An information extraction model for recommending the most applied case
- Authors: Padayachy, Thashen
- Date: 2019
- Subjects: Information technology , Information storage and retrieval systems System design
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43325 , vital:36794
- Description: The amount of information produced by different domains is constantly increasing. One domain that particularly produces large amounts of information is the legal domain, where information is mainly used for research purposes. However, too much time is spent by legal researchers on searching for useful information. Information is found by using special search engines or by consulting hard copies of legal literature. The main research question that this study addressed is “What techniques can be incorporated into a model that recommends the most applied case for a field of law?”. The Design Science Research (DSR) methodology was used to address the research objectives. The model developed is the theoretical contribution produced from following the DSR methodology. A case study organisation, called LexisNexis, was to help investigate the real-world problem. The initial investigation into the real-world problem revealed that too much time is spent on searching for the Most Applied Case (MAC) and no formal or automated processes were used. An analysis of an informal process followed by legal researchers enabled the identification of different concepts that could be combined to create a prescriptive model to recommend the MAC. A critical analysis of the literature was conducted to obtain a better understanding of the legal domain and the techniques that can be applied to assist with problems faced in this domain, related to information retrieval and extraction. This resulted in the creation of an IE Model based only on theory. Questionnaires were sent to experts to obtain a further understanding of the legal domain, highlight problems faced, and identify which attributes of a legal case can be used to help recommend the MAC. During the Design and Development activity of the DSR methodology, a prescriptive MAC Model for recommending the MAC was created based on findings from the literature review and questionnaires. The MAC Model consists of processes concerning: Information retrieval (IR); Information extraction (IE); Information storage; and Query-independent ranking. Analysis of IR and IE helped to identify problems experienced when processing text. Furthermore, appropriate techniques and algorithms were identified that can process legal documents and extract specific facts. The extracted facts were then further processed to allow for storage and processing by query-independent ranking algorithms. The processes incorporated into the model were then used to create a proof-of-concept prototype called the IE Prototype. The IE Prototype implements two processes called the IE process and the Database process. The IE process analyses different sections of a legal case to extract specific facts. The Database process then ensures that the extracted facts are stored in a document database for future querying purposes. The IE Prototype was evaluated using the technical risk and efficacy strategy from the Framework for Evaluation of Design Science. Both formative and summative evaluations were conducted. Formative evaluations were conducted to identify functional issues of the prototype whilst summative evaluations made use of real-world legal cases to test the prototype. Multiple experiments were conducted on legal cases, known as source cases, that resulted in facts from the source cases being extracted. For the purpose of the experiments, the term “source case” was used to distinguish between a legal case in its entirety and a legal case’s list of cases referred to. Two types of NoSQL databases were investigated for implementation namely, a graph database and a document database. Setting up the graph database required little time. However, development issues prevented the graph database from being successfully implemented in the proof-of-concept prototype. A document database was successfully implemented as an alternative for the proof-of-concept prototype. Analysis of the source cases used to evaluate the IE Prototype revealed that 96% of the source cases were categorised as being partially extracted. The results also revealed that the IE Prototype was capable of processing large amounts of source cases at a given time.
- Full Text:
- Date Issued: 2019
- Authors: Padayachy, Thashen
- Date: 2019
- Subjects: Information technology , Information storage and retrieval systems System design
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43325 , vital:36794
- Description: The amount of information produced by different domains is constantly increasing. One domain that particularly produces large amounts of information is the legal domain, where information is mainly used for research purposes. However, too much time is spent by legal researchers on searching for useful information. Information is found by using special search engines or by consulting hard copies of legal literature. The main research question that this study addressed is “What techniques can be incorporated into a model that recommends the most applied case for a field of law?”. The Design Science Research (DSR) methodology was used to address the research objectives. The model developed is the theoretical contribution produced from following the DSR methodology. A case study organisation, called LexisNexis, was to help investigate the real-world problem. The initial investigation into the real-world problem revealed that too much time is spent on searching for the Most Applied Case (MAC) and no formal or automated processes were used. An analysis of an informal process followed by legal researchers enabled the identification of different concepts that could be combined to create a prescriptive model to recommend the MAC. A critical analysis of the literature was conducted to obtain a better understanding of the legal domain and the techniques that can be applied to assist with problems faced in this domain, related to information retrieval and extraction. This resulted in the creation of an IE Model based only on theory. Questionnaires were sent to experts to obtain a further understanding of the legal domain, highlight problems faced, and identify which attributes of a legal case can be used to help recommend the MAC. During the Design and Development activity of the DSR methodology, a prescriptive MAC Model for recommending the MAC was created based on findings from the literature review and questionnaires. The MAC Model consists of processes concerning: Information retrieval (IR); Information extraction (IE); Information storage; and Query-independent ranking. Analysis of IR and IE helped to identify problems experienced when processing text. Furthermore, appropriate techniques and algorithms were identified that can process legal documents and extract specific facts. The extracted facts were then further processed to allow for storage and processing by query-independent ranking algorithms. The processes incorporated into the model were then used to create a proof-of-concept prototype called the IE Prototype. The IE Prototype implements two processes called the IE process and the Database process. The IE process analyses different sections of a legal case to extract specific facts. The Database process then ensures that the extracted facts are stored in a document database for future querying purposes. The IE Prototype was evaluated using the technical risk and efficacy strategy from the Framework for Evaluation of Design Science. Both formative and summative evaluations were conducted. Formative evaluations were conducted to identify functional issues of the prototype whilst summative evaluations made use of real-world legal cases to test the prototype. Multiple experiments were conducted on legal cases, known as source cases, that resulted in facts from the source cases being extracted. For the purpose of the experiments, the term “source case” was used to distinguish between a legal case in its entirety and a legal case’s list of cases referred to. Two types of NoSQL databases were investigated for implementation namely, a graph database and a document database. Setting up the graph database required little time. However, development issues prevented the graph database from being successfully implemented in the proof-of-concept prototype. A document database was successfully implemented as an alternative for the proof-of-concept prototype. Analysis of the source cases used to evaluate the IE Prototype revealed that 96% of the source cases were categorised as being partially extracted. The results also revealed that the IE Prototype was capable of processing large amounts of source cases at a given time.
- Full Text:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
An investigation into bile formation of Wistar rats for excretion of injected gold nanoparticles
- Authors: Thole, Sagoleka Thabo
- Date: 2019
- Subjects: Nanoparticles , Nanomedicine Gold -- Immunology Bile acids -- Physiological effect
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43900 , vital:37082
- Description: There is an increase in the use of nanoparticles (NPs) throughout the world. Gold nanoparticles (AuNPs) are commonly used NPs in the field of biomedicine. NPs bigger than 8 nm are excreted via the hepatobiliary system. Bile acids (BAs) are regarded as the main components of bile. If there is a decreased or increased secretion of BAs, the composition of microbiota in the gut can change. Under normal physiological condition BAs fluctuates daily without causing any harm. Nevertheless, it is the long-term changes in bile acid secretion that can affect microbiota in the gut. If there is an increased excretion of AuNPs via hepatobiliary pathway it can alter bile formation. The aim of this study was to investigate whether the hepatobiliary excretion of AuNPs will alter the bile formation two weeks after intravenous administration of 14 nm AuNPs to Wistar rats. Rat liver samples of two previous experiments were used to investigate bile formation. The rats had been injected intravenously with a single dose of citrate capped and functionalised AuNPs. These rats were killed 14 days later. Small pieces of liver were stored in RNAlater. The mRNA of different enzymes and transporters in the hepatobiliary system were quantified in these samples and compared with suitable control. As a reference the mRNA of the same enzymes and transporters were extracted and quantified in rat liver that were killed one day after injection with one of the abovementioned functionalised AuNPs. The study shows down-regulation of genes responsible for conjugation of BAs whereas the rate-limiting enzymes were not significantly changed. This was the first study to investigate the formation of bile in relation to the use of AuNPs. The effect and consequences of AuNPs on the hepatobiliary system need further investigation.
- Full Text:
- Date Issued: 2019
- Authors: Thole, Sagoleka Thabo
- Date: 2019
- Subjects: Nanoparticles , Nanomedicine Gold -- Immunology Bile acids -- Physiological effect
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43900 , vital:37082
- Description: There is an increase in the use of nanoparticles (NPs) throughout the world. Gold nanoparticles (AuNPs) are commonly used NPs in the field of biomedicine. NPs bigger than 8 nm are excreted via the hepatobiliary system. Bile acids (BAs) are regarded as the main components of bile. If there is a decreased or increased secretion of BAs, the composition of microbiota in the gut can change. Under normal physiological condition BAs fluctuates daily without causing any harm. Nevertheless, it is the long-term changes in bile acid secretion that can affect microbiota in the gut. If there is an increased excretion of AuNPs via hepatobiliary pathway it can alter bile formation. The aim of this study was to investigate whether the hepatobiliary excretion of AuNPs will alter the bile formation two weeks after intravenous administration of 14 nm AuNPs to Wistar rats. Rat liver samples of two previous experiments were used to investigate bile formation. The rats had been injected intravenously with a single dose of citrate capped and functionalised AuNPs. These rats were killed 14 days later. Small pieces of liver were stored in RNAlater. The mRNA of different enzymes and transporters in the hepatobiliary system were quantified in these samples and compared with suitable control. As a reference the mRNA of the same enzymes and transporters were extracted and quantified in rat liver that were killed one day after injection with one of the abovementioned functionalised AuNPs. The study shows down-regulation of genes responsible for conjugation of BAs whereas the rate-limiting enzymes were not significantly changed. This was the first study to investigate the formation of bile in relation to the use of AuNPs. The effect and consequences of AuNPs on the hepatobiliary system need further investigation.
