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
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
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
Categorising Network Telescope data using big data enrichment techniques
- Authors: Davis, Michael Reginald
- Date: 2019
- Subjects: Denial of service attacks , Big data , Computer networks -- Security measures
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92941 , vital:30766
- Description: Network Telescopes, Internet backbone sampling, IDS and other forms of network-sourced Threat Intelligence provide researchers with insight into the methods and intent of remote entities by capturing network traffic and analysing the resulting data. This analysis and determination of intent is made difficult by the large amounts of potentially malicious traffic, coupled with limited amount of knowledge that can be attributed to the source of the incoming data, as the source is known only by its IP address. Due to the lack of commonly available tooling, many researchers start this analysis from the beginning and so repeat and re-iterate previous research as the bulk of their work. As a result new insight into methods and approaches of analysis is gained at a high cost. Our research approaches this problem by using additional knowledge about the source IP address such as open ports, reverse and forward DNS, BGP routing tables and more, to enhance the researcher's ability to understand the traffic source. The research is a BigData experiment, where large (hundreds of GB) datasets are merged with a two month section of Network Telescope data using a set of Python scripts. The result are written to a Google BigQuery database table. Analysis of the network data is greatly simplified, with questions about the nature of the source, such as its device class (home routing device or server), potential vulnerabilities (open telnet ports or databases) and location becoming relatively easy to answer. Using this approach, researchers can focus on the questions that need answering and efficiently address them. This research could be taken further by using additional data sources such as Geo-location, WHOIS lookups, Threat Intelligence feeds and many others. Other potential areas of research include real-time categorisation of incoming packets, in order to better inform alerting and reporting systems' configuration. In conclusion, categorising Network Telescope data in this way provides insight into the intent of the (apparent) originator and as such is a valuable tool for those seeking to understand the purpose and intent of arriving packets. In particular, the ability to remove packets categorised as non-malicious (e.g. those in the Research category) from the data eliminates a known source of `noise' from the data. This allows the researcher to focus their efforts in a more productive manner.
- Full Text:
- Date Issued: 2019
- Authors: Davis, Michael Reginald
- Date: 2019
- Subjects: Denial of service attacks , Big data , Computer networks -- Security measures
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92941 , vital:30766
- Description: Network Telescopes, Internet backbone sampling, IDS and other forms of network-sourced Threat Intelligence provide researchers with insight into the methods and intent of remote entities by capturing network traffic and analysing the resulting data. This analysis and determination of intent is made difficult by the large amounts of potentially malicious traffic, coupled with limited amount of knowledge that can be attributed to the source of the incoming data, as the source is known only by its IP address. Due to the lack of commonly available tooling, many researchers start this analysis from the beginning and so repeat and re-iterate previous research as the bulk of their work. As a result new insight into methods and approaches of analysis is gained at a high cost. Our research approaches this problem by using additional knowledge about the source IP address such as open ports, reverse and forward DNS, BGP routing tables and more, to enhance the researcher's ability to understand the traffic source. The research is a BigData experiment, where large (hundreds of GB) datasets are merged with a two month section of Network Telescope data using a set of Python scripts. The result are written to a Google BigQuery database table. Analysis of the network data is greatly simplified, with questions about the nature of the source, such as its device class (home routing device or server), potential vulnerabilities (open telnet ports or databases) and location becoming relatively easy to answer. Using this approach, researchers can focus on the questions that need answering and efficiently address them. This research could be taken further by using additional data sources such as Geo-location, WHOIS lookups, Threat Intelligence feeds and many others. Other potential areas of research include real-time categorisation of incoming packets, in order to better inform alerting and reporting systems' configuration. In conclusion, categorising Network Telescope data in this way provides insight into the intent of the (apparent) originator and as such is a valuable tool for those seeking to understand the purpose and intent of arriving packets. In particular, the ability to remove packets categorised as non-malicious (e.g. those in the Research category) from the data eliminates a known source of `noise' from the data. This allows the researcher to focus their efforts in a more productive manner.
- Full Text:
- Date Issued: 2019
Targeting allosteric sites of Escherichia coli heat shock protein 70 for antibiotic development
- Authors: Okeke, Chiamaka Jessica
- Date: 2019
- Subjects: Heat shock proteins , Escherichia coli , Allosteric proteins , Antibiotics , Molecular chaperones , Ligands (Biochemistry) , Molecular dynamics , Principal components analysis , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/115998 , vital:34287
- Description: Hsp70s are members of the heat shock proteins family with a molecular weight of 70-kDa and are the most abundant group in bacterial and eukaryotic systems, hence the most extensively studied ones. These proteins are molecular chaperones that play a significant role in protein homeostasis by facilitating appropriate folding of proteins, preventing proteins from aggregating and misfolding. They are also involved in translocation of proteins into subcellular compartments and protection of cells against stress. Stress caused by environmental or biological factors affects the functionality of the cell. In response to these stressful conditions, up-regulation of Hsp70s ensures that the cells are protected by balancing out unfolded proteins giving them ample time to repair denatured proteins. Hsp70s is connected to numerous illnesses such as autoimmune and neurodegenerative diseases, bacterial infection, cancer, malaria, and obesity. The multi-functional nature of Hsp70s predisposes them as promising therapeutic targets. Hsp70s play vital roles in various cell developments, and survival pathways, therefore targeting this protein will provide a new avenue towards the discovery of active therapeutic agents for the treatment of a wide range of diseases. Allosteric sites of these proteins in its multi-conformational states have not been explored for inhibitory properties hence the aim of this study. This study aims at identifying allosteric sites that inhibit the ATPase and substrate binding activities using computational approaches. Using E. coli as a model organism, molecular docking for high throughput virtual screening was carried out using 623 compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/) against identified allosteric sites. Ligands with the highest binding affinity (good binders) interacting with critical allosteric residues that are druggable were identified. Molecular dynamics (MD) simulation was also performed on the identified hits to assess for protein-inhibitor complex stability. Finally, principal component analysis (PCA) was performed to understand the structural dynamics of the ligand-free and ligand-bound structures during MD simulation.
- Full Text:
- Date Issued: 2019
- Authors: Okeke, Chiamaka Jessica
- Date: 2019
- Subjects: Heat shock proteins , Escherichia coli , Allosteric proteins , Antibiotics , Molecular chaperones , Ligands (Biochemistry) , Molecular dynamics , Principal components analysis , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/115998 , vital:34287
- Description: Hsp70s are members of the heat shock proteins family with a molecular weight of 70-kDa and are the most abundant group in bacterial and eukaryotic systems, hence the most extensively studied ones. These proteins are molecular chaperones that play a significant role in protein homeostasis by facilitating appropriate folding of proteins, preventing proteins from aggregating and misfolding. They are also involved in translocation of proteins into subcellular compartments and protection of cells against stress. Stress caused by environmental or biological factors affects the functionality of the cell. In response to these stressful conditions, up-regulation of Hsp70s ensures that the cells are protected by balancing out unfolded proteins giving them ample time to repair denatured proteins. Hsp70s is connected to numerous illnesses such as autoimmune and neurodegenerative diseases, bacterial infection, cancer, malaria, and obesity. The multi-functional nature of Hsp70s predisposes them as promising therapeutic targets. Hsp70s play vital roles in various cell developments, and survival pathways, therefore targeting this protein will provide a new avenue towards the discovery of active therapeutic agents for the treatment of a wide range of diseases. Allosteric sites of these proteins in its multi-conformational states have not been explored for inhibitory properties hence the aim of this study. This study aims at identifying allosteric sites that inhibit the ATPase and substrate binding activities using computational approaches. Using E. coli as a model organism, molecular docking for high throughput virtual screening was carried out using 623 compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/) against identified allosteric sites. Ligands with the highest binding affinity (good binders) interacting with critical allosteric residues that are druggable were identified. Molecular dynamics (MD) simulation was also performed on the identified hits to assess for protein-inhibitor complex stability. Finally, principal component analysis (PCA) was performed to understand the structural dynamics of the ligand-free and ligand-bound structures during MD simulation.
