A 150 MHz all sky survey with the Precision Array to Probe the Epoch of Reionization
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
- Full Text:
- Date Issued: 2020
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
- Full Text:
- Date Issued: 2020
Preparation and evaluation of captopril - ion exchange resin complexes
- Chikukwa, Mellisa Tafadzwa Ruramai
- Authors: Chikukwa, Mellisa Tafadzwa Ruramai
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59146 , vital:27441
- Description: Restricted access-thesis embargoed for 2 years
- Full Text:
- Date Issued: 2017
- Authors: Chikukwa, Mellisa Tafadzwa Ruramai
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59146 , vital:27441
- Description: Restricted access-thesis embargoed for 2 years
- Full Text:
- Date Issued: 2017
Development of graphene materials and phthalocyanines for application in dye-sensitized solar cells
- Authors: Chindeka, Francis
- Date: 2020
- Subjects: Dye-sensitized solar cells , Graphene , Phthalocyanines , Molecular orbitals , Impedance spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166092 , vital:41328
- Description: Two sets of dye-sensitized solar cells (DSSCs) were fabricated. In the first set, dye-sensitized solar cells (DSSC) were fabricated by incorporating graphene materials as catalysts at the counter electrode. Platinum was also used as a catalyst for comparative purposes. Different phthalocyanines: hydroxyl indium tetracarboxyphenoxy phthalocyanine (1), chloro indium octacarboxy phthalocyanine (2) and dibenzoic acid silicon phthalocyanine (3) were used as dyes. Complex 3 gave the highest power conversion efficiency (η) of 3.19% when using nitrogen doped reduced graphene oxide nanosheets (NrGONS) as a catalyst at the counter electrode, and TiO2 containing rGONS at the anode. The value obtained is close to 3.8% obtained when using Pt catalyst instead of NrGONS at the cathode, thus confirming that NrGONS is a promising candidate to replace the more expensive Pt. The study also shows that placing rGONS on both the anode and cathode improves efficiency. In the second set, DSSCs were fabricated by using 2(3,5-biscarboxyphenoxy), 9(10), 16(17), 23(24)-tri(tertbutyl) phthalocyaninato Cu (4) and Zn (5) complexes as dyes on the ITO-TiO2 photoanodes containing reduced graphene oxide nanosheets (rGONS) or nitrogen-doped rGONS (NrGONS). The evaluation of the assembled DSSCs revealed that using ITO-TiO2-NrGONS-CuPc (4) photoanode had the highest fill factor (FF) and power conversion efficiency (ɳ) of 69 % and 4.36 % respectively. These results show that the asymmetrical phthalocyanine complexes (4) and (5) showed significant improvement on the performance of the DSSC compared to previous work on symmetrical carboxylated phthalocyanines with ɳ = 3.19%.
- Full Text:
- Date Issued: 2020
- Authors: Chindeka, Francis
- Date: 2020
- Subjects: Dye-sensitized solar cells , Graphene , Phthalocyanines , Molecular orbitals , Impedance spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166092 , vital:41328
- Description: Two sets of dye-sensitized solar cells (DSSCs) were fabricated. In the first set, dye-sensitized solar cells (DSSC) were fabricated by incorporating graphene materials as catalysts at the counter electrode. Platinum was also used as a catalyst for comparative purposes. Different phthalocyanines: hydroxyl indium tetracarboxyphenoxy phthalocyanine (1), chloro indium octacarboxy phthalocyanine (2) and dibenzoic acid silicon phthalocyanine (3) were used as dyes. Complex 3 gave the highest power conversion efficiency (η) of 3.19% when using nitrogen doped reduced graphene oxide nanosheets (NrGONS) as a catalyst at the counter electrode, and TiO2 containing rGONS at the anode. The value obtained is close to 3.8% obtained when using Pt catalyst instead of NrGONS at the cathode, thus confirming that NrGONS is a promising candidate to replace the more expensive Pt. The study also shows that placing rGONS on both the anode and cathode improves efficiency. In the second set, DSSCs were fabricated by using 2(3,5-biscarboxyphenoxy), 9(10), 16(17), 23(24)-tri(tertbutyl) phthalocyaninato Cu (4) and Zn (5) complexes as dyes on the ITO-TiO2 photoanodes containing reduced graphene oxide nanosheets (rGONS) or nitrogen-doped rGONS (NrGONS). The evaluation of the assembled DSSCs revealed that using ITO-TiO2-NrGONS-CuPc (4) photoanode had the highest fill factor (FF) and power conversion efficiency (ɳ) of 69 % and 4.36 % respectively. These results show that the asymmetrical phthalocyanine complexes (4) and (5) showed significant improvement on the performance of the DSSC compared to previous work on symmetrical carboxylated phthalocyanines with ɳ = 3.19%.
- Full Text:
- Date Issued: 2020
An investigation into the readiness of open source software to build a Telco Cloud for virtualising network functions
- Authors: Chindeka, Tapiwa C
- Date: 2020
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/124320 , vital:35593
- Description: Cloud computing offers new mechanisms that change the way networks can be created and managed. The increased demand for multimedia and Internet of Things (IoT) services using the Internet Protocol is also fueling the need to look more into a networking approach that is less reliant on physical hardware components and allows new networks and network components to be created on-demand. Network Function Virtualisation (NFV) is a networking paradigm that decouples network functions from the hardware on which they run on. This offers new approaches to telecommunication providers who are looking to new ways of improving Quality of Service (QoS) in cost effective ways. Cloud technologies have given way to more specialised cloud environments such as the telco cloud. The telco cloud is a cloud environment where telecommunication services are hosted utilising NFV techniques. As the use of telecommunication standards moves towards 5G, network services will be provided in a virtualised manner in order to keep up with the demand. Open source software is a driver for innovation as it is has a collaborative culture to support it. This research investigates the readiness of open source tools to build a telco cloud that supports functions such as autoscaling and fault tolerance. Currently available open source software was explored for the different aspects involved in building a cloud from the ground up. The ETSI NFV MANO framework is also discussed as it is a widely used guiding standard for implementing NFV. Guided by the ETSI NFV MANO framework, open source software was used in an experiment to build a resilient cloud environment in which a virtualised IP Multimedia Subsystem (vIMS) network was deployed. Through this experimentation, it is evident that open source tools are mature enough to build the cloud environment and its ETSI NFV MANO compliant orchestration. However, features such as autoscaling and fault tolerance are still fairly immature and experimental.
- Full Text:
- Date Issued: 2020
- Authors: Chindeka, Tapiwa C
- Date: 2020
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/124320 , vital:35593
- Description: Cloud computing offers new mechanisms that change the way networks can be created and managed. The increased demand for multimedia and Internet of Things (IoT) services using the Internet Protocol is also fueling the need to look more into a networking approach that is less reliant on physical hardware components and allows new networks and network components to be created on-demand. Network Function Virtualisation (NFV) is a networking paradigm that decouples network functions from the hardware on which they run on. This offers new approaches to telecommunication providers who are looking to new ways of improving Quality of Service (QoS) in cost effective ways. Cloud technologies have given way to more specialised cloud environments such as the telco cloud. The telco cloud is a cloud environment where telecommunication services are hosted utilising NFV techniques. As the use of telecommunication standards moves towards 5G, network services will be provided in a virtualised manner in order to keep up with the demand. Open source software is a driver for innovation as it is has a collaborative culture to support it. This research investigates the readiness of open source tools to build a telco cloud that supports functions such as autoscaling and fault tolerance. Currently available open source software was explored for the different aspects involved in building a cloud from the ground up. The ETSI NFV MANO framework is also discussed as it is a widely used guiding standard for implementing NFV. Guided by the ETSI NFV MANO framework, open source software was used in an experiment to build a resilient cloud environment in which a virtualised IP Multimedia Subsystem (vIMS) network was deployed. Through this experimentation, it is evident that open source tools are mature enough to build the cloud environment and its ETSI NFV MANO compliant orchestration. However, features such as autoscaling and fault tolerance are still fairly immature and experimental.
