Identification of differentially expressed proteins involved in wheat (Triticum aestivum) resistance against Russian Wheat Aphid (Diuraphis noxia) SA2 using SWATH-MS analysis
- Authors: Ntlokwana, Sitha Emmanuel
- Date: 2020
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/18872 , vital:42888
- Description: Wheat (Triticum aestivum) is the second most-consumed cereal crop in the world, second only to maize. In South Africa it is mainly produced in three provinces; the Free State, Western Cape, and the Northen Cape. The average total land area used for wheat cultivation in these three Provinces, is 533 000 hectares, with a resultant annual production of between 1.3 to 2 million tons. The total wheat requirement in South Africa is currently 2.7 million tons according to the production of wheat guidelines published by the Department of Agriculture, Forestry and Fisheries, which is higher than the total annual production. One of the primary reasons that contribute to the lower production levels is insect and pest infestation, in particular, the Russian wheat aphid (Diurophis noxis), which can result in crop loss of up to sixty percent. Russian wheat aphids (RWA) are invasive insects that feed on the phloem of the plant through their specialised thin stylet-like mouthparts and release toxic agents contained in their saliva during feeding, which disrupt cellular functions inside the host plant. This damage leads to symptoms like; chlorosis, necrosis, wilting, stunting and curling of leaves, also known as leaf rolling. This study aimed to identify differentially expressed proteins in resistant and susceptible wheat (Triticum aestivum) cultivars during Russian wheat aphid Biotype South African 2 (RWA-SA2) infestation, in order to identify proteins involved in the wheat resistant mechanism against RWA-SA2. Two wheat cultivars SST398 (resistant to RWA-SA2) and SST356 (susceptible to RWA-SA2) were used, and a total number of 126 plants were planted and divided according to four different harvest times (Control day 0; day 5; day 7 and day 12). The wheat plants were infested with approximately 10 aphids per plant at the three-leaf stage, and placed within an insect cage inside a growth chamber (Conviron, Winnipeg, Canada) set at 24ºC, light intensity of 352 µmol.m-2.sec-1, ambient CO2 levels (410 ppm) and humidity of 60% with a 16h/8h day/night cycle. Wheat leaves were harvested at various time frames, and total protein extraction was performed. The protein samples were reduced with 10 mM dithiothreitol (DTT) and alkylated with 30 mM iodoacetamide (IAA). Sample clean-up and on-bead trypsin digest were performed on megReSyn Hilic columns, over four hours. The resultant peptides were vacuum dried and resuspended in 2% acetonitrile (ACN) before submitting them to LC-MS/MS (SWATH) for analysis. A total number of 611 proteins were differentially expressed, of which 19 were identified to be involved in the resistance response of wheat, and an additional 20 involved in biotic stress responses. This study showed that reactive oxidative species (ROS) such as hydrogen peroxide and hydroxyl radicals (OH-) play a significant role in the early stages of wheat resistance against RWA-SA2 infestation. They are involved in cell wall strengthening, activation of defence genes, involvement of phytohormone signals such as salicylic and jasmonic acid, which also mediates the systemic defences such as, systemic acquired resistance (SAR), leading to the expression of pathogen-related proteins such as (thaumatin-like proteins, oxalate oxidase, defensin, chitinase, and thionins). Although up-regulation of photosynthesis proteins such as (chlorophyll a/b binding protein, photosystem I and II, rubisco and divinyl chlorophyllide a, and 8 vinyl-reductase) were seen on both infested cultivars (susceptible and resistance), higher numbers of these classes of proteins were identified in the resistance cultivar, suggesting that they also play a critical role in resistance. In conclusion, the SWATH analysis used in this study was able to identify numerous proteins involved in the wheat resistance mechanism against RWA-SA2, most of which have not yet been reported to be involved in either biotic stress or RWA-SA2 resistance responses. Future studies are required to biochemically confirm the involvement of these enzymes and proteins the specific metabolic pathways where they are found, in the wheat resistance mechanism against Russian wheat aphid Biotype 2
- Full Text:
- Date Issued: 2020
- Authors: Ntlokwana, Sitha Emmanuel
- Date: 2020
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/18872 , vital:42888
- Description: Wheat (Triticum aestivum) is the second most-consumed cereal crop in the world, second only to maize. In South Africa it is mainly produced in three provinces; the Free State, Western Cape, and the Northen Cape. The average total land area used for wheat cultivation in these three Provinces, is 533 000 hectares, with a resultant annual production of between 1.3 to 2 million tons. The total wheat requirement in South Africa is currently 2.7 million tons according to the production of wheat guidelines published by the Department of Agriculture, Forestry and Fisheries, which is higher than the total annual production. One of the primary reasons that contribute to the lower production levels is insect and pest infestation, in particular, the Russian wheat aphid (Diurophis noxis), which can result in crop loss of up to sixty percent. Russian wheat aphids (RWA) are invasive insects that feed on the phloem of the plant through their specialised thin stylet-like mouthparts and release toxic agents contained in their saliva during feeding, which disrupt cellular functions inside the host plant. This damage leads to symptoms like; chlorosis, necrosis, wilting, stunting and curling of leaves, also known as leaf rolling. This study aimed to identify differentially expressed proteins in resistant and susceptible wheat (Triticum aestivum) cultivars during Russian wheat aphid Biotype South African 2 (RWA-SA2) infestation, in order to identify proteins involved in the wheat resistant mechanism against RWA-SA2. Two wheat cultivars SST398 (resistant to RWA-SA2) and SST356 (susceptible to RWA-SA2) were used, and a total number of 126 plants were planted and divided according to four different harvest times (Control day 0; day 5; day 7 and day 12). The wheat plants were infested with approximately 10 aphids per plant at the three-leaf stage, and placed within an insect cage inside a growth chamber (Conviron, Winnipeg, Canada) set at 24ºC, light intensity of 352 µmol.m-2.sec-1, ambient CO2 levels (410 ppm) and humidity of 60% with a 16h/8h day/night cycle. Wheat leaves were harvested at various time frames, and total protein extraction was performed. The protein samples were reduced with 10 mM dithiothreitol (DTT) and alkylated with 30 mM iodoacetamide (IAA). Sample clean-up and on-bead trypsin digest were performed on megReSyn Hilic columns, over four hours. The resultant peptides were vacuum dried and resuspended in 2% acetonitrile (ACN) before submitting them to LC-MS/MS (SWATH) for analysis. A total number of 611 proteins were differentially expressed, of which 19 were identified to be involved in the resistance response of wheat, and an additional 20 involved in biotic stress responses. This study showed that reactive oxidative species (ROS) such as hydrogen peroxide and hydroxyl radicals (OH-) play a significant role in the early stages of wheat resistance against RWA-SA2 infestation. They are involved in cell wall strengthening, activation of defence genes, involvement of phytohormone signals such as salicylic and jasmonic acid, which also mediates the systemic defences such as, systemic acquired resistance (SAR), leading to the expression of pathogen-related proteins such as (thaumatin-like proteins, oxalate oxidase, defensin, chitinase, and thionins). Although up-regulation of photosynthesis proteins such as (chlorophyll a/b binding protein, photosystem I and II, rubisco and divinyl chlorophyllide a, and 8 vinyl-reductase) were seen on both infested cultivars (susceptible and resistance), higher numbers of these classes of proteins were identified in the resistance cultivar, suggesting that they also play a critical role in resistance. In conclusion, the SWATH analysis used in this study was able to identify numerous proteins involved in the wheat resistance mechanism against RWA-SA2, most of which have not yet been reported to be involved in either biotic stress or RWA-SA2 resistance responses. Future studies are required to biochemically confirm the involvement of these enzymes and proteins the specific metabolic pathways where they are found, in the wheat resistance mechanism against Russian wheat aphid Biotype 2
- Full Text:
- Date Issued: 2020
Identification of SANCDB compounds against G2019S and I2020T variants of leucine-rich repeat Kinase 2 (LRRK2) for the development of drugs against Parkinson’s Disease
- Authors: Baye, Bertha Cinthia
- Date: 2020
- Subjects: Antiparkinsonian agents , Parkinson's disease -- Treatment , Protein kinases , Parkinson's disease -- Chemotherapy , Molecules -- Models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138764 , vital:37671
- Description: Parkinson’s disease is a type of movement disorder that occurs when nerve cells in the brain stop producing dopamine. It is the second neurodegenerative disease affecting 1-2% of people above the ages of 65 years old. There is a worldwide prevalence of 7 to 10 million affected people of all cultures and race. Studies have shown that mutation that causes Parkinson’s disease result in increased kinase activity. The c.6055 G > A in exon 41 is the most prevalent LRRK2 variation which causes a substitution of glycine to serine in G2019S in the highly activated loop of its MAP kinase domain. The LRRK2 G2019S variant is the most common genetic determinant of Parkinson’s disease identified to date. This work focused on building accurate 3D models of the LRRK2 kinase domain, that were used for large-scale in silico docking against South African natural compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/). Molecular docking was performed to identify compounds that formed interactions with the active site of the protein and had the lowest binding energy scores. Molecular dynamics simulations showed different movements of the protein-ligand complexes and behavioural difference of the wildtype and the variants, all three structures proved to be compact. Network analysis was done to study residue interactions, contact maps, dynamic cross correlations, average BC and average L were used to study the residue interactions and general residue contribution to the functioning of the protein..
- Full Text:
- Date Issued: 2020
- Authors: Baye, Bertha Cinthia
- Date: 2020
- Subjects: Antiparkinsonian agents , Parkinson's disease -- Treatment , Protein kinases , Parkinson's disease -- Chemotherapy , Molecules -- Models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138764 , vital:37671
- Description: Parkinson’s disease is a type of movement disorder that occurs when nerve cells in the brain stop producing dopamine. It is the second neurodegenerative disease affecting 1-2% of people above the ages of 65 years old. There is a worldwide prevalence of 7 to 10 million affected people of all cultures and race. Studies have shown that mutation that causes Parkinson’s disease result in increased kinase activity. The c.6055 G > A in exon 41 is the most prevalent LRRK2 variation which causes a substitution of glycine to serine in G2019S in the highly activated loop of its MAP kinase domain. The LRRK2 G2019S variant is the most common genetic determinant of Parkinson’s disease identified to date. This work focused on building accurate 3D models of the LRRK2 kinase domain, that were used for large-scale in silico docking against South African natural compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/). Molecular docking was performed to identify compounds that formed interactions with the active site of the protein and had the lowest binding energy scores. Molecular dynamics simulations showed different movements of the protein-ligand complexes and behavioural difference of the wildtype and the variants, all three structures proved to be compact. Network analysis was done to study residue interactions, contact maps, dynamic cross correlations, average BC and average L were used to study the residue interactions and general residue contribution to the functioning of the protein..
