13 - 71.19) %, to (33.3 - 75.8) % after feeding. The concentration of constitutive naphthalene ranged from (0.21 - 4.79) %, to (0.92 - 2.11) % after feeding. The concentration of constitutive copaene ranged from (0.57 - 1.57) %, to (1.20 - 2.72) %. Lastly, the concentration of constitutive a-caryophyllene ranged from (1.18 - 9.03) %, to (0.78 - 5.48) % after feeding. The changes in chemical concentrations in lantana varieties indicated that feeding by the mirid on L. camara varieties causes an induction by either reducing or increasing the chemical concentrations. To determine the effect of the identified compounds on the behaviour of F. intermedia adults, olfactometer bioassays were conducted using a Y-tube technique. A significantly higher proportion of F. intermedia were attracted to undamaged leaves over damaged leaves and purified air. Undamaged leaves attracted 52 % of F. intermedia from the East London variety, 62.5 % from the Port Alfred variety, 56 % from the Whitney Farm variety, 58 % from the Lyndhurst variety and 54.5 % from the Heather Glen variety in dual choice trials versus damaged leaves. Furthermore, a significantly higher proportion of F. intermedia were attracted to damaged leaves over purified air. Damaged leaves attracted 67 % of F. intermedia from the East London variety, 67 % from the Port Alfred variety, 65.9 % from the Whitney Farm variety, 65.3 % from the Heather Glen variety and 64.5 % from the Lyndhurst variety. Olfactometer bioassays were also conducted using purified standard compounds of four chemical compounds identified from essential oils, hexane was used as a positive control as it is reported to be an insect attractant in literature. Hexane was highly attractive to the mirids compared to three standard compounds caryophyllene, caryophyllene oxide and naphthalene at the rate of 80 %, 73 % and 80 %, respectively. The standard compounds tested against F. intermedia are major compounds contained by L. camara varieties and they have proven to have a repellent effect. This may indicate that after feeding by F. intermedia, the major compounds expressed by the plant varieties repel F. intermedia contributing to the invasiveness of this weed. The increased expression of hexane and caryophyllene after feeding may also indicate increased attraction to some insects, opening up the potential for third trophic level interactions in varieties where this is the case. This is the first study on the chemical composition of essential oils of L. camara in South Africa. Therefore, we recommend that where appropriate chemical profile studies of the invasive alien plants should be considered during host specificity testing, and the vital role of chemical compounds on agent-weed interactions must be taken into consideration with other factors before and after the biological control agents are released.
- Full Text:
- Date Issued: 2017
A Systematic Visualisation Framework for Radio-Imaging Pipelines
- Authors: Andati, Lexy Acherwa Livoyi
- Date: 2021-04
- Subjects: Radio interferometers , Radio astronomy -- Data processing , Radio astronomy -- Data processing -- Software , Jupyter
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177338 , vital:42812
- Description: Pipelines for calibration and imaging of radio interferometric data produce many intermediate images and other data products (gain tables, etc.) These often contain valuable information about the quality of the data and the calibration, and can provide the user with valuable insights, if only visualised in the right way. However, the deluge of data that we’re experiencing with modern instruments means that most of these products are never looked at, and only the final images and data products are examined. Furthermore, the variety of imaging algorithms currently available, and the range of their options, means that very different results can be produced from the same set of original data. Proper understanding of this requires a systematic comparison that can be carried out both by individual users locally, and by the community globally. We address both problems by developing a systematic visualisation framework based around Jupyter notebooks, enriched with interactive plots based on the Bokeh and Datashader visualisation libraries. , Thesis (MSc) -- Faculty of Science, Department of Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Andati, Lexy Acherwa Livoyi
- Date: 2021-04
- Subjects: Radio interferometers , Radio astronomy -- Data processing , Radio astronomy -- Data processing -- Software , Jupyter
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177338 , vital:42812
- Description: Pipelines for calibration and imaging of radio interferometric data produce many intermediate images and other data products (gain tables, etc.) These often contain valuable information about the quality of the data and the calibration, and can provide the user with valuable insights, if only visualised in the right way. However, the deluge of data that we’re experiencing with modern instruments means that most of these products are never looked at, and only the final images and data products are examined. Furthermore, the variety of imaging algorithms currently available, and the range of their options, means that very different results can be produced from the same set of original data. Proper understanding of this requires a systematic comparison that can be carried out both by individual users locally, and by the community globally. We address both problems by developing a systematic visualisation framework based around Jupyter notebooks, enriched with interactive plots based on the Bokeh and Datashader visualisation libraries. , Thesis (MSc) -- Faculty of Science, Department of Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
An analysis of flood activity over the past century based on the sedimentary deposits in the Mfolozi floodplain
- Authors: Mbao, Chabala
- Date: 2017
- Subjects: Floodplain morphology -- South Africa -- Mfolozi River , Floodplains -- South Africa -- Kwazulu-Natal , Sedimentation and deposition -- South Africa -- Kwazulu-Natal , Floods -- South Africa -- Kwazulu-Natal -- Measurement , Hydrology -- Research -- South Africa -- Kwazulu-Natal , Stream measurements -- South Africa -- Kwazulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/53711 , vital:26312
