Historical perspectives and future directions for access to land, water and related ecosystem services in the Lower Sundays River Valley, South Africa: implications for human well being
- Authors: Chadzingwa, Karabo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/442 , vital:19959
- Description: The legacy of South Africa’s history has facilitated unequal access to land and water resources. In the Lower Sundays River Valley (LSRV), a predominantly commercial farming area, differential access to land and water has impacted aspects of ecosystem service access and human well‐being for disenfranchised families over time. Despite the social, political and economic reform efforts in the past two decades, severe inertia towards efforts attempting to increase equitable access to land and water has been experienced. As a result, communities have mobilized and claimed their land from the government through the land restitution process. Based on a mixed‐methods approach, this research explores the ways in which access to land and water over time has influenced current levels of human well‐being among disenfranchised families. Provisioning and cultural ecosystem services were identified as key areas of loss as a result of forced evictions from land. Freedom of choice was a central and cross‐cutting theme regarding the ability to change levels of human well‐being. Although the loss of ecosystem services associated with land and water had an impact on households, the ecosystem services which are regarded as fundamental to human well‐being do not seem to have been lost. The study recommends the wide use of freedom of choice as an indicator for well‐being in the LSRV, as well as a consideration of subjective, objective and psychological measures of well‐being with regards to natural resources and ecosystem services access. Key agents in fostering desirable pathways toward equity and sustainability in the LSRV are identified with stakeholders as private businesses; inclusive governance; empowered and skilled individuals, as well as NGOs.
- Full Text:
- Date Issued: 2016
- Authors: Chadzingwa, Karabo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/442 , vital:19959
- Description: The legacy of South Africa’s history has facilitated unequal access to land and water resources. In the Lower Sundays River Valley (LSRV), a predominantly commercial farming area, differential access to land and water has impacted aspects of ecosystem service access and human well‐being for disenfranchised families over time. Despite the social, political and economic reform efforts in the past two decades, severe inertia towards efforts attempting to increase equitable access to land and water has been experienced. As a result, communities have mobilized and claimed their land from the government through the land restitution process. Based on a mixed‐methods approach, this research explores the ways in which access to land and water over time has influenced current levels of human well‐being among disenfranchised families. Provisioning and cultural ecosystem services were identified as key areas of loss as a result of forced evictions from land. Freedom of choice was a central and cross‐cutting theme regarding the ability to change levels of human well‐being. Although the loss of ecosystem services associated with land and water had an impact on households, the ecosystem services which are regarded as fundamental to human well‐being do not seem to have been lost. The study recommends the wide use of freedom of choice as an indicator for well‐being in the LSRV, as well as a consideration of subjective, objective and psychological measures of well‐being with regards to natural resources and ecosystem services access. Key agents in fostering desirable pathways toward equity and sustainability in the LSRV are identified with stakeholders as private businesses; inclusive governance; empowered and skilled individuals, as well as NGOs.
- Full Text:
- Date Issued: 2016
Mesopredator release and the effectiveness of camera traps for estimating mammal abundances in the Eastern Cape, South Africa
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
Using bioinformatics tools to screen for trypanosomal cathepsin B cysteine protease inhibitors from the SANCDB as a novel therapeutic modality against Human African Trypanosomiasis (HAT)
- Authors: Mokhawa, Gaone
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3304 , vital:20470
- Description: Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a fatal chronic disease that is caused by flagellated protozoans, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. HAT is spread by a bite from an infected tsetse fly of the Glosina genus. Up to 60 million people in 36 countries in sub-Saharan Africa are at a risk of infection from HAT with up to 30 000 deaths reported every year. Current chemotherapy for HAT is insufficient since the available drugs exhibit unacceptable side effects (toxicity) and parasite resistance. Novel treatments and approaches for development of specific and more potent drugs for HAT are therefore required. One approach is to target vital proteins that are essential to the life cycle of the parasite. The main interest of this study is to explore Trypanosoma brucei cathepsin B-like protease (TbCatB) structural and functional properties with the primary goal of discovering non peptide small molecule inhibitors of TbCatB using bioinformatics approaches. TbCatB is a papain family C1 cysteine protease which belongs to clan CA group and it has emerged as a potential HAT drug target. Papain family cysteine proteases of Clan CA group of Trypanosoma brucei (rhodesain and TbCatB) have demonstrated potential as chemotherapeutic targets using synthetic protease inhibitors like Z-Phe-Ala-CHN2 to kill the parasite in vitro and in vivo. TbCatB has been identified as the essential cysteine protease of T. brucei since mRNA silencing of TbCatB killed the parasite and resulted in a cure in mice infected with T. brucei while mRNA silencing of rhodesain only extended mice life. TbCatB is therefore a promising drug target against HAT and the discovery and development of compounds that can selectively inhibit TbCatB without posing any danger to the human host represent a great therapeutic solution for treatment of HAT. To understand protein-inhibitor interactions, useful information can be obtained from high resolution protease-inhibitor crystal structure complexes. This study aims to use bioinformatics approaches to carry out comparative sequence, structural and functional analysis of TbCatB protease and its homologs from T. congolense, T, cruzi, T. vivax and H. sapien as well as to identify non-peptide small molecule inhibitors of TbCatB cysteine proteases from natural compounds of South African origin. Sequences of TbCatB (PDB ID: 3HHI) homologs were retrieved by a BLAST search. Human cathepsin B (PDB ID: 3CBJ) was selected from a list of templates for homology modelling found by HHpred. MODELLER version 9.10 program was used to generate a hundred models for T. congolense, T, cruzi and T. vivax cathepsin B like proteases using 3HHI and 3CBJ as templates. The best models were chosen based on their low DOPE Z scores before validation using MetaMQAPII, ANOLEA, PROCHECK and QMEAN6. The DOPE Z scores and the RMSD (RMS) values of the calculated models indicate that the models are of acceptable energy (stability) and fold (conformation). Results from the different MQAPs indicate the models are of acceptable quality and they can be used for docking studies. High throughput screening of SANCDB using AutoDock Vina revealed nine compounds, SANC00 478, 479, 480, 481, 482, 488, 489, 490 and 491, having a strong affinity for Trypanosoma spp. cathepsin B proteases than HsCatB. SANC00488 has the strongest binding to Trypanosoma spp. cathepsin B proteases and the weakest binding to HsCatB protease. Molecular dynamics (MD) simulations show that the complexes between SANC00488 and TbCatB, TcCatB, TcrCatB and TvCatB are stable and do not come apart during simulation. The complex between this compound and HsCatB however is unstable and comes apart during simulation. Residues that are important for the stability of SANC00488-TbCatB complex are Gly328 of the S2 subsite, Phe208, and Ala256. In conclusion SANC00488 is a good candidate for development of a drug against HAT.