- Full Text:
- Date Issued: 2020
Impact of fracking fluid on Karoo plants based on field and greenhouse experiments
- Authors: Liddell, Duncan Carlyle
- Date: 2020
- Subjects: Plants -- South Africa -- Little Karoo , Desert ecology -- South Africa Great Karoo (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49125 , vital:41603
- Description: Fracking fluid has been indicated to be detrimental to vegetation. In forest vegetation the fracking fluid caused ground vegetation to be extensively damaged with high mortality rates and trees showing premature leaf loss following application. A study by Martin (2017) investigated these effects on Karoo vegetation in a greenhouse and found it to increase stress and reduced the growth with some life forms being identified as sensitive. The current study followed on the work of Martin testing additional species in the same greenhouse and applying different treatments of fracking fluid to Karoo vegetation in their habitat. The plants were monitored by measuring their height, photosynthetic efficiency (stress), biomass allocation and the temperature of the sites. The greenhouse plants had increased growth associated with repeated fracking fluid treatments while having variable stress levels with different treatments of the fracking fluid. The farm had mixed results being generally more stressed due to the treatments, the repeated fracking fluid treatments showed greater growth. The farm vegetation was more sensitive due to prolonged drought which is suspected to play a large role in the different response to fracking fluid between the two sites. The several hypotheses based on the finding of Martin (2017) were not supported by the data in this study. However, the application of fracking fluid did affect the tree species as they were found to be sensitive, while the other plant species was generally stressed after the applications. The greenhouse study cannot accurately represent the effects of fracking fluid on the farm vegetation, due to the large difference in the environment thus, more field studies would need to be conducted to determine the effects of fracking fluid.
- Full Text:
- Date Issued: 2020
- Authors: Liddell, Duncan Carlyle
- Date: 2020
- Subjects: Plants -- South Africa -- Little Karoo , Desert ecology -- South Africa Great Karoo (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49125 , vital:41603
- Description: Fracking fluid has been indicated to be detrimental to vegetation. In forest vegetation the fracking fluid caused ground vegetation to be extensively damaged with high mortality rates and trees showing premature leaf loss following application. A study by Martin (2017) investigated these effects on Karoo vegetation in a greenhouse and found it to increase stress and reduced the growth with some life forms being identified as sensitive. The current study followed on the work of Martin testing additional species in the same greenhouse and applying different treatments of fracking fluid to Karoo vegetation in their habitat. The plants were monitored by measuring their height, photosynthetic efficiency (stress), biomass allocation and the temperature of the sites. The greenhouse plants had increased growth associated with repeated fracking fluid treatments while having variable stress levels with different treatments of the fracking fluid. The farm had mixed results being generally more stressed due to the treatments, the repeated fracking fluid treatments showed greater growth. The farm vegetation was more sensitive due to prolonged drought which is suspected to play a large role in the different response to fracking fluid between the two sites. The several hypotheses based on the finding of Martin (2017) were not supported by the data in this study. However, the application of fracking fluid did affect the tree species as they were found to be sensitive, while the other plant species was generally stressed after the applications. The greenhouse study cannot accurately represent the effects of fracking fluid on the farm vegetation, due to the large difference in the environment thus, more field studies would need to be conducted to determine the effects of fracking fluid.
- Full Text:
- Date Issued: 2020
Impacts of cattle grazing pressure on vegetation and soil characteristics in an arid grassland of South Africa
- Authors: Botha, Gert Stephanus
- Date: 2020
- Subjects: Grazing -- Environmental aspects -- South Africa , Cattle -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/${Handle} , vital:39749
- Description: Natural rangelands are often degraded due to the implementation of incorrect grazing systems. One potential solution is the use of short duration, high intensity grazing. The impacts of this grazing system on, inter alia, vegetation and soil properties have not yet been comprehensively tested within the arid rangelands of South Africa. This study aimed to determine the impacts of grazing intensity on vegetation composition, forage quantity and quality, and soil compaction, soil water infiltration rates and soil chemical properties in an arid grassland in South Africa. The following three grazing treatments were compared: no grazing (NG), low intensity grazing (LIG) and high intensity grazing (HIG). A total of 18 plots (six replicates per treatment) were grazed with Bonsmara cattle. Each plot, 4 ha in size, was surveyed pre-grazing, directly after grazing, and again three, six and 12 months post-grazing. The results indicated that different grazing intensities did not affect grass diversity and the veld condition a year after grazing. Phytomass was influenced by grazing intensity, with no grazing having the highest phytomass throughout the study period. Soil compaction differed among seasons but not among treatments, with summer surveys recording the lowest soil compaction rates. The soil water infiltration rates did not differ between the three different treatments, indicating that grazing intensity did not affect infiltration rates. However, grazing did seem to improve soil nutrient levels when compared to NG. The grazed treatments had higher NH4+, K+, and organic carbon than the NG treatment. Nevertheless, there was no significant difference in nutrients levels when comparing the LIG system to the HIG system. When comparing the soil nutrients levels within a treatment over time, only the HIG treatment showed an increase in soil nutrient levels (Mg2+) over time, whereas the LIG and NG treatments showed no changed throughout the study period. Generally, the study results indicated that in the short term there was no advantage to using higher grazing intensity, although the presence of grazing (as opposed to no grazing) is advantageous to arid grassland functioning.
- Full Text:
- Date Issued: 2020
- Authors: Botha, Gert Stephanus
- Date: 2020
- Subjects: Grazing -- Environmental aspects -- South Africa , Cattle -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/${Handle} , vital:39749
- Description: Natural rangelands are often degraded due to the implementation of incorrect grazing systems. One potential solution is the use of short duration, high intensity grazing. The impacts of this grazing system on, inter alia, vegetation and soil properties have not yet been comprehensively tested within the arid rangelands of South Africa. This study aimed to determine the impacts of grazing intensity on vegetation composition, forage quantity and quality, and soil compaction, soil water infiltration rates and soil chemical properties in an arid grassland in South Africa. The following three grazing treatments were compared: no grazing (NG), low intensity grazing (LIG) and high intensity grazing (HIG). A total of 18 plots (six replicates per treatment) were grazed with Bonsmara cattle. Each plot, 4 ha in size, was surveyed pre-grazing, directly after grazing, and again three, six and 12 months post-grazing. The results indicated that different grazing intensities did not affect grass diversity and the veld condition a year after grazing. Phytomass was influenced by grazing intensity, with no grazing having the highest phytomass throughout the study period. Soil compaction differed among seasons but not among treatments, with summer surveys recording the lowest soil compaction rates. The soil water infiltration rates did not differ between the three different treatments, indicating that grazing intensity did not affect infiltration rates. However, grazing did seem to improve soil nutrient levels when compared to NG. The grazed treatments had higher NH4+, K+, and organic carbon than the NG treatment. Nevertheless, there was no significant difference in nutrients levels when comparing the LIG system to the HIG system. When comparing the soil nutrients levels within a treatment over time, only the HIG treatment showed an increase in soil nutrient levels (Mg2+) over time, whereas the LIG and NG treatments showed no changed throughout the study period. Generally, the study results indicated that in the short term there was no advantage to using higher grazing intensity, although the presence of grazing (as opposed to no grazing) is advantageous to arid grassland functioning.
- Full Text:
- Date Issued: 2020
In vitro susceptibility of Staphylococcus aureus to porphyrin-silver mediated photodynamic antimicrobial chemotherapy
- Authors: Shabangu, Samuel Malewa
- Date: 2020
- Subjects: Porphyrins , Nanoparticles , Photochemotherapy , Drug resistance in microorganisms , Staphylococcus aureus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167476 , vital:41484
- Description: This work reports on the syntheses and characterization of symmetrical and unsymmetrical porphyrin complexes namely, 5,10,15,20-tetra(4-pyridyl)-porphyrinato zinc(II) (1), 5,10,15,20-tetrathienyl porphyrinato zinc(II) (2), 5-(4-hydroxyphenyl)-10, 15, 20-tris(2-thienyl) porphyrinato zinc(II) (3), 5-(4-carboxyphenyl)-10,15,20-tris(pentafluorophenyl)- porphyrinato zinc(II) (4), 5-(4-carboxyphenyl)-10,15,20-triphenyl-porphyrinato zinc(II) (5) and 5-(4-carboxyphenyl)-10, 15, 20-tris(2-thienyl)-porphyrinato zinc(II) (6). The synthesis of silver nanoparticles (AgNPs) was also undertaken in this research work. Complexes 1, 2, 3 and 6 were linked to oleic acid/oleylamine functionalized nanoparticles via self-assembly and 4-6 were linked via covalent interaction through an amide bond to glutathione capped AgNPs. The effect of nature of bond along with symmetry were investigated, of interest were the five membered thienyl substituents. The photophysical and photochemical behaviour of the complexes and their conjugates with AgNPs were investigated in dimethylformamide. The porphyrin and AgNPs conjugates afforded an increase in singlet oxygen quantum yield. Complexes 1-6 and their conjugates were used for photodynamic antimicrobial chemotherapy of Staphylococcus aureus. The antimicrobial studies were done in two different concentrations of 0.36 and 2.0 μg/mL. The thienyl substituted porphyrin complexes and their conjugates gave better photodynamic activity as compared to phenyl analogues
- Full Text:
- Date Issued: 2020
- Authors: Shabangu, Samuel Malewa
- Date: 2020
- Subjects: Porphyrins , Nanoparticles , Photochemotherapy , Drug resistance in microorganisms , Staphylococcus aureus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167476 , vital:41484
- Description: This work reports on the syntheses and characterization of symmetrical and unsymmetrical porphyrin complexes namely, 5,10,15,20-tetra(4-pyridyl)-porphyrinato zinc(II) (1), 5,10,15,20-tetrathienyl porphyrinato zinc(II) (2), 5-(4-hydroxyphenyl)-10, 15, 20-tris(2-thienyl) porphyrinato zinc(II) (3), 5-(4-carboxyphenyl)-10,15,20-tris(pentafluorophenyl)- porphyrinato zinc(II) (4), 5-(4-carboxyphenyl)-10,15,20-triphenyl-porphyrinato zinc(II) (5) and 5-(4-carboxyphenyl)-10, 15, 20-tris(2-thienyl)-porphyrinato zinc(II) (6). The synthesis of silver nanoparticles (AgNPs) was also undertaken in this research work. Complexes 1, 2, 3 and 6 were linked to oleic acid/oleylamine functionalized nanoparticles via self-assembly and 4-6 were linked via covalent interaction through an amide bond to glutathione capped AgNPs. The effect of nature of bond along with symmetry were investigated, of interest were the five membered thienyl substituents. The photophysical and photochemical behaviour of the complexes and their conjugates with AgNPs were investigated in dimethylformamide. The porphyrin and AgNPs conjugates afforded an increase in singlet oxygen quantum yield. Complexes 1-6 and their conjugates were used for photodynamic antimicrobial chemotherapy of Staphylococcus aureus. The antimicrobial studies were done in two different concentrations of 0.36 and 2.0 μg/mL. The thienyl substituted porphyrin complexes and their conjugates gave better photodynamic activity as compared to phenyl analogues
- Full Text:
- Date Issued: 2020
Influence of Tamarix species on soil physicochemical properties and mapping its distribution and density using GIS in Western Cape, South Africa
- Authors: Mlahlwa, Asiphe
- Date: 2020
- Subjects: Tamarisks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/18588 , vital:42611
- Description: Tamarix ramosissima invasion is unarguably one of the worst ecological disasters in South Africa and is classified under category 1b by the National Environmental Management: Biodiversity Act 2014 (NEM: BA). The exotic Tamarix species was introduced in South Africa during the early 1900s as an ornamental or phytoremediating plant. This study was conducted to assess Tamarix distribution and evaluate its impact on soil physicochemical properties in two sites at Leeu River and Olifant River in Western Cape, South Africa. Samples were collected from Leeu River (which consists both the exotic and native Tamarix species) and Olifant River (only exotic Tamarix species). Three transects were laid from the water point outwards, with exotic Tamarix invading the river bank (first transect), the control on the open land (second transect) and the native Tamarix at the far end of the study site (third transect) in Leeu River. In Olifant, transects were laid according to the degree of invasion, low Tamarix density transect was referred to as T1, the medium as T2 and the high density as T3. Soil samples from each transect were taken from three points, at three soil depths (0-10, 10-20 and 20-30 cm) during winter and summer. Soil physiochemical properties such as soil pH, electro-conductivity (EC), total nitrogen (TN), total carbon (TC), soil organic carbon (SOC), sodium (Na+ ), potassium (K+ ), Calcium (Ca2+), Magnesium (Mg2+), bulk density, soil texture and sodium adsorption ratio (SAR) were determined. Soil chemicals properties including EC, Na+ , SAR, K+ and Mg2+ were found significantly higher under the native and the exotic Tamarix species when compared to Tamarix free soils. In general, salinity of surface soils (0–10 cm) was greater than those in the deeper soils with 5.05 mS/cm and 4.73 mS/cm observed under exotic and native Tamarix species, respectively. High levels of EC, K+ , Ca2+, Na+ , SAR, TN, TC and SOC were observed under T3, followed by T2 with the lowest being recorded in T1 at 0-10 cm. Unlike the soil EC, the effect of Tamarix density on soil pH at 0-10 cm soil profile was not significant. Alterations of soil physicochemical properties were more pronounced under the high Tamarix density as compared to the low invasion. Increased in distance from the river was related to a higher density of the invasive species and also topography had a major role in the change of species density. An increase in Tamarix density, results in high leaf litter which in turn results in salinity and soil nutrient at 0-10 cm. Soil salinity was dramatically increased under Tamarix species. Tamarix species are capable of altering the soil properties making it conducive for their growth.