- Full Text:
- Date Issued: 2019
Recruitment of bivalve molluscs with specific emphasis on Mytilus galloprovincialis in the Knysna estuarine embayment, South Africa
- Authors: Radloff, James Victor
- Date: 2019
- Subjects: Mytilus galloprovincialis -- South Africa -- Knysna Lagoon , Introduced aquatic organisms -- South Africa -- Knysna Lagoon , Mexilhao mussel -- South Africa -- Knysna Lagoon , Oysters -- South Africa -- Knysna Lagoon , Mytilidae -- South Africa -- Knysna Lagoon , Bivalves -- South Africa -- Knysna Lagoon
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76733 , vital:30613
- Description: Alien invasive species have the ability to transform or alter environments, often causing severe ecological and/or economic impacts. Marine bioinvasions are occurring globally and are most often facilitated (intentially and accidently) through anthropogenic activities including the building of inter-oceanic canals, shipping and commerce. The Mediterranean mussel, Mytilus galloprovincialis, is a globally successful marine alien invasive species which was first recorded on the west coast of South Africa in the late 1970s and the south coast in 1988. This species is thought to have reached the Knysna Estuary in the early 2000s and has colonised all man-made hard substrata in the embayment of the estuary. Although there are studies on recruitment of M. galloprovincialis on the rocky intertidal coasts of South Africa, there is little information on recruitment of this species in more sheltered estuarine environments. This study aimed to determine recruitment levels of M. galloprovincialis and other bivalves within the Knysna estuarine embayment. To determine monthly recruitment, 10 recruit collectors/pads (plastic pot scourers) were placed at three separate locations within the embayment of the estuary for a week on a monthly basis for 20 months. In addition, recruitment of M. galloprovincialis over spring and neap tides and different lunar phases was also determined at two sites within the Knysna estuarine embayment during the main reproductive season in 2018. The pads were deployed three days before a neap/spring tide and then collected three days after the respective tide. Finally, to look at how rapidly M. galloprovincialis and other macroinvertebrates (when M. galloprovincialis was excluded) would re-colonise free space, 18 plots (15x15 cm), consisting of three treatments including a control (A,B and C), were cleared in M. galloprovincialis mussel beds and then photographed monthly for 12 months. Four bivalve taxa (Mytilus galloprovincialis, Perna perna, Ostreidae, unidentified mytilid) were recorded during the monthly study. Recruitment levels for all bivalves differed significantly (P < 0.001) between months and sites, with peak recruitment occurring from late spring to early autumn (November – March). Mytilus galloprovincialis recruitment levels were greater than other bivalves and were up to 4.5x greater than other taxa. Recruitment also varied between years possibly owing to differences in larval supply and/or environmental factors. Spatial variation in bivalve recruitment was observed throughout the study. The greatest recruitment was at the site (Thesen Island Wharf) closer to the entrance of the embayment. By contrast at the site (Railway Bridge) furthest from the entrance lower recruitment was found. This difference is possibly due to differences in hydrodynamics or other biological and/or environmental factors. A preliminary tidal study found that M. galloprovincialis had significantly higher (P < 0.001) recruitment levels over spring tides than neap tides at Thesen Island Wharf, whereas recruitment at the Railway Bridge on spring and neap tides was not significantly different. In the study undertaken in the reproductive season only, recruitment levels were high over a two week period during both a spring and neap tide, suggesting that factors other than lunar phase and the state of tide are more important in determining the timing and intensity of recruitment. The clearance plots created and photographed over a 12 month period showed that M. galloprovincialis rapidly occupied free space (eight months to virtually cover all free space) by encroachment from the adjacent mussel bed. Limpets and barnacles were only able to colonise cleared space when M. galloprovincialis was excluded, suggesting that the mussel has the ability to outcompete indigenous macrofauna for space. The high recruitment levels of M. galloprovincialis compared to other indigenous bivalves, as well as its ability to occupy space rapidly are traits that must contribute to the success of the invasion of this species within the Knysna estuarine embayment, particulary within Thesen Islands Marina and Thesen Island Wharf.
- Full Text:
- Date Issued: 2019
- Authors: Radloff, James Victor
- Date: 2019
- Subjects: Mytilus galloprovincialis -- South Africa -- Knysna Lagoon , Introduced aquatic organisms -- South Africa -- Knysna Lagoon , Mexilhao mussel -- South Africa -- Knysna Lagoon , Oysters -- South Africa -- Knysna Lagoon , Mytilidae -- South Africa -- Knysna Lagoon , Bivalves -- South Africa -- Knysna Lagoon
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76733 , vital:30613
- Description: Alien invasive species have the ability to transform or alter environments, often causing severe ecological and/or economic impacts. Marine bioinvasions are occurring globally and are most often facilitated (intentially and accidently) through anthropogenic activities including the building of inter-oceanic canals, shipping and commerce. The Mediterranean mussel, Mytilus galloprovincialis, is a globally successful marine alien invasive species which was first recorded on the west coast of South Africa in the late 1970s and the south coast in 1988. This species is thought to have reached the Knysna Estuary in the early 2000s and has colonised all man-made hard substrata in the embayment of the estuary. Although there are studies on recruitment of M. galloprovincialis on the rocky intertidal coasts of South Africa, there is little information on recruitment of this species in more sheltered estuarine environments. This study aimed to determine recruitment levels of M. galloprovincialis and other bivalves within the Knysna estuarine embayment. To determine monthly recruitment, 10 recruit collectors/pads (plastic pot scourers) were placed at three separate locations within the embayment of the estuary for a week on a monthly basis for 20 months. In addition, recruitment of M. galloprovincialis over spring and neap tides and different lunar phases was also determined at two sites within the Knysna estuarine embayment during the main reproductive season in 2018. The pads were deployed three days before a neap/spring tide and then collected three days after the respective tide. Finally, to look at how rapidly M. galloprovincialis and other macroinvertebrates (when M. galloprovincialis was excluded) would re-colonise free space, 18 plots (15x15 cm), consisting of three treatments including a control (A,B and C), were cleared in M. galloprovincialis mussel beds and then photographed monthly for 12 months. Four bivalve taxa (Mytilus galloprovincialis, Perna perna, Ostreidae, unidentified mytilid) were recorded during the monthly study. Recruitment levels for all bivalves differed significantly (P < 0.001) between months and sites, with peak recruitment occurring from late spring to early autumn (November – March). Mytilus galloprovincialis recruitment levels were greater than other bivalves and were up to 4.5x greater than other taxa. Recruitment also varied between years possibly owing to differences in larval supply and/or environmental factors. Spatial variation in bivalve recruitment was observed throughout the study. The greatest recruitment was at the site (Thesen Island Wharf) closer to the entrance of the embayment. By contrast at the site (Railway Bridge) furthest from the entrance lower recruitment was found. This difference is possibly due to differences in hydrodynamics or other biological and/or environmental factors. A preliminary tidal study found that M. galloprovincialis had significantly higher (P < 0.001) recruitment levels over spring tides than neap tides at Thesen Island Wharf, whereas recruitment at the Railway Bridge on spring and neap tides was not significantly different. In the study undertaken in the reproductive season only, recruitment levels were high over a two week period during both a spring and neap tide, suggesting that factors other than lunar phase and the state of tide are more important in determining the timing and intensity of recruitment. The clearance plots created and photographed over a 12 month period showed that M. galloprovincialis rapidly occupied free space (eight months to virtually cover all free space) by encroachment from the adjacent mussel bed. Limpets and barnacles were only able to colonise cleared space when M. galloprovincialis was excluded, suggesting that the mussel has the ability to outcompete indigenous macrofauna for space. The high recruitment levels of M. galloprovincialis compared to other indigenous bivalves, as well as its ability to occupy space rapidly are traits that must contribute to the success of the invasion of this species within the Knysna estuarine embayment, particulary within Thesen Islands Marina and Thesen Island Wharf.
- Full Text:
- Date Issued: 2019
BODIPY and porphyrin dyes for direct glucose sensing and optical limiting applications
- Authors: Ndebele, Nobuhle
- Date: 2019
- Subjects: Boron compounds , Boric acid , Porphyrins , Dyes and dying -- Chemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97221 , vital:31412
- Description: A series of BODIPY dyes functionalised with boronic acid in the 3,5-positions were successfully synthesised and characterised by using various analytical techniques. The dyes were prepared through a slight modification of the conventional acid catalysed condensation method. Phenylboronic acid moieties were added as styryl groups at the 3,5-positions of the 1,3,5,7-tetrametylBODIPY cores using a modified Knoevengal condensation method. The addition of the styryls resulted in the main absorption band of the dyes red-shifting to the 630−650 nm region. The photophysical and electrochemical properties of these dyes were studied to determine whether the dyes are suitable for use in the fluorescent, colourimetric and electrochemical detection of glucose. Boronic acid moieties were added as bioreceptor recognition elements because they have an affinity for carbohydrates and therefore would be able to bind and “detect” glucose. The series of BODIPY dyes did not show a “turn-on” fluorescence effect upon addition with glucose at the physiological pH. This was attributed on the basis of molecular modelling to the absence of an MO localised on the boronic-acid-substituted styryl moieties that lie close in energy to the HOMO and LUMO that facilitates the formation of an intramolecular charge transfer state. However, colourimetric changes that are visible to the naked eye are observed at basic pH when glucose was added to the dye solutions. The dyes exhibited favourable electrochemical behaviour and were able to detect glucose directly in this context when glassy carbon electrodes are modified through the drop dry method. A series of Sn(IV) porphyrins with thienyl and phenyl groups at the meso-positions were successfully synthesised and characterised. Pyridine and tetrabutyl axial ligands were added to the porphyrins to limit aggregation. The optical limiting properties of these porphyrins and three styrylated BODIPY dyes were studied in benzene and dichloromethane. Dyes were also embedded in polystyrene and studied as thin films to further gauge their suitability for use in optical limiting applications. Second-order hyperpolarizability, third-order susceptibly, non-linear absorption with reversible saturable absorption and the optical limiting threshold, were the parameters studied. Three of the four porphyrins and the three styrylated BODIPY dyes showed favourable optical limiting behaviour, which was further enhanced when the dyes are embedded in polymer thin films.
