Solid-phase extraction based sample preparation for the determination of drug and organic pollutant residue
- Authors: Pule, Bellah Oreeditse
- Date: 2011 , 2011-02-08
- Subjects: Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4406 , http://hdl.handle.net/10962/d1006711 , Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Description: This thesis presents solid phase extraction (SPE) methodologies based on mixed-mode polymeric sorbents; a mixed mode strong anion exchanger (Agilent SampliQ SAX) and a mixed mode strong cation exchanger (Agilent SampliQ SCX). Furthermore, dispersive-SPE based on a quick, easy, cheap, effective, rugged and safe (QuEChERS) method was assessed for applicability in the determination of drug residues. The mixed-mode polymeric sorbents were evaluated for the simultaneous fractionation of drugs that exhibit diverse polarities with acidic, basic and neutral functionalities in biological matrices (plasma and urine). The polymeric skeleton of these sorbents entails an exchanger group and therefore provides two retention mechanisms, strong cation or anion exchange retention mechanisms with hydrophobic interactions. It was demonstrated that with a sequential elution protocol for sample clean-up analytes were fractionated into acidic, basic and neutral classes. The SAX was employed for analysis of ketoprofen, naproxen (acidic drugs), nortriptyline (basic) and secobarbital (neutral) from urine sample. The SCX was used for fractionating phenobarbital, p-toluamide (acidic), amphetamine, m-toluidine (basic) and acetaminophen (neutral drug) from plasma sample. QuEChERS method was employed for quantitative determination of 16 polycyclic aromatic hydrocarbons (PAHs) from fish fillets and soil; 9 sulfonamides (SAs) from chicken muscles and acrylamide (AA) in cooking oil. The analyte recoveries ranged from 79.6 - 109% with RSDs ranging from 0.06 - 1.9% at three different fortification levels. Good linearity (r2 > 0.9990) was attained for most analytes. The limits of detection and quantification ranged from 0.03 - 0.84 μg/ml and 0.81 - 1.89 μg/ml respectively for analytes in biological samples. LODs and LOQs for analytes in food and environmental samples ranged from 0.02 to 0.39 and 0.25 to 1.30 ng/g respectively.
- Full Text:
- Authors: Pule, Bellah Oreeditse
- Date: 2011 , 2011-02-08
- Subjects: Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4406 , http://hdl.handle.net/10962/d1006711 , Food contamination , Drugs -- Analysis , Pharmaceutical chemistry , Extraction (Chemistry) , Sorbents
- Description: This thesis presents solid phase extraction (SPE) methodologies based on mixed-mode polymeric sorbents; a mixed mode strong anion exchanger (Agilent SampliQ SAX) and a mixed mode strong cation exchanger (Agilent SampliQ SCX). Furthermore, dispersive-SPE based on a quick, easy, cheap, effective, rugged and safe (QuEChERS) method was assessed for applicability in the determination of drug residues. The mixed-mode polymeric sorbents were evaluated for the simultaneous fractionation of drugs that exhibit diverse polarities with acidic, basic and neutral functionalities in biological matrices (plasma and urine). The polymeric skeleton of these sorbents entails an exchanger group and therefore provides two retention mechanisms, strong cation or anion exchange retention mechanisms with hydrophobic interactions. It was demonstrated that with a sequential elution protocol for sample clean-up analytes were fractionated into acidic, basic and neutral classes. The SAX was employed for analysis of ketoprofen, naproxen (acidic drugs), nortriptyline (basic) and secobarbital (neutral) from urine sample. The SCX was used for fractionating phenobarbital, p-toluamide (acidic), amphetamine, m-toluidine (basic) and acetaminophen (neutral drug) from plasma sample. QuEChERS method was employed for quantitative determination of 16 polycyclic aromatic hydrocarbons (PAHs) from fish fillets and soil; 9 sulfonamides (SAs) from chicken muscles and acrylamide (AA) in cooking oil. The analyte recoveries ranged from 79.6 - 109% with RSDs ranging from 0.06 - 1.9% at three different fortification levels. Good linearity (r2 > 0.9990) was attained for most analytes. The limits of detection and quantification ranged from 0.03 - 0.84 μg/ml and 0.81 - 1.89 μg/ml respectively for analytes in biological samples. LODs and LOQs for analytes in food and environmental samples ranged from 0.02 to 0.39 and 0.25 to 1.30 ng/g respectively.
- Full Text:
SphereZyme (TM) technology for enhanced enzyme immobilisation application in biosensors
- Authors: Molawa, Letshego Gloria
- Date: 2011
- Subjects: Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3989 , http://hdl.handle.net/10962/d1004048 , Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Description: Self-immobilisation enzyme technologies, such as SphereZyme™, suffer from the lack of applicability to hydrolyse large substrates. Solid support immobilisation is usually a method of choice, to produce a stable biocatalyst for large substrates hydrolysis in the industry. In order to investigate this limitation, a commercial protease called Alcalase® was chosen as a model enzyme due to its natural activity (hydrolysis of large substrates-proteins). Prior to immobilising through the SphereZyme™ technology, Alcalase® was partially purified through dialysis followed by CM Sepharose™ FF cation exchanger. Sample contaminants, such as salts and stabilisers can inhibit protein crosslinking by reacting with glutaraldehyde. Alcalase® was successfully separated into 3 proteases with the major peak correlating to a positive control run on native PAGE, indicating that it was likely subtilisin Carlsberg. A 16% alkaline protease activity for azo-casein hydrolysis was retained when 5% v/v PEI: 25% v/v glutaraldehyde solution was used as a crosslinking agent in Alcalase® SphereZyme™ production. An increase in activity was also observed for monomeric substrates (PNPA) where the highest was 55%. The highest % activities maintained when 0.33 M EDA: 25% v/v glutaraldehyde solution was initially used as crosslinking agent were 4.5% and 1.6% for monomeric and polymeric substrates, respectively. PEI is a hydrophilic branched polymer with an abundance of amine groups compared to EDA. A comparison study of immobilisation efficiencies of SphereZyme™, Eupergit® and Dendrispheres was also performed for large substrate biocatalysis. The two latter technologies are solid-support immobilisation methods. Dendrispheres reached its maximum loading capacity in the first 5 minute of the one hour binding time. Twenty minutes was chosen as a maximum binding time since there was constant protein maintained on the solid support and no enzyme loss was observed during the 1 hour binding time. PEI at pH 11.5, its native pH, gave the highest immobilisation yield and specific activity over the PEI pH range of 11.5 to 7. SphereZyme™ had the highest ratio for azocasein hydrolysis followed by Dendrispheres and Eupergit®. The SphereZyme™ was also shown to be applicable to biosensors for phenol detection. Different modifications of glassy carbon electrode (GCE) were evaluated as a benchmark for the fabrication of SphereZyme™ modified phenol biosensor. GCE modified with laccase SphereZyme™ entrapped in cellulose membrane was the best modification due to the broad catechol range (<0.950 mM), high correlation coefficient (R2, 0.995) and relative high sensitivity factor (0.305 μA.mM-1). This type of biosensor was also shown to be electroactive at pH 7.0 for which its control, free laccase, lacked electroactivity. From the catalytic constants calculated, GCE modified with laccase SphereZyme™ entrapped in cellulose membrane also gave the highest effectiveness factor (Imax/Km app) of 1.84 μA.mM-1. The modified GCE with Alcalase® SphereZyme™ was relatively more sensitive than GCE modified with free Alcalase®.
- Full Text:
- Authors: Molawa, Letshego Gloria
- Date: 2011
- Subjects: Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3989 , http://hdl.handle.net/10962/d1004048 , Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
- Description: Self-immobilisation enzyme technologies, such as SphereZyme™, suffer from the lack of applicability to hydrolyse large substrates. Solid support immobilisation is usually a method of choice, to produce a stable biocatalyst for large substrates hydrolysis in the industry. In order to investigate this limitation, a commercial protease called Alcalase® was chosen as a model enzyme due to its natural activity (hydrolysis of large substrates-proteins). Prior to immobilising through the SphereZyme™ technology, Alcalase® was partially purified through dialysis followed by CM Sepharose™ FF cation exchanger. Sample contaminants, such as salts and stabilisers can inhibit protein crosslinking by reacting with glutaraldehyde. Alcalase® was successfully separated into 3 proteases with the major peak correlating to a positive control run on native PAGE, indicating that it was likely subtilisin Carlsberg. A 16% alkaline protease activity for azo-casein hydrolysis was retained when 5% v/v PEI: 25% v/v glutaraldehyde solution was used as a crosslinking agent in Alcalase® SphereZyme™ production. An increase in activity was also observed for monomeric substrates (PNPA) where the highest was 55%. The highest % activities maintained when 0.33 M EDA: 25% v/v glutaraldehyde solution was initially used as crosslinking agent were 4.5% and 1.6% for monomeric and polymeric substrates, respectively. PEI is a hydrophilic branched polymer with an abundance of amine groups compared to EDA. A comparison study of immobilisation efficiencies of SphereZyme™, Eupergit® and Dendrispheres was also performed for large substrate biocatalysis. The two latter technologies are solid-support immobilisation methods. Dendrispheres reached its maximum loading capacity in the first 5 minute of the one hour binding time. Twenty minutes was chosen as a maximum binding time since there was constant protein maintained on the solid support and no enzyme loss was observed during the 1 hour binding time. PEI at pH 11.5, its native pH, gave the highest immobilisation yield and specific activity over the PEI pH range of 11.5 to 7. SphereZyme™ had the highest ratio for azocasein hydrolysis followed by Dendrispheres and Eupergit®. The SphereZyme™ was also shown to be applicable to biosensors for phenol detection. Different modifications of glassy carbon electrode (GCE) were evaluated as a benchmark for the fabrication of SphereZyme™ modified phenol biosensor. GCE modified with laccase SphereZyme™ entrapped in cellulose membrane was the best modification due to the broad catechol range (<0.950 mM), high correlation coefficient (R2, 0.995) and relative high sensitivity factor (0.305 μA.mM-1). This type of biosensor was also shown to be electroactive at pH 7.0 for which its control, free laccase, lacked electroactivity. From the catalytic constants calculated, GCE modified with laccase SphereZyme™ entrapped in cellulose membrane also gave the highest effectiveness factor (Imax/Km app) of 1.84 μA.mM-1. The modified GCE with Alcalase® SphereZyme™ was relatively more sensitive than GCE modified with free Alcalase®.
- Full Text:
Studies in South African marine molluscan chemistry
- Authors: Bromley, Candice Leigh
- Date: 2011
- Subjects: Mollusks -- South Africa , Marine invertebrates -- South Africa , Marine metabolites -- South Africa , Chemical oceanography -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4356 , http://hdl.handle.net/10962/d1005021
- Description: This thesis investigates the variability occurring in the secondary metabolites produced by three South African marine molluscs. Chapter Two discusses the isolation and spectroscopic structure elucidation of the metabolites isolated from two Siphonaria species. The re-investigation of Siphonaria capensis yielded siphonarienfuranone (2.2) as the only common polypropionate isolated from both the 1998 and 2009 collections of S. capensis from the same areas suggesting possible seasonal or genetic variation in polypropionate production. The sterol cholest-7-en-3,5,7- triol (2.33) was also isolated form the 2009 collection of S. capensis and this is the first time this compound has been isolated from a Siphonaria species. The second species, Siphonaria oculus is closely related to S. capensis and the investigation into the former’s secondary metaboliteproduction revealed 2.2 as a major metabolite suggesting an inter-species overlap in polypropionate production. Three new polypropionate metabolites, 2.35, 2.36 and 2.37 were also isolated from S. oculus. An unsuccessful attempt was made to establish the absolute configuration of 2.37 using the modified Mosher’s method and the limited amount of 2.37 available prevented any further attempts at resolving the absolute configuration of this compound. The 1H NMR analysis of the defensive mucus collected directly from S. oculus revealed the presence of the acyclic polypropionate 2.37 as a minor metabolite. The absence of characteristic signals for the furanone containing compounds 2.2, 2.35 and 2.36, might suggest that these compounds cyclise from a hypothetical acyclic precursor (2.38) during standard work up of bulk acetone extracts of Siphonaria species. Chapter Three discusses the re-isolation and spectroscopic structure elucidation of the metabolites isolated from the nudibranch, Leminda millecra. Three known natural products, millecrone A (3.1), 8-hydroxycalamenene (3.6) and cubebenone (3.8) were re-isolated from our 2010 collection of L. millecra, as well as the new minor metabolite 8-acetoxycalamenene (3.16). The cytotoxic prenylated toluquinones and toluhydroquinones (3.9-3.15) initially isolated from the 1998 collection of L. millecra were not found in the 2010 collection supporting the hypothesis that these compounds may be of fungal origin. L. millecra clearly shows variability in the compounds sequestered by this species with millecrone A (3.1) being the only common metabolite in the three investigations of L. millecra to date. An unsuccessful attempt was made to establish the absolute configuration of 3.1, 3.6 and 3.8 through initial LAH reduction of the ketone moiety contained in 3.1 and 3.8 and esterification of the resultant diastereomeric alcohol mixtures and the phenol functionality in 3.6 with (1S)-camphanic chloride. Crystallisation of the (S)- camphanate esters of 3.6 and 3.8 for X-ray analysis were unsuccessful, while the unexpected conjugate addition of a hydride in 3.1 resulted in complex diastereomeric mixtures which could not be separated by HPLC.