- Full Text:
- Date Issued: 2016
- Authors: Mokhawa, Gaone
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3304 , vital:20470
- Description: Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a fatal chronic disease that is caused by flagellated protozoans, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. HAT is spread by a bite from an infected tsetse fly of the Glosina genus. Up to 60 million people in 36 countries in sub-Saharan Africa are at a risk of infection from HAT with up to 30 000 deaths reported every year. Current chemotherapy for HAT is insufficient since the available drugs exhibit unacceptable side effects (toxicity) and parasite resistance. Novel treatments and approaches for development of specific and more potent drugs for HAT are therefore required. One approach is to target vital proteins that are essential to the life cycle of the parasite. The main interest of this study is to explore Trypanosoma brucei cathepsin B-like protease (TbCatB) structural and functional properties with the primary goal of discovering non peptide small molecule inhibitors of TbCatB using bioinformatics approaches. TbCatB is a papain family C1 cysteine protease which belongs to clan CA group and it has emerged as a potential HAT drug target. Papain family cysteine proteases of Clan CA group of Trypanosoma brucei (rhodesain and TbCatB) have demonstrated potential as chemotherapeutic targets using synthetic protease inhibitors like Z-Phe-Ala-CHN2 to kill the parasite in vitro and in vivo. TbCatB has been identified as the essential cysteine protease of T. brucei since mRNA silencing of TbCatB killed the parasite and resulted in a cure in mice infected with T. brucei while mRNA silencing of rhodesain only extended mice life. TbCatB is therefore a promising drug target against HAT and the discovery and development of compounds that can selectively inhibit TbCatB without posing any danger to the human host represent a great therapeutic solution for treatment of HAT. To understand protein-inhibitor interactions, useful information can be obtained from high resolution protease-inhibitor crystal structure complexes. This study aims to use bioinformatics approaches to carry out comparative sequence, structural and functional analysis of TbCatB protease and its homologs from T. congolense, T, cruzi, T. vivax and H. sapien as well as to identify non-peptide small molecule inhibitors of TbCatB cysteine proteases from natural compounds of South African origin. Sequences of TbCatB (PDB ID: 3HHI) homologs were retrieved by a BLAST search. Human cathepsin B (PDB ID: 3CBJ) was selected from a list of templates for homology modelling found by HHpred. MODELLER version 9.10 program was used to generate a hundred models for T. congolense, T, cruzi and T. vivax cathepsin B like proteases using 3HHI and 3CBJ as templates. The best models were chosen based on their low DOPE Z scores before validation using MetaMQAPII, ANOLEA, PROCHECK and QMEAN6. The DOPE Z scores and the RMSD (RMS) values of the calculated models indicate that the models are of acceptable energy (stability) and fold (conformation). Results from the different MQAPs indicate the models are of acceptable quality and they can be used for docking studies. High throughput screening of SANCDB using AutoDock Vina revealed nine compounds, SANC00 478, 479, 480, 481, 482, 488, 489, 490 and 491, having a strong affinity for Trypanosoma spp. cathepsin B proteases than HsCatB. SANC00488 has the strongest binding to Trypanosoma spp. cathepsin B proteases and the weakest binding to HsCatB protease. Molecular dynamics (MD) simulations show that the complexes between SANC00488 and TbCatB, TcCatB, TcrCatB and TvCatB are stable and do not come apart during simulation. The complex between this compound and HsCatB however is unstable and comes apart during simulation. Residues that are important for the stability of SANC00488-TbCatB complex are Gly328 of the S2 subsite, Phe208, and Ala256. In conclusion SANC00488 is a good candidate for development of a drug against HAT.
- Full Text:
- Date Issued: 2016
Localizing selected endocytosis protein candidates in Plasmodium falciparum using GFP-tagged fusion constructs
- Authors: Basson, Travis
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2680 , vital:20316
- Description: Malaria is a mosquito-borne infectious disease caused by several obligate intracellular protozoan parasites in the Plasmodium genus, with Plasmodium falciparum causing the most widespread cases and malaria deaths. In 2013 there were approximately 190 million cases of the disease and between 584,000 and 855,000 deaths. It is essential to identify novel drug targets and develop novel drug candidates due to the increase in resistance of P. falciparum parasites to the current arsenal of antimalarial drugs. Endocytosis is an essential process in eukaryotic cells in which the external environment is internalized by the cell in order to obtain various particles from the extracellular space. This extracellular cytoplasm is internalized in membrane-bound invaginations at the plasma membrane. During the blood stage of malaria infection, the parasite requires nutrients from the host red blood cell. To obtain these nutrients, the parasite internalizes haemoglobin in large amounts and degrades it in an acidic, lysosome-like organelle, known as the digestive vacuole. Whilst the exact molecular mechanism of malaria parasite endocytosis is not yet fully understood, a number of proteins have been suggested to be involved. The most expedient approach in identifying candidate endocytosis proteins is to investigate parasite homologues of proteins known to be involved in endocytosis in mammalian cells. The three proteins selected for investigation in this study were the P. falciparum homologues of coronin, dynamin 2, and μ4. The coding sequences for the candidate endocytosis proteins were amplified by PCR and cloned into the pARL2-GFP expression vector. P. falciparum 3D7 parasites were transfected with these vectors and the episomal expression of full-length GFP-tagged fusion protein was confirmed by Western blot analysis using commercially available anti-GFP antibodies. Microscopic analysis of live parasites using fluorescence and confocal microscopy was used to determine the localization of the candidate endocytosis proteins. Coronin appeared to display diffuse cytoplasmic GFP localization during the trophozoite stage, arguing against a role in endocytosis. However, distinct localization during the schizont stage at what appears to be the inner membrane complex was observed. Coronin is thus likely required to coordinate the formation of the actin network between the merozoite IMC and the plasma membrane on which the glideosome is dependant for generating the motile forces required for the merozoite motility and invasion of RBCs. Dynamin 2 displayed localization at three potential locii: the parasite periphery (plasma membrane), punctuate regions within the cytoplasm (potentially at membrane bound organelles) and at the parasite food vacuole. The data suggested that dynamin 2 is involved in endocytosis and membrane trafficking in a similar manner to classical dynamins, potentially as a vesicle scission molecule at the plasma membrane, mediating vesicle formation at the food vacuole to recycle membrane to the plasma membrane, and possibly mitochondria organelle division. μ4 displayed transient localization, cycling between cytosolic localization, and localization to distinct regions at the plasma membrane and the food vacuole. Localization of Pfμ4 to the plasma membrane is indicative of a role for μ4 as a part of an adaptor protein (AP) complex which may be responsible for recruitment of clathrin to initiate endocytosis in a manner similar to mammalian AP-2. As was observed with PfDYN2, Pfμ4 localizes to the FV, which suggests that Pfμ4 forms part of a coat complex that mediates the formation of vesicles that recycle membrane from the FV to the parasite plasma membrane. This study showed that expressing proteins as full-length GFP-tagged fusion constructs is an effective approach in the early stages of determining the localization and function of P. falciparum proteins in vitro, and distinguishing between candidates that have a potential role in endocytosis and those that are unlikely to do so.
