Studies towards the development of novel antimalarial agents
- Authors: Adeyemi, Christiana Modupe
- Date: 2015
- Subjects: Antimalarials , Malaria , Drug resistance , Drug development , Enzyme inhibitors , Plasmodium
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54645 , vital:26596
- Description: Considerable efforts have been made in the modification of existing antimalarial drugs, and the support of incentive programmes have led to a drastic decrease in malaria cases reported by WHO during the past 6 years. However, the development of drug resistance threatens the eradication of this deadly disease and has prompted research on the synthesis of novel antimalarial drugs. Our research has involved the design and synthesis of novel benzylated phosphonate esters as potential 1-deoxy-D-xylose-5-phosphate reductoisomerase (DXR) inhibitors. A series of amidoalkylphosphonate esters were obtained by reacting various 3-subsituted anilines and heterocyclic amines with chloroalkanoyl chlorides and reacting the resulting chloroalkanamides with triethyl phosphite using Michaelis-Arbuzov methodology. Benzylation of the phosphonate esters afforded a series of novel N-benzylated derivatives in good yields and these compounds were fully characterised by NMR and HRMS methods. Several approaches to the introduction of a benzyl group at the C-2 position of the phosphonate ester derivatives have been explored, leading unexpectedly to the isolation of unprecedented tetrahydrofuranyl derivatives. Studies towards the preparation of potential bi-functional PfDXR / HIV-1 RT inhibitors have also been initiated. Preliminary in silico docking studies of selected non-benzylated and benzylated phosphonated derivatives into the Pf-DXR active-site has provided useful insight into the binding potential of these ligands. Bioassays have revealed a very low toxicity for all the synthesised phosphonated compounds and a number of these ligands also exhibit a promising inhibitory activity against the Plasmodium parasite.
- Full Text:
- Date Issued: 2015
Structural bioinformatics analysis of the Hsp40 and Hsp70 molecular chaperones from humans
- Authors: Adeyemi, Samson Adebowale
- Date: 2014
- Subjects: Structural bioinformatics , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Biomolecules
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4171 , http://hdl.handle.net/10962/d1020962
- Description: HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70 isoforms will interact. We attempted to use bioinformatics to identify residues involved in the specificity of the interaction between the J domain from HSP40 and the ATPase domain from the HSP70 isoforms from humans. A total of 49 HSP40 and 13 HSP70 sequences from humans were retrieved and used for subsequent analyses. The HSP40 J domains and HSP70 ATPase domains were extracted using python scripts and classified according to the subcellular localization of the proteins using localization prediction programs. Motif analysis was carried out using the full length HSP40 proteins and Multiple Sequence Alignment (MSA) was performed to identify conserved residues that may contribute to the J domain – ATPase domain interactions. Phylogenetic inference of the proteins was also performed in order to study their evolutionary relationship. Homology models of the J domains and ATPase domains were generated. The corresponding models were docked using HADDOCK server in order to analyze possible putative interactions between the partner proteins using the Protein Interactions Calculator (PIC). The level of residue conservation was found to be higher in Type I and II HSP40 than in Type III J proteins. While highly conserved residues on helixes II and III could play critical roles in J domain interactions with corresponding HSP70s, conserved residues on helixes I and IV seemed to be significant in keeping the J domain in its right orientation for functional interactions with HSP70s. Our results also showed that helixes II and III formed the interaction interface for binding to HSP70 ATPase domain as well as the linker residues. Finally, data based docking procedures, such as applied in this study, could be an effective method to investigate protein-protein interactions complex of biomolecules.
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- Date Issued: 2014
Research projects
- Authors: Adusei-Owusu, James
- Date: 2001
- Subjects: Constructivism (Education) , Review literature , College students -- Study and teaching , Teaching -- Methods , Competency based education -- Eastern Cape (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:1740 , http://hdl.handle.net/10962/d1003624 , Constructivism (Education) , Review literature , College students -- Study and teaching , Teaching -- Methods , Competency based education -- Eastern Cape (South Africa)
- Description: RESEARCH PROJECTS: 1 RESEARCH PROJECT ONE: A literature review: Constructivism: An alternate approach to teaching and learning. Abstract The constructivist perspectives on learning have helped enhance science educators' understanding of how students make sense of their lived experiences. Constructivism purports to be a transformation of the traditional curriculum. As such this article starts with a brief overview of behaviorism: the scientific approach to education. The main tenets underlying constructivism, how constructivism guides educators to change their classroom practice, and the implications to science teaching have been reviewed. 2 RESEARCH PROJECT TWO (Empirical study): Being Constructive: College students' learning of work and heat as aspects of the energy concept based a constructivist approach. Abstract This study is an extension of a literature review on constructivism as an alternate teaching and learning approach discussed in research project one. It is an empirical study concerning the use of a learning module based on a constructivist approach to develop pre-service student teachers' understanding of work and heat as aspects of the energy concept. The data consisted mainly of transcripts of students' interviews, written responses to questionnaires designed in the form of a worksheet, and comments from non-participant observers and students. The results seem to suggest that a carefully designed learning module based on a constructivist teaching and learning approach may be a valuable tool in developing pre-service student teachers' understanding of work and heat. 3 RESEARCH PROJECT THREE (Empirical study): A College in transition: A case study of the readiness of a college in the Eastern Cape province to implement Outcomes-Based Education in an Education Development centre. Abstract Curriculum 2005 premised on Outcomes-Based Education is the new curriculum framework for South Africa. It signifies a paradigm shift in education from the traditional 'telling-listening' relationship between the teacher and the learner to one that emphasises leamer-centred approach to the teaching process. Teachers, though recognized as crucial to the educational transformation process in the country have also being identified as ill-equipped to meet the challenges posed by Outcomes-Based Education. This study starts with a brief overview of the South African curriculum and the main tenets underlying Outcomes-Based Education. The institutional conditions and whether the lecturers at a college in the Eastern Cape province perceive the need for a change in their classroom practice were also investigated. Bearing in mind the need for further research to validate the findings of this study, positive indicators that emerged from the study suggest the readiness of the college to implement Outcomes-Based Education at the proposed Education Development Centre.