- Full Text:
- Authors: Bromley, Candice Leigh
- Date: 2011
- Subjects: Mollusks -- South Africa , Marine invertebrates -- South Africa , Marine metabolites -- South Africa , Chemical oceanography -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4356 , http://hdl.handle.net/10962/d1005021
- Description: This thesis investigates the variability occurring in the secondary metabolites produced by three South African marine molluscs. Chapter Two discusses the isolation and spectroscopic structure elucidation of the metabolites isolated from two Siphonaria species. The re-investigation of Siphonaria capensis yielded siphonarienfuranone (2.2) as the only common polypropionate isolated from both the 1998 and 2009 collections of S. capensis from the same areas suggesting possible seasonal or genetic variation in polypropionate production. The sterol cholest-7-en-3,5,7- triol (2.33) was also isolated form the 2009 collection of S. capensis and this is the first time this compound has been isolated from a Siphonaria species. The second species, Siphonaria oculus is closely related to S. capensis and the investigation into the former’s secondary metaboliteproduction revealed 2.2 as a major metabolite suggesting an inter-species overlap in polypropionate production. Three new polypropionate metabolites, 2.35, 2.36 and 2.37 were also isolated from S. oculus. An unsuccessful attempt was made to establish the absolute configuration of 2.37 using the modified Mosher’s method and the limited amount of 2.37 available prevented any further attempts at resolving the absolute configuration of this compound. The 1H NMR analysis of the defensive mucus collected directly from S. oculus revealed the presence of the acyclic polypropionate 2.37 as a minor metabolite. The absence of characteristic signals for the furanone containing compounds 2.2, 2.35 and 2.36, might suggest that these compounds cyclise from a hypothetical acyclic precursor (2.38) during standard work up of bulk acetone extracts of Siphonaria species. Chapter Three discusses the re-isolation and spectroscopic structure elucidation of the metabolites isolated from the nudibranch, Leminda millecra. Three known natural products, millecrone A (3.1), 8-hydroxycalamenene (3.6) and cubebenone (3.8) were re-isolated from our 2010 collection of L. millecra, as well as the new minor metabolite 8-acetoxycalamenene (3.16). The cytotoxic prenylated toluquinones and toluhydroquinones (3.9-3.15) initially isolated from the 1998 collection of L. millecra were not found in the 2010 collection supporting the hypothesis that these compounds may be of fungal origin. L. millecra clearly shows variability in the compounds sequestered by this species with millecrone A (3.1) being the only common metabolite in the three investigations of L. millecra to date. An unsuccessful attempt was made to establish the absolute configuration of 3.1, 3.6 and 3.8 through initial LAH reduction of the ketone moiety contained in 3.1 and 3.8 and esterification of the resultant diastereomeric alcohol mixtures and the phenol functionality in 3.6 with (1S)-camphanic chloride. Crystallisation of the (S)- camphanate esters of 3.6 and 3.8 for X-ray analysis were unsuccessful, while the unexpected conjugate addition of a hydride in 3.1 resulted in complex diastereomeric mixtures which could not be separated by HPLC.
- Full Text:
Testing the existence and direction of "spill-over" of mussel recruits beyond the boundaries of marine protected areas
- Authors: Ludford, Adam
- Date: 2011
- Subjects: Marine parks and reserves -- South Africa -- Transkei , Marine resources conservation -- South Africa -- Transkei , Mussels -- Ecology -- South Africa -- Transkei , Mexilhao mussel -- Reproduction -- South Africa -- Transkei , Mexilhao mussel -- Behavior -- South Africa -- Transkei
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5786 , http://hdl.handle.net/10962/d1005474 , Marine parks and reserves -- South Africa -- Transkei , Marine resources conservation -- South Africa -- Transkei , Mussels -- Ecology -- South Africa -- Transkei , Mexilhao mussel -- Reproduction -- South Africa -- Transkei , Mexilhao mussel -- Behavior -- South Africa -- Transkei
- Description: Landscape ecology helps in predicting the influence of habitat fragmentation on populations. Marine protected areas (MPAs) are expected to create areas of good quality patches and so improve connectivity among shores. MPAs are believed not only to protect adult populations, but also to enhance recruitment both within MPAs and on surrounding exploited shores, therefore improving their ability to recover from overexploitation. As such, MPAs are a preferred management tool for the conservation of natural populations. Although MPAs have been demonstrated to enhance adult abundances, little work has been done on their ability to provide so called "spill-over" of recruits nor has the generality of the influence of MPAs been investigated in a single region with multiple control sites. The Transkei region, on the east coast of South Africa, and the intertidal mussel, Perna perna, offer an ideal system to test the generality of the influence of MPAs on surrounding shores, due to the presence of multiple MPAs and exploited control sites. Patterns of adult abundance were surveyed at four MPAs and two comparably sized exploited control sites. Adult abundances were, in general, found to be higher within MPAs than at exploited control sites, with adult abundances decreasing towards the edge of MPAs and decreasing even more on the outside shores. To simplify the sorting procedure for samples of mussel recruits, a new method using fractionated elutriation was devised and tested. This new method was found to be more accurate, although not statistically significant but also substantially more time consuming. The increase in accuracy although not statistically significant could be biologically significant, especially when looking at low numbers. This new method could, therefore, be very useful especially when [...] is low. Recruitment was estimated over three months during the main reproductive season at two of the MPAs and at appropriate control sites. I predicted that recruitment patterns would mirror the patterns found in adult abundances and that there would be directionality in patterns of recruitment, with northern sites having greater recruitment due to the direction of near-shore ocean currents. Contrary to this, there were no correlations between adult abundance and recruitment for any of the months or sites, with no clear spatial pattern of recruitment in any of the three months. There was, however, a slight trend of greater recruitment at northern sites. To explain the lack of consistency in recruitment and adult abundances, wind data were used to examine the near-shore surface currents in this area, with theoretical surface currents showing similar patterns to those observed for recruitment. From a landscape perspective, the good patches created by MPAs supply recruits to the surrounding matrix but the low quality of habitat in the matrix prevents rehabilitation. The quality of the matrix must therefore be first improved by reseeding these shores. These results emphasise that while MPAs may function in protecting adult abundances, their influence on supplying recruits and hence recovery of near-by exploited shores may be overestimated. This lack of influence on near-by exploited shores highlights the need for reseeding of shores in conjunction with suitable management plans.
- Full Text:
- Authors: Ludford, Adam
- Date: 2011
- Subjects: Marine parks and reserves -- South Africa -- Transkei , Marine resources conservation -- South Africa -- Transkei , Mussels -- Ecology -- South Africa -- Transkei , Mexilhao mussel -- Reproduction -- South Africa -- Transkei , Mexilhao mussel -- Behavior -- South Africa -- Transkei
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5786 , http://hdl.handle.net/10962/d1005474 , Marine parks and reserves -- South Africa -- Transkei , Marine resources conservation -- South Africa -- Transkei , Mussels -- Ecology -- South Africa -- Transkei , Mexilhao mussel -- Reproduction -- South Africa -- Transkei , Mexilhao mussel -- Behavior -- South Africa -- Transkei
- Description: Landscape ecology helps in predicting the influence of habitat fragmentation on populations. Marine protected areas (MPAs) are expected to create areas of good quality patches and so improve connectivity among shores. MPAs are believed not only to protect adult populations, but also to enhance recruitment both within MPAs and on surrounding exploited shores, therefore improving their ability to recover from overexploitation. As such, MPAs are a preferred management tool for the conservation of natural populations. Although MPAs have been demonstrated to enhance adult abundances, little work has been done on their ability to provide so called "spill-over" of recruits nor has the generality of the influence of MPAs been investigated in a single region with multiple control sites. The Transkei region, on the east coast of South Africa, and the intertidal mussel, Perna perna, offer an ideal system to test the generality of the influence of MPAs on surrounding shores, due to the presence of multiple MPAs and exploited control sites. Patterns of adult abundance were surveyed at four MPAs and two comparably sized exploited control sites. Adult abundances were, in general, found to be higher within MPAs than at exploited control sites, with adult abundances decreasing towards the edge of MPAs and decreasing even more on the outside shores. To simplify the sorting procedure for samples of mussel recruits, a new method using fractionated elutriation was devised and tested. This new method was found to be more accurate, although not statistically significant but also substantially more time consuming. The increase in accuracy although not statistically significant could be biologically significant, especially when looking at low numbers. This new method could, therefore, be very useful especially when [...] is low. Recruitment was estimated over three months during the main reproductive season at two of the MPAs and at appropriate control sites. I predicted that recruitment patterns would mirror the patterns found in adult abundances and that there would be directionality in patterns of recruitment, with northern sites having greater recruitment due to the direction of near-shore ocean currents. Contrary to this, there were no correlations between adult abundance and recruitment for any of the months or sites, with no clear spatial pattern of recruitment in any of the three months. There was, however, a slight trend of greater recruitment at northern sites. To explain the lack of consistency in recruitment and adult abundances, wind data were used to examine the near-shore surface currents in this area, with theoretical surface currents showing similar patterns to those observed for recruitment. From a landscape perspective, the good patches created by MPAs supply recruits to the surrounding matrix but the low quality of habitat in the matrix prevents rehabilitation. The quality of the matrix must therefore be first improved by reseeding these shores. These results emphasise that while MPAs may function in protecting adult abundances, their influence on supplying recruits and hence recovery of near-by exploited shores may be overestimated. This lack of influence on near-by exploited shores highlights the need for reseeding of shores in conjunction with suitable management plans.
- Full Text:
The critical natural capital of the Buffalo City Municipality, South Africa : harnessing local action for biodiversity conservation
- Authors: Hagen, Brett
- Date: 2011
- Subjects: Natural resources -- South Africa -- Buffalo City , Biodiversity conservation -- South Africa -- Buffalo City , Ecosystem services -- South Africa -- Buffalo City , Nature conservation -- South Africa -- Buffalo City , Environmental protection -- South Africa -- Buffalo City , Environmental degradation -- South Africa -- Buffalo City , Restoration ecology -- South Africa -- Buffalo City
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4753 , http://hdl.handle.net/10962/d1007075 , Natural resources -- South Africa -- Buffalo City , Biodiversity conservation -- South Africa -- Buffalo City , Ecosystem services -- South Africa -- Buffalo City , Nature conservation -- South Africa -- Buffalo City , Environmental protection -- South Africa -- Buffalo City , Environmental degradation -- South Africa -- Buffalo City , Restoration ecology -- South Africa -- Buffalo City
- Description: Globally, ecosystems provide services of almost twice the value of global gross national product (Costanza et al., 2006). The Buffalo City Municipality (BCM), South Africa contains biodiversity of national and international importance (Pierce, 2003; Pierce et al., 2005). Despite this, the municipality continues to experience loss of both urban and rural biodiversity (Buffalo City Municipality, 2006a). This study sought to determine the status of biodiversity, and the potential for ecosystem services to contribute to conservation, within the BCM. Biodiversity features, including ecosystem type, species of special concern and biodiversity processes, were identified and mapped using a GIS to produce a biodiversity priority index for the BCM. Current transformation status was then mapped to determine the level of ecosystem degradation within the BCM. Priority biodiversity areas as well as individual biodiversity features were spatially overlain against current transformation status and protected areas and analysed using a GIS to determine the level of degradation and protection of BCM biodiversity. In total 3.5 % of total BCM biodiversity was protected. Of the 24 ecosystem types, 11 (45%) had less than 1% under protection, while 16 (67%) had less than five percent protected. Not restorable areas, thus completely lost to biodiversity conservation, comprised just less than a quarter of the total BCM area while un-impacted areas comprised just 12.3%. Twenty five ecosystem services were identified as being provided by intact natural ecosystems within the BCM. The natural capital providing these services was identified and mapped to produce an ecosystem service index (ESI) using a GIS. This ecosystem service index and the biodiversity priority index were overlain to determine their level of correlation. Overall ESI correlation with priority biodiversity was weak although several individual ecosystem services, including carbon sequestration, showed correlation. Using the above data layers an implementation plan and conservation framework was proposed to assist the coordination of local conservation action within the BCM. It is concluded that ecosystem services are a potentially useful tool for conservationists at the local level seeking to ensure that biodiversity has relevance to and receives protection from broader society.
- Full Text:
- Authors: Hagen, Brett
- Date: 2011
- Subjects: Natural resources -- South Africa -- Buffalo City , Biodiversity conservation -- South Africa -- Buffalo City , Ecosystem services -- South Africa -- Buffalo City , Nature conservation -- South Africa -- Buffalo City , Environmental protection -- South Africa -- Buffalo City , Environmental degradation -- South Africa -- Buffalo City , Restoration ecology -- South Africa -- Buffalo City
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4753 , http://hdl.handle.net/10962/d1007075 , Natural resources -- South Africa -- Buffalo City , Biodiversity conservation -- South Africa -- Buffalo City , Ecosystem services -- South Africa -- Buffalo City , Nature conservation -- South Africa -- Buffalo City , Environmental protection -- South Africa -- Buffalo City , Environmental degradation -- South Africa -- Buffalo City , Restoration ecology -- South Africa -- Buffalo City
- Description: Globally, ecosystems provide services of almost twice the value of global gross national product (Costanza et al., 2006). The Buffalo City Municipality (BCM), South Africa contains biodiversity of national and international importance (Pierce, 2003; Pierce et al., 2005). Despite this, the municipality continues to experience loss of both urban and rural biodiversity (Buffalo City Municipality, 2006a). This study sought to determine the status of biodiversity, and the potential for ecosystem services to contribute to conservation, within the BCM. Biodiversity features, including ecosystem type, species of special concern and biodiversity processes, were identified and mapped using a GIS to produce a biodiversity priority index for the BCM. Current transformation status was then mapped to determine the level of ecosystem degradation within the BCM. Priority biodiversity areas as well as individual biodiversity features were spatially overlain against current transformation status and protected areas and analysed using a GIS to determine the level of degradation and protection of BCM biodiversity. In total 3.5 % of total BCM biodiversity was protected. Of the 24 ecosystem types, 11 (45%) had less than 1% under protection, while 16 (67%) had less than five percent protected. Not restorable areas, thus completely lost to biodiversity conservation, comprised just less than a quarter of the total BCM area while un-impacted areas comprised just 12.3%. Twenty five ecosystem services were identified as being provided by intact natural ecosystems within the BCM. The natural capital providing these services was identified and mapped to produce an ecosystem service index (ESI) using a GIS. This ecosystem service index and the biodiversity priority index were overlain to determine their level of correlation. Overall ESI correlation with priority biodiversity was weak although several individual ecosystem services, including carbon sequestration, showed correlation. Using the above data layers an implementation plan and conservation framework was proposed to assist the coordination of local conservation action within the BCM. It is concluded that ecosystem services are a potentially useful tool for conservationists at the local level seeking to ensure that biodiversity has relevance to and receives protection from broader society.
