An investigation into the replication biology of Helicoverpa armigera stunt virus
- Authors: Short, James Roswell
- Date: 2011
- Subjects: Helicoverpa armigera RNA viruses Viruses -- Reproduction Lepidoptera -- Viruses
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3967 , http://hdl.handle.net/10962/d1004026
- Description: Tetraviruses are a family of small non-enveloped positive sense RNA viruses that exclusively infect members of the order Lepidoptera. Their replication biology is poorly studied because, with the exception of Providence virus (PrV), tetraviruses are unable to replicate in tissue culture cells. The overall aim of the research described in this thesis was to develop a fundamental understanding of the replication of tetraviruses, focussing on the site of replication within host cells and in particular, the subcellular localisation of the viral replicase. Helicoverpa armigera stunt virus (HaSV, Genus: Omegatetravirus) was chosen for this study because it is the only tetravirus for which the cDNAs have been shown to be infectious. In the absence of tissue culture cell lines susceptible to HaSV infection, the approach was to use confocal fluorescence microscopy to examine the subcellular localisation of the HaSV replicase fused to enhanced green fluorescent protein (EGFP) in mammalian and insect tissue culture cells. The replicase (with EGFP fused at its C-terminus) localised to punctate structures throughout the cytoplasm of transfected HeLa and Sf9 cells. These structures were then shown – using live cell imaging and time lapse photography – to behave similarly to cellular endocytic organelles and fluorescence partially overlapped with membranes containing the late endosomal marker protein CD63. Biochemical fractionation of Sf9 cells expressing the replicase via a recombinant baculovirus (as well as transfected HeLa and Sf9 cells expressing EGFP-replicase fusion proteins) demonstrated that the replicase was strongly associated with detergentresistant membranes (DRMs) in these cells. Deletion analysis of the replicase coding sequence revealed two regions involved in the generation of the punctuate structures. Firstly, the C-terminal half of the replicase RNAdependant RNA polymerase domain was found to be essential for targeting and the tight association with DRMs while the second region, within the Nterminal 44 amino acids, enhanced localisation through a combination of secondary structural elements and sequence-specific functions. A comparative immunofluorescence study on PrV, which replicates as a persistent infection in an insect midgut cell line, showed that the PrV replicase also localised to punctate structures in the cytoplasm. Biochemical fractionation showed that the replicase was also strongly associated with DRMs. This thesis describes the development of new experimental systems for the study of tetravirus replication biology and the data lead to the conclusion that the HaSV replicase associates with DRMs derived from alternate endocytic pathway organelles.
- Full Text:
- Date Issued: 2011
- Authors: Short, James Roswell
- Date: 2011
- Subjects: Helicoverpa armigera RNA viruses Viruses -- Reproduction Lepidoptera -- Viruses
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3967 , http://hdl.handle.net/10962/d1004026
- Description: Tetraviruses are a family of small non-enveloped positive sense RNA viruses that exclusively infect members of the order Lepidoptera. Their replication biology is poorly studied because, with the exception of Providence virus (PrV), tetraviruses are unable to replicate in tissue culture cells. The overall aim of the research described in this thesis was to develop a fundamental understanding of the replication of tetraviruses, focussing on the site of replication within host cells and in particular, the subcellular localisation of the viral replicase. Helicoverpa armigera stunt virus (HaSV, Genus: Omegatetravirus) was chosen for this study because it is the only tetravirus for which the cDNAs have been shown to be infectious. In the absence of tissue culture cell lines susceptible to HaSV infection, the approach was to use confocal fluorescence microscopy to examine the subcellular localisation of the HaSV replicase fused to enhanced green fluorescent protein (EGFP) in mammalian and insect tissue culture cells. The replicase (with EGFP fused at its C-terminus) localised to punctate structures throughout the cytoplasm of transfected HeLa and Sf9 cells. These structures were then shown – using live cell imaging and time lapse photography – to behave similarly to cellular endocytic organelles and fluorescence partially overlapped with membranes containing the late endosomal marker protein CD63. Biochemical fractionation of Sf9 cells expressing the replicase via a recombinant baculovirus (as well as transfected HeLa and Sf9 cells expressing EGFP-replicase fusion proteins) demonstrated that the replicase was strongly associated with detergentresistant membranes (DRMs) in these cells. Deletion analysis of the replicase coding sequence revealed two regions involved in the generation of the punctuate structures. Firstly, the C-terminal half of the replicase RNAdependant RNA polymerase domain was found to be essential for targeting and the tight association with DRMs while the second region, within the Nterminal 44 amino acids, enhanced localisation through a combination of secondary structural elements and sequence-specific functions. A comparative immunofluorescence study on PrV, which replicates as a persistent infection in an insect midgut cell line, showed that the PrV replicase also localised to punctate structures in the cytoplasm. Biochemical fractionation showed that the replicase was also strongly associated with DRMs. This thesis describes the development of new experimental systems for the study of tetravirus replication biology and the data lead to the conclusion that the HaSV replicase associates with DRMs derived from alternate endocytic pathway organelles.
- Full Text:
- Date Issued: 2011
Application of catalysts and nanomaterials in the design of an electrochemical sensor for ochratoxin A
- Authors: Flanagan, Shane Patrick
- Date: 2011 , 2010-12-06
- Subjects: Ochratoxins , Filamentous fungi , Electrochemical sensors , Nanostructured materials , Catalysts , Food contamination
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4121 , http://hdl.handle.net/10962/d1013328
- Description: Ochratoxin A is the most potent chlorinated derivative of the ochratoxin group, consisting of a 5'-chlorinated dihydroisocoumarin moiety linked by an amide bond to l-phenylalanine. Produced as a secondary fungal metabolite by several species of Aspergillus and Penicillium, ochratoxin A has been shown to readily contaminate a large variety of commodities including cereals, groundnuts, dried fruit, spices and coffee. This has led to widespread contamination of ochratoxin in wine, beer, milk and meat products. As ochratoxin A is a potent nephrotoxin exhibiting teratogenic and carcinogenic properties, the development of a rapid screening platform for the cost effective control of ochratoxin A content in foodstuffs is therefore required. The evaluation of metallophthalocyanine and carbon nanotube electrode modification toward the development of a nanostructured biosensor capable of enhancing the electrochemical detection of ochratoxin A in complex media is presented. Cyclic voltammetry at a glassy carbon electrode allowed for the optimization of detection parameters including pH and type of supporting electrolyte. Britton-Robinson buffer was found to be the most suitable supporting electrolyte in terms of sensitivity and reproducibility obtaining a LOD of 0.28 μM as determined by differential pulse voltammetry. Subsequent analysis determined the dependence of OTA oxidation on pH in acidic media which proceeds with the transfer of two electrons to form a quinone/hydroquinone couple shown to adsorb to the electrode surface. Passivation of the electrode through adsorption of oxidation products was shown to severely limit the detection of OTA upon successive detection cycles. Comparison of various metallophthalocyanine modifiers showed an increase in sensitivity toward the detection of OTA at phthalocyanine complexes with metal based redox processes. However with the exception of NiPc and CoTCPc complexes, phthalocyanine modification was limited by the increase in deviation of current response and extent of fouling. NiPc modification showed an increase in sensitivity by two fold with fouling characteristics comparable to an unmodified electrode while low improvements in fouling was observed at CoTCPc modified electrodes with sensitivity in detection comparable to an unmodified electrode.Modification of the electrode with multi- and single walled carbon nanotubes produced a significant increase in sensitivity toward the detection of ochratoxin A. The electrocatalytic activity of nanotube modifiers was attributed to the increase in surface area and to the addition of oxygenated functional groups upon acid treatment as confirmed by Raman spectroscopy. Acid functionalization of the carbon nanotubes for a period of two hours produced the greatest increase in sensitivity obtaining a respective LOD of 0.09 μM and 0.03 μM for analysis of ochratoxin A at multi- and single walled carbon nanotube modified electrodes. Centrifugal purification of carbon nanotubes was deemed necessary to improve the electrocatalytic activity of the nanotube modifiers through the removal of carbonaceous impurities as visualized by atomic force microscopy. Furthermore, a crude lipase preparation, lipase A, was investigated as a potential biological recognition element for selective detection of ochratoxin A in complex media. Lipase A enabled the hydrolysis of ochratoxin A to the electroactive species ochratoxin α as confirmed by thin layer chromatography and voltammetric analysis. Additional isolation of a pure hydrolase from the lipase A preparation is required prior to utilization within a nanostructured biosensor platform capable of detecting ochratoxin A in complex media.
- Full Text:
- Date Issued: 2011
- Authors: Flanagan, Shane Patrick
- Date: 2011 , 2010-12-06
- Subjects: Ochratoxins , Filamentous fungi , Electrochemical sensors , Nanostructured materials , Catalysts , Food contamination
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4121 , http://hdl.handle.net/10962/d1013328
- Description: Ochratoxin A is the most potent chlorinated derivative of the ochratoxin group, consisting of a 5'-chlorinated dihydroisocoumarin moiety linked by an amide bond to l-phenylalanine. Produced as a secondary fungal metabolite by several species of Aspergillus and Penicillium, ochratoxin A has been shown to readily contaminate a large variety of commodities including cereals, groundnuts, dried fruit, spices and coffee. This has led to widespread contamination of ochratoxin in wine, beer, milk and meat products. As ochratoxin A is a potent nephrotoxin exhibiting teratogenic and carcinogenic properties, the development of a rapid screening platform for the cost effective control of ochratoxin A content in foodstuffs is therefore required. The evaluation of metallophthalocyanine and carbon nanotube electrode modification toward the development of a nanostructured biosensor capable of enhancing the electrochemical detection of ochratoxin A in complex media is presented. Cyclic voltammetry at a glassy carbon electrode allowed for the optimization of detection parameters including pH and type of supporting electrolyte. Britton-Robinson buffer was found to be the most suitable supporting electrolyte in terms of sensitivity and reproducibility obtaining a LOD of 0.28 μM as determined by differential pulse voltammetry. Subsequent analysis determined the dependence of OTA oxidation on pH in acidic media which proceeds with the transfer of two electrons to form a quinone/hydroquinone couple shown to adsorb to the electrode surface. Passivation of the electrode through adsorption of oxidation products was shown to severely limit the detection of OTA upon successive detection cycles. Comparison of various metallophthalocyanine modifiers showed an increase in sensitivity toward the detection of OTA at phthalocyanine complexes with metal based redox processes. However with the exception of NiPc and CoTCPc complexes, phthalocyanine modification was limited by the increase in deviation of current response and extent of fouling. NiPc modification showed an increase in sensitivity by two fold with fouling characteristics comparable to an unmodified electrode while low improvements in fouling was observed at CoTCPc modified electrodes with sensitivity in detection comparable to an unmodified electrode.Modification of the electrode with multi- and single walled carbon nanotubes produced a significant increase in sensitivity toward the detection of ochratoxin A. The electrocatalytic activity of nanotube modifiers was attributed to the increase in surface area and to the addition of oxygenated functional groups upon acid treatment as confirmed by Raman spectroscopy. Acid functionalization of the carbon nanotubes for a period of two hours produced the greatest increase in sensitivity obtaining a respective LOD of 0.09 μM and 0.03 μM for analysis of ochratoxin A at multi- and single walled carbon nanotube modified electrodes. Centrifugal purification of carbon nanotubes was deemed necessary to improve the electrocatalytic activity of the nanotube modifiers through the removal of carbonaceous impurities as visualized by atomic force microscopy. Furthermore, a crude lipase preparation, lipase A, was investigated as a potential biological recognition element for selective detection of ochratoxin A in complex media. Lipase A enabled the hydrolysis of ochratoxin A to the electroactive species ochratoxin α as confirmed by thin layer chromatography and voltammetric analysis. Additional isolation of a pure hydrolase from the lipase A preparation is required prior to utilization within a nanostructured biosensor platform capable of detecting ochratoxin A in complex media.
