The development of biological tools to aid in the genetic investigation of the black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros mitochondrial genomes
- Authors: Parsons, Michelle
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56059 , vital:26769
- Description: The black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are found in South Africa. A decline in the populations of these species has resulted due to human activities such as habitat fragmentation and poaching. This has contributed to the loss of genetic diversity amongst the black and white rhinoceros. Conservation and anti-poaching efforts are needed to help maintain genetic diversity. These efforts could be improved through the development of non-invasive techniques to examine DNA from threatened animals. The aim of this research was to develop a molecular technique which would allow for the identification of the black and white rhinoceros and to develop a molecular technique which would allow for intraspecies genetic variation to be examined. DNA extractions were performed on matched faecal and tissue samples that were collected from two regions in South Africa. Polymerase chain reaction (PCR) primer sets were designed to investigate several regions of the rhinoceros mitochondrial genome. PCR optimisation was completed for the target regions. Sequencing was conducted on all final PCR products. The cytochrome c oxidase subunit 1 (COIi) gene allowed for the rhinoceros family to be identified. This region was digested with the HindIII restriction enzyme, which allowed for the specific identification of either the black or white rhinoceros. A subsequent region of the cytochrome c oxidase subunit 1 (COIii) as well as the D-loop, hypervariable regions (HV1 and HV2), cytochrome b (cytb) and 16s rRNA regions were investigated. These regions displayed potential for establishing geographic origin for black rhinoceros samples, whereas the D-loop and HV2 show potential for the white rhinoceros. The white rhinoceros displayed sequence variation in the HV2 and cytb region, while variation was observed in the COIi and HV1 for the black rhinoceros. All investigated target regions allowed for the rhinoceros family to be identified. The COI (COIi and COIii), HV2 and cytb regions allowed for the subspecies of rhinoceros to be identified, however the D-loop was not able to identify the white rhinoceros species. The 16s rRNA and HV1 regions allowed for the correct subspecies of rhinoceros to be identified, however as the primers were only compatible for the black rhinoceros therefore a subsequent investigation is required for the white rhinoceros. The establishment of this novel PCR based technique to identify white and black rhinoceros will allow for efficient species identification in wildlife forensic cases. A biological method was established to study intraspecies variation for the white and black rhinoceros; however the investigated target regions did not yield sufficient genetic variation. The core techniques developed in this study will be valuable for future studies that wish to investigate genetic variation in mammal species.
- Full Text:
- Date Issued: 2015
- Authors: Parsons, Michelle
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56059 , vital:26769
- Description: The black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are found in South Africa. A decline in the populations of these species has resulted due to human activities such as habitat fragmentation and poaching. This has contributed to the loss of genetic diversity amongst the black and white rhinoceros. Conservation and anti-poaching efforts are needed to help maintain genetic diversity. These efforts could be improved through the development of non-invasive techniques to examine DNA from threatened animals. The aim of this research was to develop a molecular technique which would allow for the identification of the black and white rhinoceros and to develop a molecular technique which would allow for intraspecies genetic variation to be examined. DNA extractions were performed on matched faecal and tissue samples that were collected from two regions in South Africa. Polymerase chain reaction (PCR) primer sets were designed to investigate several regions of the rhinoceros mitochondrial genome. PCR optimisation was completed for the target regions. Sequencing was conducted on all final PCR products. The cytochrome c oxidase subunit 1 (COIi) gene allowed for the rhinoceros family to be identified. This region was digested with the HindIII restriction enzyme, which allowed for the specific identification of either the black or white rhinoceros. A subsequent region of the cytochrome c oxidase subunit 1 (COIii) as well as the D-loop, hypervariable regions (HV1 and HV2), cytochrome b (cytb) and 16s rRNA regions were investigated. These regions displayed potential for establishing geographic origin for black rhinoceros samples, whereas the D-loop and HV2 show potential for the white rhinoceros. The white rhinoceros displayed sequence variation in the HV2 and cytb region, while variation was observed in the COIi and HV1 for the black rhinoceros. All investigated target regions allowed for the rhinoceros family to be identified. The COI (COIi and COIii), HV2 and cytb regions allowed for the subspecies of rhinoceros to be identified, however the D-loop was not able to identify the white rhinoceros species. The 16s rRNA and HV1 regions allowed for the correct subspecies of rhinoceros to be identified, however as the primers were only compatible for the black rhinoceros therefore a subsequent investigation is required for the white rhinoceros. The establishment of this novel PCR based technique to identify white and black rhinoceros will allow for efficient species identification in wildlife forensic cases. A biological method was established to study intraspecies variation for the white and black rhinoceros; however the investigated target regions did not yield sufficient genetic variation. The core techniques developed in this study will be valuable for future studies that wish to investigate genetic variation in mammal species.
- Full Text:
- Date Issued: 2015
Assessment of the effects of stream channel incision on soil water levels, soil morphology and vegetation in a wetland in the Hogsback area, Eastern Cape, South Africa
- Authors: Omar, Mohamed Yussuf
- Date: 2015
- Subjects: Hydrology Wetland Soil Formation
- Language: English
- Type: Thesis , Masters , Degree
- Identifier: http://hdl.handle.net/10353/3132 , vital:28264
- Description: Wetland degradation in the form of channel incisioning can significantly alter the hydrological functioning of a wetland. In this study in a small headwater wetland in the Hogsback area, Eastern Cape Province, the impact of channel incisioning on soil water levels and soil morphology was examined. A good correlation (R2 = 0.89) exists between the depth of channel incisioning and average water table depths in most of the 21 installed piezometers. In localised cases the upslope supply of water was in equilibrium with drainage from the piezometers. Although all the studied soils show hydromorphic characteristics, those continuously saturated close to the surface exhibit redox accumulations in oxygen supplying macropores, whereas gleyic colour patterns occur deeper in soils where the water table has been lowered by channel incision. The nature and occurrence of different hydromorphic soil indicators observed confirm the contribution of soil morphology as a valuable indicator of long-term average soil water conditions. The study evaluates the effects of hydrological processes on plant species composition and distribution in a Hogsback wetland. Twenty-four circular plots with a radius of 2 m were established between March and August 2013. Within each sample plot, the habitat information and species present were recorded including Braun-Blanquet cover-abundance value for each and every species present in the plot. Plant species were identified in the field and the unknown plant species were collected, pressed, oven-dried and identified at the National Herbarium, South African Biodiversity Institute (SANBI), Pretoria and Schonland Herbarium, Rhodes University, Grahamstown. A total of 39 taxa belonging to 19 families and 34 genera were recorded from the Hogsback wetland. Of the documented taxa, three were exotic and three endemic to South Africa, indicating diversity and dynamic nature of Hogsback wetland flora. Plant families with the highest number of species were: Poaceae (11 species), Asteraceae (5 species), Onagraceae and Cyperaceae with 3 taxa each. The low number of exotic plant species in Hogsback wetland (three taxa in total) indicates limited anthropogenic influence. Unique species recorded in Hogsback wetlands are three species that are endemic to South Africa, namely, Alchemilla capensis, Helichrysum rosum and Lysimachia nutans. Five main floristic associations were identified from the Hierarchical Cluster Analysis whilst Detrenched .Correspondence Analysis (DCA) identified four groups. The Canonical Correspondence Analysis (CCA) indicates that edaphic factors, particularly in an area covered with water, erosion category, organic matter content and water table depth were the most important environmental variables measured accounting for the vegetation pattern present in the Hogsback wetland.
- Full Text:
- Date Issued: 2015
- Authors: Omar, Mohamed Yussuf
- Date: 2015
- Subjects: Hydrology Wetland Soil Formation
- Language: English
- Type: Thesis , Masters , Degree
- Identifier: http://hdl.handle.net/10353/3132 , vital:28264
- Description: Wetland degradation in the form of channel incisioning can significantly alter the hydrological functioning of a wetland. In this study in a small headwater wetland in the Hogsback area, Eastern Cape Province, the impact of channel incisioning on soil water levels and soil morphology was examined. A good correlation (R2 = 0.89) exists between the depth of channel incisioning and average water table depths in most of the 21 installed piezometers. In localised cases the upslope supply of water was in equilibrium with drainage from the piezometers. Although all the studied soils show hydromorphic characteristics, those continuously saturated close to the surface exhibit redox accumulations in oxygen supplying macropores, whereas gleyic colour patterns occur deeper in soils where the water table has been lowered by channel incision. The nature and occurrence of different hydromorphic soil indicators observed confirm the contribution of soil morphology as a valuable indicator of long-term average soil water conditions. The study evaluates the effects of hydrological processes on plant species composition and distribution in a Hogsback wetland. Twenty-four circular plots with a radius of 2 m were established between March and August 2013. Within each sample plot, the habitat information and species present were recorded including Braun-Blanquet cover-abundance value for each and every species present in the plot. Plant species were identified in the field and the unknown plant species were collected, pressed, oven-dried and identified at the National Herbarium, South African Biodiversity Institute (SANBI), Pretoria and Schonland Herbarium, Rhodes University, Grahamstown. A total of 39 taxa belonging to 19 families and 34 genera were recorded from the Hogsback wetland. Of the documented taxa, three were exotic and three endemic to South Africa, indicating diversity and dynamic nature of Hogsback wetland flora. Plant families with the highest number of species were: Poaceae (11 species), Asteraceae (5 species), Onagraceae and Cyperaceae with 3 taxa each. The low number of exotic plant species in Hogsback wetland (three taxa in total) indicates limited anthropogenic influence. Unique species recorded in Hogsback wetlands are three species that are endemic to South Africa, namely, Alchemilla capensis, Helichrysum rosum and Lysimachia nutans. Five main floristic associations were identified from the Hierarchical Cluster Analysis whilst Detrenched .Correspondence Analysis (DCA) identified four groups. The Canonical Correspondence Analysis (CCA) indicates that edaphic factors, particularly in an area covered with water, erosion category, organic matter content and water table depth were the most important environmental variables measured accounting for the vegetation pattern present in the Hogsback wetland.
