A Systematic Visualisation Framework for Radio-Imaging Pipelines
- Authors: Andati, Lexy Acherwa Livoyi
- Date: 2021-04
- Subjects: Radio interferometers , Radio astronomy -- Data processing , Radio astronomy -- Data processing -- Software , Jupyter
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177338 , vital:42812
- Description: Pipelines for calibration and imaging of radio interferometric data produce many intermediate images and other data products (gain tables, etc.) These often contain valuable information about the quality of the data and the calibration, and can provide the user with valuable insights, if only visualised in the right way. However, the deluge of data that we’re experiencing with modern instruments means that most of these products are never looked at, and only the final images and data products are examined. Furthermore, the variety of imaging algorithms currently available, and the range of their options, means that very different results can be produced from the same set of original data. Proper understanding of this requires a systematic comparison that can be carried out both by individual users locally, and by the community globally. We address both problems by developing a systematic visualisation framework based around Jupyter notebooks, enriched with interactive plots based on the Bokeh and Datashader visualisation libraries. , Thesis (MSc) -- Faculty of Science, Department of Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Andati, Lexy Acherwa Livoyi
- Date: 2021-04
- Subjects: Radio interferometers , Radio astronomy -- Data processing , Radio astronomy -- Data processing -- Software , Jupyter
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177338 , vital:42812
- Description: Pipelines for calibration and imaging of radio interferometric data produce many intermediate images and other data products (gain tables, etc.) These often contain valuable information about the quality of the data and the calibration, and can provide the user with valuable insights, if only visualised in the right way. However, the deluge of data that we’re experiencing with modern instruments means that most of these products are never looked at, and only the final images and data products are examined. Furthermore, the variety of imaging algorithms currently available, and the range of their options, means that very different results can be produced from the same set of original data. Proper understanding of this requires a systematic comparison that can be carried out both by individual users locally, and by the community globally. We address both problems by developing a systematic visualisation framework based around Jupyter notebooks, enriched with interactive plots based on the Bokeh and Datashader visualisation libraries. , Thesis (MSc) -- Faculty of Science, Department of Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
Observations of cosmic re-ionisation with the Hydrogen Epoch of Reionization Array: simulations of closure phase spectra
- Authors: Charles, Ntsikelelo
- Date: 2021-04
- Subjects: Epoch of reionization , Space interferometry , Astronomy -- Observations , Closure phase spectra
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174470 , vital:42480
- Description: The 21 cm transition from neutral Hydrogen promises to be the best observational probe of the Epoch of Reionisation. It has driven the construction of the new generation of low frequency radio interferometric arrays, including the Hydrogen Epoch of Reionization Array (HERA). The main difficulty in measuring the 21 cm signal is the presence of bright foregrounds that require very accurate interferometric calibration. Thyagarajan et al. (2018) proposed the use of closure phase quantities as a means to detect the 21 cm signal, which has the advantage of being independent (to first order) from calibration errors and therefore, bypasses the need for accurate calibration. Closure phases are, however, affected by so-called direction dependent effects, e.g. the fact that the dishes - or antennas - of an interferometric array are not identical to each other and , therefore, yield different antenna primary beam responses. In this thesis, we investigate the impact of direction dependent effects on closure quantities and simulate the impact that primary antenna beams affected by mutual coupling have on the foreground closure phase and its power spectrum i.e. the power spectrum of the bispectrum phase (Thyagarajan et al., 2020). Our simulations show that primary beams affected by mutual coupling lead to an overall leakage of foreground power in the so-called EoR window, i.e. power from smooth-spectrum foregrounds is confined to low k modes. We quantified this effect and found that the leakage is up to ~ 8 orders magnitude higher than the case of an ideal beam at kǁ > 0:5 h Mpc-1. We also found that the foreground leakage is worse when edge antennas are included, as they have a more different primary beam compared to antennas at the centre of the array. The leakage magnitude is worse when bright foregrounds appear in the antenna sidelobes, as expected. Our simulations provide a useful framework to interpret observations and assess which power spectrum region is expected to be most contaminated by foreground power leakage.
- Full Text:
- Date Issued: 2021-04
- Authors: Charles, Ntsikelelo
- Date: 2021-04
- Subjects: Epoch of reionization , Space interferometry , Astronomy -- Observations , Closure phase spectra
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174470 , vital:42480
- Description: The 21 cm transition from neutral Hydrogen promises to be the best observational probe of the Epoch of Reionisation. It has driven the construction of the new generation of low frequency radio interferometric arrays, including the Hydrogen Epoch of Reionization Array (HERA). The main difficulty in measuring the 21 cm signal is the presence of bright foregrounds that require very accurate interferometric calibration. Thyagarajan et al. (2018) proposed the use of closure phase quantities as a means to detect the 21 cm signal, which has the advantage of being independent (to first order) from calibration errors and therefore, bypasses the need for accurate calibration. Closure phases are, however, affected by so-called direction dependent effects, e.g. the fact that the dishes - or antennas - of an interferometric array are not identical to each other and , therefore, yield different antenna primary beam responses. In this thesis, we investigate the impact of direction dependent effects on closure quantities and simulate the impact that primary antenna beams affected by mutual coupling have on the foreground closure phase and its power spectrum i.e. the power spectrum of the bispectrum phase (Thyagarajan et al., 2020). Our simulations show that primary beams affected by mutual coupling lead to an overall leakage of foreground power in the so-called EoR window, i.e. power from smooth-spectrum foregrounds is confined to low k modes. We quantified this effect and found that the leakage is up to ~ 8 orders magnitude higher than the case of an ideal beam at kǁ > 0:5 h Mpc-1. We also found that the foreground leakage is worse when edge antennas are included, as they have a more different primary beam compared to antennas at the centre of the array. The leakage magnitude is worse when bright foregrounds appear in the antenna sidelobes, as expected. Our simulations provide a useful framework to interpret observations and assess which power spectrum region is expected to be most contaminated by foreground power leakage.
- Full Text:
- Date Issued: 2021-04
An assessment of the wild cyclopia subternata (vleitee) resource
- Authors: Van der Walt, Wouter
- Date: 2021-04
- Subjects: Legumes -- South Africa , Fynbos -- South Africa , Fynbos ecology -- South Africa , Fynbos -- Harvesting -- South Africa , Biodiversity conservation -- South Africa , Traditional ecological knowledge -- South Africa , Wild Cyclopia Subternata (Vleitee) , Honeybush tea industry
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176874 , vital:42767
- Description: Cyclopia spp. is used for the production of Honeybush tea, an herbal tea which is used in many cases as a substitute for rooibos tea. The wild harvesting of this fynbos plant still brings in up to 85% of the annual crop and as such needs to be carefully monitored in order to avoid over harvesting and the destruction of biodiversity within the Eastern and Western Cape mountain regions of Southern Africa. Due to the concerns of overharvesting and unsuitable use of the wild resource issues of supply security have been raised. There is a lack of formal knowledge relating to the plant, its harvesting, the industry and its economic potential. This study aimed to amend this scarcity by contributing to the knowledge of C. subternata as a wild harvested plant, the physical environment favoured by C. subternata, sustainable use through harvesting of the wild plant and harvesting methods specific to this honeybush species. The research concludes by presenting a guideline for best harvest practices of the wild C. subternata plant. , Thesis (MSc) -- Faculty of Science, Department of Geography, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Van der Walt, Wouter
- Date: 2021-04
- Subjects: Legumes -- South Africa , Fynbos -- South Africa , Fynbos ecology -- South Africa , Fynbos -- Harvesting -- South Africa , Biodiversity conservation -- South Africa , Traditional ecological knowledge -- South Africa , Wild Cyclopia Subternata (Vleitee) , Honeybush tea industry
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176874 , vital:42767