- Full Text:
- Date Issued: 2020
Gaining cyber security insight through an analysis of open source intelligence data: an East African case study
- Authors: Chindipha, Stones Dalitso
- Date: 2018
- Subjects: Open source intelligence -- Africa, East , Computer security -- Africa, East , Computer networks -- Security measures -- Africa, East , Denial of service attacks -- Africa, East , Sentient Hvper-Optimised Data Access Network (SHODAN) , Internet Background Radiation (IBR)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60618 , vital:27805
- Description: With each passing year the number of Internet users and connected devices grows, and this is particularly so in Africa. This growth brings with it an increase in the prevalence cyber-attacks. Looking at the current state of affairs, cybersecurity incidents are more likely to increase in African countries mainly due to the increased prevalence and affordability of broadband connectivity which is coupled with lack of online security awareness. The adoption of mobile banking has aggravated the situation making the continent more attractive to hackers who bank on the malpractices of users. Using Open Source Intelligence (OSINT) data sources like Sentient Hvper-Optimised Data Access Network (SHODAN) and Internet Background Radiation (IBR), this research explores the prevalence of vulnerabilities and their accessibility to evber threat actors. The research focuses on the East African Community (EAC) comprising of Tanzania, Kenya, Malawi, and Uganda, An IBR data set collected by a Rhodes University network telescope spanning over 72 months was used in this research, along with two snapshot period of data from the SHODAN project. The findings shows that there is a significant risk to systems within the EAC, particularly using the SHODAN data. The MITRE CVSS threat scoring system was applied to this research using FREAK and Heartbleed as sample vulnerabilities identified in EAC, When looking at IBR, the research has shown that attackers can use either destination ports or IP source addresses to perform an attack which if not attended to may be reused yearly until later on move to the allocated IP address space once it starts making random probes. The moment it finds one vulnerable client on the network it spreads throughout like a worm, DDoS is one the attacks that can be generated from IBR, Since the SHODAN dataset had two collection points, the study has shown the changes that have occurred in Malawi and Tanzania for a period of 14 months by using three variables i.e, device type, operating systems, and ports. The research has also identified vulnerable devices in all the four countries. Apart from that, the study identified operating systems, products, OpenSSL, ports and ISPs as some of the variables that can be used to identify vulnerabilities in systems. In the ease of OpenSSL and products, this research went further by identifying the type of attack that can occur and its associated CVE-ID.
- Full Text:
- Date Issued: 2018
- Authors: Chindipha, Stones Dalitso
- Date: 2018
- Subjects: Open source intelligence -- Africa, East , Computer security -- Africa, East , Computer networks -- Security measures -- Africa, East , Denial of service attacks -- Africa, East , Sentient Hvper-Optimised Data Access Network (SHODAN) , Internet Background Radiation (IBR)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60618 , vital:27805
- Description: With each passing year the number of Internet users and connected devices grows, and this is particularly so in Africa. This growth brings with it an increase in the prevalence cyber-attacks. Looking at the current state of affairs, cybersecurity incidents are more likely to increase in African countries mainly due to the increased prevalence and affordability of broadband connectivity which is coupled with lack of online security awareness. The adoption of mobile banking has aggravated the situation making the continent more attractive to hackers who bank on the malpractices of users. Using Open Source Intelligence (OSINT) data sources like Sentient Hvper-Optimised Data Access Network (SHODAN) and Internet Background Radiation (IBR), this research explores the prevalence of vulnerabilities and their accessibility to evber threat actors. The research focuses on the East African Community (EAC) comprising of Tanzania, Kenya, Malawi, and Uganda, An IBR data set collected by a Rhodes University network telescope spanning over 72 months was used in this research, along with two snapshot period of data from the SHODAN project. The findings shows that there is a significant risk to systems within the EAC, particularly using the SHODAN data. The MITRE CVSS threat scoring system was applied to this research using FREAK and Heartbleed as sample vulnerabilities identified in EAC, When looking at IBR, the research has shown that attackers can use either destination ports or IP source addresses to perform an attack which if not attended to may be reused yearly until later on move to the allocated IP address space once it starts making random probes. The moment it finds one vulnerable client on the network it spreads throughout like a worm, DDoS is one the attacks that can be generated from IBR, Since the SHODAN dataset had two collection points, the study has shown the changes that have occurred in Malawi and Tanzania for a period of 14 months by using three variables i.e, device type, operating systems, and ports. The research has also identified vulnerable devices in all the four countries. Apart from that, the study identified operating systems, products, OpenSSL, ports and ISPs as some of the variables that can be used to identify vulnerabilities in systems. In the ease of OpenSSL and products, this research went further by identifying the type of attack that can occur and its associated CVE-ID.
- Full Text:
- Date Issued: 2018
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
A study of why some physic concepts in the South African Physical Science curriculum are poorly understood in order to develop a targeted action-research intervention for Newton’s second law
- Authors: Cobbing, Kathleen Margaret
- Date: 2020
- Subjects: Physics -- Study and teaching (Secondary) -- South Africa , Physics -- Examinations, questions, etc. -- South Africa , Motion -- Study and teaching (Secondary) -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146903 , vital:38575
- Description: Globally, many students show a poor understanding of concepts in high school physics and lack the necessary problem-solving skills that the course demands. The application of Newton’s second law was found to be particularly problematic through document analysis of South African examination feedback reports, as well as from an analysis of the physics examinations at a pair of well-resourced South African independent schools that follow the Independent Examination Board curriculum. Through an action-research approach, a resource for use by students was designed and modified to improve students’ understanding of this concept, while modelling problemsolving methods. The resource consisted of brief revision notes, worked examples and scaffolded exercises. The design of the resource was influenced by the theory of cognitive apprenticeship, cognitive load theory and conceptual change theory. One of the aims of the resource was to encourage students to translate between the different representations of a problem situation: symbolic, abstract, model and concrete. The impact of this resource was evaluated at a pair of schools using a mixed methods approach. This incorporated pre- and post-tests for a quantitative assessment, qualitative student evaluations and the analysis of examination scripts. There was an improvement from pre- to post-test for all four iterations of the intervention and these improvements were shown to be significant. The use of the resource led to an increase in the quality and quantity of diagrams drawn by students in subsequent assessments.
- Full Text:
- Date Issued: 2020
- Authors: Cobbing, Kathleen Margaret
- Date: 2020
- Subjects: Physics -- Study and teaching (Secondary) -- South Africa , Physics -- Examinations, questions, etc. -- South Africa , Motion -- Study and teaching (Secondary) -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146903 , vital:38575
- Description: Globally, many students show a poor understanding of concepts in high school physics and lack the necessary problem-solving skills that the course demands. The application of Newton’s second law was found to be particularly problematic through document analysis of South African examination feedback reports, as well as from an analysis of the physics examinations at a pair of well-resourced South African independent schools that follow the Independent Examination Board curriculum. Through an action-research approach, a resource for use by students was designed and modified to improve students’ understanding of this concept, while modelling problemsolving methods. The resource consisted of brief revision notes, worked examples and scaffolded exercises. The design of the resource was influenced by the theory of cognitive apprenticeship, cognitive load theory and conceptual change theory. One of the aims of the resource was to encourage students to translate between the different representations of a problem situation: symbolic, abstract, model and concrete. The impact of this resource was evaluated at a pair of schools using a mixed methods approach. This incorporated pre- and post-tests for a quantitative assessment, qualitative student evaluations and the analysis of examination scripts. There was an improvement from pre- to post-test for all four iterations of the intervention and these improvements were shown to be significant. The use of the resource led to an increase in the quality and quantity of diagrams drawn by students in subsequent assessments.