- Full Text:
- Date Issued: 2015
Rhodes University Research Report 2015
- Rhodes University, Gillitt, Tarryn, Goba, Busi, Macgregor, Jill, Roberts, Jaine, Dore, Sally
- Authors: Rhodes University , Gillitt, Tarryn , Goba, Busi , Macgregor, Jill , Roberts, Jaine , Dore, Sally
- Date: 2015
- Language: English
- Type: Text
- Identifier: http://hdl.handle.net/10962/59298 , vital:27546
- Description: From Foreword by Dr Sizwe Mabizela: A further feature of research at Rhodes University has long been international collaborations, many of them responsible for raising the international competitiveness and voice of scholarship involving Rhodes academics and students. In March 2015, Rhodes University became a founder member of the African Research Universities’ Alliance (ARUA), launched at the African Higher Education Summit in Senegal. Leading universities with strong programmes of research and Postgraduate training formed the network of 16 institutions, which aim to bring together intersecting and complementary strengths in the interest of building critical mass in the key development priorities of the African continent. , A publication of the Rhodes University Research Office, compiled and edited by Tarryn Gillitt, Busi Goba, Patricia Jacob, Jill Macgregor and Jaine Roberts. Design & Layout: Sally Dore.
- Full Text:
- Date Issued: 2015
- Authors: Rhodes University , Gillitt, Tarryn , Goba, Busi , Macgregor, Jill , Roberts, Jaine , Dore, Sally
- Date: 2015
- Language: English
- Type: Text
- Identifier: http://hdl.handle.net/10962/59298 , vital:27546
- Description: From Foreword by Dr Sizwe Mabizela: A further feature of research at Rhodes University has long been international collaborations, many of them responsible for raising the international competitiveness and voice of scholarship involving Rhodes academics and students. In March 2015, Rhodes University became a founder member of the African Research Universities’ Alliance (ARUA), launched at the African Higher Education Summit in Senegal. Leading universities with strong programmes of research and Postgraduate training formed the network of 16 institutions, which aim to bring together intersecting and complementary strengths in the interest of building critical mass in the key development priorities of the African continent. , A publication of the Rhodes University Research Office, compiled and edited by Tarryn Gillitt, Busi Goba, Patricia Jacob, Jill Macgregor and Jaine Roberts. Design & Layout: Sally Dore.
- Full Text:
- Date Issued: 2015
(Ferrocenylpyrazolyl) zinc (II) benzoates as catalysts for the ring opening polymerization of ε-caprolactone
- Obuah, Collins, Lochee, Yemanlall, Jordaan, Johan H L, Otto, Daniel P, Nyokong, Tebello, Darkwa, James
- Authors: Obuah, Collins , Lochee, Yemanlall , Jordaan, Johan H L , Otto, Daniel P , Nyokong, Tebello , Darkwa, James
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189515 , vital:44853 , xlink:href="https://doi.org/10.1016/j.poly.2015.02.007"
- Description: The reaction of Zn(OAc)2 and C6H5COOH or 3,5-NO2-C6H3COOH with 3-ferrocenylpyrazolyl-methylenepyridine (L1), 3-ferrocenyl-5-methylpyrazolyl-methylenepyridine (L2), 3-ferrocenylpyrazolyl-ethylamine (L3) and 3-ferrocenyl-5-pyrazolyl-ethylamine (L4) afford the corresponding complexes [Zn(C6H5COO)2(L1)] (1), [Zn(C6H5COO)2(L2)] (2), [Zn(3,5-NO2-C6H3COO)2(L1)] (3), [Zn(3,5-NO2-C6H3 COO)2(L2)] (4), [Zn(C6H5COO)2(L3)] (5), [Zn(C6H5COO)2(L4)] (6), [Zn(3,5-NO2-C6H3COO)2(L3)] (7) and [Zn(3,5-NO2-C6H3COO)2(L4)] (8). These complexes behave as catalysts for the ring opening polymerization of e-caprolactone to produce polymers with molecular weight that range from 1480 to 7080 g mol1 and exhibited moderate to broad PDIs. Evidence of these complexes acting as catalysts was obtained from both the polymerization data and kinetic studies. The polymerization data show that variation of the [CL]/[C] from 100 to 800 produced PCL with relatively the same molecular weight indicative of a catalyst behavior. The appearance of induction period in kinetic plots strengthens the fact that these complexes are catalysts rather than initiators. MALDI-TOF MS and 1 H NMR data show di-hydroxy end groups, which support the coordination mechanism rather than insertion mechanism. To understand the broad PDIs obtained for some of the polymer, the electronic properties of the zinc complexes were investigated using cyclic voltammetry. The results show that the zinc complexes containing amine based ligands are highly electrophilic therefore making them unstable, hence the broad PDIs observed for zinc complexes containing amine based ligands. Among the eight complexes investigated, complex 7 is the most active catalyst with kp value of 1.18 107 h1 mol1 at 110 C.
- Full Text:
- Date Issued: 2015
- Authors: Obuah, Collins , Lochee, Yemanlall , Jordaan, Johan H L , Otto, Daniel P , Nyokong, Tebello , Darkwa, James
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189515 , vital:44853 , xlink:href="https://doi.org/10.1016/j.poly.2015.02.007"
- Description: The reaction of Zn(OAc)2 and C6H5COOH or 3,5-NO2-C6H3COOH with 3-ferrocenylpyrazolyl-methylenepyridine (L1), 3-ferrocenyl-5-methylpyrazolyl-methylenepyridine (L2), 3-ferrocenylpyrazolyl-ethylamine (L3) and 3-ferrocenyl-5-pyrazolyl-ethylamine (L4) afford the corresponding complexes [Zn(C6H5COO)2(L1)] (1), [Zn(C6H5COO)2(L2)] (2), [Zn(3,5-NO2-C6H3COO)2(L1)] (3), [Zn(3,5-NO2-C6H3 COO)2(L2)] (4), [Zn(C6H5COO)2(L3)] (5), [Zn(C6H5COO)2(L4)] (6), [Zn(3,5-NO2-C6H3COO)2(L3)] (7) and [Zn(3,5-NO2-C6H3COO)2(L4)] (8). These complexes behave as catalysts for the ring opening polymerization of e-caprolactone to produce polymers with molecular weight that range from 1480 to 7080 g mol1 and exhibited moderate to broad PDIs. Evidence of these complexes acting as catalysts was obtained from both the polymerization data and kinetic studies. The polymerization data show that variation of the [CL]/[C] from 100 to 800 produced PCL with relatively the same molecular weight indicative of a catalyst behavior. The appearance of induction period in kinetic plots strengthens the fact that these complexes are catalysts rather than initiators. MALDI-TOF MS and 1 H NMR data show di-hydroxy end groups, which support the coordination mechanism rather than insertion mechanism. To understand the broad PDIs obtained for some of the polymer, the electronic properties of the zinc complexes were investigated using cyclic voltammetry. The results show that the zinc complexes containing amine based ligands are highly electrophilic therefore making them unstable, hence the broad PDIs observed for zinc complexes containing amine based ligands. Among the eight complexes investigated, complex 7 is the most active catalyst with kp value of 1.18 107 h1 mol1 at 110 C.
- Full Text:
- Date Issued: 2015
Assessing symptoms of eutrophication in estuaries
- Authors: Lemley, Daniel Alan
- Date: 2015
- Subjects: Estuarine eutrophication -- South Africa , Water quality -- South Africa , Ecological integrity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/3427 , vital:20429
- Description: Water quality and ecological integrity of estuaries reflect activities within the entire upstream catchment. Much emphasis has been placed on the response of estuaries to anthropogenic stressors through the use of monitoring programmes. Key to the success of these programmes is the use of indicators as they transform data into useful information. The ultimate aim of this study was to identify eutrophic symptoms in selected estuaries in the Gouritz Water Management Area (WMA) using a multi-metric classification method. The study sites included the permanently open Duiwenhoks, Goukou, Gouritz, and Kaaimans estuaries, as well as the temporarily open/closed Hartenbos, Klein Brak, Great Brak, Gwaing, and Goukamma estuaries. Initially, the “pressure” associated with all the estuaries in the Gouritz WMA was determined (e.g. total daily nutrient loads and changes in river inflow affecting flushing time) using long-term flow and water quality monitoring data provided by the Department of Water Affairs (DWA). Subsequently, the “state” of the selected estuaries was assessed using a variety of indicators, including: inorganic nutrients (~ N and P), phytoplankton, epiphytes and microphytobenthos. Estuaries with longer flushing time suggested greater vulnerability to eutrophication. For example, the Gwaing (281.11 kg DIN d-1; 78.85 kg DIP d-1) and Hartenbos (38.33 kg DIN d-1; 21.51 kg DIP d-1) estuaries generally received the highest daily inorganic nutrient loads. However, at the time of sampling, the Hartenbos Estuary had a longer flushing time (i.e. weeks) compared to the Gwaing Estuary (i.e. couple of days). Field data confirmed the greater vulnerability to eutrophication associated with longer flushing times, as the indicators measured in the Hartenbos Estuary exceeded all the proposed ‘thresholds’ of a eutrophic system (~ overall ‘Poor’ condition). The Great Brak Estuary (~ overall ‘Fair’ condition) provided an interesting example where eutrophic symptoms were only detected when assessing the microalgal primary producers (i.e. high biomass and low diversity). Furthermore, the need to distinguish between naturally and anthropogenically induced symptoms was highlighted. One such scenario was noted in the Kaaimans Estuary, where its natural hydro-morphological characteristics (i.e. steep banks, low river inflow, and deep/narrow channel) led to the possible exaggeration of its overall eutrophic condition, i.e. received a ‘Fair’ rather than ‘Good’ rating, arising from ‘Poor’ ratings for dissolved oxygen and benthic diatom diversity. Overall, this study demonstrated the importance of adopting a holistic approach when assessing the condition and trophic status of estuaries. Studies such as these allow for the detection of vulnerable and degraded systems, which can provide important information with regards to the identification of management priorities.