- Full Text:
- Date Issued: 2011
Co-utilisation of microalgae for wastewater treatment and the production of animal feed supplements
- Authors: Johnson, Hailey E
- Date: 2011
- Subjects: Microalgae -- Biotechnology , Algae culture , Algae products , Waste products as feed , Sewage -- Purification , Organic wastes -- Recycling , Food industry and trade -- Waste disposal , Agriculture -- Waste disposal
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3940 , http://hdl.handle.net/10962/d1003999 , Microalgae -- Biotechnology , Algae culture , Algae products , Waste products as feed , Sewage -- Purification , Organic wastes -- Recycling , Food industry and trade -- Waste disposal , Agriculture -- Waste disposal
- Description: Microalgae have a variety of commercial applications, the oldest of which include utilisation as a food source and for use in wastewater treatment. These applications, however, are seldom combined due to toxicity concerns, for ethical reasons, and generally the requirement for cultivation of a single algae species for use as a feed supplement. These problems might be negated if a “safer” wastewater such as that from agricultural and/or commercial food production facilities were to be utilised and if a stable algae population can be maintained. In this investigation preliminary studies were carried out using an Integrated Algae Pond System (IAPS) for domestic wastewater treatment to determine the species composition in the associated High Rate Algae Ponds (HRAPs). The effect of different modes of operation, continuous versus batch, on nutrient removal, productivity and species composition was also investigated. Furthermore, indigenous species in the HRAP were isolated and molecularly identified as, Chlorella, Micractinium, Scenedesmus and Pediastrum. Additionally, the effect of the nor amino acid, 2-hydroxy-4-(methylthio)-butanoic acid (HMTBA) and its Cu-chelated derivative, on the growth and biochemical composition of Chlorella, Micractinium, Scenedesmus, Pediastrum and Spirulina was investigated. Species composition in the HRAP was stable under continuous operation with Micractinium dominating > 90% of the algae population. Under batch operation the population dynamic shifted; Chlorella outcompeted Micractinium possibly due to nutrient depletion and selective grazing pressures caused by proliferation of Daphnia. Higher species diversity was observed during batch mode as slower growing algae were able to establish in the HRAP. Nutrient removal efficiency and biomass productivity was higher in continuous mode, however lower nutrient levels were obtained in batch operation. HMTBA did not significantly affect growth rate, however treatment with 10 mg.L-1 resulted in slightly increased growth rate in Micractinium and increased final biomass concentrations in Chlorella, Micractinium and Spirulina (although this was not statistically significant for Micractinium and Spirulina), which are known mixotrophic species. Algae treated with Cu-HMTBA, showed reduced final biomass concentration with 10 mg.L-1, caused by Cu toxicity. Biochemical composition of the algae was species-specific and differed through the growth cycle, with high protein observed during early growth and high carbohydrate during late growth/early stationary phase. Additionally, 0.1 mg.L-1 HMTBA and Cu-HMTBA significantly reduced protein content in Chlorella, Micractinium, Scenedesmus and Pediastrum. In conclusion, operation of the HRAP in continuous culture provided suitable wastewater treatment with high productivity of an ideal species, Micractinium, for use in animal feed supplementation. This species had 40% protein content during growth (higher than the other species tested) and dominated the HRAP at > 90% of the algae population during continuous mode. Addition of HMTBA (> 1 mg.L-1) to algae cultivation systems and those treating wastewater, has the potential to improve productivity and the value of the biomass by enhancing protein content. Overall, the co-utilisation of microalgae for wastewater treatment and the generation of a biomass rich in protein, for incorporation into formulated animal feed supplements, represents a closed ecosystem which conserves nutrients and regenerates a most valuable resource, water.
- Full Text:
- Date Issued: 2011
- Authors: Johnson, Hailey E
- Date: 2011
- Subjects: Microalgae -- Biotechnology , Algae culture , Algae products , Waste products as feed , Sewage -- Purification , Organic wastes -- Recycling , Food industry and trade -- Waste disposal , Agriculture -- Waste disposal
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3940 , http://hdl.handle.net/10962/d1003999 , Microalgae -- Biotechnology , Algae culture , Algae products , Waste products as feed , Sewage -- Purification , Organic wastes -- Recycling , Food industry and trade -- Waste disposal , Agriculture -- Waste disposal
- Description: Microalgae have a variety of commercial applications, the oldest of which include utilisation as a food source and for use in wastewater treatment. These applications, however, are seldom combined due to toxicity concerns, for ethical reasons, and generally the requirement for cultivation of a single algae species for use as a feed supplement. These problems might be negated if a “safer” wastewater such as that from agricultural and/or commercial food production facilities were to be utilised and if a stable algae population can be maintained. In this investigation preliminary studies were carried out using an Integrated Algae Pond System (IAPS) for domestic wastewater treatment to determine the species composition in the associated High Rate Algae Ponds (HRAPs). The effect of different modes of operation, continuous versus batch, on nutrient removal, productivity and species composition was also investigated. Furthermore, indigenous species in the HRAP were isolated and molecularly identified as, Chlorella, Micractinium, Scenedesmus and Pediastrum. Additionally, the effect of the nor amino acid, 2-hydroxy-4-(methylthio)-butanoic acid (HMTBA) and its Cu-chelated derivative, on the growth and biochemical composition of Chlorella, Micractinium, Scenedesmus, Pediastrum and Spirulina was investigated. Species composition in the HRAP was stable under continuous operation with Micractinium dominating > 90% of the algae population. Under batch operation the population dynamic shifted; Chlorella outcompeted Micractinium possibly due to nutrient depletion and selective grazing pressures caused by proliferation of Daphnia. Higher species diversity was observed during batch mode as slower growing algae were able to establish in the HRAP. Nutrient removal efficiency and biomass productivity was higher in continuous mode, however lower nutrient levels were obtained in batch operation. HMTBA did not significantly affect growth rate, however treatment with 10 mg.L-1 resulted in slightly increased growth rate in Micractinium and increased final biomass concentrations in Chlorella, Micractinium and Spirulina (although this was not statistically significant for Micractinium and Spirulina), which are known mixotrophic species. Algae treated with Cu-HMTBA, showed reduced final biomass concentration with 10 mg.L-1, caused by Cu toxicity. Biochemical composition of the algae was species-specific and differed through the growth cycle, with high protein observed during early growth and high carbohydrate during late growth/early stationary phase. Additionally, 0.1 mg.L-1 HMTBA and Cu-HMTBA significantly reduced protein content in Chlorella, Micractinium, Scenedesmus and Pediastrum. In conclusion, operation of the HRAP in continuous culture provided suitable wastewater treatment with high productivity of an ideal species, Micractinium, for use in animal feed supplementation. This species had 40% protein content during growth (higher than the other species tested) and dominated the HRAP at > 90% of the algae population during continuous mode. Addition of HMTBA (> 1 mg.L-1) to algae cultivation systems and those treating wastewater, has the potential to improve productivity and the value of the biomass by enhancing protein content. Overall, the co-utilisation of microalgae for wastewater treatment and the generation of a biomass rich in protein, for incorporation into formulated animal feed supplements, represents a closed ecosystem which conserves nutrients and regenerates a most valuable resource, water.
- Full Text:
- Date Issued: 2011
Effect of alkaline pre-treatments on the synergistic enzymatic hydrolysis of sugarcane (Saccharum officinarum) bagasse by Clostridium cellulovorans XynA, ManA and ArfA
- Authors: Beukes, Natasha
- Date: 2011
- Subjects: Sugarcane -- Biotechnology Lignocellulose -- Biotechnology Renewable energy sources Hydrolysis Enzymes
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3952 , http://hdl.handle.net/10962/d1004011
- Description: The continual increase in industrialization and global population has increased the dependency and demand on traditional fossil fuels for energy; however, there are limited amounts of fossil fuels available. The slow depletion of fossil fuels has sparked a fresh interest in renewable sources such as lignocellulose to produce a variety of biofuels, such as biogases (e.g. methane), bioethanol, biodiesel and a variety of other solvents and economically valuable by-products. Agricultural crop wastes produced in surplus are typically lignocellulosic in composition and thus partially recalcitrant to enzymatic degradation. The recalcitrant nature of plant biomass and the inability to obtain complete enzymatic hydrolysis has led to the establishment of various pre-treatment strategies. Alkaline pre-treatments increase the accessibility of the exposed surface to enzymatic hydrolysis through the removal of acetyl and uronic acid substituents on hemicellulose. Unlike the use of steam and acid pre-treatments, alkaline pre-treatments solubilize lignin and a small percentage of the hemicellulose, increasing enzyme accessibility and thus the hydrolysis of lignocellulose. The majority of Clostridium cellulovorans associated enzyme synergy studies have been devoted to an understanding of the cellulolytic and hemi-cellulolytic degradation of plant cell walls. However, little is known about the effect of various physical and chemical pre-treatments on the synergistic enzymatic degradation of plant biomass and possible depolymerization of plant cell walls. This study investigates the use of slake lime, sodium hydroxide and ammonium hydroxide to pre-treat sugarcane bagasse under mild conditions and elucidates potentially important synergistic associations between the C. cellulovorans enzymes for the enhanced degradation of lignocellulose. The primary aims of the study were addressed using of a variety of techniques. This included suitable vector constructs for the expression and purification of recombinant C. cellulovorans enzymes, identification of the effects of various pre-treatments on enzyme synergy, and identification of the resultant reducing sugars and phenolic compounds (released during the pre-treatment of the bagasse). This study also made use of physical and chemical pre-treatment methods, protein purification using affinity, high performance liquid and thin layer chromatography, mass spectrometry, sodium dodecyl sulphate and fluorophore-assisted polyacrylamide gel electrophoresis (FACE) , enzymatic degradation and synergy studies with various substrates indirectly using the 3, 4-dinitrosalicylic acid (DNS) reducing sugar assay. From this investigation, the following conclusions were made: alkaline pre-treatment successfully solublised, redistributed and removed lignin from the bagasse, increasing the digestibility of the substrates. In summary, the most effective pre-treatment employed 0.114 M ammonium hydroxide / gram bagasse at 70°C for 36 hours, followed by hydrolysis with an enzyme cocktail containing 25% ManA and 75% XynA. This increased the production of sugars approximately 13-fold. Analysis of the sugars produced by the synergistic hydrolysis of sugarcane bagasse (SCB) indicated the presence of xylose, indicating that the enzymes are potentially bifunctional under certain conditions. This study indicated that the use of mild pre-treatment conditions sufficiently removed a large portion of lignin without affecting the hemicellulose moiety of the SCB. This facilitated the potential use of the hemicellulose component for the production of valuable products (e.g. xylitol) in addition to the production of bioethanol. Thus, the potential use of additional components of holocellulose may generate an additional biotechnological benefit and allow a certain degree of flexibility in the biofuel industry, depending on consumer and industrial needs.
