Changes in muscle recruitment, functional strength and ratings of perceived effort during an 8-over bowling spell: impact on performance
- Authors: Barford, Gareth Charles
- Date: 2013
- Subjects: Cricket -- Bowling , Sports -- Physiological aspects , Muscles -- Wounds and injuries , Fatigue , Physical fitness , Cricket injuries
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5102 , http://hdl.handle.net/10962/d1003926 , Cricket -- Bowling , Sports -- Physiological aspects , Muscles -- Wounds and injuries , Fatigue , Physical fitness , Cricket injuries
- Description: Background: The musculoskeletal demands placed on the lower limb musculature of fast bowlers over time have not received much attention. In particular, measures of muscle recruitment changes have, to the author’s knowledge, not been considered. Objective: The present study, therefore sought to establish any associations between an eight over, simulated fast bowling spell, and muscle activation patterns, power output, perceptual demands, and changes in performance. This will enable improvements in the development of training programmes. Methods: Players’ were required to attend two sessions in total. The purpose of the initial session was to collect specific demographic, anthropometric and physiological data and injury history information from each player. In addition, this first session allowed for habituation with the treadmill, the jump meter and all other equipment involved in experimentation. The second testing session involved electrode attachment sites being identified on player’s dominant leg. The areas were then shaved, wiped with an alcohol swab and left to dry, to ensure good connectivity. Pre- and post- measures of muscle activity and functional strength of the lower limbs were recorded in the Department of Human Kinetics and Ergonomics. The protocol took place at the Kingswood High Performance Centre, which is in close proximity to the initial testing site. The protocol involved players bowling eight overs (48 balls). During the protocol, accuracy, ball release speed and perceptual measures were recorded at the end of each over. After the protocol, players were driven back to the Human Kinetics and Ergonomics Department where post-testing measures were completed. The dependable variables of interest were muscle activation, functional strength of the lower limbs, ‘local’ ratings of perceived exertion (RPE), body discomfort, accuracy, and ball release speed. Results: For all muscles it was shown that, as the speed increased so did the muscle activity in players’ lower limbs. There were no significant changes in muscle activity preversus post-protocol. There was however, a general trend of decreasing muscle activity post protocol at higher testing speeds. There were significant (p<0.05) decreases in peak power following the simulated eight over bowling spell. ‘Local’ RPE displayed a significant (P<0.05) increase with each additional over and were observed to reach the ‘heavy’ category. The players’ highest discomfort area was in the lower back, with 13 players perceiving discomfort in this region following the eight over spell. The shoulder and chest were another two areas player’s indicated discomfort with eight players selecting the dominant shoulder. Seven players complained of the dominant side pectoral muscle, leading foot and dominant latissimus dorsi muscle being uncomfortable. Interestingly, the dominant pectoral showed the highest body discomfort ratings amongst players. There were no significant changes in accuracy between overs although there were large interindividual differences in accuracy points between players. The decrease in ball release speed observed during over seven was shown to be significantly (p<0.05) lower than overs one to four. Conclusion: The power output and perceived strain results of the players, appears to indicate the presence of fatigue in players. However, the results are not conclusive, as the fatigue was not shown in muscle recruitment patterns, as well as the body discomfort ratings. There was a non-significant trend observed in the lower limb muscle activation decreasing at higher speeds. Players were able to maintain accuracy. However, the significantly lower ball release speed observed during over seven showed players performance decreasing.
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Characterisation of a plasmodium falciparum type II Hsp40 chaperone exported to the cytosol of infected erythrocytes
- Authors: Maphumulo, Philile Nompumelelo
- Date: 2013
- Subjects: Erythrocytes , Heat shock proteins , Plasmodium falciparum , Molecular chaperones , Malaria -- Prevention -- Research , Protein folding , Proteins -- Analysis , Malaria -- Immunological aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4128 , http://hdl.handle.net/10962/d1015681
- Description: Heat Shock 40 kDa proteins (Hsp40s) partner with heat shock 70 kDa proteins (Hsp70s) in facilitating, among other chaperone activities; correct protein transport, productive protein folding and assembly within the cells; under both normal and stressful conditions. Hsp40 proteins regulate the ATPase activity of Hsp70 through interaction with the J-domain. Plasmodium falciparum Hsp70s (PfHsp70s) do not contain a Plasmodium export element (PEXEL) sequence although PfHsp70-1 and PfHsp70-3 have been located outside of the parasitophorous vacuole. Studies reveal that a type I P. falciparum (PfHsp40) chaperone (PF14_0359) stimulates the rate of ATP hydrolysis of the cytosolic PfHsp70 (PfHsp70-1) and that of human Hsp70A1A. PFE0055c is a PEXEL-bearing type II Hsp40 that is exported into the cytosol of P. falciparum-infected erythrocytes; where it potentially interacts with human Hsp70. Studies reveal that PFE0055c associates with structures found in the erythrocyte cytosol termed “J-dots” which are believed to be involved in trafficking parasite-encoded proteins through the erythrocyte cytosol. If P. falciparum exports PFE0055c into the host cytosol, it may be proposed that it interacts with human Hsp70, making it a possible drug target. The effect of PFE0055c on the ATPase activity of human Hsp70A1A has not been previously characterised. Central to this study was bioinformatic analysis and biochemical characterisation PFE0055c using an in vitro (ATPase assay) approach. Structural domains that classify PFE0055c as a type II Hsp40 were identified with similarity to two other exported type II PfHsp40s. Plasmids encoding the hexahistidine-tagged versions of PFE0055c and human Hsp70A1A were used for the expression and purification of these proteins from Escherichia coli. Purification was achieved using nickel affinity chromatography. The urea-denaturing method was used to obtain the purified PFE0055c whilst human Hsp70A1A was purified using the native method. PFE0055c could stimulate the ATPase activity of alfalfa Hsp70, although such was not the case for human Hsp70A1A in vitro.