- Full Text:
- Date Issued: 2015
- Authors: Lemley, Daniel Alan
- Date: 2015
- Subjects: Estuarine eutrophication -- South Africa , Water quality -- South Africa , Ecological integrity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/3427 , vital:20429
- Description: Water quality and ecological integrity of estuaries reflect activities within the entire upstream catchment. Much emphasis has been placed on the response of estuaries to anthropogenic stressors through the use of monitoring programmes. Key to the success of these programmes is the use of indicators as they transform data into useful information. The ultimate aim of this study was to identify eutrophic symptoms in selected estuaries in the Gouritz Water Management Area (WMA) using a multi-metric classification method. The study sites included the permanently open Duiwenhoks, Goukou, Gouritz, and Kaaimans estuaries, as well as the temporarily open/closed Hartenbos, Klein Brak, Great Brak, Gwaing, and Goukamma estuaries. Initially, the “pressure” associated with all the estuaries in the Gouritz WMA was determined (e.g. total daily nutrient loads and changes in river inflow affecting flushing time) using long-term flow and water quality monitoring data provided by the Department of Water Affairs (DWA). Subsequently, the “state” of the selected estuaries was assessed using a variety of indicators, including: inorganic nutrients (~ N and P), phytoplankton, epiphytes and microphytobenthos. Estuaries with longer flushing time suggested greater vulnerability to eutrophication. For example, the Gwaing (281.11 kg DIN d-1; 78.85 kg DIP d-1) and Hartenbos (38.33 kg DIN d-1; 21.51 kg DIP d-1) estuaries generally received the highest daily inorganic nutrient loads. However, at the time of sampling, the Hartenbos Estuary had a longer flushing time (i.e. weeks) compared to the Gwaing Estuary (i.e. couple of days). Field data confirmed the greater vulnerability to eutrophication associated with longer flushing times, as the indicators measured in the Hartenbos Estuary exceeded all the proposed ‘thresholds’ of a eutrophic system (~ overall ‘Poor’ condition). The Great Brak Estuary (~ overall ‘Fair’ condition) provided an interesting example where eutrophic symptoms were only detected when assessing the microalgal primary producers (i.e. high biomass and low diversity). Furthermore, the need to distinguish between naturally and anthropogenically induced symptoms was highlighted. One such scenario was noted in the Kaaimans Estuary, where its natural hydro-morphological characteristics (i.e. steep banks, low river inflow, and deep/narrow channel) led to the possible exaggeration of its overall eutrophic condition, i.e. received a ‘Fair’ rather than ‘Good’ rating, arising from ‘Poor’ ratings for dissolved oxygen and benthic diatom diversity. Overall, this study demonstrated the importance of adopting a holistic approach when assessing the condition and trophic status of estuaries. Studies such as these allow for the detection of vulnerable and degraded systems, which can provide important information with regards to the identification of management priorities.
- Full Text:
- Date Issued: 2015
Issues and concerns in developing regulated markets for endangered species products: the case of rhinoceros horns
- Collins, Alan, Fraser, Gavin C G, Snowball, Jeanette D
- Authors: Collins, Alan , Fraser, Gavin C G , Snowball, Jeanette D
- Date: 2015
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124877 , vital:35706 , https://doi.org/10.1093/cje/bev076
- Description: A proposal for addressing rhinoceros poaching is to legalise the trade in rhino horn and adopt a regulated market approach, overturning the current trade ban. This orthodox economic prescription aims to reduce incentives to poach endangered wildlife by driving down the market price of their products via auctioned stockpile releases. Biologists are clear, however, that securing a stockpile for some species needs biological success in captive breeding programmes (CBPs), which varies markedly across species and habitats. Rhinoceros herds in a CBP would need spatially extensive terrain and costly permanent security measures; this only appears feasible for the less aggressive ‘white’ rhino. We argue that the market price would actually need to be sustained at a high level to cover protection costs over the longer reproduction cycles in CBPs and that, without extensive monitoring and the correct institutional structures being in place, legalising trade may encourage, rather than prevent, poaching. Supplementary policy measures that differentiate among consumer groups would also likely prove necessary.
- Full Text:
- Date Issued: 2015
- Authors: Collins, Alan , Fraser, Gavin C G , Snowball, Jeanette D
- Date: 2015
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124877 , vital:35706 , https://doi.org/10.1093/cje/bev076
- Description: A proposal for addressing rhinoceros poaching is to legalise the trade in rhino horn and adopt a regulated market approach, overturning the current trade ban. This orthodox economic prescription aims to reduce incentives to poach endangered wildlife by driving down the market price of their products via auctioned stockpile releases. Biologists are clear, however, that securing a stockpile for some species needs biological success in captive breeding programmes (CBPs), which varies markedly across species and habitats. Rhinoceros herds in a CBP would need spatially extensive terrain and costly permanent security measures; this only appears feasible for the less aggressive ‘white’ rhino. We argue that the market price would actually need to be sustained at a high level to cover protection costs over the longer reproduction cycles in CBPs and that, without extensive monitoring and the correct institutional structures being in place, legalising trade may encourage, rather than prevent, poaching. Supplementary policy measures that differentiate among consumer groups would also likely prove necessary.
- Full Text:
- Date Issued: 2015
Isolation and molecular characterization of Bacillus cereus from cow’s raw milk
- Authors: Lukanji, Zinathi , Ndip, R N
- Date: 2015
- Subjects: Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11296 , http://hdl.handle.net/10353/d1021284 , Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Description: Bacillus cereus is a group of ubiquitous facultative anaerobic spore forming Gram-positive rods commonly found in soil. It has been detected and implicated in several contaminated food products and raw milk in dairy farms and it causes foodborne gastroenteritis by producing several toxins. This study is aimed at characterizing virulence determinants of B. cereus from cow‟s raw milk. A total of 400 raw milk samples were collected in Fort Hare Dairy Trust and Middledrift Dairy Farm; and cultured on Polymyxin pyruvate Egg-Yolk Mannitol Bromothymol Agar (PEMBA) for 48 hours at 37°C. DNA was isolated from the isolates and 16S rDNA was amplified and sent to Central Analytical Laboratory for sequencing. The gyrB gene of B. cereus was also used to confirm the identity of the isolates. Antibiotic susceptibility profiles of the isolates together with virulence genes were investigated. Multilocus Sequence typing was used to investigate the genetic relatedness of some selected isolates. Furthermore, spores of the isolates were produced, harvested and their concentrations determined. All (100%) of the isolates were identified as having a 96-99% similarity to B. cereus, B. thuringiensis and B. anthracis using sequencing; while gyrB gene was observed in all (100%) of the isolates. Three virulence genes nheA, nheB, nheC encoding for non haemolysin enterotoxin were amplified in all (100%) the isolates. All (100%) of the isolates were susceptible to doxycycline, gentamycin, tetracycline, ciprofloxacin, chloramphenicol and streptomycin. Resistance to rifampicin and penicillin G was predominant with equal rate of 100%, while susceptibility to erythromycin, clindamycin and doxycycline ranged from 60% to 100%. The selected isolates were related and are descendants of the same ancestor. All (100%) the isolates produced spores. The B. cereus isolates contain virulence genes, has multiple antibiotic drug resistance and produce spores, which poses a health risk to the public and cannot be used as probiotics.
- Full Text:
- Date Issued: 2015
- Authors: Lukanji, Zinathi , Ndip, R N
- Date: 2015
- Subjects: Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11296 , http://hdl.handle.net/10353/d1021284 , Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Description: Bacillus cereus is a group of ubiquitous facultative anaerobic spore forming Gram-positive rods commonly found in soil. It has been detected and implicated in several contaminated food products and raw milk in dairy farms and it causes foodborne gastroenteritis by producing several toxins. This study is aimed at characterizing virulence determinants of B. cereus from cow‟s raw milk. A total of 400 raw milk samples were collected in Fort Hare Dairy Trust and Middledrift Dairy Farm; and cultured on Polymyxin pyruvate Egg-Yolk Mannitol Bromothymol Agar (PEMBA) for 48 hours at 37°C. DNA was isolated from the isolates and 16S rDNA was amplified and sent to Central Analytical Laboratory for sequencing. The gyrB gene of B. cereus was also used to confirm the identity of the isolates. Antibiotic susceptibility profiles of the isolates together with virulence genes were investigated. Multilocus Sequence typing was used to investigate the genetic relatedness of some selected isolates. Furthermore, spores of the isolates were produced, harvested and their concentrations determined. All (100%) of the isolates were identified as having a 96-99% similarity to B. cereus, B. thuringiensis and B. anthracis using sequencing; while gyrB gene was observed in all (100%) of the isolates. Three virulence genes nheA, nheB, nheC encoding for non haemolysin enterotoxin were amplified in all (100%) the isolates. All (100%) of the isolates were susceptible to doxycycline, gentamycin, tetracycline, ciprofloxacin, chloramphenicol and streptomycin. Resistance to rifampicin and penicillin G was predominant with equal rate of 100%, while susceptibility to erythromycin, clindamycin and doxycycline ranged from 60% to 100%. The selected isolates were related and are descendants of the same ancestor. All (100%) the isolates produced spores. The B. cereus isolates contain virulence genes, has multiple antibiotic drug resistance and produce spores, which poses a health risk to the public and cannot be used as probiotics.
- Full Text:
- Date Issued: 2015
The synthesis and analysis of (2R,3R)-1,1,4,4- tetraphenylbutane-1,2,3,4-tetraol (tetrol) and derivatives, and a study of their host potential
- Authors: Weitz, Selwyn Herbert
- Date: 2015
- Subjects: Chemistry, Organic
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/3735 , vital:20459
- Description: This investigation focussed on the inclusion and resolution ability of (2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (TETROL), studies on the stoichiometry of its derivatives and the formation of inclusion compounds for single crystal analysis. The guest compounds that featured in the main study were cyclohexanone, 2-methylcyclohexanone, 3-methylcyclohexanone and 4-methylcyclohexanone. It was found that 3- and 4-methylcyclohexanone were trapped in their energetically unfavourable axial conformations in the inclusion crystal. Resolution experiments proved that (2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol can be used as a resolving agent for 2- and 3-methylcyclohexanone, with ee values of 13% and 22%, respectively (according to the method of Hiemstra), in favour of the R-enantiomer. Single crystal X-ray diffraction (SCXRD) studies, however, showed that 2-methylcyclohexanone was resolved with an ee of 30% in R. An ee of 56% in R was obtained for 3-methylcyclohexanone. Enantiomer enrichment of 2-methylcyclohexanone was achieved in basic medium (ee of 18% according to the method of Hiemstra) and showed that by using the host in either half or double the molar ratio of the guest, a higher ee was obtained than for a 1:1 ratio. The following TETROL derivatives were also synthesized and their stoichiometries with various guest compounds were determined: (2R,3R)-1,1,4,4-tetra(naphthalen-1-yl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(naphthalen-2-yl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(p-anisyl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(p-tolyl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(m-tolyl)butane-1,2,3,4-tetraol and; (2R,3R)-1,1,4,4-tetra(o-tolyl)butane-1,2,3,4-tetraol.