- Full Text:
- Date Issued: 2020
Understanding the extension capacity needs of the CapeNature Stewardship Programme in the Western Cape Province of South Africa
- Coetzee, Johannes Christiaan
- Authors: Coetzee, Johannes Christiaan
- Date: 2018
- Subjects: Conservation projects (Natural resources) , Psychometrics , Adaptive natural resource management , Biodiversity conservation , CapeNature Stewardship Programme
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63220 , vital:28383
- Description: There is an increasing call for conservation programmes to provide sound evidence of effectiveness, and employing empirical evaluations can assist in the transition to evidence-based conservation practices. The objectives of this research were to develop a logic model for the CapeNature Stewardship Programme which would articulate the programme's theory of operation with respect to its Stewardship Programme landholders. The second major objective was to develop psychometric instruments for assessing the motivations and satisfactions of the programme's stewardship landholders. Both objectives included the aim to provide robust and repeatable instruments for exploring landholder's psychology, and developing a programme's theory of operation to understand the programme and improve with understanding the needs of the landowners. In this regard the processes and methodologies employed represent a major component of this research. A mixed methods approach was utilized, including stakeholder and volunteer surveys, conducted via mailing hardcopies and the internet, together with three focus groups held with the programme's management, extension staff and the stewardship landholders. Analysis of the data thus collected included both qualitative and quantitative approaches, specifically coding and content analysis, together with statistical tests of internal consistency, factor analysis and doubling correspondence analysis. Robust indices for example validity and internal consistency were developed for assessing landholder’s satisfaction with extension and level of satisfaction with the stewardship programme (Babbie 2007). These indices revealed that landholders in the Stewardship Programme are not satisfied with the programme, and exhibit behaviours suggesting they act as advocates for the programme. Demographic data and additional information provided further insights into the programme. The development of a method for articulating the programme's theory of operation is represented, together with four logic models which graphically illustrate this theory. This process and theory allowed for recommendations to be provided for the programme's improvement. A platform for adaptive management and further evaluations of this, and similar programmes, represents a major outcome of this research, understanding the extension capacity needs for the conservation of biodiversity in the CapeNature Stewardship Programme to function as a model for improving the implementation of the programme across the Western Cape, South Africa. This research feeds into an evaluation of CapeNature’s Biodiveristy Stewardship programme and demonstrates the importance of incorporating psychology into conservation interventions.
- Full Text:
- Date Issued: 2018
- Authors: Coetzee, Johannes Christiaan
- Date: 2018
- Subjects: Conservation projects (Natural resources) , Psychometrics , Adaptive natural resource management , Biodiversity conservation , CapeNature Stewardship Programme
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63220 , vital:28383
- Description: There is an increasing call for conservation programmes to provide sound evidence of effectiveness, and employing empirical evaluations can assist in the transition to evidence-based conservation practices. The objectives of this research were to develop a logic model for the CapeNature Stewardship Programme which would articulate the programme's theory of operation with respect to its Stewardship Programme landholders. The second major objective was to develop psychometric instruments for assessing the motivations and satisfactions of the programme's stewardship landholders. Both objectives included the aim to provide robust and repeatable instruments for exploring landholder's psychology, and developing a programme's theory of operation to understand the programme and improve with understanding the needs of the landowners. In this regard the processes and methodologies employed represent a major component of this research. A mixed methods approach was utilized, including stakeholder and volunteer surveys, conducted via mailing hardcopies and the internet, together with three focus groups held with the programme's management, extension staff and the stewardship landholders. Analysis of the data thus collected included both qualitative and quantitative approaches, specifically coding and content analysis, together with statistical tests of internal consistency, factor analysis and doubling correspondence analysis. Robust indices for example validity and internal consistency were developed for assessing landholder’s satisfaction with extension and level of satisfaction with the stewardship programme (Babbie 2007). These indices revealed that landholders in the Stewardship Programme are not satisfied with the programme, and exhibit behaviours suggesting they act as advocates for the programme. Demographic data and additional information provided further insights into the programme. The development of a method for articulating the programme's theory of operation is represented, together with four logic models which graphically illustrate this theory. This process and theory allowed for recommendations to be provided for the programme's improvement. A platform for adaptive management and further evaluations of this, and similar programmes, represents a major outcome of this research, understanding the extension capacity needs for the conservation of biodiversity in the CapeNature Stewardship Programme to function as a model for improving the implementation of the programme across the Western Cape, South Africa. This research feeds into an evaluation of CapeNature’s Biodiveristy Stewardship programme and demonstrates the importance of incorporating psychology into conservation interventions.
- Full Text:
- Date Issued: 2018
Assessing the genetic diversity of catface rockcod epinephelus andersoni in the subtropical Western Indian Ocean and modelling the effects of climate change on their distribution
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
Assessment of the long-term response to rehabilitation of two wetlands in KwaZulu-Natal, South Africa
- Authors: Cowden, Craig
- Date: 2018
- Subjects: Wetlands -- South Africa -- KwaZulu-Natal Wetland restoration -- South Africa -- KwaZulu-Natal Wetland management -- South Africa -- KwaZulu-Natal Wetland conservation -- South Africa -- KwaZulu-Natal Wetland ecology -- South Africa -- KwaZulu-Natal Ecosystem management -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60606 , vital:27802
- Description: Assessing the outputs and outcomes of wetland rehabilitation activities is recognised by the 'Working for Wetlands' programme in South Africa as important, but to date has been limited. An assessment of the ecological outcomes and the structural outputs of the Working for Wetlands rehabilitation implemented in the Killarney and Kruisfontein wetlands, KwaZulu-Natal, in 2005 was undertaken. The assessment of outcomes included an evaluation of the changes in terms of ecological integrity and the supply of ecosystem services, using WET-Health and WET- EcoServices assessment techniques respectively, and vegetation composition. Improvements in hydrological and geomorphic integrity were recorded in both wetlands, resulting in improved ecosystem services delivery. However, investigation of vegetation composition using the Wetland Index Value and Floristic Quality Assessment Index showed that, seven years after rehabilitation, KiNamey's vegetation composition had improved, but Kruisfontein's vegetation was still largely dominated by pioneer species and appeared to be stable, but in a severely transformed state. The response of these wetlands has shown that sites for rehabilitation should be screened before work begins, and wetlands requiring intensive management of vegetation recovery should be assessed in terms of the objectives and the anticipated benefits of the project. The assessment of the outputs included an evaluation of structural integrity, survival and cost- effectiveness. Limited issues, mostly relating to deviations from the designs during construction, were identified with regards to the structural outputs at each of the wetlands. However, the spreader canals at both Killarney and Kruisfontein wetlands were not functioning as intended and concentrated flows from the spreader canals were evident in both wetlands. The use of spreader canals should therefore be carefully planned and implemented for future wetland rehabilitation projects. Consideration of ZAR per hectare equivalent re-instated/secured provided a useful initial means of determining the cost-effectiveness of the wetland rehabilitation. However, additional factors need to be considered, such as, the nature of the rehabilitation activities, the type and size of the problem being addressed, rehabilitation of priority wetlands, limitations imposed by funders, and risks that need to be addressed by the rehabilitation strategy. Furthermore, the evaluation of the Killarney and Kruisfontein wetlands highlighted the need to revise the Water Research Commission's Wetland Management Series, especially those documents or guidelines relating to rehabilitation planning (WET-RehabPlan), interventions (WET-RehabMethods), and monitoring and evaluation (WET-RehabEvaluate).