- Full Text:
- Date Issued: 2011
- Authors: Beukes, Natasha
- Date: 2011
- Subjects: Sugarcane -- Biotechnology Lignocellulose -- Biotechnology Renewable energy sources Hydrolysis Enzymes
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3952 , http://hdl.handle.net/10962/d1004011
- Description: The continual increase in industrialization and global population has increased the dependency and demand on traditional fossil fuels for energy; however, there are limited amounts of fossil fuels available. The slow depletion of fossil fuels has sparked a fresh interest in renewable sources such as lignocellulose to produce a variety of biofuels, such as biogases (e.g. methane), bioethanol, biodiesel and a variety of other solvents and economically valuable by-products. Agricultural crop wastes produced in surplus are typically lignocellulosic in composition and thus partially recalcitrant to enzymatic degradation. The recalcitrant nature of plant biomass and the inability to obtain complete enzymatic hydrolysis has led to the establishment of various pre-treatment strategies. Alkaline pre-treatments increase the accessibility of the exposed surface to enzymatic hydrolysis through the removal of acetyl and uronic acid substituents on hemicellulose. Unlike the use of steam and acid pre-treatments, alkaline pre-treatments solubilize lignin and a small percentage of the hemicellulose, increasing enzyme accessibility and thus the hydrolysis of lignocellulose. The majority of Clostridium cellulovorans associated enzyme synergy studies have been devoted to an understanding of the cellulolytic and hemi-cellulolytic degradation of plant cell walls. However, little is known about the effect of various physical and chemical pre-treatments on the synergistic enzymatic degradation of plant biomass and possible depolymerization of plant cell walls. This study investigates the use of slake lime, sodium hydroxide and ammonium hydroxide to pre-treat sugarcane bagasse under mild conditions and elucidates potentially important synergistic associations between the C. cellulovorans enzymes for the enhanced degradation of lignocellulose. The primary aims of the study were addressed using of a variety of techniques. This included suitable vector constructs for the expression and purification of recombinant C. cellulovorans enzymes, identification of the effects of various pre-treatments on enzyme synergy, and identification of the resultant reducing sugars and phenolic compounds (released during the pre-treatment of the bagasse). This study also made use of physical and chemical pre-treatment methods, protein purification using affinity, high performance liquid and thin layer chromatography, mass spectrometry, sodium dodecyl sulphate and fluorophore-assisted polyacrylamide gel electrophoresis (FACE) , enzymatic degradation and synergy studies with various substrates indirectly using the 3, 4-dinitrosalicylic acid (DNS) reducing sugar assay. From this investigation, the following conclusions were made: alkaline pre-treatment successfully solublised, redistributed and removed lignin from the bagasse, increasing the digestibility of the substrates. In summary, the most effective pre-treatment employed 0.114 M ammonium hydroxide / gram bagasse at 70°C for 36 hours, followed by hydrolysis with an enzyme cocktail containing 25% ManA and 75% XynA. This increased the production of sugars approximately 13-fold. Analysis of the sugars produced by the synergistic hydrolysis of sugarcane bagasse (SCB) indicated the presence of xylose, indicating that the enzymes are potentially bifunctional under certain conditions. This study indicated that the use of mild pre-treatment conditions sufficiently removed a large portion of lignin without affecting the hemicellulose moiety of the SCB. This facilitated the potential use of the hemicellulose component for the production of valuable products (e.g. xylitol) in addition to the production of bioethanol. Thus, the potential use of additional components of holocellulose may generate an additional biotechnological benefit and allow a certain degree of flexibility in the biofuel industry, depending on consumer and industrial needs.
- Full Text:
- Date Issued: 2011
Ericoid mycorrhizal fungi and potential for inoculation of commercial berry species (Vaccinium corymbosium L.)
- Authors: Bizabani, Christine
- Date: 2011
- Subjects: Ericaceae , Mycorrhizas , Fynbos
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4136 , http://hdl.handle.net/10962/d1016127
- Description: Ericaceous plants are the richest growth form of the fynbos vegetation of South Africa. The fynbos is characterized by highly leached acidic soils, low mineral nutrients and climatically it is a winter rainfall and dry summer region. Ericoid mycorrhizal fungi associate with Erica species enhancing their ability to access essential nutrients for survival under unfavourable growth conditions. The aim of this study was to select local Ericaceae plant species and to isolate, identify and characterize the ericoid endophytes and assess these isolates as potential inocula for commercial berry species. Two ericaceous plants Erica cerinthoides L. and Erica demmissa Klotzsch ex Benth. were identified from the Mountain Drive area of Grahamstown, Eastern Cape. Root staining was used to confirm the mycorrhizal status of both plants. Hyphal coils typical of ericoid association were observed within the epidermal cells of the hair roots under a light microscope. The endophytes were successfully isolated in pure culture on 2% malt extract agar (MEA) and modified Fontana medium. Cultural morphology and microscopy were used for initial identification. Two slow growing isolates were selected. These isolates were further subjected to molecular identification; extracted DNA was amplified using ITS1 and ITS4 fungal primers. The rDNA gene internal transcriber spacer (ITS) was then sequenced and analyzed by comparison to sequences in the GenBank. On the basis of percentage sequence identity Lachnum Retz. species and Cadophora Lagerb. & Melin species were identified as the ericoid endophytes of E. cerinthoides and E. demmissa respectively. The optimum growth parameters of the fungal isolates were determined in 2% MEA incubated at varying temperatures and pH. It was established that both species had optimum growth at 27⁰C and pH 5. The Ericaceae species are sometimes found in metal contaminated sites were ericoid fungi have been proved to alleviate toxicity of their host. The fungal isolates were grown in increasing concentration of Cu²⁺ and Zn²⁺ in 2% MEA. The growth of Lachnum species decreased with increasing Zn²⁺ ions above 2.7 mM while Cadophora species showed a change in morphology and also decreased in growth with increased ion concentration. However there were no significant differences recorded in the growth of Cadophora and Lachnum species on increasing Cu²⁺ concentration. Lachnum and Cadophora isolates were formulated into a semi solid inoculum and inoculated onto micropropagated Vaccinni corymbosum L. plantlets of 5 different varieties. Colonization was low for all varieties, Elliott and Brightwell varieties recorded the highest colonization of 35% and 31% respectively. Lachnum species infected roots showed potential ericoid structures while the Cadophora inoculated plantlets had hyphal coils within the cortical cells typical of ericoid mycorrhizas. Inoculation significantly enhanced the shoot growth of Brightwell and Elliott varieties. The Chandler variety inoculated with Lachnum species showed improved shoot dry weight. The Bluecrop and Elliott varieties inoculated with Cadophora and Lachnum accumulated more root biomass. All inoculated Bluecrop plantlets had an improved canopy growth index. Brightwell plantlets inoculated with Lachnum species also had an enhanced canopy growth index. The growth responses were variable within varieties and between varieties. Treatments with the Cadophora and Lachnum have shown potential in the promotion of growth of the Blueberry species. The findings indicate the need to conduct trials under conditions which simulate the commercial growth conditions so as explore the optimum potential of the isolates.