- Full Text:
- Date Issued: 2015
- Authors: Weitz, Selwyn Herbert
- Date: 2015
- Subjects: Chemistry, Organic
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/3735 , vital:20459
- Description: This investigation focussed on the inclusion and resolution ability of (2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (TETROL), studies on the stoichiometry of its derivatives and the formation of inclusion compounds for single crystal analysis. The guest compounds that featured in the main study were cyclohexanone, 2-methylcyclohexanone, 3-methylcyclohexanone and 4-methylcyclohexanone. It was found that 3- and 4-methylcyclohexanone were trapped in their energetically unfavourable axial conformations in the inclusion crystal. Resolution experiments proved that (2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol can be used as a resolving agent for 2- and 3-methylcyclohexanone, with ee values of 13% and 22%, respectively (according to the method of Hiemstra), in favour of the R-enantiomer. Single crystal X-ray diffraction (SCXRD) studies, however, showed that 2-methylcyclohexanone was resolved with an ee of 30% in R. An ee of 56% in R was obtained for 3-methylcyclohexanone. Enantiomer enrichment of 2-methylcyclohexanone was achieved in basic medium (ee of 18% according to the method of Hiemstra) and showed that by using the host in either half or double the molar ratio of the guest, a higher ee was obtained than for a 1:1 ratio. The following TETROL derivatives were also synthesized and their stoichiometries with various guest compounds were determined: (2R,3R)-1,1,4,4-tetra(naphthalen-1-yl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(naphthalen-2-yl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(p-anisyl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(p-tolyl)butane-1,2,3,4-tetraol; (2R,3R)-1,1,4,4-tetra(m-tolyl)butane-1,2,3,4-tetraol and; (2R,3R)-1,1,4,4-tetra(o-tolyl)butane-1,2,3,4-tetraol.
- Full Text:
- Date Issued: 2015
Chemical constituents and biological studies of Tagetes minuta L. and Rauvolfia caffra Sond
- Authors: Mlala, Sithenkosi
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Organic Chemistry)
- Identifier: vital:11358 , http://hdl.handle.net/10353/d1021325
- Description: Consequently, specific parts or the whole plant can be used for various treatments. The aim of this study was to extract, isolate and characterize the biologically active volatile and non-volatile compounds from Tagetes minuta and Rauvolfia caffra respectively. Tagetes minuta plant was considered for extraction of essential oils using hydrodistillation method. Cis-β-ocimene (38.03%), caryophyllene oxide (18.04%), alloocimene (25.35 %), isopropyl tetradecanoate (17.02 %), cis-ocimene (38.14%) and trans-β-ocimene (37.03%) were the major components of essential oil analyzed from fresh stem, dried stem, fresh leaf, dried leaf, fresh flower and dried flower respectively. The volatile compounds were identified by Gas Chromatography-Mass Spectrometry (GC-MS) and Gas Chromatography (GC). Essential oil of dried stem leaf and flower parts of T. minuta exhibit antioxidant activity as demonstrated by the DPPH and FRAP bioassays. Crude extracts were extracted from R. caffra stem bark using sequence of solvents namely n-hexane, dichloromethane, ethyl acetate, methanol and ethanol. A white powder, a β-sitosterol (non-volatile compound) was isolated by column chromatography from ethyl acetate fractions of R. caffra stem bark and identified on various spectroscopic techniques such as FTIR and (1D and 2D) NMR. Melting point was also determined to be a sharp 129-130 ºC. DCM, EA, MetOH and EtOH fractions as well as β-Sitosterol (compound SM/01), showed antioxidant activity when tested on DPPH, FRAP, total phenolic and flavonoid bioassays. This antioxidant activity might be due to the presence of hydroxyl groups in the compound and crude fractions. On the other hand, T. minuta’s essential oil showed high antioxidant activity when evaluated on the DPPH and FRAP bioassays, which can be attributed to the presence of oxygenated monoterpenes and sesquiterpenes known to act as free radical scavenging and reducing agents. The use of R. caffra stem bark extracts against hypertension and other diseases by traditional healers could be attributed to the presence of phytochemicals (polyphenols and flavonoids) with known health benefits. Thus, it is recommended that the plant should be exploited further using modern techniques involving separation and purification of compounds that can be used for drug formulation. This study supports the use of T. minuta and R. caffra as the potential natural antioxidant source to manage various diseases including hypertension.
- Full Text:
- Date Issued: 2015
- Authors: Mlala, Sithenkosi
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Organic Chemistry)
- Identifier: vital:11358 , http://hdl.handle.net/10353/d1021325
- Description: Consequently, specific parts or the whole plant can be used for various treatments. The aim of this study was to extract, isolate and characterize the biologically active volatile and non-volatile compounds from Tagetes minuta and Rauvolfia caffra respectively. Tagetes minuta plant was considered for extraction of essential oils using hydrodistillation method. Cis-β-ocimene (38.03%), caryophyllene oxide (18.04%), alloocimene (25.35 %), isopropyl tetradecanoate (17.02 %), cis-ocimene (38.14%) and trans-β-ocimene (37.03%) were the major components of essential oil analyzed from fresh stem, dried stem, fresh leaf, dried leaf, fresh flower and dried flower respectively. The volatile compounds were identified by Gas Chromatography-Mass Spectrometry (GC-MS) and Gas Chromatography (GC). Essential oil of dried stem leaf and flower parts of T. minuta exhibit antioxidant activity as demonstrated by the DPPH and FRAP bioassays. Crude extracts were extracted from R. caffra stem bark using sequence of solvents namely n-hexane, dichloromethane, ethyl acetate, methanol and ethanol. A white powder, a β-sitosterol (non-volatile compound) was isolated by column chromatography from ethyl acetate fractions of R. caffra stem bark and identified on various spectroscopic techniques such as FTIR and (1D and 2D) NMR. Melting point was also determined to be a sharp 129-130 ºC. DCM, EA, MetOH and EtOH fractions as well as β-Sitosterol (compound SM/01), showed antioxidant activity when tested on DPPH, FRAP, total phenolic and flavonoid bioassays. This antioxidant activity might be due to the presence of hydroxyl groups in the compound and crude fractions. On the other hand, T. minuta’s essential oil showed high antioxidant activity when evaluated on the DPPH and FRAP bioassays, which can be attributed to the presence of oxygenated monoterpenes and sesquiterpenes known to act as free radical scavenging and reducing agents. The use of R. caffra stem bark extracts against hypertension and other diseases by traditional healers could be attributed to the presence of phytochemicals (polyphenols and flavonoids) with known health benefits. Thus, it is recommended that the plant should be exploited further using modern techniques involving separation and purification of compounds that can be used for drug formulation. This study supports the use of T. minuta and R. caffra as the potential natural antioxidant source to manage various diseases including hypertension.
- Full Text:
- Date Issued: 2015
Invariant control systems and sub-Riemannian structures on lie groups: equivalence and isometries
- Authors: Biggs, Rory
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64815 , vital:28607
- Description: In this thesis we consider invariant optimal control problems and invariant sub-Riemannian structures on Lie groups. Primarily, we are concerned with the equivalence and classification of problems (resp. structures). In the first chapter, both the class of invariant optimal control problems and the class of invariant sub-Riemannian structures are organised as categories. The latter category is shown to be functorially equivalent to a subcategory of the former category. Via the Pontryagin Maximum Principle, we associate to each invariant optimal control problem (resp. invariant sub-Riemannian structure) a quadratic Hamilton-Poisson system on the associated Lie-Poisson space. These Hamiltonian systems are also organised as a category and hence the Pontryagin lift is realised as a contravariant functor. Basic properties of these categories are investigated. The rest of this thesis is concerned with the classification (and investigation) of certain subclasses of structures and systems. In the second chapter, the homogeneous positive semidefinite quadratic Hamilton-Poisson systems on three-dimensional Lie-Poisson spaces are classified up to compatibility with a linear isomorphism; a list of 23 normal forms is exhibited. In the third chapter, we classify the invariant sub-Riemannian structures in three dimensions and calculate the isometry group for each normal form. By comparing our results with known results, we show that most isometries (in three dimensions) are in fact the composition of a left translation and a Lie group isomorphism. In the fourth and last chapter of this thesis, we classify the sub-Riemannian and Riemannian structures on the (2n + 1)-dimensional Heisenberg groups. Furthermore, we find the isometry group and geodesics of each normal form.
- Full Text:
- Date Issued: 2015
- Authors: Biggs, Rory
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64815 , vital:28607
- Description: In this thesis we consider invariant optimal control problems and invariant sub-Riemannian structures on Lie groups. Primarily, we are concerned with the equivalence and classification of problems (resp. structures). In the first chapter, both the class of invariant optimal control problems and the class of invariant sub-Riemannian structures are organised as categories. The latter category is shown to be functorially equivalent to a subcategory of the former category. Via the Pontryagin Maximum Principle, we associate to each invariant optimal control problem (resp. invariant sub-Riemannian structure) a quadratic Hamilton-Poisson system on the associated Lie-Poisson space. These Hamiltonian systems are also organised as a category and hence the Pontryagin lift is realised as a contravariant functor. Basic properties of these categories are investigated. The rest of this thesis is concerned with the classification (and investigation) of certain subclasses of structures and systems. In the second chapter, the homogeneous positive semidefinite quadratic Hamilton-Poisson systems on three-dimensional Lie-Poisson spaces are classified up to compatibility with a linear isomorphism; a list of 23 normal forms is exhibited. In the third chapter, we classify the invariant sub-Riemannian structures in three dimensions and calculate the isometry group for each normal form. By comparing our results with known results, we show that most isometries (in three dimensions) are in fact the composition of a left translation and a Lie group isomorphism. In the fourth and last chapter of this thesis, we classify the sub-Riemannian and Riemannian structures on the (2n + 1)-dimensional Heisenberg groups. Furthermore, we find the isometry group and geodesics of each normal form.
- Full Text:
- Date Issued: 2015
An investigation into the synergistic action of cellulose-degrading enzymes on complex substrates
- Authors: Thoresen, Mariska
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Cellulosic ethanol , Saccharomyces cerevisiae , Cellulase , Enzymes -- Biotechnology , Hydrolases
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4154 , http://hdl.handle.net/10962/d1017915
- Full Text:
- Date Issued: 2015
- Authors: Thoresen, Mariska
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Cellulosic ethanol , Saccharomyces cerevisiae , Cellulase , Enzymes -- Biotechnology , Hydrolases
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4154 , http://hdl.handle.net/10962/d1017915
- Full Text:
- Date Issued: 2015
Spatial and temporal variations in trophic connectivity within an estuarine environment : benthic-pelagic and terrestrial-aquatic linkages via invertebrates and fishes
- Authors: Bergamino Roman, Leandro
- Date: 2015
- Subjects: Estuarine ecology -- South Africa , Marine invertebrates -- South Africa -- Ecology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5921 , http://hdl.handle.net/10962/d1017799
- Description: Estuarine ecosystems are among the most biologically productive areas and they provide important ecosystem services such as erosion control, habitat and refugia for several species. These environments are characterized by the presence of a variety of organic matter sources due to their transitional position between rivers and the sea. The biotic compositions can undergo spatial and seasonal changes along the estuary due to the spatial and temporal fluctuations of environmental factors such as salinity, temperature and seston loads. Therefore, the different combinations of biotic and abiotic factors make each estuary a unique ecosystem. Because of this spatial and temporal complexity, the understanding of estuarine food web structure and which factors affect the trophic relationships within the ecosystem through space and time represent challenging tasks. Furthermore, estuaries are under an increasing number of anthropogenic perturbations because of the growing concentration of human populations in coastal areas. Knowledge of ecosystem structure and functioning is essential for effective conservation and management planning of coastal areas.In this dissertation, I combine the utilization of biological tracers to examine spatial and temporal variability in the food web structure within a small temperate and microtidal estuary located in South Africa. To this end, fatty acid profiles and stable isotope signatures were measured in several primary organic matter sources and consumers (including zooplankton, fishes and benthic invertebrates) during four consecutive seasons and in three different estuarine regions: upper, middle, and lower reaches. The three reaches had distinct habitat features of vegetation type and morphology, and in particular the lower reaches were colonized by the marsh grass Spartina maritima. Isotopic mixing models were used to estimate the relative contribution of each food source to the diets of invertebrates and fishes within the estuarine food web. The isotopic and fatty acid data showed similar results. In general, the lower reaches of the estuary were characterized by a higher deposition and assimilation by brachyuran crabs of carbon derived from marsh grass detritus, whiletowards the upper reaches a mixture of microphytobenthos and particulate organic matter (phytoplankton and detritus) was deposited and sustained the pelagic and benthic fauna. The highest deposition and assimilation of marsh grass detritus in the lower reaches of the estuary occurred during periods of low freshwater discharge (autumn and winter). In the upper reaches, microphytobenthos and suspended particulate organic matter were dominant basal food resources for the food web during all seasons. These results indicated that benthic consumers incorporated mainly local carbon sources from their local habitat.To clarify isotopic and fatty acid patterns I examined the trophic behaviour of the sesarmid crab Sesarma catenata through laboratory feeding experiments. Results from these experiments validated that decomposed leaves of riparian trees and the salt marsh plant S. maritima were the preferred food of the sesarmid crabs, potentially due to high bacterial loads. The remaining leaf material not assimilated by crabs, together with faecal material, are likely important subsidies for adjacent environments, hence representing an important energy pathway involving the microbial food chain. Furthermore, this dissertation showed the importance of mobile top predators as vectors energetically connecting distinct food chains within the estuary (i.e. littoral, benthic and pelagic). I concluded that a combination of physical (i.e. patterns of freshwater discharge and estuary morphology) and biological factors (i.e. organism feeding behaviour, mobility, primary productivity, the local vegetation type) influence the pattern of dominant primary organic matter sources, and therefore the food web structure along the estuarine environment. In particular, marsh grass detritus contributed substantially to the diets of estuarine fauna during periods of low freshwater discharge. Given the importance of the salt marsh habitat in providing trophic resources, it is important to preserve this environment to sustain the natural biota and ecosystem functioning.
- Full Text:
- Date Issued: 2015
- Authors: Bergamino Roman, Leandro
- Date: 2015
- Subjects: Estuarine ecology -- South Africa , Marine invertebrates -- South Africa -- Ecology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5921 , http://hdl.handle.net/10962/d1017799
- Description: Estuarine ecosystems are among the most biologically productive areas and they provide important ecosystem services such as erosion control, habitat and refugia for several species. These environments are characterized by the presence of a variety of organic matter sources due to their transitional position between rivers and the sea. The biotic compositions can undergo spatial and seasonal changes along the estuary due to the spatial and temporal fluctuations of environmental factors such as salinity, temperature and seston loads. Therefore, the different combinations of biotic and abiotic factors make each estuary a unique ecosystem. Because of this spatial and temporal complexity, the understanding of estuarine food web structure and which factors affect the trophic relationships within the ecosystem through space and time represent challenging tasks. Furthermore, estuaries are under an increasing number of anthropogenic perturbations because of the growing concentration of human populations in coastal areas. Knowledge of ecosystem structure and functioning is essential for effective conservation and management planning of coastal areas.In this dissertation, I combine the utilization of biological tracers to examine spatial and temporal variability in the food web structure within a small temperate and microtidal estuary located in South Africa. To this end, fatty acid profiles and stable isotope signatures were measured in several primary organic matter sources and consumers (including zooplankton, fishes and benthic invertebrates) during four consecutive seasons and in three different estuarine regions: upper, middle, and lower reaches. The three reaches had distinct habitat features of vegetation type and morphology, and in particular the lower reaches were colonized by the marsh grass Spartina maritima. Isotopic mixing models were used to estimate the relative contribution of each food source to the diets of invertebrates and fishes within the estuarine food web. The isotopic and fatty acid data showed similar results. In general, the lower reaches of the estuary were characterized by a higher deposition and assimilation by brachyuran crabs of carbon derived from marsh grass detritus, whiletowards the upper reaches a mixture of microphytobenthos and particulate organic matter (phytoplankton and detritus) was deposited and sustained the pelagic and benthic fauna. The highest deposition and assimilation of marsh grass detritus in the lower reaches of the estuary occurred during periods of low freshwater discharge (autumn and winter). In the upper reaches, microphytobenthos and suspended particulate organic matter were dominant basal food resources for the food web during all seasons. These results indicated that benthic consumers incorporated mainly local carbon sources from their local habitat.To clarify isotopic and fatty acid patterns I examined the trophic behaviour of the sesarmid crab Sesarma catenata through laboratory feeding experiments. Results from these experiments validated that decomposed leaves of riparian trees and the salt marsh plant S. maritima were the preferred food of the sesarmid crabs, potentially due to high bacterial loads. The remaining leaf material not assimilated by crabs, together with faecal material, are likely important subsidies for adjacent environments, hence representing an important energy pathway involving the microbial food chain. Furthermore, this dissertation showed the importance of mobile top predators as vectors energetically connecting distinct food chains within the estuary (i.e. littoral, benthic and pelagic). I concluded that a combination of physical (i.e. patterns of freshwater discharge and estuary morphology) and biological factors (i.e. organism feeding behaviour, mobility, primary productivity, the local vegetation type) influence the pattern of dominant primary organic matter sources, and therefore the food web structure along the estuarine environment. In particular, marsh grass detritus contributed substantially to the diets of estuarine fauna during periods of low freshwater discharge. Given the importance of the salt marsh habitat in providing trophic resources, it is important to preserve this environment to sustain the natural biota and ecosystem functioning.
- Full Text:
- Date Issued: 2015
The effects of distance travelled, lairage duration and animal-related factors on pre-slaughter stress indicators, carcass characteristics, nanostructure and technological properties of beef
- Authors: Chulayo, Amanda Yucca
- Date: 2015
- Subjects: Slaughtering and slaughter-houses -- South Africa -- Eastern Cape , Meat -- Quality -- South Africa -- Eastern Cape , Beef -- Quality -- South Africa -- Eastern Cape , Nanostructured materials -- South Africa -- Eastern Cape , Livestock -- Handling -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD (Animal Science)
- Identifier: vital:11835 , http://hdl.handle.net/10353/d1021275 , Slaughtering and slaughter-houses -- South Africa -- Eastern Cape , Meat -- Quality -- South Africa -- Eastern Cape , Beef -- Quality -- South Africa -- Eastern Cape , Nanostructured materials -- South Africa -- Eastern Cape , Livestock -- Handling -- South Africa -- Eastern Cape
- Description: The main objective of the current study was to determine the effect of distance travelled (DT), lairage duration (LDhr) and animal-related factors (animal class, breed, sex) on pre-slaughter stress indicators, carcass characteristics, nanostructure and technological properties of beef. The study was conducted in an Eastern Cape abattoir under the Buffalo City District Municipality. Six genotypes of cattle (Beefmaster, Bonsmara, Brahman, Holstein-Friesian, Non-descript and Nguni) brought for slaughter at the abattoir on different days were used in the study. Slaughter weight (SWT), warm and cold carcass weight (WCW and CCW), fatness and conformation of each animal were measured and recorded. Representative samples of blood plasma and meat quality from the Muscularis thoracis et lumborum (LTL) were collected at slaughter and 24 hours after slaughter, respectively. Heat shock proteins 70kDa (HSPA1A), glucose (GLU), cortisol (CORT), creatine kinase (CK) and lactate dehydrogenase (LDH) were determined from the blood plasma. The representative LTL muscle was used to determine ultimate pH (pHu), lightness (L*), redness (a*), yellowness (b*), meat temperature (Tm), Warner Bratzler Shear Force (WBSF) and histological structure of beef. There were significant effects of distance on pHu, Tm, a*, b*, TL%, CK and LDH. Pearson correlations were observed between distance travelled (DT), creatine kinase (CK), lactate dehydrogenase (LDH), ultimate pH (pHu), colour coordinates (L*, a* and b*) and Warner Bratzler Shear Force (WBSF). Principal component analysis (PCA) revealed that the 1st (pHu), 2nd (Tm) and 3rd (L*) principal components were the critical meat quality attributes. Positive relationships between carcass weights and beef quality characteristics for bovine cattle where the cumulative percentage of the first six principal component`s (PC`s) (SWT, WCW, CCW, DP, pHu and Tm contributed to 93.4 % of the total variance. Significant correlation coefficients between DT (r = 0.15), LDhr (r = 0.29), Ta (r = -0.52), Tm (r = 0.26), L* (r = 0.33), a* (r = 0.32) and WBSF (r = -0.49) were observed. Meat from Brahman (BR), Non-descript (ND) and Nguni (NG) cows had visible skeletal muscle fibres which were thin and long indicating improved tenderness of beef. Exposing animals to longer hours of transportation did not only reduce glucose levels but also increased the expression of HSPA1A and levels of cortisol. The CK and LDH were not related to beef quality. Therefore, CK and LDH can be used as indicators of animal welfare in slaughter cattle but cannot be used to predict the quality of meat. Bulls were the heaviest, although heifers had the highest dressing percentage than cows. Furthermore, the nanostructure of beef indicated that heifers had the best muscle fibres, sarcomere length and visible intercalated discs. The observed nanostructures of Nguni genotype are an indication of tender meat. Beef from heifers of Nguni had visible and tender meat with traces of intramuscular fat while males had shorter sarcomere length and tougher meat.
- Full Text:
- Date Issued: 2015
- Authors: Chulayo, Amanda Yucca
- Date: 2015
- Subjects: Slaughtering and slaughter-houses -- South Africa -- Eastern Cape , Meat -- Quality -- South Africa -- Eastern Cape , Beef -- Quality -- South Africa -- Eastern Cape , Nanostructured materials -- South Africa -- Eastern Cape , Livestock -- Handling -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD (Animal Science)
- Identifier: vital:11835 , http://hdl.handle.net/10353/d1021275 , Slaughtering and slaughter-houses -- South Africa -- Eastern Cape , Meat -- Quality -- South Africa -- Eastern Cape , Beef -- Quality -- South Africa -- Eastern Cape , Nanostructured materials -- South Africa -- Eastern Cape , Livestock -- Handling -- South Africa -- Eastern Cape
- Description: The main objective of the current study was to determine the effect of distance travelled (DT), lairage duration (LDhr) and animal-related factors (animal class, breed, sex) on pre-slaughter stress indicators, carcass characteristics, nanostructure and technological properties of beef. The study was conducted in an Eastern Cape abattoir under the Buffalo City District Municipality. Six genotypes of cattle (Beefmaster, Bonsmara, Brahman, Holstein-Friesian, Non-descript and Nguni) brought for slaughter at the abattoir on different days were used in the study. Slaughter weight (SWT), warm and cold carcass weight (WCW and CCW), fatness and conformation of each animal were measured and recorded. Representative samples of blood plasma and meat quality from the Muscularis thoracis et lumborum (LTL) were collected at slaughter and 24 hours after slaughter, respectively. Heat shock proteins 70kDa (HSPA1A), glucose (GLU), cortisol (CORT), creatine kinase (CK) and lactate dehydrogenase (LDH) were determined from the blood plasma. The representative LTL muscle was used to determine ultimate pH (pHu), lightness (L*), redness (a*), yellowness (b*), meat temperature (Tm), Warner Bratzler Shear Force (WBSF) and histological structure of beef. There were significant effects of distance on pHu, Tm, a*, b*, TL%, CK and LDH. Pearson correlations were observed between distance travelled (DT), creatine kinase (CK), lactate dehydrogenase (LDH), ultimate pH (pHu), colour coordinates (L*, a* and b*) and Warner Bratzler Shear Force (WBSF). Principal component analysis (PCA) revealed that the 1st (pHu), 2nd (Tm) and 3rd (L*) principal components were the critical meat quality attributes. Positive relationships between carcass weights and beef quality characteristics for bovine cattle where the cumulative percentage of the first six principal component`s (PC`s) (SWT, WCW, CCW, DP, pHu and Tm contributed to 93.4 % of the total variance. Significant correlation coefficients between DT (r = 0.15), LDhr (r = 0.29), Ta (r = -0.52), Tm (r = 0.26), L* (r = 0.33), a* (r = 0.32) and WBSF (r = -0.49) were observed. Meat from Brahman (BR), Non-descript (ND) and Nguni (NG) cows had visible skeletal muscle fibres which were thin and long indicating improved tenderness of beef. Exposing animals to longer hours of transportation did not only reduce glucose levels but also increased the expression of HSPA1A and levels of cortisol. The CK and LDH were not related to beef quality. Therefore, CK and LDH can be used as indicators of animal welfare in slaughter cattle but cannot be used to predict the quality of meat. Bulls were the heaviest, although heifers had the highest dressing percentage than cows. Furthermore, the nanostructure of beef indicated that heifers had the best muscle fibres, sarcomere length and visible intercalated discs. The observed nanostructures of Nguni genotype are an indication of tender meat. Beef from heifers of Nguni had visible and tender meat with traces of intramuscular fat while males had shorter sarcomere length and tougher meat.
- Full Text:
- Date Issued: 2015
Application of Baylis-Hillman methodology in the synthesis of HIV-1 enzyme inhibitors
- Authors: Manyeruke, Meloddy Hlatini
- Date: 2015
- Subjects: HIV infections , Enzyme inhibitors , AZT (Drug) , Bioconjugates
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4540 , http://hdl.handle.net/10962/d1017920
- Description: The application of Baylis-Hillman methodology has afforded access to a range of β-hydroxypropionate ester-AZT conjugates as potential dual-action HIV-1 IN/RT inhibitors. Two families comprising a total of nine β-hydroxypropionate ester-AZT conjugates were synthesised. The first family was accessed using O-benzylated salicylaldehydes and methyl acrylate and the second from unprotected salicylaldehydes using tert-butyl acrylate as the activated alkene. Spectroscopic methods were employed to fully characterize the compounds. Propargylation of the respective Baylis-Hillman adducts was achieved via conjugate addition of propargylamine. The resulting products were then employed in Cu(I)-catalysed “click” reactions with azidothymidine (AZT) to yield the desired β-hydroxypropionate ester-AZT conjugates. Exploratory studies were also conducted to access 4-hydroxycoumarins from Baylis-Hillman derived adducts and to construct customized chiral Baylis-Hillman reaction sites. Many 4- hydroxycoumarins are known to exhibit a wide range of biological activities, and extending Baylis-Hillman methodology to access these systems is an important challenge. Two approaches were investigated. The first involved the formation of a 4-phthalimidocoumarin, aromatisation and hydrolysis of which was expected to lead to the 4-hydroxycoumarin target. The second, a variation of the first, involved the use of 4-(chrolomethyl)coumarin intermediates. Unfortunately, while various intermediates were prepared and characterised, neither approach led ultimately to the desired targets. N-substituted borneol-10-sulfonamides were constructed from camphor-10- sulfonyl chloride as chiral Baylis-Hillman reaction sites. In a preliminary study, however, none of the N-substituted borneol-10-sulfonamides exhibited Baylis-Hillman catalytic activity.
- Full Text:
- Date Issued: 2015
- Authors: Manyeruke, Meloddy Hlatini
- Date: 2015
- Subjects: HIV infections , Enzyme inhibitors , AZT (Drug) , Bioconjugates
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4540 , http://hdl.handle.net/10962/d1017920
- Description: The application of Baylis-Hillman methodology has afforded access to a range of β-hydroxypropionate ester-AZT conjugates as potential dual-action HIV-1 IN/RT inhibitors. Two families comprising a total of nine β-hydroxypropionate ester-AZT conjugates were synthesised. The first family was accessed using O-benzylated salicylaldehydes and methyl acrylate and the second from unprotected salicylaldehydes using tert-butyl acrylate as the activated alkene. Spectroscopic methods were employed to fully characterize the compounds. Propargylation of the respective Baylis-Hillman adducts was achieved via conjugate addition of propargylamine. The resulting products were then employed in Cu(I)-catalysed “click” reactions with azidothymidine (AZT) to yield the desired β-hydroxypropionate ester-AZT conjugates. Exploratory studies were also conducted to access 4-hydroxycoumarins from Baylis-Hillman derived adducts and to construct customized chiral Baylis-Hillman reaction sites. Many 4- hydroxycoumarins are known to exhibit a wide range of biological activities, and extending Baylis-Hillman methodology to access these systems is an important challenge. Two approaches were investigated. The first involved the formation of a 4-phthalimidocoumarin, aromatisation and hydrolysis of which was expected to lead to the 4-hydroxycoumarin target. The second, a variation of the first, involved the use of 4-(chrolomethyl)coumarin intermediates. Unfortunately, while various intermediates were prepared and characterised, neither approach led ultimately to the desired targets. N-substituted borneol-10-sulfonamides were constructed from camphor-10- sulfonyl chloride as chiral Baylis-Hillman reaction sites. In a preliminary study, however, none of the N-substituted borneol-10-sulfonamides exhibited Baylis-Hillman catalytic activity.
- Full Text:
- Date Issued: 2015
Studies towards the development of novel antimalarial agents
- Authors: Adeyemi, Christiana Modupe
- Date: 2015
- Subjects: Antimalarials , Malaria , Drug resistance , Drug development , Enzyme inhibitors , Plasmodium
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54645 , vital:26596
- Description: Considerable efforts have been made in the modification of existing antimalarial drugs, and the support of incentive programmes have led to a drastic decrease in malaria cases reported by WHO during the past 6 years. However, the development of drug resistance threatens the eradication of this deadly disease and has prompted research on the synthesis of novel antimalarial drugs. Our research has involved the design and synthesis of novel benzylated phosphonate esters as potential 1-deoxy-D-xylose-5-phosphate reductoisomerase (DXR) inhibitors. A series of amidoalkylphosphonate esters were obtained by reacting various 3-subsituted anilines and heterocyclic amines with chloroalkanoyl chlorides and reacting the resulting chloroalkanamides with triethyl phosphite using Michaelis-Arbuzov methodology. Benzylation of the phosphonate esters afforded a series of novel N-benzylated derivatives in good yields and these compounds were fully characterised by NMR and HRMS methods. Several approaches to the introduction of a benzyl group at the C-2 position of the phosphonate ester derivatives have been explored, leading unexpectedly to the isolation of unprecedented tetrahydrofuranyl derivatives. Studies towards the preparation of potential bi-functional PfDXR / HIV-1 RT inhibitors have also been initiated. Preliminary in silico docking studies of selected non-benzylated and benzylated phosphonated derivatives into the Pf-DXR active-site has provided useful insight into the binding potential of these ligands. Bioassays have revealed a very low toxicity for all the synthesised phosphonated compounds and a number of these ligands also exhibit a promising inhibitory activity against the Plasmodium parasite.
- Full Text:
- Date Issued: 2015
- Authors: Adeyemi, Christiana Modupe
- Date: 2015
- Subjects: Antimalarials , Malaria , Drug resistance , Drug development , Enzyme inhibitors , Plasmodium
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54645 , vital:26596
- Description: Considerable efforts have been made in the modification of existing antimalarial drugs, and the support of incentive programmes have led to a drastic decrease in malaria cases reported by WHO during the past 6 years. However, the development of drug resistance threatens the eradication of this deadly disease and has prompted research on the synthesis of novel antimalarial drugs. Our research has involved the design and synthesis of novel benzylated phosphonate esters as potential 1-deoxy-D-xylose-5-phosphate reductoisomerase (DXR) inhibitors. A series of amidoalkylphosphonate esters were obtained by reacting various 3-subsituted anilines and heterocyclic amines with chloroalkanoyl chlorides and reacting the resulting chloroalkanamides with triethyl phosphite using Michaelis-Arbuzov methodology. Benzylation of the phosphonate esters afforded a series of novel N-benzylated derivatives in good yields and these compounds were fully characterised by NMR and HRMS methods. Several approaches to the introduction of a benzyl group at the C-2 position of the phosphonate ester derivatives have been explored, leading unexpectedly to the isolation of unprecedented tetrahydrofuranyl derivatives. Studies towards the preparation of potential bi-functional PfDXR / HIV-1 RT inhibitors have also been initiated. Preliminary in silico docking studies of selected non-benzylated and benzylated phosphonated derivatives into the Pf-DXR active-site has provided useful insight into the binding potential of these ligands. Bioassays have revealed a very low toxicity for all the synthesised phosphonated compounds and a number of these ligands also exhibit a promising inhibitory activity against the Plasmodium parasite.
- Full Text:
- Date Issued: 2015
Contributions to the study of a class of optimal control problems on the orthogonal groups SO(3) and SO(4)
- Authors: Adams, Ross Montague
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64826 , vital:28608
- Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
- Full Text:
- Date Issued: 2015
- Authors: Adams, Ross Montague
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64826 , vital:28608
- Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
- Full Text:
- Date Issued: 2015
Study of the biotransformations and microbiological properties of cymbopogon citratus
- Ajayi, Emmanuel Olusegun https://orcid.org/0000-0002-0838-4948
- Authors: Ajayi, Emmanuel Olusegun https://orcid.org/0000-0002-0838-4948
- Date: 2015
- Subjects: Lemongras , Essences and essential oils
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19737 , vital:43197
- Description: Variations in the essential oil yield, chemical composition and kinetics of chemical transformation, antibacterial, and antioxidant properties of the Cymbopogon citratus cultivated in Alice, Eastern Cape of South Africa, over a period of 12 months using the solvent-free microwave extraction and the modified forms of conventional hydrodistillation methods have been evaluated. The modified forms involve variation in the pH medium to effect extraction and to obtain the whole leaf extracts of Cymbopogon citratus (lemongrass). The GC-MS analyses of the essential oils revealed the presence of 10, 11, 13, and 9 principal compounds in the microwave, extraction, hydrodistillation (water-distilled), hydrodistillation (aciddistilled and hydrodistillation (base-distilled), respectively with citral being the prominent compound in all the various extraction methods, with the water-distilled method having the highest cumulative citral content under the period specified. Each of the components of the oils varied in quantity and quality of yield at different points of the year. Different extraction methods produce different compounds. Increase in the amount of citral content was observed during the maturation stage of Cymbopogon citratus in all the extraction methods. Quantitative evaluation of antibacterial activity, minimum inhibitory concentration (MIC) values were determined on the oils and extracts of Cymbopogon citratus using agar dilution method. The essential oils obtained using all the methods of extraction showed activity against all the tested bacteria at a concentration of 10 mg mL-1. The minimum inhibitory concentrations for the acid-distilled varied between 1.25 and 5.0 mg mL-1, while those obtained by both water- and base-distilled showed equal activity on the microorganisms with the MIC ranging between 2.5 and 10 mg mL-1. The microwave extraction showed the least activity with the MIC of 10 mg mL-1. This however suggested that the oils obtained through acid-distillation showed the greatest activity than all other methods of extraction. Activity of the various extracts on bacteria showed that the ethanol extract had the highest activity on the tested organisms with MIC ranging between 0.625 and 1.25 mg mL-1. This was closely followed by the acid-extract (1.25 and 5.0 mg mL-1), methanol extract (1.25 and 10 mg mL-1), acetone extract (2.5 and 5.0 mg mL-1), and base extract (5.0 mg mL-1). Both cold water and hot water extracts showed the least activity of MIC, >10 mg mL-1. The antioxidant and free-radical scavenging activity of the obtained oils and extracts were tested by means of 1,1-diphenyl-2-picrylhydrazyl radical (DPPH+) assay, [(2,2ˊ-azino bis-(3-ethylbenzothiazoline-6-sulfonic acid)] (ABTS), nitric oxide and ferric reducing power assays. The oils and extracts showed DPPH radical scavenging ability, but not as high as the standard drugs. The base extract showed a higher reducing power than the standard drug, rutin. There were significant differences in the phytochemicals contents of the various leaf extracts. The acetone extract has the highest flavonol, proanthocyanidin, and alkaloid contents. The ethanol extract showed the highest amount of phenolic content with the acid extract, having the least. Thin layer chromatography (TLC) and column chromatography was employed to obtain different fractions of extracts using four eluent solvent systems of varying polarities: toluene, petroleum ether, hexane and ethyl acetate and sprayed with anisaldehyde. A single, visible spot of B-fraction was developed, collected and analyzed as 1-methyl-2,4,5- trinitroimidazole with renown valuable properties. , Thesis (PhD) -- Faculty of Science and Agriculture, 2015
- Full Text:
- Date Issued: 2015
- Authors: Ajayi, Emmanuel Olusegun https://orcid.org/0000-0002-0838-4948
- Date: 2015
- Subjects: Lemongras , Essences and essential oils
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19737 , vital:43197
- Description: Variations in the essential oil yield, chemical composition and kinetics of chemical transformation, antibacterial, and antioxidant properties of the Cymbopogon citratus cultivated in Alice, Eastern Cape of South Africa, over a period of 12 months using the solvent-free microwave extraction and the modified forms of conventional hydrodistillation methods have been evaluated. The modified forms involve variation in the pH medium to effect extraction and to obtain the whole leaf extracts of Cymbopogon citratus (lemongrass). The GC-MS analyses of the essential oils revealed the presence of 10, 11, 13, and 9 principal compounds in the microwave, extraction, hydrodistillation (water-distilled), hydrodistillation (aciddistilled and hydrodistillation (base-distilled), respectively with citral being the prominent compound in all the various extraction methods, with the water-distilled method having the highest cumulative citral content under the period specified. Each of the components of the oils varied in quantity and quality of yield at different points of the year. Different extraction methods produce different compounds. Increase in the amount of citral content was observed during the maturation stage of Cymbopogon citratus in all the extraction methods. Quantitative evaluation of antibacterial activity, minimum inhibitory concentration (MIC) values were determined on the oils and extracts of Cymbopogon citratus using agar dilution method. The essential oils obtained using all the methods of extraction showed activity against all the tested bacteria at a concentration of 10 mg mL-1. The minimum inhibitory concentrations for the acid-distilled varied between 1.25 and 5.0 mg mL-1, while those obtained by both water- and base-distilled showed equal activity on the microorganisms with the MIC ranging between 2.5 and 10 mg mL-1. The microwave extraction showed the least activity with the MIC of 10 mg mL-1. This however suggested that the oils obtained through acid-distillation showed the greatest activity than all other methods of extraction. Activity of the various extracts on bacteria showed that the ethanol extract had the highest activity on the tested organisms with MIC ranging between 0.625 and 1.25 mg mL-1. This was closely followed by the acid-extract (1.25 and 5.0 mg mL-1), methanol extract (1.25 and 10 mg mL-1), acetone extract (2.5 and 5.0 mg mL-1), and base extract (5.0 mg mL-1). Both cold water and hot water extracts showed the least activity of MIC, >10 mg mL-1. The antioxidant and free-radical scavenging activity of the obtained oils and extracts were tested by means of 1,1-diphenyl-2-picrylhydrazyl radical (DPPH+) assay, [(2,2ˊ-azino bis-(3-ethylbenzothiazoline-6-sulfonic acid)] (ABTS), nitric oxide and ferric reducing power assays. The oils and extracts showed DPPH radical scavenging ability, but not as high as the standard drugs. The base extract showed a higher reducing power than the standard drug, rutin. There were significant differences in the phytochemicals contents of the various leaf extracts. The acetone extract has the highest flavonol, proanthocyanidin, and alkaloid contents. The ethanol extract showed the highest amount of phenolic content with the acid extract, having the least. Thin layer chromatography (TLC) and column chromatography was employed to obtain different fractions of extracts using four eluent solvent systems of varying polarities: toluene, petroleum ether, hexane and ethyl acetate and sprayed with anisaldehyde. A single, visible spot of B-fraction was developed, collected and analyzed as 1-methyl-2,4,5- trinitroimidazole with renown valuable properties. , Thesis (PhD) -- Faculty of Science and Agriculture, 2015
- Full Text:
- Date Issued: 2015
Synthesis and biological evaluation of truncated sarganaphthoquinoic acid derivatives as Hsp90 inhibitors
- Authors: Chiwakata, Maynard T
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64708 , vital:28594
- Description: Hsp90 inhibition has been at the centre of attention in current research due to the possibility of “cracking down” on the entire process leading to the development of malignant cancers. Small underlying principles common in all types of cancers have been determined that govern the transformation of normal human cells into cancerous cells, with all relying on the ATPase activity of Hsp90 protein. Hsp90 protein is therefore an attractive drug target that if successfully inhibited can result in the remission of cancer tumours by one form of treatment. To date, no Hsp90 inhibitor has been sanctioned for cancer treatment as most are still in clinical development. Our research was therefore inspired by reports that indicated the potential of quinones / naphthoquinones to act as Hsp90 inhibitors. Preliminary results of a few selected marine natural product quinone systems i.e. sargaquinoic acid (SQA) (2.47) and lapachol (3.6) showed moderate cytotoxicity and weak interactions with the Hsp90 molecular chaperone, and evidence suggested C-terminal binding of these molecules. No correlation has been determined yet between cytotoxicity and Hsp90 inhibition, hence we aimed to develop natural product inspired molecules that exhibit both cytotoxic and Hsp90 inhibition properties. Due to limited amounts of the natural product that can be acquired from natural sources, synthetic analogues were opted for. Isolation of a few selected quinones was conducted to have material that could be used in biological assays. For structural modifications, a series of truncated naphthoquinone systems were prepared adopting the sarganaphthoquinoic acid (3.5) scaffold. The naphthoquinones were prepared via Diels-Alder reactions of relevant benzoquinones with myrcene, followed by aromatization reactions using MnO2. Various alkyl and aryl amines were then coupled to the C-2/3 position of the naphthoquinone using Michael’s addition reactions. Tricyclic naphthoquinones were also synthesized from reactions with hypotaurine and citral. Design of the analogues incorporated functionalities from known Hsp90 inhibitors e.g. geldanamycin (2.28) and its analogues. Preliminary results obtained showed that coupling of naphthoquinones with aryl-amines resulted in the most cytotoxic compounds (4.14-4.19) with IC50 values as low as 0.3 μM against Hs578T breast cancer carcinoma (triple negative). Most of the alkyl amines (4.20-4.25) had IC50 values greater than 50 μM except for 4.20 and 4.21 that showed IC50 values of 7.6 μM and 2.6 μM respectively. Tricyclic naphthoquinones (4.28-4.29) showed moderate cytotoxic activity of approximately 10 μM. Hsp90 inhibition was assessed by client protein degradation assays, of which SQA (2.47), showed the best Hsp90 inhibition properties, followed by compound 4.20. The most cytotoxic arylamino-naphthoquinone (4.16) and tricyclic naphthoquinones (4.28-4.29) showed only moderate inhibition. None of the compounds led to Hsp70 induction, suggesting possible binding to the C-terminus of Hsp90. Interactions at the binding site were assessed by molecular docking studies and saturation transfer difference (STD) NMR. Docking studies were conducted on the N-terminus of Hsp90 and better binding was observed for arylamino naphthoquinones (4.14-4.19) than for other series of compounds. Unfortunately, the co-crystal structure for the C-terminus of Hsp90 is unavailable, hence docking study comparisons on both domains could not be conducted. However, STD NMR offered a platform to assess binding interactions between the naphthoquinones and the N- or C-terminal domains of Hsp90. However no interactions were observed at both the N- and C- termini of Hsp90 due to either weak binding of ligands to the protein or poor water solubility of the ligands. From these preliminary results, naphthoquinones bind to Hsp90 protein but conclusive remarks to which terminal domain they bind to could not be made. The best candidate from amongst the series of naphthoquinones prepared that showed moderate cytotoxicity and promising Hsp90 inhibition was compound 4.20. We therefore succeeded in developing a new series of naphthoquinones that possess moderate cytotoxicity and show Hsp90 inhibition.
- Full Text:
- Date Issued: 2015
- Authors: Chiwakata, Maynard T
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64708 , vital:28594
- Description: Hsp90 inhibition has been at the centre of attention in current research due to the possibility of “cracking down” on the entire process leading to the development of malignant cancers. Small underlying principles common in all types of cancers have been determined that govern the transformation of normal human cells into cancerous cells, with all relying on the ATPase activity of Hsp90 protein. Hsp90 protein is therefore an attractive drug target that if successfully inhibited can result in the remission of cancer tumours by one form of treatment. To date, no Hsp90 inhibitor has been sanctioned for cancer treatment as most are still in clinical development. Our research was therefore inspired by reports that indicated the potential of quinones / naphthoquinones to act as Hsp90 inhibitors. Preliminary results of a few selected marine natural product quinone systems i.e. sargaquinoic acid (SQA) (2.47) and lapachol (3.6) showed moderate cytotoxicity and weak interactions with the Hsp90 molecular chaperone, and evidence suggested C-terminal binding of these molecules. No correlation has been determined yet between cytotoxicity and Hsp90 inhibition, hence we aimed to develop natural product inspired molecules that exhibit both cytotoxic and Hsp90 inhibition properties. Due to limited amounts of the natural product that can be acquired from natural sources, synthetic analogues were opted for. Isolation of a few selected quinones was conducted to have material that could be used in biological assays. For structural modifications, a series of truncated naphthoquinone systems were prepared adopting the sarganaphthoquinoic acid (3.5) scaffold. The naphthoquinones were prepared via Diels-Alder reactions of relevant benzoquinones with myrcene, followed by aromatization reactions using MnO2. Various alkyl and aryl amines were then coupled to the C-2/3 position of the naphthoquinone using Michael’s addition reactions. Tricyclic naphthoquinones were also synthesized from reactions with hypotaurine and citral. Design of the analogues incorporated functionalities from known Hsp90 inhibitors e.g. geldanamycin (2.28) and its analogues. Preliminary results obtained showed that coupling of naphthoquinones with aryl-amines resulted in the most cytotoxic compounds (4.14-4.19) with IC50 values as low as 0.3 μM against Hs578T breast cancer carcinoma (triple negative). Most of the alkyl amines (4.20-4.25) had IC50 values greater than 50 μM except for 4.20 and 4.21 that showed IC50 values of 7.6 μM and 2.6 μM respectively. Tricyclic naphthoquinones (4.28-4.29) showed moderate cytotoxic activity of approximately 10 μM. Hsp90 inhibition was assessed by client protein degradation assays, of which SQA (2.47), showed the best Hsp90 inhibition properties, followed by compound 4.20. The most cytotoxic arylamino-naphthoquinone (4.16) and tricyclic naphthoquinones (4.28-4.29) showed only moderate inhibition. None of the compounds led to Hsp70 induction, suggesting possible binding to the C-terminus of Hsp90. Interactions at the binding site were assessed by molecular docking studies and saturation transfer difference (STD) NMR. Docking studies were conducted on the N-terminus of Hsp90 and better binding was observed for arylamino naphthoquinones (4.14-4.19) than for other series of compounds. Unfortunately, the co-crystal structure for the C-terminus of Hsp90 is unavailable, hence docking study comparisons on both domains could not be conducted. However, STD NMR offered a platform to assess binding interactions between the naphthoquinones and the N- or C-terminal domains of Hsp90. However no interactions were observed at both the N- and C- termini of Hsp90 due to either weak binding of ligands to the protein or poor water solubility of the ligands. From these preliminary results, naphthoquinones bind to Hsp90 protein but conclusive remarks to which terminal domain they bind to could not be made. The best candidate from amongst the series of naphthoquinones prepared that showed moderate cytotoxicity and promising Hsp90 inhibition was compound 4.20. We therefore succeeded in developing a new series of naphthoquinones that possess moderate cytotoxicity and show Hsp90 inhibition.
- Full Text:
- Date Issued: 2015
Investigation into the characteristics and possible applications of biomass gasification by-products from a downdraft gasifier system
- Authors: Melapi, Aviwe
- Date: 2015
- Subjects: Biomass gasification -- South Africa -- Eastern Cape , Renewable energy sources -- South Africa -- Eastern Cape , Biomass energy -- South Africa -- Eastern Cape , Crop residue management -- South Africa -- Eastern Cape , Coal gasification -- South Africa -- Eastern Cape , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Chemistry)
- Identifier: vital:11348 , http://hdl.handle.net/10353/d1020174 , Biomass gasification -- South Africa -- Eastern Cape , Renewable energy sources -- South Africa -- Eastern Cape , Biomass energy -- South Africa -- Eastern Cape , Crop residue management -- South Africa -- Eastern Cape , Coal gasification -- South Africa -- Eastern Cape , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape
- Description: Biomass gasification has attracted the interest of researchers because it produces zero carbon to the atmosphere. This technology does not only produce syngas but also the byproducts which can be used for various application depending on quality.The study conducted at Melani village in Alice in the Eastern Cape of South Africa was aimed at investigating the possible applications of the gasification byproducts instead of being thrown away. Pine wood was employed as the parent feedstock material for the gasifier. Biomass gasification by-products were then collected for further analysis. The studied by-products included tar(condensate), char, soot and resin. These materials were also blended to produce strong materials.The essence of the blending was to generate ideal material that is strong but light at the same time.The elemental analysis of the samples performed by CHNS analyser revealed that carbon element is in large quantities in all samples. The FTIR spectra showed almost similar results for all the studied samples, since the samples are end products of lignocellulosegasification. SEM gave the sticky images of resin as well as porous char structures. Char showed a higher heating value of 35.37MJ/Kg when compared to other by-products samples.
- Full Text:
- Date Issued: 2015
- Authors: Melapi, Aviwe
- Date: 2015
- Subjects: Biomass gasification -- South Africa -- Eastern Cape , Renewable energy sources -- South Africa -- Eastern Cape , Biomass energy -- South Africa -- Eastern Cape , Crop residue management -- South Africa -- Eastern Cape , Coal gasification -- South Africa -- Eastern Cape , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Chemistry)
- Identifier: vital:11348 , http://hdl.handle.net/10353/d1020174 , Biomass gasification -- South Africa -- Eastern Cape , Renewable energy sources -- South Africa -- Eastern Cape , Biomass energy -- South Africa -- Eastern Cape , Crop residue management -- South Africa -- Eastern Cape , Coal gasification -- South Africa -- Eastern Cape , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape
- Description: Biomass gasification has attracted the interest of researchers because it produces zero carbon to the atmosphere. This technology does not only produce syngas but also the byproducts which can be used for various application depending on quality.The study conducted at Melani village in Alice in the Eastern Cape of South Africa was aimed at investigating the possible applications of the gasification byproducts instead of being thrown away. Pine wood was employed as the parent feedstock material for the gasifier. Biomass gasification by-products were then collected for further analysis. The studied by-products included tar(condensate), char, soot and resin. These materials were also blended to produce strong materials.The essence of the blending was to generate ideal material that is strong but light at the same time.The elemental analysis of the samples performed by CHNS analyser revealed that carbon element is in large quantities in all samples. The FTIR spectra showed almost similar results for all the studied samples, since the samples are end products of lignocellulosegasification. SEM gave the sticky images of resin as well as porous char structures. Char showed a higher heating value of 35.37MJ/Kg when compared to other by-products samples.
- Full Text:
- Date Issued: 2015
Transformation, job creation and subsidies to creative industries: the case of South Africa’s film and television sector
- Collins, Alan, Snowball, Jeanette D
- Authors: Collins, Alan , Snowball, Jeanette D
- Date: 2015
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67433 , vital:29087 , https://doi.org/10.1080/10286632.2013.874418
- Description: Pre-print , Many governments have tried to stimulate economic growth via policy on the creative industries. South Africa is no different but additionally has an overarching aim of achieving social and labour market ‘transformation’ to move away from the legacy of the apartheid era. The effectiveness of incentives provided to the film and television sector in South Africa are considered in terms of their stated objectives of job creation, skills and knowledge transfer and the attraction of foreign direct investment. Informed by empirical analysis of incentive scheme data and supplemented by elite interviews with key informants, some specific policy revisions are proposed.
- Full Text:
- Date Issued: 2015
- Authors: Collins, Alan , Snowball, Jeanette D
- Date: 2015
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67433 , vital:29087 , https://doi.org/10.1080/10286632.2013.874418
- Description: Pre-print , Many governments have tried to stimulate economic growth via policy on the creative industries. South Africa is no different but additionally has an overarching aim of achieving social and labour market ‘transformation’ to move away from the legacy of the apartheid era. The effectiveness of incentives provided to the film and television sector in South Africa are considered in terms of their stated objectives of job creation, skills and knowledge transfer and the attraction of foreign direct investment. Informed by empirical analysis of incentive scheme data and supplemented by elite interviews with key informants, some specific policy revisions are proposed.
- Full Text:
- Date Issued: 2015