- Full Text:
- Date Issued: 2018
- Authors: Cowden, Craig
- Date: 2018
- Subjects: Wetlands -- South Africa -- KwaZulu-Natal Wetland restoration -- South Africa -- KwaZulu-Natal Wetland management -- South Africa -- KwaZulu-Natal Wetland conservation -- South Africa -- KwaZulu-Natal Wetland ecology -- South Africa -- KwaZulu-Natal Ecosystem management -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60606 , vital:27802
- Description: Assessing the outputs and outcomes of wetland rehabilitation activities is recognised by the 'Working for Wetlands' programme in South Africa as important, but to date has been limited. An assessment of the ecological outcomes and the structural outputs of the Working for Wetlands rehabilitation implemented in the Killarney and Kruisfontein wetlands, KwaZulu-Natal, in 2005 was undertaken. The assessment of outcomes included an evaluation of the changes in terms of ecological integrity and the supply of ecosystem services, using WET-Health and WET- EcoServices assessment techniques respectively, and vegetation composition. Improvements in hydrological and geomorphic integrity were recorded in both wetlands, resulting in improved ecosystem services delivery. However, investigation of vegetation composition using the Wetland Index Value and Floristic Quality Assessment Index showed that, seven years after rehabilitation, KiNamey's vegetation composition had improved, but Kruisfontein's vegetation was still largely dominated by pioneer species and appeared to be stable, but in a severely transformed state. The response of these wetlands has shown that sites for rehabilitation should be screened before work begins, and wetlands requiring intensive management of vegetation recovery should be assessed in terms of the objectives and the anticipated benefits of the project. The assessment of the outputs included an evaluation of structural integrity, survival and cost- effectiveness. Limited issues, mostly relating to deviations from the designs during construction, were identified with regards to the structural outputs at each of the wetlands. However, the spreader canals at both Killarney and Kruisfontein wetlands were not functioning as intended and concentrated flows from the spreader canals were evident in both wetlands. The use of spreader canals should therefore be carefully planned and implemented for future wetland rehabilitation projects. Consideration of ZAR per hectare equivalent re-instated/secured provided a useful initial means of determining the cost-effectiveness of the wetland rehabilitation. However, additional factors need to be considered, such as, the nature of the rehabilitation activities, the type and size of the problem being addressed, rehabilitation of priority wetlands, limitations imposed by funders, and risks that need to be addressed by the rehabilitation strategy. Furthermore, the evaluation of the Killarney and Kruisfontein wetlands highlighted the need to revise the Water Research Commission's Wetland Management Series, especially those documents or guidelines relating to rehabilitation planning (WET-RehabPlan), interventions (WET-RehabMethods), and monitoring and evaluation (WET-RehabEvaluate).
- Full Text:
- Date Issued: 2018
Factors influencing estuarine and coastal connectivity of an estuarine-dependent fishery species, Pomadasys commersonnii (Haemulidae)
- Authors: Dames, Michael Henri
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62307 , vital:28153
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
- Authors: Dames, Michael Henri
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/62307 , vital:28153
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
The effect of habitat and spatial management on reef fish in an established marine protected area
- Authors: Dames, Vivienne Abigail
- Date: 2021
- Subjects: iSimangaliso Wetland Park (South Africa) -- Management , Reef fishes -- South Africa -- KwaZulu-Natal , Baited remote underwater stereo-video systems (stereo-BRUVs) , Marine parks and reserves -- Monitoring -- South Africa -- KwaZulu-Natal , Fish populations -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171150 , vital:42024
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
- Date Issued: 2021
- Authors: Dames, Vivienne Abigail
- Date: 2021
- Subjects: iSimangaliso Wetland Park (South Africa) -- Management , Reef fishes -- South Africa -- KwaZulu-Natal , Baited remote underwater stereo-video systems (stereo-BRUVs) , Marine parks and reserves -- Monitoring -- South Africa -- KwaZulu-Natal , Fish populations -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171150 , vital:42024
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
- Date Issued: 2021
Improving the cold tolerance of false codling moth, thaumatotibia leucotreta, for better performance in a sterile insect release programme
- Authors: Daniel, Claire Ashleigh
- Date: 2017
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Reproduction -- Effect of temperature on , 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
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5271 , vital:20803
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is a major pest of citrus and other important crops in Sub-Saharan Africa. The introduction of a sterile insect technique (SIT) programme for FCM in South Africa has proven to be very effective in the control of FCM. The objective was to flood citrus orchards with large numbers of sterile males resulting in a ratio of at least 10 sterile to 1 wild moth, increasing the probability of a female moth mating with a sterile male. This target is often achieved and the programme is generally successful, however there are some challenges regarding this programme. The mass rearing environment, artificial diet, handling methods and irradiation have an impact on sterile insect quality as environmental differences between the rearing facility and field, influences the insect phenotype and competitiveness. This is evident as wild male moths can theoretically actively fly at a temperature of 12°C and laboratory-reared sterilized moths, due to the radiation treatment, appear unable to fly below 20°C. As a consequence, sterile males are out-competed by wild males during the cooler months of the year. This is detrimental to the SIT programme as FCM do not undergo diapause, meaning they are active during winter and will still reproduce. Therefore, to maximize the effect of the SIT programme, it is vital to increase the flight ability of mass reared sterile males at lower temperatures. Various studies have shown that by adding cryoprotectants to the basic laboratory diets increases the cold tolerance of certain insects and thus may allow them to be mobile at lower temperatures, however it imperative that any chemical used to augment the commercial diet of the insect has no negative effects on the insect physiology and development. To investigate this detail for FCM, five generations of FCM were reared on diets augmented with various known insect cryoprotectants. These augmented FCM were subsequently used in experiments designed to determine firstly, if the cryoprotectants had a positive result on the cold tolerance of the FCM, and secondly, if they had any adverse effects on other physiological aspects such as duration of development. Laboratory trials indicated that the flight ability of male FCM was improved when larvae were reared on diets augmented with trehalose and cholesterol (with an average of 40 % of cholesterol and trehalose augmented males that flew at 15 °C where 0 % of the control flew). Results obtained during the field trials support the laboratory results as there was a significant increase in the number of trehalose augmented moths caught in the field during March and July (winter). Results also showed potential for cholesterol to be used as an additive. Other important findings show that both cholesterol and trehalose have no negative impacts on developmental rate, pupal size, and egg production and viability. Trehalose was found to increase the pupal mass of male and female FCM, as well as the number of eggs laid per female. Cholesterol was found to increase developmental rate and the number of eggs laid. The main findings of this study were that diet additives could improve the massrearing of FCM for SIT and the competitiveness of the males, especially at lower temperatures. However, the additives were expensive and cost could well be a constraint to the wide scale implementation of the new technology.
- Full Text:
- Date Issued: 2017
- Authors: Daniel, Claire Ashleigh
- Date: 2017
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Reproduction -- Effect of temperature on , 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
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5271 , vital:20803
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is a major pest of citrus and other important crops in Sub-Saharan Africa. The introduction of a sterile insect technique (SIT) programme for FCM in South Africa has proven to be very effective in the control of FCM. The objective was to flood citrus orchards with large numbers of sterile males resulting in a ratio of at least 10 sterile to 1 wild moth, increasing the probability of a female moth mating with a sterile male. This target is often achieved and the programme is generally successful, however there are some challenges regarding this programme. The mass rearing environment, artificial diet, handling methods and irradiation have an impact on sterile insect quality as environmental differences between the rearing facility and field, influences the insect phenotype and competitiveness. This is evident as wild male moths can theoretically actively fly at a temperature of 12°C and laboratory-reared sterilized moths, due to the radiation treatment, appear unable to fly below 20°C. As a consequence, sterile males are out-competed by wild males during the cooler months of the year. This is detrimental to the SIT programme as FCM do not undergo diapause, meaning they are active during winter and will still reproduce. Therefore, to maximize the effect of the SIT programme, it is vital to increase the flight ability of mass reared sterile males at lower temperatures. Various studies have shown that by adding cryoprotectants to the basic laboratory diets increases the cold tolerance of certain insects and thus may allow them to be mobile at lower temperatures, however it imperative that any chemical used to augment the commercial diet of the insect has no negative effects on the insect physiology and development. To investigate this detail for FCM, five generations of FCM were reared on diets augmented with various known insect cryoprotectants. These augmented FCM were subsequently used in experiments designed to determine firstly, if the cryoprotectants had a positive result on the cold tolerance of the FCM, and secondly, if they had any adverse effects on other physiological aspects such as duration of development. Laboratory trials indicated that the flight ability of male FCM was improved when larvae were reared on diets augmented with trehalose and cholesterol (with an average of 40 % of cholesterol and trehalose augmented males that flew at 15 °C where 0 % of the control flew). Results obtained during the field trials support the laboratory results as there was a significant increase in the number of trehalose augmented moths caught in the field during March and July (winter). Results also showed potential for cholesterol to be used as an additive. Other important findings show that both cholesterol and trehalose have no negative impacts on developmental rate, pupal size, and egg production and viability. Trehalose was found to increase the pupal mass of male and female FCM, as well as the number of eggs laid per female. Cholesterol was found to increase developmental rate and the number of eggs laid. The main findings of this study were that diet additives could improve the massrearing of FCM for SIT and the competitiveness of the males, especially at lower temperatures. However, the additives were expensive and cost could well be a constraint to the wide scale implementation of the new technology.