- Full Text:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
Applications of complex functions on problems in Banach algebras
- Authors: Snyman, Jandré Dillon
- Date: 2019
- Subjects: Banach algebras , Functions of several complex variables
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48643 , vital:41055
- Description: In this dissertation, we provide applications of complex function theory to problems in Banach algebras. We discuss the structure of analytic functions f : D → A, where D is a domain of C and A is a Banach algebra as given by Aupetit in [3]: either the set {λ ∈ D : Sp(f(λ)) is finite} is of capacity zero, or there exists an integer n such that Sp(f(λ)) has exactly n elements, for every λ, except on a closed, discrete set of capacity zero, where the spectrum has at most n−1 elements. This deep result, which describes the structure of Sp(f(λ)) for all λ ∈ D, relies heavily on subharmonic techniques, which are also included in the dissertation. Let A and B be Banach algebras. A linear mapping φ : A → B is called a Jordan homomorphism if and only if φ(xy + yx) = φ(x)φ(y) + φ(y)φ(x) for every x, y ∈ A. This is equivalent to saying that φ(x 2 ) = φ(x) 2 for every x ∈ A. The following problem, due to I. Kaplansky, is still unsolved for the general Banach algebra case: Let A and B be unital Banach algebras and φ : A → B a unital, invertibility preserving linear mapping. Under what conditions of A and B is φ a Jordan homomorphism? The author’s honours project [24] served as an exposition of the GleasonKahane-Żelazko Theorem [7, Theorem 4], which provides an answer to Kaplansky’s problem in the case where B = C. In this dissertation we look at other special cases of Kaplansky’s problem, such as the case where A and B are von Neumann algberas, as solved by Aupetit [4, Theorem 1.3] and remark that his result holds for the more general case where A is any C ∗ -algebra that has the property that every self-adjoint element is the limit of a sequence of linear combinations of orthogonal idempotents in A, and B is a semi-simple Banach algebra. This result relies heavily on complex function theory, spectral theory and holomorphic functional calculus. We also provide detailed expositions of the work of Taylor [27] in which an operator calculus on undounded, closed linear operators is developed, and the work of Allan [1] in which a holomorphic functional calculus is defined for locally convex algebras.
- Full Text:
- Date Issued: 2019
- Authors: Snyman, Jandré Dillon
- Date: 2019
- Subjects: Banach algebras , Functions of several complex variables
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48643 , vital:41055
- Description: In this dissertation, we provide applications of complex function theory to problems in Banach algebras. We discuss the structure of analytic functions f : D → A, where D is a domain of C and A is a Banach algebra as given by Aupetit in [3]: either the set {λ ∈ D : Sp(f(λ)) is finite} is of capacity zero, or there exists an integer n such that Sp(f(λ)) has exactly n elements, for every λ, except on a closed, discrete set of capacity zero, where the spectrum has at most n−1 elements. This deep result, which describes the structure of Sp(f(λ)) for all λ ∈ D, relies heavily on subharmonic techniques, which are also included in the dissertation. Let A and B be Banach algebras. A linear mapping φ : A → B is called a Jordan homomorphism if and only if φ(xy + yx) = φ(x)φ(y) + φ(y)φ(x) for every x, y ∈ A. This is equivalent to saying that φ(x 2 ) = φ(x) 2 for every x ∈ A. The following problem, due to I. Kaplansky, is still unsolved for the general Banach algebra case: Let A and B be unital Banach algebras and φ : A → B a unital, invertibility preserving linear mapping. Under what conditions of A and B is φ a Jordan homomorphism? The author’s honours project [24] served as an exposition of the GleasonKahane-Żelazko Theorem [7, Theorem 4], which provides an answer to Kaplansky’s problem in the case where B = C. In this dissertation we look at other special cases of Kaplansky’s problem, such as the case where A and B are von Neumann algberas, as solved by Aupetit [4, Theorem 1.3] and remark that his result holds for the more general case where A is any C ∗ -algebra that has the property that every self-adjoint element is the limit of a sequence of linear combinations of orthogonal idempotents in A, and B is a semi-simple Banach algebra. This result relies heavily on complex function theory, spectral theory and holomorphic functional calculus. We also provide detailed expositions of the work of Taylor [27] in which an operator calculus on undounded, closed linear operators is developed, and the work of Allan [1] in which a holomorphic functional calculus is defined for locally convex algebras.
- Full Text:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
Assessing flood vulnerability in the Nelson Mandela Bay Metro
- Authors: Zuze, Hillary
- Date: 2019
- Subjects: Floods -- South Africa -- Nelson Mandela Bay Municipality , Natural disasters Hazardous geographic environments Hazardous geographic environments -- Risk assessment , Climatic changes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44224 , vital:37135
- Description: Floods are the most frequent amongst all global natural disasters at present, causing problems such as bridge collapses, fatalities, building damages and traffic delays. Between 1995 and 2015, there were approximately 3062 global flood disasters which accounted for 56% of all declared natural disasters and these affected 2.3 billion people (almost a third of the world’s population at the time) (EMDAT, 2015). The cost of damages for this period incurred for buildings and other infrastructure was at an all-time high of R23.69 (US$1.891) trillion. It is postulated through various studies that the number of urban flood events reported is increasing significantly in comparison to the previous decades (Armah et al., 2010; Lóczy, 2013; Leaning and Guha-Sapir, 2013; EMDAT, 2015; Tanoue et al., 2016; Rogger et al., 2017). Some research has also noted an increase in the number of floods per year, which has ascended to an average of 171 in this decade, from an annual average of 127 in the previous one (Dozier, 2013; Guha Sapir et al., 2016). Sources such as the Centre of Research and Epidemiological Disasters (Guha Sapir et al., 2016) recorded that from 1995 to 2015, globally, millions of homes were vulnerable to weather-related disasters, along with 130,000 health and education facilities. During this period, urban floods accounted for 98% of houses damaged and 99.9% of education and health facilities demolished by a weather-related disaster (Davies, 2017). Flooding is particularly harmful in terms of fatalities in developing countries due to inadequate flood protection and mitigation measures (Di Baldassarre et al., 2010; Dozier, 2013). Some studies attribute the high fatalities in developing countries to the inadequate disaster management strategies implemented to counter the impacts of urban flooding (Egbinola et al., 2015; Pazzi et al., 2016; Mavhura et al., 2017). Other authors have attributed the high fatalities to the sheer number of people residing in areas prone to flooding, which has been the knock-on effect of rapidly expanding cities, overwhelmed government agencies, and a pre-existing political and social system that promotes marginalisation (Collins, 2008; Aboagye, 2012). The occupation of flood-prone areas by settlements, which is a common feature in developing countries, is the major contributor to the fatalities as it involves a degree of risk. Risk is exposure to an undesired event, in this case flooding, and contributes directly to differing levels of vulnerability (Samuels, 2018). Communities have differing perceptions of flood vulnerability because of a combination of factors. These include the magnitude of the flood experienced, the number of people or the value of assets potentially affected by flooding due to location, and the lack of socioeconomic capacity to do anything to alter their vulnerability to a disaster (Hall et al., 2005; Adger, 2006; Birkmann et al., 2013; Rogger et al., 2017). Some communities acknowledge that there are people residing in flood prone areas and take measures to reduce or eliminate the risk through social, political and economic networks. In other cases, communities are able to identify their exposure to flooding but do not have the capacity to reduce the effects (Bouchard et al., 2007; Agbaoye, 2012; Musungu et al., 2012; Siyongwana, Heijne, and Tele et al., 20155).
- Full Text:
- Date Issued: 2019
- Authors: Zuze, Hillary
- Date: 2019
- Subjects: Floods -- South Africa -- Nelson Mandela Bay Municipality , Natural disasters Hazardous geographic environments Hazardous geographic environments -- Risk assessment , Climatic changes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44224 , vital:37135
- Description: Floods are the most frequent amongst all global natural disasters at present, causing problems such as bridge collapses, fatalities, building damages and traffic delays. Between 1995 and 2015, there were approximately 3062 global flood disasters which accounted for 56% of all declared natural disasters and these affected 2.3 billion people (almost a third of the world’s population at the time) (EMDAT, 2015). The cost of damages for this period incurred for buildings and other infrastructure was at an all-time high of R23.69 (US$1.891) trillion. It is postulated through various studies that the number of urban flood events reported is increasing significantly in comparison to the previous decades (Armah et al., 2010; Lóczy, 2013; Leaning and Guha-Sapir, 2013; EMDAT, 2015; Tanoue et al., 2016; Rogger et al., 2017). Some research has also noted an increase in the number of floods per year, which has ascended to an average of 171 in this decade, from an annual average of 127 in the previous one (Dozier, 2013; Guha Sapir et al., 2016). Sources such as the Centre of Research and Epidemiological Disasters (Guha Sapir et al., 2016) recorded that from 1995 to 2015, globally, millions of homes were vulnerable to weather-related disasters, along with 130,000 health and education facilities. During this period, urban floods accounted for 98% of houses damaged and 99.9% of education and health facilities demolished by a weather-related disaster (Davies, 2017). Flooding is particularly harmful in terms of fatalities in developing countries due to inadequate flood protection and mitigation measures (Di Baldassarre et al., 2010; Dozier, 2013). Some studies attribute the high fatalities in developing countries to the inadequate disaster management strategies implemented to counter the impacts of urban flooding (Egbinola et al., 2015; Pazzi et al., 2016; Mavhura et al., 2017). Other authors have attributed the high fatalities to the sheer number of people residing in areas prone to flooding, which has been the knock-on effect of rapidly expanding cities, overwhelmed government agencies, and a pre-existing political and social system that promotes marginalisation (Collins, 2008; Aboagye, 2012). The occupation of flood-prone areas by settlements, which is a common feature in developing countries, is the major contributor to the fatalities as it involves a degree of risk. Risk is exposure to an undesired event, in this case flooding, and contributes directly to differing levels of vulnerability (Samuels, 2018). Communities have differing perceptions of flood vulnerability because of a combination of factors. These include the magnitude of the flood experienced, the number of people or the value of assets potentially affected by flooding due to location, and the lack of socioeconomic capacity to do anything to alter their vulnerability to a disaster (Hall et al., 2005; Adger, 2006; Birkmann et al., 2013; Rogger et al., 2017). Some communities acknowledge that there are people residing in flood prone areas and take measures to reduce or eliminate the risk through social, political and economic networks. In other cases, communities are able to identify their exposure to flooding but do not have the capacity to reduce the effects (Bouchard et al., 2007; Agbaoye, 2012; Musungu et al., 2012; Siyongwana, Heijne, and Tele et al., 20155).