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Characterization and application of phthalocyanine-gold nanoparticle conjugates
- Authors: Tombe, Sekai Lana
- Date: 2013
- Subjects: Phthalocyanines , Gold , Zinc , Nanoparticles , Bioconjugates , Photochemistry , Photocatalysis , Electrospinning , Polymers , Pollutants , Phenols , Azo dyes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4293 , http://hdl.handle.net/10962/d1004517 , Phthalocyanines , Gold , Zinc , Nanoparticles , Bioconjugates , Photochemistry , Photocatalysis , Electrospinning , Polymers , Pollutants , Phenols , Azo dyes
- Description: This work presents the syntheses, photophysical and photochemical characterization of arylthio zinc phthalocyanines and their gold nanoparticle conjugates. Spectroscopic and microscopic studies confirmed the formation of the phthalocyanine-gold nanoparticle conjugates which exhibited enhanced photophysicochemical properties in comparison to the phthalocyanines. The studies showed that the presence of gold nanoparticles significantly lowered fluorescence quantum yields and lifetimes. However, this interaction did not restrict the formation of excited singlet and triplet states and hence the formation of singlet oxygen required for photocatalysis. The conjugates showed significantly higher singlet oxygen quantum yields and therefore enhanced photocatalytic activity compared to the phthalocyanines. The zinc phthalocyanines and their gold nanoparticle conjugates were successfully incorporated into electrospun polymer fibers. Spectral characteristics of the functionalized electrospun fibers indicated that the phthalocyanines and phthalocyanine-gold nanoparticle conjugates were bound and their integrity was maintained within the polymeric fiber matrices. The photophysical and photochemical properties of the complexes were equally maintained within the electrospun fibers. The functionalized fibers were applied for the photoconversion of 4-chlorophenol and Orange G as model organic pollutants. , Microsoft� Word 2010 , Adobe Acrobat 9.53 Paper Capture Plug-in
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Contributions of inshore and offshore sources of primary production to the foodweb, and the trophic connectivity between various habitats along a depth-gradient, in Sodwana Bay, Kwazulu-Natal, South Africa
- Authors: Parkinson, Matthew Cameron
- Date: 2013
- Subjects: Marine ecology -- South Africa -- Sodwana Bay , Food chains (Ecology) -- South Africa -- Sodwana Bay , Coastal ecology -- South Africa -- Sodwana Bay , Stable isotopes , Dinoflagellates , Marine algae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5179 , http://hdl.handle.net/10962/d1001630 , Marine ecology -- South Africa -- Sodwana Bay , Food chains (Ecology) -- South Africa -- Sodwana Bay , Coastal ecology -- South Africa -- Sodwana Bay , Stable isotopes , Dinoflagellates , Marine algae
- Description: Sodwana Bay, situated within the iSimangaliso Wetland Park, is ecologically important as it contains high-latitude corals and the most southerly known population of coelacanths. This thesis utilised stable isotope and lipid analyses to investigate the trophic ecology of the area, in particular, understanding the relative contribution of inshore and offshore primary production to consumers inhabiting intertidal and shallow subtidal, coral reef, deep reef, canyon head and pelagic habitats. Seaweeds, excluding certain species of red seaweeds with highly depleted carbon signatures, and phytoplankton, such as diatoms, were found to be the principal sources of primary production for all consumers. Offshore production was typified by dinoflagellates. Particulate organic matter (POM) was spatio-temporally variable. Three distinct productivity periods related to nutrient cycling were noted with enriched carbon signatures and higher organic matter loads associated with warmer water. Inshore primary production was an important source of carbon to consumers in all habitats with the exception of zooplankton that were more reliant on pelagic primary production. Benthic invertebrates reflected a gradient in the utilisation of inshore production, due to the reduced availability of this source further offshore. Consumers at the furthest sites offshore were found to include a substantial quantity of inshore-derived production in their diets. Fishes, which are more mobile, were found to incorporate a similar proportion of inshore production into their diets regardless of where they were collected from.
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Deploying DNSSEC in islands of security
- Authors: Murisa, Wesley Vengayi
- Date: 2013 , 2013-03-31
- Subjects: Internet domain names , Computer security , Computer network protocols , Computer security -- Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4577 , http://hdl.handle.net/10962/d1003053 , Internet domain names , Computer security , Computer network protocols , Computer security -- Africa
- Description: The Domain Name System (DNS), a name resolution protocol is one of the vulnerable network protocols that has been subjected to many security attacks such as cache poisoning, denial of service and the 'Kaminsky' spoofing attack. When DNS was designed, security was not incorporated into its design. The DNS Security Extensions (DNSSEC) provides security to the name resolution process by using public key cryptosystems. Although DNSSEC has backward compatibility with unsecured zones, it only offers security to clients when communicating with security aware zones. Widespread deployment of DNSSEC is therefore necessary to secure the name resolution process and provide security to the Internet. Only a few Top Level Domains (TLD's) have deployed DNSSEC, this inherently makes it difficult for their sub-domains to implement the security extensions to the DNS. This study analyses mechanisms that can be used by domains in islands of security to deploy DNSSEC so that the name resolution process can be secured in two specific cases where either the TLD is not signed or the domain registrar is not able to support signed domains. The DNS client side mechanisms evaluated in this study include web browser plug-ins, local validating resolvers and domain look-aside validation. The results of the study show that web browser plug-ins cannot work on their own without local validating resolvers. The web browser validators, however, proved to be useful in indicating to the user whether a domain has been validated or not. Local resolvers present a more secure option for Internet users who cannot trust the communication channel between their stub resolvers and remote name servers. However, they do not provide a way of showing the user whether a domain name has been correctly validated or not. Based on the results of the tests conducted, it is recommended that local validators be used with browser validators for visibility and improved security. On the DNS server side, Domain Look-aside Validation (DLV) presents a viable alternative for organizations in islands of security like most countries in Africa where only two country code Top Level Domains (ccTLD) have deployed DNSSEC. This research recommends use of DLV by corporates to provide DNS security to both internal and external users accessing their web based services. , LaTeX with hyperref package , pdfTeX-1.40.10
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Development of a novel, quantitative assay for determining the rate of activity of antimalarial drugs
- Authors: Khan, Tasmiyah
- Date: 2013
- Subjects: Assay , ATP , Antimalarials -- Therapeutic use Malaria Malaria -- Drug therapy Adenosine triphosphate Luciferases Plasmodium falciparum
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3884 , http://hdl.handle.net/10962/d1001618
- Description: Malaria, caused by an intracellular Plasmodium parasite, remains a devastating disease, having claimed approximately 655 000 lives worldwide in 2010. The Medicines for Malaria Venture suggests a "single-dose radical cure" as the ideal malaria treatment since rapid clearance of blood-stage parasites and symptom relief improves patient compliance and limits drug resistance. Thus, novel antimalarials should be rapid-acting and assessing their rate of activity is critical to drug discovery. Traditional evaluation of this rate by morphological assessments is flawed by highly subjective, operator-specific interpretations, mainly due to heterogeneous parasite morphology under routine culture conditions. This study aimed to develop an alternative, quantitative assay. Energy is vital for the growth and maintenance of all living organisms. Commercially available kits allow rapid quantification of the cell's energy currency, ATP. Therefore, quantification of parasite ATP shows potential for diagnosing abnormal parasite metabolism and the kinetics of drug action. In this study, a rapid protocol for detecting ATP in Plasmodium falciparum parasites using a luminescence-based kit was developed and optimised. Furthermore, luciferase-expressing transgenic parasites, in which luciferase activity is detected using a similar kit, were acquired. The utility of both methods for evaluating the rate of drug-induced stress was explored using antimalarials with varying modes of action and, presumably, rates of activity. Results showed that parasite ATP remained unchanged, increased or decreased during drug exposure. Morphological examinations by light microscopy and a Recovery assay, aided interpretation of the drug-induced changes in parasite ATP. These investigations suggested that unchanged parasite ATP levels reflect poor drug action, increased ATP levels indicate a stress response and partially compromised viability, while significantly reduced ATP reflects severely compromised viability. Concerning the Luciferase assay, parasite luciferase activity decreased during drug exposure, even in the presence of proteasome inhibitors. Changes in parasite ATP and luciferase activity occurred at rates which suggested that chloroquine is slow-acting, mefloquine has a moderate rate of activity and artemisinin is rapid-acting. These findings are compatible with the expected rates of activity of these established antimalarials. Hence, measurement of parasite ATP and/or luciferase activity may support assessments of parasite health and the kinetics of antimalarial action during drug discovery
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Entomopathogenic fungi for control of soil-borne life stages of false codling moth, Thaumatotibia leucotreta (Meyrick) (1912) (Lepidoptera: Tortricidae)
- Authors: Coombes, Candice Anne
- Date: 2013
- Subjects: Tortricidae , Lepidoptera , Cryptophlebia leucotreta , Insect pests -- Biological control -- South Africa -- Eastern Cape , Tortricidae -- Biological control -- South Africa -- Eastern Cape , Citrus -- Diseases and pests -- Biological control -- South Africa -- Eastern Cape , Entomopathogenic fungi , Fungi as biological pest control agents , Biological pest control agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5607 , http://hdl.handle.net/10962/d1002057 , Tortricidae , Lepidoptera , Cryptophlebia leucotreta , Insect pests -- Biological control -- South Africa -- Eastern Cape , Tortricidae -- Biological control -- South Africa -- Eastern Cape , Citrus -- Diseases and pests -- Biological control -- South Africa -- Eastern Cape , Entomopathogenic fungi , Fungi as biological pest control agents , Biological pest control agents
- Description: False codling moth (FCM), Thaumatotibia leucotreta is an extremely important pest of citrus in South Africa and with the shift away from the use of chemicals, alternate control options are needed. One avenue of control which has only recently been investigated against the soil-borne life stages of FCM is the use of entomopathogenic fungi (EPF). In 2009, 12 entomopathogenic fungal isolates collected from South African citrus orchards showed good control potential during laboratory conducted bioassays. The aim of this study was to further analyse the potential of these isolates through concentration-dose and exposure-time response bioassays. After initial re-screening, concentration-dose response and exposure-time response sandconidial bioassays, three isolates were identified as exhibiting the greatest control potential against FCM in soil, Metarhizium anisopliae var. anisopliae (G 11 3 L6 and FCM Ar 23 B3) and Beauveria bassiana (G Ar 17 B3). Percentage mycosis was found to be directly related to fungal concentration as well as the amount of time FCM 5th instar larvae were exposed to the fungal conidia. LC50 values for the three isolates were not greater than 1.92 x 10⁶ conidia.ml⁻ₑ and at the LC₅₀, FCM 5th instar larvae would need to be exposed to the fungus for a maximum of 13 days to ensure a high mortality level. These isolates along with two commercially available EPF products were subjected to field persistence trials whereby net bags filled with a mixture of autoclaved sand and formulated fungal product were buried in an Eastern Cape citrus orchard. The viability of each isolate was measured on a monthly basis for a period of six months. All isolates were capable of persisting in the soil for six months with the collected isolates persisting far better than the commercially used isolates. Two of the isolates, G 11 3 L6 and G Ar 17 B3, were subjected to small scale laboratory application trials. Two formulations were investigated at two concentrations. For each isolate, each formulation and each concentration, FCM 5th instar larvae were applied and allowed to burrow into the soil to pupate before fungal application or after fungal application. Contact between fungi and FCM host is essential as, in contrast to pre-larval treatments, percentage mortality in post-larval treatments was low for both formulations and both isolates. For isolate G Ar 17 B3, a conidial suspension applied as a spray at a concentration of 1 x 10⁷ conidia.ml⁻ₑ obtained the highest percentage mortality (80 %). For isolate G 11 3 L6 however, both formulations performed equally well at a high, 1 x10⁷ conidia.ml⁻ₑ concentration (conidial suspension: 60 %; granular: 65 %) The results obtained thus far are promising for the control of FCM in citrus, but if these EPFs are to successfully integrate into current FCM control practices more research, some of which is discussed, is essential
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Evaluation of the performance of community-based natural resources management (CBNRM) projects along an aridity gradient in Botswana
- Authors: Mpofu, Khulekani
- Date: 2013
- Subjects: Community-Based Natural Resource Management in Southern Africa (Project) , Natural resources, Communal -- Botswana , Natural resources -- Management -- Botswana , Natural resources -- Management -- Economic aspects -- Botswana , Conservation of natural resources -- Botswana , Conservation of natural resources -- Economic aspects -- Botswana , Arid regions -- Botswana , Natural resources -- Management -- Citizen participation -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4740 , http://hdl.handle.net/10962/d1006063 , Community-Based Natural Resource Management in Southern Africa (Project) , Natural resources, Communal -- Botswana , Natural resources -- Management -- Botswana , Natural resources -- Management -- Economic aspects -- Botswana , Conservation of natural resources -- Botswana , Conservation of natural resources -- Economic aspects -- Botswana , Arid regions -- Botswana , Natural resources -- Management -- Citizen participation -- Botswana
- Description: The Botswana Community Based Natural Resources Management (CBNRM) programme started in 1989. Its aims were to promote sustainable development through sustainable natural resources management and utilisation to improve rural livelihoods. The country CBNRM programme has recorded mixed outcomes and this has raised questions on the programme performance throughout the country. Since the programme has been recognised as one of the eight main livelihood strategies for rural communities in Botswana, there was a need to evaluate the programme performance and determine the factors that influence it. This thesis therefore evaluated the performance of CBNRM projects along an aridity gradient in Botswana and by so doing answered the two research questions of: (1) What factors influence the performance of CBNRM? And (2) how does aridity influence the performance of CBNRM programmes? Performance was determined in terms of financial benefits generated by CBNRM projects and the projects adherence to the CBNRM principles. Data were collected from seven selected CBNRM projects covering three aridity zones (wet, medium rainfall and dry areas) in the country. Data were also collected from key informants and community based organisations (CBO) project managers. Research findings have indicated differences in the performance of CBNRM projects across the identified three aridity zones. Factors that influenced the performance of CBNRM projects varied among the three aridity zones. These factors included: existence of complimentary rules and regulations for managing CBNRM projects; literacy levels of communities involved in CBNRM; ethnic composition of the project communities; historic and current socio-economic trends within communities; collaboration between CBNRM institutions and other local level institutes; amount of benefits generated through the projects; ability of institutions to resolve outstanding issues in time and type of CBNRM project. Research results also indicated that there was variation in the performance of CBNRM projects across the three aridity zones. Aridity was found to directly influence the performance of CBNRM projects through its influence on the amount of revenues that projects generated.
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Evolution of the UG2 unit, Bushveld Complex, South Africa : mineral composition and petrological evidence
- Authors: Everitt, Simon James
- Date: 2013
- Subjects: Textures -- South Africa -- Bushveld Complex Petrology -- South Africa -- Bushveld Complex Chromite -- South Africa -- Bushveld Complex Mineralogy -- South Africa -- Bushveld Complex
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4913 , http://hdl.handle.net/10962/d1001573
- Description: Several disequilibrium textures are found to occur within the hanging wall and footwall of the UG2 chromitite layer of the Bushveld Complex, South Africa. These textures include plagioclase chadacrysts found included within orthopyroxene and clinopyroxene as well as the orthopyroxenes exhibiting round crystal boundaries that appear to be resorbed. Textures found within the UG2 stratigraphy such as linear boundaries and 120° triple junctions at interfaces of adjacent plagioclase or pyroxene grains also suggest that recrystallization has taken place. The presence of both disequilibrium textures and recrystallization textures would suggest that a complex emplacement history has occurred. Ideally, this would be expected to be manifested by minerals of the same type but which are texturally distinct showing different composition. However this has been found not to be the case; minerals that suggest disequilibrium textures show similar compositions to the minerals which appear to have formed in equilibrium. This is also the same for recrystallized crystals which show the same compositions as crystals that have not been recrystallized. For example tabular clinopyroxene, which has a compositional range of En 44.6 to En 50.5, is indistinguishable from clinopyroxene occuring as discontinuous rims, En 44.3-48.2, and as intergranular necking connecting primocrysts of orthopyroxene ( En 44.3-50.4). Similarly, plagioclase occurring as inclusions with An 66.3-76.0 is indistinguishable from plagioclase occurring as zoned or recrystallized interstitial grains ( An 69.0- An 77.4). Compositional variation has however, been found to be controlled to an extent by stratigraphy in that minerals show different compositions within one layer to the same minerals within another layer, consistent with an evolving magma composition. It is concluded therefore that while composition is not texturally controlled it is to an extent stratigraphy controlled and that the evidence collected within the study supports two models for the formation of chromite within the Bushveld complex. The evidence is consistent with a combination of the magma mixing model and magma injection model to account for the textures and compositional variations found within the study. The evidence may also show support for models involving late modification of minerals by magmatic fluids but not as prominently as for the models mentioned above , Microsoft� Word 2010 , Adobe Acrobat 9.53 Paper Capture Plug-in
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Falcipains as malarial drug targets
- Authors: Kanzi, Aquillah Mumo
- Date: 2013
- Subjects: Malaria Malaria -- Chemotherapy Plasmodium falciparum Antimalarials -- Development Cysteine proteinases Cysteine proteinases -- Inhibitors Papain Drug development Bioinformatics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3897 , http://hdl.handle.net/10962/d1003842
- Description: Malaria is an infectious disease caused by parasites of the Plasmodium genus with mortality rates of more than a million annually, hence a major global public health concern. Plasmodium falciparum (P. falciparum) accounts for over 90% of malaria incidence. Increased resistance to antimalarial drugs by the Plasmodium parasite, coupled with the lack of an effective malaria vaccine necessitates the urgent need for new research avenues to develop novel and more potent antimalarial drugs. This study focused on falcipains, a group of P. falciparum cysteine proteases that belong to the clan CA and papain family C1, that have emerged as potential drug targets due to their involvement in a range of crucial functions in the P. falciparum life cycle. Recently, falcipain-2 has been validated as a drug target but little is known of its Plasmodium orthologs. Currently, there are several falcipain inhibitors that have been identified, most of which are peptide based but none has proceeded to drug development due to associated poor pharmacological profiles and susceptibility to degradation by host cysteine proteases. Non-peptides inhibitors have been shown to be more stable in vivo but limited information exists. In vivo studies on falcipain-2 and falcipain-3 inhibitors have also been complicated by varying outcomes, thus a good understanding of the structural variations of falcipain Plasmodium orthologs at the active site could go a long way to ease in vivo results interpretation and effective inhibitor design. In this study, we use bioinformatics approaches to perform comparative sequence and structural analysis and molecular docking to characterize protein-inhibitor interactions of falcipain homologs at the active site. Known FP-2 and FP-3 small molecule nonpeptide inhibitors were used to identify residue variations and their effect on inhibitor binding. This was done with the aim of screening a collection of selected non-peptide compounds of South African natural origin to identify possible new inhibitor leads. Natural compounds with high binding affinities across all Plasmodium orthologs were identified. These compounds were then used to search the ZINC database for similar compounds which could have better binding affinities across all selected falcipain homologs. Compounds with high binding affinities across all Plasmodium orthologs were found.
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Fish and fisheries of Bangweulu wetlands, Zambia
- Authors: Huchzermeyer, Carl Friedrich
- Date: 2013
- Subjects: Bangweulu Swamps (Zambia) , Fisheries -- Zambia -- Bangweulu Swamps , Fishes -- Zambia -- Bangweulu Swamps , Fishery management -- Zambia -- Bangweulu Swamps , Fishing -- Zambia -- Bangweulu Swamps , Fishing -- Economic aspects -- Zambia -- Bangweulu Swamps , Fish stock assessment -- Zambia -- Bangweulu Swamps , Fish as food -- Zambia -- Bangweulu Swamps , Conservation of natural resources -- Zambia -- Bangweulu Swamps , Sustainable development -- Zambia -- Bangweulu Swamps
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5203 , http://hdl.handle.net/10962/d1003927 , Bangweulu Swamps (Zambia) , Fisheries -- Zambia -- Bangweulu Swamps , Fishes -- Zambia -- Bangweulu Swamps , Fishery management -- Zambia -- Bangweulu Swamps , Fishing -- Zambia -- Bangweulu Swamps , Fishing -- Economic aspects -- Zambia -- Bangweulu Swamps , Fish stock assessment -- Zambia -- Bangweulu Swamps , Fish as food -- Zambia -- Bangweulu Swamps , Conservation of natural resources -- Zambia -- Bangweulu Swamps , Sustainable development -- Zambia -- Bangweulu Swamps
- Description: Bangweulu Wetlands is a 6000 km² public-private-partnership conservation area in northeastern Zambia, lying on the south-eastern margins of the Bangweulu Swamps, Congo River system. The area is important for wildlife conservation, tourism and as a fishing ground for the local inhabitants. This study provides a baseline of the fish and fisheries of this area. The conservation area is situated on the transition zone between woodland, floodplain and swamp. A total of 42 fish species representing 12 taxonomic families were collected. The fish fauna of the area was characterised by a diversity of small cyprinids (14 species), cichlids (9 species), clariid catfishes (4 species) and mormyrids (4 species). Species such as Clarias gariepinus, C. ngamensis, Marcusenius macrolepidotus, Tilapia rendali, T. sparrmanii and several small Barbus species were shared with adjacent floodplain systems such as the upper Zambezi and Kafue rivers. Fishing was undertaken by fishing groups consisting of a fisherman and his family, or a group of men fishing together. Access to the fishing grounds was controlled by traditional fishing leaders, who collected tribute from fishermen. Fishing groups utilised fixed, distinct fishing areas determined by ancestry. The most important time for fishing was during the drawdown phase of the floodplains, from March until June. During the dry season fewer groups were engaged in fishing, with many having returned to farming activities. The main fishing methods of the floodplain fishery were basket traps and mosquito-mesh funnel nets set into earth fish barriers (fish weirs) constructed on the plains, various mesh sizes of gillnets, hook longlines and seine nets. The use of fish spears, drag baskets and piscicides was of lesser importance. Most fishing gears were constructed of a variety of natural and modern, manufactured materials. The fishery was multi-species and 23 fish species were recorded from in catch. The three most important species in the catches were C. gariepinus, T. rendalli and M. macrolepidotus. Together these contributed 67% by weight to the catch. Catch-per-unit-effort (CPUE) for the different gears was 0.4 ± 0.3 kg.trap.night⁻¹ for basket traps, 2.7 ± 4.6 kg.net.night⁻¹ for funnel nets, 0.3 ± 0.5 kg.50 m net.night⁻¹ for gill nets, 3.5 ± 6.3 kg.100 hooks.night⁻¹ for longlines, 1.79 ± 1.11 kg.haul⁻¹ for mosquito-mesh seine nets and 6.87 ± 6.27 kg.haul⁻¹ for larger-mesh seine nets. The weight of average daily landings of fishing groups, using a variety of gears was 7.8 ± 7.4 kg. Fishermen were able to maintain the same catch rate between dry and wet seasons, with no significant differences (p < 0.05) in daily landings between seasons. Yield per fisherman for a seven month season, which required 2-3 relocations due to falling water level, was 1.64 t based on catch assessment, and 1.9 t from a socio-economic survey. A tentative yield per area estimate for the area was 2I7 kg.ha⁻¹ over the three month shallow-floodplain fishing season. Most fish landed in the fishery were processed into sundried or smoke-dried products. These were used for 1) home consumption, 2) trade with village farmers (from up to 70 km inland of the fishing grounds) in exchange for staple starch meal, and 3) sold to urban fish traders, reaching markets as distant as Lubumbashi in Democratic Republic of Congo. Fish traders toured fishing camps to buy fish, supporting auxiliary industries such as transport and accommodation services. The price for dried fish at source was 3.14 ± 1.34 USDlkg and the market price reported for the Zambian Copperbelt was 6.14 ± 2.54 USD/kg. Typical returns on investment in fish trading were estimated as 68-77%. The fishery was considered to be biologically and socially sustainable. By harvesting a seasonally transient assemblage of species with high productivity and biological turnover rates and with life histories adapted to high mortality, fishermen were able to maintain a stable and viable livelihood. Management recommendations for the area were that a fisheries management plan be developed that would seek to strengthen the traditional system of rights-allocation, address problems between fishing and tourism activities, and enhance communication between fisheries and conservation stakeholders. To do this it was recommended that: 1) conservation authorities recognise the importance of the fishery, 2) no changes to current effort levels and fishing methods were necessary, 3) points 1 and 2 above be used to improve communication and trust between conservation authorities and fishermen, 4) customary resource-access mechanisms be understood and strengthened so that local inhabitants' rights to the resource are protected, 5) fishermen help formulate and accept conservation and tourism rules, 6) tourists and guides be made aware of the function of the fishery, 7) a fisheries management forum of key community, government and conservation stakeholders be formed to shape and implement the fisheries management plan, 8) locally-adapted bylaws be created to legitimise crucial floodplain gears currently considered illegal (e.g. mosquito-net gears, fish weirs), 9) no intervention to formalise fish trading be made, and 10) a trained person with a fisheries background be hired oversee the implementation of the recommendations.
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Governance and management of urban trees and green spaces in South Africa: ensuring benefits to local people and the environment
- Authors: Chishaleshale, Mwale
- Date: 2013
- Subjects: Trees in cities -- South Africa , Urban forestry -- South Africa , Community forestry -- South Africa , City planning -- South Africa , Human-plant relationships -- South Africa , Urban ecology (Biology -- South Africa , Urban ecology (Sociology) -- South Africa , Natural resources -- South Africa , Trees in cities -- Law and legislation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4739 , http://hdl.handle.net/10962/d1006035 , Trees in cities -- South Africa , Urban forestry -- South Africa , Community forestry -- South Africa , City planning -- South Africa , Human-plant relationships -- South Africa , Urban ecology (Biology -- South Africa , Urban ecology (Sociology) -- South Africa , Natural resources -- South Africa , Trees in cities -- Law and legislation -- South Africa
- Description: In the face of rapid urbanization and global climate change, urban trees and green spaces (UTGS) can contribute to the welfare of people and the urban environment. Urban trees and green spaces can assist to address urbanization challenges related to environmental degradation. While functions of UTGS have been well documented in the developed world, they have not yet received full attention in much of sub-Saharan Africa. Consequently, UTGS are under threat from urban development and fragmentation. Notably, the problems associated with UTGS also fall into the governance realm and indications are that poor governance and management of UTGS can negatively influence the potential benefits of UTGS to local people and the environment. This formed a basis for this research. The main objective of the study was to determine the current governance and management approaches to UTGS in South Africa. Through document search and review, the study determined the governance institutions influencing UTGS at national level and at provincial level (in the Limpopo and Eastern Cape Provinces). Face-to-face and online survey methods were used to determine the extent to which 28 local municipalities had adopted planned, systematic and integrated management of UTGS. The snowball approach was used to determine the key actors involved in UTGS activities and interviews were conducted to establish the roles and capabilities of these actors. A total of 540 household interviews were conducted to determine the institutional factors influencing local peoples’ ability to access, plant and use UTGS. The findings of the study showed that UTGS have not been adequately covered in existing governance institutions and practice at national and provincial levels. Local government municipalities were not managing their UTGS in a planned or systematic manner due to constraining factors such as insufficient funds, insufficient personnel, lack of equipment and lack of political support. Only 7.1 % of the surveyed municipalities had an urban tree management plan and an estimate of the urban tree stock; 32.1 % had tree policies; 28.6 % had tree bylaws; 21.4 % had tree planting schedules; 10.7 % had tree maintenance schedules and only 3.6 % had tree inspection schedules. Key actors involved in UTGS activities differed among levels of government. The actors included national and provincial government departments, local government municipalities, Non-Governmental Organizations, private sector companies and local volunteers. Most of the actors, however, either planted trees or provided tree seedlings to municipalities and the local people. Tenure security was a key institutional factor affecting peoples’ ability to plant, use or even remove trees from their residential plots. The same applied to trees in the streets and public parks. Whereas most respondents did not require permission to plant (79.8 %) or remove (75 %) trees on their residential plots, a majority of them required permission to plant and remove trees from streets (over 70 %) and public parks (over 80 %). However, with regard to planting and removing urban trees in public open spaces, 54% of the respondents indicated that permission was not required suggesting a lack of clarity among local residents on the issue. Overall, the findings of this study indicate that there is no political recognition and support for UTGS at almost all levels of government. This has resulted in the lack of incorporation of UTGS in urban planning and development and has caused UTGS to receive limited funding to permit planned and systematic management. Given the current rates of urbanization and urban development, the lowly prioritised UTGS are vulnerable to exploitation. To conserve UTGS and promote their potential contribution to local people and the environment, UTGS must be recognized and placed on political and development agendas. There is a need to develop national guidelines for UTGS management, assess the extent of the urban forest resource in local municipalities, clearly define the roles and capabilities of different actors, integrate UTGS in the urban planning and development system, and most of all seek to involve the local people in overall management and governance of UTGS.