- Description: Floods are natural phenomena that are of widespread interest to the scientific community, particularly in the context of understanding the impact of climate change as well as changing land use patterns and the security of infrastructure such as towns and roads. In northern KwaZulu-Natal, large flood events have been a reoccurring feature over the past century. The geographical position and extent of the region means that is affected by both inland and coastal weather phenomena, each with the potential to cause large flood events. While information pertaining to large floods in the region in the form of flow data is readily available, flow data is often incomplete and limited in terms of how far back in time the records extend. The Mfolozi River floodplain itself also houses a record of flood activity in the region in the form of sedimentary deposits, which have the potential to reveal flood activity over a much longer timescale, even when monitoring of flood activity in the region was not present. Establishing a link between the hydrological and sedimentary features of floods may be useful in establishing a record of flood activity extending beyond the limits of historical records. The aim of this project was to construct a record of major flood events on the Mfolozi River floodplain over the last century and determine their source. The first objective involved establishing the history of flood events in the Mfolozi River catchment utilising hydrological data recorded throughout the catchment. Thirty nine different large floods (defined as being over 800 m3.s-1) were recorded on the floodplain over the past century. The data also highlighted differences in the extent of known coastal and inland systems (tropical cyclones and cut-off lows respectively), allowing for inferences to be made about the area of the catchment most likely affected by each event; some flood events were identified as having mostly affected the upper reaches of the catchment, while others mostly affected the lower reaches, closer to the coast. The second objective was to identify the various physical, mineralogical and geochemical features of the sediment deposited on the Mfolozi floodplain. Multiple individual flood deposits were identified in the sedimentary record, with sediment tracing analysis providing insight into the source of the deposits within the catchment; no traces of igneous or metamorphic material could be found within the sediment. The source rocks were identified as mostly quartzite, with minor shale and sandstone deposits as well. This put the source of the sediment in the upper to middle reaches of the catchment. The sedimentary analysis was combined with the hydrological records to establish a chronology of flood events extending back to the 1960's. Unfortunately, this record could not be extended further due to the limited amount of sediment collected as well the limits of readily available analytical techniques; radionuclide dating methods were unsuccessful due to the low amounts of fallout radionuclides present in the sediment. The study has however successfully established a history of flood events in the region, as well as providing a link between the hydrological and sedimentary features of flood events that could potentially be useful for current and future research.
- Full Text:
- Date Issued: 2017
- Authors: Mbao, Chabala
- Date: 2017
- Subjects: Floodplain morphology -- South Africa -- Mfolozi River , Floodplains -- South Africa -- Kwazulu-Natal , Sedimentation and deposition -- South Africa -- Kwazulu-Natal , Floods -- South Africa -- Kwazulu-Natal -- Measurement , Hydrology -- Research -- South Africa -- Kwazulu-Natal , Stream measurements -- South Africa -- Kwazulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/53711 , vital:26312
- Description: Floods are natural phenomena that are of widespread interest to the scientific community, particularly in the context of understanding the impact of climate change as well as changing land use patterns and the security of infrastructure such as towns and roads. In northern KwaZulu-Natal, large flood events have been a reoccurring feature over the past century. The geographical position and extent of the region means that is affected by both inland and coastal weather phenomena, each with the potential to cause large flood events. While information pertaining to large floods in the region in the form of flow data is readily available, flow data is often incomplete and limited in terms of how far back in time the records extend. The Mfolozi River floodplain itself also houses a record of flood activity in the region in the form of sedimentary deposits, which have the potential to reveal flood activity over a much longer timescale, even when monitoring of flood activity in the region was not present. Establishing a link between the hydrological and sedimentary features of floods may be useful in establishing a record of flood activity extending beyond the limits of historical records. The aim of this project was to construct a record of major flood events on the Mfolozi River floodplain over the last century and determine their source. The first objective involved establishing the history of flood events in the Mfolozi River catchment utilising hydrological data recorded throughout the catchment. Thirty nine different large floods (defined as being over 800 m3.s-1) were recorded on the floodplain over the past century. The data also highlighted differences in the extent of known coastal and inland systems (tropical cyclones and cut-off lows respectively), allowing for inferences to be made about the area of the catchment most likely affected by each event; some flood events were identified as having mostly affected the upper reaches of the catchment, while others mostly affected the lower reaches, closer to the coast. The second objective was to identify the various physical, mineralogical and geochemical features of the sediment deposited on the Mfolozi floodplain. Multiple individual flood deposits were identified in the sedimentary record, with sediment tracing analysis providing insight into the source of the deposits within the catchment; no traces of igneous or metamorphic material could be found within the sediment. The source rocks were identified as mostly quartzite, with minor shale and sandstone deposits as well. This put the source of the sediment in the upper to middle reaches of the catchment. The sedimentary analysis was combined with the hydrological records to establish a chronology of flood events extending back to the 1960's. Unfortunately, this record could not be extended further due to the limited amount of sediment collected as well the limits of readily available analytical techniques; radionuclide dating methods were unsuccessful due to the low amounts of fallout radionuclides present in the sediment. The study has however successfully established a history of flood events in the region, as well as providing a link between the hydrological and sedimentary features of flood events that could potentially be useful for current and future research.
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- Date Issued: 2017