- Full Text:
- Date Issued: 2016
- Authors: Basson, Travis
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2680 , vital:20316
- Description: Malaria is a mosquito-borne infectious disease caused by several obligate intracellular protozoan parasites in the Plasmodium genus, with Plasmodium falciparum causing the most widespread cases and malaria deaths. In 2013 there were approximately 190 million cases of the disease and between 584,000 and 855,000 deaths. It is essential to identify novel drug targets and develop novel drug candidates due to the increase in resistance of P. falciparum parasites to the current arsenal of antimalarial drugs. Endocytosis is an essential process in eukaryotic cells in which the external environment is internalized by the cell in order to obtain various particles from the extracellular space. This extracellular cytoplasm is internalized in membrane-bound invaginations at the plasma membrane. During the blood stage of malaria infection, the parasite requires nutrients from the host red blood cell. To obtain these nutrients, the parasite internalizes haemoglobin in large amounts and degrades it in an acidic, lysosome-like organelle, known as the digestive vacuole. Whilst the exact molecular mechanism of malaria parasite endocytosis is not yet fully understood, a number of proteins have been suggested to be involved. The most expedient approach in identifying candidate endocytosis proteins is to investigate parasite homologues of proteins known to be involved in endocytosis in mammalian cells. The three proteins selected for investigation in this study were the P. falciparum homologues of coronin, dynamin 2, and μ4. The coding sequences for the candidate endocytosis proteins were amplified by PCR and cloned into the pARL2-GFP expression vector. P. falciparum 3D7 parasites were transfected with these vectors and the episomal expression of full-length GFP-tagged fusion protein was confirmed by Western blot analysis using commercially available anti-GFP antibodies. Microscopic analysis of live parasites using fluorescence and confocal microscopy was used to determine the localization of the candidate endocytosis proteins. Coronin appeared to display diffuse cytoplasmic GFP localization during the trophozoite stage, arguing against a role in endocytosis. However, distinct localization during the schizont stage at what appears to be the inner membrane complex was observed. Coronin is thus likely required to coordinate the formation of the actin network between the merozoite IMC and the plasma membrane on which the glideosome is dependant for generating the motile forces required for the merozoite motility and invasion of RBCs. Dynamin 2 displayed localization at three potential locii: the parasite periphery (plasma membrane), punctuate regions within the cytoplasm (potentially at membrane bound organelles) and at the parasite food vacuole. The data suggested that dynamin 2 is involved in endocytosis and membrane trafficking in a similar manner to classical dynamins, potentially as a vesicle scission molecule at the plasma membrane, mediating vesicle formation at the food vacuole to recycle membrane to the plasma membrane, and possibly mitochondria organelle division. μ4 displayed transient localization, cycling between cytosolic localization, and localization to distinct regions at the plasma membrane and the food vacuole. Localization of Pfμ4 to the plasma membrane is indicative of a role for μ4 as a part of an adaptor protein (AP) complex which may be responsible for recruitment of clathrin to initiate endocytosis in a manner similar to mammalian AP-2. As was observed with PfDYN2, Pfμ4 localizes to the FV, which suggests that Pfμ4 forms part of a coat complex that mediates the formation of vesicles that recycle membrane from the FV to the parasite plasma membrane. This study showed that expressing proteins as full-length GFP-tagged fusion constructs is an effective approach in the early stages of determining the localization and function of P. falciparum proteins in vitro, and distinguishing between candidates that have a potential role in endocytosis and those that are unlikely to do so.
- Full Text:
- Date Issued: 2016
Detecting derivative malware samples using deobfuscation-assisted similarity analysis
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
- Full Text:
- Date Issued: 2016
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
- Full Text:
- Date Issued: 2016
Investigating the role of Hsp90 and LRP1 in FN matrix dynamics
- Authors: Boël, Natasha Marie-Eraine
- Date: 2016
- Subjects: Extracellular matrix , Molecular chaperones , Heat shock proteins , Cancer , Fibronectins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2713 , vital:20319
- Description: Fibronectin (FN), a matrix protein responsible for regulating processes including migration and differentiation, is secreted as a soluble dimer which is assembled into an insoluble extracellular matrix. The dynamics of FN matrix assembly and degradation play a large role in cell migration and invasion contributing to the metastatic potential of cancer cells. Previous studies from our group have shown the direct binding of Hsp90 and FN in vitro and that inhibition of Hsp90 with novobiocin (NOV) caused internalisation of the FN matrix. However, the receptor mediating this internalisation is currently unknown. Low density lipoprotein 1 (LRP1) is a likely candidate as it is a ubiquitous receptor responsible for regulating internalisation of diverse ligands and is known to bind both Hsp90 and FN. We used wild type and knockout LRP1 cell lines to study the endocytosis of FN via this receptor. Here, we demonstrate that LRP1-deficient cells accumulated greatly increased levels of FN and were found to be less sensitive to pharmacological inhibition of Hsp90 by NOV. LRP1-expressing MEF-1 and Hs578T breast cancer cells experienced an increase in total FN in response to NOV, at concentrations below the EC50 value, followed by a dose-dependent loss of FN. We attributed greater FN levels to a loss of extracellular FN matrix coupled with increased internalisation of FN. Cell-surface biotinylation and DOC assays showed that loss of extracellular FN was specific to LRP1-expressing MEF-1 cells. Furthermore, we demonstrate that the loss of extracellular FN is not affected by changes in FN mRNA levels as determined by qRT-PCR, and that treatment with NOV resulted in the accelerated degradation of FN in the presence of cycloheximide. Immunoprecipitation studies reveal a putative complex exists between FN, Hsp90 and LRP1 in both cancer and non-cancer cells which is not perturbed by NOV. Western analyses revealed increased proteolytic processing of LRP1 in response to NOV which we proposed, based on literature, to modulate signalling pathways as a potential mechanism for regulating FN turnover. Moreover, using wound healing assays we identified increased migration to be one of the consequences associated with loss of extracellular FN by Hsp90 inhibition but only in cells containing LRP1. In summary, this study provides new insights into the Hsp90-LRP1 mediated loss of FN matrix and also reveals for the first time the functional consequence related to FN turnover by NOV was an increase in migration in LRP1-expressing cells.
- Full Text:
- Date Issued: 2016
- Authors: Boël, Natasha Marie-Eraine
- Date: 2016
- Subjects: Extracellular matrix , Molecular chaperones , Heat shock proteins , Cancer , Fibronectins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2713 , vital:20319
- Description: Fibronectin (FN), a matrix protein responsible for regulating processes including migration and differentiation, is secreted as a soluble dimer which is assembled into an insoluble extracellular matrix. The dynamics of FN matrix assembly and degradation play a large role in cell migration and invasion contributing to the metastatic potential of cancer cells. Previous studies from our group have shown the direct binding of Hsp90 and FN in vitro and that inhibition of Hsp90 with novobiocin (NOV) caused internalisation of the FN matrix. However, the receptor mediating this internalisation is currently unknown. Low density lipoprotein 1 (LRP1) is a likely candidate as it is a ubiquitous receptor responsible for regulating internalisation of diverse ligands and is known to bind both Hsp90 and FN. We used wild type and knockout LRP1 cell lines to study the endocytosis of FN via this receptor. Here, we demonstrate that LRP1-deficient cells accumulated greatly increased levels of FN and were found to be less sensitive to pharmacological inhibition of Hsp90 by NOV. LRP1-expressing MEF-1 and Hs578T breast cancer cells experienced an increase in total FN in response to NOV, at concentrations below the EC50 value, followed by a dose-dependent loss of FN. We attributed greater FN levels to a loss of extracellular FN matrix coupled with increased internalisation of FN. Cell-surface biotinylation and DOC assays showed that loss of extracellular FN was specific to LRP1-expressing MEF-1 cells. Furthermore, we demonstrate that the loss of extracellular FN is not affected by changes in FN mRNA levels as determined by qRT-PCR, and that treatment with NOV resulted in the accelerated degradation of FN in the presence of cycloheximide. Immunoprecipitation studies reveal a putative complex exists between FN, Hsp90 and LRP1 in both cancer and non-cancer cells which is not perturbed by NOV. Western analyses revealed increased proteolytic processing of LRP1 in response to NOV which we proposed, based on literature, to modulate signalling pathways as a potential mechanism for regulating FN turnover. Moreover, using wound healing assays we identified increased migration to be one of the consequences associated with loss of extracellular FN by Hsp90 inhibition but only in cells containing LRP1. In summary, this study provides new insights into the Hsp90-LRP1 mediated loss of FN matrix and also reveals for the first time the functional consequence related to FN turnover by NOV was an increase in migration in LRP1-expressing cells.
