No description available.

Thesis (MSc (Microbiology))--University of Stellenbosch, 2005. / Plasmid pTC-F14 is a 14.2kb promiscuous, broad-host range IncQ-like mobilizable plasmid isolated from Acidithiobacillus caldus f. At. caldus is a member of a consortium of bacteria (along with Acidithiobacillus ferrooxidans and Leptospirilum ferrooxidans) that is used industrially for decomposing metal sulphide ores and concentrates at temperatures of 40ºC or below which is now a well-established industrial process to recover metals from certain copper, uranium and gold-bearing minerals or mineral concentrates. These biomining microbes are usually obligately acidophilic, autotrophic, usually aerobic iron- or sulphur-oxidizing chemolithotrophic bacteria. Their remarkable physiology allows them to inhabit an ecological niche that is largely inorganic and differs from those environments populated by the more commonly studied non-acidophilic heterotrophic bacteria. At. caldus, is a moderately thermophilic (45 to 50ºC), highly acidophilic (pH1.5 to 2.5) sulphur-oxidizing bacterium, and its role as one of the major players in the industrial decomposition of metal sulphide ores has become evident in recent years. At. caldus f from which pTC-F14 was isolated was found to be one of two dominant organisms in a bacterial consortium undergoing pilot-scale testing for the commercial extraction of nickel from ores.

Thesis (MSc (Microbiology))--University of Stellenbosch, 2009. / Biomining organisms are generally found in metal-rich, inorganic environments such as iron and sulfur containing ores; where they play a vital role in mineralization and decomposition of minerals. They are typically obligatory acidophilic, mesophilic or thermophilic, autotrophic, usually aerobic, iron-or sulfur oxidizing chemolithotrophic bacteria. The most prominent biomining organisms used in bioleaching of metal sulfides are Acidithiobacillus ferrooxidans, At. thiooxidans, At. caldus, Sulfobacillus spp. and Leptospirillum spp. Biomining enables us to utilize low grade ores that would not have been utilized by conventional methods of mining. Research has focused on the backbone features of plasmids isolated from bacteria of biomining environments. The aim of this study is to sequence and analyze an 18 kb region of the 66 kb plasmid pTcM1 isolated from At. caldus MNG, focusing on accessory genes carried by this plasmid. Fifteen putative genes / open reading frames were identified with functions relating to metabolism and transport systems. The genes are located in two divergently located operons. The first operon carries features related to general metabolism activities and consists of a transcriptional regulator (ORF 2), a succinate / fumarate dehydrogenase-like subunit (ORF 3), two ferredoxin genes (ORF 4 and ORF 7), a putative HEAT-like repeat (ORF 6) which is interrupted by an insertion sequence (ORF 5) and a GOGAT-like subunit (ORF 8). The second operon contains an ABC-type nitrate / sulfonate bicarbonate-like gene (ORF 9), a binding protein-dependent inner membrane component-like gene, another ABC sulfonate / nitrate-like gene (ORF 12i and 12ii) which is interrupted by an insertion sequence (ORF 13) and two hypothetical proteins with unknown functions (ORF 14 and ORF 15). Southern hybridization analysis have shown that most of the genes from the two operons are found in other At caldus strains #6, “f”, C-SH12 and BC13 from different geographical locations. Expression of the GOGAT-like subunit and the succinate / fumarate-like subunit was demonstrated in At. caldus MNG showing that these genes are functional and actively transcribed. The transcriptional regulator (ORF 2) has been shown to repress the downstream genes of putative operon 1. The persistence of these genes on plasmids together with the fact that they are being expressed, represents a potential metabolic burden, which begs the question why they have been maintained on the plasmid from geographically separated strains (and perhaps also growing under very different nutrient availability conditions) and therefore what possible role they may play.

Effects of dietary supplementation with low levels of organic sources of trace minerals in place of normal levels of their inorganic salts and phytase on growth performance and mineral metabolism were evaluated in two studies using pullets of white and brown shell laying strains. The organic sources were proteinates of copper, iron, manganese and zinc and selenium yeast. A corn-soybean meal diet was fed alone, plus inorganic minerals or plus organic minerals, and with or without phytase in a 3 x 2 factorial arrangement. Twelve groups of 16 pullets, 2 weeks old, were used per treatment. Compared with inorganic minerals, feeding no mineral supplement or organic minerals significantly (P<0.05) decreased manure Cu, Fe and Zn for white pullets and Cu, Fe, Mn and Zn for brown pullets. Dietary phytase significantly reduced manure Fe, P and Ca for white pullets and Fe, Mn, Zn, P and Ca for brown pullets. Adding phytase to diets containing inorganic minerals reduced manure Zn concentration for white pullets and manure Fe, Mn, Zn, P and Ca concentrations for brown pullets. These studies indicate manure levels of trace minerals can be decreased by using low levels of organic mineral supplements and phytase in pullet diets.

No description available.

Thesis (MSc)--Stellenbosch University, 2004 / ENGLISH ABSTRACT: The main aim of this study is to establish a standard procedure for all sedimentary particle size analysis methods specifically for clay minerals and mixtures thereof. Not only will it improve accuracy and reproducibility during clay size analysis, it will also secure comparability between different operators. As a start, all the apparatus-related parameters that can affect the accuracy and reproducibility were determined for the apparatus used, viz. the Sedigraph SOOOD. Thereafter, these parameters were kept constant, and the effects of potential material-related parameters were investigated one-by-one. First to be investigated were those parameters relating specifically to sample preparation. They were: grinding intensity, chemical dissolution of cementing materials, duration of prior soaking, salt content, centrifugal washing with polar organic liquids, deflocculant type and concentration, the effect of pH, ultrasonic time, and stirring during ultrasonic treatment. Then, the influence on accuracy and reproducibility of the physical and chemical parameters related to the suspension was determined. They were: the use of the viscosity and density of water to calibrate the apparatus in stead of those of the suspension liquid, hydrolysis of the deflocculant with suspension-ageing, and the effect of solid concentration on hindered settling. During this investigation a novel method was developed to enable faster and more accurate pycnometric density determinations. Next, the unique characteristics of clays, which can influence the results of sedimentary particle size analyses, were examined. Serious problems are encountered with the accuracy of the analyses of some clay types abundantly found in nature, viz. the smectites and mixed-layered clay minerals. Due to their swelling in water, and variations in the amounts of their crystal layers, they experience unpredictable changes in particle size. The latter is caused by the following external factors: clay type, humidity, type of exchange cation, electrolyte concentration, clay concentration, pH, deflocculant type and concentration, pressure history of the swell-clay suspension, and ageing of the suspension. The effect of each of them on the accuracy and reproducibility of the sedimentary particle size analysis of clays are investigated in detail. Another problem that influences the accuracy of the sedimentary methods is that owing to swelling, the densities of smectites and mixed-layered clays change by varying degrees when suspended in water. It is, however, impossible to pycnometrically determine the density of a swell-clay since it absorbs a part of the water used for its volume determination. To solve this problem, a novel method was devised to calculate swell-clay density. This method makes use of existing Monte Carlo simulations of the swelling mechanism of montmorillonite. During all sedimentary methods, an average clay density is normally used to calculate the particle size distribution of clay mixtures. However, if there is a large enough difference between the calculated average density and that of a component, then inaccurate results will be recorded. The magnitude of this effect was investigated for a few self-made clay mixtures, which consisted of different proportions of kaolinite, illite, and montmorillonite. Based on all the above results, a practical approach to, and a standard methodology for all the sedimentary methods of particle size analysis of clay minerals are presented. Additionally, a condensed summary is provided in table-form, which contains the magnitudes of the errors associated with each of the parameters that were examined. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie is om 'n standaard prosedure daar te stel vir alle sedimentêre metodes van partikelgrootte analise, spesifiek vir gebruik met kleiminerale en mengsels daarvan. So 'n standaard prosedure sal die akkuraatheid en herhaalbaarheid van klei-analises verbeter, en die vergelykbaarheid tussen verskillende operateurs verseker. Aanvanklik is slegs die parameters bepaal wat die akkuraatheid en herhaalbaarheid van die gekose apparaat (Sedigraph 5000D) kan beïnvloed. Daarna is al hierdie parameters konstant gehou, en is die potensiële effekte van die moontlike materiaal-verwante parameters een na die ander ondersoek. Eerstens is die invloed van monstervoorbereiding op akkuraatheid en herhaalbaarheid bepaal. Verskillende parameters nl. maal-intensiteit, chemiese oplossing van sementerende materiale, sentrifugale wassing met polêre organiese vloeistowwe, tipe ontvlokker en konsentrasie, die effek van pH, ultrasoniese tyd en die effek van roer tydens ultrasonikasie is ondersoek. Vervolgens is die invloed op die akkuraatheid en herhaalbaarheid van die fisiese en chemiese parameters verwant aan die suspensie bepaal. Hierdie parameters was nl. die gebruik van die viskositeit en digtheid van water in plaas van dié van die suspensievloeistof, hidrolise van die ontvlokker tydens suspensieveroudering, asook die effek van vastestof-konsentrasie op belemmerde uitsakking. Gedurende hierdie ondersoek is ook 'n nuwe metode ontwikkel wat vinniger, en meer akkurate piknometriese digtheidsbepalings moontlik maak. Die unieke eienskappe van kleie wat die resultate van sedimentêre metodes van partikelgrootte analises kan beïnvloed, is volgende ondersoek. Tydens die analises van party kleie wat baie volop in die natuur voorkom, nl. die smektiete en menglaag-kleie, word ernstige akkuraatheids-probleme ondervind. Hul swelling in water, tesame met variasies in hul aantal kristal-lagies, veroorsaak onvoorspelbare verandering van hul partikelgroottes. Laasgenoemde word deur die volgende eksterne faktore veroorsaak: klei tipe, humiditeit, tipe uitruil-katioon, elektrolietkonsentrasie, kleikonsentrasie, pH, ontvlokker-tipe en konsentrasie, drukgeskiedenis van 'n swelklei-suspensie, en veroudering van die suspensie. Die effek van elk op die akkuraatheid en herhaalbaarheid van die sedimentêre partikelgrootte analises van kleie word in detail bespreek. 'n Verdere probleem wat die akkuraatheid van sedimentêre metodes beïnvloed, is dat wanneer smektiete en menglaag-kleie in water gesuspendeer word, hulle digthede in verskillende mates weens swelling verander. Dit is egter onmoontlik om die digtheid van swelkleie in water piknometries te bepaal, omdat swelklei 'n gedeelte van die water absorbeer wat gebruik moet word om die kleivolume mee te bepaal. Om hierdie probleem op te los, is 'n nuwe metode ontwikkelom die digtheid van swelkleie mee te bereken. Die metode maak gebruik van reedsbestaande Monte Carlo simulasies van die swelling van montmorillonite. Tydens alle sedimentêre metodes word normaalweg van 'n gemiddelde kleidigtheid gebruik gemaak om die partikelgrootte-verspreiding van kleimengsels mee te bereken. Indien die berekende gemiddelde digtheid egter genoegsaam met dié van 'n kleikomponent verskil, sal onakkurate resultate verkry word. Hierdie effek is ondersoek vir 'n paar selfgemaakte kleimengsels wat uit verskillende hoeveelhede kaoliniet, illiet, en montmorilloniet bestaan het. Laastens word 'n praktiese benadering en 'n standaard metode vir alle sedimentêre metodes voorgestel, wat gebaseer is op al die bogenoemde resultate. 'n Verkorte opsomming, met die groottes van die foute geassosieer met elke parameter wat ondersoek is, word laastens in tabelvorm verskaf.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Five areas proximal to the world class Namakwa Sands heavy mineral deposit have been studied and include the farms Houtkraal Remainder Portion 2, Houtkraal Remainder, Geelwal Karoo, Graauwduinen and Rietfontein. These are locally referred to as the satellite deposits and are sub-economic occurrences. The primary objective of the study was to quantify the mineralogy and mineral chemistry, determine the provenance of the heavy mineral suite and draw a comparison between the satellite deposits and the Namakwa Sands deposit from an exploratory point of view. Methodology used to achieve the above objectives included optical microscopy, Scanning Electron Microscope (SEM), Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS), Quantitative Evaluation of Minerals by Scanning Electron Microscopy (QEMSCAN), X- Ray Fluorescence (XRF) and Zr-geothermometry of rutile. The five satellite areas contain the same heavy mineral suite but mineral proportions differ. The total heavy mineral population (THM) are diverse and consist of ilmenite and its alteration products (hydrated ilmenite, pseudorutile and leucoxene), magnetite, hematite, spinel, rutile, tourmaline, pyroxene, amphibole, garnet, aluminosilicates, staurolite, corundum, epidote, zircon, monazite and sphene. Ilmenite and garnet are the two most dominant heavy minerals present. The valuable heavy minerals (VHM) suite consists of ilmenite, zircon, rutile and leucoxene. The mineralogy of the satellite areas and chemistry of the ore minerals (rutile, zircon, ilmenite and leucoxene) are similar to the Namakwa Sands deposit. The whole spectrum of ilmenite alteration products (hydrated ilmenite, pseudorutile, and leucoxene) is present and allowed the quantitative use of the alteration index. The indices is low (22-24%) and indicates that the surficial deposits have formed under arid to semi-arid climatological conditions which preserved the pristine character of most of the minerals. This allowed reliable provenance studies using the characteristics of most of the heavy mineral suite, which showed that the minerals were derived from a diversity of source rocks. These included mainly medium to high-grade metamorphites and felsic intrusives of the underlying Mesoproterozoic Namaqualand Metamorphic Complex and a minor contribution from the Neoproterozoic Gariep Supergroup. This relationship indicates a limited transport distance from source to depositional basin. Mineral ratios in particular the THM-VHM relationship showed that the deposits located close to the shoreline such as Geelwal Karoo, Graauwduinen and Rietfontein have a relatively low proportion of valuable heavy minerals whereas those more inland such as Houtkraal Remainder Portion 2 and Houtkraal Remainder are close to unity. Heavy mineral concentration as such is low in the satellite areas and the mechanism to increase the concentration is clearly not only a function of distance from the present shoreline but is also topographically controlled. Steep sided linear depressions channelled the unconsolidated sediments and heavy minerals were upgraded into economic concentrations by aeolian processes. The quality of the valuable heavy minerals in the satellite areas however is similar to those of the adjacent Namakwa Sands deposit. This study has demonstrated that Houtkraal Remainder is the northeasterly continuation of the red aeolian sand (RAS) associated East Mine orebody and offers the best exploration potential. / AFRIKAANSE OPSOMMING: Vyf areas proksimaal aan die Namakwa Sands swaar mineral afsetting is bestudeer en sluit in Houtkraal Remainder, Houtkraal Remainder Portion 2, Geelwal Karoo, Graauwduinen en Rietfontein. Hierdie areas word plaaslik na verwys as satelliet afsettings en is subekonomies. Die hoofdoel van hierdie studie was om die mineralogie en mineral chemie te kwantifiseer, die oorsprong van die swaar mineraal suite te bepaal asook n vergelyking te tref tussen die satelliet areas en die Namakwa Sands afsetting vanuit n verkennende eksplorasie oogpunt. Optiese mikroskopie, SEM, LA-ICP-MS, QEMSCAN, XRF en die Zr-geotermometer van rutiel is gebruik om bostaande doele te bereik. Die vyf satellite areas bestaan uit dieselfde swaar minerale maar mineral proporsies verskil. Die totale swaar mineraal populasie is divers en bestaan uit ilmeniet en ilmeniet se veranderingsprodukte (gehidreerde ilmeniet, pseudorutiel en leukokseen), magnetiet, hematiet, spinel, rutiel, toermalyn, pirokseen, amfibool, granaat, aluminiumsilikate, stauroliet, korund, epidoot, sirkoon, monasiet and sfeen. Ilmenite en granaat is die twee mees dominante swaar minerale teenwoordig. Die waardevolle swaar mineraal populasie bestaan uit ilmeniet, rutiel, sirkoon en leukokseen. Die mineralogie van die satelliet areas en die chemie van die erts minerale (rutiel, sirkoon, ilmeniet en leukokseen) is dieselfde as die van die Namakwa Sands afsetting. Die hele spektrum ilmeniet veranderingsprodukte is teenwoordig en het die kwantitatiewe gebruik van die alterasie indeks toegelaat. Die alterasie indekse is laag (22-24%) en dui aan dat die oppervak afsettings gevorm het tydens droë tot semi droë toestande wat die eertydse karakter van meeste minerale bewaar het. Deurdat die karakter van meeste minerale behoue gebly het, kon provenans studies toegepas word op die swaar mineraal suite. Provenans studies het aangedui dat die swaar minerale afkomstig is van n verskeidenheid van bron gesteentes. Dit sluit in medium tot hoë graad metamorfe gesteentes en felsiese intrusies van die Mesoproterosoïese Namakwaland Metamorfiese Kompleks met n geringe bydrae van die Neo Proterosoïese Gariep Supergroep. Hierdie verhouding dui n beperkte vervoer afstand aan vanaf die bron tot by die afsettings omgewing. Mineraal vehoudings spesifiek die totale swaar mineraal-waardevolle swaar mineraal verhoudings dui aan dat afsettings na aan die kus soos Geelwal Karoo, Graauwduinen en Rietfontien n lae inhoud van waardevolle swaar minerale het teenoor afsettings soos Houtkraal Remainder Portion 2 en Houtkraal Remainder wat meer land in is met verhoudings na aan eenheid. Swaar mineral konsentrasie is laag in die satellite areas en die meganisme verantwoordelik vir die toename in konsentrasie is nie net n funksie van die afstand van die bestaande kuslyn nie maar word ook deur topografie beheer. Steil sydige lineêre depressies kanaliseer die ongekonsolideerde sediment en swaar minerale en word opgradeer tot ekonomiese konsentrasies deur wind prossese. Die kwaliteit van die waardevolle swaar minerale in die satelliet areas is egter dieselfde as die van die aangrensende Namakwa Sands afsetting. Hierdie studie het gewys dat Houtkraal Remainder is die noordelike voortsetting van die Rooi Aeoliese Sand geassosieerde Oos Myn ertsliggam en bied die beste eksplorasie potensiaal.

Raman spectroscopy has been used to characterise both organic and geological samples in order to build a database for the future characterization of biomarker molecules that are of astrobiological relevance. Characteristic geological features and hydrated minerals recently found on the surface of Mars by the NASA planetary rovers Spirit and Opportunity suggest that a possible biosphere could have once existed there. Analytical instrumentation protocols for the unequivocal detection of biomarkers in suitable geological matrices are critical for future unmanned explorations, including the forthcoming ESA ExoMars mission scheduled for 2018. Several geological features found on the surface of Mars by planetary rovers suggest that a possible extinct biosphere could exist based on similar sources of energy as occurred on Earth. For this reason, analytical instrumental protocols for the detection of isolated biomarkers preserved in suitable geological matrices unequivocally and non-destructively have to be evaluated for future unmanned missions. Raman spectroscopy is currently part of the Pasteur instrumentation suite of the ExoMars mission for the remote detection of extant or extinct life signatures in the Martian surface and subsurface. Terrestrial analogues of Martian sites have been identified and the biogeological modifications resulting from extremophilic survival activity have been studied. Here we present the Raman spectral characterization of several examples of organic compounds which have been recorded using 785 nm, 633 nm and 514 nm laser excitation -polycyclic aromatic hydrocarbons (PAHs), organic acids, chlorophyll and carotenoids. Experimental mixtures of ß-carotene in usnic acid, PAHs in usnic acid and PAHs in mineral matrices have also been investigated. Organic compounds and PAHs located under crystalline minerals samples were identified using a 5x objective lens and 785 nm III excitation. The pure compounds and compound mixtures were also analysed using X-ray powder diffraction and scanning electron microscopy (SEM). The results of this study indicate that near infrared laser at 785 nm provided the clearest and the most informative spectra due to the reduction of fluorescence emission. Higher energy lasers operating in the visible region have resulted in the emission of significant background fluorescence. Few samples fluoresce even with the use of 785 nm excitation and FT-Raman spectroscopy remains the instrument of choice for the analysis of these samples.

The effect of magnesium, strontium, and other alkaline earths on the formation and persistence of metastable carbonates in the natural environment was investigated to determine the nature of the controlling mechanism. Barium and beryllium were studied to evaluate the effect of ionic radius; magnesium and strontium, in order to determine if the results correlate with the usual order of stability for complexes and adsorbed species. Known weights of aragonite were placed in contact with solutions of beryllium, magnesium, calcium, strontium, and barium. Samples were covered and periodically both pH and percent composition of aragonite determined; supernatant liquids and precipitates were analyzed for cation concentrations by atomic absorption spectroscopy and titrimetric methods. Results indicated that the order of effectiveness of alkaline earth metals in inhibiting recrystallization is : Be > Mg > Sr > Ba. This is the expected order of effectiveness for both surface and solution effects. A solution effect (i.e., sequestration of bicarbonate ions) is strongly suggested by the chemical behavior of each cation.

This diploma thesis deals with legal regulation of lands affected by mining activities. These activities, predominantly the extraction of minerals are by their nature very closely related to soil and land. The thesis offers a comprehensive view of the legal relations in the process of mining - from prospecting and exploration of mineral deposits to mine closure - while it discusses the key issues from the perspective of the land owner as well as the mining companies. Legal relations arising from mining activities are significantly influenced by the character of mining. Mining interferes with rights and interests related to land and ownership of land which gives rise to certain conflicts. Mining companies' interests come very often into conflict with interests of the owner of the land where the mineral deposit is located. The legal relations are further complicated by the position of the state who acts as an owner of mineral wealth and an authority defending public interests. The introductory chapter of the thesis defines the terms that are essential for the selected topic. The content of the next chapters corresponds with phases of mining activities as they are carried out in reality. Prospecting and exploration of exclusive deposits represents the first phase of mining activity. In the chapter...