- Full Text:
- Date Issued: 2011
- Authors: Bizabani, Christine
- Date: 2011
- Subjects: Ericaceae , Mycorrhizas , Fynbos
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4136 , http://hdl.handle.net/10962/d1016127
- Description: Ericaceous plants are the richest growth form of the fynbos vegetation of South Africa. The fynbos is characterized by highly leached acidic soils, low mineral nutrients and climatically it is a winter rainfall and dry summer region. Ericoid mycorrhizal fungi associate with Erica species enhancing their ability to access essential nutrients for survival under unfavourable growth conditions. The aim of this study was to select local Ericaceae plant species and to isolate, identify and characterize the ericoid endophytes and assess these isolates as potential inocula for commercial berry species. Two ericaceous plants Erica cerinthoides L. and Erica demmissa Klotzsch ex Benth. were identified from the Mountain Drive area of Grahamstown, Eastern Cape. Root staining was used to confirm the mycorrhizal status of both plants. Hyphal coils typical of ericoid association were observed within the epidermal cells of the hair roots under a light microscope. The endophytes were successfully isolated in pure culture on 2% malt extract agar (MEA) and modified Fontana medium. Cultural morphology and microscopy were used for initial identification. Two slow growing isolates were selected. These isolates were further subjected to molecular identification; extracted DNA was amplified using ITS1 and ITS4 fungal primers. The rDNA gene internal transcriber spacer (ITS) was then sequenced and analyzed by comparison to sequences in the GenBank. On the basis of percentage sequence identity Lachnum Retz. species and Cadophora Lagerb. & Melin species were identified as the ericoid endophytes of E. cerinthoides and E. demmissa respectively. The optimum growth parameters of the fungal isolates were determined in 2% MEA incubated at varying temperatures and pH. It was established that both species had optimum growth at 27⁰C and pH 5. The Ericaceae species are sometimes found in metal contaminated sites were ericoid fungi have been proved to alleviate toxicity of their host. The fungal isolates were grown in increasing concentration of Cu²⁺ and Zn²⁺ in 2% MEA. The growth of Lachnum species decreased with increasing Zn²⁺ ions above 2.7 mM while Cadophora species showed a change in morphology and also decreased in growth with increased ion concentration. However there were no significant differences recorded in the growth of Cadophora and Lachnum species on increasing Cu²⁺ concentration. Lachnum and Cadophora isolates were formulated into a semi solid inoculum and inoculated onto micropropagated Vaccinni corymbosum L. plantlets of 5 different varieties. Colonization was low for all varieties, Elliott and Brightwell varieties recorded the highest colonization of 35% and 31% respectively. Lachnum species infected roots showed potential ericoid structures while the Cadophora inoculated plantlets had hyphal coils within the cortical cells typical of ericoid mycorrhizas. Inoculation significantly enhanced the shoot growth of Brightwell and Elliott varieties. The Chandler variety inoculated with Lachnum species showed improved shoot dry weight. The Bluecrop and Elliott varieties inoculated with Cadophora and Lachnum accumulated more root biomass. All inoculated Bluecrop plantlets had an improved canopy growth index. Brightwell plantlets inoculated with Lachnum species also had an enhanced canopy growth index. The growth responses were variable within varieties and between varieties. Treatments with the Cadophora and Lachnum have shown potential in the promotion of growth of the Blueberry species. The findings indicate the need to conduct trials under conditions which simulate the commercial growth conditions so as explore the optimum potential of the isolates.
- Full Text:
- Date Issued: 2011
Expression of heat shock proteins on the plasma membrane of cancer cells : a potential multi-chaperone complex that mediates migration
- Authors: Kenyon, Amy
- Date: 2011 , 2011-03-29
- Subjects: Heat shock proteins , Protein folding , Molecular chaperones , Cancer -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4122 , http://hdl.handle.net/10962/d1013362
- Description: Current dogma suggests that the Heat Shock Protein (Hsp) molecular chaperones and associated co-chaperones function primarily within the cell, although growing evidence suggests a role for these proteins on the plasma membrane of cancer cells. Hsp90 does not function independently in vivo, but instead functions with a variety of partner chaperones and co-chaperones, that include Hsp70 and Hsp90/Hsp70 organising protein (Hop), which are thought to regulate ATP hydrolysis and the binding of Hsp90 to its client proteins. Hsp90 on the plasma membrane appears to have distinct roles in pathways leading to cell motility, invasion and metastasis. We hypothesised that Hsp90 on the plasma membrane is present as part of a multi-chaperone complex that participates in the chaperone-assisted folding of client membrane proteins in a manner analogous to the intracellular chaperone complex. This study characterised the membrane expression of Hsp90, Hsp70 and Hop in different cell models of different adhesive and migratory capacity, namely MDA-MB-231 (metastatic adherent breast cancer cell line), MCF-7 (non-metastatic adherent breast cancer cell line), U937 and THP1 (monocytic leukemia suspension cell lines). Membrane expression of the Hsps was analysed using a combination of subcellular fractionation, biotin-streptavidin affinity purification and immunofluorescence. This study provided evidence to suggest that Hsp90, Hsp70 and Hop are membrane associated in MDA-MB-231 and MCF-7 breast cancer cells. Hsp90, Hsp70 and Hop associated with the plasma membrane such that at least part of the protein is located extracellularly. Immunofluorescence analysis showed that Hsp90, Hsp70 and Hop at the leading edge may localize to membrane ruffles in MDA-MB-231 cells, in accordance with the published role of Hsp90 in migration. An increase in this response was seen in cells stimulated to migrate with SDF-1. By immunoprecipitation, we isolated a putative extracellular membrane associated complex containing Hsp90, Hsp70 and Hop. Using soluble Hsp90 and antibodies against membrane associated Hsp90, we suggested roles for soluble extracellular Hsp90 in mediating migration by wound healing assays and inducing actin reorganisation and vinculin-based focal adhesion formation. The effects of extracellular Hsp90 are mediated by signalling through an ERK1/2 dependent pathway. An anti-Hsp90 antibody against an N-terminal epitope in Hsp90 appeared to be able to overcome the death inducing effects of a combination of SDF-1 and AMD3100, while soluble Hsp90 could not overcome this effect. We propose that this study provides preliminary evidence that extracellular Hsp90 functions as part of a multi-chaperone complex that includes Hsp70 and Hop. The extracellular Hsp90 chaperone complex may mediate cell processes such as migration by modulating the conformation of cell surface receptors, leading to downstream signalling.
- Full Text:
- Date Issued: 2011
- Authors: Kenyon, Amy
- Date: 2011 , 2011-03-29
- Subjects: Heat shock proteins , Protein folding , Molecular chaperones , Cancer -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4122 , http://hdl.handle.net/10962/d1013362
- Description: Current dogma suggests that the Heat Shock Protein (Hsp) molecular chaperones and associated co-chaperones function primarily within the cell, although growing evidence suggests a role for these proteins on the plasma membrane of cancer cells. Hsp90 does not function independently in vivo, but instead functions with a variety of partner chaperones and co-chaperones, that include Hsp70 and Hsp90/Hsp70 organising protein (Hop), which are thought to regulate ATP hydrolysis and the binding of Hsp90 to its client proteins. Hsp90 on the plasma membrane appears to have distinct roles in pathways leading to cell motility, invasion and metastasis. We hypothesised that Hsp90 on the plasma membrane is present as part of a multi-chaperone complex that participates in the chaperone-assisted folding of client membrane proteins in a manner analogous to the intracellular chaperone complex. This study characterised the membrane expression of Hsp90, Hsp70 and Hop in different cell models of different adhesive and migratory capacity, namely MDA-MB-231 (metastatic adherent breast cancer cell line), MCF-7 (non-metastatic adherent breast cancer cell line), U937 and THP1 (monocytic leukemia suspension cell lines). Membrane expression of the Hsps was analysed using a combination of subcellular fractionation, biotin-streptavidin affinity purification and immunofluorescence. This study provided evidence to suggest that Hsp90, Hsp70 and Hop are membrane associated in MDA-MB-231 and MCF-7 breast cancer cells. Hsp90, Hsp70 and Hop associated with the plasma membrane such that at least part of the protein is located extracellularly. Immunofluorescence analysis showed that Hsp90, Hsp70 and Hop at the leading edge may localize to membrane ruffles in MDA-MB-231 cells, in accordance with the published role of Hsp90 in migration. An increase in this response was seen in cells stimulated to migrate with SDF-1. By immunoprecipitation, we isolated a putative extracellular membrane associated complex containing Hsp90, Hsp70 and Hop. Using soluble Hsp90 and antibodies against membrane associated Hsp90, we suggested roles for soluble extracellular Hsp90 in mediating migration by wound healing assays and inducing actin reorganisation and vinculin-based focal adhesion formation. The effects of extracellular Hsp90 are mediated by signalling through an ERK1/2 dependent pathway. An anti-Hsp90 antibody against an N-terminal epitope in Hsp90 appeared to be able to overcome the death inducing effects of a combination of SDF-1 and AMD3100, while soluble Hsp90 could not overcome this effect. We propose that this study provides preliminary evidence that extracellular Hsp90 functions as part of a multi-chaperone complex that includes Hsp70 and Hop. The extracellular Hsp90 chaperone complex may mediate cell processes such as migration by modulating the conformation of cell surface receptors, leading to downstream signalling.
- Full Text:
- Date Issued: 2011
Fundamental investigations into the factors affecting the response of laccase-based electrochemical biosensors
- Authors: Fogel, Ronen
- Date: 2011
- Subjects: Laccase Phenols Biosensors
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4073 , http://hdl.handle.net/10962/d1007166
- Description: Given their widespread effects and distribution in both natural and industrial environments, the monitoring of phenolic compounds is of considerable analytical interest. Electrochemical biosensor technologies, in particular those comprising laccase enzymes, afford many potential benefits to address this analytical need. However, several key factors affecting sensor response currently limit their applicability. This Thesis reports on the fabrication and optimisation of an electrochemical laccase-based biosensor towards the application of the monitoring of phenolic compounds. Selected factors considered to affect sensor response were investigated using the optimised biosensor. These included: electrochemical, biochemical and substrate-dependent factors, which were found to intersect in modulating biosensor response signals. Through the application of transducer-dependent and substrate-dependent parameters, the selective and simultaneous detection of a mixture of different phenolic analytes is successfully demonstrated. This Thesis also investigates the use of Quartz-Crystal Microbalance with Dissipation (QCM-D) technology, an analytical technique that measures physical parameters of thin-film structures, towards the successful monitoring of enzyme immobilisation strategies. These strategies are fundamental to the successful fabrication of biosensors, and the real-time monitoring of immobilised film formations is of considerable research interest. In the studies reported on in this Thesis, QCM-D technology was demonstrated to be an effective complementary technology in the prediction of film immobilisation techniques on the resultant biochemical kinetics of immobilised enzymes.
- Full Text:
- Date Issued: 2011
- Authors: Fogel, Ronen
- Date: 2011
- Subjects: Laccase Phenols Biosensors
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4073 , http://hdl.handle.net/10962/d1007166
- Description: Given their widespread effects and distribution in both natural and industrial environments, the monitoring of phenolic compounds is of considerable analytical interest. Electrochemical biosensor technologies, in particular those comprising laccase enzymes, afford many potential benefits to address this analytical need. However, several key factors affecting sensor response currently limit their applicability. This Thesis reports on the fabrication and optimisation of an electrochemical laccase-based biosensor towards the application of the monitoring of phenolic compounds. Selected factors considered to affect sensor response were investigated using the optimised biosensor. These included: electrochemical, biochemical and substrate-dependent factors, which were found to intersect in modulating biosensor response signals. Through the application of transducer-dependent and substrate-dependent parameters, the selective and simultaneous detection of a mixture of different phenolic analytes is successfully demonstrated. This Thesis also investigates the use of Quartz-Crystal Microbalance with Dissipation (QCM-D) technology, an analytical technique that measures physical parameters of thin-film structures, towards the successful monitoring of enzyme immobilisation strategies. These strategies are fundamental to the successful fabrication of biosensors, and the real-time monitoring of immobilised film formations is of considerable research interest. In the studies reported on in this Thesis, QCM-D technology was demonstrated to be an effective complementary technology in the prediction of film immobilisation techniques on the resultant biochemical kinetics of immobilised enzymes.
