Research Report Submitted in Partial Fulfilment of the Requirements for the Degree of Master of Science in Environmental Sciences Date: May 2016 / This study assesses the water quality status of the Hex River downstream of Kroondal Mine (KMS15, sampling point located downstream of Kroondal Mine) and the effects of mining activities (Kroondal Chrome Mine) on the water quality of the Hex River in Rustenburg, which is in the North West Province of South Africa. Potential pollutants were identified, quantified and their distribution was determined over seven years (2007 to 2013) along different sampling points upstream and downstream to the mine. Water quality-monitoring data was obtained from the mine. The surface and underground water was sampled on a monthly basis and analysed by Aquatico, (a water quality service provider of Kroondal Chrome Mine) at SANAS Accredited Testing Laboratory (No T0374). Data was collected for the Hex River and its tributary; the nearby discharge from Crocodile Farm and Farm Dam; as well as mine containment dams, slimes dams, run-off from the processing plant and water dams within the mine. Descriptive statistics (mean/average, minimum and Maximum) and box plots are used to explain the water quality at all sampling points. Water quality from sampling location points was compared against the Total Water Quality Guideline Range (TWQGR) for irrigation, livestock watering, ideal domestic use, aquatic ecosystem limits and the exemption permit issued to the Kroondal Chrome Mine by the Department of Water Affairs and Forestry (DWAF) in 2007, now Department of Water and Sanitation (DWS). The water quality of the Hex River, downstream of Kroondal, was described as neutral, alkaline, saline and very hard with a high pH, and a high concentration of Electric conductivity (EC), Total Dissolve Solids (TDS), Chlorine (Cl), Sulphate (SO4), Nitrate (NO3), Ammonium (NH3), Hardness (CaCO3) and Orthophosphate (PO4). Pollution sources and pathways were identified using the study area layout and by conducting an impact pathway analysis using annual descriptive statistical (annual mean or average values) of water quality tables generated by SAS enterprise 6.1 (a software used to analysed descriptive statistics of the mine water quality data) for a period 2007 until 2013, and box pots graphs showing monthly water-quality data for pH, EC, TDS, Cl, SO4, NO3, NH3, CaCO3 and PO4 at 15 monitoring localities between Kroondal Chrome Mine, the Hex River and its tributaries (Kroondal tributary and Sandspruit) over seven years. It was concluded that the surface/groundwater of the Kroondal Chrome Mine process – such as seepage from slimes dams, plant run-off and the vent shaft underground water dam – had an influence on the water quality of Hex River with regard to the discharge of pH modifying pollutants, EC, TDS, Cl, SO4, NO3, NH3, CaCO3 and PO4. Other pollution sources were discharge from Crocodile Farm and Hex River, as well as the Sandspruit upstream sources such as mining (platinum and chrome), industries’ municipal sewage treatment works, agricultural activities and informal settlements activities. Mine pollutants or constituents were identified as a unique example of the compound impact of weathering, hydrologic and anthropogenic processes such as the increased use of explosives containing NO3 and NH3 underground. The chemical compositions of surface water in the mine sampling location were strongly influenced by rock water in tractions, dissolution and dilution, as well as anthropogenic inputs. Key insights drawn from the study is that, cumulative impacts in the Hex River catchment present different issues, roles and responsibilities for industries, government/ regulators and community stakeholders. Practical and cooperative management of cumulative impacts by catchment stakeholders can benefit regional environments and communities of Rustenburg and the North West Province at large. This study demonstrates the usefulness of descriptive statistical techniques for analysis and interpretation of complex data sets, water quality status of the Hex River catchment, influence of the Kroondal Chrome Mine (KCM) waste water to the Hex River catchment, pollution sources and pathways from different activities around Hex River catchment. Best practice water management was recommended to form part of the Kroondal Chrome Mine environmental objects, target and management plan as well as the mine risk profile. Cumulative management dimensions, approaches and/or methods were recommended for all Hex River catchment stakeholders including Department of Water and Sanitation (DWS), mines, farmers, industries and disadvantage communities along the catchment.

