Structural assessment of the Koulekoun Gold Deposit, Guinea, West Africa
- Authors: Dopavogui, Joseph Siba
- Date: 2015
- Subjects: Avocet Mining PLC , Gold ores -- Geology -- Guinea -- Siguiri (Region) , Mines and mineral resources -- Guinea -- Siguiri (Region) , Mineralogy -- Guinea -- Siguiri (Region) , Spherical projection , Faults (Geology) -- Guinea -- Siguiri (Region) , Sedimentary rocks -- Guinea -- Siguiri (Region)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5084 , http://hdl.handle.net/10962/d1018201
- Description: The Koulekoun Gold project is the most important prospect of Avocet Mining plc. It is one of the projects within the TriK-block in Guinea (West Africa) for which an exploration permit has been granted. The Koulekoun deposit is located within the Siguiri basin of Birimian age in the Eastern Guinea region; where most Guinea’s gold mines are situated. The present study involves the investigation of structural elements (S₀, S₁, S₂, intrusive contacts, faults and veins) from selected drill cores from drill sections that intersect the Koulekoun orebody in four parts of the deposit; characterizes the principal orientations of measured structures and determines their relationships using stereonet; in order to predict important intersections to focus on in exploration programs within the TriK-block and suggests a possible structural model of the Koulekoun deposit. Raw data used for the present research was collected from half-core samples due to the absence of surface outcrop from which direct measurements could have been made. Measured data were interpreted using stereographic projection. Often no preferred orientations of structural elements exist in the area, suggesting a complex structural situation, particularly with regard to hydrothermal vein attitudes. Thus, it has been illustrated from structural data analysis and S₀ data 3d interpolation of the four sub-structural domains (North-East, North-West, Central and South) that NE-SW structures (S₂, intrusive contact, fault and vein) have controlled the occurrency of gold mineralization in the Koulekoun deposit area. Geometrical relationships between structure main cluster orientation from stereonet analysis show the majority of S₀ moderately E-dipping; intrusive contacts dip at moderate angle to the SE in all zones, except in the North-East zone where they are sub-vertical and SE-dipping. Fault planes show variable orientation of NE-SW, NW-SE and E-W, and steeply SE-dipping. Vein planes correspond to fault systems and show high variability in their orientation with numerous orders of vein direction in each domain. The cross-cutting relationships suggest two principal generations of faults: the NE-SW fault (F1) and the NW-SE fault (F2). These two fault systems and their associated vein intersection areas preferably define the ore shoot zones within the Koulekoun deposit. The proposed structural model of the Koulekoun deposit suggests the intersection and interference of major NW-SE and minor NE-SW structures. The interference of folds formed basin-dome structures with oval shape geometries striking NW-SE and that dominantly occur in North-East, North-West and Central zones. The South Zone is characterized by NE-SW gently plunging and moderately inclined folds with NW-SE striking axial surface. Gold mineralization occurs at the edges of basin-dome structures in North-East, North-West and Central zones. Mineralized porphyry intrusions are likely located within the axial surface of the South zone folds and extend toward the Central zone. The proposed model is compliant with the earlier model of the Koulekoun deposit presented by Tenova (2013); Fahey et al. (2013) describing the Koulekoun deposit as an auriferous NE-SW trending fault zone, intersecting a major NW-striking and steeply E-dipping porphyry units. The model also fits within the regional structural context suggested by Lahondere et al. (1999a) related to the E-W vein structures attributed to NW-SE fractures and to the conjugated fault of NE-SW direction. Comparatively to the three industrial gold deposits (Siguiri, Lero, Kiniero) being currently mined in the Siguiri Basin, and defined as mesothermal vein and lode mineralization hosted in Birimian meta-sedimentary rocks (Lalande, 2005), the Koulekoun gold deposit appears to be a porphyry hosted orogenic disseminated style mineralization system (Fahey et al., 2013). Although, similarities between the Koulekoun gold deposit and these three industrial deposits (Siguiri, Lero, Kiniero) constitute of the intensive extends of the weathering profile and at some stages, by the existence of numerous ring-shaped and curved lineaments enhanced by drag folding (Lero deposit for instance). It is therefore recommended that targets selection around the Koulekoun deposit and within the TriK-block for further exploration programs be concentrated along NW-SE structures, in objective to determine possible intersection zones with NE-SW structures.
- Full Text:
- Authors: Dopavogui, Joseph Siba
- Date: 2015
- Subjects: Avocet Mining PLC , Gold ores -- Geology -- Guinea -- Siguiri (Region) , Mines and mineral resources -- Guinea -- Siguiri (Region) , Mineralogy -- Guinea -- Siguiri (Region) , Spherical projection , Faults (Geology) -- Guinea -- Siguiri (Region) , Sedimentary rocks -- Guinea -- Siguiri (Region)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5084 , http://hdl.handle.net/10962/d1018201
- Description: The Koulekoun Gold project is the most important prospect of Avocet Mining plc. It is one of the projects within the TriK-block in Guinea (West Africa) for which an exploration permit has been granted. The Koulekoun deposit is located within the Siguiri basin of Birimian age in the Eastern Guinea region; where most Guinea’s gold mines are situated. The present study involves the investigation of structural elements (S₀, S₁, S₂, intrusive contacts, faults and veins) from selected drill cores from drill sections that intersect the Koulekoun orebody in four parts of the deposit; characterizes the principal orientations of measured structures and determines their relationships using stereonet; in order to predict important intersections to focus on in exploration programs within the TriK-block and suggests a possible structural model of the Koulekoun deposit. Raw data used for the present research was collected from half-core samples due to the absence of surface outcrop from which direct measurements could have been made. Measured data were interpreted using stereographic projection. Often no preferred orientations of structural elements exist in the area, suggesting a complex structural situation, particularly with regard to hydrothermal vein attitudes. Thus, it has been illustrated from structural data analysis and S₀ data 3d interpolation of the four sub-structural domains (North-East, North-West, Central and South) that NE-SW structures (S₂, intrusive contact, fault and vein) have controlled the occurrency of gold mineralization in the Koulekoun deposit area. Geometrical relationships between structure main cluster orientation from stereonet analysis show the majority of S₀ moderately E-dipping; intrusive contacts dip at moderate angle to the SE in all zones, except in the North-East zone where they are sub-vertical and SE-dipping. Fault planes show variable orientation of NE-SW, NW-SE and E-W, and steeply SE-dipping. Vein planes correspond to fault systems and show high variability in their orientation with numerous orders of vein direction in each domain. The cross-cutting relationships suggest two principal generations of faults: the NE-SW fault (F1) and the NW-SE fault (F2). These two fault systems and their associated vein intersection areas preferably define the ore shoot zones within the Koulekoun deposit. The proposed structural model of the Koulekoun deposit suggests the intersection and interference of major NW-SE and minor NE-SW structures. The interference of folds formed basin-dome structures with oval shape geometries striking NW-SE and that dominantly occur in North-East, North-West and Central zones. The South Zone is characterized by NE-SW gently plunging and moderately inclined folds with NW-SE striking axial surface. Gold mineralization occurs at the edges of basin-dome structures in North-East, North-West and Central zones. Mineralized porphyry intrusions are likely located within the axial surface of the South zone folds and extend toward the Central zone. The proposed model is compliant with the earlier model of the Koulekoun deposit presented by Tenova (2013); Fahey et al. (2013) describing the Koulekoun deposit as an auriferous NE-SW trending fault zone, intersecting a major NW-striking and steeply E-dipping porphyry units. The model also fits within the regional structural context suggested by Lahondere et al. (1999a) related to the E-W vein structures attributed to NW-SE fractures and to the conjugated fault of NE-SW direction. Comparatively to the three industrial gold deposits (Siguiri, Lero, Kiniero) being currently mined in the Siguiri Basin, and defined as mesothermal vein and lode mineralization hosted in Birimian meta-sedimentary rocks (Lalande, 2005), the Koulekoun gold deposit appears to be a porphyry hosted orogenic disseminated style mineralization system (Fahey et al., 2013). Although, similarities between the Koulekoun gold deposit and these three industrial deposits (Siguiri, Lero, Kiniero) constitute of the intensive extends of the weathering profile and at some stages, by the existence of numerous ring-shaped and curved lineaments enhanced by drag folding (Lero deposit for instance). It is therefore recommended that targets selection around the Koulekoun deposit and within the TriK-block for further exploration programs be concentrated along NW-SE structures, in objective to determine possible intersection zones with NE-SW structures.