- Full Text:
The demography and population dynamics of a re-introduced black rhinoceros population on the Great Fish River Reserve, Eastern Cape Province
- Authors: Fike, Bradley Robin
- Date: 2011
- Subjects: Black rhinoceros -- South Africa -- Great Fish River Valley , Population biology -- South Africa -- Great Fish River Valley , Black rhinoceros -- Habitat -- South Africa -- Great Fish River Valley , Black rhinoceros -- Adaptation -- South Africa -- Great Fish River Valley , Black rhinoceros -- Ecology -- South Africa -- Great Fish River Valley
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5948 , http://hdl.handle.net/10962/d1020869
- Description: The re-introduction of black rhinoceros onto the Great Fish River Reserve in the Eastern Cape, following the species absence for over a century, created an opportunity to study this species in the thicket biome, and in particular the succulent thicket of the Great Fish River valley. The thicket biome is quite different from the habitats in which other extant populations of these animals are found and where studies of their demography have been undertaken. Data collection occurred from May 1986, with the arrival of the first four animals to December 2008, when the population was estimated to be 144 individuals. A variety of monitoring techniques were used including direct ground observations, aerial helicopter census, aerial monitoring by microlight aircraft, camera traps and opportunistic observations, each with its own advantages and disadvantages. The combination of methods and effort has resulted in the population being recognized as completely known with up to 97% of the animals being located at least once per year with a mean frequency of sightings of 11.5 per animal per year. In 2008, the population was about 20% juvenile, 36% sub-adult and 44% adult with a female biased sex ratio of 1.3 females per male. Mean age at first birth was about 80 months and this increased significantly with increasing density of black rhinoceroses. Mean intercalf interval was about 28 months and 41% of adult females gave birth each year. Mortality rates were low for juveniles, higher for sub-adults and higher for males than females. There was a weak but significant positive effect of density on male mortality. Population growth rate was about 10% and was not significantly affected by density. These results suggest that this population is beginning to show the first indications of density dependant constraints and that harvesting should be implemented in order to maintain the productive tempo. A secondary goal of the Management Plan will then be realized as the population functions as a donor to establish founder populations elsewhere within the Diceros bicornis minor range.
- Full Text:
- Authors: Fike, Bradley Robin
- Date: 2011
- Subjects: Black rhinoceros -- South Africa -- Great Fish River Valley , Population biology -- South Africa -- Great Fish River Valley , Black rhinoceros -- Habitat -- South Africa -- Great Fish River Valley , Black rhinoceros -- Adaptation -- South Africa -- Great Fish River Valley , Black rhinoceros -- Ecology -- South Africa -- Great Fish River Valley
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5948 , http://hdl.handle.net/10962/d1020869
- Description: The re-introduction of black rhinoceros onto the Great Fish River Reserve in the Eastern Cape, following the species absence for over a century, created an opportunity to study this species in the thicket biome, and in particular the succulent thicket of the Great Fish River valley. The thicket biome is quite different from the habitats in which other extant populations of these animals are found and where studies of their demography have been undertaken. Data collection occurred from May 1986, with the arrival of the first four animals to December 2008, when the population was estimated to be 144 individuals. A variety of monitoring techniques were used including direct ground observations, aerial helicopter census, aerial monitoring by microlight aircraft, camera traps and opportunistic observations, each with its own advantages and disadvantages. The combination of methods and effort has resulted in the population being recognized as completely known with up to 97% of the animals being located at least once per year with a mean frequency of sightings of 11.5 per animal per year. In 2008, the population was about 20% juvenile, 36% sub-adult and 44% adult with a female biased sex ratio of 1.3 females per male. Mean age at first birth was about 80 months and this increased significantly with increasing density of black rhinoceroses. Mean intercalf interval was about 28 months and 41% of adult females gave birth each year. Mortality rates were low for juveniles, higher for sub-adults and higher for males than females. There was a weak but significant positive effect of density on male mortality. Population growth rate was about 10% and was not significantly affected by density. These results suggest that this population is beginning to show the first indications of density dependant constraints and that harvesting should be implemented in order to maintain the productive tempo. A secondary goal of the Management Plan will then be realized as the population functions as a donor to establish founder populations elsewhere within the Diceros bicornis minor range.
- Full Text:
The design and synthesis of multidentate N-heterocyclic carbenes as metathesis catalyst ligands
- Authors: Truscott, Byron John
- Date: 2011
- Subjects: Carbenes (Methylene compounds) , Heterocyclic compounds , Ligands , Ligands -- Design , Metathesis (Chemistry) , Catalysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4304 , http://hdl.handle.net/10962/d1004962 , Carbenes (Methylene compounds) , Heterocyclic compounds , Ligands , Ligands -- Design , Metathesis (Chemistry) , Catalysis
- Description: This study has focused on the design and preparation of bi– and tridentate N–Heterocyclic Carbene (NHC) ligands in order to investigate the effect of a multidentate approach to the formation, stability and catalytic activity of coordination complexes. Chapters 1 – 3 provide background information of relevant catalysis, carbene and coordination chemistry, followed by previous work performed within our research group. In Chapter 4 attention is given to the synthetic aspects of the research conducted, comprising two distinct approaches to the preparation of unsymmetrical saturated and unsaturated NHCs. Firstly, an investigation of the saturated NHC ligands yielded three novel, unsymmetrical pro–ligands, viz., two halopropyl imidazolinium salts and a bidentate hydroxypropyl imidazolinium salt. Secondly, eight imidazolium salts have been generated, including a hydroxypropyl analogue and novel decyl and tridentate malonyl derivatives. These compounds were prepared using microwave–assisted methodology for the alkylation of N– mesitylimidazole – an approach that drastically reduced reaction times (from 8 hours – 7 days to ca. 0.5 – 2 hours) and facilitated isolation of the imidazolium salts. Many of the compounds prepared in this study are novel and were fully characterized using HRMS and 1– and 2–D NMR analysis. Coordination studies using a selection of the prepared pro–ligands afforded an alkoxy–NHC silver derivative and four novel Ru–complexes, viz., Grubbs II–type Ru–complexes containing:– chloropropyl imidazolinylidene; propenyl imidazolylidene; and bidentate alkoxypropyl imidazolylidene ligands. Furthermore, a well–defined benzyl mesitylimidazolylidene Ru–complex has been isolated, which exhibited good stability in air. DFT–level geometry–optimization studies, using the Accelrys DMol3 package have given valuable insights into the likely geometries of the prepared and putative catalysts.
- Full Text:
- Authors: Truscott, Byron John
- Date: 2011
- Subjects: Carbenes (Methylene compounds) , Heterocyclic compounds , Ligands , Ligands -- Design , Metathesis (Chemistry) , Catalysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4304 , http://hdl.handle.net/10962/d1004962 , Carbenes (Methylene compounds) , Heterocyclic compounds , Ligands , Ligands -- Design , Metathesis (Chemistry) , Catalysis
- Description: This study has focused on the design and preparation of bi– and tridentate N–Heterocyclic Carbene (NHC) ligands in order to investigate the effect of a multidentate approach to the formation, stability and catalytic activity of coordination complexes. Chapters 1 – 3 provide background information of relevant catalysis, carbene and coordination chemistry, followed by previous work performed within our research group. In Chapter 4 attention is given to the synthetic aspects of the research conducted, comprising two distinct approaches to the preparation of unsymmetrical saturated and unsaturated NHCs. Firstly, an investigation of the saturated NHC ligands yielded three novel, unsymmetrical pro–ligands, viz., two halopropyl imidazolinium salts and a bidentate hydroxypropyl imidazolinium salt. Secondly, eight imidazolium salts have been generated, including a hydroxypropyl analogue and novel decyl and tridentate malonyl derivatives. These compounds were prepared using microwave–assisted methodology for the alkylation of N– mesitylimidazole – an approach that drastically reduced reaction times (from 8 hours – 7 days to ca. 0.5 – 2 hours) and facilitated isolation of the imidazolium salts. Many of the compounds prepared in this study are novel and were fully characterized using HRMS and 1– and 2–D NMR analysis. Coordination studies using a selection of the prepared pro–ligands afforded an alkoxy–NHC silver derivative and four novel Ru–complexes, viz., Grubbs II–type Ru–complexes containing:– chloropropyl imidazolinylidene; propenyl imidazolylidene; and bidentate alkoxypropyl imidazolylidene ligands. Furthermore, a well–defined benzyl mesitylimidazolylidene Ru–complex has been isolated, which exhibited good stability in air. DFT–level geometry–optimization studies, using the Accelrys DMol3 package have given valuable insights into the likely geometries of the prepared and putative catalysts.
- Full Text:
The development and assessment of a fixed dose combination tablet of Ranitidine and Metronidazole
- Authors: King'ori, Loti David
- Date: 2011 , 2011-04-07
- Subjects: Ulcers -- Treatment , Ranitidine -- Evaluation , Metronidazole -- Evaluation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3858 , http://hdl.handle.net/10962/d1013359
- Description: The oral route of drug administration is convenient since it is acceptable to most patients and the manufacturing processes used to produce tablets and capsules are relatively simple when compared to those used to manufacture other types of dosage forms. Metronidazole (MTZ) and Ranitidine (RTD) have been used in combination, as part of triple therapy for the treatment of ulcers. However the use of large numbers of tablets and long duration of therapy makes adherence to drug treatment challenging for patients. Therefore the formulation of a fixed dose combination (FDC) of MTZ and RTD may improve patient adherence to therapy and consequently may reduce morbidity and mortality due to ulcers. A stability indicating HPLC method for the simultaneous analysis of MTZ and RTD was developed and validated according to the International Conference on Harmonization (ICH) guidelines. The method was sensitive, selective, precise, accurate and linear.Preformulation studies were performed on the active pharmaceutical ingredients (API) alone and in combination with potential excipients. Differential scanning calorimetry (DSC) studies revealed a potential interaction between MTZ and RTD, however the interaction was not apparent following IR analysis of the same samples. DSC analyses of the API in combination with potential excipients revealed that the compounds were compatible with most materials with the exception of a binary mixture of RTD and Dibasic calcium phosphate (DCP) that exhibited a potential interaction. Thermal gravimetric analysis (TGA) of MTZ and RTD revealed that both compounds exhibited thermal stability. The Carrs Index (CI) and Hausner Ratio (HR) values of MTZ and RTD indicated that both compounds exhibited poor flow and compressibility properties, whereas the CI and HR values for (Microcrystalline cellulose) MCC and DCP indicated better flowability and compressibility characteristics.Direct compression and wet granulation processes were assessed to identify a suitable method of manufacture of FDC tablets of MTZ and RTD. The blends were evaluated using bulk and tapped density and the resultant tablets were evaluated for weight uniformity, crushing strength, tensile strength and disintegration time. The wet granulation method of manufacture produced tablets that showed acceptable pharmacotechnical properties: this approach was therefore used as the method of manufacture of FDC tablets of MTZ and RTD. Tablet formulations comprised of API, viz. MTZ and RTD and different compositions of MCC, DCP, Sodium starch glycolate (SSG) and Croscarmellose sodium (CCS), were manufactured in order to screen for an appropriate diluent and disintegrant composition for use in response surface studies. Assays of tablet content and in vitro drug release were undertaken using the validated HPLC method. Tablets in which MCC and CCS were used appeared to produce better assay and dissolution results as compared to those manufactured using DCP and SSG. Consequently a formulation comprised of MCC and CCS was selected and used in studies in which the effect(s) of level two formulation and composition changes as described in the Scale and Post Approval Changes for Immediate Release (SUPAC-IR) Guidelines on tablet disintegration and in vitro release were assessed. A Box-Behnken statistical design was used for the investigation of the effect of input factors, viz. CCS, (Polyvinyl pyrollidone K30) PVP-K30 and magnesium stearate on measured responses, viz. disintegration time and percent drug release in 10 minutes (Q10). CCS appeared to have an inverse linear relationship on disintegration time and a linear relationship with the Q10 for MTZ and RTD, whereas PVP-K30 and magnesium stearate appeared to have an antagonistic effect on the measured responses. Furthermore CCS and magnesium stearate exhibited an interaction that had an agonistic effect on the Q10 value for RTD. A numerical optimization approach was used to predict a formulation composition that would produce tablets that exhibited a disintegration time and Q10 values for MTZ and RTD that fell within the constraints set in our laboratory. The resultant model was found to be accurate and had a percent prediction error of < 5% for all measured response variables.FDC tablets of MTZ and RTD have been successfully produced. The disintegration of the tablet and dissolution of the API were within compendial specifications and the tablets are of suitable quality and have the potential to be further investigated to reduce the pill burden in the treatment of ulcers.