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Growth and gonad size in cultured South African abalone, Haliotis midae
- Authors: Riddin, Nicholas Alwyn
- Date: 2013
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- Growth -- South Africa , Abalones -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5180 , http://hdl.handle.net/10962/d1001651 , Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- Growth -- South Africa , Abalones -- Feeding and feeds -- South Africa
- Description: According to farm records, cultured Haliotis midae (50-70 g.abalone⁻¹) were growing 10% slower in winter when compared to summer. This reduction in growth rate also coincided with enlarged gonads. Initial trials showed that there were differences in mean monthly growth rates ranging from 1.97 – 5.14 g abalone⁻¹ month⁻¹, and gonad bulk index (GBI) also varied between months (GBI range: 26.88 ± 12.87 to 51.03 ± 34.47). The investment of energy into gonad tissue growth did not compromise whole body growth as the abalone continued to gain weight throughout the reproductive periods, probably due to gonadal growth. Growth of this size class of abalone was not influenced by water temperature or day length, suggesting favourable on-farm culture conditions (regression analyses, p > 0.05). There is no need to implement a seasonal dietary regime. Cultured H. midae were fed artificial diets with different protein sources, including only soya, only fishmeal, a combination of soya and fishmeal, and these were compared to kelp-fed abalone. Kelp-fed abalone grew slower than those fed artificial feeds (p>0.05). Gonad growth was the greatest when soya meal was included in the diet (average GBI: 74.91 ± 23.31), while the average gonad size of abalone fed the fishmealbased diet had gonads which were 38% smaller, and kelp-fed abalone had gonads which were 75% smaller than those of the abalone fed on diets containing soya meal. The increased gonad mass in abalone fed on diets including soya meal could be attributed to phytoestrogenic activity, as a result of the presence of isoflavones found in the soya plant; this remains to be tested. The use of soya in brood stock diet development is advised. The influence of dietary protein to energy ratio (1.41 – 2.46 g MJ⁻¹) on growth and gonad size was tested. Protein and energy levels within the ranges tested (22 and 33% protein; 13.5 and 15.6 MJ kg⁻¹) did not interact to influence growth rates of cultured H. midae. GBI increased from 50.67 ± 4.16 to 83.93 ± 9.35 units as a function of dietary protein to energy ratio (y = 42.02 x⁰·⁸¹; r² = 0.19; regression analysis: F₁¸₃₈ = 8.9; p = 0.005). In addition, protein level influenced gonad size, with gonad growth being greater in abalone fed the high protein diet (factorial ANOVA: F₁¸₃₂ = 7.1, p = 0.012). Canning yields were reduced by 7% when the protein content was increased, while increasing the quantity of dietary energy improved canning yields by ~ 6% (one-way ANOVA: F₁¸₂₈ = 14.4, p= 0.001). The present study provided evidence that although growth rates are varying seasonally, reproductive investment is not hindering weight gain. Gonad growth can be influenced if desired by farms, depending on the level of soya inclusion, as well as the protein to energy ratio in the diet. Monthly variation in growth and gonad size, as well as the influence of diet on gonad growth were highlighted, and the implications for farm application and further research were discussed.
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High-throughput modelling and structural investigation of cysteine protease complexes with protein inhibitors
- Authors: Kroon, Matthys Christoffel
- Date: 2013
- Subjects: Cysteine proteinases Cysteine proteinases -- Inhibitors Papain Cystatins Malaria -- Chemotherapy Homology (Biology) Protein-protein interactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3885 , http://hdl.handle.net/10962/d1001619
- Description: The papain-like cysteine protease family (C1 proteases) is highly important because of its involvement in research and industrial applications and its role in various human diseases. Protein inhibitors are an important aspect of C1 protease biology and are relevant to its clinical, industrial and research importance. To study the interaction between the proteases and the inhibitors it is very useful to have accurate structural models of the protease-inhibitor complexes. To this end, a high-throughput pipeline for modelling complexes of papain-like cysteine proteases and protein inhibitors was implemented and tested (Tastan Bishop & Kroon, 2011). The pipeline utilizes a novel technique for obtaining modelling templates by using superpositioning to combine coordinates from separate experimental structures. To test the pipeline, models of complexes with known structures (test set) were modelled using many different templates and the resultant models evaluated to compare the quality of the different templates. It was found that use of the new technique to obtain templates did not introduce significant errors, while allowing closer homologs to be used for modelling - leading to more accurate models. The test set models were also used to evaluate certain steps of the modelling protocol. The effect of Rosetta energy minimization on model accuracy and the use of Rosetta energy and DOPE Z-score values to identify accurate models were investigated. Several complexes were then modelled using the best available templates according to criteria informed by the previous results. A website was built that allows a user to download any of the metrics or models produced in the study. This website is accessible at http://rubi.ru.ac.za/cpmdb
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Identification and evaluation of key factors for rehabilitation of shores denuded of mussels (Perna perna) along the Transkei Coast, South Africa
- Authors: Macala, Lukholo
- Date: 2013
- Subjects: Mussels -- Ecology -- South Africa -- Transkei , Mussels -- Conservation -- South Africa -- Transkei , Mussels -- Growth -- South Africa -- Transkei , Mussels -- Effect of human beings on -- South Africa -- Transkei , Mussels -- Reproduction -- South Africa -- Transkei , Perna -- South Africa -- Transkei
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5611 , http://hdl.handle.net/10962/d1002966 , Mussels -- Ecology -- South Africa -- Transkei , Mussels -- Conservation -- South Africa -- Transkei , Mussels -- Growth -- South Africa -- Transkei , Mussels -- Effect of human beings on -- South Africa -- Transkei , Mussels -- Reproduction -- South Africa -- Transkei , Perna -- South Africa -- Transkei
- Description: Mussels play an important supplementary role in the diet of local communities on the Transkei coast in the Eastern Cape province of South Africa. The exploitation of mussels date back to about 1350 years ago, but in the last 3 decades, exploitation of the brown mussel Perna perna has become unsustainable with mussels collected as small as 30-40mm when they are only just sexually mature. Dye and Dyantyi (2002) developed a technique to rehabilitate areas denuded of adult mussels. The government sponsored Mussel Rehabilitation Project (MRP) to use this technique but only some sites have been successfully rehabilitated, reaching c. 80 % cover within a year whilst others only reach about 5%. At an unexploited site (Riet River), I tested the effects of mussel size and wave strength on the effectiveness of the rehabilitation technique, hypothesizing that different size classes may respond differently due to differences in their energy allocation (growth vs reproduction), while wave action determines food supply. Small (1-2cm) and large mussels (3-4cm) were deployed for rehabilitation at 2 exposed and 2 sheltered sites, separated by 100s m. A similar study was repeated in Coffee Bay where shores are exploited. Six sites were selected, 3 sites that had been successfully rehabilitated and 3 that were unsuccessful according to the MRP. Again, two size classes were used but these differed from the first experiment. Mussels of 3-4cm size were now rated as small and 5-6cm as large. Two methods were used to re-attach mussels, the original and the same method with the addition of mesh bags during mussel deployment. Treatments were examined on three occasions at approximately one month intervals. At Riet River, the sites chosen did not show differences in wave strength (measured using dynamometers) or water flux (measured using erosion of cement balls) so that water motion was excluded from the analyses. Small mussels grew faster and had weaker attachment than large mussels. There was no difference in condition index between small and large mussels, or in the numbers of recruits settling among the byssus threads of deployed mussels of the two size classes. In Coffee Bay, there was no relationship between rehabilitation success and maximum wave force, and no difference in bulk water flux among sites. Small mussels deployed using mesh bags survived better than non-meshed or large mussels of either treatment. There was no difference in condition index (CI) between mesh and no-mesh, or between small and large mussels. As in the case of Riet River, small mussels grew faster than large mussels, but large mussels attached stronger than small mussels, with no effect of mesh. Although the factors that improve reseeding of mussels can be identified (use of mesh, use of small mussels, choice of sites with high recruitment rates), successful long-term rehabilitation requires appropriate subsequent management of re-seeded sites.