- Full Text:
Structural controls of gold mineralisation in Seguelen pit of Siguiri gold mine, Guinea
- Authors: Beavogui, Massa
- Date: 2015
- Subjects: AngloGold Ashanti Ltd. , Gold mines and mining -- Guinea -- Siguiri (Region) , Geochemical surveys -- Guinea -- Siguiri (Region) , Geology, Structural -- Guinea -- Siguiri (Region) , Faults (Geology) -- Guinea -- Siguiri (Region) , Folds (Geology) -- Guinea -- Siguiri (Region) , Turbidites -- Guinea -- Siguiri (Region) , Metamorphism (Geology) -- Guinea -- Siguiri (Region) , Hydrothermal alteration -- Guinea -- Siguiri (Region)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5091 , http://hdl.handle.net/10962/d1019879
- Description: The present study provides the results of detailed mapping and analysis of structures encountered in Seguelen pit of Siguiri gold mine, Guinea, where the Siguiri mine is geo-tectonically located in the Baoulé-Mossi domain of Man Shield in West African craton. The gold deposit is hosted in low-grade metamorphic sediments of turbidites sequences which form part of the Lower Proterozoic of Birimian Super group. Three rock formations of Balato, Fatoya and Kintinian underlay the overall pits. The Siguiri gold mine is characterized by the deep weathering profile, developed over the rocks reaching 200 m below the surface in some areas and often capped by the lateritic gravel or duricrust. The rock formations at Seguelen area are characterised by strong bedding monotonously dipping towards SW and trending NW-SE. The lithology of the host rocks has strong control on the disseminated mineralisation throughout the deposit. Two domains of rock formations are clearly distinguished at Seguelen: Fatoya Formation(Ffm) domain ; and Kintinian Formation (Kfm) domain. The two domains are separated by a contact zone of 1.7 m wide parallel to bedding and characterised by the presence of quartz fragments as well as thinly sheeted shale and black shale. This contact zone is identified as disconformity. The major tectonic deformation which has affected the region is known as D2 corresponding to the Eburnean orogeny. The major D2 related structures is the regional thrust striking N-S over an area of 12 km long and 3 km wide and within which corridors all Siguiri gold Mine open pits are located. In the N-S trending structures, there is east-northeast shortening and north-northwest extension. There is pervasive hydrothermal alteration (carbonatization and sideritization) and supergene alteration in the all pits. The hydrothermal alteration attests the intensity of hydrothermal fluid-flow over the host rocks. The hydrothermal fluids flowed along the fractures and within the wall rocks through bedding plans to form numerous auriferous quartz veins bearing disseminated sulphides through chemical reaction between fluids and wall rocks, which are remarkable at Seguelen pit. Three quartz vein sets are distinguished at Seguelen: NNE-SSW quartz vein set NE-SW quartz vein set NW-SE quartz vein set The NE-SW and NNE-SSW quartz veins are often lenticular and associated with the bulk mineralisation.
- Full Text:
- Authors: Beavogui, Massa
- Date: 2015
- Subjects: AngloGold Ashanti Ltd. , Gold mines and mining -- Guinea -- Siguiri (Region) , Geochemical surveys -- Guinea -- Siguiri (Region) , Geology, Structural -- Guinea -- Siguiri (Region) , Faults (Geology) -- Guinea -- Siguiri (Region) , Folds (Geology) -- Guinea -- Siguiri (Region) , Turbidites -- Guinea -- Siguiri (Region) , Metamorphism (Geology) -- Guinea -- Siguiri (Region) , Hydrothermal alteration -- Guinea -- Siguiri (Region)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5091 , http://hdl.handle.net/10962/d1019879
- Description: The present study provides the results of detailed mapping and analysis of structures encountered in Seguelen pit of Siguiri gold mine, Guinea, where the Siguiri mine is geo-tectonically located in the Baoulé-Mossi domain of Man Shield in West African craton. The gold deposit is hosted in low-grade metamorphic sediments of turbidites sequences which form part of the Lower Proterozoic of Birimian Super group. Three rock formations of Balato, Fatoya and Kintinian underlay the overall pits. The Siguiri gold mine is characterized by the deep weathering profile, developed over the rocks reaching 200 m below the surface in some areas and often capped by the lateritic gravel or duricrust. The rock formations at Seguelen area are characterised by strong bedding monotonously dipping towards SW and trending NW-SE. The lithology of the host rocks has strong control on the disseminated mineralisation throughout the deposit. Two domains of rock formations are clearly distinguished at Seguelen: Fatoya Formation(Ffm) domain ; and Kintinian Formation (Kfm) domain. The two domains are separated by a contact zone of 1.7 m wide parallel to bedding and characterised by the presence of quartz fragments as well as thinly sheeted shale and black shale. This contact zone is identified as disconformity. The major tectonic deformation which has affected the region is known as D2 corresponding to the Eburnean orogeny. The major D2 related structures is the regional thrust striking N-S over an area of 12 km long and 3 km wide and within which corridors all Siguiri gold Mine open pits are located. In the N-S trending structures, there is east-northeast shortening and north-northwest extension. There is pervasive hydrothermal alteration (carbonatization and sideritization) and supergene alteration in the all pits. The hydrothermal alteration attests the intensity of hydrothermal fluid-flow over the host rocks. The hydrothermal fluids flowed along the fractures and within the wall rocks through bedding plans to form numerous auriferous quartz veins bearing disseminated sulphides through chemical reaction between fluids and wall rocks, which are remarkable at Seguelen pit. Three quartz vein sets are distinguished at Seguelen: NNE-SSW quartz vein set NE-SW quartz vein set NW-SE quartz vein set The NE-SW and NNE-SSW quartz veins are often lenticular and associated with the bulk mineralisation.
- Full Text:
Structural studies on yeast eIF5A using biomolecular NMR and molecular dynamics
- Authors: Sigauke, Lester Takunda
- Date: 2015
- Subjects: Molecular dynamics , Reverse transcriptase , HIV (Viruses) , HIV infections , Eukaryotic cells , Yeast
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4547 , http://hdl.handle.net/10962/d1017927
- Description: Eukaryotic initiation factor 5A, eIF5A, is a ubiquitous eukaryotic protein that has been shown to influence the translation initiation of a specific subset of mRNAs. It is the only protein known to undergo hypusination in a two-step post translational modification process involving deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) enzymes. Hypusination has been shown to influence translation of HIV-1 and HTLV-1 nuclear export signals, while the involvement of active hypusinated eIF5A in induction of IRES mediated processes that initiate pro-apoptotic process have inspired studies into the manipulation of eIF5A in anti-cancer and anti-diabetic therapies. eIF5A oligomerisation in eukaryotic systems has been shown to be influenced by hypusination and the mechanism of dimerisation is RNA dependent. Nuclear magnetic resonance spectroscopy approaches were proposed to solve the structure of the hypusinated eIF5A in solution in order to understand the influence of hypusination on the monomeric arrangement which enhances dimerisation and activates the protein. Cleavage of the 18 kDa protein monomer by introduction of thrombin cleavage site within the flexible domain was thought to give rise to 10 kDa fragments accessible to a 600 MHz NMR spectrometer. Heteronuclear single quantum correlation experiments of the mutated isotopically labelled protein expressed in E. coli showed that the eIF5A protein with a thrombin cleavage insert, eIF5AThr (eIF5A subscript Thr), was unfolded. In silico investigations of the behaviour of eIF5A and eIF5AThr (eIF5A subscript Thr) models in solution using molecular dynamics showed that the mutated model had different solution dynamics to the native model. Chemical shift predictors were used to extract atomic resolution data of solution dynamics and the introduction of rigidity in the flexible loop region of eIF5A affected solution behaviour consistent with lack of in vivo function of eIF5AThr (eIF5A subscript Thr) in yeast. Residual dipolar coupling and T₁ relaxation times were calculated in anticipation of the extraction of experimental data from RDC and relaxation dispersion experiments based on HSQC measurable restraints.
- Full Text:
- Authors: Sigauke, Lester Takunda
- Date: 2015
- Subjects: Molecular dynamics , Reverse transcriptase , HIV (Viruses) , HIV infections , Eukaryotic cells , Yeast
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4547 , http://hdl.handle.net/10962/d1017927
- Description: Eukaryotic initiation factor 5A, eIF5A, is a ubiquitous eukaryotic protein that has been shown to influence the translation initiation of a specific subset of mRNAs. It is the only protein known to undergo hypusination in a two-step post translational modification process involving deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) enzymes. Hypusination has been shown to influence translation of HIV-1 and HTLV-1 nuclear export signals, while the involvement of active hypusinated eIF5A in induction of IRES mediated processes that initiate pro-apoptotic process have inspired studies into the manipulation of eIF5A in anti-cancer and anti-diabetic therapies. eIF5A oligomerisation in eukaryotic systems has been shown to be influenced by hypusination and the mechanism of dimerisation is RNA dependent. Nuclear magnetic resonance spectroscopy approaches were proposed to solve the structure of the hypusinated eIF5A in solution in order to understand the influence of hypusination on the monomeric arrangement which enhances dimerisation and activates the protein. Cleavage of the 18 kDa protein monomer by introduction of thrombin cleavage site within the flexible domain was thought to give rise to 10 kDa fragments accessible to a 600 MHz NMR spectrometer. Heteronuclear single quantum correlation experiments of the mutated isotopically labelled protein expressed in E. coli showed that the eIF5A protein with a thrombin cleavage insert, eIF5AThr (eIF5A subscript Thr), was unfolded. In silico investigations of the behaviour of eIF5A and eIF5AThr (eIF5A subscript Thr) models in solution using molecular dynamics showed that the mutated model had different solution dynamics to the native model. Chemical shift predictors were used to extract atomic resolution data of solution dynamics and the introduction of rigidity in the flexible loop region of eIF5A affected solution behaviour consistent with lack of in vivo function of eIF5AThr (eIF5A subscript Thr) in yeast. Residual dipolar coupling and T₁ relaxation times were calculated in anticipation of the extraction of experimental data from RDC and relaxation dispersion experiments based on HSQC measurable restraints.
- Full Text:
Structure of the nucleus ¹¹⁴Sn using gamma-ray coincidence data
- Authors: Oates, Sean Benjamin
- Date: 2015
- Subjects: High spin physics , Nuclear structure , Nuclear shell theory , Neutron counters , Decay schemes (Radioactivity) , Coincidence circuits , Collective excitations , Anisotropy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5562 , http://hdl.handle.net/10962/d1019870
- Full Text:
- Authors: Oates, Sean Benjamin
- Date: 2015
- Subjects: High spin physics , Nuclear structure , Nuclear shell theory , Neutron counters , Decay schemes (Radioactivity) , Coincidence circuits , Collective excitations , Anisotropy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5562 , http://hdl.handle.net/10962/d1019870
- Full Text:
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:
- 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:
Synthesis of silver nanoparticles and their role against human and Plasmodium falciparum leucine aminopeptidase
- Authors: Mnkandhla, Dumisani
- Date: 2015
- Subjects: Silver , Nanoparticles , Plasmodium falciparum , Leucine aminopeptidase , Antimalarials , Nanotechnology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4150 , http://hdl.handle.net/10962/d1017911
- Description: Antimalarial drug discovery remains a challenging endeavour as malaria parasites continue to develop resistance to drugs, including those which are currently the last line of defence against the disease. Plasmodium falciparum is the most virulent of the malaria parasites and it delivers its deadliest impact during the erythrocytic stages of the parasite’s life cycle; a stage characterised by elevated catabolism of haemoglobin and anabolism of parasite proteins. The present study investigates the use of nanotechnology in the form of metallic silver nanoparticles (AgNPs) against P. falciparum leucine aminopeptidase (PfLAP), a validated biomedical target involved in haemoglobin metabolism. AgNPs were also tested against the human homolog cytosolic Homo sapiens leucine aminopeptidase (HsLAP) to ascertain their selective abilities. PfLAP and HsLAP were successfully expressed in Escherichia coli BL21(DE3) cells. PfLAP showed optimal thermal stability at 25 °C and optimal pH stability at pH 8.0 with a Km of 42.7 mM towards leucine-p-nitroanilide (LpNA) and a Vmax of 59.9 μmol.ml⁻¹.min⁻¹. HsLAP was optimally stable at 37 °C and at pH 7.0 with a Km of 16.7 mM and a Vmax of 17.2 μmol.ml⁻¹.min⁻¹. Both enzymes exhibited optimal activity in the presence of 2 mM Mn²⁺. On interaction with polyvinylpyrrolidone (PVP) stabilised AgNPs, both enzymes were inhibited to differing extents with PfLAP losing three fold of its catalytic efficiency relative to HsLAP. These results show the ability of AgNPs to selectively inhibit PfLAP whilst having much lesser effects on its human homolog. With the use of available targeting techniques, the present study shows the potential use of nanotechnology based approaches as “silver bullets” that can target PfLAP without adversely affecting the host. However further research needs to be conducted to better understand the mechanisms of AgNP action, drug targeting and the health and safety issues associated with nanotechnology use.
- Full Text:
- Authors: Mnkandhla, Dumisani
- Date: 2015
- Subjects: Silver , Nanoparticles , Plasmodium falciparum , Leucine aminopeptidase , Antimalarials , Nanotechnology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4150 , http://hdl.handle.net/10962/d1017911
- Description: Antimalarial drug discovery remains a challenging endeavour as malaria parasites continue to develop resistance to drugs, including those which are currently the last line of defence against the disease. Plasmodium falciparum is the most virulent of the malaria parasites and it delivers its deadliest impact during the erythrocytic stages of the parasite’s life cycle; a stage characterised by elevated catabolism of haemoglobin and anabolism of parasite proteins. The present study investigates the use of nanotechnology in the form of metallic silver nanoparticles (AgNPs) against P. falciparum leucine aminopeptidase (PfLAP), a validated biomedical target involved in haemoglobin metabolism. AgNPs were also tested against the human homolog cytosolic Homo sapiens leucine aminopeptidase (HsLAP) to ascertain their selective abilities. PfLAP and HsLAP were successfully expressed in Escherichia coli BL21(DE3) cells. PfLAP showed optimal thermal stability at 25 °C and optimal pH stability at pH 8.0 with a Km of 42.7 mM towards leucine-p-nitroanilide (LpNA) and a Vmax of 59.9 μmol.ml⁻¹.min⁻¹. HsLAP was optimally stable at 37 °C and at pH 7.0 with a Km of 16.7 mM and a Vmax of 17.2 μmol.ml⁻¹.min⁻¹. Both enzymes exhibited optimal activity in the presence of 2 mM Mn²⁺. On interaction with polyvinylpyrrolidone (PVP) stabilised AgNPs, both enzymes were inhibited to differing extents with PfLAP losing three fold of its catalytic efficiency relative to HsLAP. These results show the ability of AgNPs to selectively inhibit PfLAP whilst having much lesser effects on its human homolog. With the use of available targeting techniques, the present study shows the potential use of nanotechnology based approaches as “silver bullets” that can target PfLAP without adversely affecting the host. However further research needs to be conducted to better understand the mechanisms of AgNP action, drug targeting and the health and safety issues associated with nanotechnology use.
- Full Text:
Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae)
- Authors: Riddin, Megan Amy
- Date: 2015
- Subjects: River sardine , Molecular evolution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5930 , http://hdl.handle.net/10962/d1017808
- Description: The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.
- Full Text:
- Authors: Riddin, Megan Amy
- Date: 2015
- Subjects: River sardine , Molecular evolution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5930 , http://hdl.handle.net/10962/d1017808
- Description: The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.
- Full Text:
The acute impact of extended aerobic exercise on cognitive performance
- Tichiwanhuyi, Tendayi Stephen
- Authors: Tichiwanhuyi, Tendayi Stephen
- Date: 2015
- Subjects: Aerobic exercises , Cognition -- Effect of exercise on , Exercise -- Physiological aspects , Exercise -- Psychological aspects , Visual perception , Short-term memory , Motor ability , Human information processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5173 , http://hdl.handle.net/10962/d1018182
- Description: Previous research has established a relationship between exercise and cognition, with more emphasis on this ascertained link, being made on the effects of long term and endurance exercise on cognition. However, enhanced worker effectiveness relies on a strong acute collaboration of physical and cognitive performance during task execution. As a result, the purpose of this study was to examine the acute effects of extended aerobic exercise on visual perception, working memory and motor responses, and to achieve this 24 participants (12 males and 12 females) aged between 18 and 24 participated in a 2 bout cycling exercise. The experimental condition had cycling resistance set at 60 percent of each individual’s maximum aerobic output and the control condition had zero cycling resistance, where three cognitive tasks were performed at 10 minute intervals during the cycling exercise. The results showed that exercise did not affect any significant changes on the cognitive performance measures over the entire cycling duration, as well as during the exercise phase (cycling with resistance). However, visual perception improved significantly (p<0.05) immediately after exercise. This led to the conclusion that moderate to high intensity exercise when performed for an extended duration, has selective effects on certain cognitive performance measures, with the time at which the performance is measured during the exercise being a relevant factor to be considered for maximum activation effects of the exercise.
- Full Text:
- Authors: Tichiwanhuyi, Tendayi Stephen
- Date: 2015
- Subjects: Aerobic exercises , Cognition -- Effect of exercise on , Exercise -- Physiological aspects , Exercise -- Psychological aspects , Visual perception , Short-term memory , Motor ability , Human information processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5173 , http://hdl.handle.net/10962/d1018182
- Description: Previous research has established a relationship between exercise and cognition, with more emphasis on this ascertained link, being made on the effects of long term and endurance exercise on cognition. However, enhanced worker effectiveness relies on a strong acute collaboration of physical and cognitive performance during task execution. As a result, the purpose of this study was to examine the acute effects of extended aerobic exercise on visual perception, working memory and motor responses, and to achieve this 24 participants (12 males and 12 females) aged between 18 and 24 participated in a 2 bout cycling exercise. The experimental condition had cycling resistance set at 60 percent of each individual’s maximum aerobic output and the control condition had zero cycling resistance, where three cognitive tasks were performed at 10 minute intervals during the cycling exercise. The results showed that exercise did not affect any significant changes on the cognitive performance measures over the entire cycling duration, as well as during the exercise phase (cycling with resistance). However, visual perception improved significantly (p<0.05) immediately after exercise. This led to the conclusion that moderate to high intensity exercise when performed for an extended duration, has selective effects on certain cognitive performance measures, with the time at which the performance is measured during the exercise being a relevant factor to be considered for maximum activation effects of the exercise.
- Full Text:
The biology, behaviour and survival of pupating false codling moth, Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a citrus pest in South Africa
- Authors: Love, Claire Natalie
- Date: 2015
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Larvae -- Behavior , Citrus -- Diseases and pests , Citrus -- Diseases and pests -- Biological control , Biological pest control agents , Entomopathogenic fungi , Insect nematodes , Pupae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5941 , http://hdl.handle.net/10962/d1018907
- Description: Control of the citrus pest, false codling moth (FCM), Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is crucial for the South African citrus industry. The economic losses and phytosanitary status of this pest, coupled with increased consumer awareness and demands, has created a need for effective, IPM-compatible control measures for use against the soil-dwelling life stages of FCM. Promising developments in the field of microbial control through the use of entomopathogenic fungi (EPF) and entomopathogenic nematodes (EPNs) have highlighted the need for research regarding pupation biology, behaviour and survival of FCM, as a good understanding of biology of the target organism is an important component of any biological control programme. The aim of this study was to improve the current understanding of FCM pupation habits through the manipulation of soil texture class, ground cover, shading, soil compaction, air temperature, and soil moisture in the laboratory. These findings would then be used to aid the biological control programmes using EPF and EPNs against FCM in the soil. Three soil texture classes (sandy loam, silt loam and silty clay loam) were obtained from orchards for use in the study. FCM larvae were allowed to drop into the soil of their own accord and the pupation behaviour that followed was then captured on film with pupae formed in the soil being kept in order to measure adult eclosion. In general, very few abiotic factors had a clear influence on FCM pupation. Larval wandering time and distance was short, but also variable between individuals. Distance did increase when soils were moist. Pupation depth was shallow, with pupal cocoons generally being formed on the soil surface. Depth of pupation was less than one centimetre for all abiotic conditions, with little burrowing into soil. Eclosion success was higher for sandier soils when these were dry and uncompacted, but the addition of both moisture and soil compaction increased FCM eclosion success. FCM was sensitive to desiccation when the soils were dry and temperature limits of 15 °C and 32 °C had a strongly negative impact on eclosion success. Preferences for particular abiotic conditions were limited to only certain moisture conditions when interacting with soil texture class and a preference for pupating in soil when it is available. Limited preference was found for particular soil textures despite this having a strong influence on eclosion success, but individuals did appear to pupate in close proximity to one another. Viable direct habitat manipulation for FCM control could not be identified. These results and all of the abiotic variables measured have important implications for EPF and EPN application, survival and persistence in the soil in order to improve the ability of these biological control agents to control FCM. These are discussed in each chapter.
- Full Text:
- Authors: Love, Claire Natalie
- Date: 2015
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Larvae -- Behavior , Citrus -- Diseases and pests , Citrus -- Diseases and pests -- Biological control , Biological pest control agents , Entomopathogenic fungi , Insect nematodes , Pupae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5941 , http://hdl.handle.net/10962/d1018907
- Description: Control of the citrus pest, false codling moth (FCM), Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is crucial for the South African citrus industry. The economic losses and phytosanitary status of this pest, coupled with increased consumer awareness and demands, has created a need for effective, IPM-compatible control measures for use against the soil-dwelling life stages of FCM. Promising developments in the field of microbial control through the use of entomopathogenic fungi (EPF) and entomopathogenic nematodes (EPNs) have highlighted the need for research regarding pupation biology, behaviour and survival of FCM, as a good understanding of biology of the target organism is an important component of any biological control programme. The aim of this study was to improve the current understanding of FCM pupation habits through the manipulation of soil texture class, ground cover, shading, soil compaction, air temperature, and soil moisture in the laboratory. These findings would then be used to aid the biological control programmes using EPF and EPNs against FCM in the soil. Three soil texture classes (sandy loam, silt loam and silty clay loam) were obtained from orchards for use in the study. FCM larvae were allowed to drop into the soil of their own accord and the pupation behaviour that followed was then captured on film with pupae formed in the soil being kept in order to measure adult eclosion. In general, very few abiotic factors had a clear influence on FCM pupation. Larval wandering time and distance was short, but also variable between individuals. Distance did increase when soils were moist. Pupation depth was shallow, with pupal cocoons generally being formed on the soil surface. Depth of pupation was less than one centimetre for all abiotic conditions, with little burrowing into soil. Eclosion success was higher for sandier soils when these were dry and uncompacted, but the addition of both moisture and soil compaction increased FCM eclosion success. FCM was sensitive to desiccation when the soils were dry and temperature limits of 15 °C and 32 °C had a strongly negative impact on eclosion success. Preferences for particular abiotic conditions were limited to only certain moisture conditions when interacting with soil texture class and a preference for pupating in soil when it is available. Limited preference was found for particular soil textures despite this having a strong influence on eclosion success, but individuals did appear to pupate in close proximity to one another. Viable direct habitat manipulation for FCM control could not be identified. These results and all of the abiotic variables measured have important implications for EPF and EPN application, survival and persistence in the soil in order to improve the ability of these biological control agents to control FCM. These are discussed in each chapter.
- Full Text:
The cheetahs of the Northern Tuli Game Reserve, Botswana: population estimates, monitoring techniques and human-predator conflict
- Authors: Brassine, Eleanor I
- Date: 2015
- Subjects: Cheetah -- Botswana , Northern Tuli Game Reserve , Animal populations -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5922 , http://hdl.handle.net/10962/d1017800
- Description: Remaining viable cheetah (Acinonyx jubatus) populations in Africa are threatened by direct persecution through conflict with farmers and habitat degradation and fragmentation. Botswana is considered a stronghold for free roaming cheetahs in Africa, yet the country has had relatively limited research on its cheetahs, and information from the east of the country is lacking. Data on the current status of populations is thus required to make informed management decisions. My study provides estimates of population density, abundance, distribution and status for the demographically open cheetah population of the Northern Tuli Game Reserve (NOTUGRE) in Botswana. The effectiveness of two population monitoring methods, namely camera trapping and a photographic survey, were also investigated. Moreover, I report on the level of conflict between livestock farmers and predators on rural communal farmlands within and adjacent to NOTUGRE. Data were collected between May 2012 and November 2013. Results indicate a low population density of 0.61 ± 0.18 adult cheetahs per 100 km² and a minimum population size of 10 individuals (nine adults and one cub). Camera traps placed at cheetah scent-marking posts increased detection rates and provided ideal set up locations. This approach, together with Spatial Explicit Capture- Recapture (SECR) models, is recommended for future studies. The long-term studies that are required to better understand the status of cheetahs in Botswana do not exist. Thus, photographic surveys may provide an alternative method for providing baseline data on population numbers, distribution and demography. The third aspect of my study gathered information on levels of livestock loss and human tolerance of predators through the use of interviews (n = 80). Conflict with subsistence farmers is a concern as livestock depredation is relatively high (9.1% of total livestock owned) and farmers had an overall negative attitude towards conservation of large predators. My results suggest that human-predator conflict in this area is more complex than the direct financial loss from depredation. Hence, reducing depredation rates alone is unlikely to change farmer tolerance of wildlife on farmlands. Improved, responsible farm management, including self-responsibility for livestock rearing, and positive appreciation for wildlife are necessary. The NOTUGRE cheetah population requires further research to understand possible threats to the population. Furthermore, a better understanding of the connectivity between cheetahs of NOTUGRE, South Africa and Zimbabwe is required. The number of cheetahs within NOTUGRE is too small to sustain a viable population, hence conserving cheetahs outside of the protected area should be a priority for the conservation of the population. This can only be achieved through assistance and involvement from national authorities, local people and conservation organisations.
- Full Text:
- Authors: Brassine, Eleanor I
- Date: 2015
- Subjects: Cheetah -- Botswana , Northern Tuli Game Reserve , Animal populations -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5922 , http://hdl.handle.net/10962/d1017800
- Description: Remaining viable cheetah (Acinonyx jubatus) populations in Africa are threatened by direct persecution through conflict with farmers and habitat degradation and fragmentation. Botswana is considered a stronghold for free roaming cheetahs in Africa, yet the country has had relatively limited research on its cheetahs, and information from the east of the country is lacking. Data on the current status of populations is thus required to make informed management decisions. My study provides estimates of population density, abundance, distribution and status for the demographically open cheetah population of the Northern Tuli Game Reserve (NOTUGRE) in Botswana. The effectiveness of two population monitoring methods, namely camera trapping and a photographic survey, were also investigated. Moreover, I report on the level of conflict between livestock farmers and predators on rural communal farmlands within and adjacent to NOTUGRE. Data were collected between May 2012 and November 2013. Results indicate a low population density of 0.61 ± 0.18 adult cheetahs per 100 km² and a minimum population size of 10 individuals (nine adults and one cub). Camera traps placed at cheetah scent-marking posts increased detection rates and provided ideal set up locations. This approach, together with Spatial Explicit Capture- Recapture (SECR) models, is recommended for future studies. The long-term studies that are required to better understand the status of cheetahs in Botswana do not exist. Thus, photographic surveys may provide an alternative method for providing baseline data on population numbers, distribution and demography. The third aspect of my study gathered information on levels of livestock loss and human tolerance of predators through the use of interviews (n = 80). Conflict with subsistence farmers is a concern as livestock depredation is relatively high (9.1% of total livestock owned) and farmers had an overall negative attitude towards conservation of large predators. My results suggest that human-predator conflict in this area is more complex than the direct financial loss from depredation. Hence, reducing depredation rates alone is unlikely to change farmer tolerance of wildlife on farmlands. Improved, responsible farm management, including self-responsibility for livestock rearing, and positive appreciation for wildlife are necessary. The NOTUGRE cheetah population requires further research to understand possible threats to the population. Furthermore, a better understanding of the connectivity between cheetahs of NOTUGRE, South Africa and Zimbabwe is required. The number of cheetahs within NOTUGRE is too small to sustain a viable population, hence conserving cheetahs outside of the protected area should be a priority for the conservation of the population. This can only be achieved through assistance and involvement from national authorities, local people and conservation organisations.
- Full Text:
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:
- 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:
The diets of co-occuring anurans in a small South African river: assessments using stomach contents, stable isotope ratios and fatty acid profiles
- Authors: Sikutshwa, Likho
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54405 , vital:26562
- Description: During their life cycle amphibians change their habitat and feeding, and are important consumers in both terrestrial and aquatic habitats. The trophic ecology of anurans has been studied intensively using gut content analysis, but very little work has been done using biochemical techniques such as stable isotope and fatty acid analyses. These biochemical techniques produce data that allow for additional inferences about the trophic ecology of anurans, as they reveal what the organisms assimilated over time rather than what was recently ingested. The investigation of the feeding ecology and trophic interactions of anurans using gut content analyses together with stable isotope and fatty acid analyses will help us to better understand their ecological roles. The objective of this thesis was to assess the feeding ecology of four anurans (Amietia angolensis, Amietophyrnus rangeri, Strongylopus grayii and Xenopus laevis) in a temperate river using a combination of gut content, stable isotope and fatty acid analyses. Frogs, tadpoles and potential food sources were sampled in two sites (upstream and downstream) in the Kowie River, Eastern Cape Province, South Africa. Gut content analyses identified 147 prey items belonging to 12 prey orders in the stomachs of the sampled specimens. In both A. angolensis and S. grayii the most important prey category was Coleoptera, followed by Hemiptera, Diptera and Hymenoptera at both sites. Aquatic prey items (aquatic hemipterans, chirinomids and blackflies) were the most important food sources for X. laevis (Alimentary Index (IAi) = 6.4; 5.2; 4.2). In Am. rangeri, Hymenoptera was the most important prey category (IAi = 8.3). The trophic niche overlap between A. angolensis and S. grayii was biologically significant (> 0.6), and in the remaining species there was no significant trophic niche overlap. Amietia angolensis showed a larger trophic niche (Levin’s measure; B = 7.7 and Bst = 0.84 downstream, and upstream B = 7.6 (Bst = 0.82) compared to the other species. The gut content analyses showed that frogs feed on a variety of prey items that constitutes food sources from both aquatic and terrestrial habitats. Stable isotopes indicated that aquatic derived sources contributed significantly more towards the diets of X. laevis, A. angolensis tadpoles and S. grayii tadpoles compared with the other anurans, whereas aquatic and terrestrial derived food sources contributed equally to the diets of A. angolensis and S. grayii. Increased trophic positions in A. angolensis and S. grayii occurred throughout their development. The four different species had similar fatty acid profiles in the upstream region, and fairly similar δ13C values, suggesting that they probably consumed similar food. Fatty acid profiles of anurans in the downstream region showed distinct separations among the species. Tadpoles had high levels of diatom-associated fatty acids (20:5ω3; A. angolensis tadpole – 8.4 %, S. grayii tadpole – 9.4 % upstream and downstream; 9.1 and 6.1 % total fatty acids (TFA), respectively). All four species had substantial contributions from bacterial fatty acids, and large proportions of saturated fatty acids (30.6 - 50.0 %) including those with 14 and 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. The fatty acid profiles revealed high proportions of polyunsaturated fatty acids (PUFAs) and essential fatty acids (EFAs) in all species, indicating a good quality of food and that the quality of food consumed was similar among species. The results demonstrated the usefulness of a combination of traditional techniques (gut content techniques) and biochemical techniques (stable isotopes and fatty acid analysis) for assessing consumption and assimilation. The amphibian assemblages examined derived much of their energy from terrestrial and aquatic sources. This information will allow more precise and comprehensive assessments of trophic interactions in freshwater habitats, along with aiding in future amphibian conservation and management efforts.
- Full Text:
- Authors: Sikutshwa, Likho
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54405 , vital:26562
- Description: During their life cycle amphibians change their habitat and feeding, and are important consumers in both terrestrial and aquatic habitats. The trophic ecology of anurans has been studied intensively using gut content analysis, but very little work has been done using biochemical techniques such as stable isotope and fatty acid analyses. These biochemical techniques produce data that allow for additional inferences about the trophic ecology of anurans, as they reveal what the organisms assimilated over time rather than what was recently ingested. The investigation of the feeding ecology and trophic interactions of anurans using gut content analyses together with stable isotope and fatty acid analyses will help us to better understand their ecological roles. The objective of this thesis was to assess the feeding ecology of four anurans (Amietia angolensis, Amietophyrnus rangeri, Strongylopus grayii and Xenopus laevis) in a temperate river using a combination of gut content, stable isotope and fatty acid analyses. Frogs, tadpoles and potential food sources were sampled in two sites (upstream and downstream) in the Kowie River, Eastern Cape Province, South Africa. Gut content analyses identified 147 prey items belonging to 12 prey orders in the stomachs of the sampled specimens. In both A. angolensis and S. grayii the most important prey category was Coleoptera, followed by Hemiptera, Diptera and Hymenoptera at both sites. Aquatic prey items (aquatic hemipterans, chirinomids and blackflies) were the most important food sources for X. laevis (Alimentary Index (IAi) = 6.4; 5.2; 4.2). In Am. rangeri, Hymenoptera was the most important prey category (IAi = 8.3). The trophic niche overlap between A. angolensis and S. grayii was biologically significant (> 0.6), and in the remaining species there was no significant trophic niche overlap. Amietia angolensis showed a larger trophic niche (Levin’s measure; B = 7.7 and Bst = 0.84 downstream, and upstream B = 7.6 (Bst = 0.82) compared to the other species. The gut content analyses showed that frogs feed on a variety of prey items that constitutes food sources from both aquatic and terrestrial habitats. Stable isotopes indicated that aquatic derived sources contributed significantly more towards the diets of X. laevis, A. angolensis tadpoles and S. grayii tadpoles compared with the other anurans, whereas aquatic and terrestrial derived food sources contributed equally to the diets of A. angolensis and S. grayii. Increased trophic positions in A. angolensis and S. grayii occurred throughout their development. The four different species had similar fatty acid profiles in the upstream region, and fairly similar δ13C values, suggesting that they probably consumed similar food. Fatty acid profiles of anurans in the downstream region showed distinct separations among the species. Tadpoles had high levels of diatom-associated fatty acids (20:5ω3; A. angolensis tadpole – 8.4 %, S. grayii tadpole – 9.4 % upstream and downstream; 9.1 and 6.1 % total fatty acids (TFA), respectively). All four species had substantial contributions from bacterial fatty acids, and large proportions of saturated fatty acids (30.6 - 50.0 %) including those with 14 and 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. The fatty acid profiles revealed high proportions of polyunsaturated fatty acids (PUFAs) and essential fatty acids (EFAs) in all species, indicating a good quality of food and that the quality of food consumed was similar among species. The results demonstrated the usefulness of a combination of traditional techniques (gut content techniques) and biochemical techniques (stable isotopes and fatty acid analysis) for assessing consumption and assimilation. The amphibian assemblages examined derived much of their energy from terrestrial and aquatic sources. This information will allow more precise and comprehensive assessments of trophic interactions in freshwater habitats, along with aiding in future amphibian conservation and management efforts.
- Full Text:
The Ecca type section (Permian, South Africa) : an outcrop analogue study of conventional and unconventional hydrocarbon reservoirs
- Authors: Campbell, Stuart Alexander
- Date: 2015
- Subjects: Hydrocarbon reservoirs -- Ecca Group , Geology, Stratigraphic -- Permian , Paleogeography -- Ecca Group , Shale gas -- Ecca Group , Shale gas reservoirs -- Ecca Group , Ecca Group , Ripon Formation (South Africa) , Collingham Formation (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5083 , http://hdl.handle.net/10962/d1018199
- Description: The Karoo Basin of South Africa holds an estimated 906 billion to 11 trillion cubic meters of unconventional shale gas within the shales of the Whitehill and Collingham formations of the Ecca Group. Evaluation of this potential resource has been limited due to the lack of exploration and a scarcity of existing drill core data. In order to circumnavigate this problem this study was undertaken to evaluate the potential target horizons exposed in outcrops along the southern portion of the Karoo Basin, north of Grahamstown in the Eastern Cape Province. Detailed field logging was done on the exposed Whitehill and Collingham formations as well as a possible conventional sandstone (turbidite) reservoir, the Ripon Formation, along road cuttings of the Ecca Pass. Palaeocurrent data, jointing directions and fossil material were also documented. Samples were analysed for mineralogy, porosity, permeability, and total organic carbon content (TOC). The extensively weathered black shales of the Whitehill Formation contain a maximum TOC value of 0.9% and the Collingham Formation shales contain a maximum TOC value of 0.6%. The organic lithic arkose sandstones of the Ripon Formation are classified as ‘tight rock’ with an average porosity of 1% and an average permeability of 0.05 mD. The Whitehill Formation in the southern portion of the Karoo Basin has experienced organic matter loss due to low grade metamorphism as well as burial to extreme depths, thus reducing shale gas potential. The Ripon Formation is an unsuitable conventional reservoir along the southern basin boundary due to extensive cementation and filling of pore spaces.
- Full Text:
- Authors: Campbell, Stuart Alexander
- Date: 2015
- Subjects: Hydrocarbon reservoirs -- Ecca Group , Geology, Stratigraphic -- Permian , Paleogeography -- Ecca Group , Shale gas -- Ecca Group , Shale gas reservoirs -- Ecca Group , Ecca Group , Ripon Formation (South Africa) , Collingham Formation (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5083 , http://hdl.handle.net/10962/d1018199
- Description: The Karoo Basin of South Africa holds an estimated 906 billion to 11 trillion cubic meters of unconventional shale gas within the shales of the Whitehill and Collingham formations of the Ecca Group. Evaluation of this potential resource has been limited due to the lack of exploration and a scarcity of existing drill core data. In order to circumnavigate this problem this study was undertaken to evaluate the potential target horizons exposed in outcrops along the southern portion of the Karoo Basin, north of Grahamstown in the Eastern Cape Province. Detailed field logging was done on the exposed Whitehill and Collingham formations as well as a possible conventional sandstone (turbidite) reservoir, the Ripon Formation, along road cuttings of the Ecca Pass. Palaeocurrent data, jointing directions and fossil material were also documented. Samples were analysed for mineralogy, porosity, permeability, and total organic carbon content (TOC). The extensively weathered black shales of the Whitehill Formation contain a maximum TOC value of 0.9% and the Collingham Formation shales contain a maximum TOC value of 0.6%. The organic lithic arkose sandstones of the Ripon Formation are classified as ‘tight rock’ with an average porosity of 1% and an average permeability of 0.05 mD. The Whitehill Formation in the southern portion of the Karoo Basin has experienced organic matter loss due to low grade metamorphism as well as burial to extreme depths, thus reducing shale gas potential. The Ripon Formation is an unsuitable conventional reservoir along the southern basin boundary due to extensive cementation and filling of pore spaces.
- Full Text:
The effect of extracellular Hsp90β and TGF-β1 on colon cancer biology
- Authors: Perks, Tamarin
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55896 , vital:26753
- Description: The TGF-β signaling pathway is known to be one of the most commonly mutated pathways in human cancers, while Hsp90 is a bone fide drug target that is involved in regulating the conformation and activity of many oncoproteins. The role of intracellular Hsp90 in cancer has thus far been established and there is a growing link between extracellular Hsp90 and cancer metastasis, as well as the role of TGF-β in metastasis. This study aimed to analyse the interaction between Hsp90 (both intracellular and extracellular) and the TGF-β machinery in cancer cells, as well as to determine the effect of these proteins on cellular responses on the biology of cancer cells. This was achieved by studying the expression of Hsp90; TGF-βRII and TGF-β1 in cancer cell lines of various origins using flow cytometry, ELISA, and western blot analysis. The genetically paired SW480 and SW620 colon cancer cell lines, derived from a primary tumour and lymph node metastasis, respectively, were selected for further study due to differences in expression levels and activation of the TGF-β1 pathway. SW480 cells expressed double the level of TGF-βRII compared to SW620 cells, while SW620 expressed two times more extracellular TGF-β1 than SW480 cells. A direct interaction between TGF-β1 and Hsp90β was determined in vitro, and confirmed in vivo in SW620 cells. Growth, adhesion and migration were analysed in SW480 and SW620 cells. SW480 cells adhered significantly faster than SW620 cells, while SW620 cells had a greater rate of migration. Inhibiting the TGF-β pathway, specifically TGF-βRI, using SB 431542, as well as inhibiting Hsp90 with novobiocin, caused an increase in migration in SW480 cells. Only the addition of TGF-β1 in combination with Hsp90 as well as SB 431542 caused an increase in migration in SW620 cells. The canonical TGF-β1/TGF-βRI/TGF-βRII pathway may be constitutively active in SW620 cells and the inhibition of TGF-βRI may suggest an alternate pathway or receptor in both SW480 and SW620 cells.
- Full Text:
- Authors: Perks, Tamarin
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55896 , vital:26753
- Description: The TGF-β signaling pathway is known to be one of the most commonly mutated pathways in human cancers, while Hsp90 is a bone fide drug target that is involved in regulating the conformation and activity of many oncoproteins. The role of intracellular Hsp90 in cancer has thus far been established and there is a growing link between extracellular Hsp90 and cancer metastasis, as well as the role of TGF-β in metastasis. This study aimed to analyse the interaction between Hsp90 (both intracellular and extracellular) and the TGF-β machinery in cancer cells, as well as to determine the effect of these proteins on cellular responses on the biology of cancer cells. This was achieved by studying the expression of Hsp90; TGF-βRII and TGF-β1 in cancer cell lines of various origins using flow cytometry, ELISA, and western blot analysis. The genetically paired SW480 and SW620 colon cancer cell lines, derived from a primary tumour and lymph node metastasis, respectively, were selected for further study due to differences in expression levels and activation of the TGF-β1 pathway. SW480 cells expressed double the level of TGF-βRII compared to SW620 cells, while SW620 expressed two times more extracellular TGF-β1 than SW480 cells. A direct interaction between TGF-β1 and Hsp90β was determined in vitro, and confirmed in vivo in SW620 cells. Growth, adhesion and migration were analysed in SW480 and SW620 cells. SW480 cells adhered significantly faster than SW620 cells, while SW620 cells had a greater rate of migration. Inhibiting the TGF-β pathway, specifically TGF-βRI, using SB 431542, as well as inhibiting Hsp90 with novobiocin, caused an increase in migration in SW480 cells. Only the addition of TGF-β1 in combination with Hsp90 as well as SB 431542 caused an increase in migration in SW620 cells. The canonical TGF-β1/TGF-βRI/TGF-βRII pathway may be constitutively active in SW620 cells and the inhibition of TGF-βRI may suggest an alternate pathway or receptor in both SW480 and SW620 cells.
- Full Text:
The effect of GH family affiliations of mannanolytic enzymes on their synergistic associations during the hydrolysis of mannan-containing substrates
- Authors: Malgas, Samkelo
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Ethanol as fuel , Polysaccharides , Sugar -- Inversion , Glycosidases , Galactoglucomannans , Oligosaccharides
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4148 , http://hdl.handle.net/10962/d1017909
- Full Text:
- Authors: Malgas, Samkelo
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Ethanol as fuel , Polysaccharides , Sugar -- Inversion , Glycosidases , Galactoglucomannans , Oligosaccharides
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4148 , http://hdl.handle.net/10962/d1017909
- Full Text:
The effects of dietary soya and crystalline phytoestrogens on the growth, gonad development and histology of farmed abalone, Haliotis midae
- Wu, Yu
- Authors: Wu, Yu
- Date: 2015
- Subjects: Haliotis midae , Haliotis midae -- Feeding and feeds , Haliotis midae -- Growth , Haliotis midae -- Histology , Haliotis midae -- Effect of chemicals on , Soybean as feed , Phytoestrogens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5380 , http://hdl.handle.net/10962/d1017225
- Description: The inclusion of soya as a dietary protein source in the formulated feed, Abfeed® S34 (Marifeed Pty (Ltd), Hermanus) for farmed abalone, Haliotis midae has resulted in larger gonads during reproductive seasons compared to the gonads of abalone fed kelp or diets that included fishmeal as the only main protein source. The aim of this study was to determine if the isoflavones present in the soya were responsible for this increase in gonad size and the subsequent effects on farmed abalone growth. Animals weighing between 40-50 g were fed one of seven isonitrogenous and isoenergetic diets containing either 0, 25, 50 or 100 percent of the soya component of the commercial feed (Abfeed® S34, Marifeed Pty (Ltd), Hermanus) from September 2013 to March 2014. An additional three diets were formulated to include crystalline isoflavone (ISO). These diets were identical to the 0 percent soya diet (i.e. the fishmeal only diet - FM), only ISO was included at the same rate that ISO occurred in the three soya diets. Data were analysed using a multiple forward stepwise regression analysis (MSR) to test the effects of ISO concentration, soya concentration, time, sex, time by concentration interaction and sex by concentration interaction on growth and gonad development and to identify those variables that most contributed to the model. The inclusion of crystalline ISO failed to promote larger gonads and had no effect on abalone growth, while growth and gonad development was dose dependent on soya inclusion rates with sex and time contributing to the models. Mean monthly weight gain in males correlated with increasing soya concentrations (c) (MSR, y = 3.24 + 0.002c, r2 = 0.23, p = 0.03), ranging from 3.11 ± 0.55 g abalone-1 month-1 to 4.43 ± 0.46 g abalone-1 month-1, while both male and female monthly length gain was not influenced by soya concentration with an overall mean of 1.62 ± 0.05 mm abalone-1 month-1 (MSR, p = 0.05 and p = 0.81, respectively). By December, the whole body mass, meat mass and visceral mass in both males and females decreased with increasing soya levels. However, by February, female whole body mass, meat mass and visceral mass positively correlated with soya levels. At the end of the study, male abalone fed FM with soya equivalent to the commercial feed had the highest whole body mass (69.00 ± 2.48 g abalone-1), meat mass (41.80 ± 1.12 g abalone-1), visceral mass (9.00 ± 2.47 g abalone-1) and gonad bulk index (42.70 ± 9.82 g abalone-1), while females were not influenced by soya concentrations with an overall whole body mass of 63.46 ± 0.79 g abalone-1. Weight loss was observed in all treatments between February and March, probably due to a spawning event. The moisture content in the meat was not influenced by treatment, however, visceral water loss was effected by both ISO and soya concentration with time and sex contributing to the model. The visceral water loss of females fed graded levels of soya decreased as a function of soya from December to March, and from December to February for males, whereas females fed ISO-enriched diets decreased as a function of ISO concentration (c) at the end of the study from 74.98 ± 0.88 to 73.10 ± 0.75 percent (MSR, y = 74.97 – 0.0025c, r2 = 0.20, p = 0.048). The inclusion of crystalline ISO had no significant effect on oogenesis in female farmed Haliotis midae, while the distribution of the predominant oocyte stage, stage 7 (second last stage prior to spawning) was dose-dependent in abalone fed increasing soya concentration (c) (MSR, y = 33.38 + 0.03c, r2 = 0.32, F(1, 18) = 8.52, p = 0.01). The increase in stage 7 oocytes in abalone fed FM with soya did not reduce the number of oocytes (44.96 ± 3.01 oocytes mm-2) present within the lumen, while the number of oocytes (o) in abalone fed the FM-only based diets decreased with increasing abundance of stage 7 oocytes (MSR, y = 58.28 – 0.48c, r2 = 0.38, F(1, 18) = 12.51, p = 0.002), possibly due to the increase in size of the oocytes with thicker jelly coats. This study provided evidence that crystalline isoflavone had no influence on abalone gonad development over five months, while soya had a dose-dependent effect on growth, gonad mass and oogenesis in farmed Haliotis midae. Formulated abalone feed could be manipulated at certain times of the year to obtain maximum growth. These implications and further studies were discussed.