- Full Text:
- Date Issued: 2020
- Authors: Mlahlwa, Asiphe
- Date: 2020
- Subjects: Tamarisks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/18588 , vital:42611
- Description: Tamarix ramosissima invasion is unarguably one of the worst ecological disasters in South Africa and is classified under category 1b by the National Environmental Management: Biodiversity Act 2014 (NEM: BA). The exotic Tamarix species was introduced in South Africa during the early 1900s as an ornamental or phytoremediating plant. This study was conducted to assess Tamarix distribution and evaluate its impact on soil physicochemical properties in two sites at Leeu River and Olifant River in Western Cape, South Africa. Samples were collected from Leeu River (which consists both the exotic and native Tamarix species) and Olifant River (only exotic Tamarix species). Three transects were laid from the water point outwards, with exotic Tamarix invading the river bank (first transect), the control on the open land (second transect) and the native Tamarix at the far end of the study site (third transect) in Leeu River. In Olifant, transects were laid according to the degree of invasion, low Tamarix density transect was referred to as T1, the medium as T2 and the high density as T3. Soil samples from each transect were taken from three points, at three soil depths (0-10, 10-20 and 20-30 cm) during winter and summer. Soil physiochemical properties such as soil pH, electro-conductivity (EC), total nitrogen (TN), total carbon (TC), soil organic carbon (SOC), sodium (Na+ ), potassium (K+ ), Calcium (Ca2+), Magnesium (Mg2+), bulk density, soil texture and sodium adsorption ratio (SAR) were determined. Soil chemicals properties including EC, Na+ , SAR, K+ and Mg2+ were found significantly higher under the native and the exotic Tamarix species when compared to Tamarix free soils. In general, salinity of surface soils (0–10 cm) was greater than those in the deeper soils with 5.05 mS/cm and 4.73 mS/cm observed under exotic and native Tamarix species, respectively. High levels of EC, K+ , Ca2+, Na+ , SAR, TN, TC and SOC were observed under T3, followed by T2 with the lowest being recorded in T1 at 0-10 cm. Unlike the soil EC, the effect of Tamarix density on soil pH at 0-10 cm soil profile was not significant. Alterations of soil physicochemical properties were more pronounced under the high Tamarix density as compared to the low invasion. Increased in distance from the river was related to a higher density of the invasive species and also topography had a major role in the change of species density. An increase in Tamarix density, results in high leaf litter which in turn results in salinity and soil nutrient at 0-10 cm. Soil salinity was dramatically increased under Tamarix species. Tamarix species are capable of altering the soil properties making it conducive for their growth.
- Full Text:
- Date Issued: 2020
Initiating biological control for Nymphaea mexicana zuccarini (Nymphaeaceae) in South Africa
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
Invalid submission of extension of time claims in the South African construction industry
- Authors: Neethling, Juan Pierre
- Date: 2020
- Subjects: Construction industry -- South Africa , Construction industry -- Management Project management Building -- Superintendence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46805 , vital:39663
- Description: Most construction projects are delayed in the construction industry due to internal and/or external influences. Proving delay is not a simple task but rather a time-consuming process, as projects consist of numerous activities and a substantial amount of detail, and they interface with the many stakeholders. Several different methods can be used to prove a delay; however, these are academic and are mainly for simple projects. Proving a delay is often difficult for the contractor, who is consistently dealing with multiple project constraints. Therefore, to be effective with an extension of time claim, the contractor must establish causation and liability, and assist in demonstrating the extent of time-related damages experienced as a direct result of the delay events relied upon. The process of recording the delays is dynamic and requires solid knowledge of contract clauses, the ability to distinguish between different types of delays and the capability to identify what constitutes valid evidence. Therefore, a need arises to establish a framework that would assist contractors by standardising their submission. This would contribute to expediting the evaluation and approval process, thus limiting the negative impacts associated with prolonged delay claims. The research obtains a “lived” view from contractors who have participated with EOT claims, therefore, utilising the qualitative research method. The choice of data collection method was semi-structured one-on one face to face interviews. In deriving the findings of the research, the coding scheme techniques were used throughout the research process to manage both the secondary and primary data. The main factors which cause major problems in EOT claims are contractual knowledge, lack of supporting information, contractual compliance, employer inference and the different philosophies of contracts, which often leads to confusion and misinterpretation. There is a lack of awareness and knowledge of the analysis techniques and strategies which could assist in preparing EOT claims, even though there is a substantial amount of literature available. The concept that the industry needs a standardised submission process was welcomed by the participants; the existence of a common strategy would certainly resolve many problems in the submission process, including reducing the number of disputes. There was a consensus among all participants that there is no standard approach to submitting EOT claims in the South African construction industry and exploring a common approach was an idea that was viewed as reasonable and maybe offered a practical solution to address the submission challenges. There were several delimitations to this study. First, the sample only included individuals within the Eastern Cape region. Since the sample size was relatively small, the researcher was cautious when interpreting and generalising the results. Secondly, the targeted population for this research was selected using the purposive sampling method, as opposed to a random sampling, which means that the results of the study cannot be generally applied to a larger population. Lastly, the research was a qualitative study which relied on the interpretations of the researcher based on his understanding of the data collected.
- Full Text:
- Date Issued: 2020
- Authors: Neethling, Juan Pierre
- Date: 2020
- Subjects: Construction industry -- South Africa , Construction industry -- Management Project management Building -- Superintendence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46805 , vital:39663
- Description: Most construction projects are delayed in the construction industry due to internal and/or external influences. Proving delay is not a simple task but rather a time-consuming process, as projects consist of numerous activities and a substantial amount of detail, and they interface with the many stakeholders. Several different methods can be used to prove a delay; however, these are academic and are mainly for simple projects. Proving a delay is often difficult for the contractor, who is consistently dealing with multiple project constraints. Therefore, to be effective with an extension of time claim, the contractor must establish causation and liability, and assist in demonstrating the extent of time-related damages experienced as a direct result of the delay events relied upon. The process of recording the delays is dynamic and requires solid knowledge of contract clauses, the ability to distinguish between different types of delays and the capability to identify what constitutes valid evidence. Therefore, a need arises to establish a framework that would assist contractors by standardising their submission. This would contribute to expediting the evaluation and approval process, thus limiting the negative impacts associated with prolonged delay claims. The research obtains a “lived” view from contractors who have participated with EOT claims, therefore, utilising the qualitative research method. The choice of data collection method was semi-structured one-on one face to face interviews. In deriving the findings of the research, the coding scheme techniques were used throughout the research process to manage both the secondary and primary data. The main factors which cause major problems in EOT claims are contractual knowledge, lack of supporting information, contractual compliance, employer inference and the different philosophies of contracts, which often leads to confusion and misinterpretation. There is a lack of awareness and knowledge of the analysis techniques and strategies which could assist in preparing EOT claims, even though there is a substantial amount of literature available. The concept that the industry needs a standardised submission process was welcomed by the participants; the existence of a common strategy would certainly resolve many problems in the submission process, including reducing the number of disputes. There was a consensus among all participants that there is no standard approach to submitting EOT claims in the South African construction industry and exploring a common approach was an idea that was viewed as reasonable and maybe offered a practical solution to address the submission challenges. There were several delimitations to this study. First, the sample only included individuals within the Eastern Cape region. Since the sample size was relatively small, the researcher was cautious when interpreting and generalising the results. Secondly, the targeted population for this research was selected using the purposive sampling method, as opposed to a random sampling, which means that the results of the study cannot be generally applied to a larger population. Lastly, the research was a qualitative study which relied on the interpretations of the researcher based on his understanding of the data collected.
- Full Text:
- Date Issued: 2020
Investigation into the influence of an alien plant species on the soil microbiota of the sub-Antarctic, Marion Island
- Authors: Pienaar, Robert Daniel
- Date: 2020
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/124039 , vital:35531
- Description: Embargo applied. Embargo period to expire in April of 2021.