- Full Text:
- Authors: King'ori, Loti David
- Date: 2011 , 2011-04-07
- Subjects: Ulcers -- Treatment , Ranitidine -- Evaluation , Metronidazole -- Evaluation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3858 , http://hdl.handle.net/10962/d1013359
- Description: The oral route of drug administration is convenient since it is acceptable to most patients and the manufacturing processes used to produce tablets and capsules are relatively simple when compared to those used to manufacture other types of dosage forms. Metronidazole (MTZ) and Ranitidine (RTD) have been used in combination, as part of triple therapy for the treatment of ulcers. However the use of large numbers of tablets and long duration of therapy makes adherence to drug treatment challenging for patients. Therefore the formulation of a fixed dose combination (FDC) of MTZ and RTD may improve patient adherence to therapy and consequently may reduce morbidity and mortality due to ulcers. A stability indicating HPLC method for the simultaneous analysis of MTZ and RTD was developed and validated according to the International Conference on Harmonization (ICH) guidelines. The method was sensitive, selective, precise, accurate and linear.Preformulation studies were performed on the active pharmaceutical ingredients (API) alone and in combination with potential excipients. Differential scanning calorimetry (DSC) studies revealed a potential interaction between MTZ and RTD, however the interaction was not apparent following IR analysis of the same samples. DSC analyses of the API in combination with potential excipients revealed that the compounds were compatible with most materials with the exception of a binary mixture of RTD and Dibasic calcium phosphate (DCP) that exhibited a potential interaction. Thermal gravimetric analysis (TGA) of MTZ and RTD revealed that both compounds exhibited thermal stability. The Carrs Index (CI) and Hausner Ratio (HR) values of MTZ and RTD indicated that both compounds exhibited poor flow and compressibility properties, whereas the CI and HR values for (Microcrystalline cellulose) MCC and DCP indicated better flowability and compressibility characteristics.Direct compression and wet granulation processes were assessed to identify a suitable method of manufacture of FDC tablets of MTZ and RTD. The blends were evaluated using bulk and tapped density and the resultant tablets were evaluated for weight uniformity, crushing strength, tensile strength and disintegration time. The wet granulation method of manufacture produced tablets that showed acceptable pharmacotechnical properties: this approach was therefore used as the method of manufacture of FDC tablets of MTZ and RTD. Tablet formulations comprised of API, viz. MTZ and RTD and different compositions of MCC, DCP, Sodium starch glycolate (SSG) and Croscarmellose sodium (CCS), were manufactured in order to screen for an appropriate diluent and disintegrant composition for use in response surface studies. Assays of tablet content and in vitro drug release were undertaken using the validated HPLC method. Tablets in which MCC and CCS were used appeared to produce better assay and dissolution results as compared to those manufactured using DCP and SSG. Consequently a formulation comprised of MCC and CCS was selected and used in studies in which the effect(s) of level two formulation and composition changes as described in the Scale and Post Approval Changes for Immediate Release (SUPAC-IR) Guidelines on tablet disintegration and in vitro release were assessed. A Box-Behnken statistical design was used for the investigation of the effect of input factors, viz. CCS, (Polyvinyl pyrollidone K30) PVP-K30 and magnesium stearate on measured responses, viz. disintegration time and percent drug release in 10 minutes (Q10). CCS appeared to have an inverse linear relationship on disintegration time and a linear relationship with the Q10 for MTZ and RTD, whereas PVP-K30 and magnesium stearate appeared to have an antagonistic effect on the measured responses. Furthermore CCS and magnesium stearate exhibited an interaction that had an agonistic effect on the Q10 value for RTD. A numerical optimization approach was used to predict a formulation composition that would produce tablets that exhibited a disintegration time and Q10 values for MTZ and RTD that fell within the constraints set in our laboratory. The resultant model was found to be accurate and had a percent prediction error of < 5% for all measured response variables.FDC tablets of MTZ and RTD have been successfully produced. The disintegration of the tablet and dissolution of the API were within compendial specifications and the tablets are of suitable quality and have the potential to be further investigated to reduce the pill burden in the treatment of ulcers.
- Full Text:
The development of an in vitro system for the production of drug metabolites using microsomal enzymes from bovine liver
- Authors: Morrison, Roxanne
- Date: 2011
- Subjects: Drugs -- Metabolism , Xenobiotics -- Metabolism , Metabolites , Drugs -- Testing , Toxicity testing -- In vitro , Doping in horse racing -- Control -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4087 , http://hdl.handle.net/10962/d1007698 , Drugs -- Metabolism , Xenobiotics -- Metabolism , Metabolites , Drugs -- Testing , Toxicity testing -- In vitro , Doping in horse racing -- Control -- Research
- Description: Drug metabolism is a specialised subset of xenobiotic metabolism, pertaining to the breakdown and elimination of pharmaceutical drugs. The enzymes involved in these pathways are the cytochrome P450 family of isozymes. Metabolism is an important factor in determining the pharmacological effects of drugs. The main aim of this study was to develop a system whereby the major metabolites of drugs can be produced in vitro. An in vitro system was developed and optimised using commercially prepared microsomes from rat liver and coumarin (by monitoring its conversion to 7-hydroxycoumarin) as a model. The optimum running conditions for the incubations were 50 μM coumarin, 50 μg protein/ml microsomes, 1 mM NADP⁺, 5 mM G6P and 1U/ml G6PDH incubated for 30 minutes at 38℃. The HPLC method for the detection of coumarin and 7-hydroxycoumarin was also validated with respect to linearity, reproducibility, precision, accuracy and lower limits of detection and quantification. The system developed was then tested using microsomes prepared from fresh bovine liver on these ten drugs of interest in doping control in horse racing: diazepam, nordiazepam, oxazepam, promazine, acepromazine, chlorpromazine, morphine, codeine, etoricoxib and lumiracoxib. The bovine liver microsomes were prepared using differential centrifugation and had activity on a par with the commercial preparations. This in vitro system metabolised the drugs and produced both phase I and II metabolites, similar to those observed in humans and horses in vivo. For example, the major metabolites of the benzodiazepine drug, diazepam, nordiazepam, temazepam and oxazepam as well as the glucuronidated phase II products were all found after incubations with the bovine liver microsomes. The metabolism of the drugs was also investigated in silico using the computational procedure, MetaSite. MetaSite was able to successfully predict known metabolites for most of the drugs studied. Differences were observed from the in vitro incubations and this is most likely due to MetaSite using only human cytochrome P450s for analysis.
- Full Text:
- Authors: Morrison, Roxanne
- Date: 2011
- Subjects: Drugs -- Metabolism , Xenobiotics -- Metabolism , Metabolites , Drugs -- Testing , Toxicity testing -- In vitro , Doping in horse racing -- Control -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4087 , http://hdl.handle.net/10962/d1007698 , Drugs -- Metabolism , Xenobiotics -- Metabolism , Metabolites , Drugs -- Testing , Toxicity testing -- In vitro , Doping in horse racing -- Control -- Research
- Description: Drug metabolism is a specialised subset of xenobiotic metabolism, pertaining to the breakdown and elimination of pharmaceutical drugs. The enzymes involved in these pathways are the cytochrome P450 family of isozymes. Metabolism is an important factor in determining the pharmacological effects of drugs. The main aim of this study was to develop a system whereby the major metabolites of drugs can be produced in vitro. An in vitro system was developed and optimised using commercially prepared microsomes from rat liver and coumarin (by monitoring its conversion to 7-hydroxycoumarin) as a model. The optimum running conditions for the incubations were 50 μM coumarin, 50 μg protein/ml microsomes, 1 mM NADP⁺, 5 mM G6P and 1U/ml G6PDH incubated for 30 minutes at 38℃. The HPLC method for the detection of coumarin and 7-hydroxycoumarin was also validated with respect to linearity, reproducibility, precision, accuracy and lower limits of detection and quantification. The system developed was then tested using microsomes prepared from fresh bovine liver on these ten drugs of interest in doping control in horse racing: diazepam, nordiazepam, oxazepam, promazine, acepromazine, chlorpromazine, morphine, codeine, etoricoxib and lumiracoxib. The bovine liver microsomes were prepared using differential centrifugation and had activity on a par with the commercial preparations. This in vitro system metabolised the drugs and produced both phase I and II metabolites, similar to those observed in humans and horses in vivo. For example, the major metabolites of the benzodiazepine drug, diazepam, nordiazepam, temazepam and oxazepam as well as the glucuronidated phase II products were all found after incubations with the bovine liver microsomes. The metabolism of the drugs was also investigated in silico using the computational procedure, MetaSite. MetaSite was able to successfully predict known metabolites for most of the drugs studied. Differences were observed from the in vitro incubations and this is most likely due to MetaSite using only human cytochrome P450s for analysis.
- Full Text:
The diversity of aquatic insects in the Tsitsikamma region, with implications for aquatic ecosystem conservation
- Authors: Bellingan, Terence Andrew
- Date: 2011
- Subjects: Aquatic insects -- South Africa -- Tsitsikamma , Aquatic insects -- Classification -- South Africa -- Tsitsikamma , Aquatic ecology -- South Africa -- Tsitsikamma , Ecosystem management -- South Africa -- Tsitsikamma , Stream conservation -- South Africa -- Tsitsikamma
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5664 , http://hdl.handle.net/10962/d1005348 , Aquatic insects -- South Africa -- Tsitsikamma , Aquatic insects -- Classification -- South Africa -- Tsitsikamma , Aquatic ecology -- South Africa -- Tsitsikamma , Ecosystem management -- South Africa -- Tsitsikamma , Stream conservation -- South Africa -- Tsitsikamma
- Description: As a result of research carried out within the last decade to assess the diversity of macroinvertebrates of the Salt River in the Western Cape Province, South Africa, surveys of macroinvertebrates of 20 sites on 11 selected rivers from the same mountain range source were undertaken. This was done to make a preliminary assessment of the conservation status of the rivers of this region. Aquatic insects from the orders Ephemeroptera, Odonata, Plecoptera, Megaloptera, Trichoptera and the dipteran family Simuliidae were collected using techniques to maximize the number of taxa found. The insects collected were identified to species level where possible. Water physicochemical parameters were recorded at all sites for each sampling trip to characterize these rivers and to establish a set of baseline data for future comparisons. These parameters included measurements made on site and analysis of the concentrations of all the major ions in water samples in the laboratory. Multivariate analyses including Principle Components Analysis and Canonical Correspondence Analysis were used to reveal patterns within the water physicochemistry and species distributional data. Results include the identification of 123 species from 70 genera and 30 families. A total of 31 species were found to be undescribed, of which 17 were not previously collected and are thus completely new to science. In addition, four of these species could not be placed into any known genus. The analysis of water physicochemistry showed a clear distinction between rivers of Table Mountain sandstone and Bokkeveld shale origin. Downstream effects of anthropogenic influences were discernable too. Distinct macroinvertebrate assemblages were found based upon stream order and water chemistry composition. pH proved to be the most important driver of invertebrate assemblage composition. The high levels of endemism of the macroinvertebrates found within the upper reaches of these rivers and their degree of ecological specialization make these systems a priority for the conservation of aquatic biodiversity on a national and global scale.
- Full Text:
- Authors: Bellingan, Terence Andrew
- Date: 2011
- Subjects: Aquatic insects -- South Africa -- Tsitsikamma , Aquatic insects -- Classification -- South Africa -- Tsitsikamma , Aquatic ecology -- South Africa -- Tsitsikamma , Ecosystem management -- South Africa -- Tsitsikamma , Stream conservation -- South Africa -- Tsitsikamma
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5664 , http://hdl.handle.net/10962/d1005348 , Aquatic insects -- South Africa -- Tsitsikamma , Aquatic insects -- Classification -- South Africa -- Tsitsikamma , Aquatic ecology -- South Africa -- Tsitsikamma , Ecosystem management -- South Africa -- Tsitsikamma , Stream conservation -- South Africa -- Tsitsikamma
- Description: As a result of research carried out within the last decade to assess the diversity of macroinvertebrates of the Salt River in the Western Cape Province, South Africa, surveys of macroinvertebrates of 20 sites on 11 selected rivers from the same mountain range source were undertaken. This was done to make a preliminary assessment of the conservation status of the rivers of this region. Aquatic insects from the orders Ephemeroptera, Odonata, Plecoptera, Megaloptera, Trichoptera and the dipteran family Simuliidae were collected using techniques to maximize the number of taxa found. The insects collected were identified to species level where possible. Water physicochemical parameters were recorded at all sites for each sampling trip to characterize these rivers and to establish a set of baseline data for future comparisons. These parameters included measurements made on site and analysis of the concentrations of all the major ions in water samples in the laboratory. Multivariate analyses including Principle Components Analysis and Canonical Correspondence Analysis were used to reveal patterns within the water physicochemistry and species distributional data. Results include the identification of 123 species from 70 genera and 30 families. A total of 31 species were found to be undescribed, of which 17 were not previously collected and are thus completely new to science. In addition, four of these species could not be placed into any known genus. The analysis of water physicochemistry showed a clear distinction between rivers of Table Mountain sandstone and Bokkeveld shale origin. Downstream effects of anthropogenic influences were discernable too. Distinct macroinvertebrate assemblages were found based upon stream order and water chemistry composition. pH proved to be the most important driver of invertebrate assemblage composition. The high levels of endemism of the macroinvertebrates found within the upper reaches of these rivers and their degree of ecological specialization make these systems a priority for the conservation of aquatic biodiversity on a national and global scale.
