The role of parallel computing in bioinformatics
- Authors: Akhurst, Timothy John
- Date: 2005
- Subjects: Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3986 , http://hdl.handle.net/10962/d1004045 , Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Description: The need to intelligibly capture, manage and analyse the ever-increasing amount of publicly available genomic data is one of the challenges facing bioinformaticians today. Such analyses are in fact impractical using uniprocessor machines, which has led to an increasing reliance on clusters of commodity-priced computers. An existing network of cheap, commodity PCs was utilised as a single computational resource for parallel computing. The performance of the cluster was investigated using a whole genome-scanning program written in the Java programming language. The TSpaces framework, based on the Linda parallel programming model, was used to parallelise the application. Maximum speedup was achieved at between 30 and 50 processors, depending on the size of the genome being scanned. Together with this, the associated significant reductions in wall-clock time suggest that both parallel computing and Java have a significant role to play in the field of bioinformatics.
- Full Text:
- Date Issued: 2005
- Authors: Akhurst, Timothy John
- Date: 2005
- Subjects: Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3986 , http://hdl.handle.net/10962/d1004045 , Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Description: The need to intelligibly capture, manage and analyse the ever-increasing amount of publicly available genomic data is one of the challenges facing bioinformaticians today. Such analyses are in fact impractical using uniprocessor machines, which has led to an increasing reliance on clusters of commodity-priced computers. An existing network of cheap, commodity PCs was utilised as a single computational resource for parallel computing. The performance of the cluster was investigated using a whole genome-scanning program written in the Java programming language. The TSpaces framework, based on the Linda parallel programming model, was used to parallelise the application. Maximum speedup was achieved at between 30 and 50 processors, depending on the size of the genome being scanned. Together with this, the associated significant reductions in wall-clock time suggest that both parallel computing and Java have a significant role to play in the field of bioinformatics.
- Full Text:
- Date Issued: 2005
Marine biotechnology : evaluation and development of methods for the discovery of natural products from fungi
- Authors: Pather, Simisha
- Date: 2005 , 2013-06-18
- Subjects: Marine biotechnology , Marine fungi -- South Africa , Natural products -- South Africa , Marine plants -- South Africa , Marine metabolites -- South Africa , Cancer -- Treatment , DNA
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3839 , http://hdl.handle.net/10962/d1007652 , Marine biotechnology , Marine fungi -- South Africa , Natural products -- South Africa , Marine plants -- South Africa , Marine metabolites -- South Africa , Cancer -- Treatment , DNA
- Description: One of the major impediments in the development of marine natural products is the provision of biologically active natural products in sufficient quantity for complete pharmacological evaluation, clinical trials and eventual commercial production. Marine microorganisms show great promise in providing a renewable source of biologically active natural products. The main aim of this study was to develop and evaluate methods for the isolation, identification and cultivation of marine fungi from the South African marine environment for the production of biologically active secondary metabolites. Twenty-four species of fungi were isolated from marine algae collected from the intertidal zone near Port Alfred, South Africa. The fungi were cultivated in small-scale under static and agitated conditions and their crude intra- and extracellular organic extracts were screened by ¹H NMR and a series of bioassays. Using this as a basis, one isolate was selected for further study. By analyses of the lTS1 region of the ribosomal DNA, the fungal isolate was identified as a marine-derived isolate of Eurotium rubrum (Aspergillus ruber). Although E. rubrum has been isolated from the marine environment, no investigations have been undertaken to determine the adaptation of these isolates to the marine environment. In order to optimise productivity, creativity and incubation time, the fungus was cultivated in small-scale using a variety of carbon (glucose, fructose, lactose, sucrose, marmitol and maltose) and nitrogen sources (ammonium tartrate, urea, peptone and yeast extract). An HPLC-DAD method was developed to assess the metabolic creativity and productivity under different fermentation conditions. Distinctive variations in the range and yield of metabolites produced as well as morphology and growth time were observed. The crude extracts from all fermentations were combined and six known compounds were isolated by reversed-phase chromatography and their structures elucidated by spectroscopic techniques. The known compounds were fIavoglaucin, aspergin, isodihydroauroglaucin, isotetrahydroauroglaucin, neoechinuline A and physcion. Neoechinuline A, isodihydroauroglaucin and isotetrahydroauroglaucin showed activity against oesophageal and cervical cancer cell lines.
- Full Text:
- Date Issued: 2005
- Authors: Pather, Simisha
- Date: 2005 , 2013-06-18
- Subjects: Marine biotechnology , Marine fungi -- South Africa , Natural products -- South Africa , Marine plants -- South Africa , Marine metabolites -- South Africa , Cancer -- Treatment , DNA
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3839 , http://hdl.handle.net/10962/d1007652 , Marine biotechnology , Marine fungi -- South Africa , Natural products -- South Africa , Marine plants -- South Africa , Marine metabolites -- South Africa , Cancer -- Treatment , DNA
- Description: One of the major impediments in the development of marine natural products is the provision of biologically active natural products in sufficient quantity for complete pharmacological evaluation, clinical trials and eventual commercial production. Marine microorganisms show great promise in providing a renewable source of biologically active natural products. The main aim of this study was to develop and evaluate methods for the isolation, identification and cultivation of marine fungi from the South African marine environment for the production of biologically active secondary metabolites. Twenty-four species of fungi were isolated from marine algae collected from the intertidal zone near Port Alfred, South Africa. The fungi were cultivated in small-scale under static and agitated conditions and their crude intra- and extracellular organic extracts were screened by ¹H NMR and a series of bioassays. Using this as a basis, one isolate was selected for further study. By analyses of the lTS1 region of the ribosomal DNA, the fungal isolate was identified as a marine-derived isolate of Eurotium rubrum (Aspergillus ruber). Although E. rubrum has been isolated from the marine environment, no investigations have been undertaken to determine the adaptation of these isolates to the marine environment. In order to optimise productivity, creativity and incubation time, the fungus was cultivated in small-scale using a variety of carbon (glucose, fructose, lactose, sucrose, marmitol and maltose) and nitrogen sources (ammonium tartrate, urea, peptone and yeast extract). An HPLC-DAD method was developed to assess the metabolic creativity and productivity under different fermentation conditions. Distinctive variations in the range and yield of metabolites produced as well as morphology and growth time were observed. The crude extracts from all fermentations were combined and six known compounds were isolated by reversed-phase chromatography and their structures elucidated by spectroscopic techniques. The known compounds were fIavoglaucin, aspergin, isodihydroauroglaucin, isotetrahydroauroglaucin, neoechinuline A and physcion. Neoechinuline A, isodihydroauroglaucin and isotetrahydroauroglaucin showed activity against oesophageal and cervical cancer cell lines.
- Full Text:
- Date Issued: 2005
An investigation of hair modelling and rendering techniques with emphasis on African hairstyles
- Authors: Patrick, Deborah Michelle
- Date: 2005 , 2013-10-17
- Subjects: RenderMan , Hairstyles -- Africa , Hairstyles -- Computer simulation -- Africa , Hairdressing of Black people , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4639 , http://hdl.handle.net/10962/d1006561 , RenderMan , Hairstyles -- Africa , Hairstyles -- Computer simulation -- Africa , Hairdressing of Black people , Computer graphics
- Description: Many computer graphics applications make use of virtual humans. Methods for modelling and rendering hair are needed so that hairstyles can be added to the virtual humans. Modelling and rendering hair is challenging due to the large number of hair strands and their geometric properties, the complex lighting effects that occur among the strands of hair, and the complexity and large variation of human hairstyles. While methods have been developed for generating hair, no methods exist for generating African hair, which differs from hair of other ethnic groups. This thesis presents methods for modelling and rendering African hair. Existing hair modelling and rendering techniques are investigated, and the knowledge gained from the investigation is used to develop or enhance hair modelling and rendering techniques to produce three different forms of hair commonly found in African hairstyles. The different forms of hair identified are natural curly hair, straightened hair, and braids or twists of hair. The hair modelling techniques developed are implemented as plug-ins for the graphics program LightWave 3D. The plug-ins developed not only model the three identified forms of hair, but also add the modelled hair to a model of a head, and can be used to create a variety of African hairstyles. The plug-ins significantly reduce the time spent on hair modelling. Tests performed show that increasing the number of polygons used to model hair increases the quality of the hair produced, but also increases the rendering time. However, there is usually an upper bound to the number of polygons needed to produce a reasonable hairstyle, making it feasible to add African hairstyles to virtual humans. The rendering aspects investigated include hair illumination, texturing, shadowing and antialiasing. An anisotropic illumination model is developed that considers the properties of African hair, including the colouring, opacity and narrow width of the hair strands. Texturing is used in several instances to create the effect of individual strands of hair. Results show that texturing is useful for representing many hair strands because the density of the hair in a texture map does not have an effect on the rendering time. The importance of including a shadowing technique and applying an anti-aliasing method when rendering hair is demonstrated. The rendering techniques are implemented using the RenderMan Interface and Shading Language. A number of complete African hairstyles are shown, demonstrating that the techniques can be used to model and render African hair successfully. , GNU Ghostscript 7.07
- Full Text:
- Date Issued: 2005
- Authors: Patrick, Deborah Michelle
- Date: 2005 , 2013-10-17
- Subjects: RenderMan , Hairstyles -- Africa , Hairstyles -- Computer simulation -- Africa , Hairdressing of Black people , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4639 , http://hdl.handle.net/10962/d1006561 , RenderMan , Hairstyles -- Africa , Hairstyles -- Computer simulation -- Africa , Hairdressing of Black people , Computer graphics
- Description: Many computer graphics applications make use of virtual humans. Methods for modelling and rendering hair are needed so that hairstyles can be added to the virtual humans. Modelling and rendering hair is challenging due to the large number of hair strands and their geometric properties, the complex lighting effects that occur among the strands of hair, and the complexity and large variation of human hairstyles. While methods have been developed for generating hair, no methods exist for generating African hair, which differs from hair of other ethnic groups. This thesis presents methods for modelling and rendering African hair. Existing hair modelling and rendering techniques are investigated, and the knowledge gained from the investigation is used to develop or enhance hair modelling and rendering techniques to produce three different forms of hair commonly found in African hairstyles. The different forms of hair identified are natural curly hair, straightened hair, and braids or twists of hair. The hair modelling techniques developed are implemented as plug-ins for the graphics program LightWave 3D. The plug-ins developed not only model the three identified forms of hair, but also add the modelled hair to a model of a head, and can be used to create a variety of African hairstyles. The plug-ins significantly reduce the time spent on hair modelling. Tests performed show that increasing the number of polygons used to model hair increases the quality of the hair produced, but also increases the rendering time. However, there is usually an upper bound to the number of polygons needed to produce a reasonable hairstyle, making it feasible to add African hairstyles to virtual humans. The rendering aspects investigated include hair illumination, texturing, shadowing and antialiasing. An anisotropic illumination model is developed that considers the properties of African hair, including the colouring, opacity and narrow width of the hair strands. Texturing is used in several instances to create the effect of individual strands of hair. Results show that texturing is useful for representing many hair strands because the density of the hair in a texture map does not have an effect on the rendering time. The importance of including a shadowing technique and applying an anti-aliasing method when rendering hair is demonstrated. The rendering techniques are implemented using the RenderMan Interface and Shading Language. A number of complete African hairstyles are shown, demonstrating that the techniques can be used to model and render African hair successfully. , GNU Ghostscript 7.07
- Full Text:
- Date Issued: 2005
Enzymatic recovery of rhodium(III) from aqueous solution and industrial effluent using sulphate reducing bacteria: role of a hydrogenase enzyme
- Authors: Ngwenya, Nonhlanhla
- Date: 2005
- Subjects: Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3956 , http://hdl.handle.net/10962/d1004015 , Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Description: In an attempt to overcome the high maintenance and costs associated with traditional physico-chemical methods, much work is being done on the application of enzymes for the recovery of valuable metals from solutions and industrial effluents. One of the most widely studied enzymatic metal recovery systems uses hydrogenase enzymes, particularly from sulphate reducing bacteria (SRB). While it is known that hydrogenases from SRB mediate the reductive precipitation of metals, the mechanism of enzymatic reduction, however, is not yet fully understood. The main aim of the present study was to investigate the role of a hydrogenase enzyme in the removal of rhodium from both aqueous solution and industrial effluent. A quantitative analysis of the rate of removal of rhodium(III) by a resting SRB consortium under different initial rhodium and biomass concentrations, pH, temperature, presence and absence of SRB cells and electron donor, was studied. Rhodium speciation was found to be the main factor controlling the rate of removal of rhodium from solution. SRB cells were found to have a higher affinity for anionic rhodium species, as compared to both cationic and neutral species, which become abundant when speciation equilibrium was reached. Consequently, a pH-dependant rate of rhodium removal from solution was observed. The maximum SRB uptake capacity for rhodium was found to be 66 mg rhodium per g of resting SRB biomass. Electron microscopy studies revealed a time-dependant localization and distribution of rhodium precipitates, initially intracellularly and then extracellularly, suggesting the involvement of an enzymatic reductive precipitation process. A hydrogenase enzyme capable of reducing rhodium(III) from solution was isolated and purified by PEG, DEAE-Sephacel anion exchanger and Sephadex G200 gel exclusion. A distinct protein band with a molecular weight of 62kDa was obtained when the hydrogenase containing fractions were subjected to a 10% SDS-PAGE. Characterization studies indicated that the purified hydrogenase had an optimum pH and temperature of 8 and 40°C, respectively. A maximum of 88% of the initial rhodium in solution was removed when the purified hydrogenase was incubated under hydrogen. Due to the low pH of the industrial effluent (1.31), the enzymatic reduction of rhodium by the purified hydrogenase was greatly retarded. It was apparent that industrial effluent pretreatment was necessary before the application an enzymatic treatment method. In the present study, however, it has been established that SRB are good candidates for the enzymatic recovery of rhodium from both solution and effluent.
- Full Text:
- Date Issued: 2005
- Authors: Ngwenya, Nonhlanhla
- Date: 2005
- Subjects: Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3956 , http://hdl.handle.net/10962/d1004015 , Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Description: In an attempt to overcome the high maintenance and costs associated with traditional physico-chemical methods, much work is being done on the application of enzymes for the recovery of valuable metals from solutions and industrial effluents. One of the most widely studied enzymatic metal recovery systems uses hydrogenase enzymes, particularly from sulphate reducing bacteria (SRB). While it is known that hydrogenases from SRB mediate the reductive precipitation of metals, the mechanism of enzymatic reduction, however, is not yet fully understood. The main aim of the present study was to investigate the role of a hydrogenase enzyme in the removal of rhodium from both aqueous solution and industrial effluent. A quantitative analysis of the rate of removal of rhodium(III) by a resting SRB consortium under different initial rhodium and biomass concentrations, pH, temperature, presence and absence of SRB cells and electron donor, was studied. Rhodium speciation was found to be the main factor controlling the rate of removal of rhodium from solution. SRB cells were found to have a higher affinity for anionic rhodium species, as compared to both cationic and neutral species, which become abundant when speciation equilibrium was reached. Consequently, a pH-dependant rate of rhodium removal from solution was observed. The maximum SRB uptake capacity for rhodium was found to be 66 mg rhodium per g of resting SRB biomass. Electron microscopy studies revealed a time-dependant localization and distribution of rhodium precipitates, initially intracellularly and then extracellularly, suggesting the involvement of an enzymatic reductive precipitation process. A hydrogenase enzyme capable of reducing rhodium(III) from solution was isolated and purified by PEG, DEAE-Sephacel anion exchanger and Sephadex G200 gel exclusion. A distinct protein band with a molecular weight of 62kDa was obtained when the hydrogenase containing fractions were subjected to a 10% SDS-PAGE. Characterization studies indicated that the purified hydrogenase had an optimum pH and temperature of 8 and 40°C, respectively. A maximum of 88% of the initial rhodium in solution was removed when the purified hydrogenase was incubated under hydrogen. Due to the low pH of the industrial effluent (1.31), the enzymatic reduction of rhodium by the purified hydrogenase was greatly retarded. It was apparent that industrial effluent pretreatment was necessary before the application an enzymatic treatment method. In the present study, however, it has been established that SRB are good candidates for the enzymatic recovery of rhodium from both solution and effluent.
- Full Text:
- Date Issued: 2005
In vitro release of ketoprofen from proprietary and extemporaneously manufactured gels
- Tettey-Amlalo, Ralph Nii Okai
- Authors: Tettey-Amlalo, Ralph Nii Okai
- Date: 2005
- Subjects: Transdermal medication , Drug delivery systems , High performance liquid chromatography , Nonsteroidal anti-inflammatory agents , Rheumatoid arthritis -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3797 , http://hdl.handle.net/10962/d1003275 , Transdermal medication , Drug delivery systems , High performance liquid chromatography , Nonsteroidal anti-inflammatory agents , Rheumatoid arthritis -- Treatment
- Description: Ketoprofen is a potent non-steroidal anti-inflammatory drug which is used for the treatment of rheumatoid arthritis. The oral administration of ketoprofen can cause gastric irritation and adverse renal effects. Transdermal delivery of the drug can bypass gastrointestinal disturbances and provide relatively consistent drug concentrations at the site of administration. The release of ketoprofen from proprietary gel products from three different countries was evaluated by comparing the in vitro release profiles. Twenty extemporaneously prepared ketoprofen gel formulations using Carbopol® polymers were manufactured. The effect of polymer, drug concentration, pH and solvent systems on the in vitro release of ketoprofen from these formulations were investigated. The gels were evaluated for drug content and pH. The release of the drug from all the formulations obeyed the Higuchi principle. Two static FDA approved diffusion cells, namely the modified Franz diffusion cell and the European Pharmacopoeia diffusion cell, were compared by measuring the in vitro release rate of ketoprofen from all the gel formulations through a synthetic silicone membrane. High-performance liquid chromatography and ultraviolet spectrophotometric analytical techniques were both used for the analysis of ketoprofen. The validated methods were employed for the determination of ketoprofen in the sample solutions taken from the receptor fluid. Two of the three proprietary products registered under the same manufacturing license exhibited similar results whereas the third product differed significantly. Among the variables investigated, the vehicle pH and solvent composition were found have the most significant effect on the in vitro release of ketoprofen from Carbopol® polymers. The different grades of Carbopol® polymers showed statistically significantly different release kinetics with respect to lag time. When evaluating the proprietary products, both the modified Franz diffusion cell and the European Pharmacopoeia diffusion cell were deemed adequate although higher profiles were generally obtained from the European Pharmacopoeia diffusion cells. Smoother diffusion profiles were obtained from samples analysed by high-performance liquid chromatography than by ultraviolet spectrophotometry in both diffusion cells. Sample solutions taken from Franz diffusion cells and analysed by ultraviolet spectrophotometry also produced smooth diffusion profiles. Erratic and higher diffusion profiles were observed with samples taken from the European Pharmacopoeia diffusion cell and analysed by ultraviolet spectrophotometry. The choice of diffusion cells and analytical procedure in product development must be weighed against the relatively poor reproducibility as observed with the European Pharmacopoeia diffusion cell.
- Full Text:
- Date Issued: 2005
- Authors: Tettey-Amlalo, Ralph Nii Okai
- Date: 2005
- Subjects: Transdermal medication , Drug delivery systems , High performance liquid chromatography , Nonsteroidal anti-inflammatory agents , Rheumatoid arthritis -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3797 , http://hdl.handle.net/10962/d1003275 , Transdermal medication , Drug delivery systems , High performance liquid chromatography , Nonsteroidal anti-inflammatory agents , Rheumatoid arthritis -- Treatment
- Description: Ketoprofen is a potent non-steroidal anti-inflammatory drug which is used for the treatment of rheumatoid arthritis. The oral administration of ketoprofen can cause gastric irritation and adverse renal effects. Transdermal delivery of the drug can bypass gastrointestinal disturbances and provide relatively consistent drug concentrations at the site of administration. The release of ketoprofen from proprietary gel products from three different countries was evaluated by comparing the in vitro release profiles. Twenty extemporaneously prepared ketoprofen gel formulations using Carbopol® polymers were manufactured. The effect of polymer, drug concentration, pH and solvent systems on the in vitro release of ketoprofen from these formulations were investigated. The gels were evaluated for drug content and pH. The release of the drug from all the formulations obeyed the Higuchi principle. Two static FDA approved diffusion cells, namely the modified Franz diffusion cell and the European Pharmacopoeia diffusion cell, were compared by measuring the in vitro release rate of ketoprofen from all the gel formulations through a synthetic silicone membrane. High-performance liquid chromatography and ultraviolet spectrophotometric analytical techniques were both used for the analysis of ketoprofen. The validated methods were employed for the determination of ketoprofen in the sample solutions taken from the receptor fluid. Two of the three proprietary products registered under the same manufacturing license exhibited similar results whereas the third product differed significantly. Among the variables investigated, the vehicle pH and solvent composition were found have the most significant effect on the in vitro release of ketoprofen from Carbopol® polymers. The different grades of Carbopol® polymers showed statistically significantly different release kinetics with respect to lag time. When evaluating the proprietary products, both the modified Franz diffusion cell and the European Pharmacopoeia diffusion cell were deemed adequate although higher profiles were generally obtained from the European Pharmacopoeia diffusion cells. Smoother diffusion profiles were obtained from samples analysed by high-performance liquid chromatography than by ultraviolet spectrophotometry in both diffusion cells. Sample solutions taken from Franz diffusion cells and analysed by ultraviolet spectrophotometry also produced smooth diffusion profiles. Erratic and higher diffusion profiles were observed with samples taken from the European Pharmacopoeia diffusion cell and analysed by ultraviolet spectrophotometry. The choice of diffusion cells and analytical procedure in product development must be weighed against the relatively poor reproducibility as observed with the European Pharmacopoeia diffusion cell.
- Full Text:
- Date Issued: 2005
Tertiary treatment in integrated algal ponding systems
- Authors: Wells, Charles Digby
- Date: 2005
- Subjects: Sewage -- Purification -- Anaerobic treatment , Water -- Purification -- Biological treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4068 , http://hdl.handle.net/10962/d1006162 , Sewage -- Purification -- Anaerobic treatment , Water -- Purification -- Biological treatment
- Description: Inadequate sanitation is one of the leading causes of water pollution and consequently illness in many underdeveloped countries, including South Africa and, specifically, the Eastern Cape Province, where cholera has become endemic. As modern wastewater treatment processes are often energy intensive and expensive, they are not suitable for use in these areas. There is thus a need to develop more sustainable wastewater treatment technologies for application in smaller communities. The integrated algal ponding system (IAPS) was identified as a possible solution to this wastewater management problem and was investigated for adaptation to local conditions, at the Rhodes University Environmental Experimental Field Station in Grahamstown, South Africa. The system was monitored over a period of nine years, with various configuration adjustments of the high rate algal pond (HRAP) unit operation investigated. Under standard operating conditions, the system was able to achieve levels of nutrient and organic removal comparable with conventional wastewater treatment works. The mean nitrate level achieved in the effluent was below the 15mg.l-1 South African discharge standard, however, nitrate removal in the IAPS was found to be inconsistent. Although the system was unable to sustain chemical oxygen demand (COD) removal to below the 75mg.l-1 South African discharge standard, a removal rate of 87% was recorded, with the residual COD remaining in the form of algal biomass. Previous studies in the Eastern Cape Province have shown that few small wastewater treatment works produce effluent that meets the microbial count specification. Therefore, in addition to the collation of IAPS data from the entire nine year monitoring period, this study also investigated the use of the HRAP as an independent unit operation for disinfection of effluent from small sewage plants. It was demonstrated that the independent high rate algal pond (IHRAP) as a free standing unit operation could consistently produce water with Escherichia coli counts of 0cfu.100ml-1. The observed effect was related to a number of possible conditions prevailing in the system, including elevated pH, sunlight and dissolved oxygen. It was also found that the IHRAP greatly enhanced the nutrient removal capabilities of the conventional IAPS, making it possible to reliably and consistently maintain phosphate and ammonium levels in the final effluent to below 5mg.l-1 and 2mg.l-1 respectively (South African discharge standards are 10mg.l-1 and 3mg.l-1 in each case). The quality of the final effluent produced by the optimisation of the IAPS would allow it to be used for irrigation, thereby providing an alternative water source in water stressed areas. The system also proved to be exceptionally robust and data collected during periods of intensive and low management regimes were broadly comparable. Results of the 9 year study have demonstrated reliable performance of the IAPS and its use an appropriate, sustainable wastewater treatment option for small communities.
- Full Text:
- Date Issued: 2005
- Authors: Wells, Charles Digby
- Date: 2005
- Subjects: Sewage -- Purification -- Anaerobic treatment , Water -- Purification -- Biological treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4068 , http://hdl.handle.net/10962/d1006162 , Sewage -- Purification -- Anaerobic treatment , Water -- Purification -- Biological treatment
- Description: Inadequate sanitation is one of the leading causes of water pollution and consequently illness in many underdeveloped countries, including South Africa and, specifically, the Eastern Cape Province, where cholera has become endemic. As modern wastewater treatment processes are often energy intensive and expensive, they are not suitable for use in these areas. There is thus a need to develop more sustainable wastewater treatment technologies for application in smaller communities. The integrated algal ponding system (IAPS) was identified as a possible solution to this wastewater management problem and was investigated for adaptation to local conditions, at the Rhodes University Environmental Experimental Field Station in Grahamstown, South Africa. The system was monitored over a period of nine years, with various configuration adjustments of the high rate algal pond (HRAP) unit operation investigated. Under standard operating conditions, the system was able to achieve levels of nutrient and organic removal comparable with conventional wastewater treatment works. The mean nitrate level achieved in the effluent was below the 15mg.l-1 South African discharge standard, however, nitrate removal in the IAPS was found to be inconsistent. Although the system was unable to sustain chemical oxygen demand (COD) removal to below the 75mg.l-1 South African discharge standard, a removal rate of 87% was recorded, with the residual COD remaining in the form of algal biomass. Previous studies in the Eastern Cape Province have shown that few small wastewater treatment works produce effluent that meets the microbial count specification. Therefore, in addition to the collation of IAPS data from the entire nine year monitoring period, this study also investigated the use of the HRAP as an independent unit operation for disinfection of effluent from small sewage plants. It was demonstrated that the independent high rate algal pond (IHRAP) as a free standing unit operation could consistently produce water with Escherichia coli counts of 0cfu.100ml-1. The observed effect was related to a number of possible conditions prevailing in the system, including elevated pH, sunlight and dissolved oxygen. It was also found that the IHRAP greatly enhanced the nutrient removal capabilities of the conventional IAPS, making it possible to reliably and consistently maintain phosphate and ammonium levels in the final effluent to below 5mg.l-1 and 2mg.l-1 respectively (South African discharge standards are 10mg.l-1 and 3mg.l-1 in each case). The quality of the final effluent produced by the optimisation of the IAPS would allow it to be used for irrigation, thereby providing an alternative water source in water stressed areas. The system also proved to be exceptionally robust and data collected during periods of intensive and low management regimes were broadly comparable. Results of the 9 year study have demonstrated reliable performance of the IAPS and its use an appropriate, sustainable wastewater treatment option for small communities.
- Full Text:
- Date Issued: 2005
An investigation into improved ionospheric F1 layer predictions over Grahamstown, South Africa
- Authors: Jacobs, Linda
- Date: 2005
- Subjects: Ionosphere , Ionospheric electron density -- South Africa -- Grahamstown , Neural networks (Computer Science)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5511 , http://hdl.handle.net/10962/d1008094 , Ionosphere , Ionospheric electron density -- South Africa -- Grahamstown , Neural networks (Computer Science)
- Description: This thesis describes an analysis of the F1 layer data obtained from the Grahamstown (33.32°S, 26.500 E), South Africa ionospheric station and the use of this data in improving a Neural Network (NN) based model of the F1 layer of the ionosphere. An application for real-time ray tracing through the South African ionosphere was identified, and for this application real-time evaluation of the electron density profile is essential. Raw real-time virtual height data are provided by a Lowell Digisonde (DPS), which employs the automatic scaling software, ARTIST whose output includes the virtual-toreal height data conversion. Experience has shown that there are times when the ray tracing performance is degraded because of difficulties surrounding the real-time characterization of the F1 region by ARTIST. Therefore available DPS data from the archives of the Grahamstown station were re-scaled manually in order to establish the extent of the problem and the times and conditions under which most inaccuracies occur. The re-scaled data were used to update the F1 contribution of an existing NN based ionospheric model, the LAM model, which predicts the values of the parameters required to produce an electron density profile. This thesis describes the development of three separate NNs required to predict the ionospheric characteristics and coefficients that are required to describe the F1 layer profile. Inputs to the NNs include day number, hour and measures of solar and magnetic activity. Outputs include the value of the critical frequency of the F1 layer, foF1, the real height of reflection at the peak, hmFl, as well as information on the state of the F1 layer. All data from the Grahamstown station from 1973 to 2003 was used to train these NNs. Tests show that the predictive ability of the LAM model has been improved by incorporating the re-scaled data.
- Full Text:
- Date Issued: 2005
- Authors: Jacobs, Linda
- Date: 2005
- Subjects: Ionosphere , Ionospheric electron density -- South Africa -- Grahamstown , Neural networks (Computer Science)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5511 , http://hdl.handle.net/10962/d1008094 , Ionosphere , Ionospheric electron density -- South Africa -- Grahamstown , Neural networks (Computer Science)
- Description: This thesis describes an analysis of the F1 layer data obtained from the Grahamstown (33.32°S, 26.500 E), South Africa ionospheric station and the use of this data in improving a Neural Network (NN) based model of the F1 layer of the ionosphere. An application for real-time ray tracing through the South African ionosphere was identified, and for this application real-time evaluation of the electron density profile is essential. Raw real-time virtual height data are provided by a Lowell Digisonde (DPS), which employs the automatic scaling software, ARTIST whose output includes the virtual-toreal height data conversion. Experience has shown that there are times when the ray tracing performance is degraded because of difficulties surrounding the real-time characterization of the F1 region by ARTIST. Therefore available DPS data from the archives of the Grahamstown station were re-scaled manually in order to establish the extent of the problem and the times and conditions under which most inaccuracies occur. The re-scaled data were used to update the F1 contribution of an existing NN based ionospheric model, the LAM model, which predicts the values of the parameters required to produce an electron density profile. This thesis describes the development of three separate NNs required to predict the ionospheric characteristics and coefficients that are required to describe the F1 layer profile. Inputs to the NNs include day number, hour and measures of solar and magnetic activity. Outputs include the value of the critical frequency of the F1 layer, foF1, the real height of reflection at the peak, hmFl, as well as information on the state of the F1 layer. All data from the Grahamstown station from 1973 to 2003 was used to train these NNs. Tests show that the predictive ability of the LAM model has been improved by incorporating the re-scaled data.
- Full Text:
- Date Issued: 2005
Population dynamics of selected ichthyofaunal components in the temperate, temporarily open/closed Kasouga Estuary, South Africa
- Authors: Tweddle, Gavin Paul
- Date: 2005
- Subjects: Estuaries -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape , Estuarine ecology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5742 , http://hdl.handle.net/10962/d1005428 , Estuaries -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape , Estuarine ecology -- South Africa -- Eastern Cape
- Description: The spatial and temporal pattern of ichthyofaunal community composition in relation to selected physico-chemical (temperature and salinity) and biological variables (chlorophyll-a and zooplankton) was investigated at ten stations in the temperate temporarily open/closed Kasouga estuary. In addition, the food web structure in the estuary was investigated using stable carbon isotope analysis. Results of the 5 metre seine net survey indicated that ichthyofaunal composition and biomass in the Kasouga estuary was largely determined by seasonality and mouth condition. Maximum abundance and biomass of ichthyofauna was recorded during summer or during those periods when overtopping occurred. Overtopping coincided with the recruitment of marine estuarine dependant species, which dominated the catches both numerically and in biomass. The recruitment of these species resulted in an increase in diversity of the ichthyofaunal community. There were no significant spatial patterns in the distribution of smaller ichthyofauna (<50mm SL) identified in Bray-Curtis similarity matrices using cluster analysis (Primer 5 v5.2.4). Spearman’s correlation analysis revealed that there were no significant correlations between abundance and biomass of ichthyofauna and selected physico-chemical and biological variables other than salinity (P>0.05 in all other cases). There were two distinct spatial patterns in the distribution of the larger ichthyofauna (>50mm SL). These corresponded to a grouping associated with the mouth region and a grouping associated with the remaining regions of the estuary. Stable isotope analysis indicated that the primary source of carbon utilised by the ichthyofauna of the Kasouga estuary was derived from the channel, most likely microphytobenthic algae. The contributions of the riparian and salt marsh vegetation to the total carbon flow appear to be minimal.
- Full Text:
- Date Issued: 2005
- Authors: Tweddle, Gavin Paul
- Date: 2005
- Subjects: Estuaries -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape , Estuarine ecology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5742 , http://hdl.handle.net/10962/d1005428 , Estuaries -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape , Estuarine ecology -- South Africa -- Eastern Cape
- Description: The spatial and temporal pattern of ichthyofaunal community composition in relation to selected physico-chemical (temperature and salinity) and biological variables (chlorophyll-a and zooplankton) was investigated at ten stations in the temperate temporarily open/closed Kasouga estuary. In addition, the food web structure in the estuary was investigated using stable carbon isotope analysis. Results of the 5 metre seine net survey indicated that ichthyofaunal composition and biomass in the Kasouga estuary was largely determined by seasonality and mouth condition. Maximum abundance and biomass of ichthyofauna was recorded during summer or during those periods when overtopping occurred. Overtopping coincided with the recruitment of marine estuarine dependant species, which dominated the catches both numerically and in biomass. The recruitment of these species resulted in an increase in diversity of the ichthyofaunal community. There were no significant spatial patterns in the distribution of smaller ichthyofauna (<50mm SL) identified in Bray-Curtis similarity matrices using cluster analysis (Primer 5 v5.2.4). Spearman’s correlation analysis revealed that there were no significant correlations between abundance and biomass of ichthyofauna and selected physico-chemical and biological variables other than salinity (P>0.05 in all other cases). There were two distinct spatial patterns in the distribution of the larger ichthyofauna (>50mm SL). These corresponded to a grouping associated with the mouth region and a grouping associated with the remaining regions of the estuary. Stable isotope analysis indicated that the primary source of carbon utilised by the ichthyofauna of the Kasouga estuary was derived from the channel, most likely microphytobenthic algae. The contributions of the riparian and salt marsh vegetation to the total carbon flow appear to be minimal.
- Full Text:
- Date Issued: 2005
Synthesis, photochemical and photophysical properties of phthalocyanine derivatives
- Authors: Maqanda, Weziwe Theorine
- Date: 2005 , 2013-06-18
- Subjects: Photochemotherapy , Phthalocyanines , Zinc , Magnesium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4436 , http://hdl.handle.net/10962/d1007472 , Photochemotherapy , Phthalocyanines , Zinc , Magnesium
- Description: Substituted zinc and magnesium phthalocyanine and porphyrazine derivatives were synthesized according to the reported procedures. The magnesium and zinc phthalocyanine and porphyrazine derivatives were synthesized by ring enlargement of subphthalocyanine and statistical condensation of the two phthalonitrile derivatives. Characterization of the complexes involved the use of infrared spectroscopy, nuclear magnetic resonance spectroscopy, ultraviolet and visible spectroscopy, and Maldi-TOF spectroscopy (for selected compounds) and elemental analysis. Photochemical and photophysical properties of the complexes in non-aqueous solution was then investigated. Photobleaching quantum yields are in order of 10⁻⁵ indicating their relative photostability. Complexes containing more electron-donating substituents were more easily oxidized. For complexes 66 and 69 (as these complexes have the same number of substituents but differ in the metal center) photobleaching quantum yield for the ZincPc complex 69 was slightly less than that of the MgPc complex 66. Singlet oxygen quantum yields of the various complexes in DMSO using diphenylisobenzofuran (DPBF) as a quencher in organic solvents were determined. Singlet oxygen quantum yields of the complexes range from 0.23 to 0.67. High values of Φ[subscript]Δ ZnPc complexes was observed compared to the corresponding MgPc, complexes. This was evidenced by complexes 66 and 69 with Φ[subscript]Δ values of Φ[subscript]Δ = 0.26 and 0.40, respectively. Varying number of phenoxy substituents, complex 71 gave significantly large value of Φ[subscript]Δ compared to 70 (that is, the presence of more electron-donating substituted group, gave higher singlet oxygen quantum yields (0 .67 and 0.25 for 71 and 70 repectively). The triplet quantum yields and triplet lifetimes were determined by laser flash photolysis for selected compounds. The triplet quantum yields increase as the number of substituents increases e.g 68 > 67 > 66. Comparing porphyrazine complexes (63, 64 and 65), 63 with benzene attached to the ring, has higher triplet state lifetime (420 μs) compared to 64 and 65 containing long alkyl chain and tertbutyl substituents, 350 and 360 μs,respectively). The observed Φ[subscript]f values for 68 and 63 were quiet suprising, since low values are observed compared to the rest of the complexes (e.g 0.03 and 0.02 respectively). Although these values seem so low, they are sufficient for fluorescence imaging applications. The Φ[subscript]f values for the complexes under study are within the range reported for complexes currently used for PDT. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2005
- Authors: Maqanda, Weziwe Theorine
- Date: 2005 , 2013-06-18
- Subjects: Photochemotherapy , Phthalocyanines , Zinc , Magnesium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4436 , http://hdl.handle.net/10962/d1007472 , Photochemotherapy , Phthalocyanines , Zinc , Magnesium
- Description: Substituted zinc and magnesium phthalocyanine and porphyrazine derivatives were synthesized according to the reported procedures. The magnesium and zinc phthalocyanine and porphyrazine derivatives were synthesized by ring enlargement of subphthalocyanine and statistical condensation of the two phthalonitrile derivatives. Characterization of the complexes involved the use of infrared spectroscopy, nuclear magnetic resonance spectroscopy, ultraviolet and visible spectroscopy, and Maldi-TOF spectroscopy (for selected compounds) and elemental analysis. Photochemical and photophysical properties of the complexes in non-aqueous solution was then investigated. Photobleaching quantum yields are in order of 10⁻⁵ indicating their relative photostability. Complexes containing more electron-donating substituents were more easily oxidized. For complexes 66 and 69 (as these complexes have the same number of substituents but differ in the metal center) photobleaching quantum yield for the ZincPc complex 69 was slightly less than that of the MgPc complex 66. Singlet oxygen quantum yields of the various complexes in DMSO using diphenylisobenzofuran (DPBF) as a quencher in organic solvents were determined. Singlet oxygen quantum yields of the complexes range from 0.23 to 0.67. High values of Φ[subscript]Δ ZnPc complexes was observed compared to the corresponding MgPc, complexes. This was evidenced by complexes 66 and 69 with Φ[subscript]Δ values of Φ[subscript]Δ = 0.26 and 0.40, respectively. Varying number of phenoxy substituents, complex 71 gave significantly large value of Φ[subscript]Δ compared to 70 (that is, the presence of more electron-donating substituted group, gave higher singlet oxygen quantum yields (0 .67 and 0.25 for 71 and 70 repectively). The triplet quantum yields and triplet lifetimes were determined by laser flash photolysis for selected compounds. The triplet quantum yields increase as the number of substituents increases e.g 68 > 67 > 66. Comparing porphyrazine complexes (63, 64 and 65), 63 with benzene attached to the ring, has higher triplet state lifetime (420 μs) compared to 64 and 65 containing long alkyl chain and tertbutyl substituents, 350 and 360 μs,respectively). The observed Φ[subscript]f values for 68 and 63 were quiet suprising, since low values are observed compared to the rest of the complexes (e.g 0.03 and 0.02 respectively). Although these values seem so low, they are sufficient for fluorescence imaging applications. The Φ[subscript]f values for the complexes under study are within the range reported for complexes currently used for PDT. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2005