- Full Text:
- Date Issued: 2019
- Authors: Ndebele, Nobuhle
- Date: 2019
- Subjects: Boron compounds , Boric acid , Porphyrins , Dyes and dying -- Chemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97221 , vital:31412
- Description: A series of BODIPY dyes functionalised with boronic acid in the 3,5-positions were successfully synthesised and characterised by using various analytical techniques. The dyes were prepared through a slight modification of the conventional acid catalysed condensation method. Phenylboronic acid moieties were added as styryl groups at the 3,5-positions of the 1,3,5,7-tetrametylBODIPY cores using a modified Knoevengal condensation method. The addition of the styryls resulted in the main absorption band of the dyes red-shifting to the 630−650 nm region. The photophysical and electrochemical properties of these dyes were studied to determine whether the dyes are suitable for use in the fluorescent, colourimetric and electrochemical detection of glucose. Boronic acid moieties were added as bioreceptor recognition elements because they have an affinity for carbohydrates and therefore would be able to bind and “detect” glucose. The series of BODIPY dyes did not show a “turn-on” fluorescence effect upon addition with glucose at the physiological pH. This was attributed on the basis of molecular modelling to the absence of an MO localised on the boronic-acid-substituted styryl moieties that lie close in energy to the HOMO and LUMO that facilitates the formation of an intramolecular charge transfer state. However, colourimetric changes that are visible to the naked eye are observed at basic pH when glucose was added to the dye solutions. The dyes exhibited favourable electrochemical behaviour and were able to detect glucose directly in this context when glassy carbon electrodes are modified through the drop dry method. A series of Sn(IV) porphyrins with thienyl and phenyl groups at the meso-positions were successfully synthesised and characterised. Pyridine and tetrabutyl axial ligands were added to the porphyrins to limit aggregation. The optical limiting properties of these porphyrins and three styrylated BODIPY dyes were studied in benzene and dichloromethane. Dyes were also embedded in polystyrene and studied as thin films to further gauge their suitability for use in optical limiting applications. Second-order hyperpolarizability, third-order susceptibly, non-linear absorption with reversible saturable absorption and the optical limiting threshold, were the parameters studied. Three of the four porphyrins and the three styrylated BODIPY dyes showed favourable optical limiting behaviour, which was further enhanced when the dyes are embedded in polymer thin films.
- Full Text:
- Date Issued: 2019
Truth and reconciliation and other stories: a critical multimodal investigation of representations of post-apartheid South Africa in children's picturebooks: volume 1
- Authors: Smith, Jade
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97614 , vital:31458
- Description: Expected release date-April 2021
- Full Text: false
- Date Issued: 2019
- Authors: Smith, Jade
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97614 , vital:31458
- Description: Expected release date-April 2021
- Full Text: false
- Date Issued: 2019
Biochemical characterization of the β-mannanase activity of Bacillus paralicheniformis SVD1
- Authors: Clarke, Matthew David
- Date: 2019
- Subjects: Mycobacterium avium paratuberculosis , Enzymes -- Biotechnology , Lignocellulose -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67570 , vital:29112
- Description: Products produced via the enzymatic hydrolysis of lignocellulosic biomass, the most abundant renewable terrestrial source of carbon, can potentially replace a lot of the fuels and chemicals currently produced using non-renewable hydrocarbons. Mannan is a polysaccharide component of lignocellulose that is abundant in softwoods and legume seeds. Enzymatic hydrolysis of mannan by β-mannanases has various industrial applications, including use in biofuel and prebiotic mannooligosaccharide (MOS) production for the improvement of human and animal health. The industrial use of β-mannanases depends on their biochemical characteristics, such as their activity, stability and substrate specificity. Knowledge of their synergistic interactions with other enzymes is also useful for effective hydrolysis. Bacillus paralicheniformis SVD1 was used as a source for β-mannanases. The two mannanases of B. paralicheniformis SVD1 have not been biochemically characterized apart from minor characterization of crude β-mannanase activity. The protein sequences of the two β-mannanases, of glycosyl hydrolase family 5 and 26, have a 95% - 96% identity to the β-mannanases of B. licheniformis DSM13T (=ATCC14580T). These small protein sequence differences could lead to quite different biochemical characteristics. These mannanases were characterized as these enzymes may have industrially useful characteristics. To induce mannanase production, B. paralicheniformis SVD1 was cultured in broth containing the mannan substrate locust bean gum. Various growth curve parameters were measured over 72 h. Mannanase activity was the highest after 48 h of growth - this was the time at which mannanase activity was concentrated, using 3 kDa centrifugal filtration devices, for biochemical characterization of the crude activity. Zymography revealed that the crude concentrated mannanase fraction consisted of at least two mannanases with relative molecular weights (MWs) of 29.6 kDa and 33 kDa. This was smaller than expected – based on their theoretical molecular masses. Protease activity, which was detected in the broth, was probably the reason. There were two pH optima, pH 5.0 and pH 7.0, which also indicated the presence of two mannanases. The concentrated mannanase displayed characteristics that were expected of a B. paralicheniformis β-mannanase. The temperature optimum was 50°C and the activity loss was less than 7% at 50°C after 24 h. Substrate specificity assays revealed that there was predominantly mannanase activity present. Thin layer chromatography (TLC) analysis of mannan and MOS hydrolysis showed that mainly M2 and M3 MOS were produced; only MOS with a degree of polymerization of 4 or higher were hydrolyzed. Hydrolysis was minimal on mannoligosaccharides with galactose substituents. Activity and MOS production was the highest on soluble, low branched mannan substrates. The highest activity observed was on konjac glucomannan. Purification of the mannanase activity was then attempted using various methods. Ammonium sulfate precipitation, acetone precipitation, as well as centrifugal filtration device concentration was assessed for concentration of the mannanase activity.Concentration was not very successful due to low activity yields (≤ 20%). Anion exchange chromatography (AEC) and size exclusion chromatography (SEC) was used for purification. AEC gave good activity yield and fold purification, but SDS-PAGE analysis revealed the presence of many different proteins so further purification was necessary. SDS-PAGE analysis showed that there were only a few protein contaminants in the SEC fraction. However, the yield was too low to allow for biochemical characterization. The optimized purification procedure, which partially purified the mannanase activity, used 85% ammonium sulfate precipitation, followed by AEC. The fold purification was high (88.9) and the specific activity was 29.5 U.mg-1. A zymogram of the partially purified mannanase showed a mannanase active band with a MW of 40 - 41 kDa. A serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), was added during the purification steps. This indicated that the mannanase/s in the crude concentrate, without PMSF added, was hydrolyzed by serine protease activity. Native PAGE zymograms suggested that at least two different isoforms of mannanases were present. Additional purification would be required to determine the true characteristics of the mannanase/s. The biochemical characteristics of the crude and partially purified mannanases were similar. The pH optima of the partially purified mannanases were different; the pH optima were 6.0 and 9.0. The substrate specificities were similar, except that the partially purified mannanases displayed no cellulase and β-D-galactosidase activity, but showed a small amount of α-L-arabinase activity. The partially purified mannanase and a Cyamopsis tetragonolobus GH27 α-galactosidase synergistically hydrolyzed locust bean gum. The M50G50 combination displayed the highest extent of hydrolysis; after 24 h there was a 1.39 fold increase in reducing sugar release and the degree of synergy (DS) was 4.64. TLC analysis indicated that synergy increased the release of small MOS. These MOS could be useful as prebiotics. The synergy between the partially purified mannanase and the commercial cellulase mixture Cellic® CTec2 (Novozymes) on spent coffee grounds (SCG) was also determined. SCG is an abundant industrial waste product that has high mannan content. The SCG was pretreated using NaOH, and the monosaccharide, soluble phenolics and insoluble contents were determined. Glucose and mannose were the dominant monosaccharides in the SCG; the pretreated SCG contained 20.4% (w/w) glucose and 18.5% (w/w) mannose, respectively. The NaOH pretreatment improved mannanase hydrolysis of SCG. It resulted in the opening up and swelling of the SCG particles and removed some of the insoluble solids. The partially purified B. paralicheniformis SVD1 mannanase displayed no detectable activity on SCG, but showed synergy with CTec2, in terms of DS, on untreated and NaOH pretreated SCG. This is the first report of mannanasecellulase synergy on SCG; other studies found that increased hydrolysis was due to additive effects. The results obtained in this study are only an initial assessment of the biochemical properties of B. paralicheniformis SVD1 mannanase activity and its synergy with other enzymes. These results can be used to inform future studies.
