Natural and Agricultural Sciences

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Open Access
3D visualization of data from groundwater flow and transport models
(University of the Free State, 2000-11) Bekker, Meintjes; Messerschmidt, H. J.; Chiang, W. H.
English: Groundwater flow and transport models produce large amounts of data, which the human brain cannot possibly grasp. Taking advantage of the natural abilities of the human vision system, 3D visualization is often the tool of choice for understanding and communicating conceptual models, verifying model input, understanding model output, explaining and communicating conclusions and recommendations, and motivating expenses. A 3D visualization tool has therefore been developed for intelligence amplification of model data. The tool is based on a groundwater modeling system (Processing MODFLOW) and makes use of the results from existing groundwater flow (MODFLOW) and transport models (MT3DMS, PHT3D and RT3D.). The Visualization Toolkit (vtk), a C++ class library for visualization was used to render 3D geohydrological objects. Realistic scenes of 3D geospatial models and 3D distributions of geohydrological properties, such as hydraulic conductivity, heads and solute concentrations, can be rendered. The advantages of 3D visualization are evident by applying the visualization tool to case studies.
Open Access
A mobile application to protect groundwater during unconventional oil and gas extraction
(The Royal Society, 2022) Worthmann, Charissa; Esterhuyse, Surina
Unconventional oil and gas (UOG) is an important energy source for many countries, but requires large quantities of water for its development, and may pollute water resources. Regulations are one of the main tools to achieve government policy on natural resource protection. South Africa, which is energy-constrained, but also water-scarce, is currently considering UOG extraction as an additional energy resource. UOG development could commence as soon as regulations to protect natural resources such as water have been published. Such regulations are, however, often not effectively enforced, which negatively affects the protection of water resources during UOG extraction. This study addresses these enforcement challenges in South Africa. It focuses on the science–society–policy interface by proposing a civic informatics platform to assist with on-the-ground enforcement of regulations via a mobile application. This mobile application aims to address both groundwater monitoring and management as well as UOG extraction operations in a single platform, to enable regulators to protect groundwater resources more effectively during UOG extraction, while simultaneously enhancing transparency in the UOG industry.
Open Access
A new species and new records of Chumma (Araneae, Macrobunidae) from South Africa
(Pensoft Publishers, 2024) Marusik, Yuri M.; Haddad, Charles R.
A new species of the genus 𝘊𝘩𝘶𝘮𝘮𝘢 Jocqué, 2001, C. 𝘧𝘰𝘰𝘳𝘥𝘪 𝐬𝐩. 𝐧𝐨𝐯., is described from the Western Cape, South Africa. New distribution records for 𝘊. 𝘣𝘪𝘤𝘰𝘭𝘰𝘳 Jocqué & Alderweireldt, 2018, 𝘊. 𝘧𝘰𝘭𝘪𝘢𝘵𝘢 Jocqué & Alderweireldt, 2018 and 𝘊. 𝘨𝘢𝘴𝘵𝘳𝘰𝘱𝘦𝘳𝘧𝘰𝘳𝘢𝘵𝘢 Jocqué, 2001 are presented. The genus is recorded from the Northern Cape Province for the first time, extending its range extensively to the northwest by approximately 450 km. The distribution of all 𝘊𝘩𝘶𝘮𝘮𝘢 species is mapped.
Open Access
A South African disaster legislative perspective of information management and communication systems
(AOSIS Publishing, 2022) Kunguma, Olivia
𝗕𝗮𝗰𝗸𝗴𝗿𝗼𝘂𝗻𝗱: Establishing a disaster information management and communication system (IMCS) is a mandate of the South African National Disaster Management Framework of 2005 (NDMF). The inception of such systems is supposed to be at the initial set-up of disaster management centres. The comprehensive functioning of a disaster centre will require an interoperable system that can collect, process, store and disseminate data. The lack of such a system might result in poor disaster risk reduction (DRR) and ineffective response. 𝗢𝗯𝗷𝗲𝗰𝘁𝗶𝘃𝗲: This article identified and described IMCSs from the South African disaster policy perspective. 𝗠𝗲𝘁𝗵𝗼𝗱𝘀: Qualitative in-depth interviews were used to investigate the status quo of all nine provincial disaster management centres (PDMCs) regarding the existence, functioning and understanding of IMCSs. The NDMF informed the interview questions administered to 29 purposively selected participants. Themes from descriptions by informants were used to analyse the data. 𝗥𝗲𝘀𝘂𝗹𝘁𝘀: All the centres operating for more than 10 years lack integrated IMCSs. The disaster managers perceive IMCSs as more information technology, computers and other physical devices and less human input systems and governance capabilities. The lack of integrated and well-governed disaster information and communication affects disaster management operations and service delivery mandate. 𝗖𝗼𝗻𝗰𝗹𝘂𝘀𝗶𝗼𝗻: To date, no studies have explored the establishment and management of interoperable IMCSs in disaster management centres. Therefore, this study contributes to the literature on disaster information and communication discourse and practical contributions to improve the capacity of PDMCs. This article provides insight into the significance of IMCS for building resilient communities and recommendations for establishing and maintaining the systems.
Open Access
A taxonomic study of the genus cryptolepis (periplocoideae: apocynaceae)
(University of the Free State, 2013) Joubert, Lize; Venter, A. M.; Venter, H. J. T.; Bruyns, P. V.