- Full Text:
- Date Issued: 2020
- Authors: Pienaar, Robert Daniel
- Date: 2020
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/124039 , vital:35531
- Description: Embargo applied. Embargo period to expire in April of 2021.
- Full Text:
- Date Issued: 2020
Investigation of wild garlic plant extracts as potential devulcanizing agents
- Authors: Mpuputla, Mooketsi
- Date: 2020
- Subjects: Plant products , Plant extracts Traditional medicine
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49204 , vital:41610
- Description: Commercially available chemical compounds used as devulcanizing agents have been found to be relatively expensive, and harmful to human health. These include compounds such as diallyl disulfide (DADS) and diphenyl disulfide (DPDS). However, compounds like DADS and other sulfides are found in the readily available natural resource material, T. violacea, which is rich in sulfur-derived compounds that may exhibit potential use as devulcanizing agents. Hence, this study is aimed at examining the efficacy of the extracted sulfur compounds of T. violacea as potential devulcanizing agents. The sulfides of T. violacea were successfully extracted by means of sequential extraction using chloroform (CHCl3), ethyl acetate (EtOAc), and methanol (MeOH). Identification of present sulfides was done by phytochemical analysis, using the TLC method. The commercially available HPLC grade DADS reference standard was used to quantify the amount of DADS in each extract. Reversed-phase high-performance liquid chromatography (RP-HPLC) was used for quantification. The HPLC results showed that only the EtOAc and MeOH extracts contained DADS, while insignificant amount of DADS was seen in the CHCl3 extracts. The EtOAc roots, bulbs and leaf extracts (18.8 × 10-3, 8.84 × 10-3, 7.2 × 10-3 mg/mL) showed greater DADS concentration compared to the MeOH roots, bulbs and leaf extracts (5.3 × 10-3, 8.07 × 10-3, 1.9 × 10-3 mg/mL), respectively. RP-HPLC and Gel Permeation Chromatography (GPC) were the methods used to monitor and identify crosslink formation and devulcanizing. The vulcanization and devulcanization studies were carried out using the model compound, squalene. All extracts showed a decrease in the molecular weight distribution of the devulcanized products. The leaf extract, CHCl3 and EtOAc, showed the highest devulcanization efficacy overall, while the MeOH extracts showed least devulcanization efficacy as devulcanization agents. Thermal analysis studies were performed to investigate the interactions of the curatives used in the vulcanization system(s). Isothermal analysis of the vulcanization system was evident in a vulcanization reaction at an optimal time of 20 min, and at onset temperature of 177.6 oC. Upon devulcanization, DSC analysis gave evidence of the glass transition of squalene products. This indicates that no main-chain scission or backbone breakage occurred in reacting the vulcanized products with the devulcanizing agents.
- Full Text:
- Date Issued: 2020
- Authors: Mpuputla, Mooketsi
- Date: 2020
- Subjects: Plant products , Plant extracts Traditional medicine
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49204 , vital:41610
- Description: Commercially available chemical compounds used as devulcanizing agents have been found to be relatively expensive, and harmful to human health. These include compounds such as diallyl disulfide (DADS) and diphenyl disulfide (DPDS). However, compounds like DADS and other sulfides are found in the readily available natural resource material, T. violacea, which is rich in sulfur-derived compounds that may exhibit potential use as devulcanizing agents. Hence, this study is aimed at examining the efficacy of the extracted sulfur compounds of T. violacea as potential devulcanizing agents. The sulfides of T. violacea were successfully extracted by means of sequential extraction using chloroform (CHCl3), ethyl acetate (EtOAc), and methanol (MeOH). Identification of present sulfides was done by phytochemical analysis, using the TLC method. The commercially available HPLC grade DADS reference standard was used to quantify the amount of DADS in each extract. Reversed-phase high-performance liquid chromatography (RP-HPLC) was used for quantification. The HPLC results showed that only the EtOAc and MeOH extracts contained DADS, while insignificant amount of DADS was seen in the CHCl3 extracts. The EtOAc roots, bulbs and leaf extracts (18.8 × 10-3, 8.84 × 10-3, 7.2 × 10-3 mg/mL) showed greater DADS concentration compared to the MeOH roots, bulbs and leaf extracts (5.3 × 10-3, 8.07 × 10-3, 1.9 × 10-3 mg/mL), respectively. RP-HPLC and Gel Permeation Chromatography (GPC) were the methods used to monitor and identify crosslink formation and devulcanizing. The vulcanization and devulcanization studies were carried out using the model compound, squalene. All extracts showed a decrease in the molecular weight distribution of the devulcanized products. The leaf extract, CHCl3 and EtOAc, showed the highest devulcanization efficacy overall, while the MeOH extracts showed least devulcanization efficacy as devulcanization agents. Thermal analysis studies were performed to investigate the interactions of the curatives used in the vulcanization system(s). Isothermal analysis of the vulcanization system was evident in a vulcanization reaction at an optimal time of 20 min, and at onset temperature of 177.6 oC. Upon devulcanization, DSC analysis gave evidence of the glass transition of squalene products. This indicates that no main-chain scission or backbone breakage occurred in reacting the vulcanized products with the devulcanizing agents.
- Full Text:
- Date Issued: 2020
Learners’ perception on the effect of infrastructure development on academic performance in Port Elizabeth public secondary schools
- Authors: Goduka, Nomava
- Date: 2020
- Subjects: Infrastructure (Economics) -- Planning , School facilities -- South Africa -- Port Elizabeth -- Finance Academic achievement
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46053 , vital:39479
- Description: South Africa is striving to attain quality equal education; however, this ideal is affected by various factors such as discrimination, learner-related challenges (e.g. dilapidated rural schools, poverty, and violence), educator-related challenges (e.g. low morale and motivation, and poor administration and management of schools), and governmental issues (e.g. a lack of will, lacklustre attitudes, and an inability to deliver resources and/or services). While the National Department of Basic Education is battling to eradicate the backlog of school infrastructure and maintenance, mud schools are still prevalent in rural areas. The present state of poverty-stricken areas is most affected by the mentioned challenges and, as a result, it is necessary to determine the nature and extent of the consequences in terms of academic performance. This study, therefore, investigated the reality of the current rural school situation by investigating the perceptions of learners on the effect of infrastructure development on their academic performance in public secondary schools. Three secondary schools in the Motherwell area in Port Elizabeth were chosen for the research setting. A quantitative research approach was deemed suitable for the study, and a questionnaire was utilised for data collection. A total of 151 questionnaires were completed. The key findings derived from the data indicated that inadequate infrastructure has a negative impact on academic performance. Some of the key issues pertaining to infrastructure included inadequate leisure areas, laboratories, libraries, and sport fields. Overcrowding in classrooms were also found to be prevalent, and posed a major barrier to learning. The findings of the study provided insights into the reality of rural education and were used as a basis for offering recommendations that may assist stakeholders to improve the current situation.
- Full Text:
- Date Issued: 2020
- Authors: Goduka, Nomava
- Date: 2020
- Subjects: Infrastructure (Economics) -- Planning , School facilities -- South Africa -- Port Elizabeth -- Finance Academic achievement
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46053 , vital:39479
- Description: South Africa is striving to attain quality equal education; however, this ideal is affected by various factors such as discrimination, learner-related challenges (e.g. dilapidated rural schools, poverty, and violence), educator-related challenges (e.g. low morale and motivation, and poor administration and management of schools), and governmental issues (e.g. a lack of will, lacklustre attitudes, and an inability to deliver resources and/or services). While the National Department of Basic Education is battling to eradicate the backlog of school infrastructure and maintenance, mud schools are still prevalent in rural areas. The present state of poverty-stricken areas is most affected by the mentioned challenges and, as a result, it is necessary to determine the nature and extent of the consequences in terms of academic performance. This study, therefore, investigated the reality of the current rural school situation by investigating the perceptions of learners on the effect of infrastructure development on their academic performance in public secondary schools. Three secondary schools in the Motherwell area in Port Elizabeth were chosen for the research setting. A quantitative research approach was deemed suitable for the study, and a questionnaire was utilised for data collection. A total of 151 questionnaires were completed. The key findings derived from the data indicated that inadequate infrastructure has a negative impact on academic performance. Some of the key issues pertaining to infrastructure included inadequate leisure areas, laboratories, libraries, and sport fields. Overcrowding in classrooms were also found to be prevalent, and posed a major barrier to learning. The findings of the study provided insights into the reality of rural education and were used as a basis for offering recommendations that may assist stakeholders to improve the current situation.
- Full Text:
- Date Issued: 2020
Linking onshore and offshore crustal features, integrating seismic and borehole data in the Gamtoos basin
- Authors: Makuzeni, Manyano
- Date: 2020
- Subjects: Submarine geology , Geology Geophysics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49137 , vital:41604
- Description: The margin of the Southern Africa continent harbours the history about the fragmentation and separation of Gondwana in its basins. The integration of onshore and offshore geology is of primordial importance to understand the complete geological history and evolution of the southern African border. The study focuses on the Gamtoos Basin, where the sediment deposits on the onshore portion are generally unfossiliferous and therefore difficult to correlate with the offshore portion of the basin. In an attempt to do this, several datasets were integrated such as old 2-D seismic reflection data and borehole wells. This data, acquired by SOEKER in the 1970s was purchased from the Petroleum Agency of South Africa (PASA). Some data reprocessing involved digitization and conversion of the old seismic data from TIF format to SEG-Y format. Conventional seismic stratigraphic method (Mitchum, JR, et al., 1977) was used to identify seismic discontinuities and remarkable stratigraphic surfaces and units based on reflection configurations and facies characteristics, and ages of these surfaces were provided by well data. Seismic interpretation was first done on printed seismogram papers, and then integrated into the ‘Kingdom Suite’ software to ensure coherency at all crossing lines. Isochron and Isopach maps (using QGIS, Mirone and tools such as GMT) were created. The first results, allow us to estimate for the first time a precise age calibration of onshore deposit. Furthermore, the delimitation in 5 second-order seismic sequences along the Gamtoos Basin suggest a link between different basin filling dynamics and kinematic phases related to the opening of the Indian and Atlantic Oceans along the southern Africa margins. The study shows that the Gamtoos Basin is an essential area linking the geological histories of both East and Western parts of the Southern Africa continent.