- Full Text:
- Date Issued: 2017
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
The effect of age and maturation on anthropometric characteristics and physical abilities of youth South African footballers
- Authors: De Beer, Ashley
- Date: 2020
- Subjects: Soccer -- Physiologial aspects , Soccer players -- South Africa -- Makhanda -- Physiology , Soccer players -- South Africa -- Makhanda -- Psychophysiology , Makana Local Football Association (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/141222 , vital:37954
- Description: Currently there is limited research investigating the football related abilities of youth South African individuals. Populations from North and South America, Europe and Asia have been extensively covered in terms of their anthropometric characteristics, physical abilities, technical competency, tactical understanding as well as various personality traits. In describing these details, and especially how each is affected during the ageing and pubertal process, a more informed understanding of the talent development systems is created. A holistic approach to talent development is required to effectively and efficiently produce elite level footballers. An important consideration is the unique socio-economic environment many youth footballers experience which may impact on the talent development process. The present study therefore sought to quantify the anthropometric characteristics and the physical ability level of youth South African footballers from Local Football Association in Makhanda in the Sarah Baartman Region of the Eastern Cape province. In order to achieve this a two-factorial design was used with age and maturity status as independent variables. Anthropometric characteristics were tested by finding the height, weight, body mass index and total fat percentage of participants. Physical ability was determined by results for aerobic capacity, power, acceleration, speed and agility. All tests were football specific and had been widely used in a variety of footballing studies. Additional demographic and socio-economic information was also recorded. A total of 136 participants were placed in their respective Under 11, 13, 15 or Under 19 age groups, while the maturity status of 96 participants were stratified into five distinct categories. Statistical analyses was conducted using p-value significance, with appropriate Tukey post-hoc tests administered when necessary, while effect sizes were calculated using Cohen’s d. Significant changes and practical effect sizes were present for nearly all dependent variables when either stratified by age or by maturity. Total fat percentage was the only dependent variable which was not influenced by either age or maturity. Age and maturity effect sizes for total body fat percentage indicated practical changes present which did not occur during statistical analysis. The present results indicate poor values when compared to normative data or that of other football playing study populations. Further longitudinal research is required to better understand individual growth rates for youth South African footballers, particularly from the Makana region. Implications of the thesis may determine long term development pathways, while the delayed maturity rate is a critical finding which needs to be further researched.
- Full Text:
- Date Issued: 2020
- Authors: De Beer, Ashley
- Date: 2020
- Subjects: Soccer -- Physiologial aspects , Soccer players -- South Africa -- Makhanda -- Physiology , Soccer players -- South Africa -- Makhanda -- Psychophysiology , Makana Local Football Association (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/141222 , vital:37954
- Description: Currently there is limited research investigating the football related abilities of youth South African individuals. Populations from North and South America, Europe and Asia have been extensively covered in terms of their anthropometric characteristics, physical abilities, technical competency, tactical understanding as well as various personality traits. In describing these details, and especially how each is affected during the ageing and pubertal process, a more informed understanding of the talent development systems is created. A holistic approach to talent development is required to effectively and efficiently produce elite level footballers. An important consideration is the unique socio-economic environment many youth footballers experience which may impact on the talent development process. The present study therefore sought to quantify the anthropometric characteristics and the physical ability level of youth South African footballers from Local Football Association in Makhanda in the Sarah Baartman Region of the Eastern Cape province. In order to achieve this a two-factorial design was used with age and maturity status as independent variables. Anthropometric characteristics were tested by finding the height, weight, body mass index and total fat percentage of participants. Physical ability was determined by results for aerobic capacity, power, acceleration, speed and agility. All tests were football specific and had been widely used in a variety of footballing studies. Additional demographic and socio-economic information was also recorded. A total of 136 participants were placed in their respective Under 11, 13, 15 or Under 19 age groups, while the maturity status of 96 participants were stratified into five distinct categories. Statistical analyses was conducted using p-value significance, with appropriate Tukey post-hoc tests administered when necessary, while effect sizes were calculated using Cohen’s d. Significant changes and practical effect sizes were present for nearly all dependent variables when either stratified by age or by maturity. Total fat percentage was the only dependent variable which was not influenced by either age or maturity. Age and maturity effect sizes for total body fat percentage indicated practical changes present which did not occur during statistical analysis. The present results indicate poor values when compared to normative data or that of other football playing study populations. Further longitudinal research is required to better understand individual growth rates for youth South African footballers, particularly from the Makana region. Implications of the thesis may determine long term development pathways, while the delayed maturity rate is a critical finding which needs to be further researched.
- Full Text:
- Date Issued: 2020
The integration of effluent treatment using constructed wetlands, with crop production and aquaculture
- Authors: de Jong, Martyn
- Date: 2019
- Subjects: Recycling (Waste, etc.) , Brewery waste , Sewage -- Purification , Beets , Mozambique tilapia
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95767 , vital:31197
- Description: Breweries are major consumers of water and produce nutrient rich wastewater. Therefore, it is important to research technologies that optimise the reuse and recycling of this waste. This study compared different constructed wetlands (CWs) in terms of their potential for cleaning brewery effluent and simultaneously producing crops Beta vulgaris and fish Oreochromis mossambicus. Filling and draining times (FDT; 15 min, 30 min and 60 min) in tidal CWs were compared in Experiment 1. The 15 min FDT (6.52 ± 0.09 mg/l) and 30 min FDT (5.74 ± 0.09 mg/l) had higher dissolved oxygen (DO) than the 60 min FDT (5.40 ± 0.09 mg/l; p<0.05). This resulted in the 15 and 30 min FDT treatments reaching ammonia effluent discharge standards sooner than the 60 min FDT. Total plant harvest increased with increasing FDT; therefore, 15 min FDT was used as the FDT in tidal treatments in the following experiments. The aerated CW (5.81 ± 0.07 mg/l) and tidal CW (5.67 ± 0.07 mg/l) treatments had higher DO concentrations than the unaerated CW treatment (3.76 ± 0.07 mg/l; p<0.05) in Experiment 2. This resulted in lower ammonia concentrations on day 5 in the aerated and tidal CWs compared with the unaerated treatment (p<0.05). The tidal CW (23.97 ± 2.57 kg) had a total harvest that was approximately four times higher than the unaerated CW (p<0.05), which had the highest frequency of chlorosis and plant mortality; and was unable to treat ammonia to discharge standards. In Experiment 3, the aerated and tidal CW were compared with municipal-water as water sources for aquaculture. There were no differences in fish growth (p > 0.05). However, there were differences in water quality; with the municipal treatment having the lowest pH, EC and nitrate concentration (p<0.05); but all water quality parameters remained in a range suitably for fish production. Due to the tidal CW having the highest plant harvest and lowest frequency of chlorosis and mortality; it was the most suitable CW technology to clean the brewery effluent, and to produce B. vulgaris and water that could be used downstream in aquaculture.