- Full Text:
- Date Issued: 2011
Investigating the role of heat shock proteins (Hsps) 40, 70 and 90 in the life cycle of Theiler's murine encephalomyelitis virus (TMEV)
- Mutsvunguma, Lorraine Zvichapera
- Authors: Mutsvunguma, Lorraine Zvichapera
- Date: 2011
- Subjects: Heat shock proteins , Picornaviruses , Encephalomyelitis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3966 , http://hdl.handle.net/10962/d1004025 , Heat shock proteins , Picornaviruses , Encephalomyelitis
- Description: Introduction: Picornaviruses are a family of RNA viruses which are economically and clinically significant. Like many other viruses, picornaviruses utilise host cell machinery to facilitate their replication and assembly, including heat shock proteins (Hsps). The aim of this research was to investigate the role of Hsp40, Hsp70 and Hsp90 during picornavirus infection using the cardiovirus, Theiler’s murine encephalomyelitis virus (TMEV), as a study model. Methodology: Picornavirus VP1 capsid proteins were analysed by multiple sequence alignment and multiple structural comparisons. Protein domain architecture was used to analyse Hsp90 cellular and viral client proteins. Effects of Hsp90 inhibitors, novobiocin and geldanamycin, on TMEV growth in BHK-21 cells was observed over a 48hr period. Localisation of Hsp40, Hsp90 and Hsp70 in TMEV-infected BHK-21 cells was investigated by indirect immunofluorescence and confocal microscopy. Results and Discussion: VP1 proteins of picornaviruses are highly divergent within the family at the amino acid level, which might be linked to the protein’s function in determining virus tropism and antibody neutralisation. An eight-stranded anti-parallel beta-barrel structure was found conserved in the VP1 protein structures which might be linked to the highly conserved picornavirus capsid assembly process. Absence of a common protein domain between Hsp90 viral and cellular client proteins that might be functionally connected to Hsp90, suggests that Hsp90 most likely recognises surface features rather than sequence motifs/patterns. The Hsp90 inhibitors, novobiocin and geldanamycin, had a negative effect on virus growth as virus-induced cytopathic effect was not observed in treated cell after 48hrs. TMEV 2C protein was detected by Western analysis in infected cell lysates treated with geldanamycin but not novobiocin, suggesting novobiocin affects the translation or processing of TMEV 2C. Immunofluorescence analysis of TMEV-infected cells showed a relocalisation of Hsp40 into the nucleus during infection. Overlap of Hsp40 and TMEV P1 was observed in the perinuclear region, suggesting colocalisation between these proteins. Hsp70 converged around the replication complex during infection but did not overlap with TMEV 2C. Hsp90 concentrated in the region of the replication complex where it overlapped with TMEV 2C and this redistribution was found to be dependent on the stage of infection. The overlap between Hsp90 and TMEV 2C signals observed, suggested colocalisation between the two proteins. Conclusion: This study identified Hsp90, Hsp70 and Hsp40 as possible host factors required in TMEV replication.
- Full Text:
- Date Issued: 2011
- Authors: Mutsvunguma, Lorraine Zvichapera
- Date: 2011
- Subjects: Heat shock proteins , Picornaviruses , Encephalomyelitis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3966 , http://hdl.handle.net/10962/d1004025 , Heat shock proteins , Picornaviruses , Encephalomyelitis
- Description: Introduction: Picornaviruses are a family of RNA viruses which are economically and clinically significant. Like many other viruses, picornaviruses utilise host cell machinery to facilitate their replication and assembly, including heat shock proteins (Hsps). The aim of this research was to investigate the role of Hsp40, Hsp70 and Hsp90 during picornavirus infection using the cardiovirus, Theiler’s murine encephalomyelitis virus (TMEV), as a study model. Methodology: Picornavirus VP1 capsid proteins were analysed by multiple sequence alignment and multiple structural comparisons. Protein domain architecture was used to analyse Hsp90 cellular and viral client proteins. Effects of Hsp90 inhibitors, novobiocin and geldanamycin, on TMEV growth in BHK-21 cells was observed over a 48hr period. Localisation of Hsp40, Hsp90 and Hsp70 in TMEV-infected BHK-21 cells was investigated by indirect immunofluorescence and confocal microscopy. Results and Discussion: VP1 proteins of picornaviruses are highly divergent within the family at the amino acid level, which might be linked to the protein’s function in determining virus tropism and antibody neutralisation. An eight-stranded anti-parallel beta-barrel structure was found conserved in the VP1 protein structures which might be linked to the highly conserved picornavirus capsid assembly process. Absence of a common protein domain between Hsp90 viral and cellular client proteins that might be functionally connected to Hsp90, suggests that Hsp90 most likely recognises surface features rather than sequence motifs/patterns. The Hsp90 inhibitors, novobiocin and geldanamycin, had a negative effect on virus growth as virus-induced cytopathic effect was not observed in treated cell after 48hrs. TMEV 2C protein was detected by Western analysis in infected cell lysates treated with geldanamycin but not novobiocin, suggesting novobiocin affects the translation or processing of TMEV 2C. Immunofluorescence analysis of TMEV-infected cells showed a relocalisation of Hsp40 into the nucleus during infection. Overlap of Hsp40 and TMEV P1 was observed in the perinuclear region, suggesting colocalisation between these proteins. Hsp70 converged around the replication complex during infection but did not overlap with TMEV 2C. Hsp90 concentrated in the region of the replication complex where it overlapped with TMEV 2C and this redistribution was found to be dependent on the stage of infection. The overlap between Hsp90 and TMEV 2C signals observed, suggested colocalisation between the two proteins. Conclusion: This study identified Hsp90, Hsp70 and Hsp40 as possible host factors required in TMEV replication.
- Full Text:
- Date Issued: 2011
Nanomaterial modified electrodes : optimization of voltammetric sensors for pharmaceutical and industrial application
- Authors: Brimecombe, Rory Dennis
- Date: 2011
- Subjects: Voltammetry , Electrochemistry , Nanotubes , Nanostructured materials
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4101 , http://hdl.handle.net/10962/d1009721
- Description: Nanomaterials, in particular carbon nanotubes have been shown to exhibit favourable properties for the enhancement of electrochemical detection of target analytes in complex matrices. There is however scope for improvement in terms of the optimization thereof in electrochemical sensors surface modification. The aim of this thesis was to examine methods that would result in increased current response, lowered passivation and application of such modified surfaces with application to pharmaceutically and industrially relevant analytes. Current methods for enhancing the performance of carbon nanotubes include acid functionalization which not only increases the hydrophilicity of the nanotubes, and consequently their ability to provide stable (aqueous) suspensions, but also introduces electrochemically active sites. This particular approach is however not normalized in the literature. Over-exposure to acid treatment results in loss of structural integrity of the carbon nanotubes, and as such a fine balance exists between achieving these dual outcomes. Guided by high resolution scanning electron microscopy, atomic force microscopy, voltammetric and impedance studies, this thesis examined the role of the length of time of the acid functionalization process as well as the impact of activation of carbon nanotubes and fullerenes on electrochemical sensor performance. Based on desired charge transfer resistances, rate transfer coefficients and sensitivity towards redox probes the optimal length of acid functionalization for multiwalled carbon nanotubes was 9 hours and 4 hours for single-walled carbon nanotubes. Further improvements in the desired outcomes were achieved through electrochemical activation of the modified electrode surface by cycling in the presence of catechol, in a novel approach. By employing electrochemical impedance spectroscopy it was observed that catechol activation resulted in lowered charge transfer resistance, before and after activation, with functionalized multi-walled carbon nanotubes (9 hours) exhibiting the greatest decrease of 90 % and functionalized single-walled carbon nanotubes (4 hours), a 50 % decrease. Corresponding increases in the heterologous rate transfer coefficient showed a 770 % increase for functionalized multi-walled carbon nanotubes (9 hours), following catechol activation. Comparative observations for fullerenes following partial reduction in potassium hydroxide yielded a 30 % decrease in charge transfer resistance, with an increased heterologous rate transfer coefficient at a fullerene modified surface The performance of the nanomaterial modified electrodes was applied to the detection of wortmannin with applications in bioprocess control and in the pharmaceutical sector as well as to the detection and monitoring of the industrial dye Reactive red. Of particular relevance to these analytes was the assessment of the nanomaterial modified electrodes for enhanced stability, reproducibility, sensitivity and decreased passivation effects. In this study the first known account of wortmannin detection through electrochemical methods is reported. Voltammetric characterization of wortmannin revealed an irreversible cathodic process with a total number of 4 electrons and a diffusion coefficient of 1.19 x 10-7 cm².s⁻¹. At a functionalized multiwalled carbon nanotubes modified glassy carbon electrode a limit of detection of 0.128 nmol.cm⁻³ was obtained, and with limited surface passivation the detection scheme afforded pertinent analyses in biological media representing a substantial improvement over chromatographic detection methods. This study also provided the first account of the voltammetric detection of reactive red, competing favourably with traditional spectroscopic methods for monitoring biodegradation of this compound in real time.
