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Chong, King Wai Isaac. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 99-104). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / 論文摘要 --- p.iv / Table of Contents --- p.vi / Lists of Figures --- p.ix / List of Tables --- p.xi / List of Abbreviations --- p.xii / Chapter Chapter One: --- Introduction --- p.1 / Chapter 1.1 --- Overview of Glyceraldehyde 3-phosphate Dehydrogenases --- p.1 / Chapter 1.2 --- Properties And Molecular Structures of GAPDH --- p.3 / Chapter 1.3 --- Action Mechanism of GAPDH --- p.6 / Chapter 1.4 --- Novel Functions of GAPDH Unrelated to Carbohydrate Metabolism --- p.8 / Chapter 1.5 --- Effects of Heavy Metal on Enzyme Activity And Gene Expression of GAPDH --- p.10 / Chapter 1.6 --- Metal Binding Properties And Metal Binding Sites of GAPDH --- p.12 / Chapter 1.7 --- Isolation And Purification of GAPDH from Different Organisms --- p.13 / Chapter 1.8 --- Development of New Purification Method of GAPDH Using Immobilized Metal Affinity Chromatography --- p.15 / Chapter 1.9 --- Study of GAPDH from Chironomidae Larvae --- p.16 / Chapter 1.10 --- Aims of Study --- p.18 / Chapter Chapter Two: --- Methods And Materials --- p.19 / Chapter 2.1 --- Isolation of Native Chironomidae GAPDH --- p.19 / Chapter 2.1.1 --- Chemicals And Reagents --- p.19 / Chapter 2.1.2 --- Reagents --- p.19 / Chapter 2.1.3 --- Preparation of Crude Protein Extract from Chironomidae Larvae --- p.24 / Chapter 2.1.4 --- Immobilized Metal Affinity Chromatography --- p.24 / Chapter 2.1.5 --- Large Scale Preparation of Crude Protein Extract --- p.25 / Chapter 2.1.6 --- Ammonium Sulfate Fractionation --- p.25 / Chapter 2.1.7 --- Copper Affinity Column Chromatography --- p.26 / Chapter 2.1.8 --- Dye Affinity Column Chromatography --- p.26 / Chapter 2.2 --- Identification of Chironomidae GAPDH --- p.27 / Chapter 2.2.1 --- Chemicals And Reagents --- p.27 / Chapter 2.2.2 --- Reagents --- p.28 / Chapter 2.2.3 --- Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis --- p.32 / Chapter 2.2.4 --- Non-Denaturing Polyacrylamide Gel Electrophoresis --- p.33 / Chapter 2.2.5 --- Protein Extraction from Coosmassie Blue Stained Polyacrylamide Gel --- p.33 / Chapter 2.2.6 --- N-terminal Amino Acid Analysis --- p.33 / Chapter 2.2.7 --- Sequence Analysis --- p.34 / Chapter 2.3 --- Kinetic Analysis of Chironomidae GAPDH --- p.34 / Chapter 2.3.1 --- Chemcials And Reagents --- p.34 / Chapter 2.3.2 --- Reagents --- p.34 / Chapter 2.3.3 --- Determination of Enzyme Concentration And GAPDH Activity --- p.35 / Chapter 2.4 --- Molecular Cloning of Chironomidae GAPDH --- p.36 / Chapter 2.4.1 --- Chemicals And Reagents --- p.36 / Chapter 2.4.2 --- Reagents --- p.37 / Chapter 2.4.3 --- RNA Extraction from Chironomidae Larvae --- p.41 / Chapter 2.4.4 --- DNase I Removal of Genomic DNA