- Full Text:
- Authors: Wu, Yu
- Date: 2015
- Subjects: Haliotis midae , Haliotis midae -- Feeding and feeds , Haliotis midae -- Growth , Haliotis midae -- Histology , Haliotis midae -- Effect of chemicals on , Soybean as feed , Phytoestrogens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5380 , http://hdl.handle.net/10962/d1017225
- Description: The inclusion of soya as a dietary protein source in the formulated feed, Abfeed® S34 (Marifeed Pty (Ltd), Hermanus) for farmed abalone, Haliotis midae has resulted in larger gonads during reproductive seasons compared to the gonads of abalone fed kelp or diets that included fishmeal as the only main protein source. The aim of this study was to determine if the isoflavones present in the soya were responsible for this increase in gonad size and the subsequent effects on farmed abalone growth. Animals weighing between 40-50 g were fed one of seven isonitrogenous and isoenergetic diets containing either 0, 25, 50 or 100 percent of the soya component of the commercial feed (Abfeed® S34, Marifeed Pty (Ltd), Hermanus) from September 2013 to March 2014. An additional three diets were formulated to include crystalline isoflavone (ISO). These diets were identical to the 0 percent soya diet (i.e. the fishmeal only diet - FM), only ISO was included at the same rate that ISO occurred in the three soya diets. Data were analysed using a multiple forward stepwise regression analysis (MSR) to test the effects of ISO concentration, soya concentration, time, sex, time by concentration interaction and sex by concentration interaction on growth and gonad development and to identify those variables that most contributed to the model. The inclusion of crystalline ISO failed to promote larger gonads and had no effect on abalone growth, while growth and gonad development was dose dependent on soya inclusion rates with sex and time contributing to the models. Mean monthly weight gain in males correlated with increasing soya concentrations (c) (MSR, y = 3.24 + 0.002c, r2 = 0.23, p = 0.03), ranging from 3.11 ± 0.55 g abalone-1 month-1 to 4.43 ± 0.46 g abalone-1 month-1, while both male and female monthly length gain was not influenced by soya concentration with an overall mean of 1.62 ± 0.05 mm abalone-1 month-1 (MSR, p = 0.05 and p = 0.81, respectively). By December, the whole body mass, meat mass and visceral mass in both males and females decreased with increasing soya levels. However, by February, female whole body mass, meat mass and visceral mass positively correlated with soya levels. At the end of the study, male abalone fed FM with soya equivalent to the commercial feed had the highest whole body mass (69.00 ± 2.48 g abalone-1), meat mass (41.80 ± 1.12 g abalone-1), visceral mass (9.00 ± 2.47 g abalone-1) and gonad bulk index (42.70 ± 9.82 g abalone-1), while females were not influenced by soya concentrations with an overall whole body mass of 63.46 ± 0.79 g abalone-1. Weight loss was observed in all treatments between February and March, probably due to a spawning event. The moisture content in the meat was not influenced by treatment, however, visceral water loss was effected by both ISO and soya concentration with time and sex contributing to the model. The visceral water loss of females fed graded levels of soya decreased as a function of soya from December to March, and from December to February for males, whereas females fed ISO-enriched diets decreased as a function of ISO concentration (c) at the end of the study from 74.98 ± 0.88 to 73.10 ± 0.75 percent (MSR, y = 74.97 – 0.0025c, r2 = 0.20, p = 0.048). The inclusion of crystalline ISO had no significant effect on oogenesis in female farmed Haliotis midae, while the distribution of the predominant oocyte stage, stage 7 (second last stage prior to spawning) was dose-dependent in abalone fed increasing soya concentration (c) (MSR, y = 33.38 + 0.03c, r2 = 0.32, F(1, 18) = 8.52, p = 0.01). The increase in stage 7 oocytes in abalone fed FM with soya did not reduce the number of oocytes (44.96 ± 3.01 oocytes mm-2) present within the lumen, while the number of oocytes (o) in abalone fed the FM-only based diets decreased with increasing abundance of stage 7 oocytes (MSR, y = 58.28 – 0.48c, r2 = 0.38, F(1, 18) = 12.51, p = 0.002), possibly due to the increase in size of the oocytes with thicker jelly coats. This study provided evidence that crystalline isoflavone had no influence on abalone gonad development over five months, while soya had a dose-dependent effect on growth, gonad mass and oogenesis in farmed Haliotis midae. Formulated abalone feed could be manipulated at certain times of the year to obtain maximum growth. These implications and further studies were discussed.
- Full Text:
The influence of the physical environment, topography and time on the inshore distribution of invertebrate larvae : a multi-taxon approach
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
The isolation, genetic characterisation and biological activity of a South African Phthorimaea operculella granulovirus (PhopGV-SA) for the control of the Potato Tuber Moth, Phthorimaea operculella (Zeller)
- Authors: Jukes, Michael David
- Date: 2015
- Subjects: Potato tuberworm , Potatoes -- Diseases and pests -- South Africa , Baculoviruses , Natural pesticides , Biological pest control agents , Potato tuberworm -- Biological control , Restriction enzymes, DNA
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4147 , http://hdl.handle.net/10962/d1017908
- Description: The potato tuber moth, Phthorimaea operculella (Zeller), is a major pest of potato crops worldwide causing significant damage to both field and stored tubers. The current control method in South Africa involves chemical insecticides, however, there is growing concern on the health and environmental risks of their use. The development of novel biopesticide based control methods may offer a potential solution for the future of insecticides. In this study a baculovirus was successfully isolated from a laboratory population of P. operculella. Transmission electron micrographs revealed granulovirus-like particles. DNA was extracted from recovered occlusion bodies and used for the PCR amplification of the lef-8, lef-9, granulin and egt genes. Sequence data was obtained and submitted to BLAST identifying the virus as a South African isolate of Phthorimaea operculella granulovirus (PhopGV-SA). Phylogenetic analysis of the lef-8, lef-9 and granulin amino acid sequences grouped the South African isolate with PhopGV-1346. Comparison of egt sequence data identified PhopGV-SA as a type II egt gene. A phylogenetic analysis of egt amino acid sequences grouped all type II genes, including PhopGV-SA, into a separate clade from types I, III, IV and V. These findings suggest that type II may represent the prototype structure for this gene with the evolution of types I, III and IV a result of large internal deletion events and subsequent divergence. PhopGV-SA was also shown to be genetically more similar to South American isolates (i.e. PhopGV-CHI or PhopGV-INDO) than it is to other African isolates, suggesting that the South African isolate originated from South America. Restriction endonuclease profiles of PhopGV-SA were similar to those of PhopGV-1346 and PhopGV-JLZ9f for the enzymes BamHI, HindIII, NruI and NdeI. A preliminary full genome sequence for PhopGV-SA was determined and compared to PhopGV-136 with some gene variation observed (i.e. odv-e66 and vp91/p95). The biological activity of PhopGV-SA against P. operculella neonate larvae was evaluated with an estimated LC₅₀ of 1.87×10⁸ OBs.ml⁻¹ being determined. This study therefore reports the characterisation of a novel South African PhopGV isolate which could potentially be developed into a biopesticide for the control of P. operculella.
- Full Text:
- Authors: Jukes, Michael David
- Date: 2015
- Subjects: Potato tuberworm , Potatoes -- Diseases and pests -- South Africa , Baculoviruses , Natural pesticides , Biological pest control agents , Potato tuberworm -- Biological control , Restriction enzymes, DNA
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4147 , http://hdl.handle.net/10962/d1017908
- Description: The potato tuber moth, Phthorimaea operculella (Zeller), is a major pest of potato crops worldwide causing significant damage to both field and stored tubers. The current control method in South Africa involves chemical insecticides, however, there is growing concern on the health and environmental risks of their use. The development of novel biopesticide based control methods may offer a potential solution for the future of insecticides. In this study a baculovirus was successfully isolated from a laboratory population of P. operculella. Transmission electron micrographs revealed granulovirus-like particles. DNA was extracted from recovered occlusion bodies and used for the PCR amplification of the lef-8, lef-9, granulin and egt genes. Sequence data was obtained and submitted to BLAST identifying the virus as a South African isolate of Phthorimaea operculella granulovirus (PhopGV-SA). Phylogenetic analysis of the lef-8, lef-9 and granulin amino acid sequences grouped the South African isolate with PhopGV-1346. Comparison of egt sequence data identified PhopGV-SA as a type II egt gene. A phylogenetic analysis of egt amino acid sequences grouped all type II genes, including PhopGV-SA, into a separate clade from types I, III, IV and V. These findings suggest that type II may represent the prototype structure for this gene with the evolution of types I, III and IV a result of large internal deletion events and subsequent divergence. PhopGV-SA was also shown to be genetically more similar to South American isolates (i.e. PhopGV-CHI or PhopGV-INDO) than it is to other African isolates, suggesting that the South African isolate originated from South America. Restriction endonuclease profiles of PhopGV-SA were similar to those of PhopGV-1346 and PhopGV-JLZ9f for the enzymes BamHI, HindIII, NruI and NdeI. A preliminary full genome sequence for PhopGV-SA was determined and compared to PhopGV-136 with some gene variation observed (i.e. odv-e66 and vp91/p95). The biological activity of PhopGV-SA against P. operculella neonate larvae was evaluated with an estimated LC₅₀ of 1.87×10⁸ OBs.ml⁻¹ being determined. This study therefore reports the characterisation of a novel South African PhopGV isolate which could potentially be developed into a biopesticide for the control of P. operculella.
- Full Text:
The relative contribution of non-timber forest products, agriculture and off-farm sources of income to rural households in Koloni and Guquka, Eastern Cape
- Authors: Mtati, Nosiseko
- Date: 2015
- Subjects: Informal sector (Economics) -- South Africa -- Eastern Cape , Rural development -- South Africa -- Eastern Cape , Rural poor -- South Africa -- Eastern Cape , Households -- Economic aspects -- South Africa -- Eastern Cape , Forest products -- South Africa -- Eastern Cape , Non-timber forest products -- South Africa -- Eastern Cape , Agriculture -- Economic aspects -- South Africa -- Eastern Cape , Natural resources -- South Africa -- Eastern Cape , Income -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4785 , http://hdl.handle.net/10962/d1018193
- Description: [Partial abstract]: This study was carried out to determine the contribution of non-timber forest products (NTFPs) to household total income, other livelihood sectors were also examined simultaneously. The contribution of agriculture involved livestock and crop production. Wages and government grants were other livelihood sectors that were looked into. This study was important in determining the change in livelihood strategies in the last decade and to quantify the NTFPs used at the two sites. It was carried out in Guquka and Koloni, both part of the central Eastern Cape. Information on direct use value of the NTFPs used, the quantities and local price; crop production outputs and inputs and the costs. Data were collected via a questionnaire.
- Full Text:
- Authors: Mtati, Nosiseko
- Date: 2015
- Subjects: Informal sector (Economics) -- South Africa -- Eastern Cape , Rural development -- South Africa -- Eastern Cape , Rural poor -- South Africa -- Eastern Cape , Households -- Economic aspects -- South Africa -- Eastern Cape , Forest products -- South Africa -- Eastern Cape , Non-timber forest products -- South Africa -- Eastern Cape , Agriculture -- Economic aspects -- South Africa -- Eastern Cape , Natural resources -- South Africa -- Eastern Cape , Income -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4785 , http://hdl.handle.net/10962/d1018193
- Description: [Partial abstract]: This study was carried out to determine the contribution of non-timber forest products (NTFPs) to household total income, other livelihood sectors were also examined simultaneously. The contribution of agriculture involved livestock and crop production. Wages and government grants were other livelihood sectors that were looked into. This study was important in determining the change in livelihood strategies in the last decade and to quantify the NTFPs used at the two sites. It was carried out in Guquka and Koloni, both part of the central Eastern Cape. Information on direct use value of the NTFPs used, the quantities and local price; crop production outputs and inputs and the costs. Data were collected via a questionnaire.
- Full Text:
The role of seasonality, environmental correlates and edge effects on the diversity and abundance of small mammals in Afromontane forest patches, Eastern Cape, South Africa
- Authors: Junkuhn, Kyle Peter
- Date: 2015
- Subjects: Upland ecology -- South Africa -- Eastern Cape , Mammal populations -- South Africa -- Eastern Cape , Forest animals -- Adaptation -- South Africa -- Eastern Cape , Forest animals -- Climatic factors -- South Africa -- Eastern Cape , Forest animals -- Effect of habitat modification on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4270 , http://hdl.handle.net/10962/d1018188
- Description: The Eastern Cape contains the majority of the remaining forested areas in South Africa (95.8 percent Coastal forests and 47.6 percent Afromontane forests), however these occur in fragments. Due to the rapid rise in the human population and its needs, conversion of forests to agricultural land and the extraction of timber increases, natural vegetation are lost and this therefore leads to forests becoming fragmented into small forest patches. One of the main consequences of forest fragmentation is loss of contiguous habitat, which is the dominant threat to species globally as it negatively affects both species richness and genetic diversity. This research investigates the effects that forest fragmentation has on small mammal diversity and abundance. The study sampled small mammals in Southern Mistbelt Afromontane forest patches in the Eastern Cape. The first aim of this study was to identify which environmental variable, or combinations of variables, affect the diversity and abundance of small mammals in fragmented forest patches in the Eastern Cape during the austral summer. The second aim was to compare seasonal changes in small mammal diversity and abundance at a forest edge compared to the forest core at Beggars Bush, an Afromontane forest in the Eastern Cape, South Africa. To identify the environmental impacts that different forests have on small mammals, nine different forests were chosen in the Eastern Cape and sampled during the summer in 2013. These nine forests were: Fort Fordyce Forest, Thaba Ndoda Forest, Hogsback Forest, Dassie Kraans Forest, Langeni Forest, Burchell’s Reserve Forest, Maiden Dam Forest and Kagaberg Forest. At each site, three transects of 30 Sherman Traps each were used. Trapping periods within each forest patch lasted between three to five consecutive nights and traps were inspected once a day in the morning. Nine environmental variables were initially identified and after being tested for normality and colinearity, five variables were chosen. These variables were Altitude, Mean Annual Temperature, Gradient, Patch Size and Mean annual potential evaporation. The number of individuals captures and species richness were then incorporated as dependent variables for best subset multiple regression model selection using the Akaike Information Criterion (AIC). For the second aim, the same trapping methods were used when comparing seasonal changes to diversity and abundance within the forest core. However at the forest edge, due to the small size of the forest, only 20 Sherman traps were used in each transect with five traps (25 percent) placed in the grassland and 15 (75 percent) placed in the forest along each transect. This study was one of few to survey small mammal diversity and abundance in fragmented forests in the Eastern Cape. Gradient, patch size and mean annual potential evaporation were the variables that best predicted the individual number of small mammal captures while only gradient best explained species richness. It does however, need to be noted that capture rates and species richness were very low and this would therefore effect the analysis of environmental variables. Future studies should have a larger sample size of forest patches and include more microhabitat environmental variables to determine their effects on small mammal diversity and abundance. However, it should be noted that through climatic extinction filtering, forest mammals are resilient generalists that can tolerate fragmentation effects. Furthermore, it was found that forest edges appear to play a significant role in small mammal diversity and abundance in the Beggars Bush Afromontane forest. Some species were habitat specialists such as Rhabdomys pumilio preferring the grassland habitat and Graphiurus murinus and Aethomys namaquensis the forest habitat, while Myosorex varius was the only species that was not habitat dependant. It was found that there was a greater diversity and abundance at the forest edge compared to within the forest core throughout most of the seasons. One possible flaw was that the sampling methods were different at the edge and within the forest and therefore future studies should ensure that the method stays uniform throughout the study.
- Full Text:
- Authors: Junkuhn, Kyle Peter
- Date: 2015
- Subjects: Upland ecology -- South Africa -- Eastern Cape , Mammal populations -- South Africa -- Eastern Cape , Forest animals -- Adaptation -- South Africa -- Eastern Cape , Forest animals -- Climatic factors -- South Africa -- Eastern Cape , Forest animals -- Effect of habitat modification on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4270 , http://hdl.handle.net/10962/d1018188
- Description: The Eastern Cape contains the majority of the remaining forested areas in South Africa (95.8 percent Coastal forests and 47.6 percent Afromontane forests), however these occur in fragments. Due to the rapid rise in the human population and its needs, conversion of forests to agricultural land and the extraction of timber increases, natural vegetation are lost and this therefore leads to forests becoming fragmented into small forest patches. One of the main consequences of forest fragmentation is loss of contiguous habitat, which is the dominant threat to species globally as it negatively affects both species richness and genetic diversity. This research investigates the effects that forest fragmentation has on small mammal diversity and abundance. The study sampled small mammals in Southern Mistbelt Afromontane forest patches in the Eastern Cape. The first aim of this study was to identify which environmental variable, or combinations of variables, affect the diversity and abundance of small mammals in fragmented forest patches in the Eastern Cape during the austral summer. The second aim was to compare seasonal changes in small mammal diversity and abundance at a forest edge compared to the forest core at Beggars Bush, an Afromontane forest in the Eastern Cape, South Africa. To identify the environmental impacts that different forests have on small mammals, nine different forests were chosen in the Eastern Cape and sampled during the summer in 2013. These nine forests were: Fort Fordyce Forest, Thaba Ndoda Forest, Hogsback Forest, Dassie Kraans Forest, Langeni Forest, Burchell’s Reserve Forest, Maiden Dam Forest and Kagaberg Forest. At each site, three transects of 30 Sherman Traps each were used. Trapping periods within each forest patch lasted between three to five consecutive nights and traps were inspected once a day in the morning. Nine environmental variables were initially identified and after being tested for normality and colinearity, five variables were chosen. These variables were Altitude, Mean Annual Temperature, Gradient, Patch Size and Mean annual potential evaporation. The number of individuals captures and species richness were then incorporated as dependent variables for best subset multiple regression model selection using the Akaike Information Criterion (AIC). For the second aim, the same trapping methods were used when comparing seasonal changes to diversity and abundance within the forest core. However at the forest edge, due to the small size of the forest, only 20 Sherman traps were used in each transect with five traps (25 percent) placed in the grassland and 15 (75 percent) placed in the forest along each transect. This study was one of few to survey small mammal diversity and abundance in fragmented forests in the Eastern Cape. Gradient, patch size and mean annual potential evaporation were the variables that best predicted the individual number of small mammal captures while only gradient best explained species richness. It does however, need to be noted that capture rates and species richness were very low and this would therefore effect the analysis of environmental variables. Future studies should have a larger sample size of forest patches and include more microhabitat environmental variables to determine their effects on small mammal diversity and abundance. However, it should be noted that through climatic extinction filtering, forest mammals are resilient generalists that can tolerate fragmentation effects. Furthermore, it was found that forest edges appear to play a significant role in small mammal diversity and abundance in the Beggars Bush Afromontane forest. Some species were habitat specialists such as Rhabdomys pumilio preferring the grassland habitat and Graphiurus murinus and Aethomys namaquensis the forest habitat, while Myosorex varius was the only species that was not habitat dependant. It was found that there was a greater diversity and abundance at the forest edge compared to within the forest core throughout most of the seasons. One possible flaw was that the sampling methods were different at the edge and within the forest and therefore future studies should ensure that the method stays uniform throughout the study.
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