- Full Text:
- Date Issued: 2011
- Authors: Brimecombe, Rory Dennis
- Date: 2011
- Subjects: Voltammetry , Electrochemistry , Nanotubes , Nanostructured materials
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4101 , http://hdl.handle.net/10962/d1009721
- Description: Nanomaterials, in particular carbon nanotubes have been shown to exhibit favourable properties for the enhancement of electrochemical detection of target analytes in complex matrices. There is however scope for improvement in terms of the optimization thereof in electrochemical sensors surface modification. The aim of this thesis was to examine methods that would result in increased current response, lowered passivation and application of such modified surfaces with application to pharmaceutically and industrially relevant analytes. Current methods for enhancing the performance of carbon nanotubes include acid functionalization which not only increases the hydrophilicity of the nanotubes, and consequently their ability to provide stable (aqueous) suspensions, but also introduces electrochemically active sites. This particular approach is however not normalized in the literature. Over-exposure to acid treatment results in loss of structural integrity of the carbon nanotubes, and as such a fine balance exists between achieving these dual outcomes. Guided by high resolution scanning electron microscopy, atomic force microscopy, voltammetric and impedance studies, this thesis examined the role of the length of time of the acid functionalization process as well as the impact of activation of carbon nanotubes and fullerenes on electrochemical sensor performance. Based on desired charge transfer resistances, rate transfer coefficients and sensitivity towards redox probes the optimal length of acid functionalization for multiwalled carbon nanotubes was 9 hours and 4 hours for single-walled carbon nanotubes. Further improvements in the desired outcomes were achieved through electrochemical activation of the modified electrode surface by cycling in the presence of catechol, in a novel approach. By employing electrochemical impedance spectroscopy it was observed that catechol activation resulted in lowered charge transfer resistance, before and after activation, with functionalized multi-walled carbon nanotubes (9 hours) exhibiting the greatest decrease of 90 % and functionalized single-walled carbon nanotubes (4 hours), a 50 % decrease. Corresponding increases in the heterologous rate transfer coefficient showed a 770 % increase for functionalized multi-walled carbon nanotubes (9 hours), following catechol activation. Comparative observations for fullerenes following partial reduction in potassium hydroxide yielded a 30 % decrease in charge transfer resistance, with an increased heterologous rate transfer coefficient at a fullerene modified surface The performance of the nanomaterial modified electrodes was applied to the detection of wortmannin with applications in bioprocess control and in the pharmaceutical sector as well as to the detection and monitoring of the industrial dye Reactive red. Of particular relevance to these analytes was the assessment of the nanomaterial modified electrodes for enhanced stability, reproducibility, sensitivity and decreased passivation effects. In this study the first known account of wortmannin detection through electrochemical methods is reported. Voltammetric characterization of wortmannin revealed an irreversible cathodic process with a total number of 4 electrons and a diffusion coefficient of 1.19 x 10-7 cm².s⁻¹. At a functionalized multiwalled carbon nanotubes modified glassy carbon electrode a limit of detection of 0.128 nmol.cm⁻³ was obtained, and with limited surface passivation the detection scheme afforded pertinent analyses in biological media representing a substantial improvement over chromatographic detection methods. This study also provided the first account of the voltammetric detection of reactive red, competing favourably with traditional spectroscopic methods for monitoring biodegradation of this compound in real time.
- Full Text:
- Date Issued: 2011
Nanostructures and metallophthalocyanines : applications in microbial fuel cells
- Authors: Edwards, Sean
- Date: 2011
- Subjects: Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4107 , http://hdl.handle.net/10962/d1011742 , Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Description: Microbial fuel cells (MFCs) are a promising form of alternative energy capable of harnessing the potential energy stores in organic waste. The oxygen reduction reaction (ORR) forms an integral role in the generation of electricity in MFCs however it is also a potential obstacle in enhancing the performance of MFCs. Platinum, a commonly used catalyst for the ORR, is expensive and rare. Significant research has been conducted into developing alternative catalysts. Metallophthalocyanines (MPc) have garnered attention for use as catalysts. Iron phthalocyanine (FePc) has been shown to have catalytic activity towards the reduction of oxygen. Coupling of the catalyst to nanostructured carbon materials, such as multi-walled carbon nanotubes, has been observed to have several advantages as nanostructures have a high surface-to-volume ratio. In this study, we have attempted to assess the suitability of FePc, both its bulk and nanostructured form, as an oxygen reduction catalyst and acid functionalized multi-walled carbon nanotubes for use as a catalyst support using electrochemical techniques such as cyclic voltammetry and electrochemical impedance spectroscopy. We showed, for the first time, the catalytic nature of nanostructured FePc towards the ORR. Applying the data obtained from the electrochemical analyses, electrodes were modified using FePc and MWCNTs and applied to an Enterobacter cloacae-based MFC. Several operational parameters of the MFC, such as temperature and ionic strength, were optimized during the course of the study. We showed that optimized FePc:MWCNT-modified electrodes compared favourably to platinum-based electrodes in terms of power densities obtained in a microbial fuel cell.
- Full Text:
- Date Issued: 2011
- Authors: Edwards, Sean
- Date: 2011
- Subjects: Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4107 , http://hdl.handle.net/10962/d1011742 , Microbial fuel cells , Waste products as fuel , Nanostructured materials , Electrochemistry , Nanotubes
- Description: Microbial fuel cells (MFCs) are a promising form of alternative energy capable of harnessing the potential energy stores in organic waste. The oxygen reduction reaction (ORR) forms an integral role in the generation of electricity in MFCs however it is also a potential obstacle in enhancing the performance of MFCs. Platinum, a commonly used catalyst for the ORR, is expensive and rare. Significant research has been conducted into developing alternative catalysts. Metallophthalocyanines (MPc) have garnered attention for use as catalysts. Iron phthalocyanine (FePc) has been shown to have catalytic activity towards the reduction of oxygen. Coupling of the catalyst to nanostructured carbon materials, such as multi-walled carbon nanotubes, has been observed to have several advantages as nanostructures have a high surface-to-volume ratio. In this study, we have attempted to assess the suitability of FePc, both its bulk and nanostructured form, as an oxygen reduction catalyst and acid functionalized multi-walled carbon nanotubes for use as a catalyst support using electrochemical techniques such as cyclic voltammetry and electrochemical impedance spectroscopy. We showed, for the first time, the catalytic nature of nanostructured FePc towards the ORR. Applying the data obtained from the electrochemical analyses, electrodes were modified using FePc and MWCNTs and applied to an Enterobacter cloacae-based MFC. Several operational parameters of the MFC, such as temperature and ionic strength, were optimized during the course of the study. We showed that optimized FePc:MWCNT-modified electrodes compared favourably to platinum-based electrodes in terms of power densities obtained in a microbial fuel cell.
- Full Text:
- Date Issued: 2011
Neuronal nitric oxide synthase : a biomarker for Alzheimers disease : interaction of neuronal nitric oxide synthase with beta-amyloid peptides in the brain
- Authors: Padayachee, Eden Rebecca
- Date: 2011 , 2013-07-19
- Subjects: Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4086 , http://hdl.handle.net/10962/d1007677 , Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Description: High levels of the amino acid arginine and low levels of the product citrulline in the cerebrospinal fluid of Alzheimer's patients could mean that there is a decrease in the enzymes that metabolize this amino acid. One such enzyme is neuronal nitric oxide synthase (nNOS). In this study, neuronal nitric oxide synthase (nNOS), sourced from bovine brain was extracted and concentrated using two methods of precipitation: poly (ethylene glycol) 20 000 (PEG) and ammonium sulphate [(NH₄)₂S0₄). These two techniques gave no increase in yield nor fold purification and hence were abandoned in favour of ion exchange chromatography by DEAE-Sepharose. The enzyme was then successfully purified by anion-exchange and after dialysis produced a 38% yield and three fold purification and yielded the highest specific activity of 2.27 U/mg. Neuronal nitric oxide synthase (nNOS) was a heterodimeric protein with a total molecular mass of ± 225 kDa (95 and 130 kDa monomers). The temperature and pH optima of the enzyme were 40⁰C and 6.5, respectively. The kinetic parameters (KM and Vmax) of nNOS were 70 μM and 0.332 μmol.min⁻¹, respectively. Moreover neuronal nitric oxide synthase (nNOS) was relatively stable at 40⁰C (t½ = 3 h). It was also confirmed that β-amyloid peptides inhibited nNOS when bound to the enzyme and that nNOS behaved as a catalyst in fibril formation through association-dissociation between enzyme and β-amyloid peptide. It was further shown that Aβ₁₇₋₂₈ inhibited nNOS the most with a Ki of 1.92 μM and also had the highest Stern-Volmer value (Ksv) of 0.11 μM⁻¹ indicating tight binding affinity to nNOS and easier accessibility to fluor molecules during binding. Congo red, turbidity, thioflavin-T assays and transmission electron microscopy were successfully used to detect and visualize the presence of fibrils by studying the process of fibrillogenesis. Computerized molecular modeling successfully studied protein dynamics and conformational changes of nNOS. These results correlated with resonance energy transfer (FRET) results which revealed the distance of tryptophan residues from the arginine bound at enzyme active site. Both the aforementioned techniques revealed that in the natural state of the enzyme with arginine bound at the active site, the tryptophan residues (TRP₆₂₅ and TRP₇₂₁) were positioned at the surface of the enzyme 28 Å away from the active site. When the amyloid peptide (Aβ₁₇₋₂₈) was bound to the active site, these same two amino acids moved 14 Å closer to the active site. A five residue hydrophobic fragment Aβ₁₇₋₂₁ [Leu₁₇ - Val₁₈ - Phe₁₉ - Phe₂₀ - Ala₁] within Aβ₁₇₋₂₈ was shown by computer modeling to be critical to the binding of the peptide to the active site of nNOS.
- Full Text:
- Date Issued: 2011
- Authors: Padayachee, Eden Rebecca
- Date: 2011 , 2013-07-19
- Subjects: Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4086 , http://hdl.handle.net/10962/d1007677 , Alzheimer's disease , Nitric-oxide synthase , Biochemical markers , Amyloid beta-protein , Peptide hormones
- Description: High levels of the amino acid arginine and low levels of the product citrulline in the cerebrospinal fluid of Alzheimer's patients could mean that there is a decrease in the enzymes that metabolize this amino acid. One such enzyme is neuronal nitric oxide synthase (nNOS). In this study, neuronal nitric oxide synthase (nNOS), sourced from bovine brain was extracted and concentrated using two methods of precipitation: poly (ethylene glycol) 20 000 (PEG) and ammonium sulphate [(NH₄)₂S0₄). These two techniques gave no increase in yield nor fold purification and hence were abandoned in favour of ion exchange chromatography by DEAE-Sepharose. The enzyme was then successfully purified by anion-exchange and after dialysis produced a 38% yield and three fold purification and yielded the highest specific activity of 2.27 U/mg. Neuronal nitric oxide synthase (nNOS) was a heterodimeric protein with a total molecular mass of ± 225 kDa (95 and 130 kDa monomers). The temperature and pH optima of the enzyme were 40⁰C and 6.5, respectively. The kinetic parameters (KM and Vmax) of nNOS were 70 μM and 0.332 μmol.min⁻¹, respectively. Moreover neuronal nitric oxide synthase (nNOS) was relatively stable at 40⁰C (t½ = 3 h). It was also confirmed that β-amyloid peptides inhibited nNOS when bound to the enzyme and that nNOS behaved as a catalyst in fibril formation through association-dissociation between enzyme and β-amyloid peptide. It was further shown that Aβ₁₇₋₂₈ inhibited nNOS the most with a Ki of 1.92 μM and also had the highest Stern-Volmer value (Ksv) of 0.11 μM⁻¹ indicating tight binding affinity to nNOS and easier accessibility to fluor molecules during binding. Congo red, turbidity, thioflavin-T assays and transmission electron microscopy were successfully used to detect and visualize the presence of fibrils by studying the process of fibrillogenesis. Computerized molecular modeling successfully studied protein dynamics and conformational changes of nNOS. These results correlated with resonance energy transfer (FRET) results which revealed the distance of tryptophan residues from the arginine bound at enzyme active site. Both the aforementioned techniques revealed that in the natural state of the enzyme with arginine bound at the active site, the tryptophan residues (TRP₆₂₅ and TRP₇₂₁) were positioned at the surface of the enzyme 28 Å away from the active site. When the amyloid peptide (Aβ₁₇₋₂₈) was bound to the active site, these same two amino acids moved 14 Å closer to the active site. A five residue hydrophobic fragment Aβ₁₇₋₂₁ [Leu₁₇ - Val₁₈ - Phe₁₉ - Phe₂₀ - Ala₁] within Aβ₁₇₋₂₈ was shown by computer modeling to be critical to the binding of the peptide to the active site of nNOS.