Contamination --- p.42 / Chapter 2.4.5 --- RNA Concentration Determination And RNA Agarose Electrophoresis --- p.42 / Chapter 2.4.6 --- First Strand cDNA Synthesis --- p.43 / Chapter 2.4.7 --- pRSet A B C Vectors --- p.43 / Chapter 2.4.8 --- Cloning Primer Design --- p.45 / Chapter 2.4.9 --- Polymerase Chain Reaction --- p.45 / Chapter 2.4.10 --- DNA Agarose Electrophoresis --- p.46 / Chapter 2.4.11 --- Restriction Enzyme Digestion of Insert And Plasmid --- p.46 / Chapter 2.4.12 --- Ligation of Plasmid And Insert DNA --- p.46 / Chapter 2.4.13 --- Preparation of Chemically Competent E. coli --- p.47 / Chapter 2.4.14 --- Transformation of Plasmid by Heat Shock --- p.47 / Chapter 2.4.15 --- Colony PCR --- p.48 / Chapter 2.5 --- Recombinant Protein Expression And Purification --- p.48 / Chapter 2.5.1 --- Chemicals And Reagents --- p.48 / Chapter 2.5.2 --- Reagents --- p.49 / Chapter 2.5.3 --- Protein expression by IPTG --- p.51 / Chapter 2.5.4 --- Protein purification by Nickel Affinity Column Chromatography --- p.52 / Chapter 2.5.5 --- EnterokinaseMax ´ёØ Removal of Polyhistidine Fusion Tag --- p.52 / Chapter 2.5.6 --- Western Blotting of Protein --- p.53 / Chapter Chapter Three: --- Results --- p.54 / Chapter 3.1 --- Two Affinity Chromatography Methods for GAPDH Purification --- p.54 / Chapter 3.2 --- Isolation And Purification of Native Chironomidae GAPDH --- p.54 / Chapter 3.3 --- Identification of Chironomidae GAPDH --- p.62 / Chapter 3.3.1 --- N-terminal amino acid analysis --- p.62 / Chapter 3.3.2 --- Sequence Analysis --- p.62 / Chapter 3.4 --- Molecular Cloning of Chironomidae GAPDH --- p.63 / Chapter 3.5 --- Isolation And Purification of recombinant Chironomidae GAPDH --- p.70 / Chapter 3.6 --- Protein Gel Electrophoresis Analysis of GAPDHs --- p.74 / Chapter 3.7 --- "Effects of Heavy Metals, pH And Temperature on GAPDHs" --- p.76 / Chapter 3.7.1 --- Heavy Metal Effect --- p.76 / Chapter 3.7.2 --- pH Effect --- p.76 / Chapter 3.7.3 --- Temperature --- p.77 / Chapter 3.8 --- Kinetic Analysis of GAPDHs --- p.84 / Chapter Chapter Four: --- Discussion --- p.89 / Chapter 4.1 --- New Method for The Isolation and Purification of Chironomidae GAPDH --- p.89 / Chapter 4.2 --- "Effects of Heavy Metals, pH And Temperature on GAPDHs" --- p.91 / Chapter 4.3 --- Kinetic Analysis of GAPDHs --- p.91 / Chapter 4.4 --- Zinc Activation of Chironomidae GAPDH --- p.92 / Chapter 4.5 --- Future Study --- p.93 / Chapter 4.5.1 --- Sequence Analysis Using Prediction Programmes --- p.94 / Chapter 4.5.2 --- Protein Crystallization --- p.95 / Chapter 4.5.3 --- Site-Directed Mutagenesis --- p.95 / Chapter 4.5.4 --- Biacore Surface Plasmon Resonance --- p.95 / Chapter Chapter Five: --- Conclusion --- p.98 / Chapter Chapter Six: --- References --- p.99

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Bibliography: leaves 202-223.

Risk assessment of trace-metal contamination in soils requires predictive models that can accurately describe the complex uptake processes at the soil-plant interface, which are usually characterized by the coexistence of and interaction between multiple components. Competing cations such as Ca and H can affect metal availability to plants and subsequent rhizotoxicity. The biotic ligand model (BLM) has been proposed as a promising approach to model these interactive processes. Under the BLM assumption, we designed experiments to investigate how the solution chemistry is correlated with metal uptake and rhizotoxicity. Our first goal is to acquire a set of BLM parameters that can accurately represent the experimental data over varied solution conditions and parameters that are easy to integrate with general speciation models. The second objective is to get insight into the physical nature of the interactions. Our titration experiments revealed three types of biotic ligands in the pea roots with defined site densities and stability constants with H. Our ion sorption experiments estimated the surface-adsorption stability constants of Ca, Mg, Cd, Cu, Ni, and Zn with excised fresh pea roots. Our 48-h root growth tests have established the formation constants (KMe's) of living pea roots with Ca, Cd, Cu, Ni, and Zn. In these studies, we hypothesized and confirmed that the concentration of the metal-root complexes correlated with observed rhizotoxicity and that Ca, H, and trace metals competed for root absorption where lower solution pH decreased both Ca and metal uptake. Root elongation was found to be highly sensitive to root Ca content rather than merely to the direct toxic effects of the trace metals. It is shown that the physiological complexity arising from a living root affected our modeling so that adjustable KMe values, as a function of solution and root chemistry, are required for good model fits. The established model parameters were tested in hydroponic mixture solutions for their ability to predict the uptake of multiple metals simultaneously. The joint effects of Cd, Cu, and Ni in mixtures on root growth were studied and the potential interactions between these ions were also investigated.

As pollution becomes an ever-increasing threat to the global environment pressure is being placed upon industry to "clean-up" its act, both in terms of reducing the possibility of new pollution and cleaning up already contaminated areas. It was with this in mind that Amplats embarked on a phytoremediation project to decontaminate nickel-polluted soils at one of their mine sites in Rustenburg, using the nickel hyperaccumulating plant, Berkheya coddii, which is endemic to the serpentine areas near Barberton, Mpumalanga. Besides the applied aspects pertaining to the development of the phytoremediation process we were also interested in more academic aspects concerning the transport and storage of nickel within the plant tissues. In order that the progress of nickel could be followed through the plant, a radio-tracer of ⁶³nickel was placed in the soil and its movement within the plant followed by analysing the plant material, at set intervals, using a liquid scintillation counter. From these studies it was found that the nickel appeared to be transported from the roots to the leaves of the plant via the xylem. It appeared that the nickel was not confined to the leaf to which it was initially transported and so movement of nickel within the phloem also appears to occur in B. coddii. As nickel is generally toxic to most plants, hyperaccumulators contain elements that nullify the toxic effect of nickel. In the case of Berkheya coddii it is thought that the accumulated nickel is bound to malate to form a harmless nickel complex. With this in mind an assay for L-malic acid was developed in order that any effect on L-malic acid, caused by growing Berkheya coddii on soils containing various concentrations of nickel, could be determined. This method also enabled comparisons of L-malic acid concentrations to be made between hyperaccumulators and non-hyperaccumulators of various plant species. From the L-malic acid comparisons it was found that the nickel concentration within soils affected the levels of L-malic acid within B. coddii and that the levels of L-malic acid within B. coddii were greater than that of a closely related non-hyperaccumulator, suggesting that L-malic acid is indeed involved in the hyperaccumulation mechanism within B. coddii. B. coddii was chosen as the tool in nickel phytoremediation at Rustenburg Base Metal Refineries as it was found to accumulate up to 2.5% nickel in the dry biomass, it grows rapidly and has a large above-ground biomass with a well developed root system, and it is perennial and so does not need to be planted each season. Earlier work had shown that the nickel levels in the roots were comparatively low (up to 0.3% nickel in the dry material) and thus, for ease of harvesting and to ensure the continued vegetative growth of the plant on the planted sites, it was decided that the leaves and stems of the plants would be harvested at the end of each growing season. The plant was also found to accumulate low levels (0.006 - 0.3 %) of precious metals, including platinum, palladium and rhodium, within its above ground biomass, making it attractive for the remediation of certain soils that contain low levels of these metals. Before B. coddii could be introduced to the Rustenburg area a comparison of the climatic and soil conditions of Barberton, the area to which B. coddii is endemic, and Rustenburg needed to be made to ensure that the plant would be able to survive the new conditions. These comparisons showed that Rustenburg receives on average, 484 mm less rain per year than Barberton, indicating that irrigation was required when the Rustenburg sites were planted out with B. coddii, in order to reduce water stress. Rustenburg was also found to be, on average, 4.6°C warmer than Barberton, but as B. coddii growth responds to wet/dry seasons, as opposed to hot/cold seasons, it was not felt that this temperature difference would have a negative effect on the growth of the plants. The soil comparisons showed the contaminated Rustenburg sites to be serpentine-like in nature, with respect to Barberton, again giving confidence that the plant would adapt to the conditions occurring at the contaminated sites. However, to ensure optimal growth, nutrient experiments were also performed on B. coddii to ascertain the ideal macronutrient concentrations required, without inhibiting nickel uptake. These trials indicated that the individual addition of 250 mg/l ammonium nitrate, 600 mg/l calcium phosphate, 2 000 mg/l calcium chloride, 600 mg/l potassium chloride and 250 mg/l magnesium sulphate enhanced plant growth and nickel uptake, suggesting that, for phytoremediation purposes, these nutrients should be added to the medium in which the plants are growing. The growth-cycle of naturally occurring B. coddii plants in Barberton was also studied in order that seedlings could be germinated, in greenhouses, at the correct time of year so that the plants could be sown as the naturally occurring plants were germinating. From this information the seeds of the plants could be collected at the correct time of year and the above ground biomass harvested when the nickel concentrations were at their highest. It was found that the plants began to germinate as the first rains fell, which was generally at the beginning of September, and plant maturity was reached at about five months, after which flowers were produced. Seeds were produced from the flowers and these matured and were wind-dispersed one month to six weeks after full bloom, usually during February. The plants then started to die back and dry out and dormancy was reached about nine months after germination, generally in about mid- to late- May. It was found that the nickel concentration was at its highest about one month after the plants had begun to dry out and thus it was decided that the above ground biomass would usually be harvested at the end of April each season, in order to achieve maximum nickel recovery. Finally, in order that the plant's potential for use in phytoremediation could be fully assessed, field trials at the contaminated sites in Rustenburg were performed. Germination procedures were developed for the mass production of B. coddii and it was found that, although fully formed plants could be propagated in tissue culture, it was cheaper and faster to germinate the seeds in speedling trays, containing a zeolite germination mix, in greenhouses. It was also found that the seeds had a low germination rate, due to dehydration of the embryos and thus, in order to obtain the number of plants required, four to five times the amount of seeds needed to be sown. The two-month-old seedlings were transferred to potting bags, containing a mixture of potting soil and RBMR soil, and grown up in the greenhouse for a further three months. This growth period allowed B. coddii to adapt to the RBMR soil and also ensured that the plants were relatively healthy when transplanted into three prepared sites at RBMR. The plants were allowed to grow for the entire season after which the above ground biomass, comprising the leaves and stems, was harvested, dried and then ashed in an ashing vessel designed by the author, with the help of Mr K Ehlers. The ashed material was acid-leached with aqua regia in order that the base metals (mainly nickel) and precious metals could be removed from the silicates and carbonised material. The acid solution was then neutralised, causing the base metals (mainly nickel) and precious metals to be precipitated. This precipitate was then smelted with a flux in order that nickel buttons could be formed. Thus, from all the phytoremediation trials it was found that this process is highly successful in employing B. coddii for the clean-up of nickel-contaminated sites. This constitutes the first time that such a complete phytoremediation process has ever been successfully developed with B. coddii as the phytoremediation tool. It also appears to be the first time that phytoremediation has been performed "commercially" to produce a saleable metal product. The success of this project has stimulated Amplats to continue with, and expand it, to include more studies on phytoremediation as well as in the biomining of certain areas containing very low levels of precious metals which, with conventional techniques, were previously not worth mining. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1998.

In this thesis, the uptake kinetics of Cd by the liverwort D. hirsuta and the moss A. androgynum were investigated. In preliminary experiments, the toxicity of Cd to the bryophytes was investigated by characterising the effects of Cd on photosynthesis and K loss. Experiments were carried out to explain the existence of variation between different collections observed in uptake kinetics in the liverwort D. hirsuta. Photosynthesis in D. hirsuta was more sensitive to Cd than photosynthesis in A. androgynum. The sensitivity was directly related to intracellular Cd concentrations. D. hirsuta accumulated considerably higher concentration of intracellular Cd than A. androgynum. Cd caused intracellular K loss in D. hirsuta but not in A. androgynum. Extracellular Cd uptake was rapid and independent of metabolism. Intracellular Cd uptake as a function of Cd concentrations followed Michael is-Menten kinetics. Intracellular Cd uptake in D. hirsuta was affected by age of the plant, K pretreatment and the site where plants were collected. The moss A. androgynum displayed Cd uptake acclimation when uptake was measured at low temperatures. The results indicated that uptake kinetics could be affected by seasonal variation. Tolerance of Cd in the moss A. androgynum could be induced by pretreating the plants with low concentrations. The moss possibly excludes Cd from the cytoplasm and thus reduces the concentration of Cd in the cytoplasm to below toxic level. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1997.

Two enzymatic systems from the lactic acid bacterium Oenococcus oeni, isolated from wine, have been studied. The first one is the H+-ATPase for which the activity was characterized under various conditions of growth. The activity gradually increased by l.6 to 1.9-fold upon inoculation at pH 3.5. The H+-ATPase activity did not vary significantly in function of the growth rate or with and without malic acid. However, acidification of the medium in the absence of malic acid induced the activity by 1.5 to 2.2-fold depending on the initial pH. The partially cloned H+-ATPase genes shared high homologies with those from other bacterial F0F1-ATPases. A mRNA of about 7 kb was detected by Northern blot and its size suggests that the genetic organization of O. oeni atp operon is similar to most F0F 1-ATPases. Furthermore, the amount of atp mRNA was shown to increase in acidic conditions. O. oeni H +-ATPase activity was pH-inducible and regulation of the expression seems to occur at the level of mRNA synthesis. Thus, the results confirmed the proposed role of the H+-ATPase in acid tolerance in O. oeni. / The second system studied was a chromosome-encoded P-type ATPase (CopB) and its putative transcriptional regulator (CopR). The copB gene encodes a protein showing great similarities with other Cu2+-ATPases of the CPx-type family of heavy-metal ATPases like Enterococcus hirae copB. Another gene (copR) was found 250 bp upstream of copB and displays great similarities with proteins of the MecI/BlaI family of transcriptional regulators, including En. hirae CopY repressor. O. oeni was shown to be highly resistant to copper and growth occurred in up to 30 mM CuSO4. Northern blot analyses indicated that the amount of copB mRNA increased upon a 0.2 to 4.0 mM copper stress suggesting that expression of the enzyme might be regulated at the level of mRNA synthesis. Whether CopR is involved in this regulation remains to be determined, but the results suggest that copRB genes might be involved in copper resistance in O. oeni.

Bibliography: leaves 153-156. / ix, 156 p. : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis describes the experiments conducted to determine the mechanisms that cause the decline in shoot Zn concentration and the responses of the wheat plant to Zn deficiency and chlorosulfuron stress. Root tip extension is used as a measure of wheat root growth during exposure to the sulfonylurea herbicide chlorsulfuron. Wheat plants differing in Zn efficiency are grown in HEDTA chelate-buffered nutrient solution in controlled conditions. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1997