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A Systematic Visualisation Framework for Radio-Imaging Pipelines

- Andati, Lexy Acherwa Livoyi

Authors: Andati, Lexy Acherwa Livoyi
Date: 2021-04
Subjects: Radio interferometers , Radio astronomy -- Data processing , Radio astronomy -- Data processing -- Software , Jupyter
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/177338 , vital:42812
Description: Pipelines for calibration and imaging of radio interferometric data produce many intermediate images and other data products (gain tables, etc.) These often contain valuable information about the quality of the data and the calibration, and can provide the user with valuable insights, if only visualised in the right way. However, the deluge of data that we’re experiencing with modern instruments means that most of these products are never looked at, and only the final images and data products are examined. Furthermore, the variety of imaging algorithms currently available, and the range of their options, means that very different results can be produced from the same set of original data. Proper understanding of this requires a systematic comparison that can be carried out both by individual users locally, and by the community globally. We address both problems by developing a systematic visualisation framework based around Jupyter notebooks, enriched with interactive plots based on the Bokeh and Datashader visualisation libraries. , Thesis (MSc) -- Faculty of Science, Department of Physics and Electronics, 2021
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An assessment of the wild cyclopia subternata (vleitee) resource

- Van der Walt, Wouter

Authors: Van der Walt, Wouter
Date: 2021-04
Subjects: Legumes -- South Africa , Fynbos -- South Africa , Fynbos ecology -- South Africa , Fynbos -- Harvesting -- South Africa , Biodiversity conservation -- South Africa , Traditional ecological knowledge -- South Africa , Wild Cyclopia Subternata (Vleitee) , Honeybush tea industry
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/176874 , vital:42767
Description: Cyclopia spp. is used for the production of Honeybush tea, an herbal tea which is used in many cases as a substitute for rooibos tea. The wild harvesting of this fynbos plant still brings in up to 85% of the annual crop and as such needs to be carefully monitored in order to avoid over harvesting and the destruction of biodiversity within the Eastern and Western Cape mountain regions of Southern Africa. Due to the concerns of overharvesting and unsuitable use of the wild resource issues of supply security have been raised. There is a lack of formal knowledge relating to the plant, its harvesting, the industry and its economic potential. This study aimed to amend this scarcity by contributing to the knowledge of C. subternata as a wild harvested plant, the physical environment favoured by C. subternata, sustainable use through harvesting of the wild plant and harvesting methods specific to this honeybush species. The research concludes by presenting a guideline for best harvest practices of the wild C. subternata plant. , Thesis (MSc) -- Faculty of Science, Department of Geography, 2021
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An exploratory investigation into an Integrated Vulnerability and Patch Management Framework

- Carstens, Duane

Authors: Carstens, Duane
Date: 2021-04
Subjects: Computer security , Computer security -- Management , Computer networks -- Security measures , Patch Management , Integrated Vulnerability
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/177940 , vital:42892
Description: In the rapidly changing world of cybersecurity, the constant increase of vulnerabilities continues to be a prevalent issue for many organisations. Malicious actors are aware that most organisations cannot timeously patch known vulnerabilities and are ill-prepared to protect against newly created vulnerabilities where a signature or an available patch has not yet been created. Consequently, information security personnel face ongoing challenges to mitigate these risks. In this research, the problem of remediation in a world of increasing vulnerabilities is considered. The current paradigm of vulnerability and patch management is reviewed using a pragmatic approach to all associated variables of these services / practices and, as a result, what is working and what is not working in terms of remediation is understood. In addition to the analysis, a taxonomy is created to provide a graphical representation of all associated variables to vulnerability and patch management based on existing literature. Frameworks currently being utilised in the industry to create an effective engagement model between vulnerability and patch management services are considered. The link between quantifying a threat, vulnerability and consequence; what Microsoft has available for patching; and the action plan for resulting vulnerabilities is explored. Furthermore, the processes and means of communication between each of these services are investigated to ensure there is effective remediation of vulnerabilities, ultimately improving the security risk posture of an organisation. In order to effectively measure the security risk posture, progress is measured between each of these services through a single averaged measurement metric. The outcome of the research highlights influencing factors that impact successful vulnerability management, in line with identified themes from the research taxonomy. These influencing factors are however significantly undermined due to resources within the same organisations not having a clear and consistent understanding of their role, organisational capabilities and objectives for effective vulnerability and patch management within their organisations. , Thesis (MSc) -- Faculty of Science, Computer Science, 2021
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An investigation into the current state of web based cryptominers and cryptojacking

- Len, Robert

Authors: Len, Robert
Date: 2021-04
Subjects: Cryptocurrencies , Malware (Computer software) , Computer networks -- Security measures , Computer networks -- Monitoring , Cryptomining , Coinhive , Cryptojacking
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/178248 , vital:42924
Description: The aim of this research was to conduct a review of the current state and extent of surreptitious crypto mining software and its prevalence as a means for income generation. Income is generated through the use of a viewer's browser to execute custom JavaScript code to mine cryptocurrencies such as Monero and Bitcoin. The research aimed to measure the prevalence of illicit mining scripts being utilised for “in-browser" cryptojacking while further analysing the ecosystems that support the cryptomining environment. The extent of the research covers aspects such as the content (or type) of the sites hosting malicious “in-browser" cryptomining software as well as the occurrences of currencies utilised in the cryptographic mining and the analysis of cryptographic mining code samples. This research aims to compare the results of previous work with the current state of affairs since the closure of Coinhive in March 2018. Coinhive were at the time the market leader in such web based mining services. Beyond the analysis of the prevalence of cryptomining on the web today, research into the methodologies and techniques used to detect and counteract cryptomining are also conducted. This includes the most recent developments in malicious JavaScript de-obfuscation as well as cryptomining signature creation and detection. Methodologies for heuristic JavaScript behaviour identification and subsequent identification of potential malicious out-liars are also included within the research of the countermeasure analysis. The research revealed that although no longer functional, Coinhive remained as the most prevalent script being used for “in-browser" cryptomining services. While remaining the most prevalent, there was however a significant decline in overall occurrences compared to when coinhive.com was operational. Analysis of the ecosystem hosting \in-browser" mining websites was found to be distributed both geographically as well as in terms of domain categorisations. , Thesis (MSc) -- Faculty of Science, Computer Science, 2021
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Baculovirus synergism for improved management of false codling moth Thaumatotibia leucotreta Meyr. (Lepidoptera: Tortricidae)

- Taylor, David Graham

Authors: Taylor, David Graham
Date: 2021-04
Subjects: Baculoviruses , Cryptophlebia leucotreta , Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Codling moth , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/176942 , vital:42774
Description: Baculoviruses are an environmentally friendly and effective agent for managing lepidopteran pests. This includes the management of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a serious pest of citrus in Southern Africa and a major threat to the South African citrus export industry. For more than 15 years, CrleGV-SA- based biopesticides have been used as part of an integrated pest management strategy for the control of T. leucotreta in citrus orchards in South Africa, under the names Cryptogran™ and Cryptex®. While these biopesticides have been effective during this period, there are some areas in which baculovirus use could potentially be improved. Baculoviruses are notoriously slow to kill in comparison to chemical-based pesticides, and lately, pest resistance to baculoviruses has become a major concern with the development of resistance by Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) to its granulovirus occurring in the field in Europe. The consistent use of CrleGV-SA for more than 15 years in the field has raised concern that T. leucotreta could develop resistance to this virus, and has made it necessary to alter baculovirus-based management strategies to prevent this from occurring. A second baculovirus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV), has recently been isolated and was shown to be effective against T. leucotreta. However, the interactions between CrleGV-SA and CrpeNPV are not yet understood and so it is important to test these interactions before both viruses are applied on the same orchards. Not only is it important to know whether these viruses could negatively impact each other, but it is also important to test whether they could interact synergistically. A synergistic interaction could not only provide a potential tool for the management of resistance, but it could also be exploited to improve baculovirus-based management of T. leucotreta. In this study, a stock of CrleGV-SA was purified by glycerol gradient centrifugation from T. leucotreta cadavers, while a stock of CrpeNPV purified from Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae) cadavers was provided by River Bioscience (Pty) Ltd. These stocks were screened for purity by a multiplex polymerase chain reaction (mPCR) protocol designed to detect CrleGV-SA and CrpeNPV. The occlusion body (OB) density was then calculated using darkfield microscopy and a counting chamber. Both stocks were shown to be pure within the limits of the mPCR protocol, and the CrleGV-SA and CrpeNPV stocks were calculated to contain 3.08 × 1011 OBs/mL and 1.92 × 1011 OBs/mL respectively The first aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the dose mortality, in terms of lethal concentration. This was calculated using 7-day surface-dose biological assays for each virus and a 1:1 mixture of OBs of the two against T. leucotreta neonates. The lethal concentrations of each treatment required to kill 50 % of larvae (LC50) and 90 % of larvae (LC90) for each treatment were then calculated and compared using a probit regression. The mixed infection performed significantly better than either virus by itself, while each virus by itself did not differ significantly from the other. The LC50 for CrleGV-SA, CrpeNPV and the mixed infection were 1.53 × 104 OBs/mL, 1.15 × 104 OBs/mL and 4.38 × 103 OBs/mL respectively. The LC90 of CrleGV-SA, CrpeNPV and the mixed infection were calculated to be 4.10 × 105 OBs/mL, 1.05 × 105 OBs/mL, and 4.09 × 104 OBs/mL respectively. The second aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the speed of kill. A time-response biological assay protocol was created that allowed for effective observation of the larvae. This was then used to generate time-mortality data that were analysed by a logit regression function to calculate and compare the treatments at the time of 50 % larval mortality (LT50) and the time of 90 % mortality (LT90). Each virus by itself did not differ significantly from the other, while the mixed infection took significantly longer to kill 50 % and 90 % of the larvae, suggesting that there is competition for resources between viruses during the secondary, systemic phase of infection. The LT50 for CrleGV-SA, CrpeNPV and the mixed infection were 117.5 hours, 113.5 hours and 139.0 hours respectively. The LT90 for CrleGV-SA, CrpeNPV and the mixed infection were 153.2 hours, 159.3, and 193.4 hours respectively. Finally, the composition of OBs recovered from the cadavers produced by the time-response biological assays were investigated by mPCR. A method for extracting gDNA from OBs in neonate-sized T. leucotreta larvae is described. The presence of CrpeNPV along with CrleGV-SA was noted in 4 out of 9 larvae inoculated with only CrleGV-SA. The presence of CrleGV-SA as well as CrpeNPV was noted in all but one larva inoculated with only CrpeNPV, and both CrleGV-SA and CrpeNPV were noted in all but one larva inoculated with a 1:1 mixture of the two, with one larva only being positive for CrleGV-SA. This suggests either stock contamination or the presence of covert infections of CrleGV-SA and CrpeNPV in the T. leucotreta population used in this study. This is the second study to report an improved lethal concentration of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates, and the first study to report the slower speed of kill of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates. While the improved lethal concentration of the mixed infection is a promising step in the future improvement of baculovirus-based biopesticides, it is at the cost of a slower speed of kill. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
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Biology, ecology and management of the Keurboom moth, Leto venus Cramer and the leafhopper Molopopterus sp. Jacobi in cultivated Honeybush (Cyclopia spp.)

- Mushore, Tapiwa Gift

Authors: Mushore, Tapiwa Gift
Date: 2021-04
Subjects: Legumes , Legumes -- Diseases and pests , Hepialidae , Leafhoppers , Pests -- Biological control , Entomopathogenic fungi , Leafhoppers -- Biological control , Hepialidae -- Biological control , Keurboom moth (Leto venus Cramer) , Molopopterus sp. Jacobi , Honeybush (Cyclopia spp.)
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/177125 , vital:42792
Description: Honeybush, Cyclopia spp. Vent (Fabaceae), farmers have raised pest concerns following commercial cultivation. The Keurboom moth Leto venus Cramer (Lepidoptera: Hepialidae) and the leafhopper Molopopterus sp. Jacobi (Hemiptera: Cicadellidae), are two of the major pests identified in cultivated Honeybush. Laboratory and field studies were conducted to gain an understanding of the biology of these two pests to inform future pest management solutions. Additionally, entomopathogenic fungi were isolated from Honeybush farms and screened for virulence against Molopopterus sp. as a possible management strategy. This study showed that the L. venus infestation on Honeybush was a product of four fixed effects; stem diameter, species of Cyclopia, Farm location and age of the plants. Cyclopia subternata, had the highest likelihood of infestation. Increase in age of the plants resulted in an increase in the stem diameter and therefore a higher probability of infestation. Stem diameter was also shown to be a significant predictor of infestation likelihood. Infestation severity, determined by the number of larvae per plant, was shown to be influenced by three fixed effects; stem diameter, plant species and Farm location. The results also showed that L. venus prefers to initiate penetration at, or just aboveground level. Laboratory studies showed that the leafhopper Molopopterus sp. undergoes five nymphal instars with an average egg incubation time of 20 days, development time from 1st instar to adult of 26 days and average generation time of 47 days. Laboratory experiments revealed variations in host preference by the leafhopper over a period of 15 days. Cyclopia longifolia was identified to be the most preferred species for feeding compared to the two other commonly cultivated species, C. subternata and C. maculata. The results were consistent with those obtained from the field survey which showed that leafhopper density was influenced by four fixed effects; plant species, age of the plant, Farm location and harvesting practices. There were significant differences in leafhopper density in different species with C. longifolia having the highest number of leafhoppers per plant. There were differences in leafhopper density in different farms as 57% of the sampled farms had leafhopper infestations, of these farms, Lodestone and Kurland had the highest leafhopper densities. Harvested plants were shown to have significantly higher leafhopper density than non-harvested plants. Age was also shown to influence leafhopper density, which reduced with an increase in the age of the plants. A total of 20 fungal isolates were recovered from 98 soil samples of which 70% were from Honeybush fields and 30% were from surrounding refugia. Fusarium oxysporum isolates comprised 20% of the recovered isolates, with Metarhizium anisopliae isolates making up the remainder. Laboratory bioassays against adults and nymphs of the leafhopper, Molopopterus sp., showed that F. oxysporum isolates induced 10 – 45% mortality and M. anisopliae isolates induce 30 – 80% mortality. Metarhizium anisopliae isolates J S1, KF S3, KF S11, KF S13, LS1 and LS2 were the most virulent and induced over 60% mortality in both Molopopterus sp. nymphs and adults. The results of this study showed pest preference towards different Cyclopia species. As such, they should be managed differently. Furthermore, L. venus was observed to occur in low densities, hence, it cannot be considered a major pest. However, Molopopterus sp. recorded high population densities making it a major pest in Honeybush production. Positive results indicated that some of the isolated fungal isolates have potential for control, an avenue worth investigating further. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
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Constraining the role of carbonate assimilation on spinel stability in oxide ores of the Flatreef, Bushveld Complex, South Africa