- Full Text:
- Date Issued: 2011
Probing the biocompatibility of biomedical interfaces using the Quartz Crystal Microbalance with Dissipation
- Authors: Cromhout, Mary
- Date: 2011
- Subjects: Biomedical materials , Nanostructured materials , Biomedical engineering , Quartz crystal microbalances , Blood proteins , Nanoparticles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4102 , http://hdl.handle.net/10962/d1010660
- Description: The biomedical application of nanotechnology has come into the spotlight, with the promise of ‘personalised’ therapeutics that couple early diagnosis with targeted therapeutic activity. Due to the rapid growth of the biomedical applications of nanoparticles, along with the lack of understanding concerning their interactions with biomolecules, there is a pressing need for the development of standard methods directed at investigating the effect of introducing these unique particles into the human body. The central aim of this research is to establish a platform directed at assessing the biological fate of pioneering therapeutic particulate agents, such as metallophthalocyanines (MPcs) and multi-walled carbon nanotubes (FMWCNTs). In particular, we proposed, that Quartz Crystal Microbalance with Dissipation (QCM-D) technology may be employed to assess the composition of blood protein corona deposited on the therapeutic surface, and subsequently assess the biocompatibility of such particles. The proposed method of protein detection utilises the nanogram sensitivity of QCM-D technology to monitor highly specific antibody-antigen interactions. In particular those interactions which occur when probe antibodies are used to detect adsorbed blood proteins deposited on target particle-modified sensor surfaces. Protein detection analysis was directed toward identification of surface bound human serum albumin, complement factor C3c, and human plasma fibrinogen. Preliminary analysis of generic biomedical surfaces indicated human serum albumin demonstrates a higher binding affinity towards positively charged surfaces (i.e. cysteamine self-assembled monolayer), followed by hydrophobic surfaces. Detection of complement C3c, corresponded with literature, where lower levels were detected on negatively charged surfaces (i.e. mercapto undecanoic acid self-assembled monolayer), and higher levels of more hydrophobic surfaces (i.e. 11-amino undecane thiol self-assembled monolayer). Human plasma fibrinogen was observed to favour hydrophilic over hydrophobic self-assembled monolayer surfaces, which was in accordance with literature. Application of the proposed protein detection method for biocompatibility analysis of target therapeutic molecules, namely metallophthalocyanines and acid functionalised multi-walled carbon nanotubes, demonstrated a dependence on modified-surface film characteristics, such as surface charge and topography with regards to human serum albumin and human plasma fibrinogen analysis representing new insights into their potential biomolecular interactions The highest levels of detected human serum albumin and complement C3c were detected on the GePcSmix-modified surfaces. AlPcSmix-modified surfaces analysis suggested the highest levels of human plasma fibrinogen. Two methods of acid functionalisation were employed, using both nitric and sulphuric acid, and pure nitric acid. A general increase in detected human serum albumin, corresponding with an increase in functionalisation time, was observed. Complement C3c detection suggested an increase in deposited complement C3c, with increasing functionalisation time, when assessing nitric acid functionalised multi-walled carbon nanotubes, and a decrease, with increasing functionalisation time, when assessing nitric and sulphuric acid functionalised multi-walled carbon nanotubes. Analysis of human plasma fibrinogen was inconclusive, as were cytotoxicity experiments utilising MCF-7 cells in the presence of metallophthalocyanine complexes, raising simultaneously important considerations for their application and study. In the first such detailed examination of its kind it was concluded that the proposed method of protein detection, using QCM-D, allows for the rudimentary but rapid means of analysis of select protein corona deposited on particulate biomedical surfaces.
- Full Text:
- Date Issued: 2011
- Authors: Cromhout, Mary
- Date: 2011
- Subjects: Biomedical materials , Nanostructured materials , Biomedical engineering , Quartz crystal microbalances , Blood proteins , Nanoparticles
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4102 , http://hdl.handle.net/10962/d1010660
- Description: The biomedical application of nanotechnology has come into the spotlight, with the promise of ‘personalised’ therapeutics that couple early diagnosis with targeted therapeutic activity. Due to the rapid growth of the biomedical applications of nanoparticles, along with the lack of understanding concerning their interactions with biomolecules, there is a pressing need for the development of standard methods directed at investigating the effect of introducing these unique particles into the human body. The central aim of this research is to establish a platform directed at assessing the biological fate of pioneering therapeutic particulate agents, such as metallophthalocyanines (MPcs) and multi-walled carbon nanotubes (FMWCNTs). In particular, we proposed, that Quartz Crystal Microbalance with Dissipation (QCM-D) technology may be employed to assess the composition of blood protein corona deposited on the therapeutic surface, and subsequently assess the biocompatibility of such particles. The proposed method of protein detection utilises the nanogram sensitivity of QCM-D technology to monitor highly specific antibody-antigen interactions. In particular those interactions which occur when probe antibodies are used to detect adsorbed blood proteins deposited on target particle-modified sensor surfaces. Protein detection analysis was directed toward identification of surface bound human serum albumin, complement factor C3c, and human plasma fibrinogen. Preliminary analysis of generic biomedical surfaces indicated human serum albumin demonstrates a higher binding affinity towards positively charged surfaces (i.e. cysteamine self-assembled monolayer), followed by hydrophobic surfaces. Detection of complement C3c, corresponded with literature, where lower levels were detected on negatively charged surfaces (i.e. mercapto undecanoic acid self-assembled monolayer), and higher levels of more hydrophobic surfaces (i.e. 11-amino undecane thiol self-assembled monolayer). Human plasma fibrinogen was observed to favour hydrophilic over hydrophobic self-assembled monolayer surfaces, which was in accordance with literature. Application of the proposed protein detection method for biocompatibility analysis of target therapeutic molecules, namely metallophthalocyanines and acid functionalised multi-walled carbon nanotubes, demonstrated a dependence on modified-surface film characteristics, such as surface charge and topography with regards to human serum albumin and human plasma fibrinogen analysis representing new insights into their potential biomolecular interactions The highest levels of detected human serum albumin and complement C3c were detected on the GePcSmix-modified surfaces. AlPcSmix-modified surfaces analysis suggested the highest levels of human plasma fibrinogen. Two methods of acid functionalisation were employed, using both nitric and sulphuric acid, and pure nitric acid. A general increase in detected human serum albumin, corresponding with an increase in functionalisation time, was observed. Complement C3c detection suggested an increase in deposited complement C3c, with increasing functionalisation time, when assessing nitric acid functionalised multi-walled carbon nanotubes, and a decrease, with increasing functionalisation time, when assessing nitric and sulphuric acid functionalised multi-walled carbon nanotubes. Analysis of human plasma fibrinogen was inconclusive, as were cytotoxicity experiments utilising MCF-7 cells in the presence of metallophthalocyanine complexes, raising simultaneously important considerations for their application and study. In the first such detailed examination of its kind it was concluded that the proposed method of protein detection, using QCM-D, allows for the rudimentary but rapid means of analysis of select protein corona deposited on particulate biomedical surfaces.
- Full Text:
- Date Issued: 2011
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:
- Date Issued: 2011
- 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:
- Date Issued: 2011
Structural and functional characterisation of the protein inhibitor of activated STAT3 (PIAS3)
- Authors: Mautsa, Nicodemus
- Date: 2011
- Subjects: Cytokines Immune response Proteins Cancer cells -- Growth -- Regulation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3991 , http://hdl.handle.net/10962/d1004050
- Description: The signal transducer and activator of transcription (STAT) and protein inhibitor of STAT(PIAS) system represent an elegant regulatory mechanism of transcriptional control IN mammalian cytokine signalling. Abnormal activation of the system is associated with immune disorders and a large group of diverse tumours. PIAS3 is a multiple domain protein with distinct functions involved in regulation of cytokine-mediated gene activation pathways.Its over-expression significantly inhibits cell growth and renders cancer cells more sensitive to drugs. The objective of this study was to structurally and biochemically characterise the function of the PIAS3 protein using in silico, in vivo and in vitro analysis approaches.The conservation pattern of the PIAS protein family and critical conserved residues in the PINIT (Proline, Isoleucine, Asparagine, Isoleucine, Tyrosine) domain were identified. The PINIT domain model was generated based on the PINIT domain structure of yeast PIAS3 homologue Siz1 and structural determinants in the PIAS3-STAT3 interaction were evaluated.Guided by the in silico findings, in vivo analysis of the localisation of the PIAS3, mutantderivatives of PIAS3 (PIAS3-L97A, PIAS3-R99N, PIAS3-R99Q), PINIT and acidic domain was conducted. PIAS3 was completely localised in the nucleus while PIAS3 mutants appeared to exhibit diffuse cytoplasmic distribution. The PINIT domain was predominantly localised in the nucleus with some apparent perinuclear staining while the acidic domain exhibited a predominantly perinuclear staining pattern. Further analysis of the PINIT domain and the effect of the mutants on PIAS3-STAT3 interaction were assessed by in vitro analysis. Guided by in silico analysis, the PINIT domain and mutant derivatives of PINIT domain (PINIT-L97A, PINIT-R99N, and PINIT-R99Q) were heterologously expressed in Escherichia coli and subsequently purified using a combination of immobilized metal affinity and size exclusion based chromatography. The size and structural elements of the PINIT domain and its mutants were characterised. The 23 kDa PINIT domain was found to exist as a monomer in solution and its secondary structure was shown to consist of 66 % β-sheets by fourier transformed infrared spectroscopy consistent with the generated homology model.Using surface plasmonresonance spectroscopy (SPR) the PINIT domain was shown to bind to STAT3 in a specific concentration dependent manner. Recombinant PINIT-L97A,PINITR99N and PINIT-R99Q mutants, which exhibited similar structural integrity to the wildtype, were found to abrogate binding to STAT3. These findings suggest that these residues form part of a potential binding surface for stat3. In conclusion, this study has provided evidence that the PINIT domain is an important determinant of PIAS3 interaction with STAT3 and that the interaction is mediated by defined conserved residues directly involved in the PINITSTAT3 interaction.