- Full Text:
The effect of mussel bed structure on the associated infauna in South Africa and the interaction between mussel and epibiotic barnacles
- Jordaan, Tembisa Nomathamsanqa
- Authors: Jordaan, Tembisa Nomathamsanqa
- Date: 2011
- Subjects: Mytilidae -- South Africa , Mytilus galloprovincialis -- South Africa , Mussel culture -- South Africa , Shellfish culture -- South Africa , Perna -- South Africa , Barnacles -- South Africa , Mussels -- South Africa , Mussels -- Ecology , Barnacles -- Ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5675 , http://hdl.handle.net/10962/d1005360 , Mytilidae -- South Africa , Mytilus galloprovincialis -- South Africa , Mussel culture -- South Africa , Shellfish culture -- South Africa , Perna -- South Africa , Barnacles -- South Africa , Mussels -- South Africa , Mussels -- Ecology , Barnacles -- Ecology
- Description: Mussels are important ecological engineers on intertidal rocks where they create habitat that contributes substantially to overall biodiversity. They provide secondary substratum for other free-living, infaunal or epifaunal organisms, and increase the surface area for settlement by densely packing together into complex multilayered beds. The introduction of the alien invasive mussel Mytilus galloprovincialis has extended the upper limit of mussels on the south coast of South Africa, potentially increasing habitat for associated fauna. The aim of this study was to describe the structure of mussel beds, the general biodiversity associated with multi- and monolayered mussel beds of indigenous Perna perna and alien M. galloprovincialis, and to determine the relationship between mussels and epibiotic barnacles. This was done to determine the community structure of associated macrofauna and the role of mussels as biological facilitators. Samples were collected in Plettenberg Bay, South Africa, where M. galloprovincialis dominates the high mussel zone and P. perna the low zone. Three 15 X 15 cm quadrats were scraped off the rock in the high and low zones, and in the mid zone where the two mussel species co-exist. The samples were collected on 3 occasions. In the laboratory mussel-size was measured and sediment trapped within the samples was separated through 75 μm, 1 mm and 5 mm mesh. The macrofauna was sorted from the 1 mm and 5 mm sieves and identified to species level where possible. The epibiotic relationship between mussels and barnacles was assessed by measuring the prevalence and intensity of barnacle infestation and the condition index of infested mussels. Multivariate analysis was used on the mean abundance data of the species for each treatment (Hierarchical clustering, multidimensional scaling, analysis of similarity and similarity of percentages) and ANOVA was used for most of the statistical analyses. Overall, the results showed that tidal height influences the species composition and abundance of associated fauna. While mussel bed layering influenced the accumulation of sediments; it had no significant effect on the associated fauna. Time of collection also had a strong effect. While there was an overlap of species among samples from January, May and March, the principal species contributing to similarity among the March samples were not found in the other two months. The outcomes of this study showed that low shore mussel beds not only supported a higher abundance and diversity of species, but were also the most structurally complex. Although the condition index of mussels did not correlate to the percentage cover of barnacle epibionts, it was also evident that low shore mussels had the highest prevalence. The levels of barnacle infestation (intensity) for each mussel species were highest where it was common and lowest where it was least abundant. This is viewed as a natural artefact of the distribution patterns of P. perna and M. galloprovincialis across the shore. Mussels are more efficient as facilitators on the low mussel zone than the high mussel zone possibly because they provide habitats that are more effective in protecting the associated macrofauna from the effects of competition and predation, than they are at eliminating the effects of physical stress on the high shore. Although mussels create less stressful habitats and protect organisms from the physical stress of the high shore, there are clear limitations in their ability to provide ideal habitats. The biological associations in an ecosystem can be made weak or strong depending on the external abiotic factors and the adaptability of the affected organisms.
- Full Text:
- Authors: Jordaan, Tembisa Nomathamsanqa
- Date: 2011
- Subjects: Mytilidae -- South Africa , Mytilus galloprovincialis -- South Africa , Mussel culture -- South Africa , Shellfish culture -- South Africa , Perna -- South Africa , Barnacles -- South Africa , Mussels -- South Africa , Mussels -- Ecology , Barnacles -- Ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5675 , http://hdl.handle.net/10962/d1005360 , Mytilidae -- South Africa , Mytilus galloprovincialis -- South Africa , Mussel culture -- South Africa , Shellfish culture -- South Africa , Perna -- South Africa , Barnacles -- South Africa , Mussels -- South Africa , Mussels -- Ecology , Barnacles -- Ecology
- Description: Mussels are important ecological engineers on intertidal rocks where they create habitat that contributes substantially to overall biodiversity. They provide secondary substratum for other free-living, infaunal or epifaunal organisms, and increase the surface area for settlement by densely packing together into complex multilayered beds. The introduction of the alien invasive mussel Mytilus galloprovincialis has extended the upper limit of mussels on the south coast of South Africa, potentially increasing habitat for associated fauna. The aim of this study was to describe the structure of mussel beds, the general biodiversity associated with multi- and monolayered mussel beds of indigenous Perna perna and alien M. galloprovincialis, and to determine the relationship between mussels and epibiotic barnacles. This was done to determine the community structure of associated macrofauna and the role of mussels as biological facilitators. Samples were collected in Plettenberg Bay, South Africa, where M. galloprovincialis dominates the high mussel zone and P. perna the low zone. Three 15 X 15 cm quadrats were scraped off the rock in the high and low zones, and in the mid zone where the two mussel species co-exist. The samples were collected on 3 occasions. In the laboratory mussel-size was measured and sediment trapped within the samples was separated through 75 μm, 1 mm and 5 mm mesh. The macrofauna was sorted from the 1 mm and 5 mm sieves and identified to species level where possible. The epibiotic relationship between mussels and barnacles was assessed by measuring the prevalence and intensity of barnacle infestation and the condition index of infested mussels. Multivariate analysis was used on the mean abundance data of the species for each treatment (Hierarchical clustering, multidimensional scaling, analysis of similarity and similarity of percentages) and ANOVA was used for most of the statistical analyses. Overall, the results showed that tidal height influences the species composition and abundance of associated fauna. While mussel bed layering influenced the accumulation of sediments; it had no significant effect on the associated fauna. Time of collection also had a strong effect. While there was an overlap of species among samples from January, May and March, the principal species contributing to similarity among the March samples were not found in the other two months. The outcomes of this study showed that low shore mussel beds not only supported a higher abundance and diversity of species, but were also the most structurally complex. Although the condition index of mussels did not correlate to the percentage cover of barnacle epibionts, it was also evident that low shore mussels had the highest prevalence. The levels of barnacle infestation (intensity) for each mussel species were highest where it was common and lowest where it was least abundant. This is viewed as a natural artefact of the distribution patterns of P. perna and M. galloprovincialis across the shore. Mussels are more efficient as facilitators on the low mussel zone than the high mussel zone possibly because they provide habitats that are more effective in protecting the associated macrofauna from the effects of competition and predation, than they are at eliminating the effects of physical stress on the high shore. Although mussels create less stressful habitats and protect organisms from the physical stress of the high shore, there are clear limitations in their ability to provide ideal habitats. The biological associations in an ecosystem can be made weak or strong depending on the external abiotic factors and the adaptability of the affected organisms.
- Full Text:
The genetic diversity and conservation biology of the rare terrestrial snail genus Prestonella
- Authors: Fearon, Janine Lee
- Date: 2011
- Subjects: Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4191 , http://hdl.handle.net/10962/d1003760 , Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Description: Prestonella bowkeri and Prestonella nuptialis are montane specialists endemic to the southern Great Escarpment of South Africa. Phylogeographic analyses of these species based on mitochondrial markers CO1 and 16S reveal extremely high levels of divergence between populations indicating a lack of gene flow between populations. This is not surprising, because P. nuptialis and P. bowkeri have limited dispersal capacity, low vagility, a highly fragmented distribution and are habitat specialists that are restricted to isolated mesic refugia associated with waterfalls and montane seepages. A relaxed Bayesian clock estimate suggests that populations diverged from one another during the mid-late Miocene (12.5-7 MYA) which coincides with the modern trends of seasonal aridity which began during the Miocene. This result should be viewed with caution because the rates used are at best imprecise estimates of mutation rates in snails. There is no clear dichotomy between the two species and P. bowkeri is paraphyletic with respect to P. nuptialis, as a consequence the taxonomy is unclear. Due to the high levels of sequence divergence between populations they may be considered as evolutionary significant units (ESU’s). An assessment of haplotype diversity (h) and nucleotide diversity (π) reveals that populations in the western part of the Great Escarpment are more genetically depauperate than populations in the east. Correlations between genetic diversity and climatic variables show that genetically depauperate populations are found in areas that have lower annual rainfall, less reliable rainfall and higher potential evaporation, all factors associated with a drier, less mesic environment that increases the chances of a population bottleneck. This indicates that a shift towards a more arid environment may be a driver of genetic erosion. Historical climate change may thus have affected the amount and distribution of genetic diversity across the Great Escarpment since the Miocene. This has serious future implications for the survival of Prestonella. With predicted increase in global temperatures, climate change in South Africa is likely to result in range contraction and an eastward range shift for many species in the drier central and western areas (Erasmus et al. 2002) and regions along the Great Escarpment are likely to become more arid. Prestonella populations found living on inselbergs along the Great Escarpment are already restricted to site specific watercourses and seepages. An increase in the periods between stream flow, and increasing rainfall variability and mean annual potential evaporation are likely to have an adverse affect on species living in these habitats, resulting in further bottlenecks and possibly local extinction. An IUCN assessment of P. nuptialis and P. bowkeri suggests that these two species are probably endangered. The issue surrounding the conservation of Prestonella species is that they are threatened by global climate change, which cannot be simply restricted or prevented, which makes dealing with the threat of climate change difficult. Assisted migration (MA) may be considered as a method to prevent possible future extinctions of Prestonella populations, but will only be considered as a last resort. The thermal tolerance (Arrhenius breaking temperature and flat-line temperature) of individual snails from three Prestonella populations (one forest population and two thicket populations) were assessed using infrared sensors that detected changes in heart rate with increasing temperature. The forest population had a significantly lower Arrhenius breaking temperature (ABT) and flat-line temperature (FLT) than the two thicket population (p<0.05). Our results do not show a correlation between upper thermal limits and maximum habitat temperatures or other climatic variables in Prestonella populations. Although no correlation is found between ABT and maximum habitat temperature, it is likely that the differences seen between these populations are due to local micro-climate adaptation. The climatic variables used in this experiment are coarse estimates from GIS data and do not reflect actual microhabitat conditions. Forest environments are less heat stressed than thicket environments due to the forest canopy which may explain the lower ABT and FLT of the forest population.
- Full Text:
- Authors: Fearon, Janine Lee
- Date: 2011
- Subjects: Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4191 , http://hdl.handle.net/10962/d1003760 , Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Description: Prestonella bowkeri and Prestonella nuptialis are montane specialists endemic to the southern Great Escarpment of South Africa. Phylogeographic analyses of these species based on mitochondrial markers CO1 and 16S reveal extremely high levels of divergence between populations indicating a lack of gene flow between populations. This is not surprising, because P. nuptialis and P. bowkeri have limited dispersal capacity, low vagility, a highly fragmented distribution and are habitat specialists that are restricted to isolated mesic refugia associated with waterfalls and montane seepages. A relaxed Bayesian clock estimate suggests that populations diverged from one another during the mid-late Miocene (12.5-7 MYA) which coincides with the modern trends of seasonal aridity which began during the Miocene. This result should be viewed with caution because the rates used are at best imprecise estimates of mutation rates in snails. There is no clear dichotomy between the two species and P. bowkeri is paraphyletic with respect to P. nuptialis, as a consequence the taxonomy is unclear. Due to the high levels of sequence divergence between populations they may be considered as evolutionary significant units (ESU’s). An assessment of haplotype diversity (h) and nucleotide diversity (π) reveals that populations in the western part of the Great Escarpment are more genetically depauperate than populations in the east. Correlations between genetic diversity and climatic variables show that genetically depauperate populations are found in areas that have lower annual rainfall, less reliable rainfall and higher potential evaporation, all factors associated with a drier, less mesic environment that increases the chances of a population bottleneck. This indicates that a shift towards a more arid environment may be a driver of genetic erosion. Historical climate change may thus have affected the amount and distribution of genetic diversity across the Great Escarpment since the Miocene. This has serious future implications for the survival of Prestonella. With predicted increase in global temperatures, climate change in South Africa is likely to result in range contraction and an eastward range shift for many species in the drier central and western areas (Erasmus et al. 2002) and regions along the Great Escarpment are likely to become more arid. Prestonella populations found living on inselbergs along the Great Escarpment are already restricted to site specific watercourses and seepages. An increase in the periods between stream flow, and increasing rainfall variability and mean annual potential evaporation are likely to have an adverse affect on species living in these habitats, resulting in further bottlenecks and possibly local extinction. An IUCN assessment of P. nuptialis and P. bowkeri suggests that these two species are probably endangered. The issue surrounding the conservation of Prestonella species is that they are threatened by global climate change, which cannot be simply restricted or prevented, which makes dealing with the threat of climate change difficult. Assisted migration (MA) may be considered as a method to prevent possible future extinctions of Prestonella populations, but will only be considered as a last resort. The thermal tolerance (Arrhenius breaking temperature and flat-line temperature) of individual snails from three Prestonella populations (one forest population and two thicket populations) were assessed using infrared sensors that detected changes in heart rate with increasing temperature. The forest population had a significantly lower Arrhenius breaking temperature (ABT) and flat-line temperature (FLT) than the two thicket population (p<0.05). Our results do not show a correlation between upper thermal limits and maximum habitat temperatures or other climatic variables in Prestonella populations. Although no correlation is found between ABT and maximum habitat temperature, it is likely that the differences seen between these populations are due to local micro-climate adaptation. The climatic variables used in this experiment are coarse estimates from GIS data and do not reflect actual microhabitat conditions. Forest environments are less heat stressed than thicket environments due to the forest canopy which may explain the lower ABT and FLT of the forest population.