- Dyan, Siyasanga

Authors: Dyan, Siyasanga
Date: 2021-04
Subjects: Oxide minerals -- South Africa -- Bushveld Complex , Transvaal Supergroup (South Africa) , Magmas -- South Africa -- Bushveld Complex , Petrogenesis -- South Africa -- Bushveld Complex , Spinel group – South Africa -- South Africa -- Bushveld Complex , Dolomite -- South Africa -- Bushveld Complex
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/174578 , vital:42490
Description: The northern limb of the Bushveld Complex shows significant evidence for footwall rock- magma interaction, as a result of the emplacement of magmas onto the Transvaal Supergroup sediments. The Platreef of the northern limb is known to have involved extensive contamination of the magma. The lateral extension of the Platreef, the Flatreef, is less contaminated and comprises PGE-mineralization and thick chromitite layers. This enables successful stratigraphic correlation to the Upper Critical Zone of the eastern and western limbs of the Bushveld Complex. This study aims at addressing the influence of dolomitic floor rock contamination on the formation of spinels of the Flatreef and how they may differ to their occurrences in the Bushveld Complex elsewhere. Three main drill cores (UMT-345, UMT-335, and UMT-094) from the deep drilling program by Ivanhoe Mine, north of Turfspruit, were logged and sampled. The drill cores contained rocks contaminated by dolomite in varying degrees, depending on the proportion of carbonate xenoliths present. A total of sixty-two samples were obtained from the UG-2- equivalent chromitite seam, down into the hybrid contaminated units (Footwall Assimilation Zone; FAZ). Petrographic examination of the drill cores revealed that the feldspathic pyroxenite and chromitite layers are the most pristine lithologies in the Flatreef. The chromitite layers occur as a semi-massive to massive ores. The FAZ rocks are mainly dominated by the abundance of Al-rich Cr-spinels (Mg#30-80), clinopyroxenes with a high Ca-Tschermak component (up to 35 mol.%), olivines (Fo72-84), and plagioclase (An31-78). Geochemical characteristics of the feldspathic pyroxenite and chromitite seams include low CaO/Al2O3 and Ca/SiO2 ratios, the low abundance of REE and HFSE. In contrast, the FAZ samples display high CaO/Al2O3 and CaO/SiO2 ratios, suggesting mobilization of CaO-rich fluids derived from the associated dolomite xenoliths. Observations from lithostratigraphic element profiles indicate spikes in CaO within FAZ units relative to the feldspathic pyroxene, indicating a secondary source of CaO linked to proximity to carbonate xenoliths intersected in the core. The assimilation-fractional crystallization model performed with the Upper Critical Zone parental melt and dolomite produced assemblages dominated by spinel, olivine, clinopyroxene, and plagioclase, relating to those of the most contaminated rocks of footwall assimilation zones. The model also showed that large quantities of CO2 were produced during assimilation. High amounts of CO2-fluids mobilized in the melt would have interacted with the melt and increased the overall oxidation conditions. Oxygen fugacity (ƒO2) values were constrained from the spinels in the FAZ and chromites in chromitite seams. Spinels within the most contaminated rocks of the FAZ recorded relatively high ƒO2 values ranging between NNO-0.2 and NNO+1.8 (relative to the Nickel-Nickel-Oxide buffer. High ƒO2 values in spinels from the FAZ suggest that the melt interacted with greater amounts of oxidative CO2-fluids during decarbonation reactions. Such high redox conditions could have triggered the saturation and crystallization of spinels. Comparison of mineral compositions and ƒO2 of UG-2 chromites from the Flatreef with UG-2 from the eastern limb, western limb, chromitites from the Platreef and Uitkomst Complex reveal that Flatreef chromites are of most similar to those of the Platreef Uitkosmt Complex. The northern limb and Uitkomst Complex chromites have high ƒO2 values (NNO+0.3 to NNO+1.2), indicating their apparent link to the Malmani dolomite. Interaction of magma with the Malmani dolomite would have produced high quantities of CO2, triggering an increase in oxidizing conditions. Such an effect is most prominent in the Flatreef chromitites that are in contact with the FAZ. The chromites are characterised by high ƒO2 (NNO+1.2) and distinct compositions (low Cr2O3, high Fe3+/Fetotal, and TiO2). Thus, it is proposed that carbonate assimilation in the Flatreef triggered the precipitation of these distinctive chromites proximal to FAZ, due to liberation of substantial amounts of CO2-rich fluids with a highly oxidative capacity. Carbonate assimilation in layered intrusions can be used as a monitor potential precipitation of chromites. , Thesis (MSc)--Rhodes University, Faculty of Science, Department of Geology, 2021
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Does the Transkei population of Haliotis Midae at the eastern edge of its distributional range have a higher thermal tolerance than those in more temperate waters?

- Mathebula, Surprise

Authors: Mathebula, Surprise
Date: 2021-04
Subjects: Haliotis midae -- South Africa -- Indian Coast , Abalones -- South Africa -- Indian Coast , Haliotis midae -- Effect of temperature on -- South Africa -- Indian Coast , Haliotis midae -- Physiology -- South Africa -- Indian Coast , Haliotis midae -- Adaptation -- South Africa -- Indian Coast , Haliotis midae -- Growth -- South Africa -- Indian Coast
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/177360 , vital:42814
Description: The South African perlemoen abalone (Haliotis midae) may be vulnerable to rising temperatures on the East coast of South Africa due to climate change. H. midae is South Africa’s most valuable aquaculture species, and it is thus important to understand its physiological ability to adapt to the expected changes and to identify possible management measures to mitigate the impacts of rising temperatures. This project aimed to understand thermal tolerance and growth rates of offspring from two H. midae populations originating from the warm-temperate Central region (Port Elizabeth) and warmer Eastern edge of the species’ distribution in the Transkei region. To determine the effects of temperature on the physiological performance of the two abalone populations, growth rates, oxygen consumption rates and critical thermal maxima (CTM) were compared. A laboratory growth trial was conducted at three controlled temperatures, visibly, the ‘optimal’ temperature for H. midae growth (18 - 20℃), ‘pejus’ (stressful) temperature (21 - 22℃) and ‘critical’ temperature (23 - 24℃). Oxygen consumption rates were recorded at optimum (20℃), pejus (22℃) and critical (24℃) temperature using a respirometer. In addition, a farm growth trial with simultaneously spawned cohorts of abalone from the two populations was conducted at ambient temperature (19.5 and 20.0℃). The laboratory growth trial revealed no significant differences in growth rate between the two populations at the three temperature treatments (ANOVA, P > 0.05; df = 2). However, mortalities were high and growth rates low, indicating that the rearing conditions were sub-optimal, possibly masking genetic differences. No significant differences were observed in oxygen consumption rates (ANOVA, P = 0.18; df = 2), and CTM (t-Test, P = 0.31; df = 3) between the two populations. The CTM for both populations was between 29 - 30℃. The farm trial yielded no significant differences in growth rate during the Nursery phase (t-Test, P = 0.25; df = 2), however significant differences in growth rate were observed during the grow out phase with the Central region abalone offspring growing faster than the Eastern edge population (t-Test, P = 0.04; df = 4) indicating the possibility of a genetic difference between the two populations. Further experiments will be required to determine whether the differences observed in the growth trial were genetically or environmentally induced. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2021
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In silico identification of selective novel hits against the active site of wild type mycobacterium tuberculosis pyrazinamidase and its mutants

- Gowo, Prudence

Authors: Gowo, Prudence
Date: 2021-04
Subjects: Mycobacterium tuberculosis , Pyrazinamide , Multidrug resistance , Antitubercular agents , Molecular dynamics , Hydrogen bonding , Ligand binding (Biochemistry) , Dynamic Residue Network
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/178007 , vital:42898
Description: The World Health Organization declared Tuberculosis a global health emergency and has set a goal to eradicate it by 2035. However, effective treatment and control of the disease is being hindered by the emerging Multi-Drug Resistant and Extensively Drug Resistant strains on the most effective first line prodrug, Pyrazinamide (PZA). Studies have shown that the main cause of PZA resistance is due to mutations in the pncA gene that codes for the target protein Pyrazinamidase (PZase). Therefore, this study aimed to identify novel drug compounds that bind to the active site of wild type PZase and study the dynamics of these potential anti-TB drugs in the mutant systems of PZase. This approach will aid in identifying drugs that may be repurposed for TB therapy and/or designed to counteract PZA resistance. This was achieved by screening 2089 DrugBank compounds against the whole wild type (WT) PZase protein in molecular docking using AutoDOCK4.2. Compound screening based on docking binding energy, hydrogen bonds, molecular weight and active site proximity identified 47 compounds meeting all the set selection criteria. The stability of these compounds were analysed in Molecular Dynamic (MD) simulations and were further studied in PZase mutant systems of A3P, A134V, A146V, D8G, D49A, D49G, D63G, H51P, H137R, L85R, L116R, Q10P, R140S, T61P, V139M and Y103S. Generally, mutant-ligand systems displayed little deviation from the WT systems. The compound systems remained compact, with less fluctuations and more hydrogen bond interactions throughout the simulation (DB00255, DB00655, DB00672, DB00782, DB00977, DB01196, DB04573, DB06414, DB08981, DB11181, DB11760, DB13867, DB13952). From this research study, potential drugs that may be repurposed for TB therapy were identified. Majority of these drugs are currently used in the treatment of hypertension, menopause disorders and inflammation. To further understand the mutant-ligand dynamic systems, calculations such as Dynamic Residue Network (DRN) may be done. Also, the bioactivity of these drugs on Mycobacterium tuberculosis may be studied in wet laboratory, to understand their clinical impart in vivo experiments. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
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Inhibitor search and variant analysis of Acetylcholinesterase

- Ras, Harnaud

Authors: Ras, Harnaud
Date: 2021-04
Subjects: Acetylcholinesterase , Alzheimer's disease , Acetylcholinesterase -- Inhibitors , Alzheimer's disease -- Chemotherapy , Cerebrovascular disease -- Treatment , Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA)
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/178191 , vital:42919
Description: Acetylcholinesterase (AChE) inhibition is used to treat Alzheimer's disease by increasing the availability of acetylcholine to carry nerve signals in the brain. The response to this treatment varies widely, which may be due to altered affnity to the current drugs caused by genetic variation. Various negative side-effects limit their use. As this is one of the only available therapeutic drug targets to treat Alzheimer's disease, decreasing the negative effects is of great importance. AChE is involved in biological processes that occur after acute ischemic stroke. Stroke is the third leading cause of death worldwide, and 87% of all stroke cases belong to ischemic stroke. AchEI (cholinesterase inhibitors) have been suggested to have properties that lower the risk of stroke. AChE is one of 15 verified drug targets under study for treatment of stroke. In addition to Alzheimer's disease and stroke, Lewy body disease (LBD) may be treated using cholinesterase inhibitors. The goals of this study are to find inhibitors that can potentially be used to treat Alzheimer's disease and/or stroke and to investigate variants which may affect protein dynamics and function. Two variants were analyzed, P247L and T229S. Molecular simulation of the P247L variant resulted in a disruption in protein dynamics in comparison to the wildtype. A total of 5728 molecules were screened and 10 nanosecond simulations were used to narrow down the set of compounds. The four best performing molecules were simulated for 10 nanoseconds. MM-PBSA was performed to identify molecules with high binding free energies. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
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Larval fish dynamics within the coastal nearshore of the Eastern Cape, South Africa

- Sotshongaye, Oko

Authors: Sotshongaye, Oko
Date: 2021-04
Subjects: Fishes -- Larvae -- South Africa -- Eastern Cape , Fishes -- Larvae -- Development -- South Africa -- Eastern Cape , Fishes -- Larvae -- Ecology -- South Africa -- Eastern Cape , Coastal ecology -- South Africa -- Eastern Cape , Fishes -- Larvae -- Dispersal -- South Africa -- Eastern Cape
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/176977 , vital:42776
Description: The coastal nearshore is important for the early development of fishes as it is used for spawning and/or as a nursery. One of the central concerns in coastal ecology is understanding the role of the nearshore for larvae, ultimately providing key knowledge on population dynamics and hence helping in making decisions pertaining to conservation and resource management. The aim of this study was to investigate the alongshore and cross-shore distribution of larval fishes and the links to the physio-chemical conditions (including prevailing winds) and hydrodynamics in the region of Algoa Bay, situated on the south east coast in the warm temperate region of South Africa. Fish larvae were sampled at nine sites for the first component of the study (January 2016 –March 2017) and at four sites for the second component (November 2019), near the surface and bottom (15-50 m) of the water column as well as at two different distances from shore (~400 m/~3 km) using a set of bongo plankton nets towed behind a boat. Environmental data were simultaneously collected using and acoustic Doppler current profiler (ADCP) and conductivity, temperature, depth (CTD) profiler. Larval fish abundance generally decreased with increasing distance from the shore, however, this varied in space and time, with some larval species recorded in high abundances offshore. Close inshore the larvae of coastal fish species producing benthic eggs (CBE) including the Blenniidae and Gobiesocidae mostly dominated, while offshore the larvae of coastal fish species producing pelagic eggs (CPE) i.e. Sparidae and Cynoglossidae, as well as pelagic fish species producing pelagic eggs (PPE) i.e. Clupeidae and Engraulidae mostly dominated. Vertical distribution of larvae differed according to taxon, with the Callionymidae (CPE), Cynoglossidae and Gobiesocidae occurring at high densities at the bottom of the water column, while the Blenniidae dominated near the surface. Fluorescence, temperature and salinity varied with depth (surface/bottom), being particularly high at the surface; currents moved faster at the surface than the bottom of the water column. Increased abundances of larval fishes were evident after upwelling events (associated with easterly winds) in the Bay, while during downwelling (associated with westerly winds), low densities were generally recorded, except for the sites situated near headlands/capes where there were higher densities of fish larvae during downwelling events. Overall, the results of this study suggest that spawning mode of the adults, oceanography and environmental conditions coupled with what is known of the behaviour of fish larvae, were important in shaping the larval fish community of the Algoa Bay region. These results highlight the importance of incorporating multiple biological (developmental stage, reproductive mode, species) and physical (currents, fluorescence, wind-driven up/down-welling) factors when addressing the mechanims of transport of larval fish in the coastal nearshore. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
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Night-time gravity waves detected with multi-frequency airglow imager

- Machubeng, Karabo Pebane

Authors: Machubeng, Karabo Pebane
Date: 2021-04
Subjects: Gravity waves , Airglow , Gravity waves -- Seasonal variations , All Sky Imager
Language: English
Type: thesis , text , Masters , MSc
Identifier: http://hdl.handle.net/10962/178341 , vital:42931
Description: This thesis shows the statistics of atmospheric gravity waves (AGWs) observed in the OI emission 557.7 nm at _97 km altitude using an all-sky imager based in Sutherland, South Africa (32.37_ S, 20.81_ E) in the year 2017. The wavelengths were determined using the propagation vector method, velocity was determined using the cross correlation of 1D FFT and the period was determined using the equation that relates wavelength and velocity. It was found that the horizontal wavelength in summer was almost evenly distributed between 10 and 40 km and for autumn, winter and spring were mostly between 10 and 30 km. The favoured speeds were between 40 and 50 m/s in autumn, as well as 30 and 50 m/s in summer, but the AGWs in winter had a bimodal speed distribution of 20 - 40 and 50 - 70 m/s. The majority of periods observed in all seasons were less than 20 minutes with a dominant peak of 5 - 10 minutes in autumn and spring. There was no favoured propagation direction for spring, but AGWs favoured a southeastward propagation in summer, and a southward propagation in autumn and winter. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2021
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