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Immobilisation of electric eel acetylcholinesterase on nanofibres electrospun from a nylon and chitosan blend
- Authors: Mafuma, Tendai Simbarashe
- Date: 2013
- Subjects: Acetylcholinesterase Acetylcholinesterase -- Inhibitors Electric eel Biosensors Immobilized enzymes Pesticides -- Environmental aspects Pesticides -- Toxicology Nylon Chitosan Nanofibers Electrospinning
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3886 , http://hdl.handle.net/10962/d1001620
- Description: Organophosphates and carbamates are potent inhibitors of the neurotransmitter acetylcholinesterase. This inhibition results in the blocking of nerve signal transference into the post synaptic neuron leading to loss of muscle action and death. Because of the universal mechanisms of signal transduction in animals, these inhibitors have been widely used as agricultural pesticides as well as chemical warfare agents (nerve agents). Health issues associated with pesticide usage result from the fact that both the pesticides and their breakdown products often end up in water and food sources as well as in the soil. As a result, there has been an increase in the number of studies aimed at the detection of these pesticides in the environment. One popular research area is enzyme based biosensor construction. Some important criteria for consideration during the construction of biosensors are the importance of a suitable solid support as well as the enzyme immobilisation method. Recently, there has been increased interest in using nano-scale material e.g. using nanoparticles as enzyme support material. This is largely due to their advantages such as large surface area to volume ratio as well as reduced mass transfer resistance. Electrospinning is a straight forward and cost effective method for producing nanofibres from any soluble polymer(s). The applications of electrospun nanofibres have been reported in clinical studies, biofuel production as well as bioremediation. In this study two polymers were selected: nylon for its mechanical stability and chitosan for its biocompatibility and hydrophilicity, for the fabrication of electrospun nanofibres which would function as immobilisation support material for acetylcholinesterase. The first objective of this study was to electrospin nanofibres from a nylon-6 and chitosan blend solution. A binary solvent system consisting of formic acid and acetic acid (50:50) successfully dissolved and blended the polymers which were subsequently electrospun. Scanning electron microscopy characterisation of the nanofibres showed that (i) a nylon-6: chitosan ratio of 16%: 3% resulted in the formation of bead free nanofibres and (ii) the fibres were collected in non-woven mats characterised by different size nanofibres with average diameters of 250 nm for the main fibres and 40 nm for the smaller nanofibres. Fourier transform infra-red (FT-IR) analysis of the nanofibres indicated that a new product had been formed during the blending of the two polymers. The second aim of the study was to carry out a facile immobilisation of electric eel acetylcholinesterase via glutaraldehyde (GA) cross-linking. Glutaraldehyde solution 5% (v/v) resulted in the immobilisation of 0.334 mg/cm² of acetylcholinesterase onto the nanofibres. The immobilisation procedure was optimised with reference to acetylcholinestease and crosslinker concentrations, incubation time and the cross-linking method. A comparative investigation into the optimum pH and temperature conditions, pH and thermal stabilities, substrate and inhibition kinetics was then carried out on free and immobilised acetylcholinesterase. The final objective of this study was to determine the storage stabilities of the immobilised and free enzymes as well as the reusability characteristics of the immobilised acetylcholinesterase. Several conclusions were drawn from this study. Acetylcholinesterase was successfully immobilised onto the surface of nylon-6:chitosan nanofibres with retention of its activity. There was a shift in the pH optimum of the immobilised acetylcholineseterase by 0.5 units towards a neutral pH. Although both free and immobilised acetylcholinesterase exhibited the same optimum temperature, immobilised acetylcholinesterase showed enhanced thermal stability. In terms of pH stability, immobilised acetylcholinesterase showed greater stability at acidic pH whilst free acetylcholinesterase was more stable under alkaline pH conditions. Relative to free acetylcholinesterase, the immobilised enzyme showed considerable storage stability retaining ~50% of its activity when stored for 49 days at 4°C. Immobilised acetylcholinesterase also retained > 20% of its initial activity after 9 consecutive reuse cycles. When exposed to fixed concentrations of carbofuran or demeton-S-methyl sulfone, immobilised acetylcholinesterase showed similar inhibition characteristics to that of the free enzyme. The decrease in enzyme activity observed after immobilisation to the nanofibres may have been due to several reasons which include some enzyme molecules being immobilised in structural conformations which reduced substrate access to the catalytic site, participation of the catalytic residues in immobilisation and enzyme denaturation due to the reaction conditions used for acetylcholinesterase immobilisation. Similar observations have been widely reported in literature and this is one of the major drawbacks of enzyme immobilisation. In conclusion, nylon-6:chitosan electrospun nanofibres were shown to be suitable supports for facile acetylcholinesterase immobilisation and the immobilised enzyme has potential for use in pesticide detection. Future recommendations for this study include a comparative study of the GA cross-linking method for AChE immobilisation which will lead to more intensely bound enzyme molecules to prevent non-specific binding. An investigation into the effect of inhibitors on stored immobilised AChE, as well as reactivation and reuse studies, may also be useful for determining the cost-effectiveness of reusing immobilised AChE for pesticide detection in environmental water samples. Several models have been designed for the determination of the kinetic parameters for immobilised enzymes. These take into account the mass transfer resistance as well as the overall charge of the immobilisation matrix. The use of these models to analyse experimental data will give a clear understanding of the effects of immobilisation on enzyme activity
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In-silico analysis of Plasmodium falciparum Hop protein and its interactions with Hsp70 and Hsp90
- Authors: Clitheroe, Crystal-Leigh
- Date: 2013
- Subjects: Plasmodium falciparum , Heat shock proteins , Molecular chaperones , Homology (Biology) , Protein-protein interactions , Malaria -- Chemotherapy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3896 , http://hdl.handle.net/10962/d1003819 , Plasmodium falciparum , Heat shock proteins , Molecular chaperones , Homology (Biology) , Protein-protein interactions , Malaria -- Chemotherapy
- Description: A lessor understood co-chaperone, the Hsp70/Hsp90 organising protein (Hop), has been found to play an important role in modulating the activity and co-interaction of two essential chaperones; Hsp90 and Hsp70. The best understood aspects of Hop so far indicate that residues in the concave surfaces of the three tetratricopeptide repeat (TPR) domains in the protein bind selectively to the C-terminal motifs of Hsp70 and Hsp90. Recent research suggests that P. falciparum Hop (PfHop), PfHsp90 and PfHsp70 do interact and form complex in the P. falciparum trophozooite and are overexpressed in this infective stage. However, there has been almost no computational research on malarial Hop protein in complex with other malarial Hsps.The current work has focussed on several aspects of the in-silico characterisation of PfHop, including an in-depth multiple sequence alignment and phylogenetic analysis of the protein; which showed that Hop is very well conserved across a wide range of available phyla (four Kingdoms, 60 species). Homology modelling was employed to predict several protein structures for these interactions in P. falciparum, as well as predict structures of the relevant TPR domains of Human Hop (HsHop) in complex with its own Hsp90 and Hsp70 C-terminal peptide partners for comparison. Protein complex interaction analyses indicate that concave TPR sites bound to the C-terminal motifs of partner proteins are very similar in both species, due to the excellent conservation of the TPR domain’s “double carboxylate binding clamp”. Motif analysis was combined with phylogenetic trees and structure mapping in novel ways to attain more information on the evolutionary conservation of important structural and functional sites on Hop. Alternative sites of interaction between Hop TPR2 and Hsp90’s M and C domains are distinctly less well conserved between the two species, but still important to complex formation, making this a likely interaction site for selective drug targeting. Binding and interaction energies for all modelled complexes have been calculated; indicating that all HsHop TPR domains have higher affinities for their respective C-terminal partners than do their P. falciparum counterparts. An alternate motif corresponding to the C-terminal motif of PfHsp70-x (exported to the infected erythrocyte cytosol) in complex with both human and malarial TPR1 and TPR2B domains was analysed, and these studies suggest that the human TPR domains have a higher affinity for this motif than do the respective PfHop TPR domains. This may indicate potential for a cross species protein interaction to take place, as PfHop is not transported to the human erythrocyte cytosol.
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Information technology audits in South African higher education institutions
- Authors: Angus, Lynne
- Date: 2013 , 2013-09-11
- Subjects: Electronic data processing -- Auditing , Delphi method , Education, Higher -- Computer networks -- Security measures , Information technology -- Security measures , COBIT (Information technology management standard) , IT infrastructure library , International Organization for Standardization
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4615 , http://hdl.handle.net/10962/d1006023 , Electronic data processing -- Auditing , Delphi method , Education, Higher -- Computer networks -- Security measures , Information technology -- Security measures , COBIT (Information technology management standard) , IT infrastructure library , International Organization for Standardization
- Description: The use of technology for competitive advantage has become a necessity, not only for corporate organisations, but for higher education institutions (HEIs) as well. Consequently, corporate organisations and HEIs alike must be equipped to protect against the pervasive nature of technology. To do this, they implement controls and undergo audits to ensure these controls are implemented correctly. Although HEIs are a different kind of entity to corporate organisations, HEI information technology (IT) audits are based on the same criteria as those for corporate organisations. The primary aim of this research, therefore, was to develop a set of IT control criteria that are relevant to be tested in IT audits for South African HEIs. The research method used was the Delphi technique. Data was collected, analysed, and used as feedback on which to progress to the next round of data collection. Two lists were obtained: a list of the top IT controls relevant to be tested at any organisation, and a list of the top IT controls relevant to be tested at a South African HEI. Comparison of the two lists shows that although there are some differences in the ranking of criteria used to audit corporate organisations as opposed to HEIs, the final two lists of criteria do not differ significantly. Therefore, it was shown that the same broad IT controls are required to be tested in an IT audit for a South African HEI. However, this research suggests that the risk weighting put on particular IT controls should possibly differ for HEIs, as HEIs face differing IT risks. If further studies can be established which cater for more specific controls, then the combined effect of this study and future ones will be a valuable contribution to knowledge for IT audits in a South African higher education context.
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Interaction of metallic nanoparticles with biomedical enzyme target: neuronal nitric oxide synthase
- Authors: Ngqwala, Nosiphiwe Patience
- Date: 2013
- Subjects: Nitric-oxide synthase Alzheimer's disease Arginine Nanoparticles Biochemical markers Biochemical markers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3875 , http://hdl.handle.net/10962/d1001536
- Description: Alzheimer's disease (AD) is the most common type of dementia characterized by intracellular appearance of neurofibrillary tangles, synaptic and neuronal loss; and extracellular accumulation of amyloid-β (Aβ) peptide in senile plaques. The initial causes leading to AD are unknown, and the available treatments are only effective at slowing the degeneration process. The accumulation of arginine in the brain of Alzheimer patients indicates a possible disruption of enzymes responsible for its metabolism. One such enzyme is neuronal nitric oxide synthase (nNOS) and controlling its activity by interacting with nanoparticles may lead to a delay in the onset of the disease. Neuronal nitric oxide synthase was purified using DEAE-Sephacel ion exchange resulting in 10 % yield, 0.43 fold recovery and specific activity 0.09 U/mg. The enzyme was found to be a dimer with a molecular mass of 150 kDa. Characterisation of the nNOS showed an optimum temperature and pH of 50°C and 7.5 respectively, and it was relatively stable at the optimum conditions (t½ = 100 min). The purity was analysed by SDS-PAGE followed by Western blot. Purified nNOS was challenged with 3-7 nm silver and 4-15 nm gold nanoparticles of between synthesized chemical using AgNO3 and either sodium borohydride or sodium citrate. Results showed that gold nanoparticles are more effective at low concentration (5 μM) than silver nanoparticles due to their size difference. Incubation of different concentration of nanoparticles (5, 15, 25, 50 μM) with the purified nNOS showed an initial decrease of 5% in enzyme activity which over time was restored to 80%. This suggests that different nanoparticles are produced in different sizes and interaction over a given time may result in enzyme association–dissociation mechanism. Inhibition studies showed a strong binding of both nanoparticles with Ki values of 1.4 μM and 0.2 μM for silver and gold, respectively. Both nanoparticles inhibited the activity of nNOS extensively as they bound strongly to the inhibition site on the enzyme and were more in contact with fluorophores nanoparticles. This was confirmed by fluorimetry with binding constants of 0.0084 μM and 0.01092 μM for silver and gold, respectively. Results of this study suggest that silver and gold nanoparticles competitively inhibit nNOS.
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Interactions of arbuscular mycorrhizal fungi and spore-associated bacteria
- Authors: Ridsdale, Carmen Jane
- Date: 2013
- Subjects: Mycorrhizal fungi , Host plants , Bacteria
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4159 , http://hdl.handle.net/10962/d1018269
- Description: Arbuscular mycorrhizal (AM) fungi are naturally occurring in roots of terrestrial plants. AM fungi are capable of benefiting the host plant through various mechanisms such as enhanced nutrient supply, alleviation of environmental stress and inhibition of plant fungal pathogens. AM fungal spore-associated bacteria have been previously isolated and shown to have plant growthpromoting (PGP) abilities by several authors. Some bacterial isolates are able to promote AM fungal colonisation of host plants and are known to be mycorrhizal helper bacteria (MHB). This study focused on the isolation of AM fungal spore-associated bacteria, characterization of the isolates according to plant growth promoting abilities and evaluation of their potential to enhance plant growth and mycorrhizal colonisation. AM fungi were extracted from soils sampled from natural indigenous forest sources, raspberry (Rubus idaeus cv. Heritage) and strawberry (Fragaria ananassa) farms in South Africa and from a raspberry (Rubus idaeus cv. Autumn Bliss) plantation in Argentina. A total of 52 sporeassociated bacteria were isolated from the external and internal surfaces of AM fungal spore morphotypes from the two countries. The bacterial isolates were evaluated for their PGP abilities such as phosphate solubilisation, indole-3-acetic acid production, ammonia production and inhibition of the fungal pathogens Fusarium oxysporum and Phythophthora nicotianae through mechanisms such as siderophore and/ or hydrolytic enzyme production. A total of 23 bacterial isolates from both South Africa and Argentina showing the most potential to be PGP, were identified molecularly as belonging to the genera Acinetobacter, Alcaligenes, Bacillus, Microbacterium, Micrococcus, Serratia and Staphylococcus. The ability of ten selected bacterial isolates showing multiple PGP capacity were evaluated for their plant growth promotion and mycorrhizal colonisation enhancement ability on raspberry (Rubus idaeus cv. Meeker). Significant differences in increased shoot and root dry weights were shown by the treatments compared to the uninoculated control. The highest increase in shoot and root dry weights were shown by South African (Bacillus mycoides) and Argentinean (Alcaligenes faecalis) isolates. AM fungal colonisation was significantly enhanced by the South African (Bacillus mycoides) and Argentinean (Micrococcus luteus) isolates compared to the AM fungal singly inoculated control.
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