This minor-dissertation established the long-term (July 2002 to June 2006) as well as present day (July 2005 to June 2006) water quality conditions of the Hex River and its tributaries the Dorp-, Paardekraal- , Klipgat- and Klipfontein Spruit, upstream of the Bospoort Dam. The Hex River is situated in the North-West Province, in close proximity of the town Rustenburg. The Hex River falls within the associated Hex River catchment. Various anthropogenic activities impact negatively on the water quality of the Hex River. These impacts include agriculture, livestock production, industrial effluent, mining activities, and processing as well as residential impacts including treated and untreated sewage from the town of Rustenburg as well as informal settlements in the Hex River catchment. The various land uses for the Hex River include domestic use by informal settlements in the area, including mining concessions, livestock watering as well as irrigation and the aquatic environment of the Hex River catchment and the receiving water body the Bospoort Dam. The Hex River, therefore, not only has a effect on the environment but also on the social and economic aspects in the region. Owing to the severity of these impacts it was deemed necessary to determine the long-term water quality trends of the Hex River as well as the prevailing water quality conditions. The primary tributaries of the Hex River were included in the study to determine the source of possible pollution influx. In order to achieve the aim of the study a literature review was conducted on chemical, physical and biological water quality as well as legislative requirements controlling water quality management. A proper understanding of the various impacts as well as land uses in the area is essential in demarcating possible pollution sources. The assessment of the long-term water quality data was conducted to determine the historical water quality trends of the Hex River and associated tributaries and the deterioration in water quality over a four year period. The most recent water quality data were compared against the Target Water Quality Guideline Ranges (DWAF, 1996) for domestic use, irrigation, livestock watering as well as aquatic ecosystems. The long-term water quality trends showed a significant mine water, industrial effluent and sewage impact on the Hex River after the confluence with the tributaries. The assessment of the current water quality situation indicated non-compliance towards the Target Water Quality Guideline Ranges (TWQGR) as stipulated by the Department of Water Affairs and Forestry (DWAF, 1996a-d), rendering the water unfit for domestic use, irrigation and livestock watering. The sources feeding the tributaries iii contain water of inferior quality with a direct associated environmental risk. However, at present the risk potential is contained in the system but with a specific environmental event, such as high rainfall over a short period of time, could be released with a significant environmental impact and decrease in aquatic biodiversity. / Dr. J.M. Meeuwis

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Background: Type 2 diabetes mellitus is a metabolic disorder characterized by the rise of fasting plasma glucose from its normal range (≥125mg/dl). It is marked by insufficient production of insulin from pancreatic β-cells as a result of failed compensation due to insulin resistance. Several treatments are available for the disorder, which mainly focus on improving the sensitivity of insulin in different body tissues. Recently, probiotics were suggested as candidate treatments for type 2 diabetes and for extending lifespan as well. This experiment aims to investigate such claims using Drosophila melanogaster as a disease model.   Results: Other than the observed low average weights in treated larva samples, probiotics did not show any other significant results in affecting the length, glucose, glycogen, and trehalose levels (One-Way ANOVA and Kruskal-Wallis, p>0.05). Real-time PCR was only carried out once. Thus, no statistical tests were reliable enough to analyse the data obtained. The longevity study, on the other hand, did show significance (Log-rank (Mantel-Cox) test and Gehan-Breslow-Wilcoxon test, p<0.0001), as the probiotic Bifidobacterium lactis extended the lifespan of adult flies feeding on a high sugar diet significantly when compared to the control ones feeding on only high sugar diet without probiotics.   Conclusion: Except for weight measurements, none of the other results was reliable enough to make a concrete conclusion on whether the treatments indeed worked in reversing type 2 diabetes symptoms or not. Real-time PCR results did show some effects of some of the treatments at different developmental stages. However, unless Real-time PCR is repeated at least once using the same protocol, no deduction can be made. Additionally, the data obtained hint that the dosage used (0.025 g) was too high for larvae and adult flies and might have caused malnutrition by blocking their midgut and decreasing food absorption. Hence, false significant or non-significant results were acquired instead.   Further studies are required using a much lower probiotic dosage if Drosophila is used as a disease model. Although, other models such as mice or rats are recommended in this case, in order to reach a solid conclusion about the effectiveness of probiotics in treating type 2 diabetes mellitus. Baring these thoughts in mind and based on the results of this experiment, the null hypothesis indicating that there is no significant relationship between the use of probiotics and reversing type 2 diabetes mellitus symptoms is therefore accepted.

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Mesh adaptation techniques are used to modify complex finite element meshes to reduce analysis time and improve accuracy. Modification of all-hexahedral meshes has proven difficult to the unique connectivity constraints they exhibit. This thesis presents an automated tool for local, conformal refinement of all-hexahedral meshes based on the insertion of multi-directional twist planes into the spatial twist continuum. The contributions of this thesis are (1) the ability to conformally refine all entities of an all-hexahedral element mesh, (2) the simplification of template insertion to multi-directional refinement. The refinement algorithm is divided into single hex sheet operations, where individual refinement steps are performed completely within a single hex sheet, and parallel sheet operation, where each refinement step occurs within two parallel hex sheets. Combining these two procedures facilitates the refinement of any mesh feature. Refinement is accomplished by replacing original mesh elements with one or more of six base templates selected by the number of nodes, flagged for refinement on the element. The refinement procedures are covered in detail with representative graphics and examples that illustrate the application of the techniques and the results of the refinement.

Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2005. / The South African table grape industry exports approximately 60% of the table grapes produced. A major threat to the export of these grapes is the phytosanitary risk that insect pests pose. This study was conducted in the Hex River Valley, South Africa’s main table grape producing area. The aim of this study was to reduce the number of phytosanitary rejections from insects on table grapes from the Hex River Valley. Thus the main objectives of the study were to identify the most important phytosanitary pests in the Hex River Valley; the determination of their presence in the vineyards with possible means to control them; and to assess the possibility of using postharvest quarantine treatments in the Western Cape. Further aims were to determine the effect of different colour harvesting crates on the phytosanitary pests and whether the phytosanitary pests infested the grapes via packhouses. The most important phytosanitary pests of table grapes of the Hex River Valley are in order of importance: Phlyctinus callosus (Schonherr) (Coleoptera: Curculionidae), Epichoristodes acerbella Walker (Lepidoptera: Tortricidae), Planococcus ficus (Signoret) (Hemiptera: Pseudococcidae), Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), Gonocephalum simplex Fabricius (Coleoptera: Tenebrionidae) and Dysdercus fasciatus Signoret (Hemiptera: Pyrrhocoridae). 12.71% of rejections were from species that were not identified, while a further 33% of the rejections were possibly identified incorrectly. Phytosanitary control of P. callosus appeared to be far more effective using Plantex® than pesticides. Weather conditions appeared to affect the abundance of P. callosus, especially warm weather, while bunches harboured less P. callosus later in the day. Control of E. acerbella with DiPel® (Bacillus thuringiensis var. kurstaki) appeared to at least reduce the population within the vineyards, and so its use is recommended. P. ficus is a non-actionable species for the USA market and is not listed as a phytosanitary pest for the Israeli market and so should not be causing any phytosanitary rejections. C. capitata appeared to be successfully controlled by the fruit fly sterile release program and the cold sterilisation it currently undergoes. G. simplex caused few rejections. It is still unclear where this pest infests the grapes, as it was found in both the field and in the packhouses. D. fasciatus occurrence on grapes was probably accidental. It was shown that picking during the early and late parts of the day, when this species was less active, reduced its occurrence in bunches. Gryllus bimaculatus (De Geer) (Orthoptera: Gryllidae), although not reported as a reason for rejections in table grapes for the past two years, was an actionable species that was present in large numbers in the Hex River Valley. There was a strong correlation between increasing quantities of pesticides and higher abundances of G. bimaculatus. It appeared to be an indicator of the overuse of pesticides. Results of this study showed that infestation by the phytosanitary pests came from neighbouring vineyards. The creation of barriers to prevent the movement of these pests between vineyards is suggested. Methyl bromide is the most commonly used postharvest quarantine treatment. Owing to the ozone-depleting properties of methyl bromide, it is scheduled to be outlawed in many countries from 2005. Alternative postharvest treatments are irradiation, extreme temperatures, forced air, vapour-heat treatments and the use of controlled atmospheres. Irradiation treatments appeared to control the pests at doses that do not damage the grapes. Controlled atmosphere treatments also have a high probability of success, although more research is required on this treatment. Low temperature treatments are relatively cheap as most exported fruit already undergoes cold storage, and appears to control species in the families Pseudococcidae and Tephritidae, although further research is required for the other pest. Colour or location of the harvesting crates in the vineyards appeared not to influence the number of phytosanitary pests collected, as they were not attracted to these crates.

Cette thèse s'intéresse à la génération, à l'utilisation et à l'évaluation des maillages hex-dominants, composés d'hexaèdres et de tétraèdres, dans la cadre de la simulation numérique par la méthode des éléments finis. Les éléments finis hexaédriques sont souvent préférés aux éléments tétraédriques car ils offrent un meilleur ratio entre précision et temps de calcul dans un certain nombre de situations. Cependant, si la génération automatique de maillages tétraédriques est aujourd'hui un domaine bien maîtrisé, ce n'est pas le cas de la génération de maillages hexaédriques alignés avec le bord, qui reste un problème largement ouvert. En l'absence de progrès significatifs, les approches actuelles se contentent de maillages hex-dominants afin de tirer parti des performances supérieures des hexaèdres et de la flexibilité géométrique des tétraèdres, qui rend possible le maillage automatique. Dans une première partie, nous développons des algorithmes robustes pour la génération de maillages hex-dominants à partir de champs de directions, notamment pour l'isolement et le remplissage des régions difficiles à mailler (singularités et autres dégénérescences). Dans la seconde partie, nous essayons de déterminer dans quelles situations et dans quelle mesure les maillages hexaédriques, et hex-dominants générés précédemment, sont plus intéressants que les maillages tétraédriques. Ceci implique spécifiquement d'étudier plusieurs manières d'effectuer des simulations par éléments finis avec les maillages hybrides, dont une approche où nous utilisons des contraintes de continuité pour maillages non-conformes. Pour mesurer l'influence du maillage sur l'approximation des solutions, nous proposons une nouvelle méthode d'échantillonnage pour calculer très efficacement des distances globales entre solutions éléments finis définies sur des domaines compliqués / This thesis focuses on generation, usage and evaluation of hex-dominant meshes, which are made of hexaehedra and tetrahedra, in the context of the finite element method. Hexahedron finite elements are often preferred to tetrahedron elements because they offer a better compromise between accuracy and computation time in certain situations. However, if tetrahedral meshing is a well mastered subject, it is not the case of hexahedral meshing. Generating hexahedral meshes with elements aligned to the borders is still an open and difficult problem. Meanwhile, current automated approaches can use hex-dominant meshes in order to take advantage of both hexahedron accuracy and geometrical flexibility of tetrahedra. In the first part, we develop robust algorithms for the generation of hex-dominant meshes with elements aligned with the borders. Specifically, we propose a method to extract and fill the areas where hexahedral meshing is difficult (singularities and degeneracies). In the second part, we try to identify and to quantify the advantages of hexahedral and hex-dominant meshes over tetrehedral ones. This requires to study various ways to apply the finite element method on hybrid meshes, including one in which we propose to use continuity constraints on hexahedral-tetrahedral non-conforming meshes. To measure the impact of meshes on the finite element accuracy, we develop a new sampling method which allows to compute efficiently global distances between finite element solutions defined on complicated 3D domains

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