The aquifer vulnerability of the Molototsi (B81G) and Middle Letaba (B82D) quaternary catchments was assessed to determine the influence of the vadose zone on the groundwater regime. Anecdotal evidence indicated that the aquifers may be vulnerable to pollution. The aquifer vulnerability was assessed by developing a new method RDSS. The RDSS method was developed by combining relevant vulnerability parameters of DRASTIC, GOD, EPIK, SEEPAGE, COP and SINTACS. RDSS evaluates the vadose zone as a pathway for pollutants by using the following four parameters namely: Recharge, Depth to water table, Soil type and Slope. Recharge was estimated using the Chloride-mass balance method. Depth to water table was measured in the field using a dipmeter. For inaccessible boreholes, data was requested from Groundwater Project Consulting Company. The seepage behaviour (soil type) was determined using parameters such as hydraulic conductivity, infiltration and percolation. Percolation and hydraulic conductivity was determined by undertaking percolation tests in accordance with SABS 0252-2:1993. Infiltration was determined using the double ring infiltrometer. Slopes were determined from the digital elevation method using ArcGIS software. High recharge was revealed in the lower parts of both B81G and B82D. Shallow depth to water level was revealed on the upper part of B82D and extended towards the lower part of B81G. Soil type relates to saturated vertical hydraulic conductivity, which was rated to be high in the northeast of B81G. Gentle (high influence due to preferential infiltration to runoff) slopes extend from the south towards the northern parts of both B81G and B82D. The four parameters (recharge, depth to water table, soil type, and slope) were overlaid using Weighted Sum, Weighted Overlay and Raster Calculator to produce the final vulnerability map. When using Weighted Overlay and Weighted Sum, rasters were given different percentages of influence in different scenarios. The Weighted Overlay tool inputs multiple rasters and sets all weights equal to 100%. The Weighted Sum tool inputs multiple rasters and sets all weight equal to 1.0. When using the Raster Calculator, rasters were evaluated by being added together without multiplying by the percentage of influence. The results obtained are discussed in detail with reference to the degree of vulnerability of these two densely populated rural areas. / Dissertation (MSc)--University of Pretoria, 2013. / Geology / unrestricted

Urinary catheters are indispensable in healthcare and, with an ageing population, their use will continue to increase. However, they are commonly associated with colonisation and urinary tract infections (UTIs) caused by the attachment of bacteria to the catheter surface. Application of a novel cationic compound as a catheter coating may have a significant impact on the costs associated with treatment of UTIs and reduce the need for catheter replacement, as well as decreasing the number of UTI associated morbidity and mortality. Cationic compounds in particular are known to interact with the negatively charged outer membrane of bacteria, therefore have a broad spectrum of activity. The purpose of this study was to source and evaluate a novel cationic antimicrobial for use as a potential coating to impede biofilm formation on urinary catheters, and to investigate the cellular response to the selected lead compound. This research has demonstrated that the antimicrobial activity of commercially available Byotrol™ was superior to that of polyamines and quaternary ammonium compounds that were screened. Using high-throughput antimicrobial assays, such as the minimum inhibitory concentration and microtitre plate biofilm forming assays, the inhibitory concentrations of Byotrol™ were found to range from 3 µg/mL to 15 µg/mL for planktonic cultures, and 3 µg/mL to 20 µg/mL for the biofilm growth of uropathogenic bacteria. Furthermore, the minimum biofilm eradication concentration assay demonstrated that 200-1000 µg/mL Byotrol™ was able to eradicate an established biofilm. Byotrol™ may also have significant potential as a device coating, as pre-coating data on glass slides and microtitre plates with the compound inhibited bacterial growth on the surface at concentrations of 400 µg/mL for E. coli, and 1000 µg/mL K. pneumoniae. Atomic force microscopy validated the expectation that higher concentrations of Byotrol™ coated a surface more evenly than lower concentrations. Using two-dimensional gel electrophoresis, the metabolic protein tryptophanase was seen to be significantly over-expressed when E. coli K12 was treated with sub-inhibitory concentrations of Byotrol™. A transcriptomic approach using RNA-Seq demonstrated that a majority of the differentially expressed genes were identified in cells that were challenged with 4 times the minimum inhibitory concentration of Byotrol™. Genes associated with protein synthesis and stress response were significantly up-regulated. Interestingly, the global gene regulators AI-2 and indole were significantly up-regulated, which may have an influence on the expression of genes related to motility, biofilm formation and acid-resistance. Genes associated with chemotaxis and motility, acid-resistance and iron transport were significantly down-regulated, particularly in cells challenged with Byotrol™.Byotrol™ displayed antimicrobial activity both in suspension and as a coating. Identification of differentially expressed genes and proteins, when the bacteria were treated and challenged with Byotrol™, has, for the first time, revealed the bacterial cell’s response to this biocide. The findings may enable the development of strategies to prevent or better manage catheter associated urinary tract infection (CAUTI).