- Description: Cyclopia spp. is used for the production of Honeybush tea, an herbal tea which is used in many cases as a substitute for rooibos tea. The wild harvesting of this fynbos plant still brings in up to 85% of the annual crop and as such needs to be carefully monitored in order to avoid over harvesting and the destruction of biodiversity within the Eastern and Western Cape mountain regions of Southern Africa. Due to the concerns of overharvesting and unsuitable use of the wild resource issues of supply security have been raised. There is a lack of formal knowledge relating to the plant, its harvesting, the industry and its economic potential. This study aimed to amend this scarcity by contributing to the knowledge of C. subternata as a wild harvested plant, the physical environment favoured by C. subternata, sustainable use through harvesting of the wild plant and harvesting methods specific to this honeybush species. The research concludes by presenting a guideline for best harvest practices of the wild C. subternata plant. , Thesis (MSc) -- Faculty of Science, Department of Geography, 2021
- Full Text:
- Date Issued: 2021-04
Photodynamic antimicrobial chemotherapy against Staphylococcus aureus and Escherichia coli sensitized using indium (III) cationic porphyrins linked to core-shell magnetic nanoparticles
- Authors: Makola, Lekgowa Collen
- Date: 2021-04
- Subjects: Photochemotherapy , Photosensitizing compounds , Staphylococcus aureus , Escherichia coli , Indium , Porphyrins , Magnetic nanoparticles , Quaternize
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177225 , vital:42801
- Description: Photodynamic antimicrobial chemotherapy (PACT) is a well-known antimicrobial therapy technique used against multi-drug resistant pathogens. In this study, the syntheses, characterization, photophysicochemical properties, and the applications of symmetrically and asymmetrically substituted cationic indium (III) porphyrins linked to silver/copper ferrite core-shell (Ag/CuFe2O4) magnetic nanoparticles (MNPs) as potential photosensitizers for PACT are reported. The synthesized complexes include axially modified porphyrins quaternized through an axial ligand. All the asymmetrically substituted porphyrins were linked to the NPs via an ester bond and the symmetrically substituted porphyrins were linked (peripherally and /or axially) via self-assembly (Ag-S and/or Ag-N). The impact of axial modification, peripheral substituents, conjugation to the NPs, the number of positive charges, and the chain length of the alkyl halides quaternizing agents on PACT efficacy and photophysicochemical properties of porphyrins were studied. High singlet oxygen quantum yields and antimicrobial log reductions were observed. Lipophilicity and hydrophilicity of the porphyrins were also studies, where the complexes quaternized with methyl iodide showed relatively high hydrophilicity character. Upon in vitro PACT studies, the quaternized complexes were observed to have 0% viable colony, signifying their effectiveness. Moreover, the highest log reductions of 9.27 were observed against S. aureus and 9.58 were observed against E. coli. The findings from this work delineate that singlet oxygen generation alone is not a distinct factor on the PACT efficacy of the porphyrin complexes, since some of the complexes have practically the same singlet oxygen quantum but different PACT activity. However, other contributing factors including water solubility play a significant role. , Thesis (MSc) -- Faculty of Science, Department of Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Makola, Lekgowa Collen
- Date: 2021-04
- Subjects: Photochemotherapy , Photosensitizing compounds , Staphylococcus aureus , Escherichia coli , Indium , Porphyrins , Magnetic nanoparticles , Quaternize
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177225 , vital:42801
- Description: Photodynamic antimicrobial chemotherapy (PACT) is a well-known antimicrobial therapy technique used against multi-drug resistant pathogens. In this study, the syntheses, characterization, photophysicochemical properties, and the applications of symmetrically and asymmetrically substituted cationic indium (III) porphyrins linked to silver/copper ferrite core-shell (Ag/CuFe2O4) magnetic nanoparticles (MNPs) as potential photosensitizers for PACT are reported. The synthesized complexes include axially modified porphyrins quaternized through an axial ligand. All the asymmetrically substituted porphyrins were linked to the NPs via an ester bond and the symmetrically substituted porphyrins were linked (peripherally and /or axially) via self-assembly (Ag-S and/or Ag-N). The impact of axial modification, peripheral substituents, conjugation to the NPs, the number of positive charges, and the chain length of the alkyl halides quaternizing agents on PACT efficacy and photophysicochemical properties of porphyrins were studied. High singlet oxygen quantum yields and antimicrobial log reductions were observed. Lipophilicity and hydrophilicity of the porphyrins were also studies, where the complexes quaternized with methyl iodide showed relatively high hydrophilicity character. Upon in vitro PACT studies, the quaternized complexes were observed to have 0% viable colony, signifying their effectiveness. Moreover, the highest log reductions of 9.27 were observed against S. aureus and 9.58 were observed against E. coli. The findings from this work delineate that singlet oxygen generation alone is not a distinct factor on the PACT efficacy of the porphyrin complexes, since some of the complexes have practically the same singlet oxygen quantum but different PACT activity. However, other contributing factors including water solubility play a significant role. , Thesis (MSc) -- Faculty of Science, Department of Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
Physical activity, physical fitness, sedentary behaviour and screen time profiles of primary school children in a school within the Makana Municipality, Eastern Cape, South Africa
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Date Issued: 2021-04
Inhibitor search and variant analysis of Acetylcholinesterase
- Authors: Ras, Harnaud
- Date: 2021-04
- Subjects: Acetylcholinesterase , Alzheimer's disease , Acetylcholinesterase -- Inhibitors , Alzheimer's disease -- Chemotherapy , Cerebrovascular disease -- Treatment , Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178191 , vital:42919
- Description: Acetylcholinesterase (AChE) inhibition is used to treat Alzheimer's disease by increasing the availability of acetylcholine to carry nerve signals in the brain. The response to this treatment varies widely, which may be due to altered affnity to the current drugs caused by genetic variation. Various negative side-effects limit their use. As this is one of the only available therapeutic drug targets to treat Alzheimer's disease, decreasing the negative effects is of great importance. AChE is involved in biological processes that occur after acute ischemic stroke. Stroke is the third leading cause of death worldwide, and 87% of all stroke cases belong to ischemic stroke. AchEI (cholinesterase inhibitors) have been suggested to have properties that lower the risk of stroke. AChE is one of 15 verified drug targets under study for treatment of stroke. In addition to Alzheimer's disease and stroke, Lewy body disease (LBD) may be treated using cholinesterase inhibitors. The goals of this study are to find inhibitors that can potentially be used to treat Alzheimer's disease and/or stroke and to investigate variants which may affect protein dynamics and function. Two variants were analyzed, P247L and T229S. Molecular simulation of the P247L variant resulted in a disruption in protein dynamics in comparison to the wildtype. A total of 5728 molecules were screened and 10 nanosecond simulations were used to narrow down the set of compounds. The four best performing molecules were simulated for 10 nanoseconds. MM-PBSA was performed to identify molecules with high binding free energies. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Ras, Harnaud
- Date: 2021-04
- Subjects: Acetylcholinesterase , Alzheimer's disease , Acetylcholinesterase -- Inhibitors , Alzheimer's disease -- Chemotherapy , Cerebrovascular disease -- Treatment , Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178191 , vital:42919
- Description: Acetylcholinesterase (AChE) inhibition is used to treat Alzheimer's disease by increasing the availability of acetylcholine to carry nerve signals in the brain. The response to this treatment varies widely, which may be due to altered affnity to the current drugs caused by genetic variation. Various negative side-effects limit their use. As this is one of the only available therapeutic drug targets to treat Alzheimer's disease, decreasing the negative effects is of great importance. AChE is involved in biological processes that occur after acute ischemic stroke. Stroke is the third leading cause of death worldwide, and 87% of all stroke cases belong to ischemic stroke. AchEI (cholinesterase inhibitors) have been suggested to have properties that lower the risk of stroke. AChE is one of 15 verified drug targets under study for treatment of stroke. In addition to Alzheimer's disease and stroke, Lewy body disease (LBD) may be treated using cholinesterase inhibitors. The goals of this study are to find inhibitors that can potentially be used to treat Alzheimer's disease and/or stroke and to investigate variants which may affect protein dynamics and function. Two variants were analyzed, P247L and T229S. Molecular simulation of the P247L variant resulted in a disruption in protein dynamics in comparison to the wildtype. A total of 5728 molecules were screened and 10 nanosecond simulations were used to narrow down the set of compounds. The four best performing molecules were simulated for 10 nanoseconds. MM-PBSA was performed to identify molecules with high binding free energies. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
Biology, ecology and management of the Keurboom moth, Leto venus Cramer and the leafhopper Molopopterus sp. Jacobi in cultivated Honeybush (Cyclopia spp.)
- Authors: Mushore, Tapiwa Gift
- Date: 2021-04
- Subjects: Legumes , Legumes -- Diseases and pests , Hepialidae , Leafhoppers , Pests -- Biological control , Entomopathogenic fungi , Leafhoppers -- Biological control , Hepialidae -- Biological control , Keurboom moth (Leto venus Cramer) , Molopopterus sp. Jacobi , Honeybush (Cyclopia spp.)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177125 , vital:42792
- Description: Honeybush, Cyclopia spp. Vent (Fabaceae), farmers have raised pest concerns following commercial cultivation. The Keurboom moth Leto venus Cramer (Lepidoptera: Hepialidae) and the leafhopper Molopopterus sp. Jacobi (Hemiptera: Cicadellidae), are two of the major pests identified in cultivated Honeybush. Laboratory and field studies were conducted to gain an understanding of the biology of these two pests to inform future pest management solutions. Additionally, entomopathogenic fungi were isolated from Honeybush farms and screened for virulence against Molopopterus sp. as a possible management strategy. This study showed that the L. venus infestation on Honeybush was a product of four fixed effects; stem diameter, species of Cyclopia, Farm location and age of the plants. Cyclopia subternata, had the highest likelihood of infestation. Increase in age of the plants resulted in an increase in the stem diameter and therefore a higher probability of infestation. Stem diameter was also shown to be a significant predictor of infestation likelihood. Infestation severity, determined by the number of larvae per plant, was shown to be influenced by three fixed effects; stem diameter, plant species and Farm location. The results also showed that L. venus prefers to initiate penetration at, or just aboveground level. Laboratory studies showed that the leafhopper Molopopterus sp. undergoes five nymphal instars with an average egg incubation time of 20 days, development time from 1st instar to adult of 26 days and average generation time of 47 days. Laboratory experiments revealed variations in host preference by the leafhopper over a period of 15 days. Cyclopia longifolia was identified to be the most preferred species for feeding compared to the two other commonly cultivated species, C. subternata and C. maculata. The results were consistent with those obtained from the field survey which showed that leafhopper density was influenced by four fixed effects; plant species, age of the plant, Farm location and harvesting practices. There were significant differences in leafhopper density in different species with C. longifolia having the highest number of leafhoppers per plant. There were differences in leafhopper density in different farms as 57% of the sampled farms had leafhopper infestations, of these farms, Lodestone and Kurland had the highest leafhopper densities. Harvested plants were shown to have significantly higher leafhopper density than non-harvested plants. Age was also shown to influence leafhopper density, which reduced with an increase in the age of the plants. A total of 20 fungal isolates were recovered from 98 soil samples of which 70% were from Honeybush fields and 30% were from surrounding refugia. Fusarium oxysporum isolates comprised 20% of the recovered isolates, with Metarhizium anisopliae isolates making up the remainder. Laboratory bioassays against adults and nymphs of the leafhopper, Molopopterus sp., showed that F. oxysporum isolates induced 10 – 45% mortality and M. anisopliae isolates induce 30 – 80% mortality. Metarhizium anisopliae isolates J S1, KF S3, KF S11, KF S13, LS1 and LS2 were the most virulent and induced over 60% mortality in both Molopopterus sp. nymphs and adults. The results of this study showed pest preference towards different Cyclopia species. As such, they should be managed differently. Furthermore, L. venus was observed to occur in low densities, hence, it cannot be considered a major pest. However, Molopopterus sp. recorded high population densities making it a major pest in Honeybush production. Positive results indicated that some of the isolated fungal isolates have potential for control, an avenue worth investigating further. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Mushore, Tapiwa Gift
- Date: 2021-04
- Subjects: Legumes , Legumes -- Diseases and pests , Hepialidae , Leafhoppers , Pests -- Biological control , Entomopathogenic fungi , Leafhoppers -- Biological control , Hepialidae -- Biological control , Keurboom moth (Leto venus Cramer) , Molopopterus sp. Jacobi , Honeybush (Cyclopia spp.)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177125 , vital:42792
- Description: Honeybush, Cyclopia spp. Vent (Fabaceae), farmers have raised pest concerns following commercial cultivation. The Keurboom moth Leto venus Cramer (Lepidoptera: Hepialidae) and the leafhopper Molopopterus sp. Jacobi (Hemiptera: Cicadellidae), are two of the major pests identified in cultivated Honeybush. Laboratory and field studies were conducted to gain an understanding of the biology of these two pests to inform future pest management solutions. Additionally, entomopathogenic fungi were isolated from Honeybush farms and screened for virulence against Molopopterus sp. as a possible management strategy. This study showed that the L. venus infestation on Honeybush was a product of four fixed effects; stem diameter, species of Cyclopia, Farm location and age of the plants. Cyclopia subternata, had the highest likelihood of infestation. Increase in age of the plants resulted in an increase in the stem diameter and therefore a higher probability of infestation. Stem diameter was also shown to be a significant predictor of infestation likelihood. Infestation severity, determined by the number of larvae per plant, was shown to be influenced by three fixed effects; stem diameter, plant species and Farm location. The results also showed that L. venus prefers to initiate penetration at, or just aboveground level. Laboratory studies showed that the leafhopper Molopopterus sp. undergoes five nymphal instars with an average egg incubation time of 20 days, development time from 1st instar to adult of 26 days and average generation time of 47 days. Laboratory experiments revealed variations in host preference by the leafhopper over a period of 15 days. Cyclopia longifolia was identified to be the most preferred species for feeding compared to the two other commonly cultivated species, C. subternata and C. maculata. The results were consistent with those obtained from the field survey which showed that leafhopper density was influenced by four fixed effects; plant species, age of the plant, Farm location and harvesting practices. There were significant differences in leafhopper density in different species with C. longifolia having the highest number of leafhoppers per plant. There were differences in leafhopper density in different farms as 57% of the sampled farms had leafhopper infestations, of these farms, Lodestone and Kurland had the highest leafhopper densities. Harvested plants were shown to have significantly higher leafhopper density than non-harvested plants. Age was also shown to influence leafhopper density, which reduced with an increase in the age of the plants. A total of 20 fungal isolates were recovered from 98 soil samples of which 70% were from Honeybush fields and 30% were from surrounding refugia. Fusarium oxysporum isolates comprised 20% of the recovered isolates, with Metarhizium anisopliae isolates making up the remainder. Laboratory bioassays against adults and nymphs of the leafhopper, Molopopterus sp., showed that F. oxysporum isolates induced 10 – 45% mortality and M. anisopliae isolates induce 30 – 80% mortality. Metarhizium anisopliae isolates J S1, KF S3, KF S11, KF S13, LS1 and LS2 were the most virulent and induced over 60% mortality in both Molopopterus sp. nymphs and adults. The results of this study showed pest preference towards different Cyclopia species. As such, they should be managed differently. Furthermore, L. venus was observed to occur in low densities, hence, it cannot be considered a major pest. However, Molopopterus sp. recorded high population densities making it a major pest in Honeybush production. Positive results indicated that some of the isolated fungal isolates have potential for control, an avenue worth investigating further. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
Baculovirus synergism for improved management of false codling moth Thaumatotibia leucotreta Meyr. (Lepidoptera: Tortricidae)
- Authors: Taylor, David Graham
- Date: 2021-04
- Subjects: Baculoviruses , Cryptophlebia leucotreta , Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Codling moth , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176942 , vital:42774
- Description: Baculoviruses are an environmentally friendly and effective agent for managing lepidopteran pests. This includes the management of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a serious pest of citrus in Southern Africa and a major threat to the South African citrus export industry. For more than 15 years, CrleGV-SA- based biopesticides have been used as part of an integrated pest management strategy for the control of T. leucotreta in citrus orchards in South Africa, under the names Cryptogran™ and Cryptex®. While these biopesticides have been effective during this period, there are some areas in which baculovirus use could potentially be improved. Baculoviruses are notoriously slow to kill in comparison to chemical-based pesticides, and lately, pest resistance to baculoviruses has become a major concern with the development of resistance by Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) to its granulovirus occurring in the field in Europe. The consistent use of CrleGV-SA for more than 15 years in the field has raised concern that T. leucotreta could develop resistance to this virus, and has made it necessary to alter baculovirus-based management strategies to prevent this from occurring. A second baculovirus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV), has recently been isolated and was shown to be effective against T. leucotreta. However, the interactions between CrleGV-SA and CrpeNPV are not yet understood and so it is important to test these interactions before both viruses are applied on the same orchards. Not only is it important to know whether these viruses could negatively impact each other, but it is also important to test whether they could interact synergistically. A synergistic interaction could not only provide a potential tool for the management of resistance, but it could also be exploited to improve baculovirus-based management of T. leucotreta. In this study, a stock of CrleGV-SA was purified by glycerol gradient centrifugation from T. leucotreta cadavers, while a stock of CrpeNPV purified from Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae) cadavers was provided by River Bioscience (Pty) Ltd. These stocks were screened for purity by a multiplex polymerase chain reaction (mPCR) protocol designed to detect CrleGV-SA and CrpeNPV. The occlusion body (OB) density was then calculated using darkfield microscopy and a counting chamber. Both stocks were shown to be pure within the limits of the mPCR protocol, and the CrleGV-SA and CrpeNPV stocks were calculated to contain 3.08 × 1011 OBs/mL and 1.92 × 1011 OBs/mL respectively The first aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the dose mortality, in terms of lethal concentration. This was calculated using 7-day surface-dose biological assays for each virus and a 1:1 mixture of OBs of the two against T. leucotreta neonates. The lethal concentrations of each treatment required to kill 50 % of larvae (LC50) and 90 % of larvae (LC90) for each treatment were then calculated and compared using a probit regression. The mixed infection performed significantly better than either virus by itself, while each virus by itself did not differ significantly from the other. The LC50 for CrleGV-SA, CrpeNPV and the mixed infection were 1.53 × 104 OBs/mL, 1.15 × 104 OBs/mL and 4.38 × 103 OBs/mL respectively. The LC90 of CrleGV-SA, CrpeNPV and the mixed infection were calculated to be 4.10 × 105 OBs/mL, 1.05 × 105 OBs/mL, and 4.09 × 104 OBs/mL respectively. The second aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the speed of kill. A time-response biological assay protocol was created that allowed for effective observation of the larvae. This was then used to generate time-mortality data that were analysed by a logit regression function to calculate and compare the treatments at the time of 50 % larval mortality (LT50) and the time of 90 % mortality (LT90). Each virus by itself did not differ significantly from the other, while the mixed infection took significantly longer to kill 50 % and 90 % of the larvae, suggesting that there is competition for resources between viruses during the secondary, systemic phase of infection. The LT50 for CrleGV-SA, CrpeNPV and the mixed infection were 117.5 hours, 113.5 hours and 139.0 hours respectively. The LT90 for CrleGV-SA, CrpeNPV and the mixed infection were 153.2 hours, 159.3, and 193.4 hours respectively. Finally, the composition of OBs recovered from the cadavers produced by the time-response biological assays were investigated by mPCR. A method for extracting gDNA from OBs in neonate-sized T. leucotreta larvae is described. The presence of CrpeNPV along with CrleGV-SA was noted in 4 out of 9 larvae inoculated with only CrleGV-SA. The presence of CrleGV-SA as well as CrpeNPV was noted in all but one larva inoculated with only CrpeNPV, and both CrleGV-SA and CrpeNPV were noted in all but one larva inoculated with a 1:1 mixture of the two, with one larva only being positive for CrleGV-SA. This suggests either stock contamination or the presence of covert infections of CrleGV-SA and CrpeNPV in the T. leucotreta population used in this study. This is the second study to report an improved lethal concentration of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates, and the first study to report the slower speed of kill of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates. While the improved lethal concentration of the mixed infection is a promising step in the future improvement of baculovirus-based biopesticides, it is at the cost of a slower speed of kill. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Taylor, David Graham
- Date: 2021-04
- Subjects: Baculoviruses , Cryptophlebia leucotreta , Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Codling moth , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176942 , vital:42774
- Description: Baculoviruses are an environmentally friendly and effective agent for managing lepidopteran pests. This includes the management of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a serious pest of citrus in Southern Africa and a major threat to the South African citrus export industry. For more than 15 years, CrleGV-SA- based biopesticides have been used as part of an integrated pest management strategy for the control of T. leucotreta in citrus orchards in South Africa, under the names Cryptogran™ and Cryptex®. While these biopesticides have been effective during this period, there are some areas in which baculovirus use could potentially be improved. Baculoviruses are notoriously slow to kill in comparison to chemical-based pesticides, and lately, pest resistance to baculoviruses has become a major concern with the development of resistance by Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) to its granulovirus occurring in the field in Europe. The consistent use of CrleGV-SA for more than 15 years in the field has raised concern that T. leucotreta could develop resistance to this virus, and has made it necessary to alter baculovirus-based management strategies to prevent this from occurring. A second baculovirus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV), has recently been isolated and was shown to be effective against T. leucotreta. However, the interactions between CrleGV-SA and CrpeNPV are not yet understood and so it is important to test these interactions before both viruses are applied on the same orchards. Not only is it important to know whether these viruses could negatively impact each other, but it is also important to test whether they could interact synergistically. A synergistic interaction could not only provide a potential tool for the management of resistance, but it could also be exploited to improve baculovirus-based management of T. leucotreta. In this study, a stock of CrleGV-SA was purified by glycerol gradient centrifugation from T. leucotreta cadavers, while a stock of CrpeNPV purified from Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae) cadavers was provided by River Bioscience (Pty) Ltd. These stocks were screened for purity by a multiplex polymerase chain reaction (mPCR) protocol designed to detect CrleGV-SA and CrpeNPV. The occlusion body (OB) density was then calculated using darkfield microscopy and a counting chamber. Both stocks were shown to be pure within the limits of the mPCR protocol, and the CrleGV-SA and CrpeNPV stocks were calculated to contain 3.08 × 1011 OBs/mL and 1.92 × 1011 OBs/mL respectively The first aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the dose mortality, in terms of lethal concentration. This was calculated using 7-day surface-dose biological assays for each virus and a 1:1 mixture of OBs of the two against T. leucotreta neonates. The lethal concentrations of each treatment required to kill 50 % of larvae (LC50) and 90 % of larvae (LC90) for each treatment were then calculated and compared using a probit regression. The mixed infection performed significantly better than either virus by itself, while each virus by itself did not differ significantly from the other. The LC50 for CrleGV-SA, CrpeNPV and the mixed infection were 1.53 × 104 OBs/mL, 1.15 × 104 OBs/mL and 4.38 × 103 OBs/mL respectively. The LC90 of CrleGV-SA, CrpeNPV and the mixed infection were calculated to be 4.10 × 105 OBs/mL, 1.05 × 105 OBs/mL, and 4.09 × 104 OBs/mL respectively. The second aspect of the interaction between CrleGV-SA and CrpeNPV that was investigated was the speed of kill. A time-response biological assay protocol was created that allowed for effective observation of the larvae. This was then used to generate time-mortality data that were analysed by a logit regression function to calculate and compare the treatments at the time of 50 % larval mortality (LT50) and the time of 90 % mortality (LT90). Each virus by itself did not differ significantly from the other, while the mixed infection took significantly longer to kill 50 % and 90 % of the larvae, suggesting that there is competition for resources between viruses during the secondary, systemic phase of infection. The LT50 for CrleGV-SA, CrpeNPV and the mixed infection were 117.5 hours, 113.5 hours and 139.0 hours respectively. The LT90 for CrleGV-SA, CrpeNPV and the mixed infection were 153.2 hours, 159.3, and 193.4 hours respectively. Finally, the composition of OBs recovered from the cadavers produced by the time-response biological assays were investigated by mPCR. A method for extracting gDNA from OBs in neonate-sized T. leucotreta larvae is described. The presence of CrpeNPV along with CrleGV-SA was noted in 4 out of 9 larvae inoculated with only CrleGV-SA. The presence of CrleGV-SA as well as CrpeNPV was noted in all but one larva inoculated with only CrpeNPV, and both CrleGV-SA and CrpeNPV were noted in all but one larva inoculated with a 1:1 mixture of the two, with one larva only being positive for CrleGV-SA. This suggests either stock contamination or the presence of covert infections of CrleGV-SA and CrpeNPV in the T. leucotreta population used in this study. This is the second study to report an improved lethal concentration of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates, and the first study to report the slower speed of kill of a mixed infection of CrleGV-SA and CrpeNPV against T. leucotreta neonates. While the improved lethal concentration of the mixed infection is a promising step in the future improvement of baculovirus-based biopesticides, it is at the cost of a slower speed of kill. , Thesis (MSc) -- Faculty of Science, Department of Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
Detection and effects of selected pharmaceutical compounds from selected water bodies in the Eastern Cape Province, South Africa
- Authors: Setshedi, Koketso Josinah
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177074 , vital:42788
- Description: Theses embargoed. Release date March 2023. , Thesis (MSc) -- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Setshedi, Koketso Josinah
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177074 , vital:42788
- Description: Theses embargoed. Release date March 2023. , Thesis (MSc) -- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
The effect of plant-derived dietary protein sources on cultured abalone Haliotis midae (L. 1758) digestive physiology
- Authors: Wright, Jason Geoffrey
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa , Haliotis midae -- Nutrition -- South Africa , Haliotis midae -- Physiology -- South Africa , Haliotis midae -- South Africa -- Growth , Haliotis midae -- Digestive organs , Abalone culture -- South Africa , Plant proteins as feed
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176803 , vital:42760
- Description: The growth and feed conversion ratio of farmed abalone Haliotis midae (L. 1758) fed a formulated diet varies in feeds with different protein sources. To better understand this, the effect that various combinations of dietary soybean meal (SBM), sunflower meal (SFM) and fishmeal (FM) had on the digestive efficiency of farmed H. midae when included in a formulated feed, were assessed. The aim of this study was to investigate the effect that plant-based proteins had on abalone digestion and gut-bacterial profile of cultured adult abalone when combined with fishmeal. This was done by analysing the chymotrypsin (protease) and cellulase (carbohydrase) digestive enzyme activities from whole-gut sections of farmed abalone that were fed one of four diets for 12 months: FM-only, SBM-only, fishmeal and soybean meal (FM-SBM), and fishmeal and sunflower meal (FM-SFM). There were significant interactions between the diets, sampling date, and sex of the abalone, which had an influence on the cellulase activities in the digestive tracts of the animals. Those fed the SBM diet had the highest cellulase activity by the end of the sampling period (ANOVA; df = 9; F = 2.9; P = 0.005). The significant interactions between diet and sampling date influenced the chymotrypsin activities of abalone. Animals fed the FM diet had the highest activity of chymotrypsin for most of the sampling period (ANOVA; df = 9; F = 2.5; P = 0.01). Therefore, diet did have an impact on the cellulase and chymotrypsin activities of abalone fed either combination diets (FM-SBM; FM-SFM) or single protein diets (FM; SBM). The presence of plant material such as cellulose fibres in the diets containing plant proteins may have influenced the cellulase activity levels of each treatment as it would have stimulated endogenous and exogenous cellulase production. However, treatments with the highest crude fibre content, SBM and FM-SFM, resulted in differing activities. The activity levels of chymotrypsin may have been impacted by the protein type, presence of protein inhibitors and temporal changes in utilisation. Abalone fed the FM diet exhibited the highest chymotrypsin activities on sampling day 182, which was in summer. Animals fed the treatment diets containing fishmeal also developed their reproductive tissues, and may explain the low chymotrypsin activities in abalone fed SBM-only. Additionally, the presence of allergenic compounds would have influenced enzyme activity, as they would have negatively affected the nutrient utilisation and absorptive capacity. Fluctuations in water temperature may have had an effect on enzyme activity, as activities were highest during summer, when seawater temperatures are most variable. A change to lowered water temperatures are known to trigger the growth of digestive epithelial tissue in abalone to allow for increased enzyme secretions and nutrient absorption (Schaeffer et al. 2013). The effect that plant protein inclusion in abalone diets had on the gut-microbiota was revealed by analysing the differences in gut-bacterial community profiles, through the use of metagenomic sequencing. The relative abundance of the phylum Verrucomicrobia, class Verrcomicrobiae and the genus Rubritalea were highest in the SBM diet. These bacterial groups were also influenced by the plant material from soybean meal, as hydrolysed cellulose is broken down by cellulases, and allowed for the proliferation of Rubritalea bacteria due to them using cellobiose as an energy source. The presence of Bacteroidetes was due to the phyla having bacterial species that can breakdown proteins and species that can break down carbohydrates. The animal protein present in the composition of the FM diet had a positive influence on proteolytic Bacteroidetes growth. The high levels of cellulose from the plant fibres in the soybean meal-only diet (SBM) promoted growth of saccharolytic Bacteroidetes. Tenericutes bacteria’s prominence was due to the higher plant fibres from the soybean meal as some Mycoplasma are known to degrade polysaccharides. Therefore, exposure to formulated feeds with high levels of these plant materials would allow for high proliferation. The thesis established that plant-derived dietary proteins in formulated feeds result in an effect on digestive enzyme activity and a difference in the community structure of gut bacteria in H. midae abalone. The results from the current research highlight the importance of studying abalone gut physiology when investigating the impacts of formulated feed composition, and can be used as an additional factor when determining the efficacy of a dietary component. Further research on the gut-bacterial groups and different digestive enzymes of H. midae abalone is encouraged, in order to create a holistic view on their response to dietary plant proteins inclusion in formulated feeds, thus reducing the need for fishmeal protein. , Thesis (MSc)-- Rhodes University, Faculty of Science, Department of Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Wright, Jason Geoffrey
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa , Haliotis midae -- Nutrition -- South Africa , Haliotis midae -- Physiology -- South Africa , Haliotis midae -- South Africa -- Growth , Haliotis midae -- Digestive organs , Abalone culture -- South Africa , Plant proteins as feed
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176803 , vital:42760
- Description: The growth and feed conversion ratio of farmed abalone Haliotis midae (L. 1758) fed a formulated diet varies in feeds with different protein sources. To better understand this, the effect that various combinations of dietary soybean meal (SBM), sunflower meal (SFM) and fishmeal (FM) had on the digestive efficiency of farmed H. midae when included in a formulated feed, were assessed. The aim of this study was to investigate the effect that plant-based proteins had on abalone digestion and gut-bacterial profile of cultured adult abalone when combined with fishmeal. This was done by analysing the chymotrypsin (protease) and cellulase (carbohydrase) digestive enzyme activities from whole-gut sections of farmed abalone that were fed one of four diets for 12 months: FM-only, SBM-only, fishmeal and soybean meal (FM-SBM), and fishmeal and sunflower meal (FM-SFM). There were significant interactions between the diets, sampling date, and sex of the abalone, which had an influence on the cellulase activities in the digestive tracts of the animals. Those fed the SBM diet had the highest cellulase activity by the end of the sampling period (ANOVA; df = 9; F = 2.9; P = 0.005). The significant interactions between diet and sampling date influenced the chymotrypsin activities of abalone. Animals fed the FM diet had the highest activity of chymotrypsin for most of the sampling period (ANOVA; df = 9; F = 2.5; P = 0.01). Therefore, diet did have an impact on the cellulase and chymotrypsin activities of abalone fed either combination diets (FM-SBM; FM-SFM) or single protein diets (FM; SBM). The presence of plant material such as cellulose fibres in the diets containing plant proteins may have influenced the cellulase activity levels of each treatment as it would have stimulated endogenous and exogenous cellulase production. However, treatments with the highest crude fibre content, SBM and FM-SFM, resulted in differing activities. The activity levels of chymotrypsin may have been impacted by the protein type, presence of protein inhibitors and temporal changes in utilisation. Abalone fed the FM diet exhibited the highest chymotrypsin activities on sampling day 182, which was in summer. Animals fed the treatment diets containing fishmeal also developed their reproductive tissues, and may explain the low chymotrypsin activities in abalone fed SBM-only. Additionally, the presence of allergenic compounds would have influenced enzyme activity, as they would have negatively affected the nutrient utilisation and absorptive capacity. Fluctuations in water temperature may have had an effect on enzyme activity, as activities were highest during summer, when seawater temperatures are most variable. A change to lowered water temperatures are known to trigger the growth of digestive epithelial tissue in abalone to allow for increased enzyme secretions and nutrient absorption (Schaeffer et al. 2013). The effect that plant protein inclusion in abalone diets had on the gut-microbiota was revealed by analysing the differences in gut-bacterial community profiles, through the use of metagenomic sequencing. The relative abundance of the phylum Verrucomicrobia, class Verrcomicrobiae and the genus Rubritalea were highest in the SBM diet. These bacterial groups were also influenced by the plant material from soybean meal, as hydrolysed cellulose is broken down by cellulases, and allowed for the proliferation of Rubritalea bacteria due to them using cellobiose as an energy source. The presence of Bacteroidetes was due to the phyla having bacterial species that can breakdown proteins and species that can break down carbohydrates. The animal protein present in the composition of the FM diet had a positive influence on proteolytic Bacteroidetes growth. The high levels of cellulose from the plant fibres in the soybean meal-only diet (SBM) promoted growth of saccharolytic Bacteroidetes. Tenericutes bacteria’s prominence was due to the higher plant fibres from the soybean meal as some Mycoplasma are known to degrade polysaccharides. Therefore, exposure to formulated feeds with high levels of these plant materials would allow for high proliferation. The thesis established that plant-derived dietary proteins in formulated feeds result in an effect on digestive enzyme activity and a difference in the community structure of gut bacteria in H. midae abalone. The results from the current research highlight the importance of studying abalone gut physiology when investigating the impacts of formulated feed composition, and can be used as an additional factor when determining the efficacy of a dietary component. Further research on the gut-bacterial groups and different digestive enzymes of H. midae abalone is encouraged, in order to create a holistic view on their response to dietary plant proteins inclusion in formulated feeds, thus reducing the need for fishmeal protein. , Thesis (MSc)-- Rhodes University, Faculty of Science, Department of Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-04
Healthcare issues in disaster management : preparedness in the pharmacy profession
- Authors: Vhiriri, Eunice Paidamoyo
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178591 , vital:42953
- Description: Access restricted until April 2023. , Thesis (MSc) -- Faculty of Pharmacy, Pharmacy, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Vhiriri, Eunice Paidamoyo
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178591 , vital:42953
- Description: Access restricted until April 2023. , Thesis (MSc) -- Faculty of Pharmacy, Pharmacy, 2021
- Full Text:
- Date Issued: 2021-04
The application of Classification Trees in the Banking Sector
- Authors: Mtwa, Sithayanda
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178514 , vital:42946
- Description: Access restricted until April 2026. , Thesis (MSc) -- Faculty of Science, Statistics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Mtwa, Sithayanda
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178514 , vital:42946
- Description: Access restricted until April 2026. , Thesis (MSc) -- Faculty of Science, Statistics, 2021
- Full Text:
- Date Issued: 2021-04
The reproductive performance, demography and spatial ecology of an extralimital white rhinoceros population
- Authors: Truter, Anja
- Date: 2021-04
- Subjects: White rhinoceros -- South Africa -- Eastern Cape , White rhinoceros -- Effect of poaching on -- South Africa -- Eastern Cape , White rhinoceros -- South Africa -- Eastern Cape -- Reproduction , White rhinoceros -- Dispersal -- South Africa -- Eastern Cape , White rhinoceros -- Food -- South Africa -- Eastern Cape , White rhinoceros -- Behavior -- South Africa -- Eastern Cape , Spatial ecology -- South Africa -- Eastern Cape , Animal populations -- South Africa -- Eastern Cape , Endangered species -- South Africa -- Eastern Cape , Spatial behavior in animals -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: thesis , text , Master , MSc
- Identifier: http://hdl.handle.net/10962/177975 , vital:42895
- Description: The white rhinoceros (Ceratotherium simum) (hereafter rhino) is under threat of becoming extinct due to continued poaching for its horns. In South Africa and elsewhere in Africa private landowners have, over the last few decades, contributed to the conservation of various species, including rhinos, even in areas where they have not occurred historically (i.e., where they are extralimital). Unfortunately, very few studies have investigated the conservation contribution of extralimital white rhinos on private reserves to the overall meta-population and/or their reproductive performance. The first aim of my study was therefore to determine whether or not the white rhinos introduced to a private game reserve in the Eastern Cape Province in 1992 have been successful from a reproductive perspective. I calculated inter-calving intervals, age at first calving, conception period, sex ratio, fecundity and fertility rates for white rhinos over this 28-year period. The average annual population growth rate for the rhinos was 10%, which is higher than the recommended 5% by the Rhino Management Group. Trends in density-dependent parameters such as age at first calving and inter-calving intervals also indicated that my study population is still well below carrying capacity for white rhinos and is contributing positively to white rhino conservation in South Africa. The second aim of my study was to investigate home range size and vegetation preferences of white rhinos. Home ranges were mostly larger for all age groups compared to rhinos in their native range. Previously cultivated lands (dominated by several grass species) were preferred by all rhino age groups. The rehabilitation of these previous agricultural-based pastures has likely contributed to the successful introduction of the white rhino as an extralimital megaherbivore in the Eastern Cape. I conclude that although extralimital white rhino populations in the Eastern Cape can be successful from a reproductive perspective, their potential impact on the indigenous biodiversity of the region should be a key future research priority. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Truter, Anja
- Date: 2021-04
- Subjects: White rhinoceros -- South Africa -- Eastern Cape , White rhinoceros -- Effect of poaching on -- South Africa -- Eastern Cape , White rhinoceros -- South Africa -- Eastern Cape -- Reproduction , White rhinoceros -- Dispersal -- South Africa -- Eastern Cape , White rhinoceros -- Food -- South Africa -- Eastern Cape , White rhinoceros -- Behavior -- South Africa -- Eastern Cape , Spatial ecology -- South Africa -- Eastern Cape , Animal populations -- South Africa -- Eastern Cape , Endangered species -- South Africa -- Eastern Cape , Spatial behavior in animals -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: thesis , text , Master , MSc
- Identifier: http://hdl.handle.net/10962/177975 , vital:42895
- Description: The white rhinoceros (Ceratotherium simum) (hereafter rhino) is under threat of becoming extinct due to continued poaching for its horns. In South Africa and elsewhere in Africa private landowners have, over the last few decades, contributed to the conservation of various species, including rhinos, even in areas where they have not occurred historically (i.e., where they are extralimital). Unfortunately, very few studies have investigated the conservation contribution of extralimital white rhinos on private reserves to the overall meta-population and/or their reproductive performance. The first aim of my study was therefore to determine whether or not the white rhinos introduced to a private game reserve in the Eastern Cape Province in 1992 have been successful from a reproductive perspective. I calculated inter-calving intervals, age at first calving, conception period, sex ratio, fecundity and fertility rates for white rhinos over this 28-year period. The average annual population growth rate for the rhinos was 10%, which is higher than the recommended 5% by the Rhino Management Group. Trends in density-dependent parameters such as age at first calving and inter-calving intervals also indicated that my study population is still well below carrying capacity for white rhinos and is contributing positively to white rhino conservation in South Africa. The second aim of my study was to investigate home range size and vegetation preferences of white rhinos. Home ranges were mostly larger for all age groups compared to rhinos in their native range. Previously cultivated lands (dominated by several grass species) were preferred by all rhino age groups. The rehabilitation of these previous agricultural-based pastures has likely contributed to the successful introduction of the white rhino as an extralimital megaherbivore in the Eastern Cape. I conclude that although extralimital white rhino populations in the Eastern Cape can be successful from a reproductive perspective, their potential impact on the indigenous biodiversity of the region should be a key future research priority. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2021
- Full Text:
- Date Issued: 2021-04
Does the Transkei population of Haliotis Midae at the eastern edge of its distributional range have a higher thermal tolerance than those in more temperate waters?
- Authors: Mathebula, Surprise
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa -- Indian Coast , Abalones -- South Africa -- Indian Coast , Haliotis midae -- Effect of temperature on -- South Africa -- Indian Coast , Haliotis midae -- Physiology -- South Africa -- Indian Coast , Haliotis midae -- Adaptation -- South Africa -- Indian Coast , Haliotis midae -- Growth -- South Africa -- Indian Coast
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177360 , vital:42814
- Description: The South African perlemoen abalone (Haliotis midae) may be vulnerable to rising temperatures on the East coast of South Africa due to climate change. H. midae is South Africa’s most valuable aquaculture species, and it is thus important to understand its physiological ability to adapt to the expected changes and to identify possible management measures to mitigate the impacts of rising temperatures. This project aimed to understand thermal tolerance and growth rates of offspring from two H. midae populations originating from the warm-temperate Central region (Port Elizabeth) and warmer Eastern edge of the species’ distribution in the Transkei region. To determine the effects of temperature on the physiological performance of the two abalone populations, growth rates, oxygen consumption rates and critical thermal maxima (CTM) were compared. A laboratory growth trial was conducted at three controlled temperatures, visibly, the ‘optimal’ temperature for H. midae growth (18 - 20℃), ‘pejus’ (stressful) temperature (21 - 22℃) and ‘critical’ temperature (23 - 24℃). Oxygen consumption rates were recorded at optimum (20℃), pejus (22℃) and critical (24℃) temperature using a respirometer. In addition, a farm growth trial with simultaneously spawned cohorts of abalone from the two populations was conducted at ambient temperature (19.5 and 20.0℃). The laboratory growth trial revealed no significant differences in growth rate between the two populations at the three temperature treatments (ANOVA, P > 0.05; df = 2). However, mortalities were high and growth rates low, indicating that the rearing conditions were sub-optimal, possibly masking genetic differences. No significant differences were observed in oxygen consumption rates (ANOVA, P = 0.18; df = 2), and CTM (t-Test, P = 0.31; df = 3) between the two populations. The CTM for both populations was between 29 - 30℃. The farm trial yielded no significant differences in growth rate during the Nursery phase (t-Test, P = 0.25; df = 2), however significant differences in growth rate were observed during the grow out phase with the Central region abalone offspring growing faster than the Eastern edge population (t-Test, P = 0.04; df = 4) indicating the possibility of a genetic difference between the two populations. Further experiments will be required to determine whether the differences observed in the growth trial were genetically or environmentally induced. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Mathebula, Surprise
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa -- Indian Coast , Abalones -- South Africa -- Indian Coast , Haliotis midae -- Effect of temperature on -- South Africa -- Indian Coast , Haliotis midae -- Physiology -- South Africa -- Indian Coast , Haliotis midae -- Adaptation -- South Africa -- Indian Coast , Haliotis midae -- Growth -- South Africa -- Indian Coast
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177360 , vital:42814
- Description: The South African perlemoen abalone (Haliotis midae) may be vulnerable to rising temperatures on the East coast of South Africa due to climate change. H. midae is South Africa’s most valuable aquaculture species, and it is thus important to understand its physiological ability to adapt to the expected changes and to identify possible management measures to mitigate the impacts of rising temperatures. This project aimed to understand thermal tolerance and growth rates of offspring from two H. midae populations originating from the warm-temperate Central region (Port Elizabeth) and warmer Eastern edge of the species’ distribution in the Transkei region. To determine the effects of temperature on the physiological performance of the two abalone populations, growth rates, oxygen consumption rates and critical thermal maxima (CTM) were compared. A laboratory growth trial was conducted at three controlled temperatures, visibly, the ‘optimal’ temperature for H. midae growth (18 - 20℃), ‘pejus’ (stressful) temperature (21 - 22℃) and ‘critical’ temperature (23 - 24℃). Oxygen consumption rates were recorded at optimum (20℃), pejus (22℃) and critical (24℃) temperature using a respirometer. In addition, a farm growth trial with simultaneously spawned cohorts of abalone from the two populations was conducted at ambient temperature (19.5 and 20.0℃). The laboratory growth trial revealed no significant differences in growth rate between the two populations at the three temperature treatments (ANOVA, P > 0.05; df = 2). However, mortalities were high and growth rates low, indicating that the rearing conditions were sub-optimal, possibly masking genetic differences. No significant differences were observed in oxygen consumption rates (ANOVA, P = 0.18; df = 2), and CTM (t-Test, P = 0.31; df = 3) between the two populations. The CTM for both populations was between 29 - 30℃. The farm trial yielded no significant differences in growth rate during the Nursery phase (t-Test, P = 0.25; df = 2), however significant differences in growth rate were observed during the grow out phase with the Central region abalone offspring growing faster than the Eastern edge population (t-Test, P = 0.04; df = 4) indicating the possibility of a genetic difference between the two populations. Further experiments will be required to determine whether the differences observed in the growth trial were genetically or environmentally induced. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-04
A study of the catalysis of the Diels-Alder and Aldol Condensation Reactions
- Authors: Ndagano, Urbain Nshokano
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178525 , vital:42947
- Description: Access restricted until April 2022. , Thesis (MSc) -- Faculty of Science, Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Ndagano, Urbain Nshokano
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178525 , vital:42947
- Description: Access restricted until April 2022. , Thesis (MSc) -- Faculty of Science, Chemistry, 2021
- Full Text:
- Date Issued: 2021-04
An exploratory investigation into an Integrated Vulnerability and Patch Management Framework
- Authors: Carstens, Duane
- Date: 2021-04
- Subjects: Computer security , Computer security -- Management , Computer networks -- Security measures , Patch Management , Integrated Vulnerability
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177940 , vital:42892
- Description: In the rapidly changing world of cybersecurity, the constant increase of vulnerabilities continues to be a prevalent issue for many organisations. Malicious actors are aware that most organisations cannot timeously patch known vulnerabilities and are ill-prepared to protect against newly created vulnerabilities where a signature or an available patch has not yet been created. Consequently, information security personnel face ongoing challenges to mitigate these risks. In this research, the problem of remediation in a world of increasing vulnerabilities is considered. The current paradigm of vulnerability and patch management is reviewed using a pragmatic approach to all associated variables of these services / practices and, as a result, what is working and what is not working in terms of remediation is understood. In addition to the analysis, a taxonomy is created to provide a graphical representation of all associated variables to vulnerability and patch management based on existing literature. Frameworks currently being utilised in the industry to create an effective engagement model between vulnerability and patch management services are considered. The link between quantifying a threat, vulnerability and consequence; what Microsoft has available for patching; and the action plan for resulting vulnerabilities is explored. Furthermore, the processes and means of communication between each of these services are investigated to ensure there is effective remediation of vulnerabilities, ultimately improving the security risk posture of an organisation. In order to effectively measure the security risk posture, progress is measured between each of these services through a single averaged measurement metric. The outcome of the research highlights influencing factors that impact successful vulnerability management, in line with identified themes from the research taxonomy. These influencing factors are however significantly undermined due to resources within the same organisations not having a clear and consistent understanding of their role, organisational capabilities and objectives for effective vulnerability and patch management within their organisations. , Thesis (MSc) -- Faculty of Science, Computer Science, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Carstens, Duane
- Date: 2021-04
- Subjects: Computer security , Computer security -- Management , Computer networks -- Security measures , Patch Management , Integrated Vulnerability
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177940 , vital:42892
- Description: In the rapidly changing world of cybersecurity, the constant increase of vulnerabilities continues to be a prevalent issue for many organisations. Malicious actors are aware that most organisations cannot timeously patch known vulnerabilities and are ill-prepared to protect against newly created vulnerabilities where a signature or an available patch has not yet been created. Consequently, information security personnel face ongoing challenges to mitigate these risks. In this research, the problem of remediation in a world of increasing vulnerabilities is considered. The current paradigm of vulnerability and patch management is reviewed using a pragmatic approach to all associated variables of these services / practices and, as a result, what is working and what is not working in terms of remediation is understood. In addition to the analysis, a taxonomy is created to provide a graphical representation of all associated variables to vulnerability and patch management based on existing literature. Frameworks currently being utilised in the industry to create an effective engagement model between vulnerability and patch management services are considered. The link between quantifying a threat, vulnerability and consequence; what Microsoft has available for patching; and the action plan for resulting vulnerabilities is explored. Furthermore, the processes and means of communication between each of these services are investigated to ensure there is effective remediation of vulnerabilities, ultimately improving the security risk posture of an organisation. In order to effectively measure the security risk posture, progress is measured between each of these services through a single averaged measurement metric. The outcome of the research highlights influencing factors that impact successful vulnerability management, in line with identified themes from the research taxonomy. These influencing factors are however significantly undermined due to resources within the same organisations not having a clear and consistent understanding of their role, organisational capabilities and objectives for effective vulnerability and patch management within their organisations. , Thesis (MSc) -- Faculty of Science, Computer Science, 2021
- Full Text:
- Date Issued: 2021-04
Night-time gravity waves detected with multi-frequency airglow imager
- Authors: Machubeng, Karabo Pebane
- Date: 2021-04
- Subjects: Gravity waves , Airglow , Gravity waves -- Seasonal variations , All Sky Imager
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178341 , vital:42931
- Description: This thesis shows the statistics of atmospheric gravity waves (AGWs) observed in the OI emission 557.7 nm at _97 km altitude using an all-sky imager based in Sutherland, South Africa (32.37_ S, 20.81_ E) in the year 2017. The wavelengths were determined using the propagation vector method, velocity was determined using the cross correlation of 1D FFT and the period was determined using the equation that relates wavelength and velocity. It was found that the horizontal wavelength in summer was almost evenly distributed between 10 and 40 km and for autumn, winter and spring were mostly between 10 and 30 km. The favoured speeds were between 40 and 50 m/s in autumn, as well as 30 and 50 m/s in summer, but the AGWs in winter had a bimodal speed distribution of 20 - 40 and 50 - 70 m/s. The majority of periods observed in all seasons were less than 20 minutes with a dominant peak of 5 - 10 minutes in autumn and spring. There was no favoured propagation direction for spring, but AGWs favoured a southeastward propagation in summer, and a southward propagation in autumn and winter. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Machubeng, Karabo Pebane
- Date: 2021-04
- Subjects: Gravity waves , Airglow , Gravity waves -- Seasonal variations , All Sky Imager
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178341 , vital:42931
- Description: This thesis shows the statistics of atmospheric gravity waves (AGWs) observed in the OI emission 557.7 nm at _97 km altitude using an all-sky imager based in Sutherland, South Africa (32.37_ S, 20.81_ E) in the year 2017. The wavelengths were determined using the propagation vector method, velocity was determined using the cross correlation of 1D FFT and the period was determined using the equation that relates wavelength and velocity. It was found that the horizontal wavelength in summer was almost evenly distributed between 10 and 40 km and for autumn, winter and spring were mostly between 10 and 30 km. The favoured speeds were between 40 and 50 m/s in autumn, as well as 30 and 50 m/s in summer, but the AGWs in winter had a bimodal speed distribution of 20 - 40 and 50 - 70 m/s. The majority of periods observed in all seasons were less than 20 minutes with a dominant peak of 5 - 10 minutes in autumn and spring. There was no favoured propagation direction for spring, but AGWs favoured a southeastward propagation in summer, and a southward propagation in autumn and winter. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
Selection for improved virulence of Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) to False Codling Moth, Thaumatotibia leucotreta, by serial passage through a heterologous host
- Authors: Iita, Petrus Paulus
- Date: 2021-04
- Subjects: Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Baculoviruses , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178180 , vital:42918
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is endemic to southern Africa, and strongly associated with citrus. As South African citrus production is mainly for export to foreign markets, the market access risk due to the phytosanitary status of this pest is considerable and its control is therefore imperative. Various control measures as part of a rigorous integrated pest management (IPM) programme targeted against T. leucotreta have been effective at suppressing the pest in citrus, but there is still a growing need for continued improvement of the programme and augmentation of the available control options. Of these control options, biological control, particularly the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA), is a key component of IPM in citrus orchards and it has been very successful at reducing T. leucotreta populations in the field for almost two decades. There is however, a growing need for more baculovirus variants with an improved virulence against T. leucotreta for a more efficient pest management system. The newly identified insect virus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) offers a unique opportunity for an additional biopesticide in IPM for control of T. leucotreta in the field. This study aimed to conduct serial passaging of CrpeNPV through a heterologous host, T. leucotreta, in order to determine the potential for improved virulence or speed of kill against it. In order to select for a variant of CrpeNPV with improved virulence against T. leucotreta, a high dose (LC90) of the virus OBs was used to perform 12 serial passages through T. leucotreta larvae in surface-dose bioassays. Whole genome sequencing and analysis of the passaged virus, along with restriction endonuclease profiling in silico was performed to determine if the genetic identity of the virus had changed during serial passage, in relation to the original virus. These analyses indicated that the dominant genotype of CrpeNPV was maintained following 12 serial passages through the heterologous host. The biological activity of the passaged virus, along with the original virus was evaluated against neonate T. leucotreta in surface-dose bioassays and compared. Results from dose-response bioassays showed that the virulence of CrpeNPV did not improve after 12 serial passages. The LC50 values of the passaged virus and the original virus were estimated at 1.96 × 104 and 1.58 × 104 OBs/ml, respectively, whereas the LC90 values were estimated at 3.46 × 104 OBs/ml for the passaged virus and 3.68 × 104 for the original virus. Similarly, the results from time-response bioassays showed that the speed of kill of CrpeNPV did not improve after 12 serial passages. The LT50 values of the passaged virus and the original virus were 88.44 hours (3 days and 16 hours) and 83.74 hours (3 days and 12 hours), respectively, whereas the LT90 values were 115 hours (4 days 19 hours) for the passaged virus and 102 hours (4 days 6 hours) for the original virus. The virulence and speed of kill of the passaged virus decreased significantly, in relation to the original virus. When the full genome of the passaged virus was sequenced and analysed, only a few SNPs were detected in the viral genome, in comparison to the original virus. No detectable difference in REN digestion patterns were observed following REN analysis of gDNA of the passaged virus with several restriction enzymes in silico. The results for this study suggest that CrpeNPV may already be optimally suited to the heterologous host as it persists under these conditions without significant changes to the genome. These results have positive implications for the genetic integrity of CrpeNPV as a potential biocontrol agent in the field. This study is the first to report the virulence selection of CrpeNPV by serial passage through a heterologous host, and also the first to record bioassay data in terms of dose response (or lethal concentration) against T. leucotreta second instars. The data obtained have added to the knowledge about interactions between CrpeNPV and its heterologous host, and may be fundamental to continued investigation into the effect of serial passage on pathogenicity and genetic diversity of CrpeNPV. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Iita, Petrus Paulus
- Date: 2021-04
- Subjects: Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Baculoviruses , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178180 , vital:42918
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is endemic to southern Africa, and strongly associated with citrus. As South African citrus production is mainly for export to foreign markets, the market access risk due to the phytosanitary status of this pest is considerable and its control is therefore imperative. Various control measures as part of a rigorous integrated pest management (IPM) programme targeted against T. leucotreta have been effective at suppressing the pest in citrus, but there is still a growing need for continued improvement of the programme and augmentation of the available control options. Of these control options, biological control, particularly the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA), is a key component of IPM in citrus orchards and it has been very successful at reducing T. leucotreta populations in the field for almost two decades. There is however, a growing need for more baculovirus variants with an improved virulence against T. leucotreta for a more efficient pest management system. The newly identified insect virus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) offers a unique opportunity for an additional biopesticide in IPM for control of T. leucotreta in the field. This study aimed to conduct serial passaging of CrpeNPV through a heterologous host, T. leucotreta, in order to determine the potential for improved virulence or speed of kill against it. In order to select for a variant of CrpeNPV with improved virulence against T. leucotreta, a high dose (LC90) of the virus OBs was used to perform 12 serial passages through T. leucotreta larvae in surface-dose bioassays. Whole genome sequencing and analysis of the passaged virus, along with restriction endonuclease profiling in silico was performed to determine if the genetic identity of the virus had changed during serial passage, in relation to the original virus. These analyses indicated that the dominant genotype of CrpeNPV was maintained following 12 serial passages through the heterologous host. The biological activity of the passaged virus, along with the original virus was evaluated against neonate T. leucotreta in surface-dose bioassays and compared. Results from dose-response bioassays showed that the virulence of CrpeNPV did not improve after 12 serial passages. The LC50 values of the passaged virus and the original virus were estimated at 1.96 × 104 and 1.58 × 104 OBs/ml, respectively, whereas the LC90 values were estimated at 3.46 × 104 OBs/ml for the passaged virus and 3.68 × 104 for the original virus. Similarly, the results from time-response bioassays showed that the speed of kill of CrpeNPV did not improve after 12 serial passages. The LT50 values of the passaged virus and the original virus were 88.44 hours (3 days and 16 hours) and 83.74 hours (3 days and 12 hours), respectively, whereas the LT90 values were 115 hours (4 days 19 hours) for the passaged virus and 102 hours (4 days 6 hours) for the original virus. The virulence and speed of kill of the passaged virus decreased significantly, in relation to the original virus. When the full genome of the passaged virus was sequenced and analysed, only a few SNPs were detected in the viral genome, in comparison to the original virus. No detectable difference in REN digestion patterns were observed following REN analysis of gDNA of the passaged virus with several restriction enzymes in silico. The results for this study suggest that CrpeNPV may already be optimally suited to the heterologous host as it persists under these conditions without significant changes to the genome. These results have positive implications for the genetic integrity of CrpeNPV as a potential biocontrol agent in the field. This study is the first to report the virulence selection of CrpeNPV by serial passage through a heterologous host, and also the first to record bioassay data in terms of dose response (or lethal concentration) against T. leucotreta second instars. The data obtained have added to the knowledge about interactions between CrpeNPV and its heterologous host, and may be fundamental to continued investigation into the effect of serial passage on pathogenicity and genetic diversity of CrpeNPV. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
Characterization of the diversity and metabolic potential of hypolithic communities in dronning Maud Land, Antarctica
- Authors: Mikhari, Rito Leanah
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178490 , vital:42944
- Description: Access restricted until April 2022. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Mikhari, Rito Leanah
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178490 , vital:42944
- Description: Access restricted until April 2022. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
Constraining the role of carbonate assimilation on spinel stability in oxide ores of the Flatreef, Bushveld Complex, South Africa
- Authors: Dyan, Siyasanga
- Date: 2021-04
- Subjects: Oxide minerals -- South Africa -- Bushveld Complex , Transvaal Supergroup (South Africa) , Magmas -- South Africa -- Bushveld Complex , Petrogenesis -- South Africa -- Bushveld Complex , Spinel group – South Africa -- South Africa -- Bushveld Complex , Dolomite -- South Africa -- Bushveld Complex
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174578 , vital:42490
- Description: The northern limb of the Bushveld Complex shows significant evidence for footwall rock- magma interaction, as a result of the emplacement of magmas onto the Transvaal Supergroup sediments. The Platreef of the northern limb is known to have involved extensive contamination of the magma. The lateral extension of the Platreef, the Flatreef, is less contaminated and comprises PGE-mineralization and thick chromitite layers. This enables successful stratigraphic correlation to the Upper Critical Zone of the eastern and western limbs of the Bushveld Complex. This study aims at addressing the influence of dolomitic floor rock contamination on the formation of spinels of the Flatreef and how they may differ to their occurrences in the Bushveld Complex elsewhere. Three main drill cores (UMT-345, UMT-335, and UMT-094) from the deep drilling program by Ivanhoe Mine, north of Turfspruit, were logged and sampled. The drill cores contained rocks contaminated by dolomite in varying degrees, depending on the proportion of carbonate xenoliths present. A total of sixty-two samples were obtained from the UG-2- equivalent chromitite seam, down into the hybrid contaminated units (Footwall Assimilation Zone; FAZ). Petrographic examination of the drill cores revealed that the feldspathic pyroxenite and chromitite layers are the most pristine lithologies in the Flatreef. The chromitite layers occur as a semi-massive to massive ores. The FAZ rocks are mainly dominated by the abundance of Al-rich Cr-spinels (Mg#30-80), clinopyroxenes with a high Ca-Tschermak component (up to 35 mol.%), olivines (Fo72-84), and plagioclase (An31-78). Geochemical characteristics of the feldspathic pyroxenite and chromitite seams include low CaO/Al2O3 and Ca/SiO2 ratios, the low abundance of REE and HFSE. In contrast, the FAZ samples display high CaO/Al2O3 and CaO/SiO2 ratios, suggesting mobilization of CaO-rich fluids derived from the associated dolomite xenoliths. Observations from lithostratigraphic element profiles indicate spikes in CaO within FAZ units relative to the feldspathic pyroxene, indicating a secondary source of CaO linked to proximity to carbonate xenoliths intersected in the core. The assimilation-fractional crystallization model performed with the Upper Critical Zone parental melt and dolomite produced assemblages dominated by spinel, olivine, clinopyroxene, and plagioclase, relating to those of the most contaminated rocks of footwall assimilation zones. The model also showed that large quantities of CO2 were produced during assimilation. High amounts of CO2-fluids mobilized in the melt would have interacted with the melt and increased the overall oxidation conditions. Oxygen fugacity (ƒO2) values were constrained from the spinels in the FAZ and chromites in chromitite seams. Spinels within the most contaminated rocks of the FAZ recorded relatively high ƒO2 values ranging between NNO-0.2 and NNO+1.8 (relative to the Nickel-Nickel-Oxide buffer. High ƒO2 values in spinels from the FAZ suggest that the melt interacted with greater amounts of oxidative CO2-fluids during decarbonation reactions. Such high redox conditions could have triggered the saturation and crystallization of spinels. Comparison of mineral compositions and ƒO2 of UG-2 chromites from the Flatreef with UG-2 from the eastern limb, western limb, chromitites from the Platreef and Uitkomst Complex reveal that Flatreef chromites are of most similar to those of the Platreef Uitkosmt Complex. The northern limb and Uitkomst Complex chromites have high ƒO2 values (NNO+0.3 to NNO+1.2), indicating their apparent link to the Malmani dolomite. Interaction of magma with the Malmani dolomite would have produced high quantities of CO2, triggering an increase in oxidizing conditions. Such an effect is most prominent in the Flatreef chromitites that are in contact with the FAZ. The chromites are characterised by high ƒO2 (NNO+1.2) and distinct compositions (low Cr2O3, high Fe3+/Fetotal, and TiO2). Thus, it is proposed that carbonate assimilation in the Flatreef triggered the precipitation of these distinctive chromites proximal to FAZ, due to liberation of substantial amounts of CO2-rich fluids with a highly oxidative capacity. Carbonate assimilation in layered intrusions can be used as a monitor potential precipitation of chromites. , Thesis (MSc)--Rhodes University, Faculty of Science, Department of Geology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Dyan, Siyasanga
- Date: 2021-04
- Subjects: Oxide minerals -- South Africa -- Bushveld Complex , Transvaal Supergroup (South Africa) , Magmas -- South Africa -- Bushveld Complex , Petrogenesis -- South Africa -- Bushveld Complex , Spinel group – South Africa -- South Africa -- Bushveld Complex , Dolomite -- South Africa -- Bushveld Complex
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174578 , vital:42490
- Description: The northern limb of the Bushveld Complex shows significant evidence for footwall rock- magma interaction, as a result of the emplacement of magmas onto the Transvaal Supergroup sediments. The Platreef of the northern limb is known to have involved extensive contamination of the magma. The lateral extension of the Platreef, the Flatreef, is less contaminated and comprises PGE-mineralization and thick chromitite layers. This enables successful stratigraphic correlation to the Upper Critical Zone of the eastern and western limbs of the Bushveld Complex. This study aims at addressing the influence of dolomitic floor rock contamination on the formation of spinels of the Flatreef and how they may differ to their occurrences in the Bushveld Complex elsewhere. Three main drill cores (UMT-345, UMT-335, and UMT-094) from the deep drilling program by Ivanhoe Mine, north of Turfspruit, were logged and sampled. The drill cores contained rocks contaminated by dolomite in varying degrees, depending on the proportion of carbonate xenoliths present. A total of sixty-two samples were obtained from the UG-2- equivalent chromitite seam, down into the hybrid contaminated units (Footwall Assimilation Zone; FAZ). Petrographic examination of the drill cores revealed that the feldspathic pyroxenite and chromitite layers are the most pristine lithologies in the Flatreef. The chromitite layers occur as a semi-massive to massive ores. The FAZ rocks are mainly dominated by the abundance of Al-rich Cr-spinels (Mg#30-80), clinopyroxenes with a high Ca-Tschermak component (up to 35 mol.%), olivines (Fo72-84), and plagioclase (An31-78). Geochemical characteristics of the feldspathic pyroxenite and chromitite seams include low CaO/Al2O3 and Ca/SiO2 ratios, the low abundance of REE and HFSE. In contrast, the FAZ samples display high CaO/Al2O3 and CaO/SiO2 ratios, suggesting mobilization of CaO-rich fluids derived from the associated dolomite xenoliths. Observations from lithostratigraphic element profiles indicate spikes in CaO within FAZ units relative to the feldspathic pyroxene, indicating a secondary source of CaO linked to proximity to carbonate xenoliths intersected in the core. The assimilation-fractional crystallization model performed with the Upper Critical Zone parental melt and dolomite produced assemblages dominated by spinel, olivine, clinopyroxene, and plagioclase, relating to those of the most contaminated rocks of footwall assimilation zones. The model also showed that large quantities of CO2 were produced during assimilation. High amounts of CO2-fluids mobilized in the melt would have interacted with the melt and increased the overall oxidation conditions. Oxygen fugacity (ƒO2) values were constrained from the spinels in the FAZ and chromites in chromitite seams. Spinels within the most contaminated rocks of the FAZ recorded relatively high ƒO2 values ranging between NNO-0.2 and NNO+1.8 (relative to the Nickel-Nickel-Oxide buffer. High ƒO2 values in spinels from the FAZ suggest that the melt interacted with greater amounts of oxidative CO2-fluids during decarbonation reactions. Such high redox conditions could have triggered the saturation and crystallization of spinels. Comparison of mineral compositions and ƒO2 of UG-2 chromites from the Flatreef with UG-2 from the eastern limb, western limb, chromitites from the Platreef and Uitkomst Complex reveal that Flatreef chromites are of most similar to those of the Platreef Uitkosmt Complex. The northern limb and Uitkomst Complex chromites have high ƒO2 values (NNO+0.3 to NNO+1.2), indicating their apparent link to the Malmani dolomite. Interaction of magma with the Malmani dolomite would have produced high quantities of CO2, triggering an increase in oxidizing conditions. Such an effect is most prominent in the Flatreef chromitites that are in contact with the FAZ. The chromites are characterised by high ƒO2 (NNO+1.2) and distinct compositions (low Cr2O3, high Fe3+/Fetotal, and TiO2). Thus, it is proposed that carbonate assimilation in the Flatreef triggered the precipitation of these distinctive chromites proximal to FAZ, due to liberation of substantial amounts of CO2-rich fluids with a highly oxidative capacity. Carbonate assimilation in layered intrusions can be used as a monitor potential precipitation of chromites. , Thesis (MSc)--Rhodes University, Faculty of Science, Department of Geology, 2021
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- Date Issued: 2021-04