- Full Text:
- Date Issued: 2020
- Authors: Makuzeni, Manyano
- Date: 2020
- Subjects: Submarine geology , Geology Geophysics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49137 , vital:41604
- Description: The margin of the Southern Africa continent harbours the history about the fragmentation and separation of Gondwana in its basins. The integration of onshore and offshore geology is of primordial importance to understand the complete geological history and evolution of the southern African border. The study focuses on the Gamtoos Basin, where the sediment deposits on the onshore portion are generally unfossiliferous and therefore difficult to correlate with the offshore portion of the basin. In an attempt to do this, several datasets were integrated such as old 2-D seismic reflection data and borehole wells. This data, acquired by SOEKER in the 1970s was purchased from the Petroleum Agency of South Africa (PASA). Some data reprocessing involved digitization and conversion of the old seismic data from TIF format to SEG-Y format. Conventional seismic stratigraphic method (Mitchum, JR, et al., 1977) was used to identify seismic discontinuities and remarkable stratigraphic surfaces and units based on reflection configurations and facies characteristics, and ages of these surfaces were provided by well data. Seismic interpretation was first done on printed seismogram papers, and then integrated into the ‘Kingdom Suite’ software to ensure coherency at all crossing lines. Isochron and Isopach maps (using QGIS, Mirone and tools such as GMT) were created. The first results, allow us to estimate for the first time a precise age calibration of onshore deposit. Furthermore, the delimitation in 5 second-order seismic sequences along the Gamtoos Basin suggest a link between different basin filling dynamics and kinematic phases related to the opening of the Indian and Atlantic Oceans along the southern Africa margins. The study shows that the Gamtoos Basin is an essential area linking the geological histories of both East and Western parts of the Southern Africa continent.
- Full Text:
- Date Issued: 2020
Managing the invasive aquatic plant Sagittaria platyphylla (Engelm.) J.G. Sm(Alismataceae): problems and prospects
- Ndlovu, Mpilonhle Sinothando
- Authors: Ndlovu, Mpilonhle Sinothando
- Date: 2020
- Subjects: Aquatic weeds -- Biological control -- South Africa , Sagittaria latifolia -- Biological control -- South Africa , Noxious weeds -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa , Listronotus , Insects as biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167121 , vital:41439
- Description: Sagittaria platyphylla (Engelm.) J.G.Sm. (Alismataceae), commonly known as Delta arrowhead, is an invasive aquatic macrophyte native to southern United States of America (USA) that has become a serious weed in freshwater systems in South Africa, New Zealand, Australia, and recently China. In South Africa, the plant was first detected in Krantzkloof Nature Reserve, KwaZulu-Natal Province in 2008, and due to its known impact in other countries, it was listed as a Category 1a invader species under the National Environmental Management: Biodiversity Act 2004 (NEM: BA). This listing required mechanical and chemical control methods to be implemented by the South African National Biodiversity Institute’s (SANBI), Invasive Species Programme (ISP), with the aim of eradicating the weed. Despite the eradication efforts, by 2016, the weed was recognized as one of the country’s top 10 worst and fastest spreading invasive alien plants. Since its introduction in 2008, the plant has spread both within and between sites in South Africa, increasing from one site in 2008 to 72 sites by 2019. Once introduced into lotic systems, the plant spread rapidly downstream, in some cases up to 120km within six years, with an average of 10 km per year. Extirpation over the last ten years was only possible at a limited number of sites. Under the current management approach, the invasion is foreseen to spread to new sites within a 5 km radius of the current populations. Due to the failure of conventional control mechanisms, biological control is currently being considered as a potential control option. Four potential biological control agents are under investigation, but none have been released. Amongst them is the fruit and flower feeding weevil Listronotus appendiculatus Bohm. (Coleoptera: Curculionidae) which showed most potential as a suitable biological control agent. This study demonstrated that L. appendiculatus herbivory negatively influenced the overall fitness of S. platyphylla by reducing the plant’s growth rate and above ground biomass. Listronotus appendiculatus herbivory also reduced the plant’s size and the potential to kill adult plants. Most importantly, L. appendiculatus larval feeding damage significantly reduce viable-germinating seeds, the weed’s primary dispersal mechanism. Therefore, a biological control programme is advised to be integrated within the current management plan.
- Full Text:
- Date Issued: 2020
- Authors: Ndlovu, Mpilonhle Sinothando
- Date: 2020
- Subjects: Aquatic weeds -- Biological control -- South Africa , Sagittaria latifolia -- Biological control -- South Africa , Noxious weeds -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa , Listronotus , Insects as biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167121 , vital:41439
- Description: Sagittaria platyphylla (Engelm.) J.G.Sm. (Alismataceae), commonly known as Delta arrowhead, is an invasive aquatic macrophyte native to southern United States of America (USA) that has become a serious weed in freshwater systems in South Africa, New Zealand, Australia, and recently China. In South Africa, the plant was first detected in Krantzkloof Nature Reserve, KwaZulu-Natal Province in 2008, and due to its known impact in other countries, it was listed as a Category 1a invader species under the National Environmental Management: Biodiversity Act 2004 (NEM: BA). This listing required mechanical and chemical control methods to be implemented by the South African National Biodiversity Institute’s (SANBI), Invasive Species Programme (ISP), with the aim of eradicating the weed. Despite the eradication efforts, by 2016, the weed was recognized as one of the country’s top 10 worst and fastest spreading invasive alien plants. Since its introduction in 2008, the plant has spread both within and between sites in South Africa, increasing from one site in 2008 to 72 sites by 2019. Once introduced into lotic systems, the plant spread rapidly downstream, in some cases up to 120km within six years, with an average of 10 km per year. Extirpation over the last ten years was only possible at a limited number of sites. Under the current management approach, the invasion is foreseen to spread to new sites within a 5 km radius of the current populations. Due to the failure of conventional control mechanisms, biological control is currently being considered as a potential control option. Four potential biological control agents are under investigation, but none have been released. Amongst them is the fruit and flower feeding weevil Listronotus appendiculatus Bohm. (Coleoptera: Curculionidae) which showed most potential as a suitable biological control agent. This study demonstrated that L. appendiculatus herbivory negatively influenced the overall fitness of S. platyphylla by reducing the plant’s growth rate and above ground biomass. Listronotus appendiculatus herbivory also reduced the plant’s size and the potential to kill adult plants. Most importantly, L. appendiculatus larval feeding damage significantly reduce viable-germinating seeds, the weed’s primary dispersal mechanism. Therefore, a biological control programme is advised to be integrated within the current management plan.
- Full Text:
- Date Issued: 2020
Metallophthalocyanines linked to metal nanoparticles and folic acid for use in photodynamic therapy of cancer and photoinactivation of bacterial microorganisms.
- Authors: Matlou, Gauta Gold
- Date: 2020
- Subjects: Cancer -- Photochemotherapy , Nanoparticles , Phthalocyanines , Anti-infective agents -- Therapeutic use , Photochemotherapy , Photochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166540 , vital:41377
- Description: This thesis presents on the synthesis and characterization of novel asymmetric and symmetrical metallophthalocyanines (MPcs) substituted with carboxylic acid functional groups and centrally metallated with zinc and indium. The MPcs are further covalently linked to cysteine capped silver nanoparticles (cys-AgNPs), amino functionalized magnetic nanoparticles (AMNPs) and folic acid (FA) through an amide bond between the carboxylic group of MPcs and the amino group of FA, cys-AgNPs or AMNPs. The covalent linkage of MPcs to FA improved the water solubility of MPcs and allowed for singlet oxygen quantum yield determination in water. Asymmetric MPcs and their conjugates were found to have improved photochemical and photophysical properties compared to symmetrical MPcs and their conjugates. The heavy atom effect of AMNPs and AgNPs improved the triplet and singlet oxygen quantum yields of MPcs. MPcs and their conjugates (MPc-FA, MPc-AMNPs, MPc-AgNPs) were found to have lower in vitro dark cytotoxicity and higher photodynamic therapy (PDT) activity on MCF-7 breast cancer cells. The water soluble MPc-FA had better PDT activity when compared to MPc-AMNPs due to the active targeting of folic acid-folate binding on cancer cell surface. MPcs and MPc-AgNPs conjugates also showed excellent in vitro cytotoxicity on S. aureus under light irradiation compared to dark cytotoxicity. The photosensitizing properties of MPcs and their conjugates are demonstrated for the first time in this thesis, both on breast cancer cells (MCF-7) through photodynamic therapy and on microorganisms (S. aureus) through photodynamic antimicrobial chemotherapy.
- Full Text:
- Date Issued: 2020
- Authors: Matlou, Gauta Gold
- Date: 2020
- Subjects: Cancer -- Photochemotherapy , Nanoparticles , Phthalocyanines , Anti-infective agents -- Therapeutic use , Photochemotherapy , Photochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166540 , vital:41377
- Description: This thesis presents on the synthesis and characterization of novel asymmetric and symmetrical metallophthalocyanines (MPcs) substituted with carboxylic acid functional groups and centrally metallated with zinc and indium. The MPcs are further covalently linked to cysteine capped silver nanoparticles (cys-AgNPs), amino functionalized magnetic nanoparticles (AMNPs) and folic acid (FA) through an amide bond between the carboxylic group of MPcs and the amino group of FA, cys-AgNPs or AMNPs. The covalent linkage of MPcs to FA improved the water solubility of MPcs and allowed for singlet oxygen quantum yield determination in water. Asymmetric MPcs and their conjugates were found to have improved photochemical and photophysical properties compared to symmetrical MPcs and their conjugates. The heavy atom effect of AMNPs and AgNPs improved the triplet and singlet oxygen quantum yields of MPcs. MPcs and their conjugates (MPc-FA, MPc-AMNPs, MPc-AgNPs) were found to have lower in vitro dark cytotoxicity and higher photodynamic therapy (PDT) activity on MCF-7 breast cancer cells. The water soluble MPc-FA had better PDT activity when compared to MPc-AMNPs due to the active targeting of folic acid-folate binding on cancer cell surface. MPcs and MPc-AgNPs conjugates also showed excellent in vitro cytotoxicity on S. aureus under light irradiation compared to dark cytotoxicity. The photosensitizing properties of MPcs and their conjugates are demonstrated for the first time in this thesis, both on breast cancer cells (MCF-7) through photodynamic therapy and on microorganisms (S. aureus) through photodynamic antimicrobial chemotherapy.