- Full Text:
- Date Issued: 2019
Assessing in-vivo clearance of colorectal cancer-targeting peptide-functionalized gold nanoparticles
- Authors: Xakaza, Hlumisa Belinda
- Date: 2019
- Subjects: Nanoparticles , Gold Nanotechnology -- Health aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44323 , vital:37153
- Description: Colorectal cancer (CRC) is a major public health problem. Gold nanoparticles (AuNPs) have been proved as a possible diagnostic tool to target CRC by peptides conjugated to gold nanoparticles (p-AuNP). According to previous reports, AuNPs accumulate in internal organs and have raised serious concerns on toxicity and safety. Understanding their fate in the body and the physiology underlying their clearance is crucial for toxicological evaluation and clinical translations. Six groups of rats were intravenously injected with a single dose of 100μg/kg body weight of citrate-capped (c.c-AuNPs), PEG-coated (PEG-AuNPs), and peptide functionalized gold nanoparticles (p.L-AuNPs, p.C-AuNPs, and p.14-AuNPs), to assess their physiologic clearance over a short-term (over sequential time-points: day 1, 3, 5, 7 and 14) and long-term period (three months). The inductively coupled optical-electron spectrometry (ICP-OES) showed accumulated c.c-AuNPs in the liver tissue. Moreover, a rapid and decreasing pattern of concentration of AuNPs was observed in urine and feces, with total excretion at day 7. Elevated levels of urine urea nitrogen (UUN) and urine creatinine (UCREA) reported an impaired kidney function for the c.c-AuNP group, while H&E staining indicated chronic progressive nephropathy (CPN) in all groups, 3 months post-injection, which is in all probability related to aging. Signs of inflammation were observed in rats treated with c.c-AuNPs, 2 weeks post-injection. The overall findings showed that the clearance of c.c-AuNPs’ clearance is compromised, which can have side-effects, while the excretion profiles of the p-AuNPs were consistent with the reducing long-term retention in the excretory organs. The p-AuNPs were found to be non-toxic and therefore show promise for CRC diagnostics and therapeutic purposes.
- Full Text:
- Date Issued: 2019
Assessing in-vivo clearance of colorectal cancer-targeting peptide-functionalized gold nanoparticles
- Authors: Xakaza, Hlumisa Belinda
- Date: 2019
- Subjects: Nanoparticles , Gold Nanotechnology -- Health aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44323 , vital:37153
- Description: Colorectal cancer (CRC) is a major public health problem. Gold nanoparticles (AuNPs) have been proved as a possible diagnostic tool to target CRC by peptides conjugated to gold nanoparticles (p-AuNP). According to previous reports, AuNPs accumulate in internal organs and have raised serious concerns on toxicity and safety. Understanding their fate in the body and the physiology underlying their clearance is crucial for toxicological evaluation and clinical translations. Six groups of rats were intravenously injected with a single dose of 100μg/kg body weight of citrate-capped (c.c-AuNPs), PEG-coated (PEG-AuNPs), and peptide functionalized gold nanoparticles (p.L-AuNPs, p.C-AuNPs, and p.14-AuNPs), to assess their physiologic clearance over a short-term (over sequential time-points: day 1, 3, 5, 7 and 14) and long-term period (three months). The inductively coupled optical-electron spectrometry (ICP-OES) showed accumulated c.c-AuNPs in the liver tissue. Moreover, a rapid and decreasing pattern of concentration of AuNPs was observed in urine and feces, with total excretion at day 7. Elevated levels of urine urea nitrogen (UUN) and urine creatinine (UCREA) reported an impaired kidney function for the c.c-AuNP group, while H&E staining indicated chronic progressive nephropathy (CPN) in all groups, 3 months post-injection, which is in all probability related to aging. Signs of inflammation were observed in rats treated with c.c-AuNPs, 2 weeks post-injection. The overall findings showed that the clearance of c.c-AuNPs’ clearance is compromised, which can have side-effects, while the excretion profiles of the p-AuNPs were consistent with the reducing long-term retention in the excretory organs. The p-AuNPs were found to be non-toxic and therefore show promise for CRC diagnostics and therapeutic purposes.
- Full Text:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
Bioavailability of nutrients in a diet enriched with moringa oleifera lam. Leaves using wistar rats
- Authors: Mhlomi, Yanga Nonelela
- Date: 2019
- Subjects: Moringa Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14594 , vital:40018
- Description: This study investigated the nutritional composition and bioavailability of nutrients in Moringa oleifera leaf meal from South African ecotype. Nutritional evaluation (proximate, mineral, vitamins and antinutrients, amino acids and fatty acids analyses) was performed using AOAC, ICP-OES and GC+MS techniques respectively. Bioavailability of nutrients involved formulation of diets deficient in minerals and vitamins; and proteins supplemented with Moringa oleifera leaf meal (MOLM) at 0, 3, 5 and 10% respectively. Growth performance, hematological, biochemical and histopathological evaluations were used to assess the effect of MOLM supplementation. Proximate and mineral evaluation revealed that the leaves were rich in protein (28.72%) and carbohydrate (28.84%), calcium content was (1603.33 mg/100g), potassium (1690 mg/100g), zinc (13.03 mg/100g) and iron (21.13 mg/100g). Vitamin E content was the highest (89.43 mg/100g) followed by vitamic C (24.9 mg/100g) and vitamin A (12.98 mg/100g). Fatty acids analysis detected were fifteen of which polyunsaturated fatty acid linoleic acid (56.36) and alpha-linolenic acid (687.58) were highest and behenic acid (22:0) characteristics of Moringa (4.11%) were detected. Seven of the detected fatty acids were saturated fatty acids, though relatively low, with stearic acid having the highest value. On the other hand fifteen of the amino acids, 7 were essential (valine, leucine, isoleucine, methionine, threonine and phenylalanine) were detected; while alanine, proline, serine, aspartic acid, cysteine, glutamic acid, asparagine and tyrosine were non- essential amino acid. Moringa oleifera had low quantities of antinutrients in relation to minerals, thus nutrients will easily ne available. Amino and fatty acids profile of nutrient deficient diets supplemented with MOLM revealed that six essential amino acids were detected in the diets. However, the essential amino acid (EAA) in MOLM with the highest value was threonine (500.47±23.03mg/L), while the lowest was methionine (75.65±5.31mg/L). Leucine was highest in PD10 (234.32±27.98 mg/l) 15 and lowest in PD3. Predominant amino acid in VMD diet was glutamic acid (966.76±208.92 mg/l), while methionine was lowest (197.14±35.90). Caproic acid was the most prominent unsaturated fatty acid in the diets and was highest in the PD diet. Palmitoleic acid was highest in the control diet (8.19±0.56 mg/L) and lowest in PD3 but an increase was observed as the levels of MOLM increased in the diets. Linoleic acid values obtained were significantly higher in PD diet, lower in control diet, compared to other diets. Linolenic acid (C18-3n6) was higher in PD10 (63.48±3.84 mg/L) compared to the control diet (6.05±0.14 mg/L). The highest unsaturated fatty acid in all the feed samples was linoleic acids ranging from 54.48±5.61 to 296.26±7.20 mg/L. the highest omega-3 (n-3) fatty acid content (63.48±3.38 mg/L) was in PD10 and was almost 10 times higher than the value recorded for control. Rats treated on vitamin mineral deficient (VMD) diet showed no significant changes in growth performances and blood parameters except in certain indices. Rats on VMD diet had lowest haemoglobin levels, whereas haemoglobin increased with MOLM levels. No significant differences in haematocrit, MCH, MCHC, platelets, RDW and MPV were observed in all treatments and control. However, VMD rats showed decrease in haemoglobin, increase in WBC and platelets. Electrolytes and glucose for all treatments and control were not significantly different, but, control and VMD10 diets rats showed significantly higher values for creatinine compared to MOLM diets; total protein and albumin increased with MOLM and were higher than in VMD and control rats. Serum activities of liver, cardiac, adrenal marker enzymes were significantly lower in MOLM rats compared to VMD and control. Mild congestion in VMD and VMD3 rat’s liver and diffused congestion in the kidney of VMD diet fed rats was observed. Protein deficient diets supplemented with MOLM had a negative impact on feed intake and growth parameters. Rats fed PD and PD5 consumed significantly less diet than those fed PD10, PD3 diets respectively. White blood cells decreased with increasing levels of MOLM 16 supplementation. Differential white cell count (Neutrophils, lymphocytes, monocytes, eosinophils and basophils) followed the same trend though not statistically significant (P>0.05). Furthermore, histopathological evaluation of organs revealed that no abnormalities were in heart and liver and kidney of rats fed on the control diet, while mild congestion in the liver and myocardium (heart) were observed in rats fed with protein deficient diet. No visible abnormalities were observed in the heart, kidney and liver of animals on the PD 10 diet, but myocardial fibres showing intense eosinophilia was detected in heart muscles of rats fed PD and PD3 diets. In this study, MOLM had a negative impact on feed intake and growth performance of animals and haematology. Blood biochemistry and histology suggest that MOLM has the potential of defending the body against infection with hematinic and blood enhancing qualities. Protein deficiency led to a significant elevation in the serum lipid profile of rats especially cholesterol even with increase in MOLM. PD10 had the highest triglycerides content when compared to the control but was lower (p>0.05) to that of PD. There was an increase in crude fat, ADF, NDF and protein in faecal samples of rats supplemented with MOLM diets while a decrease in moisture and ash was observed compared to the control.Vitamin and mineral deficiency resulted in significant decrease in serum cholesterol, triglycerides and HDL-C when compared to the control. There was a slight increase in excretion for all elements with increasing MOLM. Total removal of minerals and vitamins from the VMD experimental diets seemed not to have any visible negative impact on performance of the rats probably because of residual micronutrients present in other ingredients used in the feed formulation. MOLM could not replace protein in protein deficient diets.