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- Date Issued: 2001
A structural study of the capsular antigen of Klebsiella serotype K43
- Authors: Aereboe, Michael
- Date: 1993
- Subjects: Polysaccharides , Klebsiella , Antigens , Enterobacteriaceae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3740 , http://hdl.handle.net/10962/d1003218 , Polysaccharides , Klebsiella , Antigens , Enterobacteriaceae
- Description: This thesis presents a detailed chemical and spectroscopic determination of the capsular, polysaccharide K-antigen isolated from the Klebsiella bacterium, serotype K43 (culture #2482). The repeating unit of the capsular polysaccharide was found to be of the "3 + 2" repeating unit type. A uronic acid was found as part of a disaccharide side chain and the main chain of the polysaccharide was found to be composed of a neutral trisaccharide of mannose and galactose. The work forms part of an ongoing research interest in bacterial polysaccharides of this laboratory and now completes the structural elucidation of all the Klebsiella K-antigens, bar three antigens which were originally assigned to other laboratories. These data together with the respective serological characteristics of each serotype are available to the molecular biologist, and may result in the production of: vaccine(s) against Klebsiella infections, diagnostic products and novel carrier molecules enabling targeted drug delivery.
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- Date Issued: 1993
Constituent processes of leaf senescence in Hordeum vulgare cv. Dyan
- Authors: Afitlhile, Meshack Mosimanegape
- Date: 1994
- Subjects: Leaves , Leaves -- Development
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4184 , http://hdl.handle.net/10962/d1003752
- Description: Changes in chlorophyll content, carotenoid content and composition, abscisic acid and phaseic acid levels, hydrolytic enzyme activity and polypeptide pattern were monitored during senescence of the primary attached leaves of Hordeum vulgare L. cv. Dyan. Senescence occurred due to the normal course of leaf development or was induced by incubation of leaves in darkness. Loss of chlorophyll and total leaf protein was retarded in light whereas it continued rapidly in leaves from dark-incubated seedlings. Chlorophyll alb ratio increased with the progression of senescence, suggesting that chlorophyll b was referentially degraded during this process. Loss of total protein coincided with enhanced activity of acid and neutral proteases. In contrast, loss of chlorophyll was not accompanied by an increase in· peroxidase activity, suggesting that this enzyme was not responsible for initiating chlorophyll breakdown. Carotenoid and abscisic acid levels were monitored in the same tissue extracts. The results obtained show that the increase in endogenous levels of abscisic acid, induced by senescence, correlated with enhanced epoxidation of the xanthophyll cycle, ie., increased conversion of zeaxanthin to antheraxanthin and all-trans-violaxanthin. In addition, an increase in abscisic acid levels occurred concomitant with a decrease in all-trans-violaxanthin and 9'-cis-neoxanthin, suggesting an apparent 1:1 relationship on a molar basis. It is therefore proposed that enhanced abscisic acid production, due to foliar senescence, arises from fluctuations in carotenoid turnover. Polypeptide patterns in isolated chloroplasts, purified thylakoid and stromal fractions were very similar for leaves incubated in either light or darkness. A decrease in intensity of bands was observed in isolated chloroplasts and stromal fractions. Intensity of bands in thylakoids remained unchanged with the progression of senescence. Protein standards of peroxidase and lipoxygenase co-migrated with proteins of the isolated chloroplast. Although tentative, some proteins of the chloroplast may be representative of precursors of hydrolytic enzymes which are known to increase during senescence.
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- Date Issued: 1994
Isolation and characterization of antiplasmodial metabolites from South African marine alga
- Authors: Afolayan, Anthonia Folake
- Date: 2008
- Subjects: Malaria -- Africa Antimalarials -- Therapeutic use Malaria -- Prevention Malaria -- Drug therapy Marine algae -- Therapeutic use Natural products -- Therapeutic use Plasmodium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3739 , http://hdl.handle.net/10962/d1003063
- Description: Malaria is one of the three most deadly diseases in Africa. Although there are available treatments, their efficacy has been greatly reduced over the past two decades due to the development of resistance to currently available drugs. This has necessitated the search for new and effective antimalarial agents. This project approached the search for new antimalarial compounds in two ways: (i) by screening natural products isolated from marine algae against the Plasmodium parasite and (ii) by modification of selected isolated active compounds to target 1-deoxY-đ-xylulose 5-phosphate reductoisomerase (DXR), an enzyme found in the nonmevalonate isoprenoid biosynthetic pathway of Plasmodium Jalciparum. It was envisaged that such a compound would exhibit dual action on the Plasmodium parasite. Extracts obtained from 22 marine algae were prefractionated by solvent partitioning and were screened for anti plasmodial activity against the chloroquine sensitive (CQS) P. Jalciparum D 10 strain. Overall, 50% of the algae screened produced at least one crude fraction with activity against P. Jalciparum. Extracts of the algae Sargassum heterophyllum, Plocamium cornutum, Amphiroa ephedrea and Pterosiphonia cloiophylla gave the most promising results. Fractionation of S. heterophyllum afforded three tetraprenyltoluquinols (3.1, 3.2 and 3.5) and an all-trans-fucoxanthin (3.6). Three new compounds (4.5, 4.6 and 4.7) and two known halogenated monoterpenes (4.1 and 4.4) were isolated from P. cornutum. Each of the isolated compounds from both S. heterophyllum and P. cornutum showed antiplasmodial activity with IC₅₀ values ranging from 2.0 - 15.3 μM for S. heterophyllum and 13 - 230 μM for P. cornutum. Attempts to synthetically modify halogenated monoterpene 4.4 by dihydroxylation and phosphorylation in order to inhibit the DXR enzyme was unsuccessful. However, the hemiterpene analogue (5.42) of the halogenated monoterpenes was successfully phosphorylated and dihydroxylated to give compound 5.45 which showed promising activity against DXR. The result obtained indicated that the proposed phosphorylation and dihydroxylation of the halogenated monoterpene 4.4 would result in the synthesis of a potent DXR inhibitor and therefore a potential antimalarial agent with dual mode of action on the Plasmodium parasite.
- Full Text:
- Date Issued: 2008
Biochemical characterisation of Pfj2, a Plasmodium falciparum heat shock protein 40 chaperone potentially involved in protein quality control in the endoplasmic reticulum
- Authors: Afolayan, Omolola Folasade
- Date: 2013
- Subjects: Plasmodium falciparum Endoplasmic reticulum Heat shock proteins Malaria , Mosquito-borne infectious disease
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3883 , http://hdl.handle.net/10962/d1001617
- Description: Plasmodium falciparum is a protozoan parasite that causes a severe form of malaria, a mosquito-borne infectious disease in humans. P. falciparum encodes a number of proteins to facilitate its life-cycle, including a type II heat shock protein 40 (Hsp40), Pfj2. Pfj2 shows a degree of homology to human ERdj5, a resident protein of the endoplasmic reticulum (ER) that promotes protein quality control by facilitating the degradation of misfolded proteins. The overall aim of this study was to further understand the function of Pfj2 in the P. falciparum cell by characterising it biochemically. A bioinformatic analysis of Pfj2 was carried out to enable the identification of a potential ER signal sequence and cleavage site. Furthermore, an analysis of Pfj2 protein sequence was performed to compare domain similarities and identities with typical type II Hsp40s namely, human ERdj5, S. cerevisiae Sis1, human Hsj1a and human DnaJB4. The method used included the insertion of the codon-optimised coding sequence for the processed ER form of Pfj2 into the prokaryotic expression vector, pQE30, to enable overproduction of a histidine-tagged protein. A 62 kDa His₆-Pfj2 was successfully expressed in Escherichia coli and purified using denaturing nickel affinity chromatography. ATPase assays were performed to determine the ability of His₆- Pfj2 to stimulate the chaperone activity of the ER Hsp70, also called immunoglobulin binding protein (BiP). Initial studies were conducted on readily available mammalian His₆-BiP as a control, which was shown to have an intrinsic activity of 12.07±3.92 nmolPi/min/mg. His₆- Pfj2 did not stimulate the ATPase activity of mammalian His₆-BiP, suggesting that it either could not act as a co-chaperone of mammalian His₆-BiP (specificity), or it required a misfolded substrate in the system. Therefore, ongoing studies are addressing the interaction of Pfj2 and misfolded substrates with P. falciparum BiP. The results of these studies will further our understanding of a poorly-studied parasite chaperone that represents a potential drug target for development of novel strategies for the control of a serious human disease
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- Date Issued: 2013
Potential use of carbon nanotubes as a nanofiller for natural rubber latex condoms
- Authors: Agbakoba, Victor Chike
- Date: 2018
- Subjects: Nanotubes , Rubber chemistry Nanocomposites (Materials) Nanostructured materials
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/23393 , vital:30538
- Description: The recent advancement in the field of nano-technology has raised much interest in the area of natural rubber latex (NRL) processing. This interest stems from the exceptional properties of nano-material and the promising results obtained by several researchers. Studies have shown that very low loadings of inorganic nanomaterials such as carbon nanotube (CNT) in NRL matrix leads to enhanced tensile strength, tensile modulus, tear resistance and aberration resistance. Thus providing a great prospect for reinforcement of thin film NRL articles such as condom. In this research, prevulcanised natural rubber latex (PvNRL) composite blends containing single walled carbon nanotubes (SWCNTs) were prepared via direct mixing. A progressive discolouration of PvNRL was observed with increased loadings of CNTs. Thermal analysis revealed faster drying rates for the composite blends containing SWCNT. Results from equilibrium swelling experiments also suggested a slight increase in crosslink density in the presence of SWCNT. There was a significant influence on flow behaviour of PvNRL as a result of varying loadings of SWCNT suspension. This was reflected as a change in pseudoplasticity and apparent viscosity. For Instance, apparent viscosity at a shear rate of 1 s-1 at 25°C for PvNRL with ~0.08% SWCNT was 2.5 Pa.s, compared to 0.49 Pa.s for the blends with 0.02% SWCNT. Condoms were moulded via the straight dipping technique using custom made glass formers. A series of dilutions was performed to correct the viscosity differences. This also ensured good consistency and promoted uniform deposition of PvNRL on the glass former. The average dimensions of the condoms produced in terms of length and width were ~191.17 ± 5.17 mm and 52.67 ± 5.17 mm respectively. Thickness measurement varied slightly according to the method of determination. The water leakage test suggested the absence of holes in the condoms produced. However, results from electrical leakage test contradicted those from water leak test. The results from infrared spectroscopy (FTIR) did not confirm the presence of chemical interactions between the SWCNT and PvNRL matrix. Glass transition temperature (Tg) was also unaffected across the blends. The stiffness (or modulus) was unaffected in all the condoms, as revealed by results from indentation hardness analysis. The SWCNT showed no significant influence on thermal decomposition temperatures of the condoms. Nonetheless, images from optical microscopy revealed increased surface roughness corresponding to higher loadings of SWCNT. Results from stress relaxation studies revealed improved retention of modulus under constant strain for condom samples containing SWCNT.
- Full Text:
- Date Issued: 2018
Evaluation of the physicochemical qualities and heavy metal regimes of the final effluents of some wastewater treatment facilties in Berlin, Alice and Bedford communities in the Eastern Cape, South Africa
- Authors: Agoro, Mojeed Adedoyin
- Date: 2017
- Subjects: Water -- Purification -- South Africa -- Eastern Cape Sewage -- Purification -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/5003 , vital:28924
- Description: Wastewater treatment facilities have been identified as potential source of surface water pollution worldwide. In this study, the physicochemical qualities and heavy metal (including Zinc, Cadmium, Iron, Lead and Copper) concentrations in the final effluents, as well as the reduction efficiencies of three municipal wastewater plants in the Eastern Cape, South Africa were evaluated from September 2015 to February 2016 using standard methods. Wastewater effluent and sludge samples were collected from the selected plants on monthly basis over a period of six months from September 2015 to February 2016. Standard analytical method (Atomic absorption spectroscopy [AAS]) was used to assess the concentration levels of heavy metals. The physicochemical parameters assessed include pH, Temperature, Total Dissolved Solid, Turbidity, Biochemical Oxygen Demand, Chemical Oxygen Demand, Alkalinity, Dissolved Oxygen, Free chlorine, Chloride, Sulphate, Phosphate, Ammonium and Electrical Conductivity. The results of the evaluation showed that temperature ranges from 19 to 36 °C, Electrical Conductivity from 60-1095 mS/m, Alkalinity from 2.6-20.9 mg/L, Nitrate from 0.24-26.5 mg/L, Nitrite from 0.01-90 mg/L, Phosphate from 0.02-5.12 mg/L, Ammonium from 0.06-112 mg/L, Sulphate from 3-72 mg/L, Chloride from 3.25-224 mg/L, Chemical Oxygen Demand from 17-394 mg/L and Turbidity from 1.96-715 NTU. Free chlorine concentrations and dissolved oxygen were within the recommended limits for most part of the sampling period and ranged between 0.17-0.48 mg/L and 0.19-21.9 mg/L respectively. The pH, Phosphate, Sulphate and Free chlorine were within acceptable limits while Electrical Conductivity, Temperature, Total Dissolved Solid, Turbidity, Chemical Oxygen Demand, Chloride, Ammonium, Nitrate and Nitrite were not within specified limits. The reduction efficiencies observed generally ranged between 43.9 and 100 percent at all sampling points while zinc and lead were not detected throughout the sampling period. Cadmium showed low reduction rate ranging from 0 to 11.7 percent, while the rate of Copper reduction ranged from 0 to25 percent in January and February 2016. Zinc, lead and cadmium were generally not detected in the sludge samples except in January and February which could be due to the prevailing atmospheric conditions during the sampling period. Cu and Fe were detected through the sampling months of the study. We conclude that these municipal sewage plants are sources of pollution to their receiving watersheds and threats to public and environmental health.
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- Date Issued: 2017
Perceptions and livelihood uses of an invasive alien tree (acacia dealbata) by rural communities in the Eastern Cape
- Authors: Agripa, Ngorima
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5326 , vital:20813
- Description: The negative impacts which invasive alien species have on ecosystems are well documented but there is paucity of information on their impacts on rural communities. Due to ecological impacts that may be associated with Acacia dealbata invasions the Agricultural Research Council Plant Protection Institute is considering releasing a biocontrol agent for A. dealbata. The actual social impacts of A. dealbata invasion and control are likely to be related to its importance in rural livelihoods. This thesis reports on the perceptions and livelihood uses of A. dealbata in the Eastern Cape. Three study sites were assessed, Matatiele, Mount Fletcher and Maclear. The study involved 150 household surveys, one focus group discussion and one transect walk at each site, key informant interviews and frequent house visits to acquire reliable data. Results show that 100 % of households in the three sites use Silver Wattle extensively for firewood. In Matatiele 64 %, 72 % in Mount Fletcher and 84 % of households in Maclear use Silver Wattle for fencing. To carve tools 76 % in Matatiele, 76 % in Mount Fletcher and 84 % households in Maclear use Silver Wattle. For medicinal purposes 18 % in Matatiele, 20 % in Mount Fletcher and 16 % in Maclear use Silver Wattle, whilst 78 % in Matatiele, 80 % in Mount Fletcher and 80 % in Maclear use it for fodder purposes. Many respondents felt that Silver Wattle is too abundant within their areas such that it now has many negative impacts associated with it. Perceptions of local people towards A. dealbata are neither static nor uniform, but are influenced by time since the invasion and now abundance of the species. There are no alternatives which provide the same services provided by Silver Wattle. Benefits and constraints due to A. dealbata invasion are experienced by everyone irrespective of wealth and gender. In conclusion, Silver Wattle is a valuable resource to these rural communities, but increasing abundance is incurring high costs to grazing resources and landscape accessibility.
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- Date Issued: 2017
The contribution of the trade in medicinal plants to urban livelihoods: a case study of the informal markets in Nelson Mandela Bay Municipality, Eastern Cape
- Authors: Ah Goo, Delia Felecia Stephanie
- Date: 2012
- Subjects: Medicinal plants -- South Africa -- Port Elizabeth , Informal sector (Economics) -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Port Elizabeth -- Markets
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10654 , http://hdl.handle.net/10948/d1011601 , Medicinal plants -- South Africa -- Port Elizabeth , Informal sector (Economics) -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Port Elizabeth -- Markets
- Description: The commercialisation of natural resources such as medicinal plants is a strategy that is increasingly being employed by poor people in developing countries such as South Africa, as a means of generating an income. Increasing economic hardship and a lack of employment opportunities in the formal sector of the economy has led to many urban dwellers seeking alternative means of meeting their everyday livelihood needs. Although the contribution of natural resources to subsistence economies is widely recognised, there are few studies that have examined the significance of the trade in medicinal plants to the livelihoods of poor and marginalised people. Thirty informal street traders were interviewed to investigate the role of the medicinal plant trade in sustaining the livelihoods of the traders who operate in the informal sector of the Nelson Mandela Bay Municipality, South Africa. The findings of the research indicate that the sale and collection of medicinal plants is an activity which is exploited by people with limited resources, few skills, little or no education and often without any other source of household income. Middle-aged women from impoverished, single income households dominated the trade. Although income from the trade is modest, it contributed substantially to the total household cash income of the traders. Other benefits of the trade included independence and having a sense of purpose in life, as the traders felt that they were not only helping their families but also the wider community. However, without the income from the trade, many of the traders and their families would be destitute and thus the medicinal plant trade is vital to the wellbeing of these people.
- Full Text:
- Date Issued: 2012
Statistical model for risk diversification in renewable energy
- Authors: Ahame, Edmund
- Date: 2013
- Subjects: Renewable energy sources -- Statistics , Diversification in industry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10564 , http://hdl.handle.net/10948/d1008399 , Renewable energy sources -- Statistics , Diversification in industry
- Description: The growth of the industry and population of South Africa urges to seek new sources of electric power, hence the need to look at alternative power sources. Power output from some renewable energy sources is highly volatile. For instance power output from wind turbines or photovoltaic solar panels fluctuates between zero and the maximum rated power out. To optimize the overall power output a model was designed to determine the best trade-off between production from two or more renewable energy sources putting emphasis on wind and solar. Different measures of risk, such as coefficient of variation (CV) and value at risk (VAR), were used to determine the best hybrid renewable energy system (HRES) configuration. Depending on the investors’ expected returns (demand) and risk averseness, they will be able to use the model to choose the best configuration that suites their needs. In general it was found that investing in a diversified HRES is better than investing in individual power sources.
- Full Text:
- Date Issued: 2013
Geology and ore reserve estimation of the Witwatersrand-type gold deposits with specific reference to the Welkom Goldfield
- Authors: Ainslie, L C
- Date: 1981
- Subjects: Mines and mineral resources -- Statistical methods Mine valuation -- Statistical methods Gold ores -- Geology Witwatersrand Basin (South Africa) Ores -- Sampling and estimation -- Statistical methods
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4911 , http://hdl.handle.net/10962/d1001571
- Full Text:
- Date Issued: 1981
Taxonomic and trait-based responses of the orders Ephemeroptera, Plecoptera, Odonata, And Trichoptera (EPOT) to sediment stress in the Tsitsa River and its tributaries, Eastern Cape, South Africa
- Authors: Akamagwuna, Frank Chukwuzuoke
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68082 , vital:29196
- Description: Increased urbanization and industrialisation due to human population growth and associated high demand for food have led to widespread disturbances of freshwater ecosystems and associated resources. A widely recognised consequence of these disturbances is the excessive delivery of sediments into the freshwater ecosystems, which severely affects the functioning and integrity of these systems.. The major water quality impairment in the Tsitsa River and its tributaries, situated in the Mzimvubu catchment in the Eastern Cape Province of South Africa, is known to be excessive sediment input. In this study, the application of macroinvertebrates taxonomic-based and trait-based approaches was used to assess the responses and vulnerability of Ephemeroptera, Plecoptera, Odonata and Trichoptera (EPOT) species to settled and suspended sediments stress in eight selected sampling sites in the Tsitsa River and its tributaries. The eight selected sites were Site 1 (Tsitsa upstream), Site 2 (Tsitsa downstream), Site 3 (Qurana tributary), Site 4 (Pot River upstream), Site 5 (Pot River downstream), Site 6 (Little Pot River), Site 7 (Millstream upstream) and Site 8 (Millstream downstream). The methods used in this study involved the analysis of water physico-chemical variables as well as sediment characteristics, derivation of five EPOT metrics, EPOT species-level taxonomic analysis, individual EPOT trait analysis and the development of a novel trait-based approach using a combination of traits. The sampling of EPOT taxa was done using the SASS5 protocols. Identification of EPOT was done to genus/species level and all data were subjected to relevant statistical analysis. The results of ecological categories derived for the physico-chemical variables generally indicated the ecological categories A and B, which was indicative of good water quality conditions. The result of sediment particle analysis revealed four distinct site groups: site group 1 (Tsitsa River upstream and Qurana tributary), site group 2 (Tsitsa River downstream and Millstream upstream), site group 3 (Pot River, both upstream and downstream, and Millstream downstream) and site group 4 (Little Pot River). The species-level taxonomic analysis of EPOT revealed that site group 1 was the most sediment-influenced sites whereas site group 4 was the least sediment-influenced. Species such as Paragopmhus sp., Aeshna sp. and Baetis sp. were considered sediment-tolerant with strong positive association with site group 1. The novel trait-based approach developed in this study proved useful in predicting the responses of EPOT species to sediment stress, and further discriminated between the study sites. The approach was used to group EPOT species into four vulnerability classes. The result showed that filter feeding EPOT species that have filamentous gills, preferring stone biotopes and feeding on detritus (FPOM) were mostly classified as highly vulnerable to sediment stress and indicated no significant association with the highly sediment-influenced site group 1. The TBA largely corresponded well to the predictions made with the relative abundance of the vulnerable class decreasing in the sediment-influenced sites compared to the tolerant and highly tolerant classes. Overall, the study revealed the importance of the complementary use of taxonomic and trait-based approaches to biomonitoring.
- Full Text:
- Date Issued: 2019
Stress-inducible protein 1: a bioinformatic analysis of the human, mouse and yeast STI1 gene structure
- Authors: Aken, Bronwen Louise
- Date: 2005
- Subjects: Molecular chaperones , Proteins -- Analysis , Heat shock proteins , Bioinformatics , Genetics -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3990 , http://hdl.handle.net/10962/d1004049 , Molecular chaperones , Proteins -- Analysis , Heat shock proteins , Bioinformatics , Genetics -- Data processing
- Description: Stress-inducible protein 1 (Sti1) is a 60 kDa eukaryotic protein that is important under stress and non-stress conditions. Human Sti1 is also known as the Hsp70/Hsp90 organising protein (Hop) that coordinates the functional cooperation of heat shock protein 70 (Hsp70) and heat shock protein 90 (Hsp90) during the folding of various transcription factors and kinases, including certain oncogenic proteins and prion proteins. Limited studies have been conducted on the STI1 gene structure. Thus, the aim of this study was to develop a comprehensive description of human STI1 (hSTI1), mouse STI1 (mSTI1), and yeast STI1 (ySTI1) genes, using a bioinformatic approach. Genes encoded near the STI1 loci were identified for the three organisms using National Centre for Biotechnology Information (NCBI) MapViewer and the Saccharomyces Genome Database. Exon/intron boundaries were predicted using Hidden Markov model gene prediction software (HMMGene) and Genscan, and by alignment of the mRNA sequence with the genomic DNA sequence. Transcription factor binding sites (TFBS) were predicted by scanning the region 1000 base pairs (bp) upstream of the STI1 orthologues’ transcription start site (TSS) with Alibaba, Transcription element search software (TESS) and Transcription factor search (TFSearch). The promoter region was defined by comparing the number, type and position of TFBS across the orthologous STI1 genes. Additional putative TFBS were identified for ySTI1 by searching with software that aligns nucleic acid conserved elements (AlignACE) for over-represented motifs in the region upstream of the TSS of genes thought to be co-regulated with ySTI1. This study showed that hSTI1 and mSTI1 occur in a region of synteny with a number of genes of related function. Both hSTI1 and mSTI1 comprised 14 putative exons, while ySTI1 was encoded on a single exon. Human and mouse STI1 shared a perfectly conserved 55 bp region spanning their predicted TSS, although their TATA boxes were not conserved. A putative CpG island was identified in the region from -500 to +100 bp relative to the hSTI1 and mSTI1 TSS. This region overlapped with a region of high TFBS density, suggesting that the core promoter region was located in the region approximately 100 to 200 bp upstream of the TSS. Several conserved clusters of TFBS were also identified upstream of this promoter region, including binding sites for stimulatory protein 1 (Sp1), heat shock factor (HSF), nuclear factor kappa B (NF-kappaB), and the cAMP/enhancer binding protein (C/EBP). Microarray data suggested that ySTI1 was co-regulated with several heat shock proteins and substrates of the Hsp70/Hsp90 heterocomplex, and several putative regulatory elements were identified in the upstream region of these co-regulated genes, including a motif for HSF binding. The results of this research suggest several avenues of future experimental work, including the confirmation of the proposed core promoter, upstream regulatory elements, and CpG island, and the investigation into the co-regulation of mammalian STI1 with its surrounding genes. These results could also be used to inform STI1 gene knockout experiments in mice, to assess the biological importance of mammalian STI1.
- Full Text:
- Date Issued: 2005
The role of parallel computing in bioinformatics
- Authors: Akhurst, Timothy John
- Date: 2005
- Subjects: Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3986 , http://hdl.handle.net/10962/d1004045 , Bioinformatics , Parallel programming (Computer science) , LINDA (Computer system) , Java (Computer program language) , Parallel processing (Electronic computers) , Genomics -- Data processing
- Description: The need to intelligibly capture, manage and analyse the ever-increasing amount of publicly available genomic data is one of the challenges facing bioinformaticians today. Such analyses are in fact impractical using uniprocessor machines, which has led to an increasing reliance on clusters of commodity-priced computers. An existing network of cheap, commodity PCs was utilised as a single computational resource for parallel computing. The performance of the cluster was investigated using a whole genome-scanning program written in the Java programming language. The TSpaces framework, based on the Linda parallel programming model, was used to parallelise the application. Maximum speedup was achieved at between 30 and 50 processors, depending on the size of the genome being scanned. Together with this, the associated significant reductions in wall-clock time suggest that both parallel computing and Java have a significant role to play in the field of bioinformatics.
- Full Text:
- Date Issued: 2005
A pilot wide-field VLBI survey of the GOODS-North field
- Authors: Akoto-Danso, Alexander
- Date: 2019
- Subjects: Radio astronomy , Very long baseline interferometry , Radio interometers , Imaging systems in astronomy , Hubble Space Telescope (Spacecraft) -- Observations
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72296 , vital:30027
- Description: Very Long Baseline Interferometry (VLBI) has significant advantages in disentangling active galactic nuclei (AGN) from star formation, particularly at intermediate to high-redshift due to its high angular resolution and insensitivity to dust. Surveys using VLBI arrays are only just becoming practical over wide areas with numerous developments and innovations (such as multi-phase centre techniques) in observation and data analysis techniques. However, fully automated pipelines for VLBI data analysis are based on old software packages and are unable to incorporate new calibration and imaging algorithms. In this work, the researcher developed a pipeline for VLBI data analysis which integrates a recent wide-field imaging algorithm, RFI excision, and a purpose-built source finding algorithm specifically developed for the 64kx64k wide-field VLBI images. The researcher used this novel pipeline to process 6% (~ 9 arcmin2 of the total 160 arcmin2) of the data from the CANDELS GOODS- North extragalactic field at 1.6 GHz. The milli-arcsec scale images have an average rms of a ~ 10 uJy/beam. Forty four (44) candidate sources were detected, most of which are at sub-mJy flux densities, having brightness temperatures and luminosities of >5x105 K and >6x1021 W Hz-1 respectively. This work demonstrates that automated post-processing pipelines for wide-field, uniform sensitivity VLBI surveys are feasible and indeed made more efficient with new software, wide-field imaging algorithms and more purpose-built source- finders. This broadens the discovery space for future wide-field surveys with upcoming arrays such as the African VLBI Network (AVN), MeerKAT and the Square Kilometre Array (SKA).
- Full Text:
- Date Issued: 2019
Evaluating late payment-induced waste in South Africa through lean construction principles
- Authors: Akuffo-Ntow, Eric Ayesu
- Date: 2016
- Subjects: Construction industry -- South Africa -- Finance , Lean manufacturing -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/8867 , vital:26437
- Description: Central to the sustainable and competitive growth of the South African construction industry is a predictable cash flow through on time payment by clients to contractors. However, chronic late payments, a recurring problem in the industry, especially in the public sector, is bringing untold hardship to contractors by derailing their competitiveness and also eroding the trust among the supply chain partners to the extent that some firms end up closing business in the industry. The situation is viewed from the lean construction perspective as an obstacle that is preventing the accrual of the required value to project parties in the construction industry. This research addresses the causes of late payments to contractors and the role of the quantity surveyor (QS) in terms of influencing early payment from a lean construction perspective. A mixed method approach was used for compiling the primary data for the study. Sequentially, one hundred and two (102) quantitative and twelve (12) interview questionnaires were administered to selected contractors and construction professionals working predominantly on public sector projects. The findings revealed that the approval process for evaluation and certification by the client- appointed agent and intermediary institutions is taking longer than contractually allowed, with parties independently undertaking their evaluation prior to the certification date. This is found to be adverse to achieving consensus on the values of the works for authorisation. Other significant barriers are the lack of funds to authorise payment, random auditor general’s documentation changes, lack of administrators’ system integration and capacity to handle cyclical payment processing. Also, contractors have been found to be in default of timeously submitting complete claim documents. It is therefore recommended that the client agents should partner with the contractor in regular design and documentation reviews, arranging the payment process and should also meet jointly to prepare monthly evaluations. In addition, contractors should be mentored from the onset of the project regarding all the necessary documentation and supporting documents that will be required by the client to ensure that payment approvals are not delayed. The payment authori-sation agent’s capacity should be enhanced through training and improved powers as a singular point of control to perform efficiently and their systems and processes should be integrated to ensure that all parties are implementing the same protocols.
- Full Text:
- Date Issued: 2016
Creation of clay flameless burner for vaporizing an insect repellent containing pmd as an active ingredient
- Authors: Akwi, Faith Mary
- Date: 2012
- Subjects: Insect baits and repellents , Montmorillonite
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10383 , http://hdl.handle.net/10948/d1008406 , Insect baits and repellents , Montmorillonite
- Description: Insecticide treated mosquito bed nets, insecticide aerosol sprays, repellent lotions and creams, repellent candles, vaporizable repellent essential oils, mosquito mats and coils are some of the many malaria personal protection tools that are in use. The latter of these measures are the most accessible and affordable options for the rural population in sub-Saharan Africa. It is therefore important to determine how effective these personal protection measures are by determining their ability to efficiently disperse an active ingredient when the protection measure is in use. In this study, a copper II oxide montmorillonite clay burner (CuOMontmorillonite clay burner) was created to vaporize repellent formulations containing various concentrations of p-menthane-3,8-diol (PMD) as the active ingredient with the aim of determining the percentage of the active ingredient that is released into the air and the rate of release. The performance of the CuO-Montmorillonite clay burner was also compared to that of the Lampe Berger fragrance burner (LBFB). In addition to this, the percentage of PMD released from 6 percentage wt PMD candles of diameters 40mm, 69mm and 83mm was determined and compared to that released when the CuO-Montmorillonite clay burner and Lampe Berger Fragrance burner where used to vaporize PMD repellent formulations. It was found that the rate of vaporization of the various PMD repellent formulations vaporized using the Lampe Berger fragrance burner is affected by the mass of PMD present in the repellent formulations. The 6 percentage wt PMD repellent candles released the least percentage of PMD as compared to that released when the CuO-Montmorillonite clay burner and the Lampe Berger fragrance burner were used to vaporize the PMD repellent formulations.
- Full Text:
- Date Issued: 2012
A contribution to the respiratory physiology of three South African freshwater pulmonate snails, Bulinus (Physopsis) Africanus (Krauss), Bulinus (Bulinus) Tropicus (Krauss), and Lymnaea Natalensis Krauss
- Authors: Alberts, I E
- Date: 1966
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20965 , http://hdl.handle.net/10962/5696
- Description: From Introduction: The use of chemical molluscicides in the control of schistosome transmitting snails has been largely based on empirical studies of toxicity, rather than on a clear understanding of basic physiology and biochemistry of snail hosts. It is therefore possible that purely physiological studies may in themselves provide information which could be of value in the development of more effective mollucicides. In this investigation an attempt has been made to understand some aspects of the respiratory physiology of three species of fresh-water pulmonate snails, all of which are of medical and veterinary importance in the Republic of South Africa. Bulinus (Physopsis) africanus (Krauss) is the intermediate host of Schistosoma haematobium, the causative organism of human schistosomiasis (Bilharziasis). Bulinus (Bulinus) tropicus (Krauss) is the intermediate host of the conical flukes Calicophoron calicophorum and Paramphistomum microbothrium and of the liver fluke Fasciola hepatica, while Lymnaea natalensis Krauss is the intermediate host of the liver fluke Fasciola gigantica.
- Full Text:
- Date Issued: 1966