- Full Text:
- Date Issued: 2019
- Authors: Clarke, Matthew David
- Date: 2019
- Subjects: Mycobacterium avium paratuberculosis , Enzymes -- Biotechnology , Lignocellulose -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67570 , vital:29112
- Description: Products produced via the enzymatic hydrolysis of lignocellulosic biomass, the most abundant renewable terrestrial source of carbon, can potentially replace a lot of the fuels and chemicals currently produced using non-renewable hydrocarbons. Mannan is a polysaccharide component of lignocellulose that is abundant in softwoods and legume seeds. Enzymatic hydrolysis of mannan by β-mannanases has various industrial applications, including use in biofuel and prebiotic mannooligosaccharide (MOS) production for the improvement of human and animal health. The industrial use of β-mannanases depends on their biochemical characteristics, such as their activity, stability and substrate specificity. Knowledge of their synergistic interactions with other enzymes is also useful for effective hydrolysis. Bacillus paralicheniformis SVD1 was used as a source for β-mannanases. The two mannanases of B. paralicheniformis SVD1 have not been biochemically characterized apart from minor characterization of crude β-mannanase activity. The protein sequences of the two β-mannanases, of glycosyl hydrolase family 5 and 26, have a 95% - 96% identity to the β-mannanases of B. licheniformis DSM13T (=ATCC14580T). These small protein sequence differences could lead to quite different biochemical characteristics. These mannanases were characterized as these enzymes may have industrially useful characteristics. To induce mannanase production, B. paralicheniformis SVD1 was cultured in broth containing the mannan substrate locust bean gum. Various growth curve parameters were measured over 72 h. Mannanase activity was the highest after 48 h of growth - this was the time at which mannanase activity was concentrated, using 3 kDa centrifugal filtration devices, for biochemical characterization of the crude activity. Zymography revealed that the crude concentrated mannanase fraction consisted of at least two mannanases with relative molecular weights (MWs) of 29.6 kDa and 33 kDa. This was smaller than expected – based on their theoretical molecular masses. Protease activity, which was detected in the broth, was probably the reason. There were two pH optima, pH 5.0 and pH 7.0, which also indicated the presence of two mannanases. The concentrated mannanase displayed characteristics that were expected of a B. paralicheniformis β-mannanase. The temperature optimum was 50°C and the activity loss was less than 7% at 50°C after 24 h. Substrate specificity assays revealed that there was predominantly mannanase activity present. Thin layer chromatography (TLC) analysis of mannan and MOS hydrolysis showed that mainly M2 and M3 MOS were produced; only MOS with a degree of polymerization of 4 or higher were hydrolyzed. Hydrolysis was minimal on mannoligosaccharides with galactose substituents. Activity and MOS production was the highest on soluble, low branched mannan substrates. The highest activity observed was on konjac glucomannan. Purification of the mannanase activity was then attempted using various methods. Ammonium sulfate precipitation, acetone precipitation, as well as centrifugal filtration device concentration was assessed for concentration of the mannanase activity.Concentration was not very successful due to low activity yields (≤ 20%). Anion exchange chromatography (AEC) and size exclusion chromatography (SEC) was used for purification. AEC gave good activity yield and fold purification, but SDS-PAGE analysis revealed the presence of many different proteins so further purification was necessary. SDS-PAGE analysis showed that there were only a few protein contaminants in the SEC fraction. However, the yield was too low to allow for biochemical characterization. The optimized purification procedure, which partially purified the mannanase activity, used 85% ammonium sulfate precipitation, followed by AEC. The fold purification was high (88.9) and the specific activity was 29.5 U.mg-1. A zymogram of the partially purified mannanase showed a mannanase active band with a MW of 40 - 41 kDa. A serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), was added during the purification steps. This indicated that the mannanase/s in the crude concentrate, without PMSF added, was hydrolyzed by serine protease activity. Native PAGE zymograms suggested that at least two different isoforms of mannanases were present. Additional purification would be required to determine the true characteristics of the mannanase/s. The biochemical characteristics of the crude and partially purified mannanases were similar. The pH optima of the partially purified mannanases were different; the pH optima were 6.0 and 9.0. The substrate specificities were similar, except that the partially purified mannanases displayed no cellulase and β-D-galactosidase activity, but showed a small amount of α-L-arabinase activity. The partially purified mannanase and a Cyamopsis tetragonolobus GH27 α-galactosidase synergistically hydrolyzed locust bean gum. The M50G50 combination displayed the highest extent of hydrolysis; after 24 h there was a 1.39 fold increase in reducing sugar release and the degree of synergy (DS) was 4.64. TLC analysis indicated that synergy increased the release of small MOS. These MOS could be useful as prebiotics. The synergy between the partially purified mannanase and the commercial cellulase mixture Cellic® CTec2 (Novozymes) on spent coffee grounds (SCG) was also determined. SCG is an abundant industrial waste product that has high mannan content. The SCG was pretreated using NaOH, and the monosaccharide, soluble phenolics and insoluble contents were determined. Glucose and mannose were the dominant monosaccharides in the SCG; the pretreated SCG contained 20.4% (w/w) glucose and 18.5% (w/w) mannose, respectively. The NaOH pretreatment improved mannanase hydrolysis of SCG. It resulted in the opening up and swelling of the SCG particles and removed some of the insoluble solids. The partially purified B. paralicheniformis SVD1 mannanase displayed no detectable activity on SCG, but showed synergy with CTec2, in terms of DS, on untreated and NaOH pretreated SCG. This is the first report of mannanasecellulase synergy on SCG; other studies found that increased hydrolysis was due to additive effects. The results obtained in this study are only an initial assessment of the biochemical properties of B. paralicheniformis SVD1 mannanase activity and its synergy with other enzymes. These results can be used to inform future studies.
- Full Text:
- Date Issued: 2019
Secret sex lives in the intertidal: insights into the mating systems of clinid fishes from molecular parentage analyses
- Authors: Scheeper, Martinus Johannes
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72438 , vital:30048
- Description: Expected release date-April 2020
- Full Text: false
- Date Issued: 2019
- Authors: Scheeper, Martinus Johannes
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72438 , vital:30048
- Description: Expected release date-April 2020
- Full Text: false
- Date Issued: 2019
An assessment of amount, distribution and use of urban green spaces in small towns of the Eastern Cape
- Authors: Radebe, Denis Siphosihle
- Date: 2019
- Subjects: Urban ecology (Sociology) -- South Africa -- Eastern Cape , Small cities -- South Africa -- Eastern Cape , City planning -- South Africa -- Eastern Cape , Recreation areas -- South Africa -- Eastern Cape , Open spaces -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76447 , vital:30563
- Description: Most regions of the developing world are experiencing large-scale urbanisation, with urban population growth outstripping rural growth. This is most marked in small and medium-sized towns as opposed to megacities. Urbanisation is associated with numerous changes in social, economic and ecological states and dynamics. A key one, of interest in this study, is the sustainability and liveability of the growing towns and cities. The retention, provision and maintenance of multifunctional urban green infrastructure are a core strategy in this regard. This study therefore sought to assess the amount, distribution and use of urban green spaces within South Africa using small towns of the Eastern Cape. The primary research included sixteen aerial images of which eight were historical aerial photographs and another eight were the latest aerial images of the selected study towns. Historical and latest aerial images were digitised to classify the types and calculate the amount of urban green space. GIS mapping, interviews and focus group discussions were conducted with urban residents to understand how these green spaces are used. The analytical tools in this study derived from social science included household surveys of 180 randomly selected respondents in small towns. Fifteen types of green spaces were identified in the sample towns. The study further revealed that green spaces are not distributed equally in different suburbs of small towns, generally being less green spaces, especially formal parks and recreation areas, in poorer areas. The results indicated a decline of green spaces with urbanisation, and most marked in fast growing towns. The results suggested that urban residents frequently visited urban green spaces, with most respondents favouring the use of green spaces for social and cultural benefits. How use of different spaces was strongly gender related, with males favouring less developed green space types (such as commonages and woodlands) and females for formal areas such domestic and institutional gardens and churchyards. Respondents also identified various challenges associated with using and accessing urban green spaces, with pollution, crime and lack of maintenance in particular. The study shows the importance of GIS as a mapping tool that can be used to provide information for ecological planning in rapidly changing urban environment. The research process generated several lessons that need to be taken into consideration when designing urban landscapes, most importantly relating to the diversity, quantity, quality and maintenance of urban green spaces.
- Full Text:
- Date Issued: 2019
- Authors: Radebe, Denis Siphosihle
- Date: 2019
- Subjects: Urban ecology (Sociology) -- South Africa -- Eastern Cape , Small cities -- South Africa -- Eastern Cape , City planning -- South Africa -- Eastern Cape , Recreation areas -- South Africa -- Eastern Cape , Open spaces -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76447 , vital:30563
- Description: Most regions of the developing world are experiencing large-scale urbanisation, with urban population growth outstripping rural growth. This is most marked in small and medium-sized towns as opposed to megacities. Urbanisation is associated with numerous changes in social, economic and ecological states and dynamics. A key one, of interest in this study, is the sustainability and liveability of the growing towns and cities. The retention, provision and maintenance of multifunctional urban green infrastructure are a core strategy in this regard. This study therefore sought to assess the amount, distribution and use of urban green spaces within South Africa using small towns of the Eastern Cape. The primary research included sixteen aerial images of which eight were historical aerial photographs and another eight were the latest aerial images of the selected study towns. Historical and latest aerial images were digitised to classify the types and calculate the amount of urban green space. GIS mapping, interviews and focus group discussions were conducted with urban residents to understand how these green spaces are used. The analytical tools in this study derived from social science included household surveys of 180 randomly selected respondents in small towns. Fifteen types of green spaces were identified in the sample towns. The study further revealed that green spaces are not distributed equally in different suburbs of small towns, generally being less green spaces, especially formal parks and recreation areas, in poorer areas. The results indicated a decline of green spaces with urbanisation, and most marked in fast growing towns. The results suggested that urban residents frequently visited urban green spaces, with most respondents favouring the use of green spaces for social and cultural benefits. How use of different spaces was strongly gender related, with males favouring less developed green space types (such as commonages and woodlands) and females for formal areas such domestic and institutional gardens and churchyards. Respondents also identified various challenges associated with using and accessing urban green spaces, with pollution, crime and lack of maintenance in particular. The study shows the importance of GIS as a mapping tool that can be used to provide information for ecological planning in rapidly changing urban environment. The research process generated several lessons that need to be taken into consideration when designing urban landscapes, most importantly relating to the diversity, quantity, quality and maintenance of urban green spaces.
- Full Text:
- Date Issued: 2019
Sulphide textures and compositions associated with the hydrothermal/magmatic system of the Twangiza gold deposit (South Kivu, DRC)
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
Post-release evaluation of Megamelus scutellaris Berg. (hemiptera: delphacidae): a biological control agent of water hyacinth Eichhornia crassipes (Mart.) Solms-Laub (Pontederiaceae) in South Africa
- Authors: Miller, Benjamin Erich
- Date: 2019
- Subjects: Megamelus scutellaris Berg. , Delphacidae , 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/10962/92330 , vital:30710
- Description: Water hyacinth, Eichhornia crassipes (Mart.) Solms-Laub. (Pontederiaceae) is a free-floating aquatic macrophyte from South America that was introduced to South Africa in the 1900s for its attractive ornamental flowers. The plant was classified as a serious invader in the country in the 1970s, eventually becoming the worst invasive aquatic plant in South Africa. Biological control is widely regarded as the most effective method of managing water hyacinth, as it is ecologically safe, cost-effective, and self-sustaining. To date, nine biological control agents have been released in South Africa against water hyacinth, including eight arthropods and a pathogen. Due to the cumulative effects of highly eutrophic waterbodies, which mitigate the damage caused by biological control, and the cold winters which inhibit the rate of biological control agent population build up, South Africa currently has more biological control agents released on water hyacinth than anywhere else in the world. The need for a cold-tolerant agent that can reproduce and develop quickly, while still being damaging to water hyacinth in eutrophic systems, led to the introduction of the most recently released water hyacinth biological control agent, the planthopper Megamelus scutellaris Berg (Hemiptera: Delphacidae), which was initially collected from Argentina. This thesis formed the first post-release evaluation of M. scutellaris since its release in South Africa in 2013. It included a greenhouse experiment to measure the agent’s feeding damage in relation to different nutrient levels and stocking rates, as well as a field component to evaluate both the post-winter recovery of M. scutellaris, and a nationwide survey to measure the establishment of the agent around the country in relation to climate, water quality, and plant health. In the greenhouse experiment, the feeding damage was quantified using measurements of plant growth parameters and chlorophyll fluorometry. It was found that, like other biological control agents of water hyacinth, M. scutellaris was most damaging when released in high numbers on plants grown at medium nutrient levels, and less effective on plants grown at elevated nutrient levels. A water hyacinth infestation on the Kubusi River was selected for the evaluation of the post-winter recovery of M. scutellaris. The Kubusi River is both the first site where M. scutellaris was released, and the coldest site where water hyacinth biological control agents have established successfully in South Africa. Monthly visits tracking seasonal plant health characteristics and agent population densities indicated that the populations of M. scutellaris were impacted most significantly by the season. Low temperatures led to the water hyacinth plants being of poor quality during the winter, which had a subsequent negative effect on the agent populations. The agents could only fully recover by late summer, which meant that the plants were without any significant biological control through the initial phases of the growing season, when they were most vulnerable, and a significant lag-phase occurred between the recovery of the plants and the recovery of the agent population after the winter bottleneck. A survey of all sites where M. scutellaris had been released in South Africa yielded 16 sites where the agents had successfully established, having survived at least one full winter. Among these sites were four sites where the agents were found without them having been released, indicating that they can disperse unaided to new sites. The temperature was a major factor responsible for the success or failure of establishment, with very few agents surviving in the hot areas of South Africa or in areas with a high frost incidence. The density of M. scutellaris was higher in nutrient-rich water, and on plants with more leaves, suggesting that the quality of the plants also contributed to establishment. The results of this thesis showed that M. scutellaris is able to establish successfully in South Africa, and that the agents are capable of causing significant damage to water hyacinth, making it a promising addition to the biological control programme. Novel methods of measuring subtle insect feeding damage in plants and quantifying agent populations are also discussed, along with suggestions for the future implementation of M. scutellaris in South Africa.
- Full Text:
- Date Issued: 2019
- Authors: Miller, Benjamin Erich
- Date: 2019
- Subjects: Megamelus scutellaris Berg. , Delphacidae , 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/10962/92330 , vital:30710
- Description: Water hyacinth, Eichhornia crassipes (Mart.) Solms-Laub. (Pontederiaceae) is a free-floating aquatic macrophyte from South America that was introduced to South Africa in the 1900s for its attractive ornamental flowers. The plant was classified as a serious invader in the country in the 1970s, eventually becoming the worst invasive aquatic plant in South Africa. Biological control is widely regarded as the most effective method of managing water hyacinth, as it is ecologically safe, cost-effective, and self-sustaining. To date, nine biological control agents have been released in South Africa against water hyacinth, including eight arthropods and a pathogen. Due to the cumulative effects of highly eutrophic waterbodies, which mitigate the damage caused by biological control, and the cold winters which inhibit the rate of biological control agent population build up, South Africa currently has more biological control agents released on water hyacinth than anywhere else in the world. The need for a cold-tolerant agent that can reproduce and develop quickly, while still being damaging to water hyacinth in eutrophic systems, led to the introduction of the most recently released water hyacinth biological control agent, the planthopper Megamelus scutellaris Berg (Hemiptera: Delphacidae), which was initially collected from Argentina. This thesis formed the first post-release evaluation of M. scutellaris since its release in South Africa in 2013. It included a greenhouse experiment to measure the agent’s feeding damage in relation to different nutrient levels and stocking rates, as well as a field component to evaluate both the post-winter recovery of M. scutellaris, and a nationwide survey to measure the establishment of the agent around the country in relation to climate, water quality, and plant health. In the greenhouse experiment, the feeding damage was quantified using measurements of plant growth parameters and chlorophyll fluorometry. It was found that, like other biological control agents of water hyacinth, M. scutellaris was most damaging when released in high numbers on plants grown at medium nutrient levels, and less effective on plants grown at elevated nutrient levels. A water hyacinth infestation on the Kubusi River was selected for the evaluation of the post-winter recovery of M. scutellaris. The Kubusi River is both the first site where M. scutellaris was released, and the coldest site where water hyacinth biological control agents have established successfully in South Africa. Monthly visits tracking seasonal plant health characteristics and agent population densities indicated that the populations of M. scutellaris were impacted most significantly by the season. Low temperatures led to the water hyacinth plants being of poor quality during the winter, which had a subsequent negative effect on the agent populations. The agents could only fully recover by late summer, which meant that the plants were without any significant biological control through the initial phases of the growing season, when they were most vulnerable, and a significant lag-phase occurred between the recovery of the plants and the recovery of the agent population after the winter bottleneck. A survey of all sites where M. scutellaris had been released in South Africa yielded 16 sites where the agents had successfully established, having survived at least one full winter. Among these sites were four sites where the agents were found without them having been released, indicating that they can disperse unaided to new sites. The temperature was a major factor responsible for the success or failure of establishment, with very few agents surviving in the hot areas of South Africa or in areas with a high frost incidence. The density of M. scutellaris was higher in nutrient-rich water, and on plants with more leaves, suggesting that the quality of the plants also contributed to establishment. The results of this thesis showed that M. scutellaris is able to establish successfully in South Africa, and that the agents are capable of causing significant damage to water hyacinth, making it a promising addition to the biological control programme. Novel methods of measuring subtle insect feeding damage in plants and quantifying agent populations are also discussed, along with suggestions for the future implementation of M. scutellaris in South Africa.
- Full Text:
- Date Issued: 2019
A pilot wide-field VLBI survey of the GOODS-North field
- Authors: Akoto-Danso, Alexander
- Date: 2019
- Subjects: Radio astronomy , Very long baseline interferometry , Radio interometers , Imaging systems in astronomy , Hubble Space Telescope (Spacecraft) -- Observations
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72296 , vital:30027
- Description: Very Long Baseline Interferometry (VLBI) has significant advantages in disentangling active galactic nuclei (AGN) from star formation, particularly at intermediate to high-redshift due to its high angular resolution and insensitivity to dust. Surveys using VLBI arrays are only just becoming practical over wide areas with numerous developments and innovations (such as multi-phase centre techniques) in observation and data analysis techniques. However, fully automated pipelines for VLBI data analysis are based on old software packages and are unable to incorporate new calibration and imaging algorithms. In this work, the researcher developed a pipeline for VLBI data analysis which integrates a recent wide-field imaging algorithm, RFI excision, and a purpose-built source finding algorithm specifically developed for the 64kx64k wide-field VLBI images. The researcher used this novel pipeline to process 6% (~ 9 arcmin2 of the total 160 arcmin2) of the data from the CANDELS GOODS- North extragalactic field at 1.6 GHz. The milli-arcsec scale images have an average rms of a ~ 10 uJy/beam. Forty four (44) candidate sources were detected, most of which are at sub-mJy flux densities, having brightness temperatures and luminosities of >5x105 K and >6x1021 W Hz-1 respectively. This work demonstrates that automated post-processing pipelines for wide-field, uniform sensitivity VLBI surveys are feasible and indeed made more efficient with new software, wide-field imaging algorithms and more purpose-built source- finders. This broadens the discovery space for future wide-field surveys with upcoming arrays such as the African VLBI Network (AVN), MeerKAT and the Square Kilometre Array (SKA).
- Full Text:
- Date Issued: 2019
- Authors: Akoto-Danso, Alexander
- Date: 2019
- Subjects: Radio astronomy , Very long baseline interferometry , Radio interometers , Imaging systems in astronomy , Hubble Space Telescope (Spacecraft) -- Observations
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72296 , vital:30027
- Description: Very Long Baseline Interferometry (VLBI) has significant advantages in disentangling active galactic nuclei (AGN) from star formation, particularly at intermediate to high-redshift due to its high angular resolution and insensitivity to dust. Surveys using VLBI arrays are only just becoming practical over wide areas with numerous developments and innovations (such as multi-phase centre techniques) in observation and data analysis techniques. However, fully automated pipelines for VLBI data analysis are based on old software packages and are unable to incorporate new calibration and imaging algorithms. In this work, the researcher developed a pipeline for VLBI data analysis which integrates a recent wide-field imaging algorithm, RFI excision, and a purpose-built source finding algorithm specifically developed for the 64kx64k wide-field VLBI images. The researcher used this novel pipeline to process 6% (~ 9 arcmin2 of the total 160 arcmin2) of the data from the CANDELS GOODS- North extragalactic field at 1.6 GHz. The milli-arcsec scale images have an average rms of a ~ 10 uJy/beam. Forty four (44) candidate sources were detected, most of which are at sub-mJy flux densities, having brightness temperatures and luminosities of >5x105 K and >6x1021 W Hz-1 respectively. This work demonstrates that automated post-processing pipelines for wide-field, uniform sensitivity VLBI surveys are feasible and indeed made more efficient with new software, wide-field imaging algorithms and more purpose-built source- finders. This broadens the discovery space for future wide-field surveys with upcoming arrays such as the African VLBI Network (AVN), MeerKAT and the Square Kilometre Array (SKA).
- Full Text:
- Date Issued: 2019
Using captive seabirds to assess knowledge gaps in stable isotope analysis of diets
- Authors: Micklem, Isabel Andrea
- Date: 2019
- Subjects: Stable isotopes -- Analysis African penguin -- South Africa Breeding
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65101 , vital:28686
- Description: Stable isotope (SI) ratios of carbon (δ13C) and nitrogen (δ15N) are now widely used as biomarkers in ecological studies to provide information about food web structuring. However, understanding trophic relationships using SI analysis requires not only knowledge of SI values of predator and prey, but also accurate discrimination factors (DFs), which can differ among species and by physiological state. This thesis examined three questions using captive birds from the South African Foundation for the Conservation of Coastal Birds (SANCCOB). First, the effects of ontogeny on δ13C and δ15N ratios of African penguins (Spheniscus demersus) were assessed. Blood samples were collected from penguins in four age classes (P3 chicks, blues, juveniles and adults) concurrently with their diet (sardine (Sardinops sagax) and formula). Second, to assess the influence of breeding physiology on SI ratios, the blood of ten breeding pairs of penguins was sampled over a five-month period from June to October 2016. Following laying, each pair was categorised into one of three (four for whole blood) egg production phases (initial yolk deposition, rapid yolk deposition and post-laying) and their influences on SI ratios were tested. Third, species differences in DFs were evaluated for African penguins, kelp and Hartlaub’s gulls (Larus dominicanus and L. hartlaubii), greater crested terns (Thalasseus bergii) and Cape cormorants (Phalacrocorax capensis). Flying birds were mostly fed sardine with a small but unknown amount of sardinella (Sardinella aurita), DFs were therefore estimated for a 50:50 sardine:sardinella diet, a 75:25 sardine:sardinella diet and a 100% sardine diet for each flying bird species. The DFs were assessed for the whole blood (WB), red blood cells (RBC), plasma (PL) and delipidated plasma of the penguins, and only WB for the flying birds as well as flesh, whole fish, delipidated flesh and delipidated whole fish for fish species, and for formula. Results indicated that age influenced both the δ13C and δ15N of WB, only the δ15N of RBC and the δ13C of delipidated PL. The assessment of breeding physiology yielded a significant interaction between the effects of egg production phase and sex on the δ13C of WB; females had significantly lower δ13C in the rapid yolk deposition phase than the other two phases and all males. The δ13C of PL was affected only by sex, with females having a significantly lower δ13C value than males. Neither physiological state nor sex influenced the other blood components. Differences were found among the three DFs in the non-penguin species, but not for all consumer – prey tissue combinations. There were also significant differences among species with a DF calculated from a diet with the most probable prey proportions eaten. Depending on the combination of consumer and prey tissue used to calculate the DF, a different conclusion regarding trophic information can be reached. A literature review updated with the present data showed that no general pattern or grouping of similar species with regards to DF values could be drawn, highlighting the importance of determining species- and tissue-specific DFs. Thus age, egg production, tissue and species all influenced the SI values of bird blood and therefore their DFs. Not all physiological conditions affect all blood components in the same way, making different components more or less sensitive to physiological influences. Though their influence is at a small enough scale that it is unlikely to hamper correct conclusion in ecological studies, it is crucial that these factors are considered when using SI analysis (SIA). When uncertainties exist for some coefficients in wild studies, SIA should therefore be combined to other dietary techniques to determine the food web structure as best as possible.
- Full Text:
- Date Issued: 2019
- Authors: Micklem, Isabel Andrea
- Date: 2019
- Subjects: Stable isotopes -- Analysis African penguin -- South Africa Breeding
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65101 , vital:28686
- Description: Stable isotope (SI) ratios of carbon (δ13C) and nitrogen (δ15N) are now widely used as biomarkers in ecological studies to provide information about food web structuring. However, understanding trophic relationships using SI analysis requires not only knowledge of SI values of predator and prey, but also accurate discrimination factors (DFs), which can differ among species and by physiological state. This thesis examined three questions using captive birds from the South African Foundation for the Conservation of Coastal Birds (SANCCOB). First, the effects of ontogeny on δ13C and δ15N ratios of African penguins (Spheniscus demersus) were assessed. Blood samples were collected from penguins in four age classes (P3 chicks, blues, juveniles and adults) concurrently with their diet (sardine (Sardinops sagax) and formula). Second, to assess the influence of breeding physiology on SI ratios, the blood of ten breeding pairs of penguins was sampled over a five-month period from June to October 2016. Following laying, each pair was categorised into one of three (four for whole blood) egg production phases (initial yolk deposition, rapid yolk deposition and post-laying) and their influences on SI ratios were tested. Third, species differences in DFs were evaluated for African penguins, kelp and Hartlaub’s gulls (Larus dominicanus and L. hartlaubii), greater crested terns (Thalasseus bergii) and Cape cormorants (Phalacrocorax capensis). Flying birds were mostly fed sardine with a small but unknown amount of sardinella (Sardinella aurita), DFs were therefore estimated for a 50:50 sardine:sardinella diet, a 75:25 sardine:sardinella diet and a 100% sardine diet for each flying bird species. The DFs were assessed for the whole blood (WB), red blood cells (RBC), plasma (PL) and delipidated plasma of the penguins, and only WB for the flying birds as well as flesh, whole fish, delipidated flesh and delipidated whole fish for fish species, and for formula. Results indicated that age influenced both the δ13C and δ15N of WB, only the δ15N of RBC and the δ13C of delipidated PL. The assessment of breeding physiology yielded a significant interaction between the effects of egg production phase and sex on the δ13C of WB; females had significantly lower δ13C in the rapid yolk deposition phase than the other two phases and all males. The δ13C of PL was affected only by sex, with females having a significantly lower δ13C value than males. Neither physiological state nor sex influenced the other blood components. Differences were found among the three DFs in the non-penguin species, but not for all consumer – prey tissue combinations. There were also significant differences among species with a DF calculated from a diet with the most probable prey proportions eaten. Depending on the combination of consumer and prey tissue used to calculate the DF, a different conclusion regarding trophic information can be reached. A literature review updated with the present data showed that no general pattern or grouping of similar species with regards to DF values could be drawn, highlighting the importance of determining species- and tissue-specific DFs. Thus age, egg production, tissue and species all influenced the SI values of bird blood and therefore their DFs. Not all physiological conditions affect all blood components in the same way, making different components more or less sensitive to physiological influences. Though their influence is at a small enough scale that it is unlikely to hamper correct conclusion in ecological studies, it is crucial that these factors are considered when using SI analysis (SIA). When uncertainties exist for some coefficients in wild studies, SIA should therefore be combined to other dietary techniques to determine the food web structure as best as possible.
- Full Text:
- Date Issued: 2019
The relative roles of ecosystem services and disservices in rural livelihoods in the Eastern Cape, South Africa
- Authors: Herd-Hoare, Shannon
- Date: 2019
- Subjects: Ecosystem services -- Health aspects -- South Africa , South Africa -- Rural conditions , Biodiversity -- South Africa -- Health aspects , Rural development -- South Africa -- Health aspects
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94080 , vital:30998
- Description: Since the publication of the Millennium Ecosystem Assessment report there has been a marked increase in research into various aspects of ecosystem services (ES). While ES are essential to human wellbeing, the literature has overlooked that some ecosystem goods and services also undermine human wellbeing. These are known as Ecosystem Disservices (EDS). This study aims to counter this imbalance in research, specifically in the context of rural livelihoods which are frequently dependent on local ES but often ill-equipped to manage EDS. The objectives of this study, conducted in three rural villages along a gradient of habitat diversity, were to identify a range of ES and EDS, determine their perceived contributions to or effects on the wellbeing of respondents, and identify modifications in livelihood strategies in response to EDS. The research made use of household surveys in conjunction with participatory learning and action techniques, such as focus group discussions in which ranking and trendline exercises, timelines, and participatory mapping were conducted. Findings indicated that although numerous participants were involved in the harvest of multiple ES, such as Non-Timber Forest Products (NTFPs), livestock outputs, crops and marine wildlife, they simultaneously experienced losses from EDS, such as ticks, unpalatable grass species, monkeys, and Lantana camara invasion which undermined livelihoods to varying degrees. The role of ES and EDS in livelihoods was expressed in economic terms, representing a common framework with which to illustrate the magnitude of their contribution or loss. For example, the average value of livestock goods and services, amongst those who owned and used outputs, was highest in the least biodiverse village at R9 753 per annum, while the corresponding value of potential livestock goods and services lost due to EDS, despite active implementation of prevention measures, totalled R22 426. Further, the average value of cultivated plots in the most biodiverse village could have totalled approximately R20 958, but because of EDS, represented less than 20% of this value. Further, the findings highlighted that the most biodiverse village also had the highest number of EDS, supporting Dunn (2010) who hypothesised that the number of EDS increases with the number of ES. Based on these findings, I propose that a comprehensive framework which systematically contextualises both the positive and negative contributions of ES is needed to grasp the full picture of how local people conceive and engage with nature to facilitate an understanding of the resulting practices and processes.
- Full Text:
- Date Issued: 2019
- Authors: Herd-Hoare, Shannon
- Date: 2019
- Subjects: Ecosystem services -- Health aspects -- South Africa , South Africa -- Rural conditions , Biodiversity -- South Africa -- Health aspects , Rural development -- South Africa -- Health aspects
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94080 , vital:30998
- Description: Since the publication of the Millennium Ecosystem Assessment report there has been a marked increase in research into various aspects of ecosystem services (ES). While ES are essential to human wellbeing, the literature has overlooked that some ecosystem goods and services also undermine human wellbeing. These are known as Ecosystem Disservices (EDS). This study aims to counter this imbalance in research, specifically in the context of rural livelihoods which are frequently dependent on local ES but often ill-equipped to manage EDS. The objectives of this study, conducted in three rural villages along a gradient of habitat diversity, were to identify a range of ES and EDS, determine their perceived contributions to or effects on the wellbeing of respondents, and identify modifications in livelihood strategies in response to EDS. The research made use of household surveys in conjunction with participatory learning and action techniques, such as focus group discussions in which ranking and trendline exercises, timelines, and participatory mapping were conducted. Findings indicated that although numerous participants were involved in the harvest of multiple ES, such as Non-Timber Forest Products (NTFPs), livestock outputs, crops and marine wildlife, they simultaneously experienced losses from EDS, such as ticks, unpalatable grass species, monkeys, and Lantana camara invasion which undermined livelihoods to varying degrees. The role of ES and EDS in livelihoods was expressed in economic terms, representing a common framework with which to illustrate the magnitude of their contribution or loss. For example, the average value of livestock goods and services, amongst those who owned and used outputs, was highest in the least biodiverse village at R9 753 per annum, while the corresponding value of potential livestock goods and services lost due to EDS, despite active implementation of prevention measures, totalled R22 426. Further, the average value of cultivated plots in the most biodiverse village could have totalled approximately R20 958, but because of EDS, represented less than 20% of this value. Further, the findings highlighted that the most biodiverse village also had the highest number of EDS, supporting Dunn (2010) who hypothesised that the number of EDS increases with the number of ES. Based on these findings, I propose that a comprehensive framework which systematically contextualises both the positive and negative contributions of ES is needed to grasp the full picture of how local people conceive and engage with nature to facilitate an understanding of the resulting practices and processes.
- Full Text:
- Date Issued: 2019
Environmental drivers of the composition and distribution of larval fish assemblages off the south coast of South Africa
- Authors: Trassierra, Jaqueline Anne
- Date: 2019
- Subjects: Fishes -- Larvae -- South Africa -- Eastern Cape , Fishes -- Larvae -- Migration -- South Africa -- Eastern Cape , Fishes -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68154 , vital:29207
- Description: The species composition, distribution and patterns of vertical migration of larval fish assemblages were investigated in March and in September 2013 within two adjacent log spiral bays, Algoa Bay and St Francis Bay, on the south coast of South Africa. Fish larvae were collected by means of a boat towed bongo net (57 cm diameter; mesh aperture 500 μm). An onshore (2 km) and an offshore (3 km) station were each sampled twice during the daytime (06:00 – 18:00) with two horizontal tows: near the surface (0.5 m) and close to the bottom (12 m). Tows were repeated at night (18:00 – 23:00) for onshore sites. Larval catches included 16 fish families and 40 species. A multivariate analysis indicated that the species composition was significantly different between Algoa Bay and St Francis Bay, with Engraulidae, Blenniidae, Sparidae, Soleidae and Cynoglossidae making important contributions to the larval fish catch in Algoa Bay, while Blenniidae, Engraulidae, Tripterygiidae, Sparidae and Gobiesocidae contributed significantly in St Francis Bay. Differences in assemblage composition were noted between the Spring (September–October) and Autumn (March-April) months. The species composition of larval fish assemblages was related to wind speed, wave height, cloud cover, sea water temperature, depth, average current speed and direction. Wind speed, wave height, temperature and depth significantly contributed to the variation in larval fish densities. Abundances of larval fishes were greater offshore than onshore, larvae from pelagic eggs dominated catches offshore, while larvae from demersal eggs dominated onshore catches. Habitat structure strongly influenced the composition of larval fishes between the bays and abundances were significantly greater at night than during the day. Most larval fishes displayed a reverse diel vertical migration pattern and were most influenced by predators, wind speed and cloud cover. This study shows that larval fish assemblages are highly complex and patchy. Spawning mode, individual species behaviour, diel vertical migration, current structure, depth, temperature, wind speed, cloud cover and type of habitat substratum all influence larval fish composition and distribution in the nearshore waters of South Africa.
- Full Text:
- Date Issued: 2019
- Authors: Trassierra, Jaqueline Anne
- Date: 2019
- Subjects: Fishes -- Larvae -- South Africa -- Eastern Cape , Fishes -- Larvae -- Migration -- South Africa -- Eastern Cape , Fishes -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68154 , vital:29207
- Description: The species composition, distribution and patterns of vertical migration of larval fish assemblages were investigated in March and in September 2013 within two adjacent log spiral bays, Algoa Bay and St Francis Bay, on the south coast of South Africa. Fish larvae were collected by means of a boat towed bongo net (57 cm diameter; mesh aperture 500 μm). An onshore (2 km) and an offshore (3 km) station were each sampled twice during the daytime (06:00 – 18:00) with two horizontal tows: near the surface (0.5 m) and close to the bottom (12 m). Tows were repeated at night (18:00 – 23:00) for onshore sites. Larval catches included 16 fish families and 40 species. A multivariate analysis indicated that the species composition was significantly different between Algoa Bay and St Francis Bay, with Engraulidae, Blenniidae, Sparidae, Soleidae and Cynoglossidae making important contributions to the larval fish catch in Algoa Bay, while Blenniidae, Engraulidae, Tripterygiidae, Sparidae and Gobiesocidae contributed significantly in St Francis Bay. Differences in assemblage composition were noted between the Spring (September–October) and Autumn (March-April) months. The species composition of larval fish assemblages was related to wind speed, wave height, cloud cover, sea water temperature, depth, average current speed and direction. Wind speed, wave height, temperature and depth significantly contributed to the variation in larval fish densities. Abundances of larval fishes were greater offshore than onshore, larvae from pelagic eggs dominated catches offshore, while larvae from demersal eggs dominated onshore catches. Habitat structure strongly influenced the composition of larval fishes between the bays and abundances were significantly greater at night than during the day. Most larval fishes displayed a reverse diel vertical migration pattern and were most influenced by predators, wind speed and cloud cover. This study shows that larval fish assemblages are highly complex and patchy. Spawning mode, individual species behaviour, diel vertical migration, current structure, depth, temperature, wind speed, cloud cover and type of habitat substratum all influence larval fish composition and distribution in the nearshore waters of South Africa.
- Full Text:
- Date Issued: 2019
Interaction between the root-feeding beetle, Longitarsus bethae (Coleoptera: Chrysomelidae) and the root-knot nematode, Meloidogyne javanica (Nematoda: Heteroderidae): Implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa
- Authors: Musedeli, Jufter
- Date: 2019
- Subjects: Insect-plant relationships , Insects -- Host plants , Flea beetles , Symbiosis , Longitarsus , Chrysomelidae , Lantana camara -- Biological control -- South Africa , Heteroderidae , Root-knot nematodes , Weeds -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/71130 , vital:29788
- Description: Plants often are simultaneously attacked by several herbivores that can affect each other’s performance, and their interaction may affect their host plant fitness. The current study was conducted to determine the interaction between the root-feeding beetle, Longitarsus bethae Savini & Escalona (Coleoptera: Chrysomelidae) and a root-knot nematode, Meloidogyne javanica (Treub) Chitwood (Tylenchida: Heteroderidae), with implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa. The studies were conducted under quarantine conditions at the Agricultural Research Council-PHP, Roodeplaat, Pretoria, South Africa. Specifically, the study determined; (i) whether root damage by the flea beetle enhanced infection by M. javanica, (ii) whether L. camara roots infected with the nematode enhanced the performance of the beetle, (iii) whether single or combined effect of the two organisms (i.e. L. bethae and M. javanica) had an overall effect on the growth and biomass of their shared host, L. camara, and (iv) the susceptibility of 10 L. camara varieties that are commonly found in South Africa to M. javanica. The study found that galling on the roots of L. camara by the nematode occurs at the highest inoculation of 300 eggs of L. bethae per plant, and no galling occurred at inoculation of 200 eggs per plant and below. The findings also showed that L. bethae performed better on M. javanica-infected than on healthy L. camara roots, and that more L. bethae adult progeny with slightly bigger body size emerged from M. javanica-infected, than from healthy plants. Fresh weight (galls) of plant roots from treatments where both species (i.e., L. bethae and M. javanica) were combined was significantly higher than that from plants infected with the nematode only, suggesting that the combination of both species induces more galling than the nematode does alone. The above-ground dry biomass was significantly lower both in combined and M. javanica only treatments, than in L. bethae only treatment. The study also found that selected L. camara varieties were infected with M. javanica, albeit at varying degrees of infection. Among the 10 L. camara varieties, Orange Red OR 015 was the most susceptible. Other susceptible varieties included Light Pink 009 LP, Total Pink 021 TP and Dark Pink 018 DP, and these, together with variety Orange Red OR 015, constituted 40% of the L. camara varieties evaluated in the current study. Fifty percent of the varieties displayed slight to moderate susceptibility to M. javanica, while 10% displayed lack of susceptibility. The study concluded that the symbiotic relationship between L. bethae and M. javanica was mutual, resulting in increase in the fitness of the beetle. The combined herbivory by L. bethae and M. javanica was also found to be additive on one of the most common varieties of L. camara in South Africa, and therefore co-infestation by both species might enhance the biological control of this weed in South Africa. The study further concluded that the suitability of some invasive L. camara cultivars such as Light Pink 009 LP and Orange Red 015 OR for M. javanica, might also contribute towards biological control of this weed in South Africa, particularly in areas where the two herbivores species co-exist.
- Full Text:
- Date Issued: 2019
- Authors: Musedeli, Jufter
- Date: 2019
- Subjects: Insect-plant relationships , Insects -- Host plants , Flea beetles , Symbiosis , Longitarsus , Chrysomelidae , Lantana camara -- Biological control -- South Africa , Heteroderidae , Root-knot nematodes , Weeds -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/71130 , vital:29788
- Description: Plants often are simultaneously attacked by several herbivores that can affect each other’s performance, and their interaction may affect their host plant fitness. The current study was conducted to determine the interaction between the root-feeding beetle, Longitarsus bethae Savini & Escalona (Coleoptera: Chrysomelidae) and a root-knot nematode, Meloidogyne javanica (Treub) Chitwood (Tylenchida: Heteroderidae), with implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa. The studies were conducted under quarantine conditions at the Agricultural Research Council-PHP, Roodeplaat, Pretoria, South Africa. Specifically, the study determined; (i) whether root damage by the flea beetle enhanced infection by M. javanica, (ii) whether L. camara roots infected with the nematode enhanced the performance of the beetle, (iii) whether single or combined effect of the two organisms (i.e. L. bethae and M. javanica) had an overall effect on the growth and biomass of their shared host, L. camara, and (iv) the susceptibility of 10 L. camara varieties that are commonly found in South Africa to M. javanica. The study found that galling on the roots of L. camara by the nematode occurs at the highest inoculation of 300 eggs of L. bethae per plant, and no galling occurred at inoculation of 200 eggs per plant and below. The findings also showed that L. bethae performed better on M. javanica-infected than on healthy L. camara roots, and that more L. bethae adult progeny with slightly bigger body size emerged from M. javanica-infected, than from healthy plants. Fresh weight (galls) of plant roots from treatments where both species (i.e., L. bethae and M. javanica) were combined was significantly higher than that from plants infected with the nematode only, suggesting that the combination of both species induces more galling than the nematode does alone. The above-ground dry biomass was significantly lower both in combined and M. javanica only treatments, than in L. bethae only treatment. The study also found that selected L. camara varieties were infected with M. javanica, albeit at varying degrees of infection. Among the 10 L. camara varieties, Orange Red OR 015 was the most susceptible. Other susceptible varieties included Light Pink 009 LP, Total Pink 021 TP and Dark Pink 018 DP, and these, together with variety Orange Red OR 015, constituted 40% of the L. camara varieties evaluated in the current study. Fifty percent of the varieties displayed slight to moderate susceptibility to M. javanica, while 10% displayed lack of susceptibility. The study concluded that the symbiotic relationship between L. bethae and M. javanica was mutual, resulting in increase in the fitness of the beetle. The combined herbivory by L. bethae and M. javanica was also found to be additive on one of the most common varieties of L. camara in South Africa, and therefore co-infestation by both species might enhance the biological control of this weed in South Africa. The study further concluded that the suitability of some invasive L. camara cultivars such as Light Pink 009 LP and Orange Red 015 OR for M. javanica, might also contribute towards biological control of this weed in South Africa, particularly in areas where the two herbivores species co-exist.
- Full Text:
- Date Issued: 2019
Statistical study of traveling ionospheric disturbances over South Africa
- Authors: Mahlangu, Daniel Fiso
- Date: 2019
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Gravity waves , Magnetic storms
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76387 , vital:30556
- Description: This thesis provides a statistical analysis of traveling ionospheric disturbances (TIDs) in South Africa. The velocities of the TIDs were determined from total electron content (TEC) maps using particle image velocimetry (PIV). The periods were determined using Morlet function in wavelet analysis. The TIDs were grouped into four categories: daytime, twilight, nighttime TIDs, and those TIDs that occurred during magnetic storms. It was found that daytime medium scale TIDs (MSTIDs) propagated equatorward in all seasons (summer, autumn, winter, and spring), with velocities of about 114 to 213 m/s. Their maximum occurrence was in winter between 15:00 and 16:00 LT. The daytime large scale (TIDs) LSTIDs propagated equatorward with velocities of approximately 455 to 767 m/s. Their highest occurrence was in summer, between 12:00-13:00 LT. Most of the these TIDs (about 78%) were observed during the passing of the morning solar terminator. This implied that the morning terminator was more effective in instigating TIDs. Only a few nighttime TIDs were observed and therefore their behavior could not be statistically inferred. The TIDs that occurred during magnetically disturbed conditions propagated equatorward. This indicated that their source mechanism was atmospheric gravity waves generated at the onset of geomagnetic storms.
- Full Text:
- Date Issued: 2019
- Authors: Mahlangu, Daniel Fiso
- Date: 2019
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Gravity waves , Magnetic storms
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76387 , vital:30556
- Description: This thesis provides a statistical analysis of traveling ionospheric disturbances (TIDs) in South Africa. The velocities of the TIDs were determined from total electron content (TEC) maps using particle image velocimetry (PIV). The periods were determined using Morlet function in wavelet analysis. The TIDs were grouped into four categories: daytime, twilight, nighttime TIDs, and those TIDs that occurred during magnetic storms. It was found that daytime medium scale TIDs (MSTIDs) propagated equatorward in all seasons (summer, autumn, winter, and spring), with velocities of about 114 to 213 m/s. Their maximum occurrence was in winter between 15:00 and 16:00 LT. The daytime large scale (TIDs) LSTIDs propagated equatorward with velocities of approximately 455 to 767 m/s. Their highest occurrence was in summer, between 12:00-13:00 LT. Most of the these TIDs (about 78%) were observed during the passing of the morning solar terminator. This implied that the morning terminator was more effective in instigating TIDs. Only a few nighttime TIDs were observed and therefore their behavior could not be statistically inferred. The TIDs that occurred during magnetically disturbed conditions propagated equatorward. This indicated that their source mechanism was atmospheric gravity waves generated at the onset of geomagnetic storms.
- Full Text:
- Date Issued: 2019