- Full Text:
- Date Issued: 2019
- Authors: Mhlomi, Yanga Nonelela
- Date: 2019
- Subjects: Moringa Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14594 , vital:40018
- Description: This study investigated the nutritional composition and bioavailability of nutrients in Moringa oleifera leaf meal from South African ecotype. Nutritional evaluation (proximate, mineral, vitamins and antinutrients, amino acids and fatty acids analyses) was performed using AOAC, ICP-OES and GC+MS techniques respectively. Bioavailability of nutrients involved formulation of diets deficient in minerals and vitamins; and proteins supplemented with Moringa oleifera leaf meal (MOLM) at 0, 3, 5 and 10% respectively. Growth performance, hematological, biochemical and histopathological evaluations were used to assess the effect of MOLM supplementation. Proximate and mineral evaluation revealed that the leaves were rich in protein (28.72%) and carbohydrate (28.84%), calcium content was (1603.33 mg/100g), potassium (1690 mg/100g), zinc (13.03 mg/100g) and iron (21.13 mg/100g). Vitamin E content was the highest (89.43 mg/100g) followed by vitamic C (24.9 mg/100g) and vitamin A (12.98 mg/100g). Fatty acids analysis detected were fifteen of which polyunsaturated fatty acid linoleic acid (56.36) and alpha-linolenic acid (687.58) were highest and behenic acid (22:0) characteristics of Moringa (4.11%) were detected. Seven of the detected fatty acids were saturated fatty acids, though relatively low, with stearic acid having the highest value. On the other hand fifteen of the amino acids, 7 were essential (valine, leucine, isoleucine, methionine, threonine and phenylalanine) were detected; while alanine, proline, serine, aspartic acid, cysteine, glutamic acid, asparagine and tyrosine were non- essential amino acid. Moringa oleifera had low quantities of antinutrients in relation to minerals, thus nutrients will easily ne available. Amino and fatty acids profile of nutrient deficient diets supplemented with MOLM revealed that six essential amino acids were detected in the diets. However, the essential amino acid (EAA) in MOLM with the highest value was threonine (500.47±23.03mg/L), while the lowest was methionine (75.65±5.31mg/L). Leucine was highest in PD10 (234.32±27.98 mg/l) 15 and lowest in PD3. Predominant amino acid in VMD diet was glutamic acid (966.76±208.92 mg/l), while methionine was lowest (197.14±35.90). Caproic acid was the most prominent unsaturated fatty acid in the diets and was highest in the PD diet. Palmitoleic acid was highest in the control diet (8.19±0.56 mg/L) and lowest in PD3 but an increase was observed as the levels of MOLM increased in the diets. Linoleic acid values obtained were significantly higher in PD diet, lower in control diet, compared to other diets. Linolenic acid (C18-3n6) was higher in PD10 (63.48±3.84 mg/L) compared to the control diet (6.05±0.14 mg/L). The highest unsaturated fatty acid in all the feed samples was linoleic acids ranging from 54.48±5.61 to 296.26±7.20 mg/L. the highest omega-3 (n-3) fatty acid content (63.48±3.38 mg/L) was in PD10 and was almost 10 times higher than the value recorded for control. Rats treated on vitamin mineral deficient (VMD) diet showed no significant changes in growth performances and blood parameters except in certain indices. Rats on VMD diet had lowest haemoglobin levels, whereas haemoglobin increased with MOLM levels. No significant differences in haematocrit, MCH, MCHC, platelets, RDW and MPV were observed in all treatments and control. However, VMD rats showed decrease in haemoglobin, increase in WBC and platelets. Electrolytes and glucose for all treatments and control were not significantly different, but, control and VMD10 diets rats showed significantly higher values for creatinine compared to MOLM diets; total protein and albumin increased with MOLM and were higher than in VMD and control rats. Serum activities of liver, cardiac, adrenal marker enzymes were significantly lower in MOLM rats compared to VMD and control. Mild congestion in VMD and VMD3 rat’s liver and diffused congestion in the kidney of VMD diet fed rats was observed. Protein deficient diets supplemented with MOLM had a negative impact on feed intake and growth parameters. Rats fed PD and PD5 consumed significantly less diet than those fed PD10, PD3 diets respectively. White blood cells decreased with increasing levels of MOLM 16 supplementation. Differential white cell count (Neutrophils, lymphocytes, monocytes, eosinophils and basophils) followed the same trend though not statistically significant (P>0.05). Furthermore, histopathological evaluation of organs revealed that no abnormalities were in heart and liver and kidney of rats fed on the control diet, while mild congestion in the liver and myocardium (heart) were observed in rats fed with protein deficient diet. No visible abnormalities were observed in the heart, kidney and liver of animals on the PD 10 diet, but myocardial fibres showing intense eosinophilia was detected in heart muscles of rats fed PD and PD3 diets. In this study, MOLM had a negative impact on feed intake and growth performance of animals and haematology. Blood biochemistry and histology suggest that MOLM has the potential of defending the body against infection with hematinic and blood enhancing qualities. Protein deficiency led to a significant elevation in the serum lipid profile of rats especially cholesterol even with increase in MOLM. PD10 had the highest triglycerides content when compared to the control but was lower (p>0.05) to that of PD. There was an increase in crude fat, ADF, NDF and protein in faecal samples of rats supplemented with MOLM diets while a decrease in moisture and ash was observed compared to the control.Vitamin and mineral deficiency resulted in significant decrease in serum cholesterol, triglycerides and HDL-C when compared to the control. There was a slight increase in excretion for all elements with increasing MOLM. Total removal of minerals and vitamins from the VMD experimental diets seemed not to have any visible negative impact on performance of the rats probably because of residual micronutrients present in other ingredients used in the feed formulation. MOLM could not replace protein in protein deficient diets.
- Full Text:
- Date Issued: 2019
Biochemical characterization of the β-mannanase activity of Bacillus paralicheniformis SVD1
- Authors: Clarke, Matthew David
- Date: 2019
- Subjects: Mycobacterium avium paratuberculosis , Enzymes -- Biotechnology , Lignocellulose -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67570 , vital:29112
- Description: Products produced via the enzymatic hydrolysis of lignocellulosic biomass, the most abundant renewable terrestrial source of carbon, can potentially replace a lot of the fuels and chemicals currently produced using non-renewable hydrocarbons. Mannan is a polysaccharide component of lignocellulose that is abundant in softwoods and legume seeds. Enzymatic hydrolysis of mannan by β-mannanases has various industrial applications, including use in biofuel and prebiotic mannooligosaccharide (MOS) production for the improvement of human and animal health. The industrial use of β-mannanases depends on their biochemical characteristics, such as their activity, stability and substrate specificity. Knowledge of their synergistic interactions with other enzymes is also useful for effective hydrolysis. Bacillus paralicheniformis SVD1 was used as a source for β-mannanases. The two mannanases of B. paralicheniformis SVD1 have not been biochemically characterized apart from minor characterization of crude β-mannanase activity. The protein sequences of the two β-mannanases, of glycosyl hydrolase family 5 and 26, have a 95% - 96% identity to the β-mannanases of B. licheniformis DSM13T (=ATCC14580T). These small protein sequence differences could lead to quite different biochemical characteristics. These mannanases were characterized as these enzymes may have industrially useful characteristics. To induce mannanase production, B. paralicheniformis SVD1 was cultured in broth containing the mannan substrate locust bean gum. Various growth curve parameters were measured over 72 h. Mannanase activity was the highest after 48 h of growth - this was the time at which mannanase activity was concentrated, using 3 kDa centrifugal filtration devices, for biochemical characterization of the crude activity. Zymography revealed that the crude concentrated mannanase fraction consisted of at least two mannanases with relative molecular weights (MWs) of 29.6 kDa and 33 kDa. This was smaller than expected – based on their theoretical molecular masses. Protease activity, which was detected in the broth, was probably the reason. There were two pH optima, pH 5.0 and pH 7.0, which also indicated the presence of two mannanases. The concentrated mannanase displayed characteristics that were expected of a B. paralicheniformis β-mannanase. The temperature optimum was 50°C and the activity loss was less than 7% at 50°C after 24 h. Substrate specificity assays revealed that there was predominantly mannanase activity present. Thin layer chromatography (TLC) analysis of mannan and MOS hydrolysis showed that mainly M2 and M3 MOS were produced; only MOS with a degree of polymerization of 4 or higher were hydrolyzed. Hydrolysis was minimal on mannoligosaccharides with galactose substituents. Activity and MOS production was the highest on soluble, low branched mannan substrates. The highest activity observed was on konjac glucomannan. Purification of the mannanase activity was then attempted using various methods. Ammonium sulfate precipitation, acetone precipitation, as well as centrifugal filtration device concentration was assessed for concentration of the mannanase activity.Concentration was not very successful due to low activity yields (≤ 20%). Anion exchange chromatography (AEC) and size exclusion chromatography (SEC) was used for purification. AEC gave good activity yield and fold purification, but SDS-PAGE analysis revealed the presence of many different proteins so further purification was necessary. SDS-PAGE analysis showed that there were only a few protein contaminants in the SEC fraction. However, the yield was too low to allow for biochemical characterization. The optimized purification procedure, which partially purified the mannanase activity, used 85% ammonium sulfate precipitation, followed by AEC. The fold purification was high (88.9) and the specific activity was 29.5 U.mg-1. A zymogram of the partially purified mannanase showed a mannanase active band with a MW of 40 - 41 kDa. A serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), was added during the purification steps. This indicated that the mannanase/s in the crude concentrate, without PMSF added, was hydrolyzed by serine protease activity. Native PAGE zymograms suggested that at least two different isoforms of mannanases were present. Additional purification would be required to determine the true characteristics of the mannanase/s. The biochemical characteristics of the crude and partially purified mannanases were similar. The pH optima of the partially purified mannanases were different; the pH optima were 6.0 and 9.0. The substrate specificities were similar, except that the partially purified mannanases displayed no cellulase and β-D-galactosidase activity, but showed a small amount of α-L-arabinase activity. The partially purified mannanase and a Cyamopsis tetragonolobus GH27 α-galactosidase synergistically hydrolyzed locust bean gum. The M50G50 combination displayed the highest extent of hydrolysis; after 24 h there was a 1.39 fold increase in reducing sugar release and the degree of synergy (DS) was 4.64. TLC analysis indicated that synergy increased the release of small MOS. These MOS could be useful as prebiotics. The synergy between the partially purified mannanase and the commercial cellulase mixture Cellic® CTec2 (Novozymes) on spent coffee grounds (SCG) was also determined. SCG is an abundant industrial waste product that has high mannan content. The SCG was pretreated using NaOH, and the monosaccharide, soluble phenolics and insoluble contents were determined. Glucose and mannose were the dominant monosaccharides in the SCG; the pretreated SCG contained 20.4% (w/w) glucose and 18.5% (w/w) mannose, respectively. The NaOH pretreatment improved mannanase hydrolysis of SCG. It resulted in the opening up and swelling of the SCG particles and removed some of the insoluble solids. The partially purified B. paralicheniformis SVD1 mannanase displayed no detectable activity on SCG, but showed synergy with CTec2, in terms of DS, on untreated and NaOH pretreated SCG. This is the first report of mannanasecellulase synergy on SCG; other studies found that increased hydrolysis was due to additive effects. The results obtained in this study are only an initial assessment of the biochemical properties of B. paralicheniformis SVD1 mannanase activity and its synergy with other enzymes. These results can be used to inform future studies.
- Full Text:
- Date Issued: 2019
- Authors: Clarke, Matthew David
- Date: 2019
- Subjects: Mycobacterium avium paratuberculosis , Enzymes -- Biotechnology , Lignocellulose -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67570 , vital:29112
- Description: Products produced via the enzymatic hydrolysis of lignocellulosic biomass, the most abundant renewable terrestrial source of carbon, can potentially replace a lot of the fuels and chemicals currently produced using non-renewable hydrocarbons. Mannan is a polysaccharide component of lignocellulose that is abundant in softwoods and legume seeds. Enzymatic hydrolysis of mannan by β-mannanases has various industrial applications, including use in biofuel and prebiotic mannooligosaccharide (MOS) production for the improvement of human and animal health. The industrial use of β-mannanases depends on their biochemical characteristics, such as their activity, stability and substrate specificity. Knowledge of their synergistic interactions with other enzymes is also useful for effective hydrolysis. Bacillus paralicheniformis SVD1 was used as a source for β-mannanases. The two mannanases of B. paralicheniformis SVD1 have not been biochemically characterized apart from minor characterization of crude β-mannanase activity. The protein sequences of the two β-mannanases, of glycosyl hydrolase family 5 and 26, have a 95% - 96% identity to the β-mannanases of B. licheniformis DSM13T (=ATCC14580T). These small protein sequence differences could lead to quite different biochemical characteristics. These mannanases were characterized as these enzymes may have industrially useful characteristics. To induce mannanase production, B. paralicheniformis SVD1 was cultured in broth containing the mannan substrate locust bean gum. Various growth curve parameters were measured over 72 h. Mannanase activity was the highest after 48 h of growth - this was the time at which mannanase activity was concentrated, using 3 kDa centrifugal filtration devices, for biochemical characterization of the crude activity. Zymography revealed that the crude concentrated mannanase fraction consisted of at least two mannanases with relative molecular weights (MWs) of 29.6 kDa and 33 kDa. This was smaller than expected – based on their theoretical molecular masses. Protease activity, which was detected in the broth, was probably the reason. There were two pH optima, pH 5.0 and pH 7.0, which also indicated the presence of two mannanases. The concentrated mannanase displayed characteristics that were expected of a B. paralicheniformis β-mannanase. The temperature optimum was 50°C and the activity loss was less than 7% at 50°C after 24 h. Substrate specificity assays revealed that there was predominantly mannanase activity present. Thin layer chromatography (TLC) analysis of mannan and MOS hydrolysis showed that mainly M2 and M3 MOS were produced; only MOS with a degree of polymerization of 4 or higher were hydrolyzed. Hydrolysis was minimal on mannoligosaccharides with galactose substituents. Activity and MOS production was the highest on soluble, low branched mannan substrates. The highest activity observed was on konjac glucomannan. Purification of the mannanase activity was then attempted using various methods. Ammonium sulfate precipitation, acetone precipitation, as well as centrifugal filtration device concentration was assessed for concentration of the mannanase activity.Concentration was not very successful due to low activity yields (≤ 20%). Anion exchange chromatography (AEC) and size exclusion chromatography (SEC) was used for purification. AEC gave good activity yield and fold purification, but SDS-PAGE analysis revealed the presence of many different proteins so further purification was necessary. SDS-PAGE analysis showed that there were only a few protein contaminants in the SEC fraction. However, the yield was too low to allow for biochemical characterization. The optimized purification procedure, which partially purified the mannanase activity, used 85% ammonium sulfate precipitation, followed by AEC. The fold purification was high (88.9) and the specific activity was 29.5 U.mg-1. A zymogram of the partially purified mannanase showed a mannanase active band with a MW of 40 - 41 kDa. A serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), was added during the purification steps. This indicated that the mannanase/s in the crude concentrate, without PMSF added, was hydrolyzed by serine protease activity. Native PAGE zymograms suggested that at least two different isoforms of mannanases were present. Additional purification would be required to determine the true characteristics of the mannanase/s. The biochemical characteristics of the crude and partially purified mannanases were similar. The pH optima of the partially purified mannanases were different; the pH optima were 6.0 and 9.0. The substrate specificities were similar, except that the partially purified mannanases displayed no cellulase and β-D-galactosidase activity, but showed a small amount of α-L-arabinase activity. The partially purified mannanase and a Cyamopsis tetragonolobus GH27 α-galactosidase synergistically hydrolyzed locust bean gum. The M50G50 combination displayed the highest extent of hydrolysis; after 24 h there was a 1.39 fold increase in reducing sugar release and the degree of synergy (DS) was 4.64. TLC analysis indicated that synergy increased the release of small MOS. These MOS could be useful as prebiotics. The synergy between the partially purified mannanase and the commercial cellulase mixture Cellic® CTec2 (Novozymes) on spent coffee grounds (SCG) was also determined. SCG is an abundant industrial waste product that has high mannan content. The SCG was pretreated using NaOH, and the monosaccharide, soluble phenolics and insoluble contents were determined. Glucose and mannose were the dominant monosaccharides in the SCG; the pretreated SCG contained 20.4% (w/w) glucose and 18.5% (w/w) mannose, respectively. The NaOH pretreatment improved mannanase hydrolysis of SCG. It resulted in the opening up and swelling of the SCG particles and removed some of the insoluble solids. The partially purified B. paralicheniformis SVD1 mannanase displayed no detectable activity on SCG, but showed synergy with CTec2, in terms of DS, on untreated and NaOH pretreated SCG. This is the first report of mannanasecellulase synergy on SCG; other studies found that increased hydrolysis was due to additive effects. The results obtained in this study are only an initial assessment of the biochemical properties of B. paralicheniformis SVD1 mannanase activity and its synergy with other enzymes. These results can be used to inform future studies.
- Full Text:
- Date Issued: 2019
Bioinformatic analysis, isolation and kinetic characterisation of red algae (Gelidium capense) dehydrogenases
- Authors: Gogela, Yanga
- Date: 2019
- Subjects: Bioinformatics Chondrus crispus
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19164 , vital:39878
- Description: Lactate and alcohol dehydrogenases have attracted much attention in various industries and scientific research for their ability to produce chirally pure compounds and be assayed for activity using more straightforward and reproducible assay methods. These enzymes have been previously isolated and purified from various plants, animals and microorganisms. So far, the molecular and biochemical properties of enzymes from these dehydrogenase families in red algae are mostly unknown. Red macroalgae have been used for centuries for the treatment of various diseases and as a source of ingredients in the food industry. The aim of this study was to identify genes in the sequenced red algae genomes that encode dehydrogenases, to use bioinformatic tools to confirm that the proteins encoded are dehydrogenases and to isolate and kinetically purify alcohol or lactate dehydrogenase from red algae species found along the coastline of the Eastern Cape Province. A combination of bioinformatics tools, molecular and biochemical techniques were used to identify, purify, and characterise ADH and LDH enzymes. Bioinformatics analysis revealed two alcohol dehydrogenase genes and two hypothetical genes encoding functional domains similar to D-lactate dehydrogenases from other species. The ADH and LDH-like genes shared low sequence identity at the protein level with medium-chain dehydrogenases/reductases (MDRs) and 2-hydroxy acid dehydrogenases, respectively. These two dehydrogenase genes showed a highly conserved NAD-binding motif (Rossmann-fold) similar to many other NAD-dependent dehydrogenases. The ADH and LDH proteins contained no signal peptides and may be located in the cytoplasm. The phylogenetic tree analysis showed that the two ADH genes belonged to cinnamyl and class III alcohol dehydrogenases, whereas the LDHlike genes were grouped with D-lactate dehydrogenases from other organisms. The ADH and LDH gene family showed cis-acting regulatory elements that are mostly involved in stress response and hormonal response. Structural analysis showed that the dehydrogenases 3D structure predicted models comprise of two domains, namely the substrate binding and the coenzyme binding domains that are rich in beta-strands secondary structure elements. The LDH from red algae was purified approximately 4-fold with a specific activity of 0.044 U/mg. The purified LDH enzyme had a molecular weight of approximately 37kDa. The LDH was active across a broad pH range from 5-9 with a pH optimum observed at 7.5. The LDH ii enzyme in red algae exhibits a temperature optimum of 40 ⁰C and heat stability up to 40 ⁰C. Above 50 °C the LDH activity rapidly decreased showing that the LDH in red algae is not thermostable. The LDH enzyme showed a Km value of 0.8 mM and Vmax of 0.0067 mM.min-1 when using sodium pyruvate as a substrate.