- Full Text:
- Date Issued: 2020
Mineralogy, geochemistry and origin of the Neoproterozoic Xaudum iron-formation in Botswana
- Authors: Ntantiso, Mawande
- Date: 2020
- Subjects: Xaudum iron-formation , Iron ores -- Botswana , Formations (Geology) -- Botswana , Mineralogy -- Botswana , Paleoclimatology -- Proterozoic
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167211 , vital:41447
- Description: Banded iron-formations (BIF) formed in three different geological periods in the Earth’s history, namely the Archean, Paleoproterozoic and Neoproterozoic. Each of these periods has a corresponding index BIF type attributed to them. The oldest is the Archean Algoma-type BIF which is typically dominated by smaller-volume BIF deposits associated with volcanic rocks and greenstone belts. The next is the volumetrically far more abundant Superior-type BIF of the Paleoproterozoic lacking any obvious volcanic relation. The youngest BIFs were deposited after a hiatus of a billion years in the Neoproterozoic and are believed to be genetically linked to Marinoan ice-age. The global re-introduction and distribution of BIF in the Neoproterozoic highlights a shift in the Earth’s tectonics, climate, biosphere and ocean chemistry from the older Archean and Paleoproterozoic counterparts. Various models have been postulated by researchers in attempts to explain how Neoproterozoic iron-formations formed. In all the available models, the Snowball Earth Hypothesis initially proposed by Kirshvink (1992) is an overarching concept. In this study, four cores from the Neoproterozoic Xaudum iron-formation (XIF) in Ngamiland, northwest of Botswana, were sampled and analysed following a partnership between Postgraduate Research in Iron and Manganese Ore Resources (PRIMOR) and Tsodilo Resources Ltd. The study sets out to explore the mineralogy and chemistry of XIF in order to determine its origin, constrain the redox conditions in the paleo-basin, assess it in the context of other Neoproterozoic iron-formations and older Archean and Paleoproterozoic iron-formations, and inform metallurgical processing. The mineralogy of XIF consists of magnetite, quartz, amphibole, garnet, biotite and chlorite in decreasing abundance. This mineral assemblage is characteristic of medium grade metamorphosed iron-formations. Algoma and Superior-type BIFs which experienced late-diagenetic and very low-grade metamorphism have a complex mineral assemblage consisting of hematite, magnetite, quartz, and several carbonate (dolomite-ankerite series and siderite) and silicate phases (greenalite, riebeckite and stilpnomelane). The geochemical results show that XIF has higher Mn3O4 and Al2O3 average contents when compared to Algoma and Superior type BIF. The detrital components in XIF correlate with High Field Strength Elements (HFSE) suggesting increased delivery of siliciclastic material during deposition. This trend is comparable to other NIF deposits suggesting a global high input of siliciclastic material into Neoproterozoic paleodepositional environments. This trend is different from Archean and Paleoproterozoic BIF deposits which are close to pure chemical sediments lacking measurable detrital contributions. In the XIF, bulk-rock Mn3O4 and Al2O3 in drillcore SW have higher averages of 2.4 and 2.6 wt. % respectively, compared to the other three cores. The Mn3O4 shows a positive statistical relationship with Co, suggesting that Neoproterozoic oceans and atmosphere were possibly more oxic than in the Archean and Paleoproterozoic. The Mn3O4 shows an antithetic relationship with Fe2O3 suggesting that the paleobasin was chemically heterogeneous in terms of redox conditions, with Fe2O3 depositing presumably in deeper parts removed from a detrital source, and Mn3O4 depositing possibly more proximal to a paleo-shoreline in a shallower setting where there was higher delivery of siliciclastic material from the continent due to correspondingly higher Al2O3 and TiO2 contents. The REE patterns of XIF show positive-sloping trends of depletion in LREE and enrichment in HREE which resemble those of seawater. However, the REE slope becomes a lot flatter and resembles closer the signature of PAAS and adjacent diamictite facies, which agrees with the idea of high siliciclastic input in the paleobasin comparable to other NIF. XIF also appears to lack clear Ce or Eu anomalies. The lack of the former points to the oceans possibly not being oxic enough to drive the fractionation of Ce into Mn oxides like in the modern oceans, or that the Ce behaviour is obscured by the high siliciclastic input in XIF. Similarly, the lack of positive Eu anomaly shows a weak to absent hydrothermal signal into to modern shallow seawater where Fe and Si were sourced, or detritally derived REE contamination. Extensive weathering under hot and humid climate during glacial retreat is shown by the low K2O/Al2O3 ratios and high CIA values ranging from 80-99. Re-glaciation signifies the return of cold and arid and it is represented by high K2O/Al2O3 ratios and low CIA values ranging from 64-78. The previous genetic models of NIF by Klein (1993), Baldwin et al. (2012) and Lechte and Wallace (2015) provide an essential foundation for the development of a XIF genetic model. The genetic model of XIF proposes deposition on an open continental shelf characterized by a steady influx of detrital material. The seawater has been anoxic since the Paleoproterozoic and further induced by basin stagnation due to the ice covering the basin. Two overlapping oxidative stages are assumed for the precipitation of Fe and Mn across lateral redox gradients in the paleobasin. The exact oxidative pathways and mechanisms for the above processes remains unconstrained.
- Full Text:
- Date Issued: 2020
- Authors: Ntantiso, Mawande
- Date: 2020
- Subjects: Xaudum iron-formation , Iron ores -- Botswana , Formations (Geology) -- Botswana , Mineralogy -- Botswana , Paleoclimatology -- Proterozoic
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167211 , vital:41447
- Description: Banded iron-formations (BIF) formed in three different geological periods in the Earth’s history, namely the Archean, Paleoproterozoic and Neoproterozoic. Each of these periods has a corresponding index BIF type attributed to them. The oldest is the Archean Algoma-type BIF which is typically dominated by smaller-volume BIF deposits associated with volcanic rocks and greenstone belts. The next is the volumetrically far more abundant Superior-type BIF of the Paleoproterozoic lacking any obvious volcanic relation. The youngest BIFs were deposited after a hiatus of a billion years in the Neoproterozoic and are believed to be genetically linked to Marinoan ice-age. The global re-introduction and distribution of BIF in the Neoproterozoic highlights a shift in the Earth’s tectonics, climate, biosphere and ocean chemistry from the older Archean and Paleoproterozoic counterparts. Various models have been postulated by researchers in attempts to explain how Neoproterozoic iron-formations formed. In all the available models, the Snowball Earth Hypothesis initially proposed by Kirshvink (1992) is an overarching concept. In this study, four cores from the Neoproterozoic Xaudum iron-formation (XIF) in Ngamiland, northwest of Botswana, were sampled and analysed following a partnership between Postgraduate Research in Iron and Manganese Ore Resources (PRIMOR) and Tsodilo Resources Ltd. The study sets out to explore the mineralogy and chemistry of XIF in order to determine its origin, constrain the redox conditions in the paleo-basin, assess it in the context of other Neoproterozoic iron-formations and older Archean and Paleoproterozoic iron-formations, and inform metallurgical processing. The mineralogy of XIF consists of magnetite, quartz, amphibole, garnet, biotite and chlorite in decreasing abundance. This mineral assemblage is characteristic of medium grade metamorphosed iron-formations. Algoma and Superior-type BIFs which experienced late-diagenetic and very low-grade metamorphism have a complex mineral assemblage consisting of hematite, magnetite, quartz, and several carbonate (dolomite-ankerite series and siderite) and silicate phases (greenalite, riebeckite and stilpnomelane). The geochemical results show that XIF has higher Mn3O4 and Al2O3 average contents when compared to Algoma and Superior type BIF. The detrital components in XIF correlate with High Field Strength Elements (HFSE) suggesting increased delivery of siliciclastic material during deposition. This trend is comparable to other NIF deposits suggesting a global high input of siliciclastic material into Neoproterozoic paleodepositional environments. This trend is different from Archean and Paleoproterozoic BIF deposits which are close to pure chemical sediments lacking measurable detrital contributions. In the XIF, bulk-rock Mn3O4 and Al2O3 in drillcore SW have higher averages of 2.4 and 2.6 wt. % respectively, compared to the other three cores. The Mn3O4 shows a positive statistical relationship with Co, suggesting that Neoproterozoic oceans and atmosphere were possibly more oxic than in the Archean and Paleoproterozoic. The Mn3O4 shows an antithetic relationship with Fe2O3 suggesting that the paleobasin was chemically heterogeneous in terms of redox conditions, with Fe2O3 depositing presumably in deeper parts removed from a detrital source, and Mn3O4 depositing possibly more proximal to a paleo-shoreline in a shallower setting where there was higher delivery of siliciclastic material from the continent due to correspondingly higher Al2O3 and TiO2 contents. The REE patterns of XIF show positive-sloping trends of depletion in LREE and enrichment in HREE which resemble those of seawater. However, the REE slope becomes a lot flatter and resembles closer the signature of PAAS and adjacent diamictite facies, which agrees with the idea of high siliciclastic input in the paleobasin comparable to other NIF. XIF also appears to lack clear Ce or Eu anomalies. The lack of the former points to the oceans possibly not being oxic enough to drive the fractionation of Ce into Mn oxides like in the modern oceans, or that the Ce behaviour is obscured by the high siliciclastic input in XIF. Similarly, the lack of positive Eu anomaly shows a weak to absent hydrothermal signal into to modern shallow seawater where Fe and Si were sourced, or detritally derived REE contamination. Extensive weathering under hot and humid climate during glacial retreat is shown by the low K2O/Al2O3 ratios and high CIA values ranging from 80-99. Re-glaciation signifies the return of cold and arid and it is represented by high K2O/Al2O3 ratios and low CIA values ranging from 64-78. The previous genetic models of NIF by Klein (1993), Baldwin et al. (2012) and Lechte and Wallace (2015) provide an essential foundation for the development of a XIF genetic model. The genetic model of XIF proposes deposition on an open continental shelf characterized by a steady influx of detrital material. The seawater has been anoxic since the Paleoproterozoic and further induced by basin stagnation due to the ice covering the basin. Two overlapping oxidative stages are assumed for the precipitation of Fe and Mn across lateral redox gradients in the paleobasin. The exact oxidative pathways and mechanisms for the above processes remains unconstrained.
- Full Text:
- Date Issued: 2020
Molecular simulations of potential agents and targets of Alzheimer’s disease
- Authors: Carlisle, Tanya
- Date: 2020
- Subjects: Alzheimer's disease -- Treatment , Alzheimer's disease -- Molecular aspects , Amyloid beta-protein precurs , Amyloid beta-protein
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140025 , vital:37825
- Description: The World Alzheimer Report statedin 2016 that approximately 46.8 million people were living with dementia and this figure is expected to triple by 2050. Alzheimer’s Disease was discovered to be a precursor to dementia in 1976 and since then efforts to understand Alzheimer’s have been prioritized. To date, there are very few effective forms of treatment for Alzheimer’s, many are known to offer only mild calming of the symptoms and have side effects such as diarrhea, nausea, loss of appetite and sleep disturbances. This has been due to lack of understanding on how Alzheimer’s is caused. With the two main hallmarks of the disease now being more understood it has opened the doorway into the discovery of new treatments for this disease. This study focuses on the hallmark involving the aggregation of the β-amyloid protein to form plaques surrounding the neurons of the brain. Copper, Zinc and Iron have also been found in high concentrations in and surrounding these plaques. This study focused on the screening of the South African Natural Compound database (SANCDB) to discover hits that have potential destabilizing action against the Beta-amyloid aggregate. If one of these compounds could prove to have destabilizing action on the aggregate it could open the doorway to new potential forms of treatment. Over 700 SANCDB compounds were docked, and the top hits were taken to molecular dynamics to further study the interactions of the compounds and the aggregate. However, the hits identified had strong binding to the aggregate causing it to become stable instead of the desired effect of destabilizing the structure. This information, however, does not rule out the possibility of these compounds preventing the formation of the aggregates. Further, interactions of copper with β-amyloid and copper were determined by solubilizing the aggregate and introducing copper ions in a dynamics simulation. Possible interactions between copper and the methionine residues were visualised.
- Full Text:
- Date Issued: 2020
- Authors: Carlisle, Tanya
- Date: 2020
- Subjects: Alzheimer's disease -- Treatment , Alzheimer's disease -- Molecular aspects , Amyloid beta-protein precurs , Amyloid beta-protein
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140025 , vital:37825
- Description: The World Alzheimer Report statedin 2016 that approximately 46.8 million people were living with dementia and this figure is expected to triple by 2050. Alzheimer’s Disease was discovered to be a precursor to dementia in 1976 and since then efforts to understand Alzheimer’s have been prioritized. To date, there are very few effective forms of treatment for Alzheimer’s, many are known to offer only mild calming of the symptoms and have side effects such as diarrhea, nausea, loss of appetite and sleep disturbances. This has been due to lack of understanding on how Alzheimer’s is caused. With the two main hallmarks of the disease now being more understood it has opened the doorway into the discovery of new treatments for this disease. This study focuses on the hallmark involving the aggregation of the β-amyloid protein to form plaques surrounding the neurons of the brain. Copper, Zinc and Iron have also been found in high concentrations in and surrounding these plaques. This study focused on the screening of the South African Natural Compound database (SANCDB) to discover hits that have potential destabilizing action against the Beta-amyloid aggregate. If one of these compounds could prove to have destabilizing action on the aggregate it could open the doorway to new potential forms of treatment. Over 700 SANCDB compounds were docked, and the top hits were taken to molecular dynamics to further study the interactions of the compounds and the aggregate. However, the hits identified had strong binding to the aggregate causing it to become stable instead of the desired effect of destabilizing the structure. This information, however, does not rule out the possibility of these compounds preventing the formation of the aggregates. Further, interactions of copper with β-amyloid and copper were determined by solubilizing the aggregate and introducing copper ions in a dynamics simulation. Possible interactions between copper and the methionine residues were visualised.
- Full Text:
- Date Issued: 2020
Molecular simulations of potential agents and targets of Alzheimer’s disease
- Authors: Joli, Luxolo
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Ligands (Biochemistry) , Proteins -- Chemistry , Molecular dynamics -- Simulation methods
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146411 , vital:38523
- Description: Alzheimer's Disease (AD) is a neurodegenerative brain disorder that was first discovered in 1901 by Dr Aloïs Alzheimer and was later reported publicly in 1906. The German doctor had a 51-yearold woman patient called Auguste Deter, who was suffering from a rare brain disorder with early signs of memory loss and cognition. Alzheimer's Disease is the most common type of dementia that affects people with the age of 65 years and older. There is no single known cause of Alzheimer’s disease however, amyloid β-peptide (Aβ1–40/42) was found to be at the centre of AD pathogenesis and this connection was referred as “amyloid hypothesis”. It is suspected that an accumulation of amyloid β-peptide is a major contributor to neuronal dysfunction and degeneration. Alzheimer’s disease is complex and therefore, currently there is no medication available that treats the disease. However, there are approaches that focus on helping people maintain mental function, manage behavioral symptoms, and slow down the symptoms of disease. According to South Africa’s 2011 census, there are approximately 2.2 million people in South Africa with some form of dementia and therefore there is a need to find a treatment for the disease. This study aims to find agents and targets of Alzheimer’s Disease by using different computational techniques such as molecular modelling. The study will use compounds from the South African Compounds Database (SANCDB) and the following therapeutic targets α-, β- and γ-secretase, acetylcholinesterase, tau protein and neprilysin. A successful High-throughput Virtual Screening (HTVS) study to determine lead compounds was performed using a computational program called KNIME. Molecular docking was achieved with GLIDE as it allows for exhaustive ligand flexibility. The docking calculations were carried out using the high level of precision XP (extra precision) for enhanced docking accuracy. The binding affinities (docking scores) for the best bound ligands obtained from docking were in the order of -5 kcal/mol or less. The ligandSANC00370 was the best binding ligand against the protein 1J1C_B and had the best binding energy of -13.94 kcal/mol compared to others. The receptor-ligand complexes were analyzed using the interaction diagrams obtained from the Discovery Studio Visualizer and Maestro programs. Molecular Dynamics simulations were performed on the complexes obtained from docking to help in optimizing their interactions. The simulations were performed using the Desmond tool with the OPLS3 force field. 100 ns simulations were performed for six systems with the best docking score results epresenting each of the therapeutic targets and for the other complex systems, 50 ns simulations were performed. The Desmond simulations were analyzed using the Simulations Interaction Diagrams such as PL-RMSD, L-RMSF, P-RMSF, L-Torsions, P-SSE, LP-Contacts and L-Properties. Maestro was used to visualize the stability of the ligands in the active site during the simulation. All 13 Desmond simulations were successful however, there were 9 simulations which produced satisfactory results while the others were nsatisfactory. Based on the molecular docking and Molecular Dynamics results of this study, 9 potential targets and 6 potential agents were obtained successfully and can be studied further as therapeutics for Alzheimer’s Disease.
- Full Text:
- Date Issued: 2020
- Authors: Joli, Luxolo
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Ligands (Biochemistry) , Proteins -- Chemistry , Molecular dynamics -- Simulation methods
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146411 , vital:38523
- Description: Alzheimer's Disease (AD) is a neurodegenerative brain disorder that was first discovered in 1901 by Dr Aloïs Alzheimer and was later reported publicly in 1906. The German doctor had a 51-yearold woman patient called Auguste Deter, who was suffering from a rare brain disorder with early signs of memory loss and cognition. Alzheimer's Disease is the most common type of dementia that affects people with the age of 65 years and older. There is no single known cause of Alzheimer’s disease however, amyloid β-peptide (Aβ1–40/42) was found to be at the centre of AD pathogenesis and this connection was referred as “amyloid hypothesis”. It is suspected that an accumulation of amyloid β-peptide is a major contributor to neuronal dysfunction and degeneration. Alzheimer’s disease is complex and therefore, currently there is no medication available that treats the disease. However, there are approaches that focus on helping people maintain mental function, manage behavioral symptoms, and slow down the symptoms of disease. According to South Africa’s 2011 census, there are approximately 2.2 million people in South Africa with some form of dementia and therefore there is a need to find a treatment for the disease. This study aims to find agents and targets of Alzheimer’s Disease by using different computational techniques such as molecular modelling. The study will use compounds from the South African Compounds Database (SANCDB) and the following therapeutic targets α-, β- and γ-secretase, acetylcholinesterase, tau protein and neprilysin. A successful High-throughput Virtual Screening (HTVS) study to determine lead compounds was performed using a computational program called KNIME. Molecular docking was achieved with GLIDE as it allows for exhaustive ligand flexibility. The docking calculations were carried out using the high level of precision XP (extra precision) for enhanced docking accuracy. The binding affinities (docking scores) for the best bound ligands obtained from docking were in the order of -5 kcal/mol or less. The ligandSANC00370 was the best binding ligand against the protein 1J1C_B and had the best binding energy of -13.94 kcal/mol compared to others. The receptor-ligand complexes were analyzed using the interaction diagrams obtained from the Discovery Studio Visualizer and Maestro programs. Molecular Dynamics simulations were performed on the complexes obtained from docking to help in optimizing their interactions. The simulations were performed using the Desmond tool with the OPLS3 force field. 100 ns simulations were performed for six systems with the best docking score results epresenting each of the therapeutic targets and for the other complex systems, 50 ns simulations were performed. The Desmond simulations were analyzed using the Simulations Interaction Diagrams such as PL-RMSD, L-RMSF, P-RMSF, L-Torsions, P-SSE, LP-Contacts and L-Properties. Maestro was used to visualize the stability of the ligands in the active site during the simulation. All 13 Desmond simulations were successful however, there were 9 simulations which produced satisfactory results while the others were nsatisfactory. Based on the molecular docking and Molecular Dynamics results of this study, 9 potential targets and 6 potential agents were obtained successfully and can be studied further as therapeutics for Alzheimer’s Disease.
- Full Text:
- Date Issued: 2020
Nutrient removal and biofuel potential of MaB-floc biomass from an integrated algal pond system treating domestic sewage
- Authors: Sibelo, Linda
- Date: 2020
- Subjects: Biomass energy , Waste products as fuel , Algal biofuels , Sewage -- Purification -- Nutrient removal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144955 , vital:38395
- Description: Integrated algal pond systems (IAPS) are a passive water treatment technology derived from the Oswald designed advanced integrated wastewater pond systems (AIWPS®) and effect wastewater treatment based on biological activity of microorganisms within the system, solar energy and gravity. The technology consists of an advanced facultative pond (AFP), a series of interconnected high rate algal oxidation ponds (HRAOP) and algal settling ponds. The symbiotic relationship between microalgae and bacteria facilitated by paddlewheel mixing of HRAOP results in the formation of biomass aggregates known as MaB-flocs. MaB-floc formation enhances nutrient abstraction, gravitational sedimentation and separation from water hence forming two product streams; recyclable water and biomass, both with valorisation potential. This work aimed to determine the suitability of MaB-floc biomass generated in the HRAOP of an IAPS treating domestic sewage as feedstock for biofuel production based on the content of carbohydrate and lipid. Nutrient removal efficiency, biomass productivity and bulk lipid and carbohydrate concentration were monitored for two consecutive three-month periods in the winter and summer seasons of 2018/19. Maximum removal efficiencies of nitrogen and phosphorus were determined as 71% and 75% respectively, demonstrating the efficiency of IAPS as a wastewater treatment technology. MaB-floc biomass productivity in winter and summer was 9.4 g/m2/d and 16.5 g/m2/d respectively indicating the heavy influence of seasonal temperature, possibly day length, and solar irradiation on biomass productivity in the HRAOP. Summer productivity was lower than the maximum theoretical productivity of 25 g/m2/d possibly due to photoinhibition of photosynthesis as well as grazing pressures caused by the proliferation of rotifers mainly of the Brachionus genus. MaB-floc biomass consistently contained higher amounts of carbohydrate than lipid despite the changes in species dominance from Scenedesmus sp. and Desmodesmus sp. in winter to Pediastrum sp. in summer. Variations in MaB-floc biomass carbohydrate content were linked to changes in nitrogen concentration, mainly in the form of nitrates. Lower nitrogen concentration significantly increased the carbohydrate content of MaB-floc biomass from 17.5 ± 0.15% to 33.5 ± 0.3 % recorded in summer. In winter, biomass carbohydrate increased from 18.3 ± 1.2% to 35.8 ± 0.3%.To induce accumulation of carbohydrates through nitrogen starvation, isolated microalgal species native to the HRAOPs of the IAPS at Institute for Environmental Biotechnology Rhodes University(EBRU) were used. The outcome from the laboratory studies showed that carbon partitioning within isolated strains could be altered from carbohydrate to lipid which is more energy-rich. Hence, exploring the biodiesel production option using HRAOP MaB-floc biomass, which had a lipid content ranging between 12.1 ± 0.64 % and 13.9 ± 0.5 %, would require a preconditioning step in the form of nitrogen starvation to enhance its lipid content. Overall, the outcome of outdoor monitoring studies on biomass biochemical composition indicated that HRAOPs operating under natural environmental conditions preferentially generated a biomass rich in carbohydrate. Therefore, anaerobic digestion may be a more viable option for HRAOP MaB-floc biomass because of the high carbohydrate levels ranging between 24.9 ± 0.6 % and 25.6 ± 1.3 % of the dry MaB-floc biomass weight. Despite the low biomass C/N ratio (7.1 to 7.8), the MaB-floc biomass can be anaerobically co-digested with a higher C/N ratio (24) substrate such as in-pond digester sludge, to improve methane yields calculated to be between 0.31 m3 CH4/ kg MaB-floc biomass and 0.33 m3 CH4/ kg MaB-floc biomass. Anaerobic digestion of biomass also produces CO2 which can be recovered and added to HRAOPs to enhance MaB-floc biomass productivity while lowering greenhouse gas emissions from a wastewater treatment plant. The digestate from the anaerobic process, which is rich in nitrogen and phosphorus can be used as a biofertiliser. Thus, a potential MaB-floc biomass biorefinery consisting of biogas and bio-fertiliser pathways can be established using IAPS treating sewage as the platform technology. IAPS is a system designed to operate in a way that is passive and without substantial environmental impact but technological innovations and a reduction in the size of the system are required to make the technology more acceptable.