- Full Text:
- Date Issued: 2019
- Authors: de Jong, Martyn
- Date: 2019
- Subjects: Recycling (Waste, etc.) , Brewery waste , Sewage -- Purification , Beets , Mozambique tilapia
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95767 , vital:31197
- Description: Breweries are major consumers of water and produce nutrient rich wastewater. Therefore, it is important to research technologies that optimise the reuse and recycling of this waste. This study compared different constructed wetlands (CWs) in terms of their potential for cleaning brewery effluent and simultaneously producing crops Beta vulgaris and fish Oreochromis mossambicus. Filling and draining times (FDT; 15 min, 30 min and 60 min) in tidal CWs were compared in Experiment 1. The 15 min FDT (6.52 ± 0.09 mg/l) and 30 min FDT (5.74 ± 0.09 mg/l) had higher dissolved oxygen (DO) than the 60 min FDT (5.40 ± 0.09 mg/l; p<0.05). This resulted in the 15 and 30 min FDT treatments reaching ammonia effluent discharge standards sooner than the 60 min FDT. Total plant harvest increased with increasing FDT; therefore, 15 min FDT was used as the FDT in tidal treatments in the following experiments. The aerated CW (5.81 ± 0.07 mg/l) and tidal CW (5.67 ± 0.07 mg/l) treatments had higher DO concentrations than the unaerated CW treatment (3.76 ± 0.07 mg/l; p<0.05) in Experiment 2. This resulted in lower ammonia concentrations on day 5 in the aerated and tidal CWs compared with the unaerated treatment (p<0.05). The tidal CW (23.97 ± 2.57 kg) had a total harvest that was approximately four times higher than the unaerated CW (p<0.05), which had the highest frequency of chlorosis and plant mortality; and was unable to treat ammonia to discharge standards. In Experiment 3, the aerated and tidal CW were compared with municipal-water as water sources for aquaculture. There were no differences in fish growth (p > 0.05). However, there were differences in water quality; with the municipal treatment having the lowest pH, EC and nitrate concentration (p<0.05); but all water quality parameters remained in a range suitably for fish production. Due to the tidal CW having the highest plant harvest and lowest frequency of chlorosis and mortality; it was the most suitable CW technology to clean the brewery effluent, and to produce B. vulgaris and water that could be used downstream in aquaculture.
- Full Text:
- Date Issued: 2019
Ecological engineering: an assessment of the ecological impact of Reno mattress structures used in erosion control in the Keurbooms Estuary, South Africa
- Authors: De Villiers, Nina
- Date: 2020
- Subjects: Sediments (Geology) -- Management , Sediments (Geology) -- South Africa -- Keurboomstrand , Coast changes -- South Africa -- Keurboomstrand , Shore protection -- South Africa -- Keurboomstrand , Coastal engineering-- South Africa -- Keurboomstrand , Coastal zone management-- South Africa -- Keurboomstrand , Estuarine ecology-- South Africa -- Keurboomstrand , Eelgrass -- South Africa -- Keurboomstrand , Reno Mattresses
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166138 , vital:41332
- Description: Global climate changes have been associated with ocean warming and sea-level rise. Armouring of coastlines has become common practice with the increasing threat of coastal erosion. The transformation of soft sediment habitats to hard, artificial habitats because of coastline armouring can lead to changes in species diversity, composition and distribution. It is, therefore, essential to assess changes to habitats from coastal development as well as the ecological impact erosion control structures have within coastal systems. Ecological engineering attempts to combine engineering principals and ecological processes to reduce environmental impacts from coastal development and the implementation of artificial structures. Estuaries are particularly vulnerable to anthropogenic impacts through development, and are extremely important systems offering nursery and foraging grounds for many species. These systems are, however, particularly vulnerable to anthropogenic impacts from urbanisation and development. Within South Africa many estuaries are being transformed by the addition of artificial structures to combat erosion, one such structure is the Reno mattress (a flattened wire box filled with rocks). This study compared the fish diversity and abundances of existing Reno mattress structures and natural eelgrass (Zostera capensis) habitat in the Keurbooms Estuary, South Africa. Benthic invertebrates were sampled using standard core sampling and an adapted suction sampling approach within the two habitats. The non-destructive method of mini Baited Remote Underwater Video Systems (BRUVs) was used to sample fish. Seasonal benthic invertebrate and fish abundances and assemblages were assessed from winter 2018 to spring 2019 with greater abundances of both recorded in summer. Significantly greater abundances, diversity, and richness of fish were found in the Reno mattress habitat compared to Z. capensis. Invertebrate taxa displayed some overlap between habitats, however, three higher taxonomic groups were only recorded within Reno mattress habitat and one only within the eelgrass habitat. Fish assemblages differed significantly between the two established habitats. A Before-After-Control-Impact (BACI) investigation was used to assess the ecological impact of newly installed Reno mattresses in the Keurbooms Estuary. Zostera capensis extent was sampled by determining the percentage cover of 0.5 m X 0.5 m quadrats and measurements of eelgrass blades. Percentage cover and blade length decreased during the installation of Reno mattress, but then recovered shortly after completion of the installation. Abundances, richness and diversity of invertebrates and fish were found to be similar before and after the installation which suggests that the installation had no net negative impact on the site. The Reno mattresses were found to attract fauna typical of rocky shore environments as well as a few invasive alien invertebrate species. This study noted that a hybrid habitat of Reno mattress and eelgrass was created and may in fact provide the positives of both to a system. In any coastal development it will be important to balance the demands of a growing population and the protection of natural habitats. The results of this study suggest that complex artificial structures such as Reno mattresses do provide habitat for fish and invertebrates. However, the use of these structures should be in combination with natural vegetation (e.g. as a hybrid habitat) and not one that replaces intertidal and subtidal natural habitat especially eelgrass. There is limited information regarding the ecological impacts of using Reno mattresses in estuaries and this study provides new information on their ecological efficacy that should be valuable for future coastal erosion control practices.
- Full Text:
- Date Issued: 2020
- Authors: De Villiers, Nina
- Date: 2020
- Subjects: Sediments (Geology) -- Management , Sediments (Geology) -- South Africa -- Keurboomstrand , Coast changes -- South Africa -- Keurboomstrand , Shore protection -- South Africa -- Keurboomstrand , Coastal engineering-- South Africa -- Keurboomstrand , Coastal zone management-- South Africa -- Keurboomstrand , Estuarine ecology-- South Africa -- Keurboomstrand , Eelgrass -- South Africa -- Keurboomstrand , Reno Mattresses
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166138 , vital:41332
- Description: Global climate changes have been associated with ocean warming and sea-level rise. Armouring of coastlines has become common practice with the increasing threat of coastal erosion. The transformation of soft sediment habitats to hard, artificial habitats because of coastline armouring can lead to changes in species diversity, composition and distribution. It is, therefore, essential to assess changes to habitats from coastal development as well as the ecological impact erosion control structures have within coastal systems. Ecological engineering attempts to combine engineering principals and ecological processes to reduce environmental impacts from coastal development and the implementation of artificial structures. Estuaries are particularly vulnerable to anthropogenic impacts through development, and are extremely important systems offering nursery and foraging grounds for many species. These systems are, however, particularly vulnerable to anthropogenic impacts from urbanisation and development. Within South Africa many estuaries are being transformed by the addition of artificial structures to combat erosion, one such structure is the Reno mattress (a flattened wire box filled with rocks). This study compared the fish diversity and abundances of existing Reno mattress structures and natural eelgrass (Zostera capensis) habitat in the Keurbooms Estuary, South Africa. Benthic invertebrates were sampled using standard core sampling and an adapted suction sampling approach within the two habitats. The non-destructive method of mini Baited Remote Underwater Video Systems (BRUVs) was used to sample fish. Seasonal benthic invertebrate and fish abundances and assemblages were assessed from winter 2018 to spring 2019 with greater abundances of both recorded in summer. Significantly greater abundances, diversity, and richness of fish were found in the Reno mattress habitat compared to Z. capensis. Invertebrate taxa displayed some overlap between habitats, however, three higher taxonomic groups were only recorded within Reno mattress habitat and one only within the eelgrass habitat. Fish assemblages differed significantly between the two established habitats. A Before-After-Control-Impact (BACI) investigation was used to assess the ecological impact of newly installed Reno mattresses in the Keurbooms Estuary. Zostera capensis extent was sampled by determining the percentage cover of 0.5 m X 0.5 m quadrats and measurements of eelgrass blades. Percentage cover and blade length decreased during the installation of Reno mattress, but then recovered shortly after completion of the installation. Abundances, richness and diversity of invertebrates and fish were found to be similar before and after the installation which suggests that the installation had no net negative impact on the site. The Reno mattresses were found to attract fauna typical of rocky shore environments as well as a few invasive alien invertebrate species. This study noted that a hybrid habitat of Reno mattress and eelgrass was created and may in fact provide the positives of both to a system. In any coastal development it will be important to balance the demands of a growing population and the protection of natural habitats. The results of this study suggest that complex artificial structures such as Reno mattresses do provide habitat for fish and invertebrates. However, the use of these structures should be in combination with natural vegetation (e.g. as a hybrid habitat) and not one that replaces intertidal and subtidal natural habitat especially eelgrass. There is limited information regarding the ecological impacts of using Reno mattresses in estuaries and this study provides new information on their ecological efficacy that should be valuable for future coastal erosion control practices.
- Full Text:
- Date Issued: 2020
Generation of a virtual library of terpenes using graph theory, and its application in exploration of the mechanisms of terpene biosynthesis
- Authors: Dendera, Washington
- Date: 2020
- Subjects: Terpenes , Plants -- Metabolism , Computational biology , Bioinformatics , Organic compounds -- Synthesis , Monoterpenes , Molecular biology -- Computer simulation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/123453 , vital:35439
- Description: Terpenes form a large group of organic compounds which have proven to be of use to many living organisms being used by plants for metabolism (Pichersky and Gershenzon, 1934; McGarvey and Croteau, 1995; Gershenzon and Dudareva, 2007), defence or as a means to attract pollinators and also used by humans in medical, pharmaceutical and food industry (Bicas, Dionísio and Pastore, 2009; Marmulla and Harder, 2014; Kandi et al., 2015). Following on literature methods to generate chemical libraries using graph theoretic techniques, complete libraries of all possible terpene isomers have been constructed with the goal of construction of derivative libraries of possible carbocation intermediates which are important in the elucidation of mechanisms in the biosynthesis of terpenes. Virtual library generation of monoterpenes was first achieved by generating graphs of order 7, 8, 9 and 10 using the Nauty and Traces suite. These were screened and processed with a set of collated Python scripts written to recognize the graphs in text format and translate them to molecules, minimizing through Tinker whilst discarding graphs that violate chemistry laws. As a result of the computational time required only order 7 and order 10 graphs were processed. Out of the 873 graphs generated from order seven, 353 were converted to molecules and from the 11,7 million produced from order 10 half were processed resulting in the production of 442928 compounds (repeats included). For screening, 55 366 compounds were docked in the active site of limonene synthase; of these 2355 ligands had a good Vina docking score with a binding energy of between -7.0 and -7.4 kcal.mol-1. When these best docked molecules were overlaid in the active site a map of possible ligand positions within the active site of limonene synthase was traced out.
- Full Text:
- Date Issued: 2020
- Authors: Dendera, Washington
- Date: 2020
- Subjects: Terpenes , Plants -- Metabolism , Computational biology , Bioinformatics , Organic compounds -- Synthesis , Monoterpenes , Molecular biology -- Computer simulation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/123453 , vital:35439
- Description: Terpenes form a large group of organic compounds which have proven to be of use to many living organisms being used by plants for metabolism (Pichersky and Gershenzon, 1934; McGarvey and Croteau, 1995; Gershenzon and Dudareva, 2007), defence or as a means to attract pollinators and also used by humans in medical, pharmaceutical and food industry (Bicas, Dionísio and Pastore, 2009; Marmulla and Harder, 2014; Kandi et al., 2015). Following on literature methods to generate chemical libraries using graph theoretic techniques, complete libraries of all possible terpene isomers have been constructed with the goal of construction of derivative libraries of possible carbocation intermediates which are important in the elucidation of mechanisms in the biosynthesis of terpenes. Virtual library generation of monoterpenes was first achieved by generating graphs of order 7, 8, 9 and 10 using the Nauty and Traces suite. These were screened and processed with a set of collated Python scripts written to recognize the graphs in text format and translate them to molecules, minimizing through Tinker whilst discarding graphs that violate chemistry laws. As a result of the computational time required only order 7 and order 10 graphs were processed. Out of the 873 graphs generated from order seven, 353 were converted to molecules and from the 11,7 million produced from order 10 half were processed resulting in the production of 442928 compounds (repeats included). For screening, 55 366 compounds were docked in the active site of limonene synthase; of these 2355 ligands had a good Vina docking score with a binding energy of between -7.0 and -7.4 kcal.mol-1. When these best docked molecules were overlaid in the active site a map of possible ligand positions within the active site of limonene synthase was traced out.
- Full Text:
- Date Issued: 2020
Investigating assay formats for screening malaria Hsp90-Hop interaction inhibitors
- Authors: Derry, Leigh-Anne Tracy Kim
- Date: 2019
- Subjects: Antimalarials , Heat shock proteins , Drug interactions , Drug resistance , Plasmodium falciparum , High throughput screening (Drug development) , Bioluminescence resonance energy transfer (BRET) , Fluorescence resonance energy transfer (FRET)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63345 , vital:28395
- Description: Although significant gains have been made in the combat against malaria in the last decade, the persistent threat of drug and insecticide resistance continues to motivate the search for new classes of antimalarial drug compounds and targets. Due to their predominance in cellular reactions, protein-protein interactions (P-PIs) are emerging as a promising general target class for therapeutic development. The P-PI which is the focus of this project is the interaction between the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Hsp70/Hsp90 organising protein (Hop). Hop binds to Hsp70 and Hsp90 and facilitates the transfer of client proteins (proteins undergoing folding) from the former to the latter and also regulates nucleotide exchange on Hsp90. Due to its role in correcting protein misfolding during cell stress, Hsp90 is being pursued as a cancer drug target and compounds that inhibit its ATPase activity have entered clinical trials. However, it has been proposed that inhibiting the interaction between Hsp90 and Hop may be alternative approach for inhibiting Hsp90 function for cancer therapy. The malaria parasite Plasmodium falciparum experiences temperature fluctuations during vector-host transitions and febrile episodes and cell stress due to rapid growth and immune responses. Hence, it also depends on chaperones, including PfHsp90, to maintain protein functionality and pathogenesis, demonstrated inter alia by the sensitivity of parasites to Hsp90 inhibitors. In addition, PfHsp90 exists as a complex with the malarial Hop homologue, PfHop, in parasite lysates. Consequently, the purpose of this study was to explore P-PI assay formats that can confirm the interaction of PfHsp90 and PfHop and can be used to identify inhibitors of the interaction, preferably in a medium- to high-throughput screening mode. As a first approach, cell-based bioluminescence and fluorescence resonance energy transfer (BRET and FRET) assays were performed in HeLa cells. To facilitate this, expression plasmid constructs containing coding sequences of P. falciparum and mammalian Hsp90 and Hop and their interacting domains (Hsp90 C-domain and Hop TPR2A domain) fused to the BRET and FRET reporter proteins – yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and Renilla luciferase (Rluc) - were prepared and used for HeLa cell transient transfections. The FRET assay produced positive interaction signals for the full-length P. falciparum and mammalian Hsp90-Hop interactions. However, C-domain-TPR2A domain interactions were not detected, no interactions could be demonstrated with the BRET assay and western blotting experiments failed to detect expression of all the interaction partners in transiently transfected HeLa cells. Consequently, an alternative in vitro FRET assay format using recombinant proteins was investigated. Expression constructs for the P. falciparum and mammalian C-domains and TPR2A domains fused respectively to YFP and CFP were prepared and the corresponding fusion proteins expressed and purified from E. coli. No interaction was found with the mammalian interaction partners, but interaction of the P. falciparum C-domain and TPR2A domain was consistently detected with a robust Z’ factor value of 0.54. A peptide corresponding to the PfTPR2A domain sequence primarily responsible for Hsp90 binding (based on a human TPR2A peptide described by Horibe et al., 2011) was designed and showed dose-dependent inhibition of the interaction, with 53.7% inhibition at 100 μM. The components of the assay are limited to the purified recombinant proteins, requires minimal liquid steps and may thus be a useful primary screening format for identifying inhibitors of P. falciparum Hsp90-Hop interaction.
- Full Text:
- Date Issued: 2019
- Authors: Derry, Leigh-Anne Tracy Kim
- Date: 2019
- Subjects: Antimalarials , Heat shock proteins , Drug interactions , Drug resistance , Plasmodium falciparum , High throughput screening (Drug development) , Bioluminescence resonance energy transfer (BRET) , Fluorescence resonance energy transfer (FRET)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63345 , vital:28395
- Description: Although significant gains have been made in the combat against malaria in the last decade, the persistent threat of drug and insecticide resistance continues to motivate the search for new classes of antimalarial drug compounds and targets. Due to their predominance in cellular reactions, protein-protein interactions (P-PIs) are emerging as a promising general target class for therapeutic development. The P-PI which is the focus of this project is the interaction between the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Hsp70/Hsp90 organising protein (Hop). Hop binds to Hsp70 and Hsp90 and facilitates the transfer of client proteins (proteins undergoing folding) from the former to the latter and also regulates nucleotide exchange on Hsp90. Due to its role in correcting protein misfolding during cell stress, Hsp90 is being pursued as a cancer drug target and compounds that inhibit its ATPase activity have entered clinical trials. However, it has been proposed that inhibiting the interaction between Hsp90 and Hop may be alternative approach for inhibiting Hsp90 function for cancer therapy. The malaria parasite Plasmodium falciparum experiences temperature fluctuations during vector-host transitions and febrile episodes and cell stress due to rapid growth and immune responses. Hence, it also depends on chaperones, including PfHsp90, to maintain protein functionality and pathogenesis, demonstrated inter alia by the sensitivity of parasites to Hsp90 inhibitors. In addition, PfHsp90 exists as a complex with the malarial Hop homologue, PfHop, in parasite lysates. Consequently, the purpose of this study was to explore P-PI assay formats that can confirm the interaction of PfHsp90 and PfHop and can be used to identify inhibitors of the interaction, preferably in a medium- to high-throughput screening mode. As a first approach, cell-based bioluminescence and fluorescence resonance energy transfer (BRET and FRET) assays were performed in HeLa cells. To facilitate this, expression plasmid constructs containing coding sequences of P. falciparum and mammalian Hsp90 and Hop and their interacting domains (Hsp90 C-domain and Hop TPR2A domain) fused to the BRET and FRET reporter proteins – yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and Renilla luciferase (Rluc) - were prepared and used for HeLa cell transient transfections. The FRET assay produced positive interaction signals for the full-length P. falciparum and mammalian Hsp90-Hop interactions. However, C-domain-TPR2A domain interactions were not detected, no interactions could be demonstrated with the BRET assay and western blotting experiments failed to detect expression of all the interaction partners in transiently transfected HeLa cells. Consequently, an alternative in vitro FRET assay format using recombinant proteins was investigated. Expression constructs for the P. falciparum and mammalian C-domains and TPR2A domains fused respectively to YFP and CFP were prepared and the corresponding fusion proteins expressed and purified from E. coli. No interaction was found with the mammalian interaction partners, but interaction of the P. falciparum C-domain and TPR2A domain was consistently detected with a robust Z’ factor value of 0.54. A peptide corresponding to the PfTPR2A domain sequence primarily responsible for Hsp90 binding (based on a human TPR2A peptide described by Horibe et al., 2011) was designed and showed dose-dependent inhibition of the interaction, with 53.7% inhibition at 100 μM. The components of the assay are limited to the purified recombinant proteins, requires minimal liquid steps and may thus be a useful primary screening format for identifying inhibitors of P. falciparum Hsp90-Hop interaction.
- Full Text:
- Date Issued: 2019
Using four different methods to reach a taxonomic conclusion in dung beetles (Scarabaeinae)
- Authors: Deschodt, Christian Michel
- Date: 2019
- Subjects: Dung beetles -- Classification , Scarabaeidae -- Classification
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67845 , vital:29156
- Description: Four different techniques to make taxonomic decisions concerning different species in Scarabaeinae are being investigated. Firstly, I made measurements of the body dimensions which are plotted on a two dimensional graph. This method is successfully used to erect one new species, Copris crassus Deschodt and Davis, 2015, and to establish the synonymy of Copris bihamatus Balthasar, 1965 with Copris fidius (Olivier, 1789). Thereafter the classical or traditional comparative method is used to propose seven new species Scarabaeolus soutpansbergensis (Deschodt and Davis 2015), Scarabaeolus megaparvulus (Davis and Deschodt 2015), Scarabaeolus niemandi (Deschodt and Davis 2015), Scarabaeolus carniphilus (Davis and Deschodt 2015), Scarabaeolus ermienae (Deschodt and Davis 2015), Scarabaeolus planipennis (Davis and Deschodt 2015) and Scarabaeolus afronitidus (Davis and Deschodt 2015) and formally synonymise Scarabaeolus vansoni (Ferreira, 1958) with Scarabaeolus lucidulus (Boheman, 1860) and Scarabaeolus xavieri (Ferreira, 1968) with Scarabaeolus andreaei (zur Strassen, 1963). Morphometric measurements of external structures of a group of flightless relict beetles in the tribe Canthonini are used to compile a nexus file which is analysed with computer software. The interpretation of these results is used here to support the erection of a new genus Drogo Deschodt, Davis & Scholtz 2016, Lastly I analysed the DNA sequences of specimens from different species belonging to a species complex in the genus Epirinus Reiche, 1841 occurring over a wide geographic range. These sequences are used together with external morphological characters to propose the synonymy of Epirinus hluhluwensis Medina & Scholtz 2005 and Epirinus ngomae Medina & Scholtz 2005 with Epirinus davisi Scholtz & Howden 1987.
- Full Text:
- Date Issued: 2019
- Authors: Deschodt, Christian Michel
- Date: 2019
- Subjects: Dung beetles -- Classification , Scarabaeidae -- Classification
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67845 , vital:29156
- Description: Four different techniques to make taxonomic decisions concerning different species in Scarabaeinae are being investigated. Firstly, I made measurements of the body dimensions which are plotted on a two dimensional graph. This method is successfully used to erect one new species, Copris crassus Deschodt and Davis, 2015, and to establish the synonymy of Copris bihamatus Balthasar, 1965 with Copris fidius (Olivier, 1789). Thereafter the classical or traditional comparative method is used to propose seven new species Scarabaeolus soutpansbergensis (Deschodt and Davis 2015), Scarabaeolus megaparvulus (Davis and Deschodt 2015), Scarabaeolus niemandi (Deschodt and Davis 2015), Scarabaeolus carniphilus (Davis and Deschodt 2015), Scarabaeolus ermienae (Deschodt and Davis 2015), Scarabaeolus planipennis (Davis and Deschodt 2015) and Scarabaeolus afronitidus (Davis and Deschodt 2015) and formally synonymise Scarabaeolus vansoni (Ferreira, 1958) with Scarabaeolus lucidulus (Boheman, 1860) and Scarabaeolus xavieri (Ferreira, 1968) with Scarabaeolus andreaei (zur Strassen, 1963). Morphometric measurements of external structures of a group of flightless relict beetles in the tribe Canthonini are used to compile a nexus file which is analysed with computer software. The interpretation of these results is used here to support the erection of a new genus Drogo Deschodt, Davis & Scholtz 2016, Lastly I analysed the DNA sequences of specimens from different species belonging to a species complex in the genus Epirinus Reiche, 1841 occurring over a wide geographic range. These sequences are used together with external morphological characters to propose the synonymy of Epirinus hluhluwensis Medina & Scholtz 2005 and Epirinus ngomae Medina & Scholtz 2005 with Epirinus davisi Scholtz & Howden 1987.
- Full Text:
- Date Issued: 2019