Five periods of ice advance in the North Klondike-upper Blackstone basins of the Ogilvie Mountains are recognized by the downvalley sequence of progressively older moraines. The youngest occurred during the last millennium and is represented by glacierets and fresh moraines. The other advances are of the Pleistocene Epoch; from youngest to oldest they are: Age I (valley glacier stage), Age II (transection glacier), Age IIA (transection glacier with piedmont) and Age III (mountain ice cap). Evidence for Age III is limited to the north slope of the ranges. Age IIA was recognized only on the north slope and may represent a slightly older pulse of the Age II. This chronosequence is tentatively correlated with those elsewhere in the northern Cordillera. Within the region an array of surficial elements indicates that a continuous and discontinuous mosaic of processes have operated interdependently during the Quaternary. A product of these processes is mapped under one of eight facies - attention being directed to the varieties of features associated with the glacial and periglacial cycles. Of the latter, active, inactive and degradational forms exist. Strong correlations between the distribution of some types of surficial features and the underlying bedrock geology are recognized. No changes in morphology, permafrost distribution, pebble weathering, pedogenesis and floral succession could be related to the ages of the Pleistocene moraines. The influence of permafrost on all ages of moraines, the variability in their environment of deposition, and an edaphic and climatic discontinuity produce greater differences than does the age factor. In the northern half of the study area, permafrost and associated phenomena were observed to greatly retard chemical alteration; on the other hand, they permit the development of only a vegetational and pedological "polyclimax", rather than a single mesic climax, in a time span of less than 11,000-15,000 years. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Azotobacter vinelandii, grown with ammonium as a nitrogen source, was shown to possess an active transport system which could concentrate ammonium 44 to 58 fold. Ammonium uptake was inhibited by the glutamate analog methionine sulfone. The properties of the ammonium uptake system (transport and metabolism) were investigated using the ammonium analog methylammonium. The uptake of methylammonium was inhibited by arsenate indicating that phosphate bond energy was required. Methylammonium uptake was also inhibited by the electron transport inhibitor, cyanide, and the uncoupler, carbonyl cyanide- m-chlorophenyl hydrazone. However, it was shown that these agents served to deplete ATP pools in A. vinelandii. Uptake of methylammonium was sensitive to a Tris-Mg⁺⁺ shock treatment suggesting the possible involvement of a periplasmic binding protein, however, methylammonium-binding activity was not found in periplasmic extracts. A. vinelandii was shown to exhibit a positive chemotactic response toward ammonium as well as acetate, glucose and sucrose. Comparison of outer membrane proteins from nitrogen-fixing cells and ammonium-grown cells revealed the production of a 44,000 dalton protein in membranes from nitrogen-fixing cells. Inner membranes from nitrogen-fixing cells contained a 41,000 dalton protein which was present in low amounts in the membranes of ammonium-grown cells. It was shown that the outer membranes of ammonium-grown cells contained a major protein which was "heat modifiable" in that its mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis was determined by the temperature of solubilization prior to electrophoresis. Methylammonium was shown to be metabolized to N-methylglutamine. Strain JK301, an L-methionine-D,L-sulfoximine-resistant mutant of A. vinelandii, was unable to catalyse N-methylglutamine synthesis in vivo or in cell-free extracts and lacked detectable methylammonium uptake activity. Glutamine synthetase in cell-free extracts of JK301 had a Km for glutamate approximately three-fold higher and a Vmax approximately fourfold lower than enzyme from the wild type strain. It was concluded that methylammonium uptake reflects, in part, metabolism to N-methylglutamine by glutamine synthetase. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Sediments from the northern end of Juan de Fuca Ridge are Late Quaternary in age and contain widely correlatable cycles of turbidity current and hemipelagic sedimentation. Sediments from the Ridge were examined for their mineralogy, structure, components of the sand fraction, rates of sedimentation and grain size distribution to establish processes of sedimentation, stratigraphy, correlation and local hydrothermal relationships. Ten gravity and Phleger core sites along two profiles of the Ridge were examined in detail, one section was perpendicular to West Valley, the main spreading centre, and one section was within and parallel to West Valley. Sediment from Cascadia Basin was compared to the results of the Ridge study. Changes in sedimentation defined by core X-radiograph structure, components of the sand fraction and grain size distribution, indicated cycles of relatively coarse sediment overlain by finer bioturbated sediment with a repeated stratigraphic relationship in all but one Juan de Fuca Ridge core. Changes in sediment composition are attributed to brief, episodic, continent derived turbidity current deposition followed by lengthy periods of hemipelagic sedimentation for each cycle. Differences in composition exist between sediment of ridges and valleys, with a greater winnowed foraminiferal-hemipelagic and a lesser turbidity current influence in the former area. Radiocarbon dated foraminiferal-rich intervals from ridge sediments were exclusively Late Pleistocene with Middle Ridge sediment having an inferred 9000-9500 B.P. Late Pleistocene-Holocene boundary. Similar sedimentation cycles between Middle Ridge and valley localities enabled correlation of ridge and valley stratigraphy and the Late Pleistocene-Holocene boundary. A stratigraphic relationship based on the episodic deposition of continent derived turbidites exists between the northern end of Juan de Fuca Ridge and the continental Pacific Northwest. Pulses of turbidity current sedimentation coincide with initial interglacial warming trends during the Late Pleistocene. Holocene sedimentation for Juan de Fuca Ridge is of hemipelagic origin with rare local turbidity current deposition. Hydrothermal minerals were not detected. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

North American black bears (U. americanus) and brown bears (U. arctos) can be difficult to distinguish in the fossil record due to similar dental and skeletal morphologies. Challenges identifying ursid material from Oregon Caves National Monument (ORCA) called for an accurate tool to distinguish the species. Ursid teeth have a high degree of variability and morphological features are not always diagnostic. This study utilized a large database of lower tooth lengths (p4, m1, m2, and m3) and ratios (p4/m1, m2/m1, m3/m1, p4/m3, m2/m3) in an attempt to differentiate U. americanus and U. arctos in North America. Further, this project examined how these linear measurements differ in response to ecoregion, latitude, and climate. Analysis of variance (ANOVA) found significant differences between U. americanus and U. arctos from across North America for every variable studied. Stepwise discriminant analyses (DA) found lengths separated species better than ratios with 99.1% correct classification versus 77.5% correct classification for ratios. When sexes were analyzed, ANOVA only found significant differences for lengths while DA found lengths and ratios could not accurately distinguish between sexes; only 72.1% of sexes were classified correctly while utilizing lengths and 61% for ratios. Seventeen previously identified fossil specimens from across North America, in addition to the ORCA specimen, demonstrated the utility of this study, confirming several identifications and rejecting others, proposing the need for new designations.

Two sets of cores were recovered from the southern Kenya Rift (Koora and Magadi basins) through the Hominid Sites and Paleolakes Drilling Project and the Olorgesailie Drilling Project. These contain a detailed environmental Quaternary history with records of up to ~1 million years. This period correlates with much of the Olorgesailie Formation record of 1.2 Ma in the Olorgesailie Basin. The Magadi cores reached trachyte at ~ 194 and 133 m with this project focussed on the longer core, MAG14-2A, which includes limestone, zeolitic, laminated and massive clay and silt, massive mud, chert, trona, gravel and sand. The Koora Core (OLO12-1A) extended to depths of 166.14 m and contains laminated and massive diatomites, fine to coarse sands; lime and siliciclastic muds with pumice-rich gravels. The two cores are particularly important because they provide environmental records that help to fill erosional gaps in the history of the Olorgesailie Basin, which includes important evidence for changing hominin cultures and evolution. The high-resolution lacustrine-terrestrial stratigraphies of the two basins have shown how landscapes were transformed because of complex interactions between tectonic and climatic processes. Volcanism also had a significant impact, partially damming lakes at Olorgesailie. Diatoms are present in much of the Koora Basin sequence and large parts of the Magadi sediments. These are dominated by a variety of planktonic Aulacoseira, Cyclotella and Thalassiosira taxa in both basins. Species comprising these genera and other planktonic, benthonic and epiphytic taxa preserve a detailed record of lakes that fluctuated in depth, extent and chemistry. The data document the presence of freshwater and saline lakes as well as wetlands. Diatom transfer functions from the Koora and Magadi basins indicate that these water bodies fluctuated widely in conductivity between ~200 to >20,000 µs cm−1, with pH changing between about 7.5 and 11.5. The palaeolakes also periodically exceeded diatom tolerance limits and intermittently dried out. Pollen are generally lacking in the Koora basin sediments, but deposits in the Magadi core contain common pollen that document a wide range of habitats, including forests, woodlands and grasslands that could have supported the presence of hominins and their activities in the region. Fungal spore data support pollen inferences and indicate periods when large mammals might have been common. The microfossil record shows that there was a broad trend towards more arid conditions in the southern Kenya Rift after about 510 Ka, interrupted by periodic wetter conditions. A major episode of desiccation developed between about 450 Ka to 400 Ka that partially correlates with a period of mammal extinctions and a change from Acheulean to Middle Stone Age toolkits in the Olorgesailie Basin, suggesting that these changes might have been related to environmental conditions at that time.

Rockshelters are capable of preserving excellent environmental records within their sediments. But the matter of interpreting an environmental record from rockshelter sediments presents a significant hurdle in the form of dating. An “age-depth model” is typically used to estimate the age of environmental information extending through the deposit. An age-depth model calculates the changes in time between direct ages (like a radiocarbon age) and can provide an estimated age for any depth. While radiocarbon dating can provide an age for organic remains, optically stimulated luminescence (OSL) can provide a direct age on quartz sand deposition and is particularly effective when applied to deposits formed by the wind. This study compares radiocarbon and OSL age-depth models from Last Canyon Cave (LCC) in the Pryor Mountains of south-central Montana. While radiocarbon ages are quite frequently used to construct age-depth models, it is possible they fail to provide accurate ages for the environmental material they aim to date. I re-evaluated the stratigraphy at LCC and then collected OSL samples as well as samples for grain-size analysis from three different sedimentary exposures. Radiocarbon ages had already been produced for one of the exposures (Kornfeld et al. 2012). The OSL samples were most reliable when analyzed on a single-grain level. After creating age-depth models and collecting the grain-size data, I applied ages to all of the grain-size samples according to each of the three age-depth models. Ultimately, the single-grain OSL proved to be fundamentally different than the radiocarbon age-depth model, thereby challenging the current paleoenvironmental reconstruction of the site (Minckley et al. 2015). I conclude that the radiocarbon and single-grain OSL age-depth models were not sufficiently similar, and therefore both dating methods should always be used together when investigating deposits in rockshelters in order to understand how they relate to one another and to the site formation. The use of granulometry also proved to be an important part of reconstruction site formation history. Ultimately, both single-grain OSL and granulometry were determined to be essential parts of studying environmental records in sedimentary deposits in rockshelters.

Philosophiae Doctor - PhD / Background: Oropharyngeal candidiasis, caused by the fungus Candida, is the most common opportunistic infection affecting the quality of life of immunocompromised patients. Fluconazole is widely used as the first line of treatment for fungal infections. However, the inappropriate and misguided use of the drug has led to the evolvement of fluconazole-resistant Candida organisms. This arising resistance resulted in the urgent need for the development of new antimicrobial drugs. The aim of the present study was to investigate the antifungal action of K21, a novel antimicrobial quarternary ammonium compound, on fluconazole-resistant Candida species.

Mastodons (family Mammutidae) are widespread and abundant in of Pleistocene faunas across North America, exhibiting considerable variation in morphology over their broad geographic and temporal range. Mandibular tusks are a notably variable feature among mastodons; these tusks vary in size and shape, and many mastodons lack them entirely, or possess only one. Patterns in mandibular tusk distribution could potentially indicate important selective controls on different populations. Various hypotheses have been proposed to explain the distribution of mastodon mandibular tusks, attributing their presence to geographic, temporal, and sexual variation, but there have been no analyses investigating whether there is statistical support for patterns of mandibular tusk distribution. We analyze a dataset of more than 100 mastodons from throughout North America. Mandibles were coded for the presence/absence of mandibular tusks. These data were used to test whether tusk presence was related to geographic or chronological patterns. The most statistically-significant differences were recorded between interglacial- and late glacial-interval mastodons. Interglacial mastodons had mean differences of 0.958 and 0.827 from last glacial maximum and post-last glacial maximum mastodons, respectively, with essentially 0 p-values for both. Though this study is preliminary and uses simple statistical tests, it shows that patterns do exist in the presence of mandibular tusks among mastodons, and that this variability warrants further investigation, particularly with regards to differences in paleoenvironment and paleoecology between interglacial and glacial mastodons that may be responsible for their apparent differences in mandibular tusk presence.