- Full Text:
The genetic integrity of Labeo capensis and L. umbratus (Cyprinidae) in South Africa in relation to inter-basin water transfer schemes
- Authors: Ramoejane, Mpho
- Date: 2011
- Subjects: Cyprinidae -- South Africa -- Darlington Dam , Cyprinidae -- Namibia -- Hardap Dam , Labeo -- South Africa -- Darlington Dam , Labeo -- Namibia -- Hardap Dam , Fishes -- Hybridisation -- South Africa -- Darlington Dam , Fishes -- Hybridisation -- Namibia -- Hardap Dam , Fishes -- Anatomy -- South Africa -- Darlington Dam , Fishes -- Anatomy -- Namibia -- Hardap Dam , Water transfer -- South Africa-- Darlington Dam , Water transfer -- Namibia -- Hardap Dam
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5367 , http://hdl.handle.net/10962/d1013049
- Description: The Orange-Fish and Cookhouse tunnels that are part of a major inter-basin water transfer scheme (IBT) act as a pathway for several fish species from the Orange River system to enter the Great Fish and Sundays River systems in South Africa. These include Labeo capensis and L. umbratus. Labeo capensis was restricted to the Orange River system before the inter-basin water transfer scheme. Labeo umbratus occurred naturally in the Orange River and in southern flowing river systems. Previous studies showed that the two species hybridise in Hardap Dam, located in a tributary of the Orange River system in Namibia. There are also unconfirmed reports of hybrids from Darlington Dam on the Sundays River system. The aim of the thesis was to confirm hybridisation in Hardap Dam, assess whether hybridisation between L. capensis and L. umbratus has occurred in Darlington Dam and to gain a better understanding of the diversity of these two species. Morphology (morphometrics and meristics), a nuclear S7 intron and the mitochondrial cytochrome ♭ gene were used to assess for hybridisation. A total of 275 specimens were analysed from across the geographical range of the two species. The two species could be distinguished using morphometrics (dorsal fin base, interorbital width and operculum to eye distance) and meristics (lateral line, origin of the dorsal fin to lateral line, origin of the pelvic fin to lateral line and caudal peduncle scale counts) characters. Hybrids from Hardap and Darlington dams were placed between the two species clusters. Labeo umbratus from the Orange River and southern flowing rivers formed a single cluster. The two species could also be distinguished from each other with six nuclear DNA mutations and hybrids were heterozygous at such sites in both dams. Labeo umbratus populations from the Orange River and southern flowing rivers (Gouritz, Gamtoos, Sundays, Bushmans, Great Fish and Nahoon) formed a single lineage. Analysis of mitochondrial DNA, however, revealed that L. umbratus populations from the Orange River and southern flowing rivers were two lineages that differ from each other by 5 mutations. Labeo capensis could be differentiated from both these lineages. Being maternally inherited, mitochondrial DNA did not reveal hybridisation, but ten specimens with L. capensis haplotypes were found in the Darlington Dam. In Hardap Dam, however, it appears that only L. capensis mitochondrial DNA haplotypes persist, despite morphological and nuclear DNA analysis suggesting that both morphs and hybrids of the two species occur. The genetic integrity of these Labeo species has therefore been compromised in at least Hardap and Darlington dams. The Great Fish and Sundays populations are considered to be under threat of complete introgression. The Kat River and Slagboom Dam populations that were isolated before the IBTs have to remain isolated to protect the genetic integrity of the southern lineage of L. umbratus in these two systems.
- Full Text:
- Authors: Ramoejane, Mpho
- Date: 2011
- Subjects: Cyprinidae -- South Africa -- Darlington Dam , Cyprinidae -- Namibia -- Hardap Dam , Labeo -- South Africa -- Darlington Dam , Labeo -- Namibia -- Hardap Dam , Fishes -- Hybridisation -- South Africa -- Darlington Dam , Fishes -- Hybridisation -- Namibia -- Hardap Dam , Fishes -- Anatomy -- South Africa -- Darlington Dam , Fishes -- Anatomy -- Namibia -- Hardap Dam , Water transfer -- South Africa-- Darlington Dam , Water transfer -- Namibia -- Hardap Dam
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5367 , http://hdl.handle.net/10962/d1013049
- Description: The Orange-Fish and Cookhouse tunnels that are part of a major inter-basin water transfer scheme (IBT) act as a pathway for several fish species from the Orange River system to enter the Great Fish and Sundays River systems in South Africa. These include Labeo capensis and L. umbratus. Labeo capensis was restricted to the Orange River system before the inter-basin water transfer scheme. Labeo umbratus occurred naturally in the Orange River and in southern flowing river systems. Previous studies showed that the two species hybridise in Hardap Dam, located in a tributary of the Orange River system in Namibia. There are also unconfirmed reports of hybrids from Darlington Dam on the Sundays River system. The aim of the thesis was to confirm hybridisation in Hardap Dam, assess whether hybridisation between L. capensis and L. umbratus has occurred in Darlington Dam and to gain a better understanding of the diversity of these two species. Morphology (morphometrics and meristics), a nuclear S7 intron and the mitochondrial cytochrome ♭ gene were used to assess for hybridisation. A total of 275 specimens were analysed from across the geographical range of the two species. The two species could be distinguished using morphometrics (dorsal fin base, interorbital width and operculum to eye distance) and meristics (lateral line, origin of the dorsal fin to lateral line, origin of the pelvic fin to lateral line and caudal peduncle scale counts) characters. Hybrids from Hardap and Darlington dams were placed between the two species clusters. Labeo umbratus from the Orange River and southern flowing rivers formed a single cluster. The two species could also be distinguished from each other with six nuclear DNA mutations and hybrids were heterozygous at such sites in both dams. Labeo umbratus populations from the Orange River and southern flowing rivers (Gouritz, Gamtoos, Sundays, Bushmans, Great Fish and Nahoon) formed a single lineage. Analysis of mitochondrial DNA, however, revealed that L. umbratus populations from the Orange River and southern flowing rivers were two lineages that differ from each other by 5 mutations. Labeo capensis could be differentiated from both these lineages. Being maternally inherited, mitochondrial DNA did not reveal hybridisation, but ten specimens with L. capensis haplotypes were found in the Darlington Dam. In Hardap Dam, however, it appears that only L. capensis mitochondrial DNA haplotypes persist, despite morphological and nuclear DNA analysis suggesting that both morphs and hybrids of the two species occur. The genetic integrity of these Labeo species has therefore been compromised in at least Hardap and Darlington dams. The Great Fish and Sundays populations are considered to be under threat of complete introgression. The Kat River and Slagboom Dam populations that were isolated before the IBTs have to remain isolated to protect the genetic integrity of the southern lineage of L. umbratus in these two systems.
- Full Text:
The impact of forest degradation on carbon stocks of forests in the Matiwane area of the Transkei, South Africa
- Authors: Mangwale, Kagiso
- Date: 2011
- Subjects: Forest degradation -- Control -- South Africa -- Transkei , Forest ecology -- South Africa -- Transkei , Carbon sequestration -- South Africa -- Transkei , Forest conservation -- South Africa -- Transkei
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4781 , http://hdl.handle.net/10962/d1012799 , Forest degradation -- Control -- South Africa -- Transkei , Forest ecology -- South Africa -- Transkei , Carbon sequestration -- South Africa -- Transkei , Forest conservation -- South Africa -- Transkei
- Description: This study focused on assessing the condition and creating a carbon inventory of forests in the Matiwane area of the Transkei. This entailed the use of aerial photography in tracing forest cover change from 1942 to 2007 coupled with ground-truthing to assess whether the forests have in any way endured degradation over the years with a potential reduction in carbon stocks as a result. This study revealed both the loss and gain of biomass in the area with a general trend of forests being continuously converted to agricultural fields resulting in reduced forest area, stem density, tree density and carbon loss in different pools of the forests, reflecting that these forests are degraded. The conversion has resulted in the reduction in the number of species from a mean of 11±0.57 species/200m² in intact forests to 1±0.23species/200m² plot in degraded forests. It was also revealed that approximately 5.2 % (791 hectares) of 15 352 hectares of forest area was lost as a result of the conversion of forest land to agricultural fields from 1942 to 2007 with 99 % of the clearing occurring in the last 33 years (1974-2007) and of which 60 % ( 4 77 hectares) occurred from 1995 to 2007, indicating that forest degradation in these forests is on the increase. The assessment also revealed some areas that were nonforest in 1942 that have accumulated woody biomass (BAA), composed mainly of Acacia sp accounting for 51.18 MgC.ha⁻¹ (Megagrams of carbon per hectare) and total carbon stocks of 0.02 TgC (Teragrams of carbon). The degradation of these forests induced a reduction in carbon stocks from 311.68±23.69 MgC.ha⁻¹ (to a soil depth 0-50 cm) in intact forest to 73.46±12.34 MgC.ha⁻¹ in degraded forests. The total carbon stocks in the degraded forests were approximated at 0.06 TgC and the BAA areas 0.02 TgC with 4.7 TgC in intact forests. The degradation of these forests has resulted in the net carbon loss of 0.19 TgC between 1942 and 2007 but 4.76 TgC is still locked in these forests. The large difference in carbon stocks between intact and degraded forests indicated the need to reduce the degradation of these forests to prevent further carbon loss and reduction of the carbon sequestration potential of these forests.
- Full Text:
- Authors: Mangwale, Kagiso
- Date: 2011
- Subjects: Forest degradation -- Control -- South Africa -- Transkei , Forest ecology -- South Africa -- Transkei , Carbon sequestration -- South Africa -- Transkei , Forest conservation -- South Africa -- Transkei
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4781 , http://hdl.handle.net/10962/d1012799 , Forest degradation -- Control -- South Africa -- Transkei , Forest ecology -- South Africa -- Transkei , Carbon sequestration -- South Africa -- Transkei , Forest conservation -- South Africa -- Transkei
- Description: This study focused on assessing the condition and creating a carbon inventory of forests in the Matiwane area of the Transkei. This entailed the use of aerial photography in tracing forest cover change from 1942 to 2007 coupled with ground-truthing to assess whether the forests have in any way endured degradation over the years with a potential reduction in carbon stocks as a result. This study revealed both the loss and gain of biomass in the area with a general trend of forests being continuously converted to agricultural fields resulting in reduced forest area, stem density, tree density and carbon loss in different pools of the forests, reflecting that these forests are degraded. The conversion has resulted in the reduction in the number of species from a mean of 11±0.57 species/200m² in intact forests to 1±0.23species/200m² plot in degraded forests. It was also revealed that approximately 5.2 % (791 hectares) of 15 352 hectares of forest area was lost as a result of the conversion of forest land to agricultural fields from 1942 to 2007 with 99 % of the clearing occurring in the last 33 years (1974-2007) and of which 60 % ( 4 77 hectares) occurred from 1995 to 2007, indicating that forest degradation in these forests is on the increase. The assessment also revealed some areas that were nonforest in 1942 that have accumulated woody biomass (BAA), composed mainly of Acacia sp accounting for 51.18 MgC.ha⁻¹ (Megagrams of carbon per hectare) and total carbon stocks of 0.02 TgC (Teragrams of carbon). The degradation of these forests induced a reduction in carbon stocks from 311.68±23.69 MgC.ha⁻¹ (to a soil depth 0-50 cm) in intact forest to 73.46±12.34 MgC.ha⁻¹ in degraded forests. The total carbon stocks in the degraded forests were approximated at 0.06 TgC and the BAA areas 0.02 TgC with 4.7 TgC in intact forests. The degradation of these forests has resulted in the net carbon loss of 0.19 TgC between 1942 and 2007 but 4.76 TgC is still locked in these forests. The large difference in carbon stocks between intact and degraded forests indicated the need to reduce the degradation of these forests to prevent further carbon loss and reduction of the carbon sequestration potential of these forests.
- Full Text:
The implementation and evaluation of a service-learning component in a second year undergraduate organic chemistry course
- Authors: Abel, Sarah Ruth
- Date: 2011 , 2010-10-03
- Subjects: Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4393 , http://hdl.handle.net/10962/d1006008 , Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Description: The project describes the action research implementation, and evaluation of learning, of a service-learning component in a second year undergraduate organic chemistry course. The research aims to explore the learning that takes place in a service-learning context while utilizing an action research methodology within the critical theory paradigm. This occurs in response to the world-wide call for Higher Education to produce people with civic competencies and responsiveness to the society in which they live (Boyer 1996). Educating young Chemists to see the importance of their knowledge and their responsibilities in society is an important pedagogical step in the effort to cross boundaries and make connections between people communities (Eyler and Giles 1999). The goal of this project was to explore and categorize the learning that takes place in a service-learning context and discover how these areas of learning impact the awareness of the parties involved with regard to the discipline of chemistry as well as social issues. The project makes use of Kolb‘s (1984) Experiential Learning Theory, and Eyler and Giles‘ (1999) categories of learning in service-learning and results indicate that service-learning can be a powerful pedagogical tool to increase learning in chemistry as well as in the areas of critical thinking, personal and social development, reflection and citizenship. Students‘ perceptions of themselves, their discipline and their responsibility to society were transformed by their experience of service-learning in their undergraduate chemistry course.
- Full Text:
- Authors: Abel, Sarah Ruth
- Date: 2011 , 2010-10-03
- Subjects: Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4393 , http://hdl.handle.net/10962/d1006008 , Chemistry, Organic -- Study and teaching (Higher) -- South Africa , Action research in education -- South Africa , Experiential learning -- South Africa , Service learning -- South Africa
- Description: The project describes the action research implementation, and evaluation of learning, of a service-learning component in a second year undergraduate organic chemistry course. The research aims to explore the learning that takes place in a service-learning context while utilizing an action research methodology within the critical theory paradigm. This occurs in response to the world-wide call for Higher Education to produce people with civic competencies and responsiveness to the society in which they live (Boyer 1996). Educating young Chemists to see the importance of their knowledge and their responsibilities in society is an important pedagogical step in the effort to cross boundaries and make connections between people communities (Eyler and Giles 1999). The goal of this project was to explore and categorize the learning that takes place in a service-learning context and discover how these areas of learning impact the awareness of the parties involved with regard to the discipline of chemistry as well as social issues. The project makes use of Kolb‘s (1984) Experiential Learning Theory, and Eyler and Giles‘ (1999) categories of learning in service-learning and results indicate that service-learning can be a powerful pedagogical tool to increase learning in chemistry as well as in the areas of critical thinking, personal and social development, reflection and citizenship. Students‘ perceptions of themselves, their discipline and their responsibility to society were transformed by their experience of service-learning in their undergraduate chemistry course.
- Full Text:
The photophysical properties of low symmetry phthalocyanines in conjunction with quantum dots
- Authors: D'Souza, Sarah
- Date: 2011
- Subjects: Phthalocyanines , Photochemistry , Zinc , Quantum dots , Spectrum analysis , Nanoparticles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4331 , http://hdl.handle.net/10962/d1004992 , Phthalocyanines , Photochemistry , Zinc , Quantum dots , Spectrum analysis , Nanoparticles
- Description: he synthesis, extensive spectroscopic characterization and photophysical studies of low symmetry zinc phthalocyanine have been conducted. Comparisons have been made taking into consideration the influence of the solvent properties as well as substituent type and position. Photosensitizing properties of the zinc phthalocyanine derivatives in the presence of thiol capped CdTe quantum dots (QDs) were compared. The QDs were used as energy transfer donors and to facilitate with energy transfer through Förster resonance energy transfer (FRET) from the QDs to the MPcs. The linkage of unsymmetrically substituted 4-monoaminophenoxy zinc phthalocyanine (ZnAPPc) to CdTe quantum dots capped with mercaptopropionic acid (MPA), L-cysteine (L-cys) or thioglycolic acid (TGA) has been achieved using the coupling agents ethyl-N3 dimethylaminopropyl)carbodiimide (EDC) and N-hydroxy succinimide (NHS), which facilitate formation of an amide bond to form the QD-ZnAPPc-linked complex. The formation of the amide bond was confirmed using UV-Vis, Raman and IR spectroscopies, as well as AFM (atomic force microscopy). Förster resonance energy transfer (FRET) resulted in stimulated emission of ZnAPPc in both the linked (QDZnAPPc-linked) and mixed (QD:ZnAPPc-mixed) conjugates for MPA only. The linked L-cys and TGA complexes (QD-ZnAPPc-linked) gave the largest FRET efficiencies hence showing the advantages of covalent linking. Fluorescence quantum yields of QDs were decreased in QD:ZnAPPc-mixed and QD:ZnAPPc-linked. High triplet state quantum yields were obtained for the linked QD-phthalocyanine derivatives (ZnAPPc)and monoaminozinc phthalocyanine (ZnAPc) compared to when ZnAPPc and ZnAPc were mixed with MPA QDs without a chemical bond.
- Full Text:
- Authors: D'Souza, Sarah
- Date: 2011
- Subjects: Phthalocyanines , Photochemistry , Zinc , Quantum dots , Spectrum analysis , Nanoparticles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4331 , http://hdl.handle.net/10962/d1004992 , Phthalocyanines , Photochemistry , Zinc , Quantum dots , Spectrum analysis , Nanoparticles
- Description: he synthesis, extensive spectroscopic characterization and photophysical studies of low symmetry zinc phthalocyanine have been conducted. Comparisons have been made taking into consideration the influence of the solvent properties as well as substituent type and position. Photosensitizing properties of the zinc phthalocyanine derivatives in the presence of thiol capped CdTe quantum dots (QDs) were compared. The QDs were used as energy transfer donors and to facilitate with energy transfer through Förster resonance energy transfer (FRET) from the QDs to the MPcs. The linkage of unsymmetrically substituted 4-monoaminophenoxy zinc phthalocyanine (ZnAPPc) to CdTe quantum dots capped with mercaptopropionic acid (MPA), L-cysteine (L-cys) or thioglycolic acid (TGA) has been achieved using the coupling agents ethyl-N3 dimethylaminopropyl)carbodiimide (EDC) and N-hydroxy succinimide (NHS), which facilitate formation of an amide bond to form the QD-ZnAPPc-linked complex. The formation of the amide bond was confirmed using UV-Vis, Raman and IR spectroscopies, as well as AFM (atomic force microscopy). Förster resonance energy transfer (FRET) resulted in stimulated emission of ZnAPPc in both the linked (QDZnAPPc-linked) and mixed (QD:ZnAPPc-mixed) conjugates for MPA only. The linked L-cys and TGA complexes (QD-ZnAPPc-linked) gave the largest FRET efficiencies hence showing the advantages of covalent linking. Fluorescence quantum yields of QDs were decreased in QD:ZnAPPc-mixed and QD:ZnAPPc-linked. High triplet state quantum yields were obtained for the linked QD-phthalocyanine derivatives (ZnAPPc)and monoaminozinc phthalocyanine (ZnAPc) compared to when ZnAPPc and ZnAPc were mixed with MPA QDs without a chemical bond.
- Full Text:
The role of Hsp90 in the Wnt pathway of MCF7 breast cancer cells
- Authors: Cooper, Leanne Claire
- Date: 2011
- Subjects: Cancer -- Treatment , Heat shock proteins , Cancer cells , Molecular chaperones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3985 , http://hdl.handle.net/10962/d1004044 , Cancer -- Treatment , Heat shock proteins , Cancer cells , Molecular chaperones
- Description: Breast cancer is one of the most common forms of cancer in not only South African women, but women all over the world. The molecular chaperone heat shock protein 90 (HSP90) is upregulated in cancer and is almost exclusively associated with proteins involved in intracellular signal transduction, thus it plays an important role in signalling pathways within the cell. In cancer, there is an aberrant activation of the Wnt signaling pathway, which results in stabilized β-catenin being able to translocate to the nucleus where it can trigger the transcription of oncogenes found to be involved in the self-renewal of cells. The level of β-catenin is usually kept in check by a destruction complex comprising glycogen synthase kinase 3-beta (GSK-3β), axin1, adenomatous polyposis coli (APC) which phosphorylate β-catenin, resulting in its ubiquitination and degradation. HSP90 has been found to be associated with GSK-3β, but whether this association is only transient is debatable. Very little is known about the association of HSP90 with other members of the Wnt pathway in breast cancer. In this study, we have attempted to further identify the direct associations between HSP90 and GSK-3β, β-catenin, p-β-catenin and axin1. Immunofluorescence and confocal microscopy co-localization studies suggested a potential association between HSP90 and these proteins. Treatment with HSP90 inhibitors, 17-AAG and novobiocin resulted in a shift of axin1 to what appeared to be the plasma membrane. The associations of HSP90 with GSK-3β, β-catenin, p-β-catenin and axin1 were confirmed biochemically by co-immunoprecipitation and inhibition using 17-AAG, geldanamycin and novobiocin. We showed, for the first time that HSP90 is associated in a possible complex with β-catenin, p-β-catenin and axin1 therefore is potentially involved in the modulation of p-β-catenin in the Wnt pathway through the stabilization of the destruction complex.
- Full Text:
- Authors: Cooper, Leanne Claire
- Date: 2011
- Subjects: Cancer -- Treatment , Heat shock proteins , Cancer cells , Molecular chaperones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3985 , http://hdl.handle.net/10962/d1004044 , Cancer -- Treatment , Heat shock proteins , Cancer cells , Molecular chaperones
- Description: Breast cancer is one of the most common forms of cancer in not only South African women, but women all over the world. The molecular chaperone heat shock protein 90 (HSP90) is upregulated in cancer and is almost exclusively associated with proteins involved in intracellular signal transduction, thus it plays an important role in signalling pathways within the cell. In cancer, there is an aberrant activation of the Wnt signaling pathway, which results in stabilized β-catenin being able to translocate to the nucleus where it can trigger the transcription of oncogenes found to be involved in the self-renewal of cells. The level of β-catenin is usually kept in check by a destruction complex comprising glycogen synthase kinase 3-beta (GSK-3β), axin1, adenomatous polyposis coli (APC) which phosphorylate β-catenin, resulting in its ubiquitination and degradation. HSP90 has been found to be associated with GSK-3β, but whether this association is only transient is debatable. Very little is known about the association of HSP90 with other members of the Wnt pathway in breast cancer. In this study, we have attempted to further identify the direct associations between HSP90 and GSK-3β, β-catenin, p-β-catenin and axin1. Immunofluorescence and confocal microscopy co-localization studies suggested a potential association between HSP90 and these proteins. Treatment with HSP90 inhibitors, 17-AAG and novobiocin resulted in a shift of axin1 to what appeared to be the plasma membrane. The associations of HSP90 with GSK-3β, β-catenin, p-β-catenin and axin1 were confirmed biochemically by co-immunoprecipitation and inhibition using 17-AAG, geldanamycin and novobiocin. We showed, for the first time that HSP90 is associated in a possible complex with β-catenin, p-β-catenin and axin1 therefore is potentially involved in the modulation of p-β-catenin in the Wnt pathway through the stabilization of the destruction complex.
- Full Text:
The spatial evolution of the chemotaxis proteins of the Bacillus subtilis group
- Yssel, Anna Elizabeth Johanna
- Authors: Yssel, Anna Elizabeth Johanna
- Date: 2011
- Subjects: Chemotaxis , Bacillus subtilis , Bacillus (Bacteria) , Homology (Biology) , Plants -- Microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4027 , http://hdl.handle.net/10962/d1004087 , Chemotaxis , Bacillus subtilis , Bacillus (Bacteria) , Homology (Biology) , Plants -- Microbiology
- Description: The aim of this work was to study spatial evolution of the chemotaxis proteins of a group of plant-associated soil-dwelling bacteria vernacularly referred to as the B. subtilis group. This was achieved by creating homology models for the chemotaxis proteins if a suitable template was available, and by analysing the selective forces (positive, purifying or neutral) acting upon the chemotaxis proteins. Chemotaxis is the phenomenon in which bacteria direct their movement towards more favourable conditions, and is critical for processes such as obtaining nutrients, escaping toxic compounds, host colonization and bio-film formation. Members of the B. subtilis group exhibit different preferences for certain host plants, and it is therefore feasible that their chemotactic machinery are fine-tuned to respond optimally to the conditions of the various niches that the strains inhabit. Homology models were inferred for the plant growth promoting B. amyloliquefaciens FZB42 proteins CheB, CheC, CheD, CheR, CheW and CheY. The interactions between: CheC-CheD, the P1 and P2 domains of CheA with CheY and CheB, and the P4 and P5 domains of CheA with CheW were also modelled. The hydrophobic interactions contributing to intra- and inter-protein contacts were analysed. The models of the interactions between CheB and the various domains of CheA are of particular interest, because to date no structures have been solved that show an interaction between a histidine kinase (such as CheA) and a multidomain response regulator (such as CheB). Furthermore, evidence that phospho-CheB may inhibit the formation of phospho-CheY by competitively binding to the P2 domain of CheA is also presented. Proteins were analysed to determine if individual amino acid sites are under positive, neutral or purifying selection. The Methyl Accepting Chemotaxis Proteins (MCPs), CheA and CheV were also analyzed, but due to a lack of suitable templates, no homology models were constructed. Site-specific positive and purifying selection were estimated by comparing the ratios of non-synonymous to synonymous substitutions at each site in the sequences for the chemotaxis proteins as well as for the receptors McpA, McpB, and McpC. Homology models were coloured according to intensity of selective forces. It was found that the chemotaxis proteins of member of the B. subtilis group are under strong evolutionary constraints, hence it is unlikely that positive selection in these proteins are responsible for the differences in habitat preference that these organism exhibit.
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- Authors: Yssel, Anna Elizabeth Johanna
- Date: 2011
- Subjects: Chemotaxis , Bacillus subtilis , Bacillus (Bacteria) , Homology (Biology) , Plants -- Microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4027 , http://hdl.handle.net/10962/d1004087 , Chemotaxis , Bacillus subtilis , Bacillus (Bacteria) , Homology (Biology) , Plants -- Microbiology
- Description: The aim of this work was to study spatial evolution of the chemotaxis proteins of a group of plant-associated soil-dwelling bacteria vernacularly referred to as the B. subtilis group. This was achieved by creating homology models for the chemotaxis proteins if a suitable template was available, and by analysing the selective forces (positive, purifying or neutral) acting upon the chemotaxis proteins. Chemotaxis is the phenomenon in which bacteria direct their movement towards more favourable conditions, and is critical for processes such as obtaining nutrients, escaping toxic compounds, host colonization and bio-film formation. Members of the B. subtilis group exhibit different preferences for certain host plants, and it is therefore feasible that their chemotactic machinery are fine-tuned to respond optimally to the conditions of the various niches that the strains inhabit. Homology models were inferred for the plant growth promoting B. amyloliquefaciens FZB42 proteins CheB, CheC, CheD, CheR, CheW and CheY. The interactions between: CheC-CheD, the P1 and P2 domains of CheA with CheY and CheB, and the P4 and P5 domains of CheA with CheW were also modelled. The hydrophobic interactions contributing to intra- and inter-protein contacts were analysed. The models of the interactions between CheB and the various domains of CheA are of particular interest, because to date no structures have been solved that show an interaction between a histidine kinase (such as CheA) and a multidomain response regulator (such as CheB). Furthermore, evidence that phospho-CheB may inhibit the formation of phospho-CheY by competitively binding to the P2 domain of CheA is also presented. Proteins were analysed to determine if individual amino acid sites are under positive, neutral or purifying selection. The Methyl Accepting Chemotaxis Proteins (MCPs), CheA and CheV were also analyzed, but due to a lack of suitable templates, no homology models were constructed. Site-specific positive and purifying selection were estimated by comparing the ratios of non-synonymous to synonymous substitutions at each site in the sequences for the chemotaxis proteins as well as for the receptors McpA, McpB, and McpC. Homology models were coloured according to intensity of selective forces. It was found that the chemotaxis proteins of member of the B. subtilis group are under strong evolutionary constraints, hence it is unlikely that positive selection in these proteins are responsible for the differences in habitat preference that these organism exhibit.
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The zoogeography of the cetaceans in Algoa Bay
- Authors: Melly, Brigitte Leigh
- Date: 2011
- Subjects: Cetacea -- South Africa -- Algoa Bay , Cetacea -- Behavior -- South Africa -- Algoa Bay , Cetacea -- South Africa -- Algoa Bay -- Geographical distribution , Cetacea -- Counting -- South Africa -- Algoa Bay
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4858 , http://hdl.handle.net/10962/d1005534 , Cetacea -- South Africa -- Algoa Bay , Cetacea -- Behavior -- South Africa -- Algoa Bay , Cetacea -- South Africa -- Algoa Bay -- Geographical distribution , Cetacea -- Counting -- South Africa -- Algoa Bay
- Description: The most recent study on cetaceans in Algoa Bay, South Africa, was conducted over 14 years ago. Consequently, knowledge of the cetacean species visiting this bay is currently based on incidental observations and stranding data. A number of developments in recent years: a deepwater port, proposed oil refinery, increased boating and fishing (commercial and recreational), a proposed Marine Protected Area, and the release of a whale-watching permit, all of which may impact these animals in some way, highlight the need for a baseline study on cetaceans. Therefore, the aim of this study was to determine the spatial and temporal distribution, and habitat preference of cetaceans in Algoa Bay. Boat-based surveys were conducted monthly between March 2009 and July 2010. At each sighting the GPS location, species, group size and composition, and behaviour were recorded. Using GIS, the sighting data was related to data layers of geographical variables such as sea surface temperature, depth and sea-floor substrate. Approximately 365 hours of search effort were completed over 57 surveys, with a total of 346 sightings. Species observed were: southern right whales (Eubalaena australis), humpback whales (Megaptera novaeangliae), Bryde’s whales (Balaenoptera brydei), Indian Ocean bottlenose dolphins (Tursiops aduncus), Indo-Pacific humpback dolphins (Sousa chinensis), and longbeaked common dolphins (Delphinus capensis). Southern right whales were observed during austral winter, utilising the shallow, protected areas of the bay as a mating and nursery ground. Humpback whales were also recorded extensively during winter, in more offshore waters, with a significant number of mother-calf pairs sighted. Bryde’s whales were recorded in offshore waters during summer and autumn, where they were primarily observed travelling and foraging. Bottlenose dolphins were the most prolific species sighted. They were recorded year-round throughout the inshore waters of the bay, with large group sizes (up to 500 animals), and displayed a wide variety of behaviours. Humpback dolphins were observed in extremely shallow and inshore waters (mean bottom depth of 6.6 m) along the south-west corner of the bay, in small groups of approximately three individuals. Common dolphins were the least observed species, and were mainly observed foraging in large groups of up to 800 individuals. The results of this study indicate how cetaceans utilise the bay in significantly different ways. Geographical and anthropogenic factors have influenced the spatial and temporal distribution of these animals and have resulted in habitat preferences, as well as potential key habitats, in the bay. Thus, this study has provided baseline information for future research and for better informed conservation and management strategies in Algoa Bay.
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- Authors: Melly, Brigitte Leigh
- Date: 2011
- Subjects: Cetacea -- South Africa -- Algoa Bay , Cetacea -- Behavior -- South Africa -- Algoa Bay , Cetacea -- South Africa -- Algoa Bay -- Geographical distribution , Cetacea -- Counting -- South Africa -- Algoa Bay
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4858 , http://hdl.handle.net/10962/d1005534 , Cetacea -- South Africa -- Algoa Bay , Cetacea -- Behavior -- South Africa -- Algoa Bay , Cetacea -- South Africa -- Algoa Bay -- Geographical distribution , Cetacea -- Counting -- South Africa -- Algoa Bay
- Description: The most recent study on cetaceans in Algoa Bay, South Africa, was conducted over 14 years ago. Consequently, knowledge of the cetacean species visiting this bay is currently based on incidental observations and stranding data. A number of developments in recent years: a deepwater port, proposed oil refinery, increased boating and fishing (commercial and recreational), a proposed Marine Protected Area, and the release of a whale-watching permit, all of which may impact these animals in some way, highlight the need for a baseline study on cetaceans. Therefore, the aim of this study was to determine the spatial and temporal distribution, and habitat preference of cetaceans in Algoa Bay. Boat-based surveys were conducted monthly between March 2009 and July 2010. At each sighting the GPS location, species, group size and composition, and behaviour were recorded. Using GIS, the sighting data was related to data layers of geographical variables such as sea surface temperature, depth and sea-floor substrate. Approximately 365 hours of search effort were completed over 57 surveys, with a total of 346 sightings. Species observed were: southern right whales (Eubalaena australis), humpback whales (Megaptera novaeangliae), Bryde’s whales (Balaenoptera brydei), Indian Ocean bottlenose dolphins (Tursiops aduncus), Indo-Pacific humpback dolphins (Sousa chinensis), and longbeaked common dolphins (Delphinus capensis). Southern right whales were observed during austral winter, utilising the shallow, protected areas of the bay as a mating and nursery ground. Humpback whales were also recorded extensively during winter, in more offshore waters, with a significant number of mother-calf pairs sighted. Bryde’s whales were recorded in offshore waters during summer and autumn, where they were primarily observed travelling and foraging. Bottlenose dolphins were the most prolific species sighted. They were recorded year-round throughout the inshore waters of the bay, with large group sizes (up to 500 animals), and displayed a wide variety of behaviours. Humpback dolphins were observed in extremely shallow and inshore waters (mean bottom depth of 6.6 m) along the south-west corner of the bay, in small groups of approximately three individuals. Common dolphins were the least observed species, and were mainly observed foraging in large groups of up to 800 individuals. The results of this study indicate how cetaceans utilise the bay in significantly different ways. Geographical and anthropogenic factors have influenced the spatial and temporal distribution of these animals and have resulted in habitat preferences, as well as potential key habitats, in the bay. Thus, this study has provided baseline information for future research and for better informed conservation and management strategies in Algoa Bay.
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Towards a sustainable bioprocess for the remediation of acid mine drainage
- Authors: Mambo, Mutsa Prudence
- Date: 2011
- Subjects: Acid mine drainage , Algae culture , Reduction (Chemistry) , Hydrolysis , ASPAM model (Acid mine drainage) , Water -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5955 , http://hdl.handle.net/10962/d1006167 , Acid mine drainage , Algae culture , Reduction (Chemistry) , Hydrolysis , ASPAM model (Acid mine drainage) , Water -- Purification
- Description: Acid mine drainage is of growing concern for both developing and developed economies. Thus there is increasing pressure to develop alternative remediation strategies. Biological sulphidogenic mechanisms have long since been studied but, very few have been implemented on a large scale. Limitations are due to the inability to acquire a suitable, low cost, environmentally friendly, renewable carbon source. The present study investigated the use of an algae biomass generated by the HRAOP of an IAPS as a carbon source for the EBRU 00AB/06 SRB consortium. The algae biomass and consortium were utilized together to remediate simulated AMD. Remediation involved decreasing the sulphate and metal concentrations in solution and decreasing the acidity of a simulated AMD. Experiments were carried out to investigate the capability of the EBRU 00AB/06 SRB consortium for sulphate reduction and sulphide generation. The consortium produced colonies when grown under anaerobic conditions in Petri dishes containing modified lactate SRB medium. The SRB consortium reduced the sulphate concentration of modified Postgates medium B and generated sulphide. Further analysis of the EBRU 00AB/06 SRB consortium revealed that the consortium was minimally impacted at pH 5 and by sulphate and iron at 3 g.L-1 and 0.5 g.L-1 respectively. The EBRU 00AB/06 SRB consortium was exposed to Actinomycin D and Ethidium Bromide to determine whether transcription and translation of proteins was required for sulphate reduction. Results indicated that sulphide generation and sulphate reduction were inducible. Analysis of the algae biomass used in this study revealed the empirical formula C1.0H1.91N0.084S0.003O0.36 indicating a carbon source rich in the nutrients required to sustain microbial development. Light microscopy revealed that algae cell walls and in particular those of Pediastrum were susceptible to acid hydrolysis. Dinitrosalicylic acid, Nile red, Bradford and Ninhydrin assays were used to determine the reducing sugar, lipid, protein and amino acid content respectively, of the mixed algae biomass. Results showed that upon exposure of the biomass to simulated AMD at pH 1 and pH 3, the concentration of reducing sugars and amino acids in solution increased. Whereas levels of lipids remained unchanged while the protein concentration decreased, indicating that, upon exposure of algae biomass to AMD, simulated or otherwise, cells ruptured, proteins were hydrolyzed and polysaccharides were broken down to sugars which are immediately available for SRB utilization. Exposure of biomass to simulated AMD revealed further that the presence of algae biomass increased the pH of simulated AMD (pH 3) to pH 7.67 after 4 d. Likewise, the pH of simulated AMD at 1 increased to 1.77 after 2 d while pH of the neutral control increased to 8.1 after 4 d. A direct comparison between lactate and algae biomass revealed 94 % sulphate removal after 23 d in the presence of algae biomass while 82 % sulphate removal was measured in the presence of lactate. Thus the EBRU 00AB/06 SRB consortium successfully utilized algae biomass for sulphate reduction and sulphide generation. In another experiment to establish if the consortium could remediate simulated AMD (pH 5) containing 0.5 g.L-1 iron and 3 g.L-1 sulphate while utilizing an algae biomass as the carbon source no residual iron was detected after 14 d and by day 23, an 89.07 % reduction in sulphate was measured. The results of this investigation are discussed in terms of utilizing a readily available and renewable biomass in the form of microalgae produced in HRAOPs as an effective carbon source in the SRB catalysed remediation of AMD.
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- Authors: Mambo, Mutsa Prudence
- Date: 2011
- Subjects: Acid mine drainage , Algae culture , Reduction (Chemistry) , Hydrolysis , ASPAM model (Acid mine drainage) , Water -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5955 , http://hdl.handle.net/10962/d1006167 , Acid mine drainage , Algae culture , Reduction (Chemistry) , Hydrolysis , ASPAM model (Acid mine drainage) , Water -- Purification
- Description: Acid mine drainage is of growing concern for both developing and developed economies. Thus there is increasing pressure to develop alternative remediation strategies. Biological sulphidogenic mechanisms have long since been studied but, very few have been implemented on a large scale. Limitations are due to the inability to acquire a suitable, low cost, environmentally friendly, renewable carbon source. The present study investigated the use of an algae biomass generated by the HRAOP of an IAPS as a carbon source for the EBRU 00AB/06 SRB consortium. The algae biomass and consortium were utilized together to remediate simulated AMD. Remediation involved decreasing the sulphate and metal concentrations in solution and decreasing the acidity of a simulated AMD. Experiments were carried out to investigate the capability of the EBRU 00AB/06 SRB consortium for sulphate reduction and sulphide generation. The consortium produced colonies when grown under anaerobic conditions in Petri dishes containing modified lactate SRB medium. The SRB consortium reduced the sulphate concentration of modified Postgates medium B and generated sulphide. Further analysis of the EBRU 00AB/06 SRB consortium revealed that the consortium was minimally impacted at pH 5 and by sulphate and iron at 3 g.L-1 and 0.5 g.L-1 respectively. The EBRU 00AB/06 SRB consortium was exposed to Actinomycin D and Ethidium Bromide to determine whether transcription and translation of proteins was required for sulphate reduction. Results indicated that sulphide generation and sulphate reduction were inducible. Analysis of the algae biomass used in this study revealed the empirical formula C1.0H1.91N0.084S0.003O0.36 indicating a carbon source rich in the nutrients required to sustain microbial development. Light microscopy revealed that algae cell walls and in particular those of Pediastrum were susceptible to acid hydrolysis. Dinitrosalicylic acid, Nile red, Bradford and Ninhydrin assays were used to determine the reducing sugar, lipid, protein and amino acid content respectively, of the mixed algae biomass. Results showed that upon exposure of the biomass to simulated AMD at pH 1 and pH 3, the concentration of reducing sugars and amino acids in solution increased. Whereas levels of lipids remained unchanged while the protein concentration decreased, indicating that, upon exposure of algae biomass to AMD, simulated or otherwise, cells ruptured, proteins were hydrolyzed and polysaccharides were broken down to sugars which are immediately available for SRB utilization. Exposure of biomass to simulated AMD revealed further that the presence of algae biomass increased the pH of simulated AMD (pH 3) to pH 7.67 after 4 d. Likewise, the pH of simulated AMD at 1 increased to 1.77 after 2 d while pH of the neutral control increased to 8.1 after 4 d. A direct comparison between lactate and algae biomass revealed 94 % sulphate removal after 23 d in the presence of algae biomass while 82 % sulphate removal was measured in the presence of lactate. Thus the EBRU 00AB/06 SRB consortium successfully utilized algae biomass for sulphate reduction and sulphide generation. In another experiment to establish if the consortium could remediate simulated AMD (pH 5) containing 0.5 g.L-1 iron and 3 g.L-1 sulphate while utilizing an algae biomass as the carbon source no residual iron was detected after 14 d and by day 23, an 89.07 % reduction in sulphate was measured. The results of this investigation are discussed in terms of utilizing a readily available and renewable biomass in the form of microalgae produced in HRAOPs as an effective carbon source in the SRB catalysed remediation of AMD.
- Full Text: