Re-surveying the insectivorous bats of northern Kruger National Park, South Africa
- Authors: Brinkley, Erin Reed
- Date: 2019
- Subjects: Bats -- South Africa , Bats -- Behavior , Bats -- South Africa -- Ecology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/115697 , vital:34216
- Description: With over 1,300 known species, the order Chiroptera makes up about 20 percent of all mammalian species. Due to its sub-tropical climate, the northern part of Kruger National Park (KNP) in South Africa is believed to have the highest bat species richness in the country. However, the last comprehensive assessment of bat diversity in the region was conducted more than 30 years ago. In 2017 and 2018, I undertook the first detailed re-assessment of the bat communities of the northern KNP since the early 1980’s. I used both live-capture (harp traps and mist-netting) and acoustic technology (SM2 and SM4 Songmeters, Wildlife Acoustics. MA, USA) to sample bats at 24 sites across the northern region of KNP. Through live-capture (336 trapping hours), 155 bats representing 13 species from five families were recorded including Cloetis pervicali, which has never been recorded within the borders of the KNP before. The echolocation calls of all captured bats were recorded to develop a site-specific call reference library that was used (in combination with existing reference calls) as a guide for the identification of bat calls recorded using the acoustic detectors set across 24 sites (278 sampling nights). The acoustic monitoring identified 22 species from six families and two unknown sets of calls. Compared to the historical data of 40 documented species (collected over a 30-year period), the current survey (27 species) resulted in a lower species richness. However, this is likely due to the lower overall sampling effort during my survey. By re-surveying the bats of northern KNP, I have contributed towards an overall bat species inventory for this region. In addition, I have generated an important baseline dataset for the future monitoring of bat diversity across the KNP. Due to bats being important biological indicators, increased research on the various species and their behaviours is essential for improving our understanding of climate change effects as well as the overall health of the environment, especially in protected areas.
- Full Text:
- Date Issued: 2019
- Authors: Brinkley, Erin Reed
- Date: 2019
- Subjects: Bats -- South Africa , Bats -- Behavior , Bats -- South Africa -- Ecology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/115697 , vital:34216
- Description: With over 1,300 known species, the order Chiroptera makes up about 20 percent of all mammalian species. Due to its sub-tropical climate, the northern part of Kruger National Park (KNP) in South Africa is believed to have the highest bat species richness in the country. However, the last comprehensive assessment of bat diversity in the region was conducted more than 30 years ago. In 2017 and 2018, I undertook the first detailed re-assessment of the bat communities of the northern KNP since the early 1980’s. I used both live-capture (harp traps and mist-netting) and acoustic technology (SM2 and SM4 Songmeters, Wildlife Acoustics. MA, USA) to sample bats at 24 sites across the northern region of KNP. Through live-capture (336 trapping hours), 155 bats representing 13 species from five families were recorded including Cloetis pervicali, which has never been recorded within the borders of the KNP before. The echolocation calls of all captured bats were recorded to develop a site-specific call reference library that was used (in combination with existing reference calls) as a guide for the identification of bat calls recorded using the acoustic detectors set across 24 sites (278 sampling nights). The acoustic monitoring identified 22 species from six families and two unknown sets of calls. Compared to the historical data of 40 documented species (collected over a 30-year period), the current survey (27 species) resulted in a lower species richness. However, this is likely due to the lower overall sampling effort during my survey. By re-surveying the bats of northern KNP, I have contributed towards an overall bat species inventory for this region. In addition, I have generated an important baseline dataset for the future monitoring of bat diversity across the KNP. Due to bats being important biological indicators, increased research on the various species and their behaviours is essential for improving our understanding of climate change effects as well as the overall health of the environment, especially in protected areas.
- Full Text:
- Date Issued: 2019
Recovery and molecular identification of Aichi virus 1, enteric human bocaviruses and enteric human adenoviruses in untreated sewage and mussel samples collected in the Eastern Cape Province of South Africa
- Authors: Onosi, Oikwathaile
- Date: 2019
- Subjects: Sewage -- Analysis -- South Africa -- Eastern Cape , Sewage -- Microbiology -- South Africa -- Eastern Cape , Viral pollution of water -- South Africa -- Eastern Cape , Sewage disposal in rivers, lakes, etc. -- South Africa -- Eastern Cape , Enteroviruses -- South Africa -- Eastern Cape , Picornaviruses -- South Africa -- Eastern Cape , Aichi virus 1 , Parvoviruses -- South Africa -- Eastern Cape , Adenoviruses -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69456 , vital:29539
- Description: Gastroenteritis, commonly known as diarrhoeal disease, is one of the top killers responsible for substantial human morbidity and mortality especially in third world countries where most people do not have access to potable water and where hygiene levels are low. Many bacterial, viral and protozoal agents are known causes of gastroenteritis and viral gastroenteritis is responsible for over 70% of cases. Rotaviruses are the main causes of viral gastroenteritis and are responsible for most of the cases worldwide. Other viral agents associated with this disease include human noroviruses, Aichi virus 1, enteric human bocavirus, enteric human adenovirus and many other emerging viral agents such as klassivirus, Saffold virus, cosavirus and others. In 2009 the South African government introduced a rotavirus vaccine, RotaRixTM into the expanded programme on immunisation (EPI). More than a 50% decrease in diarrhoea related morbidity and mortality due to rotavirus infections was noted during surveillance studies on the efficacy of the vaccine. However, over 40% of cases of gastroenteritis are of unknown aetiology. The present study aimed to perform a preliminary study to investigate the presence of Aichi virus 1 and enteric human bocaviruses in the Eastern Cape Province by the use of molecular techniques. Furthermore, the study aimed to add to the limited molecular data about enteric adenoviruses in South Africa. Samples used in this study were swab samples collected from Belmont Valley Wastewater Treatment Plant in Grahamstown, South Africa, as well as mussel samples collected from the Swartkops River in Port Elizabeth, South Africa. Both raw sewage and shellfish give a broad idea of what microbes are circulating in the communities. In the present study, twenty swabs and twenty mussel samples were prepared by centrifugation, sonication and filtration. Samples were then subjected to transmission electron microscopy (TEM) analysis, for which the electron micrographs revealed presence of viral particles with diameters ranging from around 20 nm to just over 100 nm. Viral nucleic acids were extracted from 140 μL of the twenty swabs and twenty mussels samples using the QIAamp® Viral RNA Mini Kit, following manufacturer‟s instructions. For detection of Aichi virus 1 from the swab and mussel samples three reverse transcriptase- polymerase chain reaction (RT-PCR) assays using the Verso 1-Step RT-PCR Hot-Start Kit were developed. The first RT-PCR assay targeted amplification of the highly conserved 5′ UTR using published primers. However, despite many amplification attempts no positive results were obtained from both swab and mussel samples. It was only after the addition of DMSO (to a final concentration of 10%) that one swab sample was positive for this assay. In addition, a 2-step RT-PCR was developed using the Maxima H Minus First Strand cDNA Synthesis Kit. By using this 2-step RT-PCR assay, an additional swab sample was positive for the Aichi virus 1 5′ UTR. Using Basic Logarithm Alignment Search Tool (BLAST) analysis these two samples were 98% identical to an Aichi virus isolate from South Korea. The second one-step RT-PCR assay targeted amplification of the 266 bp partial 3CD coding region of Aichi virus 1 using published primers. By using this assay, positive results were obtained from both the swab and mussel samples, which when analysed by BLAST were all 99% identical to various Aichi virus 1 isolates in GenBank. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. The third assay was a semi-nested RT-PCR assay that targeted amplification of the hypervariable VP1 coding region of Aichi virus 1 using a combination of published primers and those designed in the present study. Amplicons which were 472 bp in size were produced from two swab samples. When analysed by BLAST, these two swab samples had percentage identities of 98% to an Aichi virus isolate from South Korea. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. This was consistent with phylogenetic results discussed above which were based on the partial 3CD region. For detection of enteric human bocaviruses from the swab and mussel samples a nested polymerase chain reaction (PCR) assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed based on PCR amplification of the 382 bp partial VP1/VP2 coding region using published primers. A total of six swab samples and six mussel samples were analysed for which five swabs and six mussel samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 98% and 99% to an enteric human bocavirus 3 strain from China while the mussel samples were all 99% identical to an enteric human bocavirus 2 isolate from Australia. A phylogenetic tree constructed based on this VP1/VP2 region showed that isolates from the present study clustered with human bocavirus 2 and human bocavirus 3 isolates in GenBank for those isolated from swab samples and mussel samples respectively. Lastly, for detection of enteric human adenoviruses from the swab and mussel samples a nested PCR assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed. This reaction was based on PCR amplification of the 168 bp partial hexon coding region using published primers for which ten swab samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 96% and 99% to enteric human adenoviruses in GenBank. A phylogenetic tree constructed based on the hexon coding region showed that isolates from the present study clustered with subtypes C, D and F which are associated with gastroenteritis worldwide. Despite several amplification attempts no positive results were obtained from mussel samples. The results from the present study show that Aichi virus 1, enteric bocaviruses and enteric adenoviruses are present in the Eastern Cape Province of South Africa. These viruses could possibly be responsible for enteric infections in South Africa. Although only a few samples were analysed, this study is the first to confirm the presence of Aichi virus 1 and enteric bocaviruses in South Africa and provides a platform for further investigation into prevalence and epidemiology of these viruses in the country.
- Full Text:
- Date Issued: 2019
- Authors: Onosi, Oikwathaile
- Date: 2019
- Subjects: Sewage -- Analysis -- South Africa -- Eastern Cape , Sewage -- Microbiology -- South Africa -- Eastern Cape , Viral pollution of water -- South Africa -- Eastern Cape , Sewage disposal in rivers, lakes, etc. -- South Africa -- Eastern Cape , Enteroviruses -- South Africa -- Eastern Cape , Picornaviruses -- South Africa -- Eastern Cape , Aichi virus 1 , Parvoviruses -- South Africa -- Eastern Cape , Adenoviruses -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69456 , vital:29539
- Description: Gastroenteritis, commonly known as diarrhoeal disease, is one of the top killers responsible for substantial human morbidity and mortality especially in third world countries where most people do not have access to potable water and where hygiene levels are low. Many bacterial, viral and protozoal agents are known causes of gastroenteritis and viral gastroenteritis is responsible for over 70% of cases. Rotaviruses are the main causes of viral gastroenteritis and are responsible for most of the cases worldwide. Other viral agents associated with this disease include human noroviruses, Aichi virus 1, enteric human bocavirus, enteric human adenovirus and many other emerging viral agents such as klassivirus, Saffold virus, cosavirus and others. In 2009 the South African government introduced a rotavirus vaccine, RotaRixTM into the expanded programme on immunisation (EPI). More than a 50% decrease in diarrhoea related morbidity and mortality due to rotavirus infections was noted during surveillance studies on the efficacy of the vaccine. However, over 40% of cases of gastroenteritis are of unknown aetiology. The present study aimed to perform a preliminary study to investigate the presence of Aichi virus 1 and enteric human bocaviruses in the Eastern Cape Province by the use of molecular techniques. Furthermore, the study aimed to add to the limited molecular data about enteric adenoviruses in South Africa. Samples used in this study were swab samples collected from Belmont Valley Wastewater Treatment Plant in Grahamstown, South Africa, as well as mussel samples collected from the Swartkops River in Port Elizabeth, South Africa. Both raw sewage and shellfish give a broad idea of what microbes are circulating in the communities. In the present study, twenty swabs and twenty mussel samples were prepared by centrifugation, sonication and filtration. Samples were then subjected to transmission electron microscopy (TEM) analysis, for which the electron micrographs revealed presence of viral particles with diameters ranging from around 20 nm to just over 100 nm. Viral nucleic acids were extracted from 140 μL of the twenty swabs and twenty mussels samples using the QIAamp® Viral RNA Mini Kit, following manufacturer‟s instructions. For detection of Aichi virus 1 from the swab and mussel samples three reverse transcriptase- polymerase chain reaction (RT-PCR) assays using the Verso 1-Step RT-PCR Hot-Start Kit were developed. The first RT-PCR assay targeted amplification of the highly conserved 5′ UTR using published primers. However, despite many amplification attempts no positive results were obtained from both swab and mussel samples. It was only after the addition of DMSO (to a final concentration of 10%) that one swab sample was positive for this assay. In addition, a 2-step RT-PCR was developed using the Maxima H Minus First Strand cDNA Synthesis Kit. By using this 2-step RT-PCR assay, an additional swab sample was positive for the Aichi virus 1 5′ UTR. Using Basic Logarithm Alignment Search Tool (BLAST) analysis these two samples were 98% identical to an Aichi virus isolate from South Korea. The second one-step RT-PCR assay targeted amplification of the 266 bp partial 3CD coding region of Aichi virus 1 using published primers. By using this assay, positive results were obtained from both the swab and mussel samples, which when analysed by BLAST were all 99% identical to various Aichi virus 1 isolates in GenBank. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. The third assay was a semi-nested RT-PCR assay that targeted amplification of the hypervariable VP1 coding region of Aichi virus 1 using a combination of published primers and those designed in the present study. Amplicons which were 472 bp in size were produced from two swab samples. When analysed by BLAST, these two swab samples had percentage identities of 98% to an Aichi virus isolate from South Korea. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. This was consistent with phylogenetic results discussed above which were based on the partial 3CD region. For detection of enteric human bocaviruses from the swab and mussel samples a nested polymerase chain reaction (PCR) assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed based on PCR amplification of the 382 bp partial VP1/VP2 coding region using published primers. A total of six swab samples and six mussel samples were analysed for which five swabs and six mussel samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 98% and 99% to an enteric human bocavirus 3 strain from China while the mussel samples were all 99% identical to an enteric human bocavirus 2 isolate from Australia. A phylogenetic tree constructed based on this VP1/VP2 region showed that isolates from the present study clustered with human bocavirus 2 and human bocavirus 3 isolates in GenBank for those isolated from swab samples and mussel samples respectively. Lastly, for detection of enteric human adenoviruses from the swab and mussel samples a nested PCR assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed. This reaction was based on PCR amplification of the 168 bp partial hexon coding region using published primers for which ten swab samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 96% and 99% to enteric human adenoviruses in GenBank. A phylogenetic tree constructed based on the hexon coding region showed that isolates from the present study clustered with subtypes C, D and F which are associated with gastroenteritis worldwide. Despite several amplification attempts no positive results were obtained from mussel samples. The results from the present study show that Aichi virus 1, enteric bocaviruses and enteric adenoviruses are present in the Eastern Cape Province of South Africa. These viruses could possibly be responsible for enteric infections in South Africa. Although only a few samples were analysed, this study is the first to confirm the presence of Aichi virus 1 and enteric bocaviruses in South Africa and provides a platform for further investigation into prevalence and epidemiology of these viruses in the country.
- Full Text:
- Date Issued: 2019
Recruitment of bivalve molluscs with specific emphasis on Mytilus galloprovincialis in the Knysna estuarine embayment, South Africa
- Authors: Radloff, James Victor
- Date: 2019
- Subjects: Mytilus galloprovincialis -- South Africa -- Knysna Lagoon , Introduced aquatic organisms -- South Africa -- Knysna Lagoon , Mexilhao mussel -- South Africa -- Knysna Lagoon , Oysters -- South Africa -- Knysna Lagoon , Mytilidae -- South Africa -- Knysna Lagoon , Bivalves -- South Africa -- Knysna Lagoon
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76733 , vital:30613
- Description: Alien invasive species have the ability to transform or alter environments, often causing severe ecological and/or economic impacts. Marine bioinvasions are occurring globally and are most often facilitated (intentially and accidently) through anthropogenic activities including the building of inter-oceanic canals, shipping and commerce. The Mediterranean mussel, Mytilus galloprovincialis, is a globally successful marine alien invasive species which was first recorded on the west coast of South Africa in the late 1970s and the south coast in 1988. This species is thought to have reached the Knysna Estuary in the early 2000s and has colonised all man-made hard substrata in the embayment of the estuary. Although there are studies on recruitment of M. galloprovincialis on the rocky intertidal coasts of South Africa, there is little information on recruitment of this species in more sheltered estuarine environments. This study aimed to determine recruitment levels of M. galloprovincialis and other bivalves within the Knysna estuarine embayment. To determine monthly recruitment, 10 recruit collectors/pads (plastic pot scourers) were placed at three separate locations within the embayment of the estuary for a week on a monthly basis for 20 months. In addition, recruitment of M. galloprovincialis over spring and neap tides and different lunar phases was also determined at two sites within the Knysna estuarine embayment during the main reproductive season in 2018. The pads were deployed three days before a neap/spring tide and then collected three days after the respective tide. Finally, to look at how rapidly M. galloprovincialis and other macroinvertebrates (when M. galloprovincialis was excluded) would re-colonise free space, 18 plots (15x15 cm), consisting of three treatments including a control (A,B and C), were cleared in M. galloprovincialis mussel beds and then photographed monthly for 12 months. Four bivalve taxa (Mytilus galloprovincialis, Perna perna, Ostreidae, unidentified mytilid) were recorded during the monthly study. Recruitment levels for all bivalves differed significantly (P < 0.001) between months and sites, with peak recruitment occurring from late spring to early autumn (November – March). Mytilus galloprovincialis recruitment levels were greater than other bivalves and were up to 4.5x greater than other taxa. Recruitment also varied between years possibly owing to differences in larval supply and/or environmental factors. Spatial variation in bivalve recruitment was observed throughout the study. The greatest recruitment was at the site (Thesen Island Wharf) closer to the entrance of the embayment. By contrast at the site (Railway Bridge) furthest from the entrance lower recruitment was found. This difference is possibly due to differences in hydrodynamics or other biological and/or environmental factors. A preliminary tidal study found that M. galloprovincialis had significantly higher (P < 0.001) recruitment levels over spring tides than neap tides at Thesen Island Wharf, whereas recruitment at the Railway Bridge on spring and neap tides was not significantly different. In the study undertaken in the reproductive season only, recruitment levels were high over a two week period during both a spring and neap tide, suggesting that factors other than lunar phase and the state of tide are more important in determining the timing and intensity of recruitment. The clearance plots created and photographed over a 12 month period showed that M. galloprovincialis rapidly occupied free space (eight months to virtually cover all free space) by encroachment from the adjacent mussel bed. Limpets and barnacles were only able to colonise cleared space when M. galloprovincialis was excluded, suggesting that the mussel has the ability to outcompete indigenous macrofauna for space. The high recruitment levels of M. galloprovincialis compared to other indigenous bivalves, as well as its ability to occupy space rapidly are traits that must contribute to the success of the invasion of this species within the Knysna estuarine embayment, particulary within Thesen Islands Marina and Thesen Island Wharf.
- Full Text:
- Date Issued: 2019
- Authors: Radloff, James Victor
- Date: 2019
- Subjects: Mytilus galloprovincialis -- South Africa -- Knysna Lagoon , Introduced aquatic organisms -- South Africa -- Knysna Lagoon , Mexilhao mussel -- South Africa -- Knysna Lagoon , Oysters -- South Africa -- Knysna Lagoon , Mytilidae -- South Africa -- Knysna Lagoon , Bivalves -- South Africa -- Knysna Lagoon
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76733 , vital:30613
- Description: Alien invasive species have the ability to transform or alter environments, often causing severe ecological and/or economic impacts. Marine bioinvasions are occurring globally and are most often facilitated (intentially and accidently) through anthropogenic activities including the building of inter-oceanic canals, shipping and commerce. The Mediterranean mussel, Mytilus galloprovincialis, is a globally successful marine alien invasive species which was first recorded on the west coast of South Africa in the late 1970s and the south coast in 1988. This species is thought to have reached the Knysna Estuary in the early 2000s and has colonised all man-made hard substrata in the embayment of the estuary. Although there are studies on recruitment of M. galloprovincialis on the rocky intertidal coasts of South Africa, there is little information on recruitment of this species in more sheltered estuarine environments. This study aimed to determine recruitment levels of M. galloprovincialis and other bivalves within the Knysna estuarine embayment. To determine monthly recruitment, 10 recruit collectors/pads (plastic pot scourers) were placed at three separate locations within the embayment of the estuary for a week on a monthly basis for 20 months. In addition, recruitment of M. galloprovincialis over spring and neap tides and different lunar phases was also determined at two sites within the Knysna estuarine embayment during the main reproductive season in 2018. The pads were deployed three days before a neap/spring tide and then collected three days after the respective tide. Finally, to look at how rapidly M. galloprovincialis and other macroinvertebrates (when M. galloprovincialis was excluded) would re-colonise free space, 18 plots (15x15 cm), consisting of three treatments including a control (A,B and C), were cleared in M. galloprovincialis mussel beds and then photographed monthly for 12 months. Four bivalve taxa (Mytilus galloprovincialis, Perna perna, Ostreidae, unidentified mytilid) were recorded during the monthly study. Recruitment levels for all bivalves differed significantly (P < 0.001) between months and sites, with peak recruitment occurring from late spring to early autumn (November – March). Mytilus galloprovincialis recruitment levels were greater than other bivalves and were up to 4.5x greater than other taxa. Recruitment also varied between years possibly owing to differences in larval supply and/or environmental factors. Spatial variation in bivalve recruitment was observed throughout the study. The greatest recruitment was at the site (Thesen Island Wharf) closer to the entrance of the embayment. By contrast at the site (Railway Bridge) furthest from the entrance lower recruitment was found. This difference is possibly due to differences in hydrodynamics or other biological and/or environmental factors. A preliminary tidal study found that M. galloprovincialis had significantly higher (P < 0.001) recruitment levels over spring tides than neap tides at Thesen Island Wharf, whereas recruitment at the Railway Bridge on spring and neap tides was not significantly different. In the study undertaken in the reproductive season only, recruitment levels were high over a two week period during both a spring and neap tide, suggesting that factors other than lunar phase and the state of tide are more important in determining the timing and intensity of recruitment. The clearance plots created and photographed over a 12 month period showed that M. galloprovincialis rapidly occupied free space (eight months to virtually cover all free space) by encroachment from the adjacent mussel bed. Limpets and barnacles were only able to colonise cleared space when M. galloprovincialis was excluded, suggesting that the mussel has the ability to outcompete indigenous macrofauna for space. The high recruitment levels of M. galloprovincialis compared to other indigenous bivalves, as well as its ability to occupy space rapidly are traits that must contribute to the success of the invasion of this species within the Knysna estuarine embayment, particulary within Thesen Islands Marina and Thesen Island Wharf.
- Full Text:
- Date Issued: 2019
Red tape in upgrading of informal settlements in Nelson Mandela Bay
- Authors: Mangezi, Wilfred
- Date: 2019
- Subjects: Housing development -- South Africa -- Nelson Mandela Bay Municipality , Squatter settlements -- South Africa -- Nelson Mandela Bay Municipality Squatters -- South Africa -- Nelson Mandela Bay Municipality Housing -- South Africa -- Nelson Mandela Bay Municipality
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/33375 , vital:32745
- Description: Even though there is general acknowledgement of the existence of red tape in low cost housing, very little effort has been made to seek-out its underlying causes. The purpose of this study was to investigate red tape in specific Informal Settlement Upgrading Programme (ISUP) developments within the Nelson Mandela Bay, to uncover the underlying causes of red tape and ultimately suggest possible remedies to reduce red tape and its adverse effects. Administrative red tape in ISUP projects is hampering the government’s efforts to improve informal settlement dwellers’ standard of living, as evidenced by the slow pace of housing delivery to such intended beneficiaries. Furthermore, red tape also causes frustration to Small, Medium, and Micro Enterprises (SMME’s) that are involved in the low-cost housing delivery value chain who suffer cash flow problems due to delays incurred from payment of their services by the local authority. This hindrance does not spare the majority of municipal employees whose roles are dependent on the performance of other departments. Of great concern are the residents within the municipality who have developed a culture of expressing their frustration caused by such delays through violent demonstrations so much to the detriment of the peaceful environment that has over time characterised this friendly tourist destination of South Africa. Applying a qualitative research strategy, the researcher undertook data collection through document review and face to face interviews from targeted respondents across various departments within and outside the municipality that deals with ISUP developments. The study revealed that, red tape in ISUP projects is a result of a variety of factors which include; inept internal management procedures, misinterpretation of legislation, silo mentality and lack of capacity in housing delivery. Thus the rules, legislation and procedures prevailing are failing to keep pace with the changing macro environment. To reduce the impact of red tape the researcher believes that it would be of paramount importance for the NMBM to consider; realignment of their internal procedures to counter the pressure posed by the residents, integrate project teams or functional departments dealing with housing, engage beneficiaries from the onset of the projects, invest in training staff and acquisition of new technology. The core of reducing red tape lies in upgrading of rules and administrative procedures in dealing with ISUP projects within the municipality so as to adopt to the dynamism that characterise the built environment.
- Full Text:
- Date Issued: 2019
- Authors: Mangezi, Wilfred
- Date: 2019
- Subjects: Housing development -- South Africa -- Nelson Mandela Bay Municipality , Squatter settlements -- South Africa -- Nelson Mandela Bay Municipality Squatters -- South Africa -- Nelson Mandela Bay Municipality Housing -- South Africa -- Nelson Mandela Bay Municipality
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/33375 , vital:32745
- Description: Even though there is general acknowledgement of the existence of red tape in low cost housing, very little effort has been made to seek-out its underlying causes. The purpose of this study was to investigate red tape in specific Informal Settlement Upgrading Programme (ISUP) developments within the Nelson Mandela Bay, to uncover the underlying causes of red tape and ultimately suggest possible remedies to reduce red tape and its adverse effects. Administrative red tape in ISUP projects is hampering the government’s efforts to improve informal settlement dwellers’ standard of living, as evidenced by the slow pace of housing delivery to such intended beneficiaries. Furthermore, red tape also causes frustration to Small, Medium, and Micro Enterprises (SMME’s) that are involved in the low-cost housing delivery value chain who suffer cash flow problems due to delays incurred from payment of their services by the local authority. This hindrance does not spare the majority of municipal employees whose roles are dependent on the performance of other departments. Of great concern are the residents within the municipality who have developed a culture of expressing their frustration caused by such delays through violent demonstrations so much to the detriment of the peaceful environment that has over time characterised this friendly tourist destination of South Africa. Applying a qualitative research strategy, the researcher undertook data collection through document review and face to face interviews from targeted respondents across various departments within and outside the municipality that deals with ISUP developments. The study revealed that, red tape in ISUP projects is a result of a variety of factors which include; inept internal management procedures, misinterpretation of legislation, silo mentality and lack of capacity in housing delivery. Thus the rules, legislation and procedures prevailing are failing to keep pace with the changing macro environment. To reduce the impact of red tape the researcher believes that it would be of paramount importance for the NMBM to consider; realignment of their internal procedures to counter the pressure posed by the residents, integrate project teams or functional departments dealing with housing, engage beneficiaries from the onset of the projects, invest in training staff and acquisition of new technology. The core of reducing red tape lies in upgrading of rules and administrative procedures in dealing with ISUP projects within the municipality so as to adopt to the dynamism that characterise the built environment.
- Full Text:
- Date Issued: 2019
Reproductive isolation mechanisms of two cryptic species of Eccritotarsus (Hemiptera: Miridae), biological control agents of water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae)
- Authors: Mnguni, Sandiso
- Date: 2019
- Subjects: Eccritotarsus , Meridae , Noxious weeds -- Biological control -- South Africa , Aquatic weeds -- Biological control -- South Africa , Water hyacinth -- Biological control -- South Africa , Biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68133 , vital:29202
- Description: Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae), is one of the world’s worst alien invasive plants. It is indigenous to the Amazon basin in South America but has become a problematic alien invasive in other parts of the world. As such, several host-specific biological control agents have been sourced from the native distributions in South America and have been released to control this plant where it has become problematic. Two of these agents include the geographically and reproductively isolated cryptic species of Eccritotarsus (Hemiptera: Miridae). One of these species was collected in the upper reaches of the Amazon River in Peru, while the other was collected over 3500km away from that site, in Florianopolis, southern Brazil. These cryptic species were thought to be a single species until recently, when DNA barcoding indicated that they were likely to be two species, and the species status has now been confirmed by interbreeding experiments and detailed morphological studies. The Brazilian population remains Eccritotarsus catarinensis (Carvalho), while the Peruvian population is now known as Eccritotarsus eichhorniae (Henry). The aim of this project was to investigate the mating behaviour and other behavioural traits of the two species that have resulted in reproductive isolation, and which could have led to speciation. In addition, investigations involving analysis of chemical compound compositions of the two species aimed to determine the extent to which the compounds played a role in the development and maintenance of reproductive isolation. To achieve the aims, behavioural-observation experiments were conducted in the form of no-choice, bi-choice and multi-choice tests in 1:1, 2:1 and 3:1 sex ratio assessments, both within and between species. Chemical compound compositions of E. catarinensis and E. eichhorniae were also assessed using Nuclear Magnetic Resonance (NMR), Solid-phase micro-extraction (SPME) and Gas-Chromatography Mass-Spectrometry (GC-MS) techniques. In no-choice experiments, the highest number of single and multiple copula incidences, and average total copula duration was found within species while copulation between species was much rarer. In bi-choice experiments, E. eichhorniae females and E. catarinensis males only chose to mate with their respective conspecifics, and within species copulations continued to have higher average total copula duration. In multi-choice experiments, the highest number of single and multiple copula incidences and average total copula duration was also found within species. GC-MS analysis suggested that E. catarinensis females and E. eichhorniae males have unique chemical compounds missing in their conspecifics and same sex of the other species. Further analysis suggested that E. catarinensis females and E. eichhorniae males have similar chemical compound compositions, whereas as E. eichhorniae females and E. catarinensis males have similar chemical compound compositions. These results suggest that there are behavioural differences that led to the development and maintenance of prezygotic reproductive isolation mechanisms, and that this is probably driven by pheromones in chemical compound compositions. These two species were geographically isolated in the native range and the populations have diverged to the point that they are now reproductively incompatible and therefore, distinct species. The main driver of the speciation is most likely mate recognition and attraction, as only reproductively important traits such as pheromones, genitalia, the scent glands and antennae have changed, while other traits, including host range and morphology, have remained remarkably stable. This provides evidence that differences in sexual selection in isolated populations may be important drivers of speciation and reproductive isolation in cryptic species.
- Full Text:
- Date Issued: 2019
- Authors: Mnguni, Sandiso
- Date: 2019
- Subjects: Eccritotarsus , Meridae , Noxious weeds -- Biological control -- South Africa , Aquatic weeds -- Biological control -- South Africa , Water hyacinth -- Biological control -- South Africa , Biological pest control agents
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68133 , vital:29202
- Description: Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae), is one of the world’s worst alien invasive plants. It is indigenous to the Amazon basin in South America but has become a problematic alien invasive in other parts of the world. As such, several host-specific biological control agents have been sourced from the native distributions in South America and have been released to control this plant where it has become problematic. Two of these agents include the geographically and reproductively isolated cryptic species of Eccritotarsus (Hemiptera: Miridae). One of these species was collected in the upper reaches of the Amazon River in Peru, while the other was collected over 3500km away from that site, in Florianopolis, southern Brazil. These cryptic species were thought to be a single species until recently, when DNA barcoding indicated that they were likely to be two species, and the species status has now been confirmed by interbreeding experiments and detailed morphological studies. The Brazilian population remains Eccritotarsus catarinensis (Carvalho), while the Peruvian population is now known as Eccritotarsus eichhorniae (Henry). The aim of this project was to investigate the mating behaviour and other behavioural traits of the two species that have resulted in reproductive isolation, and which could have led to speciation. In addition, investigations involving analysis of chemical compound compositions of the two species aimed to determine the extent to which the compounds played a role in the development and maintenance of reproductive isolation. To achieve the aims, behavioural-observation experiments were conducted in the form of no-choice, bi-choice and multi-choice tests in 1:1, 2:1 and 3:1 sex ratio assessments, both within and between species. Chemical compound compositions of E. catarinensis and E. eichhorniae were also assessed using Nuclear Magnetic Resonance (NMR), Solid-phase micro-extraction (SPME) and Gas-Chromatography Mass-Spectrometry (GC-MS) techniques. In no-choice experiments, the highest number of single and multiple copula incidences, and average total copula duration was found within species while copulation between species was much rarer. In bi-choice experiments, E. eichhorniae females and E. catarinensis males only chose to mate with their respective conspecifics, and within species copulations continued to have higher average total copula duration. In multi-choice experiments, the highest number of single and multiple copula incidences and average total copula duration was also found within species. GC-MS analysis suggested that E. catarinensis females and E. eichhorniae males have unique chemical compounds missing in their conspecifics and same sex of the other species. Further analysis suggested that E. catarinensis females and E. eichhorniae males have similar chemical compound compositions, whereas as E. eichhorniae females and E. catarinensis males have similar chemical compound compositions. These results suggest that there are behavioural differences that led to the development and maintenance of prezygotic reproductive isolation mechanisms, and that this is probably driven by pheromones in chemical compound compositions. These two species were geographically isolated in the native range and the populations have diverged to the point that they are now reproductively incompatible and therefore, distinct species. The main driver of the speciation is most likely mate recognition and attraction, as only reproductively important traits such as pheromones, genitalia, the scent glands and antennae have changed, while other traits, including host range and morphology, have remained remarkably stable. This provides evidence that differences in sexual selection in isolated populations may be important drivers of speciation and reproductive isolation in cryptic species.
- Full Text:
- Date Issued: 2019
Response of black wildebeest, a specialised grazer, to grass availability
- Authors: Barnardo, Toshka
- Date: 2019
- Subjects: Grasslands -- Research -- South Africa , Grassland ecology -- Research -- South Africa Food habits -- Research -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30876 , vital:31192
- Description: The black wildebeest Connochaetes gnou, a southern African endemic largely confined to the Grassland biome, was used as a model species to assess the response of a specialised grazer to grass availability, as an indicator of habitat quality. The occurrence of animals in low-quality habitats may have detrimental effects on population performance and persistence. Robust techniques are therefore required to assess the response of animals to varying habitat quality, to ensure sustainability of populations and species. Black wildebeest habitat use was assessed in relation to grass availability and visibility, and faecal analysis was used to estimate variation in diet composition and quality, parasite loads, and faecal pellet dimensions, across a grass gradient. Grass consumption, diet quality, and faecal pellet size and weight of black wildebeest increased with increasing grass availability. While black wildebeest consumed up to 55% browse at grass-poor sites, they consistently preferred grasses, potentially resulting in an increased intake of low-quality grasses at grass-poor sites. This, combined with the increased intake of indigestible fibres in browse, may explain the observed trends in diet quality, which in turn may explain variation in faecal pellet size and weight (indicators of body size and weight). Furthermore, black wildebeest population trends within the study area suggest that populations in grass-poor habitats, outside their natural distribution range, may exhibit reduced population performance. These findings suggest that grass availability may be a useful indicator of habitat quality for specialised grazers. The study also provided an opportunity to explore the utility of various diet assessment techniques for estimating herbivore diet composition and quality. Caution should be applied when interpreting and comparing estimates of diet composition and quality that were estimated using different techniques, because different techniques may yield different diet estimates. The study also suggests that black wildebeest may switch to C3 grasses in the winter (as indicated by isotope analysis).
- Full Text:
- Date Issued: 2019
- Authors: Barnardo, Toshka
- Date: 2019
- Subjects: Grasslands -- Research -- South Africa , Grassland ecology -- Research -- South Africa Food habits -- Research -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30876 , vital:31192
- Description: The black wildebeest Connochaetes gnou, a southern African endemic largely confined to the Grassland biome, was used as a model species to assess the response of a specialised grazer to grass availability, as an indicator of habitat quality. The occurrence of animals in low-quality habitats may have detrimental effects on population performance and persistence. Robust techniques are therefore required to assess the response of animals to varying habitat quality, to ensure sustainability of populations and species. Black wildebeest habitat use was assessed in relation to grass availability and visibility, and faecal analysis was used to estimate variation in diet composition and quality, parasite loads, and faecal pellet dimensions, across a grass gradient. Grass consumption, diet quality, and faecal pellet size and weight of black wildebeest increased with increasing grass availability. While black wildebeest consumed up to 55% browse at grass-poor sites, they consistently preferred grasses, potentially resulting in an increased intake of low-quality grasses at grass-poor sites. This, combined with the increased intake of indigestible fibres in browse, may explain the observed trends in diet quality, which in turn may explain variation in faecal pellet size and weight (indicators of body size and weight). Furthermore, black wildebeest population trends within the study area suggest that populations in grass-poor habitats, outside their natural distribution range, may exhibit reduced population performance. These findings suggest that grass availability may be a useful indicator of habitat quality for specialised grazers. The study also provided an opportunity to explore the utility of various diet assessment techniques for estimating herbivore diet composition and quality. Caution should be applied when interpreting and comparing estimates of diet composition and quality that were estimated using different techniques, because different techniques may yield different diet estimates. The study also suggests that black wildebeest may switch to C3 grasses in the winter (as indicated by isotope analysis).
- Full Text:
- Date Issued: 2019
Rural household dietary diversity and food security in Raymond Mhlaba local municipality
- Authors: Mnukwa, Minentle Lwando
- Date: 2019
- Subjects: Food security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17282 , vital:40872
- Description: In order to formulate or implement relevant food security programmes in rural areas, it is important to have a deep understanding of the food security status of rural households. Accordingly, this study was conducted to assess the food security status of rural households in Raymond Mhlaba Local Municipality. The study also sought to identify the socio-economic characteristics that influence household food security status. The research relied on primary data. Primary data were collected by using a structured questionnaire, which covered both demographic features of respondent households, and their recent food consumption patterns. The household survey was conducted among 272 participants of Raymond Mhlaba Local Municipality. Statistical tools employed in this study included both descriptive and inferential statistics. The main descriptive statistics used were frequency tables, means and percentages in relation to a number of demographic characteristics and food security indicators. The main indicator of food security/insecurity used in the study was the Household Dietary Diversity Score (HDDS). After calculating the HDDS for each household, households were defined as either food secure or insecure depending on whether their HDDS was above or below the average HDDS. A logistic regression model (binary or dichotomous) was then used to identify socio-economic factors that influence some households to have above-average rather than below-average food security levels. The Binary logistic regression model revealed that four out of eight variables included in the model were significant in explaining the variation in the food security situation of households in the study areas, namely age of household head, education level of household head, household income and household size. Of these, the first three were positively associated with aboveaverage food security status, while household size had a negative association. A Tobit model was further used to identify the determinants of the household dietary diversity score. The exact same variables were significant from the Tobit analysis, and in the same manner.
- Full Text:
- Date Issued: 2019
- Authors: Mnukwa, Minentle Lwando
- Date: 2019
- Subjects: Food security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17282 , vital:40872
- Description: In order to formulate or implement relevant food security programmes in rural areas, it is important to have a deep understanding of the food security status of rural households. Accordingly, this study was conducted to assess the food security status of rural households in Raymond Mhlaba Local Municipality. The study also sought to identify the socio-economic characteristics that influence household food security status. The research relied on primary data. Primary data were collected by using a structured questionnaire, which covered both demographic features of respondent households, and their recent food consumption patterns. The household survey was conducted among 272 participants of Raymond Mhlaba Local Municipality. Statistical tools employed in this study included both descriptive and inferential statistics. The main descriptive statistics used were frequency tables, means and percentages in relation to a number of demographic characteristics and food security indicators. The main indicator of food security/insecurity used in the study was the Household Dietary Diversity Score (HDDS). After calculating the HDDS for each household, households were defined as either food secure or insecure depending on whether their HDDS was above or below the average HDDS. A logistic regression model (binary or dichotomous) was then used to identify socio-economic factors that influence some households to have above-average rather than below-average food security levels. The Binary logistic regression model revealed that four out of eight variables included in the model were significant in explaining the variation in the food security situation of households in the study areas, namely age of household head, education level of household head, household income and household size. Of these, the first three were positively associated with aboveaverage food security status, while household size had a negative association. A Tobit model was further used to identify the determinants of the household dietary diversity score. The exact same variables were significant from the Tobit analysis, and in the same manner.
- Full Text:
- Date Issued: 2019
Sedimentology and shale gas potential of the Ecca Group, Karoo Supergroup in the Eastern Cape, South Africa
- Authors: Nemanashi , Tshisikhaiwe
- Date: 2019
- Subjects: Sedimentology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14616 , vital:40023
- Description: The aim of the study was to establish a deeper understanding on the stratigraphy, sedimentology, petrology, organic geochemistry and diagenesis of the Ecca Group, and to provide new insight on the shale gas occurrence and potential of the Ecca Group, Karoo Supergroup in the southern Karoo Basin. The Ecca Group stratigraphy is divided into five formations from the bottom upwards, namely the Prince Albert, Whitehill, Collingham, Ripon and the Fort Brown Formations. The stratigraphy of the five studied stratigraphy’s formations is now sub-divided into two new different members each. These subdivision was based on field investigation of lithological features, sedimentary structures, facies characteristics and stratigraphic correlation points. Each member has been assigned a lithological name. Sixteen sedimentary facies have been identified in the study area and were subdivided into six distinctive facies associations (FA 1, FA 2, FA 3, FA 4, FA 5 and FA 6). Sedimentological characteristics of facies associations identified indicate that the Ecca Group sediments initially accumulated in a deep marine environment, progressed through turbidite, shallow marine and ended in lacustrine and deltaic environments. The stratigraphic succession of the Ecca Group constitutes a perfect regression sequence, indicating that the marine water gradually retreated and the sea-level gradually dropped. Grain size analysis was performed on twenty four Ecca Group sandstone samples. Statistical parameters of grain-size statistical parameters, linear discriminate functions, passega diagrams and bivariate analysis were used to reveal the hydrodynamic conditions and depositional environments. The results indicated that the Ecca Group sandstones are mostly fine to very fine grained, near-symmetrical, mesokurtic and indicative of dominance of low energy environments. The linear discriminate function analysis for the Prince Albert, Whitehill, Collingham and Ripon Formations samples indicates that the majority of the deposits were by turbidity currents all in a deep marine environment; whilst of the Fort Brown Formation samples are lacustrine/deltaic deposits. The depositional mechanism C-M plot indicates that majority of the Ecca Group sediments clustered in the PQ and QR field suggesting deposition mainly by suspension, rolling or saltation as well as graded suspension. Modal mineral composition analysis indicates that the main framework grains of the Ecca Group sandstones are quartz, feldspar as well as lithic fragments derived from metamorphic, igneous and sedimentary rocks with a few from volcanic origin. The Ecca Group sandstones iii are immature compositionally and can be classified as feldspathic wackes and lithic wackes. The QFL ternary diagram revealed a dissected and recycled orogen arc provenance; whereas QmFLt ternary diagram point to dissected arc and transitional arc sources to an active continental margin as well as recycled provenance. These provenance characteristics suggest a metamorphic and plutonic terrains influence as the main source rock with minor debris derived from recycled sedimentary rocks. The weathering diagram and semi-quantitative weathering index suggests that the sandstones from the Ecca are mostly from a plutonic source area under arid to humid climatic conditions. The detrital modal compositions of these Ecca Group sandstones are related to a strike-slip setting, back arc to continental margin setting. Diagenetic features of the Ecca sandstones and shales are subdivided into early, late (burial) and uplift-related diagenetic stages. Mechanical compaction, recrystallization, cementation, replacement and the dissolution of framework grains or cements are some of the main diagenetic processes that largely affected the Ecca sediments. Early diagenetic processes include cementation, point/planar contact, formation of pyrite, hematite cements and mineral inversions. Recrystallization, replacement, compaction, overgrowth, albitization, seritisation, illitization, concave-convex and suture contacts as well as dissolution took place mostly in the later diagenetic stage due to increase of temperature and pressure as burial depth increased. The uplift-related diagenetic stage was mostly affected by deformation and fracturing, calcitization, dissolution, erosion and weathering. Diagenetic processes largely affected the porosity and permeability of the reservoir rock properties of the Ecca Group. Organic geochemistry results indicate that the sediments were highly weathered and the TOC values ranging from 0.10 to 7.35 wt% with mostly less than 0.5%, which indicate the source rocks have poor oil potential. The majority of the Ecca Shales have HI values less than 50 mg HC/g, TOC indicating Type-IV kerogen mostly derived from reworked organic matter with very little hydrocarbon generation potential. The relatively high Tmax (oC) and vitrinite reflective values indicate that most shales are thermally over-matured thus they have low hydrocarbon pontential.
- Full Text:
- Date Issued: 2019
- Authors: Nemanashi , Tshisikhaiwe
- Date: 2019
- Subjects: Sedimentology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14616 , vital:40023
- Description: The aim of the study was to establish a deeper understanding on the stratigraphy, sedimentology, petrology, organic geochemistry and diagenesis of the Ecca Group, and to provide new insight on the shale gas occurrence and potential of the Ecca Group, Karoo Supergroup in the southern Karoo Basin. The Ecca Group stratigraphy is divided into five formations from the bottom upwards, namely the Prince Albert, Whitehill, Collingham, Ripon and the Fort Brown Formations. The stratigraphy of the five studied stratigraphy’s formations is now sub-divided into two new different members each. These subdivision was based on field investigation of lithological features, sedimentary structures, facies characteristics and stratigraphic correlation points. Each member has been assigned a lithological name. Sixteen sedimentary facies have been identified in the study area and were subdivided into six distinctive facies associations (FA 1, FA 2, FA 3, FA 4, FA 5 and FA 6). Sedimentological characteristics of facies associations identified indicate that the Ecca Group sediments initially accumulated in a deep marine environment, progressed through turbidite, shallow marine and ended in lacustrine and deltaic environments. The stratigraphic succession of the Ecca Group constitutes a perfect regression sequence, indicating that the marine water gradually retreated and the sea-level gradually dropped. Grain size analysis was performed on twenty four Ecca Group sandstone samples. Statistical parameters of grain-size statistical parameters, linear discriminate functions, passega diagrams and bivariate analysis were used to reveal the hydrodynamic conditions and depositional environments. The results indicated that the Ecca Group sandstones are mostly fine to very fine grained, near-symmetrical, mesokurtic and indicative of dominance of low energy environments. The linear discriminate function analysis for the Prince Albert, Whitehill, Collingham and Ripon Formations samples indicates that the majority of the deposits were by turbidity currents all in a deep marine environment; whilst of the Fort Brown Formation samples are lacustrine/deltaic deposits. The depositional mechanism C-M plot indicates that majority of the Ecca Group sediments clustered in the PQ and QR field suggesting deposition mainly by suspension, rolling or saltation as well as graded suspension. Modal mineral composition analysis indicates that the main framework grains of the Ecca Group sandstones are quartz, feldspar as well as lithic fragments derived from metamorphic, igneous and sedimentary rocks with a few from volcanic origin. The Ecca Group sandstones iii are immature compositionally and can be classified as feldspathic wackes and lithic wackes. The QFL ternary diagram revealed a dissected and recycled orogen arc provenance; whereas QmFLt ternary diagram point to dissected arc and transitional arc sources to an active continental margin as well as recycled provenance. These provenance characteristics suggest a metamorphic and plutonic terrains influence as the main source rock with minor debris derived from recycled sedimentary rocks. The weathering diagram and semi-quantitative weathering index suggests that the sandstones from the Ecca are mostly from a plutonic source area under arid to humid climatic conditions. The detrital modal compositions of these Ecca Group sandstones are related to a strike-slip setting, back arc to continental margin setting. Diagenetic features of the Ecca sandstones and shales are subdivided into early, late (burial) and uplift-related diagenetic stages. Mechanical compaction, recrystallization, cementation, replacement and the dissolution of framework grains or cements are some of the main diagenetic processes that largely affected the Ecca sediments. Early diagenetic processes include cementation, point/planar contact, formation of pyrite, hematite cements and mineral inversions. Recrystallization, replacement, compaction, overgrowth, albitization, seritisation, illitization, concave-convex and suture contacts as well as dissolution took place mostly in the later diagenetic stage due to increase of temperature and pressure as burial depth increased. The uplift-related diagenetic stage was mostly affected by deformation and fracturing, calcitization, dissolution, erosion and weathering. Diagenetic processes largely affected the porosity and permeability of the reservoir rock properties of the Ecca Group. Organic geochemistry results indicate that the sediments were highly weathered and the TOC values ranging from 0.10 to 7.35 wt% with mostly less than 0.5%, which indicate the source rocks have poor oil potential. The majority of the Ecca Shales have HI values less than 50 mg HC/g, TOC indicating Type-IV kerogen mostly derived from reworked organic matter with very little hydrocarbon generation potential. The relatively high Tmax (oC) and vitrinite reflective values indicate that most shales are thermally over-matured thus they have low hydrocarbon pontential.
- Full Text:
- Date Issued: 2019
Sequencing, assembly and annotation of the mitochondrial and plastid genomes of Gelidium pristoides (Turner) Kützing from Kenton-on-Sea, South Africa
- Authors: Mangali, Sandisiwe
- Date: 2019
- Subjects: Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19109 , vital:39883
- Description: The genome is the complete set of an organism's hereditary information that contains all the information necessary for the functioning of that organism. Complete nuclear, mitochondrial and plastid DNA constitute the three main types of genomes which play interconnected roles in an organism. Genome sequencing enables researchers to understand the regulation and expression of the various genes and the proteins they encode. It allows researchers to extract and analyse genes of interests for a variety of studies including molecular, biotechnological, bioinformatics and conservation and evolutionary studies. Genome sequencing of Rhodophyta has received little attention. To date, no published studies are focusing on both whole genome sequencing and sequencing of the organellar genomes of Rhodophyta species found in along the South African coastline. This study focused on genome sequencing, assembly and annotation mitochondrial and plastid genomes of Gelidium pristoides. Gelidium pristoides was collected from Kenton-on-Sea and was morphologically identified at Rhodes University. Its genomic DNA was extracted using the Nucleospin® Plant II kit and quantified using Qubit 2.0, Nanodrop and 1% agarose gel electrophoresis. The Ion Plus Fragment Library kit was used for the preparation of a 600 bp library, which was sequenced in two separate runs through the Ion S5 platform. The produced reads were quality-controlled through the Ion Torrent server version 5.6. and assessed using the FASTQC program. The SPAdes version 3.11.1 assembler was used to assemble the quality-controlled reads, and the resultant genome assembly was quality-assessed using the QUAST 4.1 software. The mitochondrial genome was selected from the produced Gelidium pristoides draft genome using mitochondrial genomes of other Gelidiales as search queries on the local BLAST algorithm of the BioEdit software. Contigs matching the organellar genomes were ordered according to the mitochondrial genomes of other Gelidiales using the trial version of Geneious R11.12 software. The plastid genome was also selected following the same approach but using plastid genomes of Gelidium elegans and Gelidium vagum as search queries. Gaps observed in the organellar genomes were closed by amplification of the relevant gap using polymerase chain reaction with newly designed primers and Sanger sequencing. Open reading frames for both organellar genomes were annotated using the NCBI ORF-Finder and alignments obtained from BlastN and BlastX searches from the NCBI database, while the tRNAs and rRNAs were identified using the tRNAscan-SE1.21 vi and the RNAmmer 1.2 servers. The circular physical map of the mitochondrial genome was constructed using the CGView server. Lastly, in silico analysis of cytochrome c oxidase 3 and Heat Shock Protein 70 was performed using the PRIMO and the SWISS-MODEL pipelines respectively. Their phylogenies were analysed through Clustal omega and the trees viewed on TreeView 1.6.6 software. Qubit and Nanodrop genomic DNA qualification revealed A260/A280 and A230/A260 ratios of 1.81 and 1.52 respectively. The 1% agarose gel electrophoresis further confirmed the good quality of the genomic DNA used for library preparation and sequencing. Pre-assembly quality control of reads resulted in a total of 30 792 074 high-quality reads which were assembled into a total of 94140 contigs, making up an estimated genome length of 217.06 Mb. The largest contig covered up to 13.17 kb of the draft genome, and an N50 statistic value of 3.17 kb was obtained. The G.pristoides mitochondrial genome mapped into a circular molecule of 25012 bp, with an overall GC content of 31.04% and a total of 45 genes distributed into 20 tRNA-coding, 2 rRNAcoding genes and 23 protein-coding genes, mostly adopting the modified genetic code of Rhodophyta. The SecY and rps12 genes overlapped by 41 bp. This study presents a partial plastid genome composed of 89 (38%) fully annotated genes, of which 71 are protein-coding, and 18 are distributed among 15 tRNA-coding, 2 rRNA-coding and 1 RNaseP RNA-coding genes. Sixty-one (26%) partial protein-coding genes were predicted, while approximately 84 (36%) genes are not yet predicted. In silico analysis of the cytochrome c oxidase and heat shock protein 70 showed that the gene sequences obtained in this study and the resultant transcribed protein have sequences and structures that are similar to those from several other different species, thus validating the integrity of the genome sequences. This study provides genomic data necessary for understanding the genomic constituent of G.pristoides and serve as a foundation for studies of individual genes and for resolving evolutionary relationships.
- Full Text:
- Date Issued: 2019
- Authors: Mangali, Sandisiwe
- Date: 2019
- Subjects: Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19109 , vital:39883
- Description: The genome is the complete set of an organism's hereditary information that contains all the information necessary for the functioning of that organism. Complete nuclear, mitochondrial and plastid DNA constitute the three main types of genomes which play interconnected roles in an organism. Genome sequencing enables researchers to understand the regulation and expression of the various genes and the proteins they encode. It allows researchers to extract and analyse genes of interests for a variety of studies including molecular, biotechnological, bioinformatics and conservation and evolutionary studies. Genome sequencing of Rhodophyta has received little attention. To date, no published studies are focusing on both whole genome sequencing and sequencing of the organellar genomes of Rhodophyta species found in along the South African coastline. This study focused on genome sequencing, assembly and annotation mitochondrial and plastid genomes of Gelidium pristoides. Gelidium pristoides was collected from Kenton-on-Sea and was morphologically identified at Rhodes University. Its genomic DNA was extracted using the Nucleospin® Plant II kit and quantified using Qubit 2.0, Nanodrop and 1% agarose gel electrophoresis. The Ion Plus Fragment Library kit was used for the preparation of a 600 bp library, which was sequenced in two separate runs through the Ion S5 platform. The produced reads were quality-controlled through the Ion Torrent server version 5.6. and assessed using the FASTQC program. The SPAdes version 3.11.1 assembler was used to assemble the quality-controlled reads, and the resultant genome assembly was quality-assessed using the QUAST 4.1 software. The mitochondrial genome was selected from the produced Gelidium pristoides draft genome using mitochondrial genomes of other Gelidiales as search queries on the local BLAST algorithm of the BioEdit software. Contigs matching the organellar genomes were ordered according to the mitochondrial genomes of other Gelidiales using the trial version of Geneious R11.12 software. The plastid genome was also selected following the same approach but using plastid genomes of Gelidium elegans and Gelidium vagum as search queries. Gaps observed in the organellar genomes were closed by amplification of the relevant gap using polymerase chain reaction with newly designed primers and Sanger sequencing. Open reading frames for both organellar genomes were annotated using the NCBI ORF-Finder and alignments obtained from BlastN and BlastX searches from the NCBI database, while the tRNAs and rRNAs were identified using the tRNAscan-SE1.21 vi and the RNAmmer 1.2 servers. The circular physical map of the mitochondrial genome was constructed using the CGView server. Lastly, in silico analysis of cytochrome c oxidase 3 and Heat Shock Protein 70 was performed using the PRIMO and the SWISS-MODEL pipelines respectively. Their phylogenies were analysed through Clustal omega and the trees viewed on TreeView 1.6.6 software. Qubit and Nanodrop genomic DNA qualification revealed A260/A280 and A230/A260 ratios of 1.81 and 1.52 respectively. The 1% agarose gel electrophoresis further confirmed the good quality of the genomic DNA used for library preparation and sequencing. Pre-assembly quality control of reads resulted in a total of 30 792 074 high-quality reads which were assembled into a total of 94140 contigs, making up an estimated genome length of 217.06 Mb. The largest contig covered up to 13.17 kb of the draft genome, and an N50 statistic value of 3.17 kb was obtained. The G.pristoides mitochondrial genome mapped into a circular molecule of 25012 bp, with an overall GC content of 31.04% and a total of 45 genes distributed into 20 tRNA-coding, 2 rRNAcoding genes and 23 protein-coding genes, mostly adopting the modified genetic code of Rhodophyta. The SecY and rps12 genes overlapped by 41 bp. This study presents a partial plastid genome composed of 89 (38%) fully annotated genes, of which 71 are protein-coding, and 18 are distributed among 15 tRNA-coding, 2 rRNA-coding and 1 RNaseP RNA-coding genes. Sixty-one (26%) partial protein-coding genes were predicted, while approximately 84 (36%) genes are not yet predicted. In silico analysis of the cytochrome c oxidase and heat shock protein 70 showed that the gene sequences obtained in this study and the resultant transcribed protein have sequences and structures that are similar to those from several other different species, thus validating the integrity of the genome sequences. This study provides genomic data necessary for understanding the genomic constituent of G.pristoides and serve as a foundation for studies of individual genes and for resolving evolutionary relationships.
- Full Text:
- Date Issued: 2019
Spectroscopy based mapping of selected dominant rock types in the Balfour Formation (Beaufort Group), Eastern Cape Province, South Africa
- Authors: Qabaqaba, Mcebisi
- Date: 2019
- Subjects: spectrum Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14693 , vital:40057
- Description: Lithological mapping of areas is crucial for both mineral resource identification and determination of ore concentrations. Without adequate knowledge on the extent of an area’s lithology, the above applications cannot be meaningfully accomplished. Spectroscopy-based mapping of rocks involves the use of portable reflectance spectrometers and digital maps to analyze, assess and map changes in rocks. Thereafter, understand and interpret the geochemical, physical and environmental processes that have an impact on the reflectance of the rocks while also making spatial and spectral links. Mapping lithology using remote sensing involves identification of rocks in remotely sensed images with lithological mapping being achievable through field and laboratory spectroscopy and creation of a spectral library. The main goal of this study was to measure, extract and analyze spectral signatures of dominant rocks within the Balfour Formation in order to create a spectral library that is capable of enabling, fast and cost-effective mapping of the spatial distributions of rocks within the Balfour Formation. The spectra of dominant rocks of the Balfour Formation were measured using the SR 3500 spectroradiometer. Different pre-processing techniques were applied to the acquired spectra such as smoothing, scatter correction and outlier detection. Random Forest classifier was used in the classification of the different rocks. Analysis of Variance and Bonferroni post hoc test were applied on the spectral signatures of different rocks to ascertain if there were any spectral differences between the absorption features in the spectra of the rocks. Landsat 8 imagery was used for classification of the different rocks within the Balfour Formation, maximum likelihood and spectral angle mapper were the two classifiers that were XI used. Maximum likelihood presented an accuracy of 76.19 % and 66.67 % for spectral angle mapper.
- Full Text:
- Date Issued: 2019
- Authors: Qabaqaba, Mcebisi
- Date: 2019
- Subjects: spectrum Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14693 , vital:40057
- Description: Lithological mapping of areas is crucial for both mineral resource identification and determination of ore concentrations. Without adequate knowledge on the extent of an area’s lithology, the above applications cannot be meaningfully accomplished. Spectroscopy-based mapping of rocks involves the use of portable reflectance spectrometers and digital maps to analyze, assess and map changes in rocks. Thereafter, understand and interpret the geochemical, physical and environmental processes that have an impact on the reflectance of the rocks while also making spatial and spectral links. Mapping lithology using remote sensing involves identification of rocks in remotely sensed images with lithological mapping being achievable through field and laboratory spectroscopy and creation of a spectral library. The main goal of this study was to measure, extract and analyze spectral signatures of dominant rocks within the Balfour Formation in order to create a spectral library that is capable of enabling, fast and cost-effective mapping of the spatial distributions of rocks within the Balfour Formation. The spectra of dominant rocks of the Balfour Formation were measured using the SR 3500 spectroradiometer. Different pre-processing techniques were applied to the acquired spectra such as smoothing, scatter correction and outlier detection. Random Forest classifier was used in the classification of the different rocks. Analysis of Variance and Bonferroni post hoc test were applied on the spectral signatures of different rocks to ascertain if there were any spectral differences between the absorption features in the spectra of the rocks. Landsat 8 imagery was used for classification of the different rocks within the Balfour Formation, maximum likelihood and spectral angle mapper were the two classifiers that were XI used. Maximum likelihood presented an accuracy of 76.19 % and 66.67 % for spectral angle mapper.
- Full Text:
- Date Issued: 2019
Statistical optimisation of a terbinafine-containing cream
- Authors: Strydom, Lana
- Date: 2019
- Subjects: Chemicals -- Physiological effect , Pharmaceutical chemistry Medical microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44067 , vital:37101
- Description: Terbinafine hydrochloride (TBH) belongs to the allylamine class of antifungals and displays a favourable dermatopharmacokinetic profile, being both lipophilic and keratinophilic. It has thus been included in a variety of topical dosage forms for the treatment of dermatomycoses, many of which have been the subject of optimisation studies, with the purpose of improving the product. Since a TBH-containing cream had not been found in literature to have been optimised before, the aim of this study was to optimise a TBH cream formulation. A TBH cream formulation, suitable for optimisation, was developed. Preformulation tests were undertaken, including active-excipient compatibility testing using a combined thermal method consisting of both differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA), as well as isothermal stress testing (IST). With the confirmation of the suitability of the selected excipients, development of a suitable TBH cream took place largely by a trial-and-error approach. The choice of a suitable formulation was made based on the physical appearance and viscosity of the cream, for which a viscosity specification was set. The identified TBH cream formulation was evaluated for its physical appearance and physicochemical aspects to confirm its appropriateness for the purpose of further optimisation. Based on literature and observations from the preformulation and formulation stage, factors and responses for study during the optimisation stage were identified to study using a circumscribed central composite design (CCCD) at five levels (-1.612, -1, 0, +1, +1.612). Total percentage of surfactant (TPS), homogenisation speed (HS) and cooling rate (CR), were selected as factors to study their influence on cream viscosity, in vitro TBH release from the cream, as well as the chemical stability of TBH within the cream formulation. Following the application of stepwise multiple linear regression to the mathematical models, a suitable prediction model was only obtained for one response, cream viscosity at a shear rate of 20 s-1. A linear model was also found to fit the data for % in vitro TBH release after one hour, although a low R2 of 0.497 made the model unsuitable for prediction purposes. No mathematical model could be fit to the results for the response assessing the change in TBH concentration following seven days’ storage at accelerated stability conditions. The determination of the optimum TBH cream formulation was made chiefly on the basis of the results for cream viscosity and the optimised formulation was identified to have a predicted viscosity of 8.33 Pa.s and the factor settings to obtain this cream were a CR of 1.3 °C/min, HS set at 3400 rpm, and TPS of 4.2 %. Validation of the optimised TBH cream formulation was performed for cream viscosity at a shear rate of 20 s-1 and revealed that there was good agreement between the measured and predicted viscosity values. The optimised TBH cream underwent rheological characterisation and was compared to the innovator, Lamisil® cream, with both creams found to meet the desirable rheological profile. In vitro release testing (IVRT) was used to compare the release of TBH from the optimised TBH cream and Lamisil® cream, and the optimised TBH cream was found to show much greater TBH release over a six-hour time period than Lamisil® cream. Stability testing of the optimised TBH cream took place at accelerated stability testing conditions of 40 °C ± 2 °C and 75 ± 5 % relative humidity (RH). To assay the formulation and determine content uniformity over the three-month storage period, a suitable stability-indicating reversed-phase high performance liquid chromatography (RP-HPLC) method was developed and validated. Other cream properties which were tested included: qualitative aspects, viscosity, pH and microbial limits. At the end of the three-month stability testing period, the cream was found to meet most of the specifications set, except for cream homogeneity and viscosity. A TBH cream formulation was thus developed and optimised to meet a certain viscosity specification. Although this formulation was found to meet the viscosity specification on the day after its manufacture, the viscosity was found to increase on storage, such that it was outside the set viscosity specification range.
- Full Text:
- Date Issued: 2019
- Authors: Strydom, Lana
- Date: 2019
- Subjects: Chemicals -- Physiological effect , Pharmaceutical chemistry Medical microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44067 , vital:37101
- Description: Terbinafine hydrochloride (TBH) belongs to the allylamine class of antifungals and displays a favourable dermatopharmacokinetic profile, being both lipophilic and keratinophilic. It has thus been included in a variety of topical dosage forms for the treatment of dermatomycoses, many of which have been the subject of optimisation studies, with the purpose of improving the product. Since a TBH-containing cream had not been found in literature to have been optimised before, the aim of this study was to optimise a TBH cream formulation. A TBH cream formulation, suitable for optimisation, was developed. Preformulation tests were undertaken, including active-excipient compatibility testing using a combined thermal method consisting of both differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA), as well as isothermal stress testing (IST). With the confirmation of the suitability of the selected excipients, development of a suitable TBH cream took place largely by a trial-and-error approach. The choice of a suitable formulation was made based on the physical appearance and viscosity of the cream, for which a viscosity specification was set. The identified TBH cream formulation was evaluated for its physical appearance and physicochemical aspects to confirm its appropriateness for the purpose of further optimisation. Based on literature and observations from the preformulation and formulation stage, factors and responses for study during the optimisation stage were identified to study using a circumscribed central composite design (CCCD) at five levels (-1.612, -1, 0, +1, +1.612). Total percentage of surfactant (TPS), homogenisation speed (HS) and cooling rate (CR), were selected as factors to study their influence on cream viscosity, in vitro TBH release from the cream, as well as the chemical stability of TBH within the cream formulation. Following the application of stepwise multiple linear regression to the mathematical models, a suitable prediction model was only obtained for one response, cream viscosity at a shear rate of 20 s-1. A linear model was also found to fit the data for % in vitro TBH release after one hour, although a low R2 of 0.497 made the model unsuitable for prediction purposes. No mathematical model could be fit to the results for the response assessing the change in TBH concentration following seven days’ storage at accelerated stability conditions. The determination of the optimum TBH cream formulation was made chiefly on the basis of the results for cream viscosity and the optimised formulation was identified to have a predicted viscosity of 8.33 Pa.s and the factor settings to obtain this cream were a CR of 1.3 °C/min, HS set at 3400 rpm, and TPS of 4.2 %. Validation of the optimised TBH cream formulation was performed for cream viscosity at a shear rate of 20 s-1 and revealed that there was good agreement between the measured and predicted viscosity values. The optimised TBH cream underwent rheological characterisation and was compared to the innovator, Lamisil® cream, with both creams found to meet the desirable rheological profile. In vitro release testing (IVRT) was used to compare the release of TBH from the optimised TBH cream and Lamisil® cream, and the optimised TBH cream was found to show much greater TBH release over a six-hour time period than Lamisil® cream. Stability testing of the optimised TBH cream took place at accelerated stability testing conditions of 40 °C ± 2 °C and 75 ± 5 % relative humidity (RH). To assay the formulation and determine content uniformity over the three-month storage period, a suitable stability-indicating reversed-phase high performance liquid chromatography (RP-HPLC) method was developed and validated. Other cream properties which were tested included: qualitative aspects, viscosity, pH and microbial limits. At the end of the three-month stability testing period, the cream was found to meet most of the specifications set, except for cream homogeneity and viscosity. A TBH cream formulation was thus developed and optimised to meet a certain viscosity specification. Although this formulation was found to meet the viscosity specification on the day after its manufacture, the viscosity was found to increase on storage, such that it was outside the set viscosity specification range.
- Full Text:
- Date Issued: 2019
Statistical study of traveling ionospheric disturbances over South Africa
- Authors: Mahlangu, Daniel Fiso
- Date: 2019
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Gravity waves , Magnetic storms
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76387 , vital:30556
- Description: This thesis provides a statistical analysis of traveling ionospheric disturbances (TIDs) in South Africa. The velocities of the TIDs were determined from total electron content (TEC) maps using particle image velocimetry (PIV). The periods were determined using Morlet function in wavelet analysis. The TIDs were grouped into four categories: daytime, twilight, nighttime TIDs, and those TIDs that occurred during magnetic storms. It was found that daytime medium scale TIDs (MSTIDs) propagated equatorward in all seasons (summer, autumn, winter, and spring), with velocities of about 114 to 213 m/s. Their maximum occurrence was in winter between 15:00 and 16:00 LT. The daytime large scale (TIDs) LSTIDs propagated equatorward with velocities of approximately 455 to 767 m/s. Their highest occurrence was in summer, between 12:00-13:00 LT. Most of the these TIDs (about 78%) were observed during the passing of the morning solar terminator. This implied that the morning terminator was more effective in instigating TIDs. Only a few nighttime TIDs were observed and therefore their behavior could not be statistically inferred. The TIDs that occurred during magnetically disturbed conditions propagated equatorward. This indicated that their source mechanism was atmospheric gravity waves generated at the onset of geomagnetic storms.
- Full Text:
- Date Issued: 2019
- Authors: Mahlangu, Daniel Fiso
- Date: 2019
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Gravity waves , Magnetic storms
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76387 , vital:30556
- Description: This thesis provides a statistical analysis of traveling ionospheric disturbances (TIDs) in South Africa. The velocities of the TIDs were determined from total electron content (TEC) maps using particle image velocimetry (PIV). The periods were determined using Morlet function in wavelet analysis. The TIDs were grouped into four categories: daytime, twilight, nighttime TIDs, and those TIDs that occurred during magnetic storms. It was found that daytime medium scale TIDs (MSTIDs) propagated equatorward in all seasons (summer, autumn, winter, and spring), with velocities of about 114 to 213 m/s. Their maximum occurrence was in winter between 15:00 and 16:00 LT. The daytime large scale (TIDs) LSTIDs propagated equatorward with velocities of approximately 455 to 767 m/s. Their highest occurrence was in summer, between 12:00-13:00 LT. Most of the these TIDs (about 78%) were observed during the passing of the morning solar terminator. This implied that the morning terminator was more effective in instigating TIDs. Only a few nighttime TIDs were observed and therefore their behavior could not be statistically inferred. The TIDs that occurred during magnetically disturbed conditions propagated equatorward. This indicated that their source mechanism was atmospheric gravity waves generated at the onset of geomagnetic storms.
- Full Text:
- Date Issued: 2019
Substituent effects on the electrocatalytic activity of cobalt phthalocyanine in the presence of graphene quantum dots
- Centane, Sixolile Sibongiseni
- Authors: Centane, Sixolile Sibongiseni
- Date: 2019
- Subjects: Phthalocyanines , Quantum dots , Electrocatalysis , Electrochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67614 , vital:29121
- Description: The electrocatalytic activity of metallophthalocyanines derivatives is explored. Cobalt monocarboxyphenoxy phthalocyanine (1), cobalt tetracarboxyphenoxy phthalocyanine (2), cobalt tetraaminophenoxy phthalocyanine (3) and cobalt tris-(tert-butylphenoxy) monocarboxyphenoxy phthalocyanine (4) are the phthalocyanines employed in this work. The metallophthalocyanines were employed alone as well as in the presence of the carbon based graphene quantum dots. The electrocatalytic behaviour of functionalized GQDs is also explored herein. The catalytic processes studies were conducted on a glassy carbon electrode surface. Modification of the electrode was achieved by the adsorption method. The materials were adsorbed either alone, as premixed/covalently linked GQDs/Pc conjugates or sequentially. Sequentially adsorbed electrodes involved the phthalocyanines on top or beneath GQDs. Sequentially modified electrodes where the phthalocyanine had higher currents and low detection limits than when the phthalocyanine is underneath. Premixed conjugates showed better activity than the covalently formed conjugates. The nanomaterials synthesized and used in this work were characterized using transmission electron microscopy, UV-Vis spectroscopy, dynamic light scattering, Raman spectroscopy, X-ray diffraction, Atomic Force Microscopy and X-ray photoelectron spectroscopy. The modified electrodes were characterized using cyclic voltammetry and scanning electrochemical spectroscopy. The electrocatalytic activity of the modified electrodes towards the oxidation of hydrazine was evaluated using cyclic voltammetry and chronoamperometry. Superior catalytic activity was observed for the conjugates compared to that of the individual conjugates.
- Full Text:
- Date Issued: 2019
- Authors: Centane, Sixolile Sibongiseni
- Date: 2019
- Subjects: Phthalocyanines , Quantum dots , Electrocatalysis , Electrochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67614 , vital:29121
- Description: The electrocatalytic activity of metallophthalocyanines derivatives is explored. Cobalt monocarboxyphenoxy phthalocyanine (1), cobalt tetracarboxyphenoxy phthalocyanine (2), cobalt tetraaminophenoxy phthalocyanine (3) and cobalt tris-(tert-butylphenoxy) monocarboxyphenoxy phthalocyanine (4) are the phthalocyanines employed in this work. The metallophthalocyanines were employed alone as well as in the presence of the carbon based graphene quantum dots. The electrocatalytic behaviour of functionalized GQDs is also explored herein. The catalytic processes studies were conducted on a glassy carbon electrode surface. Modification of the electrode was achieved by the adsorption method. The materials were adsorbed either alone, as premixed/covalently linked GQDs/Pc conjugates or sequentially. Sequentially adsorbed electrodes involved the phthalocyanines on top or beneath GQDs. Sequentially modified electrodes where the phthalocyanine had higher currents and low detection limits than when the phthalocyanine is underneath. Premixed conjugates showed better activity than the covalently formed conjugates. The nanomaterials synthesized and used in this work were characterized using transmission electron microscopy, UV-Vis spectroscopy, dynamic light scattering, Raman spectroscopy, X-ray diffraction, Atomic Force Microscopy and X-ray photoelectron spectroscopy. The modified electrodes were characterized using cyclic voltammetry and scanning electrochemical spectroscopy. The electrocatalytic activity of the modified electrodes towards the oxidation of hydrazine was evaluated using cyclic voltammetry and chronoamperometry. Superior catalytic activity was observed for the conjugates compared to that of the individual conjugates.
- Full Text:
- Date Issued: 2019
Sulphide textures and compositions associated with the hydrothermal/magmatic system of the Twangiza gold deposit (South Kivu, DRC)
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
Syntheses and photophysico-chemical properties of phthalocyanines in the presence of silica nanoparticles
- Authors: Peteni, Siwaphiwe
- Date: 2019
- Subjects: Phthalocyanines , Silica , Nanoparticles , Bioconjugates
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67592 , vital:29118
- Description: This thesis reports on the syntheses and characterizationof symmetrical (charged and neutral), asymmetrical (neutral) metallophthalocyanines (MPcs) and subphthalocyanines (SubPcs). The charged and neutral Pcs were physically doped onto silica nanoparticles (SiNPs). The asymmetrical MPc was also chemically linked to SiNPs. Spectroscopic and microscopic techniques were used to confirm the formation of SiNPs-MPc conjugates. The photophysics and photochemistry of the MPcs were assessed when alone and in conjugates (with SiNPs). The studies showed no significant changes in fluorescence quantum yields (ϕF) and fluorescence lifetimes (ϕF) of MPcs following doping except for 2-SiNPs (2 = Zn tetraaminophenoxyphthalocyanines) and 6-SiNPs (doped) (6 = Zn tris[(4-(pyridine-4-ylthio)2-thio-4-methylthiazol-5yl) acetic acid phthalocyanine) where there was a decrease in the ϕF value. Also for 1-SiNPs (1 = unsubstituted ZnPc) there was an elongation in τF which could be due to the protection offered by SiNPs. Both charged/neutral MPcs displayed high triplet quantum yields (ϕT) and singlet quantum yields (ϕΔ) following doping except for 2-SiNPs where there was a decrease in the latter. For 1-SiNPs there was an increase in ϕT but a decrease inϕΔ .There wasa decrease in ϕT and an increase in ϕΔfor4-SiNPs (4 = Zn tetrasulfophenoxyphthalocyanine), the decrease in ϕT could be due to the orientation of theMPc in SiNPs. An increase in both ϕT and ϕΔ for 6-SiNPs (linked) compared to 6-SiNPs (doped) was observed. Complex 5 (5 = Zn tetra-kis-(dodecylmercapto) phthalocyanine) showed a low ϕΔ value.
- Full Text:
- Date Issued: 2019
- Authors: Peteni, Siwaphiwe
- Date: 2019
- Subjects: Phthalocyanines , Silica , Nanoparticles , Bioconjugates
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67592 , vital:29118
- Description: This thesis reports on the syntheses and characterizationof symmetrical (charged and neutral), asymmetrical (neutral) metallophthalocyanines (MPcs) and subphthalocyanines (SubPcs). The charged and neutral Pcs were physically doped onto silica nanoparticles (SiNPs). The asymmetrical MPc was also chemically linked to SiNPs. Spectroscopic and microscopic techniques were used to confirm the formation of SiNPs-MPc conjugates. The photophysics and photochemistry of the MPcs were assessed when alone and in conjugates (with SiNPs). The studies showed no significant changes in fluorescence quantum yields (ϕF) and fluorescence lifetimes (ϕF) of MPcs following doping except for 2-SiNPs (2 = Zn tetraaminophenoxyphthalocyanines) and 6-SiNPs (doped) (6 = Zn tris[(4-(pyridine-4-ylthio)2-thio-4-methylthiazol-5yl) acetic acid phthalocyanine) where there was a decrease in the ϕF value. Also for 1-SiNPs (1 = unsubstituted ZnPc) there was an elongation in τF which could be due to the protection offered by SiNPs. Both charged/neutral MPcs displayed high triplet quantum yields (ϕT) and singlet quantum yields (ϕΔ) following doping except for 2-SiNPs where there was a decrease in the latter. For 1-SiNPs there was an increase in ϕT but a decrease inϕΔ .There wasa decrease in ϕT and an increase in ϕΔfor4-SiNPs (4 = Zn tetrasulfophenoxyphthalocyanine), the decrease in ϕT could be due to the orientation of theMPc in SiNPs. An increase in both ϕT and ϕΔ for 6-SiNPs (linked) compared to 6-SiNPs (doped) was observed. Complex 5 (5 = Zn tetra-kis-(dodecylmercapto) phthalocyanine) showed a low ϕΔ value.
- Full Text:
- Date Issued: 2019
Synthesis of indium phthalocyanines for photodynamic antimicrobial chemotherapy and photo-oxidation of pollutants
- Authors: Sindelo, Azole
- Date: 2019
- Subjects: Phthalocyanines , Azo dyes , Indium compounds , Photochemotherapy , Nanoparticles , Photodegradation , Pollutants , Water -- Purification
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67581 , vital:29116
- Description: Indium (III) octacarboxyl phthalocyanine (ClInOCPc) alone and when conjugated to magnetic nanoparticles (MNP-ClInOCPc), 2(3),9(10),16(17),23(24)-octapyridylsulfanyl phthalocyaninato chloroindium (III) (ClInOPyPc) and its quaternized derivative 2(3),9(10),16(17),23(24)-octamethylpyridylsulfanyl phthalocyaninato chloroindium (III) (ClInOMePyPc) were synthesized. All Pcs were tested for both photodynamic antimicrobial chemotherapy (PACT) of an unknown water sample and photo-degradation of methyl red (MR). The singlet quantum yield (ΦΔ) for the ClInOCPc and MNP-ClInOCPc in PAN polymer fibers were 0.36 and 0.20 respectively using ADMA as a quencher in water. The photo-inactivation of bacteria in a water sample with unknown microbes was tested, with the MNP-ClInOCPc inactivating 90.6 % of the microbes and the ClInOCPc with 84.8 %. When embedded to the polymer, there was 48% bacterial clearance for ClInOCPc and 64% clearance for the MNP-ClInOCPc. The rate of degradation of MR increased with decrease of the MR concentration, with the MNP-ClInOCPc having the fastest rate. For ClInOPyPc and ClInOMePyPc, the singlet quantum yields were 0.46 and 0.33 in dimethylformamide (DMF), respectively. The PACT activity of ClInOMePyPc (containing 8 positive charges) was compared to those of 9(10),16(17),23(24)-tri-N-methyl-4-pyridylsulfanyl-2(3)-(4-aminophenoxy) phthalocyaninato chloro indium (III) triiodide (1) (containing 3 positive charges) and 2-[4-(N-methylpyridyloxy) phthalocyaninato] chloroindium (III) iodide (2) (containing 4 positive charges). When comparing ClInOMePyPc, 1 and 2, the largest log reduction for E. coli were obtained for complex 2 containing four positive charges hence showing it is not always the charge that determines the PACT activity, but the bridging atom in the phthalocyanine plays a role.
- Full Text:
- Date Issued: 2019
- Authors: Sindelo, Azole
- Date: 2019
- Subjects: Phthalocyanines , Azo dyes , Indium compounds , Photochemotherapy , Nanoparticles , Photodegradation , Pollutants , Water -- Purification
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67581 , vital:29116
- Description: Indium (III) octacarboxyl phthalocyanine (ClInOCPc) alone and when conjugated to magnetic nanoparticles (MNP-ClInOCPc), 2(3),9(10),16(17),23(24)-octapyridylsulfanyl phthalocyaninato chloroindium (III) (ClInOPyPc) and its quaternized derivative 2(3),9(10),16(17),23(24)-octamethylpyridylsulfanyl phthalocyaninato chloroindium (III) (ClInOMePyPc) were synthesized. All Pcs were tested for both photodynamic antimicrobial chemotherapy (PACT) of an unknown water sample and photo-degradation of methyl red (MR). The singlet quantum yield (ΦΔ) for the ClInOCPc and MNP-ClInOCPc in PAN polymer fibers were 0.36 and 0.20 respectively using ADMA as a quencher in water. The photo-inactivation of bacteria in a water sample with unknown microbes was tested, with the MNP-ClInOCPc inactivating 90.6 % of the microbes and the ClInOCPc with 84.8 %. When embedded to the polymer, there was 48% bacterial clearance for ClInOCPc and 64% clearance for the MNP-ClInOCPc. The rate of degradation of MR increased with decrease of the MR concentration, with the MNP-ClInOCPc having the fastest rate. For ClInOPyPc and ClInOMePyPc, the singlet quantum yields were 0.46 and 0.33 in dimethylformamide (DMF), respectively. The PACT activity of ClInOMePyPc (containing 8 positive charges) was compared to those of 9(10),16(17),23(24)-tri-N-methyl-4-pyridylsulfanyl-2(3)-(4-aminophenoxy) phthalocyaninato chloro indium (III) triiodide (1) (containing 3 positive charges) and 2-[4-(N-methylpyridyloxy) phthalocyaninato] chloroindium (III) iodide (2) (containing 4 positive charges). When comparing ClInOMePyPc, 1 and 2, the largest log reduction for E. coli were obtained for complex 2 containing four positive charges hence showing it is not always the charge that determines the PACT activity, but the bridging atom in the phthalocyanine plays a role.
- Full Text:
- Date Issued: 2019
Synthesis, characterisation and spectroscopic studies of diazine-N-oxide complexes of iron(II) towards the development of sensors
- Authors: Mpiti, Unako Bongani
- Date: 2019
- Subjects: Diazines , Ligands , Iron
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94753 , vital:31075
- Description: The characteristic magnetic and spectroscopic features associated with the red monomeric or dimeric, and polymeric pyrazine-N-oxide (PyzNO) iron(II) perchlorate complexes; Fen(μ1,1-pyzNO)2n-2(pyzNO)3n+2(ClO4)2n (n = {1, 2}*, and the novel compound {Fe(μ-pyzNO-κN,κO)n-1(pyzNO-κN)2(pyzNO-κO)2}n(ClO4)2n†, respectively, were investigated. These properties are altered substantially when the complexes are hydrated; for instance, by atmospheric exposure. The resulting species; Fe(pyzNO)5(H2O)3(ClO4)2* and [Fe(pyzNO-κN)4(H2O)2](ClO4)2.2H2O†, which have different hues of a bright yellow colour, were found to exhibit strong paramagnetism, in contrast to their anhydrous precursors, which are ‘EPR silent’. A low spin → high spin crossover (LS→HS, SCO) transition was therefore proposed to occur as the complexes become hydrated by atmospheric moisture. The red→yellow colour change is reversible, and dehydration of the yellow species by heating regenerates the red variant, a feature which lends itself to the potential applicability of the system as a sensor. Further emphasis on this potential derives from the fact that the hydration/dehydration process, and its accompanying physical changes, appears reversible even after many such treatments. It became of interest, then, to determine if these changes were limited to water-exposed samples, or if they occurred under more diverse solvent atmospheres. The reversibility of such exposure on the structure of the novel polynuclear complex was therefore investigated. In general, it was found that there occurred a strong solvent-complex association for the more polar solvents. Red→yellow, LS→HS events were seen when the complex was exposed to the vapours of p-dioxane, acetaldehyde and formaldehyde, and to a lesser extent, to that of methanol. In each case, significant structural changes were seen, as evidenced be comparative XRPD and thermo-analytical studies. Some of these changes have however been ascribed to the effects of partial dissolution upon extended exposure of the complex to the associated media. Exposure to less polar solvent atmospheres, such as those of cyclohexane, toluene, diethyl ether, etc., showed some signs of mild solvent surface adhesion, but were unaccompanied by discernible magnetic and colour changes. Another novel complex was produced during attempts to synthesize the PyzNO complexes from a mixture of a 2,2’-dimethoxypropane (DMP) and ethanol (1:1, v/v), rather than the methanol/DMP mixture which had been alternately used. The formula of the resulting complex is Fe(pyzNO)6(ClO4)2.3EtOH*. This EPR inactive product was orange in colour, and transformed into a bright yellow, strongly paramagnetic species upon atmospheric exposure. Further solvent studies showed that this species interacted significantly with all solvents tested, but generally more strongly with increasing solvent polarity. Orange→yellow colour changes occurred in environments saturated with p-dioxane, acetaldehyde and formaldehyde vapours. The DMSO-exposed sample transformed to dark red, due to suspected PyzNO substitution by the solvent. The red→yellow and orange→yellow colour changes were ascribed to the formal substitution of O-coordinated PyzNO (μ-PyzNO in the polymeric complex) by the incoming solvent. The resulting structural and geometric changes stimulated a redistribution of d electrons among the new constituent molecular orbitals of altered energy and symmetry. Therefore, although the colour changes were not conventionally solvatochromic - in that the original structure was lost on exposure – data suggested that it was the coordination of species of higher donor strength that produced the observed bathochromic shifts. A novel 4,4’-bipyridine-N-oxide Fe(II) perchlorate complex, Fe2(bipyNO)5(ClO4)4.6MeOH†, was also produced, primarily for physicochemical comparison with the PyzNO complexes. No colour or magnetic changes were seen on atmospheric exposure. The original complex was observed to be inherently paramagnetic, and no SCO events occurred upon solvent exposure. Despite this, thermal analyses showed that the complex did exhibit the strong uptake of polar solvents in general, but particularly with acetaldehyde. Significant structural changes upon exposure were limited to surface phenomena, with the exception of the acetaldehyde-exposed sample.
- Full Text:
- Date Issued: 2019
- Authors: Mpiti, Unako Bongani
- Date: 2019
- Subjects: Diazines , Ligands , Iron
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94753 , vital:31075
- Description: The characteristic magnetic and spectroscopic features associated with the red monomeric or dimeric, and polymeric pyrazine-N-oxide (PyzNO) iron(II) perchlorate complexes; Fen(μ1,1-pyzNO)2n-2(pyzNO)3n+2(ClO4)2n (n = {1, 2}*, and the novel compound {Fe(μ-pyzNO-κN,κO)n-1(pyzNO-κN)2(pyzNO-κO)2}n(ClO4)2n†, respectively, were investigated. These properties are altered substantially when the complexes are hydrated; for instance, by atmospheric exposure. The resulting species; Fe(pyzNO)5(H2O)3(ClO4)2* and [Fe(pyzNO-κN)4(H2O)2](ClO4)2.2H2O†, which have different hues of a bright yellow colour, were found to exhibit strong paramagnetism, in contrast to their anhydrous precursors, which are ‘EPR silent’. A low spin → high spin crossover (LS→HS, SCO) transition was therefore proposed to occur as the complexes become hydrated by atmospheric moisture. The red→yellow colour change is reversible, and dehydration of the yellow species by heating regenerates the red variant, a feature which lends itself to the potential applicability of the system as a sensor. Further emphasis on this potential derives from the fact that the hydration/dehydration process, and its accompanying physical changes, appears reversible even after many such treatments. It became of interest, then, to determine if these changes were limited to water-exposed samples, or if they occurred under more diverse solvent atmospheres. The reversibility of such exposure on the structure of the novel polynuclear complex was therefore investigated. In general, it was found that there occurred a strong solvent-complex association for the more polar solvents. Red→yellow, LS→HS events were seen when the complex was exposed to the vapours of p-dioxane, acetaldehyde and formaldehyde, and to a lesser extent, to that of methanol. In each case, significant structural changes were seen, as evidenced be comparative XRPD and thermo-analytical studies. Some of these changes have however been ascribed to the effects of partial dissolution upon extended exposure of the complex to the associated media. Exposure to less polar solvent atmospheres, such as those of cyclohexane, toluene, diethyl ether, etc., showed some signs of mild solvent surface adhesion, but were unaccompanied by discernible magnetic and colour changes. Another novel complex was produced during attempts to synthesize the PyzNO complexes from a mixture of a 2,2’-dimethoxypropane (DMP) and ethanol (1:1, v/v), rather than the methanol/DMP mixture which had been alternately used. The formula of the resulting complex is Fe(pyzNO)6(ClO4)2.3EtOH*. This EPR inactive product was orange in colour, and transformed into a bright yellow, strongly paramagnetic species upon atmospheric exposure. Further solvent studies showed that this species interacted significantly with all solvents tested, but generally more strongly with increasing solvent polarity. Orange→yellow colour changes occurred in environments saturated with p-dioxane, acetaldehyde and formaldehyde vapours. The DMSO-exposed sample transformed to dark red, due to suspected PyzNO substitution by the solvent. The red→yellow and orange→yellow colour changes were ascribed to the formal substitution of O-coordinated PyzNO (μ-PyzNO in the polymeric complex) by the incoming solvent. The resulting structural and geometric changes stimulated a redistribution of d electrons among the new constituent molecular orbitals of altered energy and symmetry. Therefore, although the colour changes were not conventionally solvatochromic - in that the original structure was lost on exposure – data suggested that it was the coordination of species of higher donor strength that produced the observed bathochromic shifts. A novel 4,4’-bipyridine-N-oxide Fe(II) perchlorate complex, Fe2(bipyNO)5(ClO4)4.6MeOH†, was also produced, primarily for physicochemical comparison with the PyzNO complexes. No colour or magnetic changes were seen on atmospheric exposure. The original complex was observed to be inherently paramagnetic, and no SCO events occurred upon solvent exposure. Despite this, thermal analyses showed that the complex did exhibit the strong uptake of polar solvents in general, but particularly with acetaldehyde. Significant structural changes upon exposure were limited to surface phenomena, with the exception of the acetaldehyde-exposed sample.
- Full Text:
- Date Issued: 2019
Synthesis, characterization and anticancer studies of Oxovanadium(iv) Dithiocarbamate complexes
- Authors: Hlobo, Priscilla Vuyiswa
- Date: 2019
- Subjects: Inorganic compounds -- Synthesis Chemistry, Inorganic
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19131 , vital:39880
- Description: Eight new oxovanadium(IV) dithiocarbamate complexes, formed by the interaction of vanadyl sulfate pentahydrate and as-synthesized dithiocarbamate ligands, potassium N-morpholine-4- dithiocarbamate ligand (L1), potassium N-piperidinedithiocarbamate (L2), potassium N-(4- methoxyphenyl)dithiocarbamate ligand (L3), potassium N-diallyldithiocarbamate ligand (L4), potassium N-phenyldithiocarbamate ligand (L5), potassium N-dibenzylminedithiocarbamate ligand (L6), potassium N-(4-methylphenyl)dithiocarbamate ligand (L7), N-(1Himidazoledithiocarbamate) fluoride ligand (L8) in aqueous ethanol are described. The resulting complexes were elemental analyses, molar conductance, infrared, electronic, and nuclear magnetic resonance spectral studies. The spectral studies confirmed the formation of the ligands and complexes. Four complexes [VO(L1)2], [VO(L3)2], [VO(L6)2], and [VO(L8)2] derived from potassium N-morpholine-4-dithiocarbamate ligand (L1), potassium N-(4- methoxyphenyl)dithiocarbamate ligand (L3), potassium N-dibenzylminedithiocarbamate ligand (L6), and N-(1H-imidazoledithiocarbamate) fluoride ligand (L8) were characterized using cyclic voltammetry, to study their electrochemical behavior. Square pyramid oxovanadium(IV) complexes were proposed with the metal ion coordinated to two bidentate dithiocarbamate ligands through sulphur to complete its square pyramidal geometry. The anticancer screening of four oxovanadium(IV) dithiocarbamate complexes [VO(L1)2], [VO(L3)2], [VO(L6)2], and [VO(L8)2] are described.
- Full Text:
- Date Issued: 2019
- Authors: Hlobo, Priscilla Vuyiswa
- Date: 2019
- Subjects: Inorganic compounds -- Synthesis Chemistry, Inorganic
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19131 , vital:39880
- Description: Eight new oxovanadium(IV) dithiocarbamate complexes, formed by the interaction of vanadyl sulfate pentahydrate and as-synthesized dithiocarbamate ligands, potassium N-morpholine-4- dithiocarbamate ligand (L1), potassium N-piperidinedithiocarbamate (L2), potassium N-(4- methoxyphenyl)dithiocarbamate ligand (L3), potassium N-diallyldithiocarbamate ligand (L4), potassium N-phenyldithiocarbamate ligand (L5), potassium N-dibenzylminedithiocarbamate ligand (L6), potassium N-(4-methylphenyl)dithiocarbamate ligand (L7), N-(1Himidazoledithiocarbamate) fluoride ligand (L8) in aqueous ethanol are described. The resulting complexes were elemental analyses, molar conductance, infrared, electronic, and nuclear magnetic resonance spectral studies. The spectral studies confirmed the formation of the ligands and complexes. Four complexes [VO(L1)2], [VO(L3)2], [VO(L6)2], and [VO(L8)2] derived from potassium N-morpholine-4-dithiocarbamate ligand (L1), potassium N-(4- methoxyphenyl)dithiocarbamate ligand (L3), potassium N-dibenzylminedithiocarbamate ligand (L6), and N-(1H-imidazoledithiocarbamate) fluoride ligand (L8) were characterized using cyclic voltammetry, to study their electrochemical behavior. Square pyramid oxovanadium(IV) complexes were proposed with the metal ion coordinated to two bidentate dithiocarbamate ligands through sulphur to complete its square pyramidal geometry. The anticancer screening of four oxovanadium(IV) dithiocarbamate complexes [VO(L1)2], [VO(L3)2], [VO(L6)2], and [VO(L8)2] are described.
- Full Text:
- Date Issued: 2019
Synthesis, characterization and in vitro antibacterial analysis of carvacrol based-hybrid analogues
- Authors: Mbese, Zintle
- Date: 2019
- Subjects: Medicinal plants Herbs -- Therapeutic use
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14527 , vital:39998
- Description: he focus of this research was to synthesize and characterize carvacrol hybrid analogues. Twenty-one (21) carvacrol analogues were synthesized by reacting carvacrol with (1. 4- aminosalicylic acid, 2. ferrocene keto-butanoic acid, 3. Ferrocene butanoic acid, 4. succinic anhydride, 5. folic acid, 6. cinnamic acid, 7. leucovorin, 8. oleanolic acid, 9. artesunate, 10. cholesterol, 11. cholesterol succinate, 12. curcumin, 13. curcumin succinate, 14. zidovudine, 15. Zidovudine succinate, 16. 8-hydroxyquinoline, 17. 8-hydroxyquinoline succinate, 18. 2- (7-chloroquinolin-4-ylamino)ethyl 5-isopropyl-2-methylphenyl, 19. 2-(7-chloroquinolin-4- ylamino)ethyl 5-isopropyl-2-methylphenyl succinate, 20. 2-(2-(7-chloroquinolin-4- ylamino)ethoxy)ethyl 5-isopropyl-2-methylphenyl, 21. 2-(2-(7-chloroquinolin-4- ylamino)ethoxy)ethyl 5-isopropyl-2-methylphenyl succinate). The carvacrol analogues were characterized using FTIR, UHPLC-HRMS, 1H- and 13C-NMR spectroscopy. The antibacterial analysis was performed to evaluate the carvacrol analogues against bacterial strains. FTIR spectra of carvacrol analogues were found to exhibit peaks of C-O stretch and Ar-C in a range of 1014-1280 cm-1 and a range of 1414-1697 cm-1 which confirm the successful formation of esters. The proposed structures of carvacrol analogues were confirmed by the 1H- and 13C-NMR. The selected 1H-NMR signal for aromatic protons ranged at 6.00-8.95 ppm/δ. The selected 13C-NMR signal for ester carbon and aromatic carbons ranged at 160.0-175.0 ppm/δ and at 110.00-154.00 ppm/δ. The structures were also confirmed by UHPLC-HRMS. Carvacrol analogues exhibited the highest inhibitory effect against Gram-positive and Gram-negative tested bacterial strains.
- Full Text:
- Date Issued: 2019
- Authors: Mbese, Zintle
- Date: 2019
- Subjects: Medicinal plants Herbs -- Therapeutic use
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14527 , vital:39998
- Description: he focus of this research was to synthesize and characterize carvacrol hybrid analogues. Twenty-one (21) carvacrol analogues were synthesized by reacting carvacrol with (1. 4- aminosalicylic acid, 2. ferrocene keto-butanoic acid, 3. Ferrocene butanoic acid, 4. succinic anhydride, 5. folic acid, 6. cinnamic acid, 7. leucovorin, 8. oleanolic acid, 9. artesunate, 10. cholesterol, 11. cholesterol succinate, 12. curcumin, 13. curcumin succinate, 14. zidovudine, 15. Zidovudine succinate, 16. 8-hydroxyquinoline, 17. 8-hydroxyquinoline succinate, 18. 2- (7-chloroquinolin-4-ylamino)ethyl 5-isopropyl-2-methylphenyl, 19. 2-(7-chloroquinolin-4- ylamino)ethyl 5-isopropyl-2-methylphenyl succinate, 20. 2-(2-(7-chloroquinolin-4- ylamino)ethoxy)ethyl 5-isopropyl-2-methylphenyl, 21. 2-(2-(7-chloroquinolin-4- ylamino)ethoxy)ethyl 5-isopropyl-2-methylphenyl succinate). The carvacrol analogues were characterized using FTIR, UHPLC-HRMS, 1H- and 13C-NMR spectroscopy. The antibacterial analysis was performed to evaluate the carvacrol analogues against bacterial strains. FTIR spectra of carvacrol analogues were found to exhibit peaks of C-O stretch and Ar-C in a range of 1014-1280 cm-1 and a range of 1414-1697 cm-1 which confirm the successful formation of esters. The proposed structures of carvacrol analogues were confirmed by the 1H- and 13C-NMR. The selected 1H-NMR signal for aromatic protons ranged at 6.00-8.95 ppm/δ. The selected 13C-NMR signal for ester carbon and aromatic carbons ranged at 160.0-175.0 ppm/δ and at 110.00-154.00 ppm/δ. The structures were also confirmed by UHPLC-HRMS. Carvacrol analogues exhibited the highest inhibitory effect against Gram-positive and Gram-negative tested bacterial strains.
- Full Text:
- Date Issued: 2019
Targeted attack detection by means of free and open source solutions
- Authors: Bernardo, Louis F
- Date: 2019
- Subjects: Computer networks -- Security measures , Information technology -- Security measures , Computer security -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92269 , vital:30703
- Description: Compliance requirements are part of everyday business requirements for various areas, such as retail and medical services. As part of compliance it may be required to have infrastructure in place to monitor the activities in the environment to ensure that the relevant data and environment is sufficiently protected. At the core of such monitoring solutions one would find some type of data repository, or database, to store and ultimately correlate the captured events. Such solutions are commonly called Security Information and Event Management, or SIEM for short. Larger companies have been known to use commercial solutions such as IBM's Qradar, Logrythm, or Splunk. However, these come at significant cost and arent suitable for smaller businesses with limited budgets. These solutions require manual configuration of event correlation for detection of activities that place the environment in danger. This usually requires vendor implementation assistance that also would come at a cost. Alternatively, there are open source solutions that provide the required functionality. This research will demonstrate building an open source solution, with minimal to no cost for hardware or software, while still maintaining the capability of detecting targeted attacks. The solution presented in this research includes Wazuh, which is a combination of OSSEC and the ELK stack, integrated with an Network Intrusion Detection System (NIDS). The success of the integration, is determined by measuring postive attack detection based on each different configuration options. To perform the testing, a deliberately vulnerable platform named Metasploitable will be used as a victim host. The victim host vulnerabilities were created specifically to serve as target for Metasploit. The attacks were generated by utilising Metasploit Framework on a prebuilt Kali Linux host.
- Full Text:
- Date Issued: 2019
- Authors: Bernardo, Louis F
- Date: 2019
- Subjects: Computer networks -- Security measures , Information technology -- Security measures , Computer security -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92269 , vital:30703
- Description: Compliance requirements are part of everyday business requirements for various areas, such as retail and medical services. As part of compliance it may be required to have infrastructure in place to monitor the activities in the environment to ensure that the relevant data and environment is sufficiently protected. At the core of such monitoring solutions one would find some type of data repository, or database, to store and ultimately correlate the captured events. Such solutions are commonly called Security Information and Event Management, or SIEM for short. Larger companies have been known to use commercial solutions such as IBM's Qradar, Logrythm, or Splunk. However, these come at significant cost and arent suitable for smaller businesses with limited budgets. These solutions require manual configuration of event correlation for detection of activities that place the environment in danger. This usually requires vendor implementation assistance that also would come at a cost. Alternatively, there are open source solutions that provide the required functionality. This research will demonstrate building an open source solution, with minimal to no cost for hardware or software, while still maintaining the capability of detecting targeted attacks. The solution presented in this research includes Wazuh, which is a combination of OSSEC and the ELK stack, integrated with an Network Intrusion Detection System (NIDS). The success of the integration, is determined by measuring postive attack detection based on each different configuration options. To perform the testing, a deliberately vulnerable platform named Metasploitable will be used as a victim host. The victim host vulnerabilities were created specifically to serve as target for Metasploit. The attacks were generated by utilising Metasploit Framework on a prebuilt Kali Linux host.
- Full Text:
- Date Issued: 2019