- Full Text:
- Date Issued: 2020
- Authors: Sibelo, Linda
- Date: 2020
- Subjects: Biomass energy , Waste products as fuel , Algal biofuels , Sewage -- Purification -- Nutrient removal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144955 , vital:38395
- Description: Integrated algal pond systems (IAPS) are a passive water treatment technology derived from the Oswald designed advanced integrated wastewater pond systems (AIWPS®) and effect wastewater treatment based on biological activity of microorganisms within the system, solar energy and gravity. The technology consists of an advanced facultative pond (AFP), a series of interconnected high rate algal oxidation ponds (HRAOP) and algal settling ponds. The symbiotic relationship between microalgae and bacteria facilitated by paddlewheel mixing of HRAOP results in the formation of biomass aggregates known as MaB-flocs. MaB-floc formation enhances nutrient abstraction, gravitational sedimentation and separation from water hence forming two product streams; recyclable water and biomass, both with valorisation potential. This work aimed to determine the suitability of MaB-floc biomass generated in the HRAOP of an IAPS treating domestic sewage as feedstock for biofuel production based on the content of carbohydrate and lipid. Nutrient removal efficiency, biomass productivity and bulk lipid and carbohydrate concentration were monitored for two consecutive three-month periods in the winter and summer seasons of 2018/19. Maximum removal efficiencies of nitrogen and phosphorus were determined as 71% and 75% respectively, demonstrating the efficiency of IAPS as a wastewater treatment technology. MaB-floc biomass productivity in winter and summer was 9.4 g/m2/d and 16.5 g/m2/d respectively indicating the heavy influence of seasonal temperature, possibly day length, and solar irradiation on biomass productivity in the HRAOP. Summer productivity was lower than the maximum theoretical productivity of 25 g/m2/d possibly due to photoinhibition of photosynthesis as well as grazing pressures caused by the proliferation of rotifers mainly of the Brachionus genus. MaB-floc biomass consistently contained higher amounts of carbohydrate than lipid despite the changes in species dominance from Scenedesmus sp. and Desmodesmus sp. in winter to Pediastrum sp. in summer. Variations in MaB-floc biomass carbohydrate content were linked to changes in nitrogen concentration, mainly in the form of nitrates. Lower nitrogen concentration significantly increased the carbohydrate content of MaB-floc biomass from 17.5 ± 0.15% to 33.5 ± 0.3 % recorded in summer. In winter, biomass carbohydrate increased from 18.3 ± 1.2% to 35.8 ± 0.3%.To induce accumulation of carbohydrates through nitrogen starvation, isolated microalgal species native to the HRAOPs of the IAPS at Institute for Environmental Biotechnology Rhodes University(EBRU) were used. The outcome from the laboratory studies showed that carbon partitioning within isolated strains could be altered from carbohydrate to lipid which is more energy-rich. Hence, exploring the biodiesel production option using HRAOP MaB-floc biomass, which had a lipid content ranging between 12.1 ± 0.64 % and 13.9 ± 0.5 %, would require a preconditioning step in the form of nitrogen starvation to enhance its lipid content. Overall, the outcome of outdoor monitoring studies on biomass biochemical composition indicated that HRAOPs operating under natural environmental conditions preferentially generated a biomass rich in carbohydrate. Therefore, anaerobic digestion may be a more viable option for HRAOP MaB-floc biomass because of the high carbohydrate levels ranging between 24.9 ± 0.6 % and 25.6 ± 1.3 % of the dry MaB-floc biomass weight. Despite the low biomass C/N ratio (7.1 to 7.8), the MaB-floc biomass can be anaerobically co-digested with a higher C/N ratio (24) substrate such as in-pond digester sludge, to improve methane yields calculated to be between 0.31 m3 CH4/ kg MaB-floc biomass and 0.33 m3 CH4/ kg MaB-floc biomass. Anaerobic digestion of biomass also produces CO2 which can be recovered and added to HRAOPs to enhance MaB-floc biomass productivity while lowering greenhouse gas emissions from a wastewater treatment plant. The digestate from the anaerobic process, which is rich in nitrogen and phosphorus can be used as a biofertiliser. Thus, a potential MaB-floc biomass biorefinery consisting of biogas and bio-fertiliser pathways can be established using IAPS treating sewage as the platform technology. IAPS is a system designed to operate in a way that is passive and without substantial environmental impact but technological innovations and a reduction in the size of the system are required to make the technology more acceptable.
- Full Text:
- Date Issued: 2020
Observations of diffuse radio emission in the Abell 773 galaxy cluster
- Authors: Sichone, Gift L
- Date: 2020
- Subjects: Galaxies -- Clusters -- Observations , Radio astronomy -- Observations , Astrophysics -- South Africa , Westerbork Radio Telescope , A773 galaxy cluster , Astronomy -- Observations , Radio sources (Astronomy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144945 , vital:38394
- Description: In this thesis, we present 18 and 21 cm observations of the A773 galaxy cluster observed with the Westerbork radio telescope. The final 18 and 21 cm images achieve a noise level of 0.018 mJy beam‾ 1 and 0.025 mJy beam-1 respectively. After subtracting the compact sources, the low resolution images show evidence of a radio halo at 18 cm, whereas its presence is more uncertain in the low resolution 21 cm images due the presence of residual sidelobes from bright sources. In the joint analysis of both frequencies, the radio halo has a 5.37 arcmin2 area with a 6.76 mJy flux density. Further observations and analysis are, however, required to fully characterize its properties.
- Full Text:
- Date Issued: 2020
- Authors: Sichone, Gift L
- Date: 2020
- Subjects: Galaxies -- Clusters -- Observations , Radio astronomy -- Observations , Astrophysics -- South Africa , Westerbork Radio Telescope , A773 galaxy cluster , Astronomy -- Observations , Radio sources (Astronomy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144945 , vital:38394
- Description: In this thesis, we present 18 and 21 cm observations of the A773 galaxy cluster observed with the Westerbork radio telescope. The final 18 and 21 cm images achieve a noise level of 0.018 mJy beam‾ 1 and 0.025 mJy beam-1 respectively. After subtracting the compact sources, the low resolution images show evidence of a radio halo at 18 cm, whereas its presence is more uncertain in the low resolution 21 cm images due the presence of residual sidelobes from bright sources. In the joint analysis of both frequencies, the radio halo has a 5.37 arcmin2 area with a 6.76 mJy flux density. Further observations and analysis are, however, required to fully characterize its properties.
- Full Text:
- Date Issued: 2020
Observations of diffuse radio emission in the Perseus Galaxy Cluster
- Authors: Mungwariri, Clemence
- Date: 2020
- Subjects: Galaxies -- Clusters , Radio sources (Astronomy) , Radio interferometers , Perseus Galaxy Cluster , Diffuse radio emission
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143325 , vital:38233
- Description: In this thesis we analysed Westerbork observations of the Perseus Galaxy Cluster at 1380 MHz. Observations consist of two different pointings, covering a total of ∼ 0.5 square degrees, one including the known mini halo and the source 3C 84, the other centred on the source 3C 83.1 B. We obtained images with 83 μJy beam⁻¹ and 240 μJy beam⁻¹ noise rms for the two pointings respectively. We achieved a 60000 : 1 dynamic range in the image containing the bright 3C 84 source. We imaged the mini halo surrounding 3C 84 at high sensitivity, measuring its diameter to be ∼140 kpc and its power 4 x 10²⁴ W Hz⁻¹. Its morphology agrees quite well with that observed at 240 MHz (e.g. Gendron-Marsolais et al., 2017). We measured the flux density of 3C 84 to be 20.5 ± 0.4 Jy at the 2007 epoch, consistent with a factor of ∼2 increase since the 1960s.
- Full Text:
- Date Issued: 2020
- Authors: Mungwariri, Clemence
- Date: 2020
- Subjects: Galaxies -- Clusters , Radio sources (Astronomy) , Radio interferometers , Perseus Galaxy Cluster , Diffuse radio emission
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143325 , vital:38233
- Description: In this thesis we analysed Westerbork observations of the Perseus Galaxy Cluster at 1380 MHz. Observations consist of two different pointings, covering a total of ∼ 0.5 square degrees, one including the known mini halo and the source 3C 84, the other centred on the source 3C 83.1 B. We obtained images with 83 μJy beam⁻¹ and 240 μJy beam⁻¹ noise rms for the two pointings respectively. We achieved a 60000 : 1 dynamic range in the image containing the bright 3C 84 source. We imaged the mini halo surrounding 3C 84 at high sensitivity, measuring its diameter to be ∼140 kpc and its power 4 x 10²⁴ W Hz⁻¹. Its morphology agrees quite well with that observed at 240 MHz (e.g. Gendron-Marsolais et al., 2017). We measured the flux density of 3C 84 to be 20.5 ± 0.4 Jy at the 2007 epoch, consistent with a factor of ∼2 increase since the 1960s.
- Full Text:
- Date Issued: 2020