Cryptolepis R.Br. (Apocynaceae, Periplocoideae) was taxonomically revised. Detailed descriptions of macro and micro-morphology, palynology, geographic distribution and ecological characteristics were presented. An identification key to the species was compiled and the nomenclature of all species was revised while all available type material was studied and lectotypes and neotypes were designated where necessary. Molecular phylogenetic analyses, based on the gene regions ITS, trnD–T and trnT–F, of representative species of 28 periplocoid genera and 22 Cryptolepis species were presented and the monophyly of Cryptolepis was evaluated. Historically a total of 81 species names and four subspecies names were published for Cryptolepis. However, a large number of species names were later placed in synonymy or transferred to other genera, while several new combinations were published. This resulted in a total of 29 accepted Cryptolepis species at the commencement of this study. Three new species, C. ibayana, C. thulinii and C. villosa, resulted from this study and the latter two were described in this thesis. One species, C. producta, was synonymised with C. oblongifolia. Cryptolepis, therefore, comprises a total of 31 species at present. In terms of species diversity, distribution and potential pharmaceutical and economic value, Cryptolepis is one of the most significant genera in the Periplocoideae. Cryptolepis grows throughout sub-Saharan Africa, the southern parts of Yemen, the island archipelago of Socotra, and southern Asia ranging from India to southern China, Taiwan, the Philippines and Indonesia. Most of the species grow in tropical forests or savannah, but 13 species are also adapted to arid environments. The majority of Cryptolepis species are concentrated in four centres of diversity along the east coast of Africa and on Socotra. These hotspots are associated with both arid and forest refugia in areas which have been regarded as local centres of endemism for a number of other plant taxa. The phylogenetic analysis of Cryptolepis indicates that most of these hotspots were colonized repeatedly by different Cryptolepis groups. In addition to the influence of climate shifts, edaphic conditions and also fire had a significant influence on species diversity and distribution in Cryptolepis. Macro and micro-morphological investigations indicated that numerous characters, including growth form, leaf shape and size, leaf epidermal characters, venation, inflorescence structure, floral structure and seed coat surface characters, are of diagnostic value at species level in Cryptolepis. However, the species can only be accurately identified by using a combination of these characters. The molecular phylogenetic analyses revealed that Cryptolepis is paraphyletic and, in order to establish a monophyletic genus, it was proposed that the circumscription of the genus be broadened to include Parquetina as a synonym of Cryptolepis. Several vegetative and reproductive characters showed a high degree of homoplasy, suggesting a high degree of morphological plasticity. This plasticity was also found at species level in C. oblongifolia, which showed significant variation in vegetative and reproductive features. This, together with a high tolerance for disturbance, has resulted in C. oblongifolia becoming the most widely distributed of all Cryptolepis species.
Open Access
The ability of a novel compound to enhance the effect of urea on nitrogen deficient tomatoes
(University of the Free State, 2012-03-22) Pretorius, Hendri; Potgieter, G. P.
English: A company, Elementol (Pty) Ltd, requested the evaluation of their novel product, Pheroids. Pheroids can apparently facilitate the transport of phytological beneficial substances over membranes. Information regarding the chemical attributes was withheld as patent registration is still pending. Pheroids is apparently a microemulsion containing free fatty acids (FFA’s) and or fatty acid derivatives. It apparently encapsulates a substance and facilitates its transport over the membrane. The exact mechanism involving encapsulation, transport and release of the substances inside the cells is still vague due to little information available on it. The aim of this study was to evaluate the ability of Pheroids to facilitate the transport of additional nitrogen, urea in this case, in tomatoes grown under nitrogen limiting conditions. Tomatoes (Lycopersicon esculentum cv. Rodade Star) were cultivated in a greenhouse using a circulating ebb and flow hydroponic setup, which supplied the plants with either a control- or nitrogen limiting nutrient solutions. The plants cultivated in the nitrogen limiting conditions showed a remarkable reduction in vegetative development and yield. To alleviate the effect of nitrogen limiting conditions on yield, the plants were foliarly sprayed with 0.5% and 1% urea solutions, singly or mixed with Pheroids, once every two weeks. The purpose of these foliar treatments was to determine whether Pheroids can further enhance the absorption and transport of urea across membranes of the leaves to alleviate the effect of limiting nitrogen supply. Plants grown under nitrogen adequate conditions (control) were also foliarly treated with a 0.5% urea solution, singly and mixed with Pheroids, to determine to which extent control plants react to the additional nitrogen supplied. The reduction in yield, as a result of limited nitrogen supply, was partially alleviated by spraying nitrogen deficient plants with the 0.5% and 1% urea solutions. However, mixing the 0.5% and 1% urea solutions with Pheroids, not only improved vegetative growth and generative development, but also improved yield, suggesting that Pheroids indeed has the ability to improve the uptake of urea. The 0.5% urea / Pheroids solution specifically proved to have the best ability in alleviating the effect of nitrogen limiting conditions on yield without compromising fruit quality. Although the reducing effect was not completely alleviated, the yield and loss in income as a result of nitrogen limiting conditions was prevented to a large extent. Spraying control plants with 0.5% urea, singly or mixed with Pheroids, also improved yield, without compromising fruit quality. In addition, Pheroids itself, without mixing it with any substance, also resulted in increased yields in both control- and plants grown under nitrogen limiting conditions. In summary, it appeared that Pheroids has the ability to facilitate the transport of phytological beneficial substances, in this case urea, over plant membranes and enhances cellular nitrogen content, but this needs further detailed analyses. This phenomenon was more evident in plants grown under nitrogen limiting conditions than in plants grown under control conditions. Taking into consideration that most crops frequently may suffer from nitrogen limiting conditions in standard agricultural practices, Pheroids may have numerous potential applications in the agricultural industry.
Open Access
Abiotic stress tolerance and nutritional traits of newly developed quality protein maize hybrids in sub-Saharan Africa
(University of the Free State, 2022) Engida, Bitew Tilahun; Labuschagne, M. T.; Terekegn, A.; Van Biljon, A.; Wegary, D.
Drought and poor soil fertility are some of the most serious maize production challenges in sub-Saharan Africa (SSA). Identification and development of quality protein maize (QPM) cultivars that have high yield potential and tolerance to these stresses is a reliable and affordable option to improve food security and malnutrition problems in the region, especially for small scale farming communities. Although several stress tolerant maize varieties have been released and disseminated for commercial production in SSA so far, limited development and release of stress tolerant and high yielding QPM varieties compared to normal maize varieties is evident. Limited attention has also been given to the development of nutritionally enriched varieties compared to grain yield improvement. Therefore, the main goal of this study was to study 40 newly developed QPM hybrids obtained from the International Maize and Wheat Improvement Center (CIMMYT) – Zimbabwe, under stressed and non-stressed environments to allow selection of QPM hybrids that could outperform the existing commercial QPM and normal maize cultivars with respect to grain yield and concentrations of tryptophan, iron (Fe), zinc (Zn) and molar ratios of Fe and Zn to phytic acid. The specific objectives were: (1) to determine variability and performance of QPM hybrids for grain yield and agronomic traits under stressed and non-stressed environments, (2) to determine tryptophan, Zn and Fe concentrations, and molar ratios of Zn and Fe to phytic acid in QPM hybrids grown under stressed and non-stressed environments, (3) to analyse genotype by environment interaction and grain yield stability of QPM hybrids and (4) to determine correlations among grain yield, agronomic and nutritional traits in QPM hybrids evaluated under stressed and non-stressed environments. Significant variation was seen for grain yield, and almost all studied agronomic and nutritional traits under stressed and non-stressed environments. Phenotypic coefficient of variation (PCV) was higher than genotypic coefficient of variation (GCV) for grain yield and all other agronomic and nutritional traits under all conditions, indicating that environment effect was higher than genotype effect on the expression of the traits under stressed and non-stressed environments. Broad sense heritability of grain yield was higher than 0.6 across all environments, with the exception of managed drought conditions. Anthesis silking interval (ASI) had relatively high GCV estimates and genetic advance, as a percentage of the mean, across all conditions. This indicated that the presence of sufficient genetic variability among genotypes can improve synchronization under different management conditions through selection. Grain yield was reduced by 47% under random stress, 68% under managed drought and 71% under low N conditions. Protein and tryptophan concentrations in the grain were decreased by 36.0% and 21% respectively under low N conditions and Fe and Zn concentration also decreased by 48% and 36% under low N stress and 63% and 9% under random stress, respectively. Some QPM hybrids showed better or comparable performance in terms of grain yield potential and nutritional quality traits compared with the best QPM and normal maize checks under different management conditions, indicating the genetic gain that has been made in the QPM breeding programme. Based on Additive Main effect and Multiplicative Interaction (AMMI) analysis and Genotype and Genotype by Environment interaction (GGE) biplot analysis entries 10 (CZH142238Q) and 14 (CZH15142Q) under optimum; 23 (CZH17192Q) under random stress; 19 (CZH17188Q) and 40 (CZH17209Q) under managed drought and 14 (CZH15142Q) under low N were the most stable and the highest yielding hybrids. Environments Kwekwe (KW), Bindura (BIN), Chokwe (CHO) and Bako (BK2) were identified as discriminating and representative sites for optimum conditions, random stress, managed drought and low N stress conditions, respectively, therefore these environments are promising for selecting well adapted genotypes in the respective management conditions. Grain yield was significant and positive correlated with number of ears per plant and negatively with days to anthesis and silking under low N stress. This confirmed the importance of these secondary traits in developing high yielding and early maturing genotypes. Grain yield was not significantly correlated with most of the nutritional quality traits under all management conditions, indicating a lack of common genes for simultaneous improvement of grain yield and these nutritional traits. Significant and positive correlations were observed between Fe and Zn under low N and random stress conditions.
Open Access
The acceptability of earth constructed houses in central areas of South Africa
(University of the Free State, 2015) Bosman, Gerhard; Steÿn, Das; Van der Westhuizen, Diaan; Atkinson, Doreen
English: The traditional earth building techniques of South Africans are well documented, but little research reflects the current perceptions of these building materials and techniques. The thesis explores the factors (independent variables) that can be addressed in order to make earth constructed houses in general more acceptable in central areas of South Africa. The thesis draws on data obtained from the SANPAD project (South Africa-Netherlands Research Programme on Alternatives in Development) with a household survey (n=1790) from respondents regarding their perceptions and attitudes towards earth construction. Multiple qualitative and quantitative responses were recorded both for and against the use of sun dried earth blocks (adobe). Correlation and regression analyses were used to test for the characteristics (significant variables) that influence the acceptability of earth constructed houses. The findings show that respondents regard traditional earth building materials as inferior. Negative attitudes were found to be linked to the structural performance of unbaked earth materials regarding stability in wet conditions and maintenance. Limited other studies confirmed the low acceptability of traditional earth constructed walls. Regression analysis could not confirm that personal and household characteristics are associated with the housing, context and acceptability characteristics. Correlation analyses confirmed that certain housing characteristics (basic services such as water born toilets connected to sewerage systems, running water and electricity) influence the acceptability of traditional earth constructed houses. Correlation analyses confirmed that context characteristics (location and area types) influence the acceptability of traditional earth constructed houses. Furthermore, the data and literature confirm that the building culture (available material and buildings skills) and upward social mobility together with Reconstruction and Development Programme (RDP) houses (with basic services) influence the acceptability of traditional earth constructed housing. The findings concluded that attitudes toward traditional earth construction are more positive in 1) informal urban areas where informal houses do not have access to basic services and 2) rural households where the building culture dictates the norm even without basic services. The effects of conformity, imitation and upward social mobility were confirmed, as stated by the literature and the data. Together with upgraded earth construction techniques (such as cement stabilised compressed earth blocks or bricks) wall components for earth buildings in parts of central South Africa may be more acceptable. The hypothesis is that if the influencing factors on the acceptability of traditional earth constructed housing are known, it can be used in the promotion of contemporary earth construction. The thesis aims to promote contemporary earth construction techniques. This thesis states that the public should be equipped and educated about the importance of preserving existing forms and methods of earth construction, in order to support useful applications within contemporary architecture.
Open Access
Acceptance, attitudes and nutritional content of novel nixtamalized maize products developed for the South African consumer
(University of the Free State, 2023) Colbert, Taylon Anthony; Du Toit, Alba; Bothma, Carina; van Niekerk, Johan; Swanepoel, Jan Willem
South Africa is well-known for its good quality maize that serves as a staple crop for over 80% of the country’s population. Additionally, South Africa is also Africa’s top maize producer. However, maize provides an unbalanced supply of essential nutrients, such as the essential amino acids lysine and tryptophan. Moreover, the water-soluble vitamin B₃ is biologically unavailable to humans. Therefore, long-term consumption of maize-based diets, deficient in these nutrients, can result in pellagra, a disease manifested by the characteristic symptom dermatitis, on sun-exposed skin. The process of nixtamalization improves the nutritional, textural and sensory quality, and the physicochemical properties of maize products. Nixtamalization is the traditional process of preparing maize in Mexico. It involves cooking and soaking maize kernels in an alkaline solution, typically calcium hydroxide or slaked lime. The process allows bound nutrients to be more readily available for absorption, improves flavour and texture, as well as digestion. This study was divided into three essential phases: (I) the development of consumer-acceptable novel nixtamalized maize products; (II) the determination of consumer attitudes, knowledge and awareness towards nixtamalization and nixtamalized maize products, through the administration of a questionnaire; and (III) the analysis of the nutritional content of a novel consumer accepted nixtamalized maize product. The first phase aimed to explore South African consumers' acceptance of nixtamalization and novel nixtamalized maize products. Three nixtamalized maize products were developed: a vegetarian patty; a vegetarian nugget; and a maize chip. To evaluate the consumers' sensory acceptance of various attributes, including taste, aroma, texture, and appearance, the study employed the Just-About-Right (JAR) scales and a 9-point hedonic scale. Among the three products evaluated, the maize chip received the most acceptable JAR results, although improvements were required for its appearance attribute. Furthermore, correlation and penalty analysis revealed that appearance and taste played significant roles in the acceptance of nixtamalized maize products, among South African consumers. Consequently, the chips were flavoured with seasonings to improve taste and appearance, with different flavours, such as chutney and tomato. Notably, the chutney-flavoured maize chip achieved an acceptance rate of >70.0% for all four attributes, rendering it “just-about-right”. The study's second phase involved determining consumers’ attitudes toward nixtamalization and nixtamalized maize products. The data was collected online, using an Evasys© questionnaire, which was anonymously completed by respondents, during the sensory tasting of the maize chips. Quantitative analysis concluded that most respondents were open to nixtamalization as a new processing technique and to newly developed maize products produced, through nixtamalization. Specifically, respondents indicated that the safety aspect of nixtamalization played a crucial role in their willingness to consume nixtamalized maize, in the future. Moreover, the results indicated that the respondents were willing to incorporate nixtamalized products into their future consumption, and recommend them to friends and family. After achieving consumer acceptance, the third phase of the study focused on conducting nutritional analysis of the novel nixtamalized maize chip. The analysis revealed several noteworthy findings. The chips exhibited a high energy content of 2303 kJ/100 g and protein content of 6.64 g/100 g. Compared to two commercial chips, the nixtamalized maize chip displayed a higher insoluble fibre content of 15.87 g/100 g of NDF and 1.32 g/100 g of ADF. Additionally, the sodium content of the maize chip (706.67 mg/100 g), fell within the permissible limit set out by South African salt legislation (<800 mg/100 g), for savoury snack foods. Moreover, the chips demonstrated favourable potassium, calcium, phosphorus, and magnesium levels. The higher fat content of 23.72 g/100 g in the chips was attributed to the deep-frying process, used during preparation.
Open Access
Access to credit and agricultural production in Lesotho
(University of the Free State, 2012-01) Motsoari, Charmaine; Van Schalkwyk, H. D.; Cloete, P. C.
English: One of the factors hindering development in Lesotho is the limited access to credit. The development of the rural economy in developing countries depends on growth and development in the agricultural sector and other small and medium enterprises. These enterprises constitute the engine of growth, employment and income for the rural community. In an effort to make the landscape of rural finance more attractive and to fulfil the national objectives of increased production, policy makers and donors adopted the conventional approach of advancing credit, where all practices and operational procedures were geared towards the interests of the borrower. The initiatives to advance credit include amongst others, an emphasis on project appraisals, relaxing collateral requirements and the charging of close to market interest rates. Despite the changes, the problem of limited access to financial services still exists. In fact, these approaches (policies) invariably resulted in distortions in the financial markets, and reduced the number of financial products and services to which farmers have access. The purpose of this study therefore, was to examine factors that influence small-scale farmers’ access to credit, thereby affecting their productivity and to make suggestions for government interventions and for the reduction of market failures in the rural financial markets of Lesotho. The study was conducted in two agro-ecological zones in Lesotho, namely; the Lowlands and the Highlands regions. A random sample of districts in the regions was done to select representative districts in each region. Leribe, Mafeteng, and Berea districts represented the Lowlands while Mohale’s Hoek and Thaba-Tseka districts represented the Highlands region. Stratified random sampling was employed to select borrowers and non-borrowers for the study. The study employed the logistic regression model (logit) within the principal component regression (PCR) framework to assess factors affecting small-scale farmers’ access to credit. PCR was used to take care of the multicollinearity between the variables. Firstly, the variables included in the logit model were subjected to principal component analysis (PCA) in order to reduce the variables into a few uncorrelated principal components (PCs). After principal components (PCs) were calculated, PCs with the smallest eigenvalues were eliminated and then PCR was fitted using standardised variables to improve the estimation power of the logit model. The empirical evidence of the study indicates that non-farm income, savings and remittances and pensions confirmed that increasing the household’s total income reduces the probability of a household being credit constrained. This shows that a better household situation affects the decision of the lender to ration the loan or that the household has less demand for loans because of its own equity capital accumulated through past income earnings. Farm income on the other hand, is positive, confirming that a higher farm income may improve the farmer’s creditworthiness and in some cases create a demand to expand production, thus increasing the demand for credit. The study revealed that farm income values of borrowers are higher than those of nonborrowers but lack of baseline data makes it difficult to associate the differences to the loans obtained by borrowers. However, the changes in income among borrowers are linked to the use of credit, confirming the hypothesis that credit has a positive effect on income and improvement of living conditions of credit users. Research into the behaviour of credit institutions in Lesotho will help to explain some of the actions taken by credit institutions, and at the same time assist policy-makers in formulating appropriate interventions.
Open Access
Acid-base potential characterisation in the Southern highveld coalfield of Mpumalanga
(University of the Free State, 2017-07) Ntwaeaborwa, Gaonkile Molly; Deysel, Lore-Mari
Pyrite, iron disulphide is the most common mineral in the metal sulphite and coal deposit. The oxidation of Pyrite and other metal-sulphide minerals by oxygen has a large environmental impact and plays a key role in Acid Mine Drainage (AMD). Environmental impact shows that soil acidity, toxic metal concentrations and vegetation damage are the predominant negative impact of AMD. AMD is a major concern for the mining industry because mining activities tend to increase the amount of rock surface exposed to air and water. Mining companies are increasingly required to evaluate the AMD potential at future mine sites and provide detailed plans to prevent or minimise AMD at all phases of mine operation as part of the environmental Impact assessment (EIA) process. An investigation was conducted in two mine (Mine 1 and Mine 2) areas in the Southern Highveld Coalfield of Mpumalanga. Mine 1 is an underground coal mine and is situated 10 km outside Trichardt on the road to Bethel. It was established in May 2012 and its shaft supply coal to Sasol Synfuels. Mine 2 is an open-cast coal mine and is situated between 2 towns, amely Trichardt and Kriel. Construction activities started in 1990 and the mine reached full production in September 1992. Both Mines fall in the Karoo Supergroup which comprises of Ecca group formation and consist dominantly of sandstone, siltstone, shale and coal. The aim of this study was to investigate the acid-base potential of these two Mines. 118 samples were collected from Mine 1 borehole core and 71 samples were collected from Mine 2 borehole core to conduct mineralogical and Acid Base Accounting (ABA) analysis. Acid- base potential leachate were further analysed for major and trace elements using Inductively Coupled Plasma-Optical Emission Spectrometer (ICP-OES). Most of the samples analysed for Mine 1 have been found to have High AMD risk at the interburden and these samples have low NNP values, all these samples consisted of coal and they contained pyrite mineral as indicated in the mineralogical analysis. These samples must be taken into consideration to minimise oxidation. Samples (Mine 1) that contained layers of sandstone, siltstone and shale have the highest NNP values and these layers can be used as a buffer to neutralise the AMD. Therefore Mine 1 will produce an AMD at the coal seam once exposed during mining. Mine 2 shows that 3 samples have High AMD risk at the interburden while 2 boreholes show the risk between 20m and 60m, and these samples were coal samples and others were sandstone samples and they contained pyrite. These samples that have coal showed low NNP. Therefore most of the acid generation would be mainly found at the coal seams. Layers that show high NNP values consisted of sandstone, siltstone and shale. They showed no indication of acid generation, therefore they will work as buffers to neutralise the any AMD that will be produced. Mine 2 also indicate that AMD will be produced at the interburden at layers that contains coal, therefore more consideration is needed when these layers are exposed during mining. With such condition it is possible for the mines to predict the types of situations that might arise concerning groundwater quality, and implement proper prevention or remediation programs.
Open Access
Acoustic sanctuary: the South African Ayres sensory facility located on the foot of Naval Hill
(University of the Free State, 2022) Coertz, Henry Reginald; Smit, J. D.; Jooste-Smit, P.; Bitzer, M.; Raubenheimer, H.; Auret, H. A.
This project centres around repurposing a historical water reservoir and pumpstation located on the foot of Naval Hill, Bloemfontein into an alternative speech therapy centre, where architecture plays a critical role in speech therapy arguably equal to that of any professional pathologist. Apart from a reimagined speech pathologist office, the South African – Ares Sensory facility (SA-AS Facility) also incorporates a sensory park. The impetus of this project is the sensory park and the freedom of therapy that it represents. Freedom to mend a speech disorder at the tempo of the patient, though neurologically stimulating garden structures. Similar to gymnasium equipment, these follies allow patients to exercise their neurological network of senses that all contribute to address speech disorder, hence the phonic gymnasium description of this SA-AS facility. This dissertation covers complex therapeutic and theoretical topics, and the information from each chapter contains the chronologically necessary information to understand the chapters that follow. Chapter one directly starts with what is known about speech sound disorders. Chapter two contains the reinterpretation of Frank Lloyd Wright’s concepts of organic architecture in order to establish a physical form of the essence of this dissertation. From here, the discourse starts to question the communication process at an anatomical level and therefore translates the auditory defect of speech impairments to that of musical melodies and architectural rhythm. These phonic applications are then explored within architectural precedents while being related back into sound correction (Speech therapy) and mobility (occupational therapy). Chapter 3 clarifies and analysis the project goals and location within these mentioned ideals. While chapter 4 refines all the information provided into three conceptual models. These physical manifestations investigate the architectural application of scientific research and therapeutic discourse. The final chapters explain the design development and folly rationale before leading to the final design.
Open Access
Activation of the SARS-CoV-2 spike protein by 𝘤𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘯𝘦𝘰𝘧𝘰𝘳𝘮𝘢𝘯𝘴 secreted proteases
(University of the Free State, 2023) Mjokane, Nozethu; Sebolai, O. M.; Pohl, C. H.; Albertyn, J.; Gcilitshana, O. M. N.
The thesis is not structured in a classical way. As such, it is composed of a literature review section (Chapter 1) and two research chapters (Chapters 2 and 3). A general discussion section (Chapter 4) and addendums are also included. As some chapters are in a publication format, repetition of essential information could not be avoided. Chapter 1 reviews the emergence of SARS-CoV-2 and its impact. In particular, it considers the co-infection of this virus with respiratory fungal pathogens, which are major independent risk factors that complicate COVID-19 by causing a more severe infection resulting in higher mortality than that of either infection on its own. These fungal pathogens secreted furin-like proteases to further their virulence during host invasion. In this context, the thesis argues that it is foreseeable that the virus could also access these fungal furin-like proteases and pervert them in order to activate its latent spike protein. Therefore, this set up a number of questions, which are addressed in the thesis concerning the possible activation of the viral latent spike protein by fungal furin-like proteases. In Chapter 2, it was sought to characterise 𝘊𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 (𝘊.) neoformans proteases and assess if they could theoretically bind to the SARS-CoV-2 spike protein. To be specific, previous papers reporting on cryptococcal serine proteases were perused, and this made it possible to select a number of proteases, namely cryptococcal serine carboxypeptidase (CNBF4600), cryptococcal cerevisin (CNBJ2870) and cryptococcal peptidase (CNBA1340), cryptococcal peptidase (CNAG_00150) and cryptococcal cerevisin (CNAG_04625). By designing specific primers, it was possible to show that these serine proteases were expressed in 𝘊𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘯𝘦𝘰𝘧𝘰𝘳𝘮𝘢𝘯𝘴 H99, the prototypical cryptococcal strain used in this thesis. Therefore, the expressed gene products were expected to be secreted into the culture media. This was important for the work that follows in Chapter 3. Through using the computational programme, High Ambiguity Driven protein-protein DOCKing (HADDOCK), it was possible to show that some of the selected cryptococcal serine proteases could interact with the coronavirus spike protein and yield a binding affinity greater than and comparable to furin. However, as HADDOCK is a computational programme, the predicted binding affinities might not correlate with the experimental binding affinities in solution, more so since the used 𝘊𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘯𝘦𝘰𝘧𝘰𝘳𝘮𝘢𝘯𝘴 proteases structures were predicted and not solved. To account for this, Chapter 3 sought to provide enzymatic evidence using the collected culture media – in the form of supernatant. To do this, a mimetic fluorogenic peptide of the SARS-CoV-2 spike protein was designed and modified to have intra-molecular fluorescence quenching capability using 7-methoxycoumarin-4-yl acetyl (MCA) at the N-terminus and N-2,4-dinitrophenyl (DNP) at the C-terminus. The assay was performed using the cryptococcal supernatant. For reference, recombinant furin was included as this is the serine protease present in humans that catalyses the activation of the spike protein. Here, it was determined that cryptococcal serine proteases present in the supernatant could cleave the mimetic spike protein at S1/S2 site with biochemical efficiency comparable to furin. To test the veracity of these data, SARS-CoV-2 pseudovirion containing a full-length spike protein was used. It was possible to show that the pseudovirion could be transduced into HEK-293T cells in the presence of the cryptococcal supernatant. Chapter 4 takes into account the obtained results and provides a summary of the major observations. Of note, the thesis theorises that yeast kexin proteases are responsible for the observed activity. This is because there is a functional homology between yeast kexin proteases and furin (both are convertases); thus, it is reasonable that the supernatant (which contains yeast kexin proteases) could activate the latent SARS-CoV-2 spike protein. The thesis further proves that other respiratory fungal pathogens have yeast kexin proteases that activate the spike protein. This evidence is documented in Addendum no. 1. All things considered, the findings point to the regulation of protease activity as a viable approach to control the activation of the spike protein by either mammalian protease or fungal proteases. To this end, protease inhibitors could be used to control unwanted proteolysis. Addendum no. 2 attempted to show this. Here, it was possible to show that the South African-based medicinal plant Artemisia tea infusion extract and its active compound artemisinin could control the activation of the mimetic SARS-CoV-2 spike protein by furin but not the supernatant. The latter highlights the need to purify the supernatant and isolate yeast kexin proteases. The idea of exploring the control of unwanted proteolysis is also an interventional measure considered by Pfizer, the pharmaceutical company. This American multinational pharmaceutical and biotechnology corporation successfully piloted Paxlovid to control SARS-CoV-2. This drug contains an anti-protease (PF-07321332) that inhibits the protease (SARS-CoV-2 3CLp) responsible for viral replication.
Open Access
Activity patterns of birds in the central Free State, South Africa
(University of the Free State, 2009-11) Van Niekerk, Daniël Johan; Kok, O. B.
Activity patterns of bird species were studied at Glen Agricultural College within the grassland area of the central Free State, South Africa, during a period of 11 years (July 1997 - July 2008). The study focused on a specific grassland locality where 5-minute checklists were compiled continuously from dawn to dusk at least once a week for a total of 656 days. Data were also collected each minute for selected species. Additional observations in an adjacent tree and shrub dominated drainage line included I-minute checklists compiled during transects over a two-year period (late autumn 2000/1 to mid-autumn 2002/3) as well as surveys from a fixed position from dawn to approximately 70 minutes after sunrise during 2007/8. The central aim of the study was to quantify and explain annual, seasonal and daily activity patterns of all bird species recorded in the study area. This data is summarised in separate species accounts where aspects of the annual cycle, particularly breeding and moulting, were also considered. In addition, the potential influence of rainfall was investigated. The study reveals, for the first time, how the activity patterns of a southern African bird community change through time, and how the amount and timing of rainfall can influence these patterns. In spite of similarities amongst species when daily, seasonal and annual patterns are considered separately, the study also shows that each species is unique when all its data is considered simultaneously. Because activity patterns can have a substantial influence on the detectability of a species, the accuracy and usefulness of surveys aimed at estimating bird numbers is consequently questioned. The study at Glen also shows how activity patterns can be used to help unravel the annual cycle of species in a time and cost effective way.
Open Access
Actuarial risk management of investment guarantees in life insurance
(University of the Free State, 2010-11) Bekker, Kobus Nel; Dhaene, Jan; Finkelstein, Maxim
Investment guarantees in life insurance business have generated a lot of research in recent years due to the earlier mispricing of such products. These guarantees generally take the form of exotic options and are therefore difficult to price analytically, even in a simplified setting. A possible solution to the risk management problem of investment guarantees contingent on death and survival is proposed through the use of a conditional lower bound approximation of the corresponding embedded option value. The derivation of the conditional lower bound approximation is outlined in the case of regular premiums with asset-based charges and the implementation is illustrated in a Black-Scheles-Merton setting. The derived conditional lower bound approximation also facilitates verifying economic scenario generator based pricing and valuation, as well as sensitivity measures for hedging solutions.
Open Access
Adaptation to climate change and impact on smallholder farmers' food security in South Africa
(MDPI, 2022) Ogundeji, Abiodun A.
If not adequately managed, climate change is predicted to have a large negative impact on smallholder subsistence farmers, posing a significant danger to household food security. However, the role of adaptive techniques used by farming households to reduce these negative effects and, as a result, their food insecurity status has not been sufficiently evaluated. This study explores the factors that influence smallholder farmers’ adoption of climate change adaptation measures, as well as their impact on household food security. Using an endogenous treatment-effect ordered probit model, agricultural households’ food security status is likely to significantly improve when they employ measures to adapt to adverse climatic conditions. The empirical findings also show that the gender makeup of the household, age, tropical livestock unit, and access to climatic information improve the likelihood of smallholder farmers adopting climate change adaptation measures. Based on the findings, this study advocates that governments and non-governmental organizations (NGOs) support smallholder farmers’ Indigenous adaptation options with various institutional, regulatory, and technological assistance, with a particular emphasis on female-headed households.
Open Access
Adaptation, coping strategies and resilience of agricultural drought in South Africa: implication for the sustainability of livestock sector
(Elsevier Ltd., 2021) Bahta, Yonas T.; Myeki, Vuyiseka A.
Agricultural drought has put sub-Saharan African under significant pressure, and without adaptation, will negatively influence a future generation. Hence, it is crucial to assess the adaptation and coping strategies, the resilience of agricultural drought, its implication on the sustainability of the livestock sector, and developing future interventions. Data of 217 smallholder livestock farmers were used in a principal component analysis to estimate the agricultural drought resilience index as an outcome variable against social wellbeing, economic outcome, environmental variable and adaptive capacity variables. The results found that 21% of the livestock farming households sold their livestock as an adaptation and coping strategy. In contrast, 20% of the farming households used alternative land use as an adaptation, and coping strategy, 20% stored food, 17% asked for animal feed, 6% sought employment, 6% migrated, 5% kept drought-tolerant breeds, 3% received relief grants, 2% used their savings and investments, and 1% leased their farms. When natural, economic and social sustainability was viewed as a resilience process, the three pillars positively and significantly impacted households' agricultural drought resilience. This implied that the more smallholder farmers participated in social networks and cooperatives, the higher the resilience to agricultural drought. Further, the more resources, income, access to land, access to water, access to credit, and additional types of farming, the higher the households’ resilience to agricultural drought and adaptive capacity. Thus, the three pillars of sustainability are crucial for enhancing the resilience and adaptability of smallholder livestock farmers. The study recommends that government aid reduce vulnerability to agricultural drought via access to agricultural credit and encourage farmers to be part of social networks and cooperatives. Additionally, the government could improve access to land and water rights to boost the resilience of smallholder farmers to agricultural drought. This could be achieved through collaboration and coordination among all role players.
Open Access
Adaptive dynamics for an age-structured population model with a Shepherd recruitment function
(University of the Free State, 2013-06-07) Ellis, Michelle Heidi; Schoombie, S. W.
English: In this study the evolution of the genetic composition of certain species will be replaced by the evolution of the traits that represent these genetic compositions. Depending on the nature of the trait of interest, a scalar valued parameter called the strategy parameter will be assigned to this trait making the simulation of strategy evolution possible. The trait of interest, and therefore the strategy associated, will be the ability of a population to keep its densities within the carrying capacity of the environment they find themselves in. The Shepherd function, on account of its wide use in population simulations as well as composing of exactly such a density parameter, will be the density curbing mechanism of choice in the age-structured population model designed here. An algorithm will be designed to simulate strategy evolution towards an evolutionary stable strategy or ESS that will ensure not only an optimal fit for this environment but also render the population immune against future invasion by other members of the population practising slight variations of this strategy. There are two ways to come by such an optimal strategy without directly involving genetics. The first is game theory, allowing strategists to compete for this position, and the second is with the use of adaptive dynamics, converting winning and loosing instead into tangible mathematics. Combining these two classics will show that the quest is an exercise in strategy optimization, not only from the point of view of an already established population but also from the point of view of an initially small one. It will be interesting!
Open Access
ADH2 regulation in the yeast Saccharomyces cerevisiae
(University of the Free State, 2004-05) Khoboko, Mojabatho Portia; Albertyn, J.; Du Preez, J. C.
English: The aim of this study was to investigate the ability of ethanol to repress the expression of ADH2 in the genome of Saccharomyces cerevisiae. To achieve this, an expression cassette (ADH2::LacZ) using LacZ as a reporter gene was constructed using the YIp356R shuttle vector. A 1000 bp up and downstream region, flanking the open reading frame of ADH2, was fused to the 5’-end and 3’-end of the LacZ gene in the YIp356R shuttle vector. Numerous attempts were made to transform the expression cassette (ADH2::LacZ) into S. cerevisiae (strain W303) containing a deleted ADH2 (adh2Δ::URA3), to displace the deletion cassette through homologous recombination, thereby placing ADH2::LacZ in the place of the ADH2 in genome of S. cerevisiae. This was unfortunately not successful and it was decided to use an alternative approach. In this case the expression cassette was cloned into the integrative vector YIplac211 and transformed into S. cerevisiae. For initial confirmation, the yeast transformants were grown on selective plates containing X-gal, which allows for the detection of β-galactosidase activity through the production of blue coloured colonies. The detection of the blue colour confirmed that the expression cassette was successfully constructed and integrated into the genome. Two randomly selected transformants were cultivated on 20 g glucose l-1 as sole carbon source, to study glucose repression and on three different ethanol concentrations to study the effect of ethanol on the expression of ADH2. Selection was maintained by growing the yeast in a URA– chemically defined media (pH 5.5) at 30ºC. Samples were taken at appropriate intervals to perform β-galactosidase assay, assess utilization of substrate (ethanol and glucose), ethanol formation and biomass determination. During growth on 20 g glucose l-1 the production of β-galactosidase was apparent only when glucose concentrations were very low (2.3 g l-1), indicating that glucose levels have to decrease to a critical level before ADH2 expression can resume. The highest final biomass was produced during growth on 20 g glucose l-1. During growth on the three different ethanol concentrations the highest β-galactosidase maximum specific activity was obtained during growth on 20 g ethanol l-1 (3 643 U mg-1) and the lowest during growth on 5 g ethanol l-1 (2 533 U mg-1). Although the maximum specific activity obtained during growth on 30 g ethanol l-1 were higher than that obtained during growth on 5 g l-1, the production rate was the lowest (93 U mg-1h-1) during growth on 30 g ethanol l-1, suggesting that 30 g ethanol l-1 concentration has negative effect on the expression of ADH2. However this slow production might have been due to the slow growth during this cultivation and not due to ethanol repression. The possible repression of ADH2 is further disputed by the high β-galactosidase production on 30 g ethanol l-1.
Open Access
Adult-plant resistance to Puccinia recondita f. sp. tritici in a collection of wild Triticum species
(University of the Free State, 1999-05) Barnard, Johanna Elizabeth; Pretorius, Z. A.; Kloppers, F. J.
English: The ability of rust pathogens to mutate and form new and virulent races, necessitates the broadening of the genetic base of resistance in common wheat to rust diseases. The wild relatives offer a rich reservoir of resistance genes. In an attempt to identify new sources of resistance to Puccinia recondita f. sp. tritici, 353 Triticum accessions, comprising diploid, tetraploid and hexaploid species were evaluated for seedling and adult-plant resistance to a mixture of pathotypes UVPrt2, 3, 9, and 13. In addition to infection type studies, plant height, growth habit and head type of adult plants were also recorded. One hundred and twenty six of the accessions were resistant to moderately resistant as seedlings to the pathotype mixture, whereas 180 were resistant or moderately resistant as adult plants. The number of days from planting to flag leaf stage varied from 54 to 187. High levels of resistance were observed in adult plants of T. longissimum, T. sharonense, T. searsii and T. turgidum ssp. compactum. Triticum kotschyi and T. ventricosum expressed hypersensitive infection types. Partial resistance (small pustules without any apparent chlorosis), was observed in T. turgidum ssp. durum, T. turgidum ssp. pyramidale and T. tauschii. In T. turgidum, which comprised 14 subspecies and 272 accessions, approximately 44% of the adult plants were resistant to moderately resistant compared to 24% of the seedlings. According to these results 13 accessions, producing smaller or fewer leaf rust pustules, without the characteristic chlorosis and necrosis associated with hypersensitive resistance, were selected. Adult plants were quantitatively inoculated with pathotype UVPrt13 of P. recondita f. sp. tritici. Palmiet, a bread wheat cultivar susceptible to UVPrt13, was included as a control. Latent period of leaf rust, uredium size and density, and infection type were determined in two experiments. In the first experiment latent period ranged from 309 h to 401 h compared to 258 h in the susceptible control, Palmiet. In the second experiment Palmiet had a latent period of 244 h whereas those in the Triticum accessions ranged between 175 hand 372 h. Most accessions supported more uredia per ern" flag leaf surface than Palmiet in the first, but not in the second experiment. However, pustules were significantly smaller on most of the lines. Based on these components, T. timopheevii ssp. araraticum v. tumanianii, T. turgidum ssp. durum v. obscurum, and T. turgidum ssp. persicum v. stramineum, showed high levels of partial resistance. Triticum turgidum and T. timopheevii accessions rated as potentially valuable sources of resistance were selected for histological studies on mechanisms of resistance. Penetration and establishment of the leaf rust pathogen were studied in flag leaves of T. timopheevii, T. turgidum ssp. dicoccum, T. turgidum ssp. durum and T. turgidum ssp. compactum. The T. aestivum wheats Thatcher (Tc) (susceptible common wheat control) and TcLr19 (resistant common wheat control) were included in the experiment. Using fluorescence microscopy, infection sites of pathotype UVPrt13 were examined for the percentage prestomatal exclusion (germtubes not forming appressoria and appressoria not forming over stomata), abortive penetration (non penetrating appressoria and aborted substomatal vesicles), early abortion (six or less haustorium mother cells per infection site) and infection sites successfully culminating in colonies. Flag leaf sections were prepared for phase-contrast microscopy by staining with either Trypan blue alone or in combination with a solution of picric acid in methyl salicylate. To confirm and expand light microscopy observations, upper and inner surfaces of epidermal tissue of T. timopheevii and T. turgidum ssp. dicoccum were fixed and prepared for scanning electron microscopy. Observations showed that resistance in T. timopheevii was typically hypersensitive and may thus not be durable. The prehaustorial resistance exhibited in T. turgidum ssp. durum and T. turgidum ssp. compactum, may be valuable sources of nonhypersensitive resistance when transferred to cultivated wheat.