- Full Text:
- Date Issued: 2016
Assessing estuarine nursery habitats for Cape Stumpnose (Rhabdosargus holubi), (Pisces: Sparidae) in a warm-temperate estuary in the Eastern Cape, South Africa
- Authors: Leslie, Timothy David
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3178 , vital:20381
- Description: The nursery role hypothesis provides an approach for assessing the nursery function of habitat types within estuaries. This study attempted to assess the nursery value of the dominant estuarine habitats in the Bushmans Estuary for Rhabdosargus holubi (Steindachner 1881) by analysing habitat complexity, relative abundance and behaviour of R. holubi and using stomach contents analysis and dietary diatom composition as indicative of feeding habitat. Structural habitat complexity was assessed in Zostera capensis (Setchell) seagrass and Spartina maritima (Curtis Fernald) salt marsh by sampling above-ground stem density and length, and total cover per unit area (Ct/At). Dimensionless habitat complexity indices such as the interstitial spatial index (ISI) at three magnifications and fractal geometry at two magnifications were used to further analyse habitat complexity. Above-ground biomass (P<0.05) in each season and canopy height (P<0.001) were significantly higher in salt marsh than in seagrass whilst stem density was significantly higher in seagrass than in salt marsh in each season (P<0.001). Each dimensionless index indicated that complexity is notably higher in seagrass than in the salt marsh. Using dimensionless indices that analyse complexity at different spatial scales provided a better analysis of habitat complexity than canopy height and biomass as it allowed for direct comparisons between habitat types. Underwater video cameras were deployed in seagrass, salt marsh and sand flat habitats to assess the relative abundance and behaviour of R. holubi. The relative abundance of R. holubi was significantly higher in seagrass than salt marsh and sand flats, whilst the behaviour of R. holubi indicated a high degree of habitat use in structured habitats and a low degree of habitat use in unstructured sand flat habitats. This indicated that not only are juvenile R. holubi a vegetation-associated species, but also a species that prefers seagrass to salt marsh.
- Full Text:
- Date Issued: 2016
- Authors: Leslie, Timothy David
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3178 , vital:20381
- Description: The nursery role hypothesis provides an approach for assessing the nursery function of habitat types within estuaries. This study attempted to assess the nursery value of the dominant estuarine habitats in the Bushmans Estuary for Rhabdosargus holubi (Steindachner 1881) by analysing habitat complexity, relative abundance and behaviour of R. holubi and using stomach contents analysis and dietary diatom composition as indicative of feeding habitat. Structural habitat complexity was assessed in Zostera capensis (Setchell) seagrass and Spartina maritima (Curtis Fernald) salt marsh by sampling above-ground stem density and length, and total cover per unit area (Ct/At). Dimensionless habitat complexity indices such as the interstitial spatial index (ISI) at three magnifications and fractal geometry at two magnifications were used to further analyse habitat complexity. Above-ground biomass (P<0.05) in each season and canopy height (P<0.001) were significantly higher in salt marsh than in seagrass whilst stem density was significantly higher in seagrass than in salt marsh in each season (P<0.001). Each dimensionless index indicated that complexity is notably higher in seagrass than in the salt marsh. Using dimensionless indices that analyse complexity at different spatial scales provided a better analysis of habitat complexity than canopy height and biomass as it allowed for direct comparisons between habitat types. Underwater video cameras were deployed in seagrass, salt marsh and sand flat habitats to assess the relative abundance and behaviour of R. holubi. The relative abundance of R. holubi was significantly higher in seagrass than salt marsh and sand flats, whilst the behaviour of R. holubi indicated a high degree of habitat use in structured habitats and a low degree of habitat use in unstructured sand flat habitats. This indicated that not only are juvenile R. holubi a vegetation-associated species, but also a species that prefers seagrass to salt marsh.
- Full Text:
- Date Issued: 2016
The use of treated brewery effluent as a water and nutrient source in crop irrigation
- Authors: Taylor, Richard Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5390 , http://hdl.handle.net/10962/d1021265
- Description: Brewery effluent (BE) needs to be treated before it can be released into the environment, reused or used in down-stream activities. Current technologies used to address this concern at the experimental wastewater treatment plant at Ibahyi Brewery (SAB Ltd) include anaerobic digestion (AD), primary facultative ponds (PFP), high rate algal ponds (HRAP) and constructed wetlands (CW). The aim of this work was to determine if BE treated in these systems might be suitable for crop irrigation. A test crop, cabbage (Brassica oleracea cv. Star 3301), grew best on post-AD and post-PFP BE compared to those irrigated with post-HRAP or post-CW effluent. However, the yield was 13% lower than cabbage plants irrigated with a commercial nutrient solution and fresh water. The relatively high conductivity (3019.05 ± 48.72 μs/cm2) of BE may be the main factor reducing the cabbage yields. Post-HRAP and post-CW BE were the least suitable for irrigated crop production due to the higher conductivity and lower nutrient content of these treated effluents. After three months, soils irrigated with post-AD and post-PFP BE had a significantly higher sodium content and sodium adsorption ratio (3919 ± 94.77 mg/kg & 8.18 ± 0.17) than soil irrigated with a commercial nutrient solution (920.58 ± 27.46 mg/kg & 2.20 ± 0.05; p<0.05). However, this was not accompanied by a deterioration in the soil’s hydro-physical properties, nor a change in the metabolic community structure of the soil (p>0.05). After prolonged irrigation with treated BE, sodium is likely to build up in the soil and this can be expected to be accompanied by a deterioration in the soil physical structure. However, crops species such as millet (Echinochloa esculenta), lucerne (Medicago sativa) and saltbush (Atriplex nummularia) reduced the build-up of sodium in the soil. The results suggest that sodium was mainly removed from the soil through plant-assisted leaching. Of the crops grown, lucerne showed the most promise because it improved the soil physical properties, is able to grow well in alkaline environments, is a popular fodder crop and can be harvested multiple times from a single stand. Brewery effluent is more suitable for soil production systems than hydroponic production systems because the soil was able to act as a buffer against the high pH of post-AD BE, whereas in a hydroponics systems the high pH reduced the availability of key minerals to plants. In conclusion brewery effluent contains sufficient plants nutrients to support the growth of cabbages, saltbush, lucerne and millet. However the sodium content of BE is a concern as it accumulates in the soil, and in the long-term it may lead to soil degradation. It is suggested that the brewery change the pH neutralising treatment of BE from sodium hydroxide to potassium hydroxide, or dolomitic lime (calcium and magnesium carbonate) because this would reduce the introduction of sodium into the system, and would increase the suitability of BE for crop production, given potassium and calcium are plant nutrients. The benefits of developing this nutrient and water resource could contribute to cost-reductions at the brewery, more efficient water, nutrient and energy management, create job opportunities with the potential of improving food security in the local community.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Richard Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5390 , http://hdl.handle.net/10962/d1021265
- Description: Brewery effluent (BE) needs to be treated before it can be released into the environment, reused or used in down-stream activities. Current technologies used to address this concern at the experimental wastewater treatment plant at Ibahyi Brewery (SAB Ltd) include anaerobic digestion (AD), primary facultative ponds (PFP), high rate algal ponds (HRAP) and constructed wetlands (CW). The aim of this work was to determine if BE treated in these systems might be suitable for crop irrigation. A test crop, cabbage (Brassica oleracea cv. Star 3301), grew best on post-AD and post-PFP BE compared to those irrigated with post-HRAP or post-CW effluent. However, the yield was 13% lower than cabbage plants irrigated with a commercial nutrient solution and fresh water. The relatively high conductivity (3019.05 ± 48.72 μs/cm2) of BE may be the main factor reducing the cabbage yields. Post-HRAP and post-CW BE were the least suitable for irrigated crop production due to the higher conductivity and lower nutrient content of these treated effluents. After three months, soils irrigated with post-AD and post-PFP BE had a significantly higher sodium content and sodium adsorption ratio (3919 ± 94.77 mg/kg & 8.18 ± 0.17) than soil irrigated with a commercial nutrient solution (920.58 ± 27.46 mg/kg & 2.20 ± 0.05; p<0.05). However, this was not accompanied by a deterioration in the soil’s hydro-physical properties, nor a change in the metabolic community structure of the soil (p>0.05). After prolonged irrigation with treated BE, sodium is likely to build up in the soil and this can be expected to be accompanied by a deterioration in the soil physical structure. However, crops species such as millet (Echinochloa esculenta), lucerne (Medicago sativa) and saltbush (Atriplex nummularia) reduced the build-up of sodium in the soil. The results suggest that sodium was mainly removed from the soil through plant-assisted leaching. Of the crops grown, lucerne showed the most promise because it improved the soil physical properties, is able to grow well in alkaline environments, is a popular fodder crop and can be harvested multiple times from a single stand. Brewery effluent is more suitable for soil production systems than hydroponic production systems because the soil was able to act as a buffer against the high pH of post-AD BE, whereas in a hydroponics systems the high pH reduced the availability of key minerals to plants. In conclusion brewery effluent contains sufficient plants nutrients to support the growth of cabbages, saltbush, lucerne and millet. However the sodium content of BE is a concern as it accumulates in the soil, and in the long-term it may lead to soil degradation. It is suggested that the brewery change the pH neutralising treatment of BE from sodium hydroxide to potassium hydroxide, or dolomitic lime (calcium and magnesium carbonate) because this would reduce the introduction of sodium into the system, and would increase the suitability of BE for crop production, given potassium and calcium are plant nutrients. The benefits of developing this nutrient and water resource could contribute to cost-reductions at the brewery, more efficient water, nutrient and energy management, create job opportunities with the potential of improving food security in the local community.
- Full Text:
- Date Issued: 2016
Cosmological structure formation using spectral methods
- Authors: Funcke, Michelle
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2969 , vital:20348
- Description: Numerical simulations are becoming an increasingly important tool for understanding the growth and development of structure in the universe. Common practice is to discretize the space-time using physical variables. The discreteness is embodied by considering the dynamical variables as fields on a fixed spatial and time resolution, or by constructing the matter fields by a large number of particles which interact gravitationally (N-body methods). Recognizing that the physical quantities of interest are related to the spectrum of perturbations, we propose an alternate discretization in the frequency domain, using standard spectral methods. This approach is further aided by periodic boundary conditions which allows a straightforward decomposition of variables in a Fourier basis. Fixed resources require a high-frequency cut-off which lead to aliasing effects in non-linear equations, such as the ones considered here. This thesis describes the implementation of a 3D cosmological model based on Newtonian hydrodynamic equations in an expanding background. Initial data is constructed as a spectrum of perturbations, and evolved in the frequency domain using a pseudo-spectral evolution scheme and an explicit Runge-Kutta time integrator. The code is found to converge for both linear and non-linear evolutions, and the convergence rate is determined. The correct growth rates expected from analytical calculations are recovered in the linear case. In the non-linear model, we observe close correspondence with linear growth and are able to monitor the growth on features associated with the non-linearity. High-frequency aliasing effects were evident in the non-linear evolutions, leading to a study of two potential resolutions to this problem: a boxcar filter which adheres to“Orszag’s two thirds rule” and an exponential window function, the exponential filter suggested by Hou and Li [1], and a shifted version of the exponential filter suggested, which has the potential to alleviate high frequency- ripples resulting from the Gibbs’ phenomenon. We found that the filters were somewhat successful at reducing aliasing effects but that the Gibbs’ phenomenon could not be entirely removed by the choice of filters.
- Full Text:
- Date Issued: 2016
- Authors: Funcke, Michelle
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2969 , vital:20348
- Description: Numerical simulations are becoming an increasingly important tool for understanding the growth and development of structure in the universe. Common practice is to discretize the space-time using physical variables. The discreteness is embodied by considering the dynamical variables as fields on a fixed spatial and time resolution, or by constructing the matter fields by a large number of particles which interact gravitationally (N-body methods). Recognizing that the physical quantities of interest are related to the spectrum of perturbations, we propose an alternate discretization in the frequency domain, using standard spectral methods. This approach is further aided by periodic boundary conditions which allows a straightforward decomposition of variables in a Fourier basis. Fixed resources require a high-frequency cut-off which lead to aliasing effects in non-linear equations, such as the ones considered here. This thesis describes the implementation of a 3D cosmological model based on Newtonian hydrodynamic equations in an expanding background. Initial data is constructed as a spectrum of perturbations, and evolved in the frequency domain using a pseudo-spectral evolution scheme and an explicit Runge-Kutta time integrator. The code is found to converge for both linear and non-linear evolutions, and the convergence rate is determined. The correct growth rates expected from analytical calculations are recovered in the linear case. In the non-linear model, we observe close correspondence with linear growth and are able to monitor the growth on features associated with the non-linearity. High-frequency aliasing effects were evident in the non-linear evolutions, leading to a study of two potential resolutions to this problem: a boxcar filter which adheres to“Orszag’s two thirds rule” and an exponential window function, the exponential filter suggested by Hou and Li [1], and a shifted version of the exponential filter suggested, which has the potential to alleviate high frequency- ripples resulting from the Gibbs’ phenomenon. We found that the filters were somewhat successful at reducing aliasing effects but that the Gibbs’ phenomenon could not be entirely removed by the choice of filters.
- Full Text:
- Date Issued: 2016
Thermoluminescence of annealed synthetic quartz
- Atang, Elizabeth Fende Midiki
- Authors: Atang, Elizabeth Fende Midiki
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/420 , vital:19957
- Description: The kinetic and dosimetric features of the main thermoluminescent peak of synthetic quartz have been investigated in quartz ordinarily annealed at 500_C as well as quartz annealed at 500_C for 10 minutes. The main peak is found at 78 _C for the samples annealed at 500_C for 10 minutes irradiated to 10 Gy and heated at 1.0 _C/s. For the samples ordinarily annealed at 500_C the main peak is found at 106 _C after the sample has been irradiated to 30 Gy and heated at 5.0 _C/s. In these samples, the intensity of the main peak is enhanced with repetitive measurement whereas its maximum temperature is unaffected. The peak position of the main peak in the sample is independent of the irradiation dose and this, together with its fading characteristics, are consistent with first-order kinetics. For doses between 5 and 25 Gy, the dose response of the main peak of the annealed sample is superlinear. The half-life of the main TL peak of the annealed sample is about 1 h. The activation energy E of the main peak is around 0.90 eV. For a heating rate of 0.4 _C/s, its order of kinetics b derived from the whole curve method of analysis is 1.0. Following irradiation, preheating and illumination with 470 nm blue light, the main peak in the annealed sample is regenerated during heating. The resulting phototransferred peak occurs at the same temperature as the original peak and has similar kinetic and dosimetric features, with a half-life of about 1 h. For a preheat temperature of 200 _C, the intensity of the phototransferred peak in the sample increases with illumination time up to a maximum and decreases thereafter. At longer illumination times, no further decrease in the intensity of the phototransferred peak is observed. The traps associated with the 325 _C peak are the main source of the electrons responsible for the regenerated peak.
- Full Text:
- Date Issued: 2016
- Authors: Atang, Elizabeth Fende Midiki
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/420 , vital:19957
- Description: The kinetic and dosimetric features of the main thermoluminescent peak of synthetic quartz have been investigated in quartz ordinarily annealed at 500_C as well as quartz annealed at 500_C for 10 minutes. The main peak is found at 78 _C for the samples annealed at 500_C for 10 minutes irradiated to 10 Gy and heated at 1.0 _C/s. For the samples ordinarily annealed at 500_C the main peak is found at 106 _C after the sample has been irradiated to 30 Gy and heated at 5.0 _C/s. In these samples, the intensity of the main peak is enhanced with repetitive measurement whereas its maximum temperature is unaffected. The peak position of the main peak in the sample is independent of the irradiation dose and this, together with its fading characteristics, are consistent with first-order kinetics. For doses between 5 and 25 Gy, the dose response of the main peak of the annealed sample is superlinear. The half-life of the main TL peak of the annealed sample is about 1 h. The activation energy E of the main peak is around 0.90 eV. For a heating rate of 0.4 _C/s, its order of kinetics b derived from the whole curve method of analysis is 1.0. Following irradiation, preheating and illumination with 470 nm blue light, the main peak in the annealed sample is regenerated during heating. The resulting phototransferred peak occurs at the same temperature as the original peak and has similar kinetic and dosimetric features, with a half-life of about 1 h. For a preheat temperature of 200 _C, the intensity of the phototransferred peak in the sample increases with illumination time up to a maximum and decreases thereafter. At longer illumination times, no further decrease in the intensity of the phototransferred peak is observed. The traps associated with the 325 _C peak are the main source of the electrons responsible for the regenerated peak.
- Full Text:
- Date Issued: 2016
Biology and ecology of Glossogobius callidus (Smith 1937) in irrigation impoundments in the Sundays River Valley of the Eastern Cape
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Date Issued: 2016
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Date Issued: 2016
Geochemical exploration for copper - cobalt in the Democratic Republic of Congo, Central African Copperbelt: a case study on PR851
- Authors: Katombe-Kisumbule, Paul
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3035 , vital:20354
- Description: The PR851 licence area is located at about 80 km west from the town of Likasi in the district of Haut-Katanga and 175 km north-west of Lubumbashi, the capital city of Katanga Province in the Democratic Republic of Congo. The exploration licence was granted by the government of the Democratic Republic of Congo to First Quantum Minerals Ltd through its Congolese subsidiary Compagnie Minière de Sakania Sprl (CoMiSa Sprl) under certificate N˚ CAMI/CR/70/2003 on the 10th of October 2003 for a period of 5 years with a possibility of renewal for 3 years in respect to the new Congolese mining code. The PR851 area lies on fragments of Mines Subgroup rocks of the Roan Group in the Congolese Copperbelt where most of the Cu-Co and stratiform-stratabound deposits such as Kipushi, Ruashi-Etoile, Kinsevere, Kipoi, Luishya, Luswishi, Shituru, Kamoya, Kambove, Tenke- Fungurume, Shinkolobwe, Swambo, Mindingi and Kamoto among others are found. During the 20th century, the Union Minière du Haut Katanga (U.M.H.K.) undertook mineral exploration in the Congolese Copperbelt and numerous copper- and cobalt-occurrences were identified (for instance Kibamba copper occurrence in PR851 area). From 2003, the Compagnie Minière de Sakania Sprl initiated a grassroots exploration program in PR851 area and geochemical exploration survey as one of the mineral exploration tools was implemented to aim at detecting copper and cobalt concentration in soil. The B horizon of the thick tropical soil in the area was sampled and soil samples were sent to Genalysis laboratories in Johannesburg, Republic of South Africa for main chemical analysis of Cu and Co only, whereas 10% of analyzed samples were dispatched to Perth, Western Australia for quality control analysis. Thresholds for anomalies of copper and cobalt were defined by literature comparison, standard deviations and spatial analysis. The anomalies were tested at a later stage by reverse circulation / diamond drilling during the year of 2005 to 2008 and the Cu-Co resources were estimated by Digital Mining Services of Harare, Zimbabwe in the year of 2008. Geological logging of chips from reverse circulation and diamond drill cores revealed that copper mineralization is represented by malachite, chrysocolla, chalcopyrite and bornite whereas cobalt mineralization appeared in form of heterogenite. The source of supergene mineralization remains unknown. Recommendations have been made to undertake more geological exploration work in order to fully investigate the geological setting and structural architecture of the region, which may result in a better understanding of the Cu-Co mineralization system and ore genesis. The latter has been no consensus up-to-date and different theories have been proposed to discuss the ore genesis, including syn- and dia- genetic, synorogenic and sulphide remobilization to late-to-post- orogenic Cu-Zn-Pb Kipushi-type deposit. However, geological observations favored that the diagenetic and syngenetic models are applicable to numerous deposits in the Central African Copperbelt.
- Full Text:
- Date Issued: 2016
- Authors: Katombe-Kisumbule, Paul
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3035 , vital:20354
- Description: The PR851 licence area is located at about 80 km west from the town of Likasi in the district of Haut-Katanga and 175 km north-west of Lubumbashi, the capital city of Katanga Province in the Democratic Republic of Congo. The exploration licence was granted by the government of the Democratic Republic of Congo to First Quantum Minerals Ltd through its Congolese subsidiary Compagnie Minière de Sakania Sprl (CoMiSa Sprl) under certificate N˚ CAMI/CR/70/2003 on the 10th of October 2003 for a period of 5 years with a possibility of renewal for 3 years in respect to the new Congolese mining code. The PR851 area lies on fragments of Mines Subgroup rocks of the Roan Group in the Congolese Copperbelt where most of the Cu-Co and stratiform-stratabound deposits such as Kipushi, Ruashi-Etoile, Kinsevere, Kipoi, Luishya, Luswishi, Shituru, Kamoya, Kambove, Tenke- Fungurume, Shinkolobwe, Swambo, Mindingi and Kamoto among others are found. During the 20th century, the Union Minière du Haut Katanga (U.M.H.K.) undertook mineral exploration in the Congolese Copperbelt and numerous copper- and cobalt-occurrences were identified (for instance Kibamba copper occurrence in PR851 area). From 2003, the Compagnie Minière de Sakania Sprl initiated a grassroots exploration program in PR851 area and geochemical exploration survey as one of the mineral exploration tools was implemented to aim at detecting copper and cobalt concentration in soil. The B horizon of the thick tropical soil in the area was sampled and soil samples were sent to Genalysis laboratories in Johannesburg, Republic of South Africa for main chemical analysis of Cu and Co only, whereas 10% of analyzed samples were dispatched to Perth, Western Australia for quality control analysis. Thresholds for anomalies of copper and cobalt were defined by literature comparison, standard deviations and spatial analysis. The anomalies were tested at a later stage by reverse circulation / diamond drilling during the year of 2005 to 2008 and the Cu-Co resources were estimated by Digital Mining Services of Harare, Zimbabwe in the year of 2008. Geological logging of chips from reverse circulation and diamond drill cores revealed that copper mineralization is represented by malachite, chrysocolla, chalcopyrite and bornite whereas cobalt mineralization appeared in form of heterogenite. The source of supergene mineralization remains unknown. Recommendations have been made to undertake more geological exploration work in order to fully investigate the geological setting and structural architecture of the region, which may result in a better understanding of the Cu-Co mineralization system and ore genesis. The latter has been no consensus up-to-date and different theories have been proposed to discuss the ore genesis, including syn- and dia- genetic, synorogenic and sulphide remobilization to late-to-post- orogenic Cu-Zn-Pb Kipushi-type deposit. However, geological observations favored that the diagenetic and syngenetic models are applicable to numerous deposits in the Central African Copperbelt.
- Full Text:
- Date Issued: 2016
An assessment of the invasion state and fisheries suitability in four dams and a natural lake in the Western Cape, South Africa
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
- Date Issued: 2016
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
- Date Issued: 2016
Local versus landscape effects of bush encroachment on plant available light, soil moisture, frost occurrence and herbaceous productivity and composition
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
Investigating soil microbial interactions of Portulacaria afra
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
- Date Issued: 2016
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
- Date Issued: 2016
Synthesis, spectroscopic and nonlinear optical properties of metal-free and nickel β substituted binuclear phthalocyanines
- Authors: Kabwe, Kapambwe Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3013 , vital:20352
- Description: In this project, nickel and metal-free 4β-(4-tert-butylphenoxy) phthalocyanine, biphenyl bridged binuclear 4-tert-butylphenoxy phthalocyanine and naphthalene bridged binuclear 4-tert-butylphenoxy phthalocyanine have been synthesised. The Z-scan technique has been employed to comparatively study their second order nonlinear optical (NLO) properties. This work, shows that the presence of H-aggregation in binuclear Pcs of metal-free and nickel 4β-(4-tertbutylphenoxy) phthalocyanines do not have an effect on the magnitude of second order nonlinear absorption coefficient (β) as compared to monomeric Pcs. Density functional (DFT) calculations of dipolar/octupolar contributions were performed, in order to explain experimentally determined β values. Spectroscopic and photophysical properties of the synthesised compounds have been determined using a range of different spectroscopic techniques, including magnetic circular dichroism (MCD), time correlated single photon counting spectroscopy (TCSPC), UV-visible absorption spectroscopy, mass spectroscopy and IR Spectroscopy.
- Full Text:
- Date Issued: 2016
- Authors: Kabwe, Kapambwe Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3013 , vital:20352
- Description: In this project, nickel and metal-free 4β-(4-tert-butylphenoxy) phthalocyanine, biphenyl bridged binuclear 4-tert-butylphenoxy phthalocyanine and naphthalene bridged binuclear 4-tert-butylphenoxy phthalocyanine have been synthesised. The Z-scan technique has been employed to comparatively study their second order nonlinear optical (NLO) properties. This work, shows that the presence of H-aggregation in binuclear Pcs of metal-free and nickel 4β-(4-tertbutylphenoxy) phthalocyanines do not have an effect on the magnitude of second order nonlinear absorption coefficient (β) as compared to monomeric Pcs. Density functional (DFT) calculations of dipolar/octupolar contributions were performed, in order to explain experimentally determined β values. Spectroscopic and photophysical properties of the synthesised compounds have been determined using a range of different spectroscopic techniques, including magnetic circular dichroism (MCD), time correlated single photon counting spectroscopy (TCSPC), UV-visible absorption spectroscopy, mass spectroscopy and IR Spectroscopy.
- Full Text:
- Date Issued: 2016
Identification of potential novel roles for Hsp70/Hsp90 organising protein (Hop) using proteomic analysis in human cells
- Authors: Wingate, Ianthe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64758 , vital:28598
- Description: Expected release date-May 2018
- Full Text:
- Date Issued: 2016
- Authors: Wingate, Ianthe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64758 , vital:28598
- Description: Expected release date-May 2018
- Full Text:
- Date Issued: 2016
In silico analysis of the effects of non-synonymous single nucleotide polymorphisms on the human macrophage migration inhibitory factor gene and their possible role in human African trypanosomiasis susceptibility
- Authors: Kimuda, Magambo Philip
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3047 , vital:20355
- Description: Human African trypanosomiasis (HAT) is a public health problem in sub-Saharan Africa, with approximately 10,000 cases being reported per year. The Macrophage Migration Inhibitory Factor (MIF) which is encoded by a functionally polymorphic gene is important in both innate andadaptive immune responses, and has been implicated in affecting the outcome and processes of several inflammatory conditions. A recent study in mice to that effect showed that MIF deficient and anti-MIF antibody treated mice showed lowered inflammatory responses, liver damage and anaemia than the wild type mice when experimentally challenged with Trypanosomes. These findings could mean that the transcript levels and/or polymorphisms in this gene can possibly affect individual risk to trypanosomiasis. This is especially of interest because there have been reports of spontaneous recovery i.e self-cure/resistance in some HAT cases in West Africa. Prior to this discovery the general paradigm was that trypanosomiasis is fatal if left untreated. The aim of this study was to gain insights into how human genetic variation in forms of nonsynonymous SNPs affects the MIF structure and function and possibly HAT susceptibility. NsSNPs in the mif gene were obtained from dbSNP. Through homology modeling, SNP prediction tools, protein interface analysis, alanine scanning, changes in free energy of folding, protein interactions calculator (PIC), and molecular dynamics simulations, SNP effects on the protein structure and function were studied. The study cohort comprised of human genome sequence data from 50 North Western Uganda Lugbara endemic individuals of whom 20 were cases (previous HAT patients) and 30 were controls (HAT free individuals). None of the 26 nsSNPs retrieved from dbSNP (July 2015) were present in the mif gene region in the study cohort. Out of the eight variants called in the mif coding region there was only one missense variant rs36065127 whose clinical significance is unknown. It was not possible to test for association of this variant with HAT due to its low global MAF that was less than 0.05. Alanine scanning provided a fast and computationally cheap means of quickly assessing nsSNPs of importance. NsSNPs that were interface residues were more likely to be hotspots (important in protein stability). Assessment of possible compensatory mutations using PIC analysis showed that some nsSNP sites were interacting with others, but this requires further experimentation. Analysis of changes in free energy using FOLDX was not enough to predict which nsSNPs would adversely affect protein structure, function and kinetics. The MD simulations were unfortunately too short to glean any meaningful inferences. This was the first genetic study carried out on the people of Lugbara ethnicity from North Western Uganda.
- Full Text:
- Date Issued: 2016
- Authors: Kimuda, Magambo Philip
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3047 , vital:20355
- Description: Human African trypanosomiasis (HAT) is a public health problem in sub-Saharan Africa, with approximately 10,000 cases being reported per year. The Macrophage Migration Inhibitory Factor (MIF) which is encoded by a functionally polymorphic gene is important in both innate andadaptive immune responses, and has been implicated in affecting the outcome and processes of several inflammatory conditions. A recent study in mice to that effect showed that MIF deficient and anti-MIF antibody treated mice showed lowered inflammatory responses, liver damage and anaemia than the wild type mice when experimentally challenged with Trypanosomes. These findings could mean that the transcript levels and/or polymorphisms in this gene can possibly affect individual risk to trypanosomiasis. This is especially of interest because there have been reports of spontaneous recovery i.e self-cure/resistance in some HAT cases in West Africa. Prior to this discovery the general paradigm was that trypanosomiasis is fatal if left untreated. The aim of this study was to gain insights into how human genetic variation in forms of nonsynonymous SNPs affects the MIF structure and function and possibly HAT susceptibility. NsSNPs in the mif gene were obtained from dbSNP. Through homology modeling, SNP prediction tools, protein interface analysis, alanine scanning, changes in free energy of folding, protein interactions calculator (PIC), and molecular dynamics simulations, SNP effects on the protein structure and function were studied. The study cohort comprised of human genome sequence data from 50 North Western Uganda Lugbara endemic individuals of whom 20 were cases (previous HAT patients) and 30 were controls (HAT free individuals). None of the 26 nsSNPs retrieved from dbSNP (July 2015) were present in the mif gene region in the study cohort. Out of the eight variants called in the mif coding region there was only one missense variant rs36065127 whose clinical significance is unknown. It was not possible to test for association of this variant with HAT due to its low global MAF that was less than 0.05. Alanine scanning provided a fast and computationally cheap means of quickly assessing nsSNPs of importance. NsSNPs that were interface residues were more likely to be hotspots (important in protein stability). Assessment of possible compensatory mutations using PIC analysis showed that some nsSNP sites were interacting with others, but this requires further experimentation. Analysis of changes in free energy using FOLDX was not enough to predict which nsSNPs would adversely affect protein structure, function and kinetics. The MD simulations were unfortunately too short to glean any meaningful inferences. This was the first genetic study carried out on the people of Lugbara ethnicity from North Western Uganda.
- Full Text:
- Date Issued: 2016
The efficacy of a community based eccentric hamstring strengthening program in peri-urban Black South African soccer players
- Authors: Ryan, Bennett
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3573 , vital:20526
- Description: Introduction: Hamstring injury prevalence in soccer remains a major concern. Research in this context has focused on Caucasian populations with little attention given to other ethnic groups. The compatibility and applicability of such research to the South African context, particularly at an amateur level, may be minimal due to fundamental differences in physical characteristics, as well as complexities with regards to implementation. The aim of this investigation was therefore twofold. 1) Identify the lower extremity strength and performance profile of Peri-urban Amateur South African Players, and 2) Assess the efficacy of a community based intervention through the use of the Nordic Hamstring Exercise. Methods: 19 Black male Eastern Cape amateur players participated in a 12 week randomly controlled trial (9 = Control, 10 = Intervention). All participants completed regular training, while the intervention group, in addition, performed the Nordic Hamstring exercise post warm up. The incremental program design was taken from Mjolsnes et al. (2004), with a progressive increase in both sets and repetitions. Compliance was defined as completion of the required exercises for that session. Isokinetic strength evaluations (at 60°.s-1 and 180°.s-1) including assessment of peak torque and total work, as well as performance measures of countermovement and squat jump, were completed pre and post intervention, with the profile of the Peri-urban player the combined responses of both groups at baseline. Additionally, both the functional ratio (Eccentric Hamstrings/Concentric Quadriceps) and eccentric utilization ratio (Countermovement Jump/Squat Jump) were calculated. Results: Concentric quadriceps peak torque at baseline reported values of 195 (±22) Nm and 141 (±21) Nm at 60°.s-1 and 180°.s-1. Values of 162 (±21) Nm were observed for peak torque of the eccentric hamstrings at 60°.s-1, while 157 (±18) Nm was indicated at 180°.s-1. Mean functional ratio responses were observed as 0.83 (±0.11) and 1.12 (±0.16) for 60°.s-1 and 180°.s-1 respectively. Additionally, the eccentric utilization ratio responses were recorded as 1.04 (±0.08). Regarding the intervention, concentric quadriceps total work of the dominant limb significantly improved over the time course of experimentation within the intervention group. Other quadriceps variables, concentric hamstrings, squat jump capability and performance measures all reported no significant changes (p>0.05) over the course of assessment when compared to the control. Eccentric hamstrings peak torque observed significant improvements (p<0.05) of between 5.72 and 12.82 % within the intervention group, while the countermovement jump indicated a significant 15.59 % increase (p<0.05). Additionally, the functional ratio and the eccentric utilization ratio both indicated no significant changes (p>0.05), with a 2.48-7.66 % and 5.33 % improvement noted following completion of assessment. Conclusion: Isokinetic responses at baseline observed decreased quadriceps strength, and increased hamstring strength when compared to both amateur and professional populations examined in previous studies, for both isokinetic testing speeds. Additionally, performance measures indicated similar responses to other amateur populations. Regarding the intervention, significant improvements in eccentric hamstring peak torque and countermovement jump indicate the partial success of the present intervention. Additionally, while the functional ratio and eccentric utilization ratio reported no significant changes, improvements were noted within the intervention group while the control noted no change. The Nordic hamstring lower therefore resulted in strength improvements within the eccentric hamstrings, reported as a significant factor for injury risk, however, such changes were not sufficient to significantly impact the functional ratio. It can be concluded that community based programs within South Africa have the potential to be effective; however, there are many barriers to implementation, including, language, ethnic and cultural differences, while a lack of resources and infrastructure play a significant role in a lack of development. More research of this nature is required to provide scientific support for structures and guidelines for the peri-urban community based South African player, to ensure the efficacy of internationally successful interventions such as the Nordic exercise.
- Full Text:
- Date Issued: 2016
- Authors: Ryan, Bennett
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3573 , vital:20526
- Description: Introduction: Hamstring injury prevalence in soccer remains a major concern. Research in this context has focused on Caucasian populations with little attention given to other ethnic groups. The compatibility and applicability of such research to the South African context, particularly at an amateur level, may be minimal due to fundamental differences in physical characteristics, as well as complexities with regards to implementation. The aim of this investigation was therefore twofold. 1) Identify the lower extremity strength and performance profile of Peri-urban Amateur South African Players, and 2) Assess the efficacy of a community based intervention through the use of the Nordic Hamstring Exercise. Methods: 19 Black male Eastern Cape amateur players participated in a 12 week randomly controlled trial (9 = Control, 10 = Intervention). All participants completed regular training, while the intervention group, in addition, performed the Nordic Hamstring exercise post warm up. The incremental program design was taken from Mjolsnes et al. (2004), with a progressive increase in both sets and repetitions. Compliance was defined as completion of the required exercises for that session. Isokinetic strength evaluations (at 60°.s-1 and 180°.s-1) including assessment of peak torque and total work, as well as performance measures of countermovement and squat jump, were completed pre and post intervention, with the profile of the Peri-urban player the combined responses of both groups at baseline. Additionally, both the functional ratio (Eccentric Hamstrings/Concentric Quadriceps) and eccentric utilization ratio (Countermovement Jump/Squat Jump) were calculated. Results: Concentric quadriceps peak torque at baseline reported values of 195 (±22) Nm and 141 (±21) Nm at 60°.s-1 and 180°.s-1. Values of 162 (±21) Nm were observed for peak torque of the eccentric hamstrings at 60°.s-1, while 157 (±18) Nm was indicated at 180°.s-1. Mean functional ratio responses were observed as 0.83 (±0.11) and 1.12 (±0.16) for 60°.s-1 and 180°.s-1 respectively. Additionally, the eccentric utilization ratio responses were recorded as 1.04 (±0.08). Regarding the intervention, concentric quadriceps total work of the dominant limb significantly improved over the time course of experimentation within the intervention group. Other quadriceps variables, concentric hamstrings, squat jump capability and performance measures all reported no significant changes (p>0.05) over the course of assessment when compared to the control. Eccentric hamstrings peak torque observed significant improvements (p<0.05) of between 5.72 and 12.82 % within the intervention group, while the countermovement jump indicated a significant 15.59 % increase (p<0.05). Additionally, the functional ratio and the eccentric utilization ratio both indicated no significant changes (p>0.05), with a 2.48-7.66 % and 5.33 % improvement noted following completion of assessment. Conclusion: Isokinetic responses at baseline observed decreased quadriceps strength, and increased hamstring strength when compared to both amateur and professional populations examined in previous studies, for both isokinetic testing speeds. Additionally, performance measures indicated similar responses to other amateur populations. Regarding the intervention, significant improvements in eccentric hamstring peak torque and countermovement jump indicate the partial success of the present intervention. Additionally, while the functional ratio and eccentric utilization ratio reported no significant changes, improvements were noted within the intervention group while the control noted no change. The Nordic hamstring lower therefore resulted in strength improvements within the eccentric hamstrings, reported as a significant factor for injury risk, however, such changes were not sufficient to significantly impact the functional ratio. It can be concluded that community based programs within South Africa have the potential to be effective; however, there are many barriers to implementation, including, language, ethnic and cultural differences, while a lack of resources and infrastructure play a significant role in a lack of development. More research of this nature is required to provide scientific support for structures and guidelines for the peri-urban community based South African player, to ensure the efficacy of internationally successful interventions such as the Nordic exercise.
- Full Text:
- Date Issued: 2016
Toward an automated botnet analysis framework: a darkcomet case-study
- Authors: du Bruyn, Jeremy Cecil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2937 , vital:20344
- Full Text:
- Date Issued: 2016
- Authors: du Bruyn, Jeremy Cecil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2937 , vital:20344
- Full Text:
- Date Issued: 2016