- Full Text:
- Date Issued: 2019
- Authors: Gogela, Yanga
- Date: 2019
- Subjects: Bioinformatics Chondrus crispus
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19164 , vital:39878
- Description: Lactate and alcohol dehydrogenases have attracted much attention in various industries and scientific research for their ability to produce chirally pure compounds and be assayed for activity using more straightforward and reproducible assay methods. These enzymes have been previously isolated and purified from various plants, animals and microorganisms. So far, the molecular and biochemical properties of enzymes from these dehydrogenase families in red algae are mostly unknown. Red macroalgae have been used for centuries for the treatment of various diseases and as a source of ingredients in the food industry. The aim of this study was to identify genes in the sequenced red algae genomes that encode dehydrogenases, to use bioinformatic tools to confirm that the proteins encoded are dehydrogenases and to isolate and kinetically purify alcohol or lactate dehydrogenase from red algae species found along the coastline of the Eastern Cape Province. A combination of bioinformatics tools, molecular and biochemical techniques were used to identify, purify, and characterise ADH and LDH enzymes. Bioinformatics analysis revealed two alcohol dehydrogenase genes and two hypothetical genes encoding functional domains similar to D-lactate dehydrogenases from other species. The ADH and LDH-like genes shared low sequence identity at the protein level with medium-chain dehydrogenases/reductases (MDRs) and 2-hydroxy acid dehydrogenases, respectively. These two dehydrogenase genes showed a highly conserved NAD-binding motif (Rossmann-fold) similar to many other NAD-dependent dehydrogenases. The ADH and LDH proteins contained no signal peptides and may be located in the cytoplasm. The phylogenetic tree analysis showed that the two ADH genes belonged to cinnamyl and class III alcohol dehydrogenases, whereas the LDHlike genes were grouped with D-lactate dehydrogenases from other organisms. The ADH and LDH gene family showed cis-acting regulatory elements that are mostly involved in stress response and hormonal response. Structural analysis showed that the dehydrogenases 3D structure predicted models comprise of two domains, namely the substrate binding and the coenzyme binding domains that are rich in beta-strands secondary structure elements. The LDH from red algae was purified approximately 4-fold with a specific activity of 0.044 U/mg. The purified LDH enzyme had a molecular weight of approximately 37kDa. The LDH was active across a broad pH range from 5-9 with a pH optimum observed at 7.5. The LDH ii enzyme in red algae exhibits a temperature optimum of 40 ⁰C and heat stability up to 40 ⁰C. Above 50 °C the LDH activity rapidly decreased showing that the LDH in red algae is not thermostable. The LDH enzyme showed a Km value of 0.8 mM and Vmax of 0.0067 mM.min-1 when using sodium pyruvate as a substrate.
- Full Text:
- Date Issued: 2019
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:
- Date Issued: 2019
- 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:
- Date Issued: 2019
Block copolymer templates for metal oxide nanostructures
- Authors: Talla, Assane
- Date: 2019
- Subjects: Nanotechnology , Nanostructured materials Metal oxide semiconductors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43889 , vital:37075
- Description: Recent advances in technology have increased the need for fabrication of devices with feature sizes of tens of nanometers, such as ultra-fine filters or membranes, and high density data storage media, to name a few. For this reason, research is now focused on block copolymer nanolithographic processes, particularly the fabrication of nanoscale templates with domains well below 100 nm. Block copolymers have the tendency to self-organise into various structures, such as lamellae, spheres or cylinders on a nanometer scale. Among these possible configurations, the perpendicular cylindrical structure is most desirable, because it can be used for templates or masks for feature development, in particular, oriented wires or rods. In this work, the aim is to create a nano-mask from a di-block copolymer thin film, for zinc oxide nanorods growth. For this purpose poly (styrene-block-methylmethacrylate) (PS-b-PMMA) was investigated as a potential nano-mask. Samples were characterized using X-ray reflectometry to determine the thicknesses of the PS-b-PMMA thin films, while scanning probe microscopy and scanning electron microscopy was used to investigate the surface morphology of the samples. PS-b-PMMA thin films were produced on a random copolymer (poly (styrene-random-methylmethacrylate) (PS-r-PMMA) coated onto a silicon substrate. The PS-r-PMMA permits a non-preferential interaction between the di-block constituents and the substrate. Thermal annealing in vacuum of PS-b-PMMA on PS-r-PMMA led to perpendicular cylinders of PMMA within a PS matrix in the di-block. The typical thicknesses measured for the di-block copolymer films ranged between 33 nm and 37 nm. During this study, a perpendicular orientation of the di-block components was also produced when PS-b-PMMA was spun onto a layer of zinc oxide nanoparticles and thermally annealed in vacuum. It was shown that the ZnO nanoparticles created a corrugated surface on silicon which induced perpendicular cylinders of PMMA within the PS matrix. This was possible for a specific surface roughness parameter and film thickness. In this case, the typical thickness determined for the di-block copolymer ranged between 33 and 35 nm and the surface roughness parameter was 0.07. For the fabrication of a di-block template or PS nano-mask, the vertically oriented PMMA cylindrical nanodomains in the PS matrix were removed by exposing the film to ultraviolet radiation at an adequate dose, followed successively by washing in acetic acid and de-ionized water. It was shown that ultraviolet exposure is necessary to ensure the degradation of PMMA. A subsequent rinse in glacial acetic acid and DI water of the film exposed to ultraviolet, left an array of ordered nanoscopic pores with sizes ranging between 10 nm and 20 nm. Finally, the growth of ZnO nanorods on the di-block template produced on zinc oxide nanoparticles, was attempted using an aqueous solution based-method, namely chemical bath deposition. The rods did not grow inside the nanopores, probably due to poor capillary action. In additional experiments, the di-block template was removed by toluene (a selective solvent for PS) followed by the growth of ZnO rods on the exposed nanoparticle surface. Vertical and well separated ZnO rods formed on this surface, in places where the underlying seed layer had been attacked by the acetic acid treatment during removal of the PMMA. The observed ZnO rod morphology can be used in applications such as solar cell.
- Full Text:
- Date Issued: 2019
- Authors: Talla, Assane
- Date: 2019
- Subjects: Nanotechnology , Nanostructured materials Metal oxide semiconductors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43889 , vital:37075
- Description: Recent advances in technology have increased the need for fabrication of devices with feature sizes of tens of nanometers, such as ultra-fine filters or membranes, and high density data storage media, to name a few. For this reason, research is now focused on block copolymer nanolithographic processes, particularly the fabrication of nanoscale templates with domains well below 100 nm. Block copolymers have the tendency to self-organise into various structures, such as lamellae, spheres or cylinders on a nanometer scale. Among these possible configurations, the perpendicular cylindrical structure is most desirable, because it can be used for templates or masks for feature development, in particular, oriented wires or rods. In this work, the aim is to create a nano-mask from a di-block copolymer thin film, for zinc oxide nanorods growth. For this purpose poly (styrene-block-methylmethacrylate) (PS-b-PMMA) was investigated as a potential nano-mask. Samples were characterized using X-ray reflectometry to determine the thicknesses of the PS-b-PMMA thin films, while scanning probe microscopy and scanning electron microscopy was used to investigate the surface morphology of the samples. PS-b-PMMA thin films were produced on a random copolymer (poly (styrene-random-methylmethacrylate) (PS-r-PMMA) coated onto a silicon substrate. The PS-r-PMMA permits a non-preferential interaction between the di-block constituents and the substrate. Thermal annealing in vacuum of PS-b-PMMA on PS-r-PMMA led to perpendicular cylinders of PMMA within a PS matrix in the di-block. The typical thicknesses measured for the di-block copolymer films ranged between 33 nm and 37 nm. During this study, a perpendicular orientation of the di-block components was also produced when PS-b-PMMA was spun onto a layer of zinc oxide nanoparticles and thermally annealed in vacuum. It was shown that the ZnO nanoparticles created a corrugated surface on silicon which induced perpendicular cylinders of PMMA within the PS matrix. This was possible for a specific surface roughness parameter and film thickness. In this case, the typical thickness determined for the di-block copolymer ranged between 33 and 35 nm and the surface roughness parameter was 0.07. For the fabrication of a di-block template or PS nano-mask, the vertically oriented PMMA cylindrical nanodomains in the PS matrix were removed by exposing the film to ultraviolet radiation at an adequate dose, followed successively by washing in acetic acid and de-ionized water. It was shown that ultraviolet exposure is necessary to ensure the degradation of PMMA. A subsequent rinse in glacial acetic acid and DI water of the film exposed to ultraviolet, left an array of ordered nanoscopic pores with sizes ranging between 10 nm and 20 nm. Finally, the growth of ZnO nanorods on the di-block template produced on zinc oxide nanoparticles, was attempted using an aqueous solution based-method, namely chemical bath deposition. The rods did not grow inside the nanopores, probably due to poor capillary action. In additional experiments, the di-block template was removed by toluene (a selective solvent for PS) followed by the growth of ZnO rods on the exposed nanoparticle surface. Vertical and well separated ZnO rods formed on this surface, in places where the underlying seed layer had been attacked by the acetic acid treatment during removal of the PMMA. The observed ZnO rod morphology can be used in applications such as solar cell.
- Full Text:
- Date Issued: 2019
BODIPY and porphyrin dyes for direct glucose sensing and optical limiting applications
- Authors: Ndebele, Nobuhle
- Date: 2019
- Subjects: Boron compounds , Boric acid , Porphyrins , Dyes and dying -- Chemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97221 , vital:31412
- Description: A series of BODIPY dyes functionalised with boronic acid in the 3,5-positions were successfully synthesised and characterised by using various analytical techniques. The dyes were prepared through a slight modification of the conventional acid catalysed condensation method. Phenylboronic acid moieties were added as styryl groups at the 3,5-positions of the 1,3,5,7-tetrametylBODIPY cores using a modified Knoevengal condensation method. The addition of the styryls resulted in the main absorption band of the dyes red-shifting to the 630−650 nm region. The photophysical and electrochemical properties of these dyes were studied to determine whether the dyes are suitable for use in the fluorescent, colourimetric and electrochemical detection of glucose. Boronic acid moieties were added as bioreceptor recognition elements because they have an affinity for carbohydrates and therefore would be able to bind and “detect” glucose. The series of BODIPY dyes did not show a “turn-on” fluorescence effect upon addition with glucose at the physiological pH. This was attributed on the basis of molecular modelling to the absence of an MO localised on the boronic-acid-substituted styryl moieties that lie close in energy to the HOMO and LUMO that facilitates the formation of an intramolecular charge transfer state. However, colourimetric changes that are visible to the naked eye are observed at basic pH when glucose was added to the dye solutions. The dyes exhibited favourable electrochemical behaviour and were able to detect glucose directly in this context when glassy carbon electrodes are modified through the drop dry method. A series of Sn(IV) porphyrins with thienyl and phenyl groups at the meso-positions were successfully synthesised and characterised. Pyridine and tetrabutyl axial ligands were added to the porphyrins to limit aggregation. The optical limiting properties of these porphyrins and three styrylated BODIPY dyes were studied in benzene and dichloromethane. Dyes were also embedded in polystyrene and studied as thin films to further gauge their suitability for use in optical limiting applications. Second-order hyperpolarizability, third-order susceptibly, non-linear absorption with reversible saturable absorption and the optical limiting threshold, were the parameters studied. Three of the four porphyrins and the three styrylated BODIPY dyes showed favourable optical limiting behaviour, which was further enhanced when the dyes are embedded in polymer thin films.
- Full Text:
- Date Issued: 2019
- Authors: Ndebele, Nobuhle
- Date: 2019
- Subjects: Boron compounds , Boric acid , Porphyrins , Dyes and dying -- Chemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97221 , vital:31412
- Description: A series of BODIPY dyes functionalised with boronic acid in the 3,5-positions were successfully synthesised and characterised by using various analytical techniques. The dyes were prepared through a slight modification of the conventional acid catalysed condensation method. Phenylboronic acid moieties were added as styryl groups at the 3,5-positions of the 1,3,5,7-tetrametylBODIPY cores using a modified Knoevengal condensation method. The addition of the styryls resulted in the main absorption band of the dyes red-shifting to the 630−650 nm region. The photophysical and electrochemical properties of these dyes were studied to determine whether the dyes are suitable for use in the fluorescent, colourimetric and electrochemical detection of glucose. Boronic acid moieties were added as bioreceptor recognition elements because they have an affinity for carbohydrates and therefore would be able to bind and “detect” glucose. The series of BODIPY dyes did not show a “turn-on” fluorescence effect upon addition with glucose at the physiological pH. This was attributed on the basis of molecular modelling to the absence of an MO localised on the boronic-acid-substituted styryl moieties that lie close in energy to the HOMO and LUMO that facilitates the formation of an intramolecular charge transfer state. However, colourimetric changes that are visible to the naked eye are observed at basic pH when glucose was added to the dye solutions. The dyes exhibited favourable electrochemical behaviour and were able to detect glucose directly in this context when glassy carbon electrodes are modified through the drop dry method. A series of Sn(IV) porphyrins with thienyl and phenyl groups at the meso-positions were successfully synthesised and characterised. Pyridine and tetrabutyl axial ligands were added to the porphyrins to limit aggregation. The optical limiting properties of these porphyrins and three styrylated BODIPY dyes were studied in benzene and dichloromethane. Dyes were also embedded in polystyrene and studied as thin films to further gauge their suitability for use in optical limiting applications. Second-order hyperpolarizability, third-order susceptibly, non-linear absorption with reversible saturable absorption and the optical limiting threshold, were the parameters studied. Three of the four porphyrins and the three styrylated BODIPY dyes showed favourable optical limiting behaviour, which was further enhanced when the dyes are embedded in polymer thin films.
- Full Text:
- Date Issued: 2019
Bootstrap-based tolerance intervals for photovoltaic energy yield assessments
- Authors: Deyzel, Jani Igna
- Date: 2019
- Subjects: Bootstrap (Statistics) , Mathematical statistics Photovoltaic power systems
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39469 , vital:35256
- Description: The assessment of the energy yield of a photovoltaic (PV) system is one of the key assessments required by investors and developers. Currently, available methods used for this assessment only provide a point estimate as the final assessment. This study proposes a statistical technique which provides an additional energy yield assessment method by using tolerance intervals. Variance component models are used to better account for the variability present in the daily and hourly energy yields of three different PV modules. A bootstrap-based technique is used to obtain 𝛽-expectation and (𝛼,𝛽) two-sided tolerance intervals. These tolerance intervals provided more information with a content and confidence level for seasonal and yearly time-periods. In addition, the comparisons of the PV modules provide valuable information to investors and developers.
- Full Text:
- Date Issued: 2019
- Authors: Deyzel, Jani Igna
- Date: 2019
- Subjects: Bootstrap (Statistics) , Mathematical statistics Photovoltaic power systems
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39469 , vital:35256
- Description: The assessment of the energy yield of a photovoltaic (PV) system is one of the key assessments required by investors and developers. Currently, available methods used for this assessment only provide a point estimate as the final assessment. This study proposes a statistical technique which provides an additional energy yield assessment method by using tolerance intervals. Variance component models are used to better account for the variability present in the daily and hourly energy yields of three different PV modules. A bootstrap-based technique is used to obtain 𝛽-expectation and (𝛼,𝛽) two-sided tolerance intervals. These tolerance intervals provided more information with a content and confidence level for seasonal and yearly time-periods. In addition, the comparisons of the PV modules provide valuable information to investors and developers.
- Full Text:
- Date Issued: 2019
Carbon and nutrient storage of the Swartkops Estuary salt marsh and seagrass habitats
- Authors: Els, Jessica
- Date: 2019
- Subjects: Estuarine ecology -- South Africa -- Swartkops River Estuary , Salt marsh ecology -- South Africa -- Swartkops River Estuary Seagrasses -- Ecology Seagrasses -- Conservation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42196 , vital:36634
- Description: Coastal wetlands play an important role in filtering nutrient contaminants from water bodies and are also effective carbon sinks. These systems are known as blue carbon ecosystems. Blue carbon is defined as the carbon stored and sequestered by coastal vegetated habitats such as seagrasses, salt marsh and mangroves. These habitats are being lost on a global scale due to climate change and other anthropogenic pressures. Quantifying ecosystem services provided by these habitats may lead to better conservation and restoration strategies. Research on this topic has escalated over the past decade but there are no published studies in South Africa. The aim of this study was to quantify the carbon, nitrogen, and phosphorus stocks in the above and below ground tissues of Zostera capensis, Spartina maritima, and Salicornia tegetaria — a seagrass, salt marsh grass, and salt marsh succulent. This was done in both summer and winter to understand the variability of carbon and nutrient storage. The organic carbon stock of the sediment beneath these three species was also quantified. Results showed that S. maritima, S. tegetaria, and Z. capensis stored 16 ± 2.9 Mg C. ha-1, 4.3 ± 0.7 Mg C. ha-1, and 2.1 ± 0.5 Mg C. ha-1 in their respective biomass, and 247 ± 48 Mg C. ha-1, 212 ± 44 Mg C. ha-1, and 224 ± 38 Mg C. ha-1 respectively in the sediment beneath these habitats. This was determined by elemental analysis and the loss on ignition method (LOI). The sediment made up the dominant carbon pool in the estuary and there was very little seasonal variation, however spatial variation was evident. The sediment carbon stocks were similar to the global mean for salt marsh (255 Mg C. ha-1) and greater than the global mean for seagrass (108 Mg C. ha-1). The Swartkops Estuary stored a total (biomass and sediment carbon combined) of 14 094 Mg C in the Z. capensis area of 62 ha, 25 286 Mg C in the S. maritima area of 96 ha, and 5 916 Mg C in the S. tegetaria, covering an area of 27 ha. This is significantly less than what has been found globally in estuaries, but this is largely due to the smaller area cover of these macrophytes. The amount of carbon stored per hectare is much larger in this South African system than in many international studies — possibly due to the high levels of pollution coming into the system. Nitrogen and phosphorus stocks in the plants fluctuated seasonally in relation to the nutrient input to the estuary, with the greatest stocks found in winter in Z. capensis, S. maritima, and S. tegetaria (0.42 ± 0.03 Mg N. ha-1, 1.6 ± 0.13 Mg N. ha-1, and 0.37 ± 0.02 Mg N. ha-1, respectively; and 0.4 ± 0.03 Mg P. ha-1, 1.2 ± 0.10 Mg P. ha-1 in Z. capensis and S. maritima respectively) because nutrient inputs to the system were highest in winter, however the P stocks in S. tegetaria were greatest in summer (0.35 ± 0.04 Mg P. ha-1). The reason for this difference is because of their ability to store phosphorus better than nitrogen and for longer periods of time due to luxury uptake. Salicornia tegetaria N and P stocks were also lower than the other two species, possibly due to its placement along the intertidal gradient, as it is not tidally inundated for as long as the other two species. The Z. capensis and S. maritima at Site 1 showed extremely high amounts of nitrogen in their tissues (105.3 ± 1.6 g kg-1 and 74.91 ± 4.1 g kg-1 respectively). This is due to the area being a depositional site as it was an old oyster farm and experiences little tidal flushing from the sea despite its proximity to the mouth. Nutrient ratios and N: biomass were determined as an indication of nutrient pollution. The N: biomass was low in both seasons in Z. capensis, S. maritima, and S. tegetaria (0.08, 0.02, 0.04 respectively) indicating consistant eutrophic conditions in the estuary. Plant biomass was a better indicator of nutrient pollution than epiphytes which were very low in the Swartkops Estuary and did not prove as a useful indicator of nutrient enrichment. These results can inform local management plans of the ecosystem service potential of these species and how they should be protected for future and current sustainable use as filters for nutrient pollution to keep the water quality in a better state. It also outlines the current state of blue carbon and nutrient stocks in an urban South African estuary.
- Full Text:
- Date Issued: 2019
- Authors: Els, Jessica
- Date: 2019
- Subjects: Estuarine ecology -- South Africa -- Swartkops River Estuary , Salt marsh ecology -- South Africa -- Swartkops River Estuary Seagrasses -- Ecology Seagrasses -- Conservation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42196 , vital:36634
- Description: Coastal wetlands play an important role in filtering nutrient contaminants from water bodies and are also effective carbon sinks. These systems are known as blue carbon ecosystems. Blue carbon is defined as the carbon stored and sequestered by coastal vegetated habitats such as seagrasses, salt marsh and mangroves. These habitats are being lost on a global scale due to climate change and other anthropogenic pressures. Quantifying ecosystem services provided by these habitats may lead to better conservation and restoration strategies. Research on this topic has escalated over the past decade but there are no published studies in South Africa. The aim of this study was to quantify the carbon, nitrogen, and phosphorus stocks in the above and below ground tissues of Zostera capensis, Spartina maritima, and Salicornia tegetaria — a seagrass, salt marsh grass, and salt marsh succulent. This was done in both summer and winter to understand the variability of carbon and nutrient storage. The organic carbon stock of the sediment beneath these three species was also quantified. Results showed that S. maritima, S. tegetaria, and Z. capensis stored 16 ± 2.9 Mg C. ha-1, 4.3 ± 0.7 Mg C. ha-1, and 2.1 ± 0.5 Mg C. ha-1 in their respective biomass, and 247 ± 48 Mg C. ha-1, 212 ± 44 Mg C. ha-1, and 224 ± 38 Mg C. ha-1 respectively in the sediment beneath these habitats. This was determined by elemental analysis and the loss on ignition method (LOI). The sediment made up the dominant carbon pool in the estuary and there was very little seasonal variation, however spatial variation was evident. The sediment carbon stocks were similar to the global mean for salt marsh (255 Mg C. ha-1) and greater than the global mean for seagrass (108 Mg C. ha-1). The Swartkops Estuary stored a total (biomass and sediment carbon combined) of 14 094 Mg C in the Z. capensis area of 62 ha, 25 286 Mg C in the S. maritima area of 96 ha, and 5 916 Mg C in the S. tegetaria, covering an area of 27 ha. This is significantly less than what has been found globally in estuaries, but this is largely due to the smaller area cover of these macrophytes. The amount of carbon stored per hectare is much larger in this South African system than in many international studies — possibly due to the high levels of pollution coming into the system. Nitrogen and phosphorus stocks in the plants fluctuated seasonally in relation to the nutrient input to the estuary, with the greatest stocks found in winter in Z. capensis, S. maritima, and S. tegetaria (0.42 ± 0.03 Mg N. ha-1, 1.6 ± 0.13 Mg N. ha-1, and 0.37 ± 0.02 Mg N. ha-1, respectively; and 0.4 ± 0.03 Mg P. ha-1, 1.2 ± 0.10 Mg P. ha-1 in Z. capensis and S. maritima respectively) because nutrient inputs to the system were highest in winter, however the P stocks in S. tegetaria were greatest in summer (0.35 ± 0.04 Mg P. ha-1). The reason for this difference is because of their ability to store phosphorus better than nitrogen and for longer periods of time due to luxury uptake. Salicornia tegetaria N and P stocks were also lower than the other two species, possibly due to its placement along the intertidal gradient, as it is not tidally inundated for as long as the other two species. The Z. capensis and S. maritima at Site 1 showed extremely high amounts of nitrogen in their tissues (105.3 ± 1.6 g kg-1 and 74.91 ± 4.1 g kg-1 respectively). This is due to the area being a depositional site as it was an old oyster farm and experiences little tidal flushing from the sea despite its proximity to the mouth. Nutrient ratios and N: biomass were determined as an indication of nutrient pollution. The N: biomass was low in both seasons in Z. capensis, S. maritima, and S. tegetaria (0.08, 0.02, 0.04 respectively) indicating consistant eutrophic conditions in the estuary. Plant biomass was a better indicator of nutrient pollution than epiphytes which were very low in the Swartkops Estuary and did not prove as a useful indicator of nutrient enrichment. These results can inform local management plans of the ecosystem service potential of these species and how they should be protected for future and current sustainable use as filters for nutrient pollution to keep the water quality in a better state. It also outlines the current state of blue carbon and nutrient stocks in an urban South African estuary.
- Full Text:
- Date Issued: 2019
Categorising Network Telescope data using big data enrichment techniques
- Authors: Davis, Michael Reginald
- Date: 2019
- Subjects: Denial of service attacks , Big data , Computer networks -- Security measures
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92941 , vital:30766
- Description: Network Telescopes, Internet backbone sampling, IDS and other forms of network-sourced Threat Intelligence provide researchers with insight into the methods and intent of remote entities by capturing network traffic and analysing the resulting data. This analysis and determination of intent is made difficult by the large amounts of potentially malicious traffic, coupled with limited amount of knowledge that can be attributed to the source of the incoming data, as the source is known only by its IP address. Due to the lack of commonly available tooling, many researchers start this analysis from the beginning and so repeat and re-iterate previous research as the bulk of their work. As a result new insight into methods and approaches of analysis is gained at a high cost. Our research approaches this problem by using additional knowledge about the source IP address such as open ports, reverse and forward DNS, BGP routing tables and more, to enhance the researcher's ability to understand the traffic source. The research is a BigData experiment, where large (hundreds of GB) datasets are merged with a two month section of Network Telescope data using a set of Python scripts. The result are written to a Google BigQuery database table. Analysis of the network data is greatly simplified, with questions about the nature of the source, such as its device class (home routing device or server), potential vulnerabilities (open telnet ports or databases) and location becoming relatively easy to answer. Using this approach, researchers can focus on the questions that need answering and efficiently address them. This research could be taken further by using additional data sources such as Geo-location, WHOIS lookups, Threat Intelligence feeds and many others. Other potential areas of research include real-time categorisation of incoming packets, in order to better inform alerting and reporting systems' configuration. In conclusion, categorising Network Telescope data in this way provides insight into the intent of the (apparent) originator and as such is a valuable tool for those seeking to understand the purpose and intent of arriving packets. In particular, the ability to remove packets categorised as non-malicious (e.g. those in the Research category) from the data eliminates a known source of `noise' from the data. This allows the researcher to focus their efforts in a more productive manner.
- Full Text:
- Date Issued: 2019
- Authors: Davis, Michael Reginald
- Date: 2019
- Subjects: Denial of service attacks , Big data , Computer networks -- Security measures
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92941 , vital:30766
- Description: Network Telescopes, Internet backbone sampling, IDS and other forms of network-sourced Threat Intelligence provide researchers with insight into the methods and intent of remote entities by capturing network traffic and analysing the resulting data. This analysis and determination of intent is made difficult by the large amounts of potentially malicious traffic, coupled with limited amount of knowledge that can be attributed to the source of the incoming data, as the source is known only by its IP address. Due to the lack of commonly available tooling, many researchers start this analysis from the beginning and so repeat and re-iterate previous research as the bulk of their work. As a result new insight into methods and approaches of analysis is gained at a high cost. Our research approaches this problem by using additional knowledge about the source IP address such as open ports, reverse and forward DNS, BGP routing tables and more, to enhance the researcher's ability to understand the traffic source. The research is a BigData experiment, where large (hundreds of GB) datasets are merged with a two month section of Network Telescope data using a set of Python scripts. The result are written to a Google BigQuery database table. Analysis of the network data is greatly simplified, with questions about the nature of the source, such as its device class (home routing device or server), potential vulnerabilities (open telnet ports or databases) and location becoming relatively easy to answer. Using this approach, researchers can focus on the questions that need answering and efficiently address them. This research could be taken further by using additional data sources such as Geo-location, WHOIS lookups, Threat Intelligence feeds and many others. Other potential areas of research include real-time categorisation of incoming packets, in order to better inform alerting and reporting systems' configuration. In conclusion, categorising Network Telescope data in this way provides insight into the intent of the (apparent) originator and as such is a valuable tool for those seeking to understand the purpose and intent of arriving packets. In particular, the ability to remove packets categorised as non-malicious (e.g. those in the Research category) from the data eliminates a known source of `noise' from the data. This allows the researcher to focus their efforts in a more productive manner.
- Full Text:
- Date Issued: 2019