A study of malicious software on the macOS operating system
- Authors: Regensberg, Mark Alan
- Date: 2019
- Subjects: Malware (Computer software) , Computer security , Computer viruses , Mac OS
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92302 , vital:30701
- Description: Much of the published malware research begins with a common refrain: the cost, quantum and complexity of threats are increasing, and research and practice should prioritise efforts to automate and reduce times to detect and prevent malware, while improving the consistency of categories and taxonomies applied to modern malware. Existing work related to malware targeting Apple's macOS platform has not been spared this approach, although limited research has been conducted on the true nature of threats faced by users of the operating system. While macOS focused research available consistently notes an increase in macOS users, devices and ultimately in threats, an opportunity exists to understand the real nature of threats faced by macOS users and suggest potential avenues for future work. This research provides a view of the current state of macOS malware by analysing and exploring a dataset of malware detections on macOS endpoints captured over a period of eleven months by an anti-malware software vendor. The dataset is augmented with malware information provided by the widely used Virus. Total service, as well as the application of prior automated malware categorisation work, AVClass to categorise and SSDeep to cluster and report on observed data. With Windows and Android platforms frequently in the spotlight as targets for highly disruptive malware like botnets, ransomware and cryptominers, research and intuition seem to suggest the threat of malware on this increasingly popular platform should be growing and evolving accordingly. Findings suggests that the direction and nature of growth and evolution may not be entirely as clear as industry reports suggest. Adware and Potentially Unwanted Applications (PUAs) make up the vast majority of the detected threats, with remote access trojans (RATs), ransomware and cryptocurrency miners comprising a relatively small proportion of the detected malware. This provides a number of avenues for potential future work to compare and contrast with research on other platforms, as well as identification of key factors that may influence its growth in the future.
- Full Text:
- Authors: Regensberg, Mark Alan
- Date: 2019
- Subjects: Malware (Computer software) , Computer security , Computer viruses , Mac OS
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92302 , vital:30701
- Description: Much of the published malware research begins with a common refrain: the cost, quantum and complexity of threats are increasing, and research and practice should prioritise efforts to automate and reduce times to detect and prevent malware, while improving the consistency of categories and taxonomies applied to modern malware. Existing work related to malware targeting Apple's macOS platform has not been spared this approach, although limited research has been conducted on the true nature of threats faced by users of the operating system. While macOS focused research available consistently notes an increase in macOS users, devices and ultimately in threats, an opportunity exists to understand the real nature of threats faced by macOS users and suggest potential avenues for future work. This research provides a view of the current state of macOS malware by analysing and exploring a dataset of malware detections on macOS endpoints captured over a period of eleven months by an anti-malware software vendor. The dataset is augmented with malware information provided by the widely used Virus. Total service, as well as the application of prior automated malware categorisation work, AVClass to categorise and SSDeep to cluster and report on observed data. With Windows and Android platforms frequently in the spotlight as targets for highly disruptive malware like botnets, ransomware and cryptominers, research and intuition seem to suggest the threat of malware on this increasingly popular platform should be growing and evolving accordingly. Findings suggests that the direction and nature of growth and evolution may not be entirely as clear as industry reports suggest. Adware and Potentially Unwanted Applications (PUAs) make up the vast majority of the detected threats, with remote access trojans (RATs), ransomware and cryptocurrency miners comprising a relatively small proportion of the detected malware. This provides a number of avenues for potential future work to compare and contrast with research on other platforms, as well as identification of key factors that may influence its growth in the future.
- Full Text:
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:
- 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:
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:
- 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:
An Integrated Management System to reduce False Codling Moth, Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) infested citrus fruit from being packed for export
- Authors: Mac Aleer, Clint
- Date: 2019
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Biological control -- South Africa , Citrus -- Diseases and pests -- Biological control -- South Africa , Insect pests -- Biological control -- South Africa , Insecticides , Citrus fruit industry -- South Africa , South Africa -- Commerce -- European Economic Community Countries
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92219 , vital:30691
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is indigenous to southern Africa and is an important pest of citrus in this region. As a result of its endemism to sub-Saharan Africa, several countries to which South Africa exports citrus, regulate it as a phytosanitary pest. Consequently, it is necessary to ship fruit to these markets under cold-disinfestation protocols. This has been possible, as until recently, all of these markets could be considered relatively small niche markets. The South African citrus industry exports approximately 130 million cartons of fruit (15 kg equivalent) annually. During the 2017 season, a total of 48 million cartons were exported to the European Union (EU), which is the equivalent of 41% of South Africa’s total export volume, thus making the EU South Africa’s most important export market. In 2013 the European and Mediterranean Plant Protection Organisation (EPPO) conducted a pest risk analysis (PRA) on FCM, leading to the EU declaring it an officially regulated pest for this region, effective of 1 January 2018. Citrus is regarded as a preferred non-native host of FCM and South African citrus was identified as a primary focus due to large volumes being exported to Europe. Shipping under cold disinfestation is not possible with such large volumes of fruit. Additionally, several cultivars would suffer high levels of chilling injury under such conditions. In this study, an Integrated Management System was tested with pre- and postharvest controls to test the hypothesis that pre-harvest interventions resulted in lower post-harvest infection. Thirty orchards ranging from soft citrus cultivars such as Nule and Nova Mandarins, to Navel orange cultivars such as Newhall, Palmer and Late Navel and ending with Valencia cultivars such as Midknight and Delta, were identified for this study. This system relies on pre-harvest inspections such as FCM trap counts and fruit infestation on data trees in every orchard, with associated thresholds for action or continued compliance. Inspections were conducted on a weekly basis. There was a significant relationship between the moth catches and FCM infestation for the full monitoring period, using a two-week lag period for infestation. Inspections of harvested fruit were conducted at the packhouse to determine FCM infestation. This included inspection of the fruit on delivery to the packhouse, on the packing line, and a final fruit sample taken from the packed product and inspected for FCM. The highest levels of infestation were recorded on the Navel cultivars, thus confirming that Navels cultivars are a preferred host for FCM. Significant positive relationships were recorded between FCM infestation during the last 4 weeks before harvest and the level of infestation in the fruit delivered to the packhouse and between the fruit delivered to the packhouse and in the fruit packed in a carton for export. There was a substantial reduction in infestation between the fruit delivered to the packhouse and the fruit packed in a carton for export, with certain orchards recording as much as a 93% reduction in the fruit packed in a carton, which indicated that the packhouse could effectively identify and remove FCM infested fruit. The outcome of the study is that a holistic management approach minimizes the risk of FCM in citrus fruit destined for export and therefore mitigate the risk associated with FCM.
- Full Text:
- Authors: Mac Aleer, Clint
- Date: 2019
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Biological control -- South Africa , Citrus -- Diseases and pests -- Biological control -- South Africa , Insect pests -- Biological control -- South Africa , Insecticides , Citrus fruit industry -- South Africa , South Africa -- Commerce -- European Economic Community Countries
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92219 , vital:30691
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is indigenous to southern Africa and is an important pest of citrus in this region. As a result of its endemism to sub-Saharan Africa, several countries to which South Africa exports citrus, regulate it as a phytosanitary pest. Consequently, it is necessary to ship fruit to these markets under cold-disinfestation protocols. This has been possible, as until recently, all of these markets could be considered relatively small niche markets. The South African citrus industry exports approximately 130 million cartons of fruit (15 kg equivalent) annually. During the 2017 season, a total of 48 million cartons were exported to the European Union (EU), which is the equivalent of 41% of South Africa’s total export volume, thus making the EU South Africa’s most important export market. In 2013 the European and Mediterranean Plant Protection Organisation (EPPO) conducted a pest risk analysis (PRA) on FCM, leading to the EU declaring it an officially regulated pest for this region, effective of 1 January 2018. Citrus is regarded as a preferred non-native host of FCM and South African citrus was identified as a primary focus due to large volumes being exported to Europe. Shipping under cold disinfestation is not possible with such large volumes of fruit. Additionally, several cultivars would suffer high levels of chilling injury under such conditions. In this study, an Integrated Management System was tested with pre- and postharvest controls to test the hypothesis that pre-harvest interventions resulted in lower post-harvest infection. Thirty orchards ranging from soft citrus cultivars such as Nule and Nova Mandarins, to Navel orange cultivars such as Newhall, Palmer and Late Navel and ending with Valencia cultivars such as Midknight and Delta, were identified for this study. This system relies on pre-harvest inspections such as FCM trap counts and fruit infestation on data trees in every orchard, with associated thresholds for action or continued compliance. Inspections were conducted on a weekly basis. There was a significant relationship between the moth catches and FCM infestation for the full monitoring period, using a two-week lag period for infestation. Inspections of harvested fruit were conducted at the packhouse to determine FCM infestation. This included inspection of the fruit on delivery to the packhouse, on the packing line, and a final fruit sample taken from the packed product and inspected for FCM. The highest levels of infestation were recorded on the Navel cultivars, thus confirming that Navels cultivars are a preferred host for FCM. Significant positive relationships were recorded between FCM infestation during the last 4 weeks before harvest and the level of infestation in the fruit delivered to the packhouse and between the fruit delivered to the packhouse and in the fruit packed in a carton for export. There was a substantial reduction in infestation between the fruit delivered to the packhouse and the fruit packed in a carton for export, with certain orchards recording as much as a 93% reduction in the fruit packed in a carton, which indicated that the packhouse could effectively identify and remove FCM infested fruit. The outcome of the study is that a holistic management approach minimizes the risk of FCM in citrus fruit destined for export and therefore mitigate the risk associated with FCM.