- Full Text:
- Date Issued: 2011
- Authors: Mautsa, Nicodemus
- Date: 2011
- Subjects: Cytokines Immune response Proteins Cancer cells -- Growth -- Regulation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3991 , http://hdl.handle.net/10962/d1004050
- Description: The signal transducer and activator of transcription (STAT) and protein inhibitor of STAT(PIAS) system represent an elegant regulatory mechanism of transcriptional control IN mammalian cytokine signalling. Abnormal activation of the system is associated with immune disorders and a large group of diverse tumours. PIAS3 is a multiple domain protein with distinct functions involved in regulation of cytokine-mediated gene activation pathways.Its over-expression significantly inhibits cell growth and renders cancer cells more sensitive to drugs. The objective of this study was to structurally and biochemically characterise the function of the PIAS3 protein using in silico, in vivo and in vitro analysis approaches.The conservation pattern of the PIAS protein family and critical conserved residues in the PINIT (Proline, Isoleucine, Asparagine, Isoleucine, Tyrosine) domain were identified. The PINIT domain model was generated based on the PINIT domain structure of yeast PIAS3 homologue Siz1 and structural determinants in the PIAS3-STAT3 interaction were evaluated.Guided by the in silico findings, in vivo analysis of the localisation of the PIAS3, mutantderivatives of PIAS3 (PIAS3-L97A, PIAS3-R99N, PIAS3-R99Q), PINIT and acidic domain was conducted. PIAS3 was completely localised in the nucleus while PIAS3 mutants appeared to exhibit diffuse cytoplasmic distribution. The PINIT domain was predominantly localised in the nucleus with some apparent perinuclear staining while the acidic domain exhibited a predominantly perinuclear staining pattern. Further analysis of the PINIT domain and the effect of the mutants on PIAS3-STAT3 interaction were assessed by in vitro analysis. Guided by in silico analysis, the PINIT domain and mutant derivatives of PINIT domain (PINIT-L97A, PINIT-R99N, and PINIT-R99Q) were heterologously expressed in Escherichia coli and subsequently purified using a combination of immobilized metal affinity and size exclusion based chromatography. The size and structural elements of the PINIT domain and its mutants were characterised. The 23 kDa PINIT domain was found to exist as a monomer in solution and its secondary structure was shown to consist of 66 % β-sheets by fourier transformed infrared spectroscopy consistent with the generated homology model.Using surface plasmonresonance spectroscopy (SPR) the PINIT domain was shown to bind to STAT3 in a specific concentration dependent manner. Recombinant PINIT-L97A,PINITR99N and PINIT-R99Q mutants, which exhibited similar structural integrity to the wildtype, were found to abrogate binding to STAT3. These findings suggest that these residues form part of a potential binding surface for stat3. In conclusion, this study has provided evidence that the PINIT domain is an important determinant of PIAS3 interaction with STAT3 and that the interaction is mediated by defined conserved residues directly involved in the PINITSTAT3 interaction.
- Full Text:
- Date Issued: 2011
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:
- Date Issued: 2011
- 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:
- Date Issued: 2011
The druggable antimalarial target 1-deoxy-D-xylulose-5-phosphate reductoisomerase: purfication, kinetic characterization and inhibition studies
- Authors: Goble, Jessica Leigh
- Date: 2011
- Subjects: Antimalarials -- Development Plasmodium falciparum Drug development Plasmodium falciparum -- Purification Plasmodium falciparum -- Inhibitors Enzyme kinetics Malaria -- Chemotherapy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3949 , http://hdl.handle.net/10962/d1004008
- Description: Plasmodium falciparum 1–deoxy–D–xylulose–5 phosphatereductoisomerase (PfDXR) plays a role in isoprenoid biosynthesis in the malaria parasite and is absent in the human host, making this parasite enzyme an attractive target for antimalarial drug design. To characterize PfDXR, it is necessary to produce large quantities of the enzyme in a soluble and functional form. However, the over–production of malarial proteins in prokaryotic host systems often results in the formation of truncated proteins or insoluble protein aggregates. A heterologous expression system was developed for the production of active PfDXR using codon harmonization and tight control of expression in the presence of lac repressor. Yields of up to 2 mg/l of enzyme were reported using the optimised expression system, which is 8 to 10– fold greater than previously reported yields. The kinetic parameters Km, Vmax and kcat were determined for PfDXR; values reported in this study were consistent with those reported in the literature for other DXR enzymes. A three–dimensional model of the malarial drug target protein PfDXR was generated, and validated using structure–checking programs and protein docking studies. Structural and functional features unique to PfDXR were identified using the model and comparative sequence analyses with apicomplexan and non–apicomplexan DXR proteins. Residues Val44 and Asn45, essential for NADPH binding; and catalytic hatch residues Lys224 and Lys226, which are unique to the species of Plasmodium, were mutated to resemble those of E. coli DXR. Interestingly,these mutations resulted in significant reductions in substrate affinity, when compared to the unmutated PfDXR. Mutant enzymes PfDXR(VN43,44AG) and PfDXR(KK224,226NS) also demonstrated a decreased ability to turnover substrate by 4–fold and 2–fold respectively. This study indicates a difference in the role of the catalytic hatch of PfDXR with regards to the way in which it captures substrates. The study also highlights subtle differences in cofactor binding to PfDXR, compared with the well characterized EcDXR enzyme. The validated PfDXR model was also used to develop a novel efficient in silico screening method for potential tool compounds for use in the rational design of novel DXR inhibitors. Following in silico screening of 46 potential DXR inhibitors, a two–tiered in vitro screening approach was undertaken. DXR inhibition was assessed for the 46 novel compounds using an NADPH– ependant DXP enzyme inhibition assay and antimalarial potential was assessed using P.falciparum–infected erythrocyte growth assays. Select compounds were tested in human cells in order to determine whether they were toxic to the host. From the parallel in silico and in vitro drug screening, it was evident that only a single compound demonstrated reasonable potential binding to DXR (determined using in silico docking), inhibited DXR in vitro and inhibited P. falciparum growth, without being toxic to human cells. Its potential as a lead compound in antimalarial drug development is therefore feasible. Two outcomes were evident from this work. Firstly, analogues of known antimalarial natural products can be screened against malaria, which may then lead towards the rational design of novel compounds that are effective against a specific antimalarial drug target enzyme, such as PfDXR. Secondly, the rational design of novel compounds against a specific antimalarial drug target enzyme can be untaken by adopting a coupled in silico and in vitro approach to drug discovery.
- Full Text:
- Date Issued: 2011
- Authors: Goble, Jessica Leigh
- Date: 2011
- Subjects: Antimalarials -- Development Plasmodium falciparum Drug development Plasmodium falciparum -- Purification Plasmodium falciparum -- Inhibitors Enzyme kinetics Malaria -- Chemotherapy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3949 , http://hdl.handle.net/10962/d1004008
- Description: Plasmodium falciparum 1–deoxy–D–xylulose–5 phosphatereductoisomerase (PfDXR) plays a role in isoprenoid biosynthesis in the malaria parasite and is absent in the human host, making this parasite enzyme an attractive target for antimalarial drug design. To characterize PfDXR, it is necessary to produce large quantities of the enzyme in a soluble and functional form. However, the over–production of malarial proteins in prokaryotic host systems often results in the formation of truncated proteins or insoluble protein aggregates. A heterologous expression system was developed for the production of active PfDXR using codon harmonization and tight control of expression in the presence of lac repressor. Yields of up to 2 mg/l of enzyme were reported using the optimised expression system, which is 8 to 10– fold greater than previously reported yields. The kinetic parameters Km, Vmax and kcat were determined for PfDXR; values reported in this study were consistent with those reported in the literature for other DXR enzymes. A three–dimensional model of the malarial drug target protein PfDXR was generated, and validated using structure–checking programs and protein docking studies. Structural and functional features unique to PfDXR were identified using the model and comparative sequence analyses with apicomplexan and non–apicomplexan DXR proteins. Residues Val44 and Asn45, essential for NADPH binding; and catalytic hatch residues Lys224 and Lys226, which are unique to the species of Plasmodium, were mutated to resemble those of E. coli DXR. Interestingly,these mutations resulted in significant reductions in substrate affinity, when compared to the unmutated PfDXR. Mutant enzymes PfDXR(VN43,44AG) and PfDXR(KK224,226NS) also demonstrated a decreased ability to turnover substrate by 4–fold and 2–fold respectively. This study indicates a difference in the role of the catalytic hatch of PfDXR with regards to the way in which it captures substrates. The study also highlights subtle differences in cofactor binding to PfDXR, compared with the well characterized EcDXR enzyme. The validated PfDXR model was also used to develop a novel efficient in silico screening method for potential tool compounds for use in the rational design of novel DXR inhibitors. Following in silico screening of 46 potential DXR inhibitors, a two–tiered in vitro screening approach was undertaken. DXR inhibition was assessed for the 46 novel compounds using an NADPH– ependant DXP enzyme inhibition assay and antimalarial potential was assessed using P.falciparum–infected erythrocyte growth assays. Select compounds were tested in human cells in order to determine whether they were toxic to the host. From the parallel in silico and in vitro drug screening, it was evident that only a single compound demonstrated reasonable potential binding to DXR (determined using in silico docking), inhibited DXR in vitro and inhibited P. falciparum growth, without being toxic to human cells. Its potential as a lead compound in antimalarial drug development is therefore feasible. Two outcomes were evident from this work. Firstly, analogues of known antimalarial natural products can be screened against malaria, which may then lead towards the rational design of novel compounds that are effective against a specific antimalarial drug target enzyme, such as PfDXR. Secondly, the rational design of novel compounds against a specific antimalarial drug target enzyme can be untaken by adopting a coupled in silico and in vitro approach to drug discovery.
- Full Text:
- Date Issued: 2011
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:
- Date Issued: 2011
- 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:
- Date Issued: 2011
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.
- Full Text:
- Date Issued: 2011
- 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.
- Full Text:
- Date Issued: 2011
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