- Full Text:
An investigation into the interaction partners of the scaffold protein human CNK1 in the NF-κB pathway
- Authors: Moodley, Holisha
- Date: 2019
- Subjects: CNK1 , Scaffold proteins
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/96031 , vital:31228
- Description: The protein connector enhancer of KSR1 (CNK1) plays a role in a number of signalling pathways including those involved in cell proliferation, cell growth and differentiation. De-regulation of these pathways has been linked to the promotion of oncogenic signalling. The involvement of CNK1 in all of these diverse pathways indicates a need to better understand the role of this protein within the cell and within key signalling networks. The research provides a platform to understand the intricate relationships that occur between these key signalling networks with the potential to identify new drug targets. CNK1 is multifunctional scaffolding protein that has binding domains that mediate and co-ordinate signalling within the MAPK, Hippo, PI3K/AKT, JNK and NF-κB pathways as well as downstream of the AT2 receptor. The activity of CNK1 is regulated through its interactions with a range of different binding partners within these pathways. Of particular interest to this research is the role of CNK1 in NF-κB signalling. The deregulation of the NF-κB pathway is implicated in chronic inflammation, tissue damage and induction of cervical and breast cancer. CNK1 has been reported to regulate the non-canonical branch of the NF-κB pathway, upstream of the IKK complex however new findings lead to uncertainty about these conclusions. In addition, the interacting partner of CNK1 in the NF-κB pathway has not been elucidated. In this thesis, we aim to identify the binding partners of CNK1 in the NF-κB pathway. First, we validate an epitope-tagged CNK1-expression construct to express elevated levels of CNK1 in cervical cancer cells. We report that the expression of myc-CNK1 is comparable to endogenous CNK1. Cells expressing elevated CNK1 levels were used in traditional co-immunoprecipitation reactions to identify potential CNK1-interacting proteins. We present data that indicates a potential role for NIK in the CNK1 signalling complex. We discuss the weaknesses of the traditional co-immunoprecipitation reactions and design an alternative co-immunoprecipitation technique with which to study CNK1-interacting partners. In this system, a promiscuous biotin ligase fused to the protein sequence for CNK1 (BirA-CNK1) is used to label proteins proximal to CNK1 with biotin. Using this BirA- CNK1-expressing construct in cervical cancer cells, we demonstrate that CNK1 interacts with IKKα-IKKβ in the NF-κB pathway.
- Full Text:
- Authors: Moodley, Holisha
- Date: 2019
- Subjects: CNK1 , Scaffold proteins
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/96031 , vital:31228
- Description: The protein connector enhancer of KSR1 (CNK1) plays a role in a number of signalling pathways including those involved in cell proliferation, cell growth and differentiation. De-regulation of these pathways has been linked to the promotion of oncogenic signalling. The involvement of CNK1 in all of these diverse pathways indicates a need to better understand the role of this protein within the cell and within key signalling networks. The research provides a platform to understand the intricate relationships that occur between these key signalling networks with the potential to identify new drug targets. CNK1 is multifunctional scaffolding protein that has binding domains that mediate and co-ordinate signalling within the MAPK, Hippo, PI3K/AKT, JNK and NF-κB pathways as well as downstream of the AT2 receptor. The activity of CNK1 is regulated through its interactions with a range of different binding partners within these pathways. Of particular interest to this research is the role of CNK1 in NF-κB signalling. The deregulation of the NF-κB pathway is implicated in chronic inflammation, tissue damage and induction of cervical and breast cancer. CNK1 has been reported to regulate the non-canonical branch of the NF-κB pathway, upstream of the IKK complex however new findings lead to uncertainty about these conclusions. In addition, the interacting partner of CNK1 in the NF-κB pathway has not been elucidated. In this thesis, we aim to identify the binding partners of CNK1 in the NF-κB pathway. First, we validate an epitope-tagged CNK1-expression construct to express elevated levels of CNK1 in cervical cancer cells. We report that the expression of myc-CNK1 is comparable to endogenous CNK1. Cells expressing elevated CNK1 levels were used in traditional co-immunoprecipitation reactions to identify potential CNK1-interacting proteins. We present data that indicates a potential role for NIK in the CNK1 signalling complex. We discuss the weaknesses of the traditional co-immunoprecipitation reactions and design an alternative co-immunoprecipitation technique with which to study CNK1-interacting partners. In this system, a promiscuous biotin ligase fused to the protein sequence for CNK1 (BirA-CNK1) is used to label proteins proximal to CNK1 with biotin. Using this BirA- CNK1-expressing construct in cervical cancer cells, we demonstrate that CNK1 interacts with IKKα-IKKβ in the NF-κB pathway.
- Full Text:
An investigation of the security of passwords derived from African languages
- Authors: Sishi, Sibusiso Teboho
- Date: 2019
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163273 , vital:41024
- Description: Password authentication has become ubiquitous in the cyber age. To-date, there have been several studies on country based passwords by authors who studied, amongst others, English, Finnish, Italian and Chinese based passwords. However, there has been a lack of focused study on the type of passwords that are being created in Africa and whether there are benefits in creating passwords in an African language. For this research, password databases containing LAN Manager (LM) and NT LAN Manager (NTLM) hashes extracted from South African organisations in a variety of sectors in the economy, were obtained to gain an understanding of user behaviour in creating passwords. Analysis of the passwords obtained from these hashes (using several cracking methods) showed that many organisational passwords are based on the English language. This is understandable considering that the business language in South Africa is English even though South Africa has 11 official languages. African language based passwords were derived from known English weak passwords and some of the passwords were appended with numbers and special characters. The African based passwords created using eight Southern African languages were then uploaded to the Internet to test the security around using passwords based on African languages. Since most of the passwords were able to be cracked by third party researchers, we conclude that any password that is derived from known weak English words marked no improvement in the security of a password written in an African language, especially the more widely spoken languages, namely, isiZulu, isiXhosa and Setswana.
- Full Text:
- Authors: Sishi, Sibusiso Teboho
- Date: 2019
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163273 , vital:41024
- Description: Password authentication has become ubiquitous in the cyber age. To-date, there have been several studies on country based passwords by authors who studied, amongst others, English, Finnish, Italian and Chinese based passwords. However, there has been a lack of focused study on the type of passwords that are being created in Africa and whether there are benefits in creating passwords in an African language. For this research, password databases containing LAN Manager (LM) and NT LAN Manager (NTLM) hashes extracted from South African organisations in a variety of sectors in the economy, were obtained to gain an understanding of user behaviour in creating passwords. Analysis of the passwords obtained from these hashes (using several cracking methods) showed that many organisational passwords are based on the English language. This is understandable considering that the business language in South Africa is English even though South Africa has 11 official languages. African language based passwords were derived from known English weak passwords and some of the passwords were appended with numbers and special characters. The African based passwords created using eight Southern African languages were then uploaded to the Internet to test the security around using passwords based on African languages. Since most of the passwords were able to be cracked by third party researchers, we conclude that any password that is derived from known weak English words marked no improvement in the security of a password written in an African language, especially the more widely spoken languages, namely, isiZulu, isiXhosa and Setswana.
- Full Text:
Arbuscular mycorrhizal fungi as a bio-indicator of soil health under agricultural management practices in South Africa
- Authors: Sekgota, Wendy Maphefo
- Date: 2019
- Subjects: Soils -- Quality -- South Africa , Soil fertility -- South Africa , Fungi in agriculture -- South Africa , Mycorrhizal fungi , Vesicular-arbuscular mycorrhizas , Fungi -- Spores , Soils -- Agricultural chemical content
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72161 , vital:30011
- Description: This study investigated the activity of arbuscular mycorrhizal (AM) fungi as a potential biological indicator of soil health under conventional and conservation agricultural management in South Africa. An experimental trial consisting of three replicates plots under conventional and reduced tillage subdivided into twelve treatments of six crops and two fertilizer inputs was assessed over four growing seasons for various AM fungal parameters such as spore density, most probable number (MPN) of propagules percentage root colonisation and easily extractable glomalin (EEG). Cropping combinations were maize monoculture; maize soybean rotation; maize cowpea rotation; maize cowpea intercropping; maize oats intercropping and maize vetch intercropping. Resident AM fungal spore numbers and EEG protein levels were very low and no root colonization was recorded in the first two growing seasons. These findings prompted the need for the inoculation of the study site in the third growing season with a commercial AM fungal product (MycorootTM). Spore numbers, EEG concentrations and percentage root colonisation increased 8 weeks after inoculation but were significantly reduced in the fourth growing season that was not inoculated. MPN infectivity increased with inoculation particularly under conventional tillage and maize monoculture. Resident spore taxa were morphologically identified into three genera Gigaspora, Scutellospora, and Glomus. For the first two growing seasons, the maize roots were heavily colonized by a pathogenic fungus after mycorrhizal inoculation no evidence of pathogenic fungi was observed. In the fourth growing season which did not receive inoculation, root colonization started to decline. Reduced tillage, high fertilizer input combined with maize cowpea rotation (MC) and maize hairy vetch intercropping (Mv) had a significant effect (P = 0.01) on AM fungal spore numbers. Cropping systems and high fertilizer input had a significant effect on EEG concentrations in the second growing season. Overall, fertilizer application and crop type had implications for mycorrhizal activity. The soil health status in this study site was deemed low as measured by the impaired mycorrhizal activity due to agricultural management practices. Field inoculation combined with classical and molecular tools could provide a more realistic assessment of the effect of agricultural management practices on AM fungi as potential bioindicators of soil health. Therefore, AM fungi could be used as bioindicators of soil health under agricultural management practices in South African soil conditions.
- Full Text:
- Authors: Sekgota, Wendy Maphefo
- Date: 2019
- Subjects: Soils -- Quality -- South Africa , Soil fertility -- South Africa , Fungi in agriculture -- South Africa , Mycorrhizal fungi , Vesicular-arbuscular mycorrhizas , Fungi -- Spores , Soils -- Agricultural chemical content
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72161 , vital:30011
- Description: This study investigated the activity of arbuscular mycorrhizal (AM) fungi as a potential biological indicator of soil health under conventional and conservation agricultural management in South Africa. An experimental trial consisting of three replicates plots under conventional and reduced tillage subdivided into twelve treatments of six crops and two fertilizer inputs was assessed over four growing seasons for various AM fungal parameters such as spore density, most probable number (MPN) of propagules percentage root colonisation and easily extractable glomalin (EEG). Cropping combinations were maize monoculture; maize soybean rotation; maize cowpea rotation; maize cowpea intercropping; maize oats intercropping and maize vetch intercropping. Resident AM fungal spore numbers and EEG protein levels were very low and no root colonization was recorded in the first two growing seasons. These findings prompted the need for the inoculation of the study site in the third growing season with a commercial AM fungal product (MycorootTM). Spore numbers, EEG concentrations and percentage root colonisation increased 8 weeks after inoculation but were significantly reduced in the fourth growing season that was not inoculated. MPN infectivity increased with inoculation particularly under conventional tillage and maize monoculture. Resident spore taxa were morphologically identified into three genera Gigaspora, Scutellospora, and Glomus. For the first two growing seasons, the maize roots were heavily colonized by a pathogenic fungus after mycorrhizal inoculation no evidence of pathogenic fungi was observed. In the fourth growing season which did not receive inoculation, root colonization started to decline. Reduced tillage, high fertilizer input combined with maize cowpea rotation (MC) and maize hairy vetch intercropping (Mv) had a significant effect (P = 0.01) on AM fungal spore numbers. Cropping systems and high fertilizer input had a significant effect on EEG concentrations in the second growing season. Overall, fertilizer application and crop type had implications for mycorrhizal activity. The soil health status in this study site was deemed low as measured by the impaired mycorrhizal activity due to agricultural management practices. Field inoculation combined with classical and molecular tools could provide a more realistic assessment of the effect of agricultural management practices on AM fungi as potential bioindicators of soil health. Therefore, AM fungi could be used as bioindicators of soil health under agricultural management practices in South African soil conditions.
- Full Text:
Assessing the abundance of non-timber forest products in relation to forest succession on the Wild Coast, South Africa
- Authors: Njwaxu, Afika
- Date: 2019
- Subjects: Non-timber forest products -- South Africa -- Eastern Cape , Forest ecology -- South Africa -- Eastern Cape , Rural development -- South Africa -- Eastern Cape , Non-timber forest products -- South Africa -- Willowvale , Forest ecology -- South Africa -- Willowvale , Rural development -- South Africa -- Willowvale , Forest plants -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94090 , vital:30999
- Description: The number of people in the Eastern Cape, South Africa, that are engaging in arable cropping has declined markedly over the last few decades. This is due to a number of factors such as a decrease in human capital because of migration of able-bodied people to urban areas, disinclination to participate in farming, raiding of crops by livestock and lack of equipment. This has resulted in abandoned croplands being invaded by trees and shrubs as the start of forest succession leading to a change in species composition and the ecosystem benefits reaped from these sites. Key amongst these benefits is a variety of non-timber forests products (NTFPs) which are an integral part of livelihoods in the area. The study was conducted in Willowvale, on the Wild Coast, South Africa. Aerial photographs were used to determine when cessation of cropping occurred in local fields and when revegetation began in order to determine the age of old fields. Botanical inventory and Braun-Blanquet scale were used to assess species richness, composition and abundance of vegetation in fields abandoned at different times. Focus groups were used to identify NTFPs found in these old fields, their uses as well as rank their importance to the local people. Results showed an increase in woody cover with time since field abandonment. Species richness also increased with age of the old field with approximately three species gained per decade. When species richness was disaggregated by growth forms, herbaceous plants were abundant in the early stages of succession, shrubs in the mature stages and trees increased steadily with time. A total of 177 species were recorded from 50 plots that were sampled during the ecological data collection. Of these, 70 species (39.6%) were identified by the focus group participants as NTFPs. The participants grouped the NTFPs into six categories namely: food, building, medicinal, craft, cultural and energy. There was an increase of richness of NTFPs with forest succession; however the proportion of NTFPs decreased with age suggesting an increase in non-useful species. This suggests that harvesting from plots of different ages would be the optimal way for local people to get access to a large variety of NTFPs.
- Full Text:
- Authors: Njwaxu, Afika
- Date: 2019
- Subjects: Non-timber forest products -- South Africa -- Eastern Cape , Forest ecology -- South Africa -- Eastern Cape , Rural development -- South Africa -- Eastern Cape , Non-timber forest products -- South Africa -- Willowvale , Forest ecology -- South Africa -- Willowvale , Rural development -- South Africa -- Willowvale , Forest plants -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94090 , vital:30999
- Description: The number of people in the Eastern Cape, South Africa, that are engaging in arable cropping has declined markedly over the last few decades. This is due to a number of factors such as a decrease in human capital because of migration of able-bodied people to urban areas, disinclination to participate in farming, raiding of crops by livestock and lack of equipment. This has resulted in abandoned croplands being invaded by trees and shrubs as the start of forest succession leading to a change in species composition and the ecosystem benefits reaped from these sites. Key amongst these benefits is a variety of non-timber forests products (NTFPs) which are an integral part of livelihoods in the area. The study was conducted in Willowvale, on the Wild Coast, South Africa. Aerial photographs were used to determine when cessation of cropping occurred in local fields and when revegetation began in order to determine the age of old fields. Botanical inventory and Braun-Blanquet scale were used to assess species richness, composition and abundance of vegetation in fields abandoned at different times. Focus groups were used to identify NTFPs found in these old fields, their uses as well as rank their importance to the local people. Results showed an increase in woody cover with time since field abandonment. Species richness also increased with age of the old field with approximately three species gained per decade. When species richness was disaggregated by growth forms, herbaceous plants were abundant in the early stages of succession, shrubs in the mature stages and trees increased steadily with time. A total of 177 species were recorded from 50 plots that were sampled during the ecological data collection. Of these, 70 species (39.6%) were identified by the focus group participants as NTFPs. The participants grouped the NTFPs into six categories namely: food, building, medicinal, craft, cultural and energy. There was an increase of richness of NTFPs with forest succession; however the proportion of NTFPs decreased with age suggesting an increase in non-useful species. This suggests that harvesting from plots of different ages would be the optimal way for local people to get access to a large variety of NTFPs.
- Full Text:
Augmentative releases of Dactylopius austrinus De Lotto (Dactylopiidae; Hemiptera) for biological control of Opuntia aurantiaca Lindley (Cactaceae), in South Africa
- Authors: Mulateli, Thifhelimbilu
- Date: 2019
- Subjects: Opuntia aurantiaca -- Biolotical control -- South Africa , Invasive plants -- Biolotical control -- South Africa , Dactylopius austrinus De Lotto -- South Africa , Dactylopius -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92931 , vital:30765
- Description: Opuntia aurantiaca Lindely (Cactaceae) is an invasive alien cactus which has detrimental effects on agroecosystems and indigenous biodiversity in South Africa. Dense infestations over large areas reduce grazing capacity and indigenous biodiversity. Despite the release of a biological control agent, the cochineal insect Dactylopius austrinus De Lotto (Dactylopiidae), the weed is still considered a major problem in many parts of the country. Biological control has relied heavily on classical biological control, with little augmentative biological control implemented. This study investigated the outcome of mass-rearing and augmentative releases of D. austrinus for the control of O. aurantiaca. Augmentative releases are thought to improve the level of control by increasing agent densities in the field and thus increasing the level of damage inflicted to the plants. All data were collected with the intention to optimize release strategies so that the maximum benefit from the biological control agent could be achieved. An impact study was conducted using potted plants in a greenhouse to quantify the efficacy of multiple releases of the agent on the target weed. All three of the release treatments showed consistently higher proportion of cochineal than the controls, as well as the insect exclusion treatments, and these differences were statistically significant. The number of cladodes per plant increased significantly for the insect exclusion and control treatment over the period of the study, whilst all three release treatments decreased steadily over the same period. This study indicated that the agent is damaging to O. aurantiaca and that a single release event was beneficial but that multiple releases did not result in greater levels of control. A post-release evaluation was carried out to quantify the impact of releases of D. austrinus on O. aurantiaca in the field. Plots where the agent was excluded were compared with those where the agent was left at natural field densities and three treatments where agent populations were augmented to varying degrees through releases. The percentage of cochineal infested cladodes for all treatments decreased over time from the initiation of the experiment in October 2017 until the end of the experiment in October 2018. Opuntia aurantiaca densities also decreased over time for all treatments. The insect exclusion treatment had the greatest number of plants for the duration of the study, but this was not significantly different from other treatments. Dactylopius austrinus was damaging to O. aurantiaca, but climatic conditions in the field limited the efficacy of releases. Although O. aurantiaca density decreased during the experiment, it was evident that the reduced number of plants was not due to augmentation of the cochineal populations from the releases that were conducted. The experiment was conducted over a very dry period, when cochineal was particularly effective, so although augmentative releases did not improve the level of control, the natural population of cochineal was high and very damaging to O. aurantiaca over the course of the experiment. Releasing during wet periods, when the agent is less effective, could augment agent populations at a time when natural populations would be low, and hence improve levels of control further. Although this study was limited to a short period of two years, the results of this study suggest that the number of releases is less important than the timing of releases. Releasing immediately after periods of high rainfall is likely to be beneficial, while releasing during dry periods, or during winter when temperatures are low, is less effective. Dactylopius austrinus populations should be constantly monitored so that releases can be conducted when cochineal populations are low and the climatic conditions are correct. If the timing of release events is appropriate, then the over level of control of O. aurantiaca using D. austrinus could be improved.
- Full Text:
- Authors: Mulateli, Thifhelimbilu
- Date: 2019
- Subjects: Opuntia aurantiaca -- Biolotical control -- South Africa , Invasive plants -- Biolotical control -- South Africa , Dactylopius austrinus De Lotto -- South Africa , Dactylopius -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92931 , vital:30765
- Description: Opuntia aurantiaca Lindely (Cactaceae) is an invasive alien cactus which has detrimental effects on agroecosystems and indigenous biodiversity in South Africa. Dense infestations over large areas reduce grazing capacity and indigenous biodiversity. Despite the release of a biological control agent, the cochineal insect Dactylopius austrinus De Lotto (Dactylopiidae), the weed is still considered a major problem in many parts of the country. Biological control has relied heavily on classical biological control, with little augmentative biological control implemented. This study investigated the outcome of mass-rearing and augmentative releases of D. austrinus for the control of O. aurantiaca. Augmentative releases are thought to improve the level of control by increasing agent densities in the field and thus increasing the level of damage inflicted to the plants. All data were collected with the intention to optimize release strategies so that the maximum benefit from the biological control agent could be achieved. An impact study was conducted using potted plants in a greenhouse to quantify the efficacy of multiple releases of the agent on the target weed. All three of the release treatments showed consistently higher proportion of cochineal than the controls, as well as the insect exclusion treatments, and these differences were statistically significant. The number of cladodes per plant increased significantly for the insect exclusion and control treatment over the period of the study, whilst all three release treatments decreased steadily over the same period. This study indicated that the agent is damaging to O. aurantiaca and that a single release event was beneficial but that multiple releases did not result in greater levels of control. A post-release evaluation was carried out to quantify the impact of releases of D. austrinus on O. aurantiaca in the field. Plots where the agent was excluded were compared with those where the agent was left at natural field densities and three treatments where agent populations were augmented to varying degrees through releases. The percentage of cochineal infested cladodes for all treatments decreased over time from the initiation of the experiment in October 2017 until the end of the experiment in October 2018. Opuntia aurantiaca densities also decreased over time for all treatments. The insect exclusion treatment had the greatest number of plants for the duration of the study, but this was not significantly different from other treatments. Dactylopius austrinus was damaging to O. aurantiaca, but climatic conditions in the field limited the efficacy of releases. Although O. aurantiaca density decreased during the experiment, it was evident that the reduced number of plants was not due to augmentation of the cochineal populations from the releases that were conducted. The experiment was conducted over a very dry period, when cochineal was particularly effective, so although augmentative releases did not improve the level of control, the natural population of cochineal was high and very damaging to O. aurantiaca over the course of the experiment. Releasing during wet periods, when the agent is less effective, could augment agent populations at a time when natural populations would be low, and hence improve levels of control further. Although this study was limited to a short period of two years, the results of this study suggest that the number of releases is less important than the timing of releases. Releasing immediately after periods of high rainfall is likely to be beneficial, while releasing during dry periods, or during winter when temperatures are low, is less effective. Dactylopius austrinus populations should be constantly monitored so that releases can be conducted when cochineal populations are low and the climatic conditions are correct. If the timing of release events is appropriate, then the over level of control of O. aurantiaca using D. austrinus could be improved.
- Full Text:
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:
- 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:
Biological properties and interactions of Kalaharituber pfeilii
- Authors: Krele, Viwe
- Date: 2019
- Subjects: Kalaharituber pfeilii , Pezizales -- South Africa , Desert plants -- South Africa , Truffle culture -- South Africa , Plant biochemical genetics , Enzymes -- Analysis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72257 , vital:30022
- Description: Dessert truffles are seasonal macro fungi and have been identified in several parts of the world including South Africa. The first part of the present study dealt with the assessment of the biologically active compounds of the Kalahari truffles found in the Northern Cape of South Africa. Truffles extracts (methanol, ethanol, aqueous) were investigated for their antimicrobial properties towards Gram-positive and Gram-negative bacteria. The results demonstrated that the truffle extracts tested had no inhibitory effects against the bacterial isolates. The truffle mycelial growth was also noted to be ineffective against the selected bacteria. The bacteria tested in the present study showed some antagonistic effects against the fungus. Cultures of K. pfeilii were also screened for enzyme production including amylase, protease, cellulose, and laccase. Evaluation of the potential of K. pfeilii mycelia to produce these industrially and economically important enzymes demonstrated both amylase and protease activity. However, for laccase and cellulose, no activity was detected. The second part of the present study aimed at optimizing biomass production by K. pfeilii in liquid culture media. FF Microplate containing 95 discreet carbon sources were employed to test for substrate utilization. Blanked readings above 0.1 were regarded as positive for utilization, and 4 substrates were selected as potential substrates and were included in liquid media. Media was evaluated for mycelial biomass production. Of the carbon sources tested sucrose proved to be the most suitable for supporting mycelial growth. The third part of the current study included investigating the diversity of microbial communities colonizing the rhizosheath of Stipagrostis ciliata var. capensis (the host plant of K. pfeilii) and these were identified by means of next-generation sequencing using Illumina Miseq. Bioinformatics tools were utilized in analyzing the data. Actinobacteria were found to be the most dominant bacterial phylum, followed by unclassified bacteria, Proteobacteria, and Acidobacteria. The top 25 sequences were selected and clustered into bacterial OTUs (at 97% threshold) which were assigned into 1 phylum (Actinobacteria), 1 family (Geodermatophilaceae) and 23 genera. This phylum is well known for its secondary metabolites. Streptomyces sp. was the most frequently encountered genus. The results from this study necessitate further investigations with regards to the function and evolution of fungal-bacterial associations. Wheather these bacteria have a contribution towards the truffle development, it is still not confirmed.
- Full Text:
- Authors: Krele, Viwe
- Date: 2019
- Subjects: Kalaharituber pfeilii , Pezizales -- South Africa , Desert plants -- South Africa , Truffle culture -- South Africa , Plant biochemical genetics , Enzymes -- Analysis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72257 , vital:30022
- Description: Dessert truffles are seasonal macro fungi and have been identified in several parts of the world including South Africa. The first part of the present study dealt with the assessment of the biologically active compounds of the Kalahari truffles found in the Northern Cape of South Africa. Truffles extracts (methanol, ethanol, aqueous) were investigated for their antimicrobial properties towards Gram-positive and Gram-negative bacteria. The results demonstrated that the truffle extracts tested had no inhibitory effects against the bacterial isolates. The truffle mycelial growth was also noted to be ineffective against the selected bacteria. The bacteria tested in the present study showed some antagonistic effects against the fungus. Cultures of K. pfeilii were also screened for enzyme production including amylase, protease, cellulose, and laccase. Evaluation of the potential of K. pfeilii mycelia to produce these industrially and economically important enzymes demonstrated both amylase and protease activity. However, for laccase and cellulose, no activity was detected. The second part of the present study aimed at optimizing biomass production by K. pfeilii in liquid culture media. FF Microplate containing 95 discreet carbon sources were employed to test for substrate utilization. Blanked readings above 0.1 were regarded as positive for utilization, and 4 substrates were selected as potential substrates and were included in liquid media. Media was evaluated for mycelial biomass production. Of the carbon sources tested sucrose proved to be the most suitable for supporting mycelial growth. The third part of the current study included investigating the diversity of microbial communities colonizing the rhizosheath of Stipagrostis ciliata var. capensis (the host plant of K. pfeilii) and these were identified by means of next-generation sequencing using Illumina Miseq. Bioinformatics tools were utilized in analyzing the data. Actinobacteria were found to be the most dominant bacterial phylum, followed by unclassified bacteria, Proteobacteria, and Acidobacteria. The top 25 sequences were selected and clustered into bacterial OTUs (at 97% threshold) which were assigned into 1 phylum (Actinobacteria), 1 family (Geodermatophilaceae) and 23 genera. This phylum is well known for its secondary metabolites. Streptomyces sp. was the most frequently encountered genus. The results from this study necessitate further investigations with regards to the function and evolution of fungal-bacterial associations. Wheather these bacteria have a contribution towards the truffle development, it is still not confirmed.
- Full Text:
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:
- 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:
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:
- 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:
Chitin hydrolysis with chitinolytic enzymes for the production of chitooligomers with antimicrobial properties
- Authors: Oree, Glynis
- Date: 2019
- Subjects: Chitin -- Biotechnology , Enzymes -- Biotechnology , Hydrolysis , Chitooligomers -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67887 , vital:29165
- Description: There are many diseases and illnesses in the world that require new drug treatments and chitin has been shown to produce chitooligomeric derivatives which exhibit promising antimicrobial and immune-enhancing properties. However, the rate-limiting step is associated with the high recalcitrance of chitinous substrates, and low hydrolytic activities of chitinolytic enzymes, resulting in low product release. To improve and create a more sustainable and economical process, enhancing chitin hydrolysis through various treatment procedures is essential for obtaining high enzyme hydrolysis rates, resulting in a higher yield of chitooligomers (CHOS). In literature, pre-treatment of insoluble biomass is generally associated with an increase in accessibility of the carbohydrate to hydrolytic enzymes, thus generating more products. The first part of this study investigated the effect of alkali- (NaOH) and acid pre-treatments (HCl and phosphoric acid) on chitin biomass, and chemical and morphological modifications were assessed by the employment of scanning electron microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), Energy-Dispersive X-ray spectrometery (EDX) and x-ray diffraction (XRD). Data obtained confirmed that pre-treated substrates were more chemically and morphologically modified. These results confirmed the fact that pre-treatment of chitin disrupts the structure of the biomass, rendering the polymer more accessible for enzymatic hydrolysis. The commercial chitinases from Bacillus cereus and Streptomyces griseus (CHB and CHS) are costly. Bio-prospecting for other chitin-degrading enzymes from alternate sources such as Oidiodendron maius, or the recombinant expression of CHOS, was a more economically feasible avenue. The chit1 gene from Thermomyces lanuginosus, expressed in Pichia pastoris, produced a large range CHOS with a degree of polymerisation (DP) ranging from 1 to above 6. TLC analysis showed that O. maius exhibited chitin-degrading properties by producing CHOS with a DP length of 1 to 3. These two sources were therefore successful in producing chitin-degrading enzymes. The physico-chemical properties of commercial (CHB and CHS) and expressed (Chit1) chitinolytic enzymes were investigated, to determine under which biochemical conditions and on which type of biomass they can function on optimally, for the production of value-added products such as CHOS. Substrate affinity assays were conducted on the un-treated and pre-treated biomass. TLC revealed that chitosan hydrolysis by the commercial chitinases produced the largest range of CHOS with a DP length ranging from 1 to 6. A range of temperatures (35-90oC) were investigated and CHB, CHS and Chit1 displayed optimum activities at 50, 40 and 45 oC, respectively. Thermostability studies that were conducted at 37 and 50oC revealed that CHB and CHS were most stable at 37oC. Chit1 showed great thermostablity at both temperatures, rendering this enzyme suitable for industrial processes at high temperatures. pH optima studies demonstrated that the pH optima for CHB, CHS and Chit1 was at a pH of 5.0, with specific activities of 33.459, 46.2 and 5.776 μmol/h/mg, respectively. The chain cleaving patterns of the commercial enzymes were determined and exo-chitinase activity was exhibited, due to the production of CHOS that were predominantly of a DP length of 2. Enzyme binary synergy studies were conducted with commercial chitinases (CHB and CHS) on colloidal chitin. Studies illustrated that the simultaneous combination of CHB 75%: CHS 25% produced the highest specific activity (3.526 μmol/h/mg), with no synergy. TLC analysis of this enzyme combination over time revealed that predominantly chitobiose was produced. This suggested that the substrate crystallinity and morphology played an important role in the way the enzymes cleaved the carbohydrate. Since CHOS have shown great promise for their antimicrobial properties, the CHOS generated from the chitinous substrates were tested for antimicrobial properties on Bacillus subtilis, Escherichia coli, Klebsiella and Staphlococcus aureus. This study revealed that certain CHOS produced have inhibitory effects on certain bacteria and could potentially be used in the pharamceutical or medical industries. In conclusion, this study revealed that chitinases can be produced and found in alternate sources and be used for the hydrolysis of chitinous biomass in a more sustainabe and economically viable manner. The chitinases investigated (CHB, CHS and Chit1) exhibited different cleaving patterns of the chitinous substrates due to the chemical and morphological properties of the biomass. CHOS produced from chitinous biomass exhibited some inhibitory effects on bacterial growth and show potential for use in the medical industry.
- Full Text:
- Authors: Oree, Glynis
- Date: 2019
- Subjects: Chitin -- Biotechnology , Enzymes -- Biotechnology , Hydrolysis , Chitooligomers -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67887 , vital:29165
- Description: There are many diseases and illnesses in the world that require new drug treatments and chitin has been shown to produce chitooligomeric derivatives which exhibit promising antimicrobial and immune-enhancing properties. However, the rate-limiting step is associated with the high recalcitrance of chitinous substrates, and low hydrolytic activities of chitinolytic enzymes, resulting in low product release. To improve and create a more sustainable and economical process, enhancing chitin hydrolysis through various treatment procedures is essential for obtaining high enzyme hydrolysis rates, resulting in a higher yield of chitooligomers (CHOS). In literature, pre-treatment of insoluble biomass is generally associated with an increase in accessibility of the carbohydrate to hydrolytic enzymes, thus generating more products. The first part of this study investigated the effect of alkali- (NaOH) and acid pre-treatments (HCl and phosphoric acid) on chitin biomass, and chemical and morphological modifications were assessed by the employment of scanning electron microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), Energy-Dispersive X-ray spectrometery (EDX) and x-ray diffraction (XRD). Data obtained confirmed that pre-treated substrates were more chemically and morphologically modified. These results confirmed the fact that pre-treatment of chitin disrupts the structure of the biomass, rendering the polymer more accessible for enzymatic hydrolysis. The commercial chitinases from Bacillus cereus and Streptomyces griseus (CHB and CHS) are costly. Bio-prospecting for other chitin-degrading enzymes from alternate sources such as Oidiodendron maius, or the recombinant expression of CHOS, was a more economically feasible avenue. The chit1 gene from Thermomyces lanuginosus, expressed in Pichia pastoris, produced a large range CHOS with a degree of polymerisation (DP) ranging from 1 to above 6. TLC analysis showed that O. maius exhibited chitin-degrading properties by producing CHOS with a DP length of 1 to 3. These two sources were therefore successful in producing chitin-degrading enzymes. The physico-chemical properties of commercial (CHB and CHS) and expressed (Chit1) chitinolytic enzymes were investigated, to determine under which biochemical conditions and on which type of biomass they can function on optimally, for the production of value-added products such as CHOS. Substrate affinity assays were conducted on the un-treated and pre-treated biomass. TLC revealed that chitosan hydrolysis by the commercial chitinases produced the largest range of CHOS with a DP length ranging from 1 to 6. A range of temperatures (35-90oC) were investigated and CHB, CHS and Chit1 displayed optimum activities at 50, 40 and 45 oC, respectively. Thermostability studies that were conducted at 37 and 50oC revealed that CHB and CHS were most stable at 37oC. Chit1 showed great thermostablity at both temperatures, rendering this enzyme suitable for industrial processes at high temperatures. pH optima studies demonstrated that the pH optima for CHB, CHS and Chit1 was at a pH of 5.0, with specific activities of 33.459, 46.2 and 5.776 μmol/h/mg, respectively. The chain cleaving patterns of the commercial enzymes were determined and exo-chitinase activity was exhibited, due to the production of CHOS that were predominantly of a DP length of 2. Enzyme binary synergy studies were conducted with commercial chitinases (CHB and CHS) on colloidal chitin. Studies illustrated that the simultaneous combination of CHB 75%: CHS 25% produced the highest specific activity (3.526 μmol/h/mg), with no synergy. TLC analysis of this enzyme combination over time revealed that predominantly chitobiose was produced. This suggested that the substrate crystallinity and morphology played an important role in the way the enzymes cleaved the carbohydrate. Since CHOS have shown great promise for their antimicrobial properties, the CHOS generated from the chitinous substrates were tested for antimicrobial properties on Bacillus subtilis, Escherichia coli, Klebsiella and Staphlococcus aureus. This study revealed that certain CHOS produced have inhibitory effects on certain bacteria and could potentially be used in the pharamceutical or medical industries. In conclusion, this study revealed that chitinases can be produced and found in alternate sources and be used for the hydrolysis of chitinous biomass in a more sustainabe and economically viable manner. The chitinases investigated (CHB, CHS and Chit1) exhibited different cleaving patterns of the chitinous substrates due to the chemical and morphological properties of the biomass. CHOS produced from chitinous biomass exhibited some inhibitory effects on bacterial growth and show potential for use in the medical industry.
- Full Text:
Climatic suitability of Dichrorampha odorata Brown and Zachariades (Lepidoptera: Tortricidae), a shoot-boring moth for the biological control of Chromolaena odorata (L.) R.M. King and H. Robinson (Asteraceae) in South Africa
- Authors: Nqayi, Slindile Brightness
- Date: 2019
- Subjects: CLIMEX , Chromolaena odorata -- Biological control -- South Africa , Tortricidae -- South Africa , Bioclimatology -- Software
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92208 , vital:30681
- Description: Biological control using natural enemies introduced from the native range is an integral component of the management of Chromolaena odorata, a serious invader in the eastern regions of South Africa. A number of biological control agents for C. odorata have been released in South Africa, and one of them, Dichrorampha odorata, has failed to establish. To understand if D. odorata failed to establish due to climate incompatibility, its thermal physiology was investigated. Thermal tolerance data were used to determine the developmental thresholds and number of generations that D. odorata is capable of going through in South Africa per year. These predictions were generated using CLIMEX temperature data and the degree-day parameters K and t0. Developmental time decreased with increasing temperatures ranging from 20 °C to 30°C, with immature stages not able to complete development at 18°C and 32°C. The developmental threshold, to, was determined as 8.45 °C with 872.4 degree-days required to complete development (K), indicating that D. odorata is capable of producing a maximum number of 6.5 generations per year in South Africa. The CLIMEX data indicated that the east coast regions of South Africa, which are the heaviest invaded areas by C. odorata in South Africa, were climatically most suitable for D. odorata to. D. odorata lower (LLT50) and upper (ULT50) lethal temperatures were -4.5°C and 39.64°C for larvae and 1.83 and 41.02°C for adults, and D. odorata adults were able to maintain locomotory functioning at 4.4 to 43.7°C, respectively. Acclimation at low and high temperatures indicate that when D. odorata was kept at a lower temperature of 20°C for 7 days, it became tolerant to warmer and cooler temperatures (1.95 and 44.41°C) when compared to D. odorata reared at 25°C (3.36 and 43.67°C) and 30°C (5.92 and 42.93°C). Dichrorampha odorata is therefore climatically suitable for release and should establish in South Africa to control C. odorata. The establishment and persistence of D. odorata will not be limited by climatic conditions but rather the distribution of its host weed, C. odorata in South Africa. Also, this study presents a decision-making protocol for the release of D. odorata to allow better performance in the field.
- Full Text:
- Authors: Nqayi, Slindile Brightness
- Date: 2019
- Subjects: CLIMEX , Chromolaena odorata -- Biological control -- South Africa , Tortricidae -- South Africa , Bioclimatology -- Software
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92208 , vital:30681
- Description: Biological control using natural enemies introduced from the native range is an integral component of the management of Chromolaena odorata, a serious invader in the eastern regions of South Africa. A number of biological control agents for C. odorata have been released in South Africa, and one of them, Dichrorampha odorata, has failed to establish. To understand if D. odorata failed to establish due to climate incompatibility, its thermal physiology was investigated. Thermal tolerance data were used to determine the developmental thresholds and number of generations that D. odorata is capable of going through in South Africa per year. These predictions were generated using CLIMEX temperature data and the degree-day parameters K and t0. Developmental time decreased with increasing temperatures ranging from 20 °C to 30°C, with immature stages not able to complete development at 18°C and 32°C. The developmental threshold, to, was determined as 8.45 °C with 872.4 degree-days required to complete development (K), indicating that D. odorata is capable of producing a maximum number of 6.5 generations per year in South Africa. The CLIMEX data indicated that the east coast regions of South Africa, which are the heaviest invaded areas by C. odorata in South Africa, were climatically most suitable for D. odorata to. D. odorata lower (LLT50) and upper (ULT50) lethal temperatures were -4.5°C and 39.64°C for larvae and 1.83 and 41.02°C for adults, and D. odorata adults were able to maintain locomotory functioning at 4.4 to 43.7°C, respectively. Acclimation at low and high temperatures indicate that when D. odorata was kept at a lower temperature of 20°C for 7 days, it became tolerant to warmer and cooler temperatures (1.95 and 44.41°C) when compared to D. odorata reared at 25°C (3.36 and 43.67°C) and 30°C (5.92 and 42.93°C). Dichrorampha odorata is therefore climatically suitable for release and should establish in South Africa to control C. odorata. The establishment and persistence of D. odorata will not be limited by climatic conditions but rather the distribution of its host weed, C. odorata in South Africa. Also, this study presents a decision-making protocol for the release of D. odorata to allow better performance in the field.
- Full Text:
Determining the hydrological functioning of the palmiet wetlands in the Eastern and Western Cape South Africa
- Authors: Smith, Caitlin
- Date: 2019
- Subjects: Wetlands -- South Africa -- Eastern Cape , Wetland ecology -- South Africa -- Eastern Cape , Wetland management -- South Africa -- Eastern Cape , Prioniaceae -- South Africa -- Eastern Cape , Prionium serratum -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95956 , vital:31218
- Description: Wetlands provide a range of supporting, regulating and provisioning ecosystem services, including hydrological benefits such as flood attenuation and sustaining base flows. Despite their value, wetlands are one of the most vulnerable ecosystems in South Africa. Palmiet wetlands in the Eastern and Western Cape are particularly threatened. Palmiet (Prionium serratum) is a robust perennial plant that is endemic to wetlands and rivers located in the sandstones and quartzites of the Table Mountain Group (TMG), in the Eastern and Western Cape as well as the Natal Group sandstones in KwaZulu-Natal. Palmiet is described as an ecosystem engineer because of its ability to alter its environment and create large valley-bottom wetlands. The Krom River is an important water source for the city of Port Elizabeth and there has been a decline in palmiet wetlands along the Krom River as a result of alien vegetation invasion, agricultural activity, and gully erosion. Working for Water has been clearing alien vegetation and Working for Wetlands has been installing rehabilitation structures in the Krom River catchment for a number of years. There are, however, serious knowledge gaps in the understanding of palmiet wetland structure and function, particularly in respect of the hydrological functioning of these wetland systems. The aim of this study was to investigate the hydrology (surface and groundwater) behind these wetland systems. The investigation focussed on small-scale dynamics of the palmiet wetland system in order to increase general understanding of the surface water and groundwater processes of these wetland systems. Field work was concentrated on the Kompanjiesdrif and Krugersland palmiet wetlands in the upper K90A Krom River catchment. The investigation involved the installation of piezometers, water quality and stable isotope sampling and analysis, an Electrical Resistivity Tomography survey, and hydrological and mixing cell modelling. The results of the investigation indicate that the hydrological functioning of palmiet wetlands is closely linked with high sub-surface discharges typically associated with TMG aquifers. It is proposed that the palmiet wetlands are sustained by significant amounts of sub-surface water (both groundwater and interflow) moving through preferential flow paths in the alluvial fans and tributaries, which are in turn sustained by groundwater discharge from the surrounding sandstones and quartzites of the Nardouw Sub-group and Peninsula Formation. The palmiet wetlands clearly retain a significant amount of water, leading to the maintenance of prolonged flows, and a larger baseflow. However, it is hypothesised that the occurrence of palmiet as the dominant species in these wetlands is due to the sustained low flows related to catchment geology and high hydrological connectivity between the catchment and the wetland that is enabled by flow paths that allow the free flow of water from the catchment to the wetland. It is further proposed that palmiet is possibly more reliant on a consistent water supply for its existence and survival than it is on acidic nutrient-poor water and soils as stated by other authors.
- Full Text:
- Authors: Smith, Caitlin
- Date: 2019
- Subjects: Wetlands -- South Africa -- Eastern Cape , Wetland ecology -- South Africa -- Eastern Cape , Wetland management -- South Africa -- Eastern Cape , Prioniaceae -- South Africa -- Eastern Cape , Prionium serratum -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95956 , vital:31218
- Description: Wetlands provide a range of supporting, regulating and provisioning ecosystem services, including hydrological benefits such as flood attenuation and sustaining base flows. Despite their value, wetlands are one of the most vulnerable ecosystems in South Africa. Palmiet wetlands in the Eastern and Western Cape are particularly threatened. Palmiet (Prionium serratum) is a robust perennial plant that is endemic to wetlands and rivers located in the sandstones and quartzites of the Table Mountain Group (TMG), in the Eastern and Western Cape as well as the Natal Group sandstones in KwaZulu-Natal. Palmiet is described as an ecosystem engineer because of its ability to alter its environment and create large valley-bottom wetlands. The Krom River is an important water source for the city of Port Elizabeth and there has been a decline in palmiet wetlands along the Krom River as a result of alien vegetation invasion, agricultural activity, and gully erosion. Working for Water has been clearing alien vegetation and Working for Wetlands has been installing rehabilitation structures in the Krom River catchment for a number of years. There are, however, serious knowledge gaps in the understanding of palmiet wetland structure and function, particularly in respect of the hydrological functioning of these wetland systems. The aim of this study was to investigate the hydrology (surface and groundwater) behind these wetland systems. The investigation focussed on small-scale dynamics of the palmiet wetland system in order to increase general understanding of the surface water and groundwater processes of these wetland systems. Field work was concentrated on the Kompanjiesdrif and Krugersland palmiet wetlands in the upper K90A Krom River catchment. The investigation involved the installation of piezometers, water quality and stable isotope sampling and analysis, an Electrical Resistivity Tomography survey, and hydrological and mixing cell modelling. The results of the investigation indicate that the hydrological functioning of palmiet wetlands is closely linked with high sub-surface discharges typically associated with TMG aquifers. It is proposed that the palmiet wetlands are sustained by significant amounts of sub-surface water (both groundwater and interflow) moving through preferential flow paths in the alluvial fans and tributaries, which are in turn sustained by groundwater discharge from the surrounding sandstones and quartzites of the Nardouw Sub-group and Peninsula Formation. The palmiet wetlands clearly retain a significant amount of water, leading to the maintenance of prolonged flows, and a larger baseflow. However, it is hypothesised that the occurrence of palmiet as the dominant species in these wetlands is due to the sustained low flows related to catchment geology and high hydrological connectivity between the catchment and the wetland that is enabled by flow paths that allow the free flow of water from the catchment to the wetland. It is further proposed that palmiet is possibly more reliant on a consistent water supply for its existence and survival than it is on acidic nutrient-poor water and soils as stated by other authors.
- Full Text:
Effect of substituents on the photophysical properties and nonlinear optical properties of asymmetrical zinc(II) phthalocyanine when conjugated to semiconductor quantum dots
- Authors: Mgidlana, Sithi
- Date: 2019
- Subjects: Nonlinear optics , Quantum dots , Phthalocyanines , Zinc
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97152 , vital:31404
- Description: Various characterization techniques have been used to characterize the synthesized asymmetrical zinc phthalocyanines (ZnPc) derivatives. Techniques include Ultraviolet-visible (UV-vis) spectrophotometry, matrix assisted laser desorption time of flight mass spectrometry (MALD-TOF MS), proton nuclear magnetic resonance (1H-NMR), elemental analysis and Fourier-transform infra-red spectroscopy (FT-IR). The complexes are covalently linked to core/shell and core/shell/shell semiconductor quantum dots (SQDs) via amide bond formation. Photophysical properties of complexes improved in the presence of semiconductor quantum dots (SQDs). SQDs contain cadmium/telluride (CdTe) as core, coated in the first shell with zinc selenide (ZnSe) or zinc sulfide (ZnS) and with zinc oxide (ZnO) in second shell. The photophysical properties of the phthalocyanine (Pc) complexes and their conjugates with SQDs are investigated in solution. Triplet quantum yields of complexes improved in the presence of semiconductor quantum dots. The optical limiting behaviour of the Pc complexes and conjugates are assessed using the open aperture Z–scan technique at laser excitation wavelength of 532 nm with 10 ns pulse. Pcs complexes showed good nonlinear optical response with higher nonlinear absorption coefficient. The conjugates afforded higher nonlinear absorption coefficient than Pc complexes alone.
- Full Text:
- Authors: Mgidlana, Sithi
- Date: 2019
- Subjects: Nonlinear optics , Quantum dots , Phthalocyanines , Zinc
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97152 , vital:31404
- Description: Various characterization techniques have been used to characterize the synthesized asymmetrical zinc phthalocyanines (ZnPc) derivatives. Techniques include Ultraviolet-visible (UV-vis) spectrophotometry, matrix assisted laser desorption time of flight mass spectrometry (MALD-TOF MS), proton nuclear magnetic resonance (1H-NMR), elemental analysis and Fourier-transform infra-red spectroscopy (FT-IR). The complexes are covalently linked to core/shell and core/shell/shell semiconductor quantum dots (SQDs) via amide bond formation. Photophysical properties of complexes improved in the presence of semiconductor quantum dots (SQDs). SQDs contain cadmium/telluride (CdTe) as core, coated in the first shell with zinc selenide (ZnSe) or zinc sulfide (ZnS) and with zinc oxide (ZnO) in second shell. The photophysical properties of the phthalocyanine (Pc) complexes and their conjugates with SQDs are investigated in solution. Triplet quantum yields of complexes improved in the presence of semiconductor quantum dots. The optical limiting behaviour of the Pc complexes and conjugates are assessed using the open aperture Z–scan technique at laser excitation wavelength of 532 nm with 10 ns pulse. Pcs complexes showed good nonlinear optical response with higher nonlinear absorption coefficient. The conjugates afforded higher nonlinear absorption coefficient than Pc complexes alone.
- Full Text:
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:
- 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.
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Exploration of challenges in bringing traditional medicine into SA’s healthcare system, using medicinal plants for treatment of waterborne diarrhoeal diseases as a case study
- Authors: Keche, Priscilla
- Date: 2019
- Subjects: Traditional medicine -- South Africa , Waterborne infection -- South Africa , Diarrhea -- South Africa , Healers -- South Africa , Medical care -- Quality control , Medicinal plants -- South Africa , Diarrhea in children -- South Africa , World Health Organization
- Language: English
- Type: thesis , text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/118035 , vital:34588
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre (RUBIC), 2019.
- Full Text:
- Authors: Keche, Priscilla
- Date: 2019
- Subjects: Traditional medicine -- South Africa , Waterborne infection -- South Africa , Diarrhea -- South Africa , Healers -- South Africa , Medical care -- Quality control , Medicinal plants -- South Africa , Diarrhea in children -- South Africa , World Health Organization
- Language: English
- Type: thesis , text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/118035 , vital:34588
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre (RUBIC), 2019.
- Full Text:
Factors influencing survivorship of Portulacaria afra cuttings in restoration of degraded lands
- Authors: Sholto-Douglas, Craig
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92230 , vital:30692
- Description: Heavy over-browsing, over-grazing, and over-trampling has caused the degradation of vast areas of subtropical thicket, including parts of the Greater Addo Elephant National Park (GAENP). Severe degradation has resulted in the loss of vegetation cover and the deterioration of soils and soil functioning. The South African Department of Environmental Affairs (DEA), and specifically the Natural Resource Management Programme (NRM), have invested in restoration initiatives such as the Subtropical Thicket Restoration Programme (STRP), which has aimed to demonstrate the logistical and practical feasibility of restoring these degraded thickets by planting en masse Portulacaria afra (spekboom) cuttings. However, the planted P. afra cuttings often succumb to various abiotic and biotic stresses. This project aimed to identify various factors which may influence the survival of P. afra cuttings, including i) soil properties, ii) water (rainfall, infiltration, run-off, etc.), iii) browsing by mega-herbivores, iv) topographical features such as slope and aspect, or v) plant species or communities. Biodiversity and carbon baselines were carried out at 50 plots within the Main Camp, Darlington and Kabouga sections of the GAENP, providing pre-planting vegetation and soil data. The en masse planting of P. afra occurred following the completion of the baselines. Following a minimum rest period of three months after planting, survivorship counts were carried out at all plots. Infiltration rate had a significant positive relationship with planted P. afra survivorship across all of the sites. Positive trends between increases in litter and root biomass and planted P. afra cuttings survivorship in Kabouga were also evident. Magnesium, water-holding capacity and increasing soil clay percentage were found to have a significant negative relationship with planted P. afra survivorship in Kabouga. Aluminium, magnesium, and boron all had significant positive relationships with planted P. afra cuttings survivorship in Addo Main Camp. No soil variables had any significant relationship with survivorship of planted P. afra cuttings at Darlington. The presence of elephants (Loxidonta africana) had a significant negative relationship with planted P. afra survivorship. Plant communities in more ‘moderately’ degraded states, characterized by the retention of canopy dominant species, woody vegetation cover, limited bareground and higher cover of litter had higher survivorship of planted P. afra cuttings than those in more severely degraded states. The grass Panicum maximum, and forb Atriplex semibaccata were associated with positive relationships with planted P. afra survivorship across all sites. Future research should aim to develop matrices which plot likely survivorship percentages with parameters of measurable variables, such as infiltration, severity of soil capping, browsing densities, chemical indicators, and degradation severity, to identify suitable biophysical planting conditions for P. afra cuttings. Further research should assess whether the presence of elephants, in high densities, can reduce the economic feasibility of the en masse plantings of P. afra cuttings in attempts to restore degraded landscapes.
- Full Text:
- Authors: Sholto-Douglas, Craig
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92230 , vital:30692
- Description: Heavy over-browsing, over-grazing, and over-trampling has caused the degradation of vast areas of subtropical thicket, including parts of the Greater Addo Elephant National Park (GAENP). Severe degradation has resulted in the loss of vegetation cover and the deterioration of soils and soil functioning. The South African Department of Environmental Affairs (DEA), and specifically the Natural Resource Management Programme (NRM), have invested in restoration initiatives such as the Subtropical Thicket Restoration Programme (STRP), which has aimed to demonstrate the logistical and practical feasibility of restoring these degraded thickets by planting en masse Portulacaria afra (spekboom) cuttings. However, the planted P. afra cuttings often succumb to various abiotic and biotic stresses. This project aimed to identify various factors which may influence the survival of P. afra cuttings, including i) soil properties, ii) water (rainfall, infiltration, run-off, etc.), iii) browsing by mega-herbivores, iv) topographical features such as slope and aspect, or v) plant species or communities. Biodiversity and carbon baselines were carried out at 50 plots within the Main Camp, Darlington and Kabouga sections of the GAENP, providing pre-planting vegetation and soil data. The en masse planting of P. afra occurred following the completion of the baselines. Following a minimum rest period of three months after planting, survivorship counts were carried out at all plots. Infiltration rate had a significant positive relationship with planted P. afra survivorship across all of the sites. Positive trends between increases in litter and root biomass and planted P. afra cuttings survivorship in Kabouga were also evident. Magnesium, water-holding capacity and increasing soil clay percentage were found to have a significant negative relationship with planted P. afra survivorship in Kabouga. Aluminium, magnesium, and boron all had significant positive relationships with planted P. afra cuttings survivorship in Addo Main Camp. No soil variables had any significant relationship with survivorship of planted P. afra cuttings at Darlington. The presence of elephants (Loxidonta africana) had a significant negative relationship with planted P. afra survivorship. Plant communities in more ‘moderately’ degraded states, characterized by the retention of canopy dominant species, woody vegetation cover, limited bareground and higher cover of litter had higher survivorship of planted P. afra cuttings than those in more severely degraded states. The grass Panicum maximum, and forb Atriplex semibaccata were associated with positive relationships with planted P. afra survivorship across all sites. Future research should aim to develop matrices which plot likely survivorship percentages with parameters of measurable variables, such as infiltration, severity of soil capping, browsing densities, chemical indicators, and degradation severity, to identify suitable biophysical planting conditions for P. afra cuttings. Further research should assess whether the presence of elephants, in high densities, can reduce the economic feasibility of the en masse plantings of P. afra cuttings in attempts to restore degraded landscapes.
- Full Text: