Submitted in complete fulfilment for Masters Degree in Technology: Biotechnology, Durban University of Technology, 2013. / A comparative thermostability analysis of different partially purified xylanases from Rhodothermus marinus, Bacillus halodurans, Thermomyces lanuginosus and Pulpzyme HC was studied using differential scanning fluorometry (DSF), fluorescence spectroscopy and circular dichroism (CD). The R. marinus xylanase was found to have an optimum temperature and pH of 90oC and 6 respectively while the B. halodurans xylanase was optimally active at 70oC and a broad range of alkaline pH of 8 - 10. The commercially available xylanase from T. lanuginosus showed optimal activity at 50oC and pH 7 while the Novozyme xylanase Pulpzyme HC showed optimal activity at 60oC and pH 7. Fluorescence spectroscopy monitored the microenvironment and fluorescence emission of Trp residues. In their native folded state, Trp are generally located in the core of the protein but during unfolding they become exposed. The fluorescence changes as the enzyme undergoes denaturation due to conformational changes and exposure of Trp residues. Differential scanning fluorometry (DSF) monitors thermal unfolding of proteins in the presence of a fluorescent dye such as Spyro Orange. A wide range of buffers were tested for their ability to increase the xylanase stability. T. lanuginosus had the greatest increase in melting temperature with 0.73M Bis Tris pH 6.5 and peaked highest at 78°C. The B. halodurans xylanase exhibited high pH stability (pH 4-10) and exhibited very little change in melting temperature, from 74°C-77°C over the twenty four different conditions. The R. marinus xylanase had no increase in melting temperature showing a maximum melting temperature of 90oC. Circular dichroism (CD) measures unequal absorption of right- and left-handed circularly polarized light by the molecule. The xylanase from R. marinus exhibited the lowest ΔG of 34.71kJ at 90°C as was expected. The B. halodurans xylanase showed a much higher ΔG of -52.71 at its optimum temperature of 70°C when compared with the xylanases from R. marinus and T. lanuginosus. When comparing the three xylanases activities at 70°C, it can be seen that the B. halodurans xylanase exhibited a lower relative activity then both R. marinus and T. lanuginosus xylanases. All three techniques offered different information on the structure and function relationship. Fluorescence spectroscopy, the change in conformation due to fluorescence emission as a result of increased temperature and salt concentrations. DSF, optimal conditions for increased stability and activity at higher temperatures and CD, conformational changes, the fraction of folded protein and change in Gibbs free energy over a range of temperature. / National Research Foundation

The extensive use of nanoparticles (NPs) has started receiving increased attention because of the knowledge gaps regarding their fate in the environment and the possible impact on the environment and human health. The production of silver nanoparticles (AgNPs) and titanium dioxide nanoparticles (TiO2-NPs) is increasing and it is expected that, due to their great number of applications, their concentration in waste streams will increase in the future. The presence of NPs in waste streams may affect the treatment process (e.g., composting) and, if they are not successfully removed from the waste streams, their presence in the treated waste (e.g., compost) may present an environmental risk. Composting of the biodegradable fractions of municipal solid waste (MSW) is a widely used waste management practice, mainly because it is a cost-effective treatment technology and the final product (i.e., compost) presents several benefits to the environment, particularly as a soil conditioner. The overall aim of this thesis is to assess the effect of Ag-TiO2NPs and AgNPs that may be present in the biodegradable fractions of municipal solid waste on composting and subsequent soil application of compost. For that purpose in-vessel composting of artificial municipal solid waste contaminated with commercial nanoparticles was investigated at laboratory scale, simulating a range of relevant concentration levels. Subsequently, the fate of NPs present in mature compost use as a top-layer soil conditioner was investigated using a column approach at laboratory scale. The toxicity effect of NPs present mature compost on plant growth was further investigated. The impact of NPs during composting was assessed by monitoring the temporal dynamics of organic matter (OM) using Excitation Emission Matrix (EEM) fluorescence spectroscopy. The fate of NPs following application of contaminated mature compost as a top-soil conditioner and potential release to groundwater was investigated using a column leaching experiment while the phytotoxicity of mature compost contaminated with NPs was assessed using a seed germination bioassay. Finally, to investigate further possible environmental impacts due to the application of mature compost contaminated with NPs to soils, a Life Cycle Assessment (LCA) was conducted. The impact of commercial Ag-TiO2 NPs and AgNPs on the in-vessel composting of biodegradable municipal solid waste was investigated over 21 days, using initial concentrations of 0, 5, 10, 20 and 50 mg Ag / kg of OM. Microbial activity was inhibited in the biodegradable waste reactors using 2% NaN3 to evaluate abiotic losses. Physicochemical parameters such as pH, ash content, weight loss, and the formation of humic substances (HS) were determined after 0, 4, 7, 14 and 21 days of composting and after a maturation phase. The results indicated that the presence of 2% NaN3 in biodegradable MSW inhibited effectively the microbial activity during the first week of composting. The microbial population was activated during the second week of composting but the decomposition rate was so low that did not result in the formation of humic substances (HS) following 21 days of composting when 2% NaN3 was used. Both treatments, using Ag-TiO2-NPs and AgNPs, did not show any inhibition of the decomposition process for all the tested concentrations and EEM peaks shifted towards the HS region during in-vessel composting. Higher inorganic carbon removal resulted from NP-contaminated compost with higher NP concentrations. This may indicate that the formation of humins was higher for non-contaminated compost and decreased as the NP concentration in waste increased. The shift of the peaks towards the HS region during composting for all the treatments suggested that NPs did not have an effect on humification and therefore on compost stability. The leaching properties of the NP-contaminated compost were investigated using a column leaching test. Five samples of leachate, of 50 mL each, were collected. The highest concentrations of HS were observed in the first two leaching samples. The leaching results suggested that only a low percentage of the total NPs (in weight) in compost, up to ca. 5% for Ag and up to ca. 15% for Ti, leached out from the columns, which was assumed the amount that potentially could leach to the environment. These results suggested that NPs will mainly accumulate in soils’ top layers following application of compost contaminated with NP. The phytotoxicity of NP-contaminated compost was assessed using a seed germination bioassay and the germination index was then calculated. The results indicated that the NP-contaminated compost did not present any toxic effects to cress germination. The possible environmental impacts due to the NP-contaminated compost application to soils were investigated by conducting a comparative LCA study. The LCA study indicated that the effects of NP-contaminated compost to human health and ecosystems endpoint categories increased due to the presence of NPs. The risks are associated with terrestrial ecotoxicity and human toxicity midpoint categories and are mainly attributed to the accumulation of Ag to soils.

Calcium (Ca2+), a crucial effector for many biological systems, has been associated with diseases such as cardiovascular disease, Alzheimer’s, Parkinson’s, cancer, and osteoporosis. It is important to develop calcium sensors to measure intracellular Ca2+ dynamics at various biological and pathological states. Our lab has engineered such probes by designing a Ca2+ binding site into fluorescent proteins such as Enhanced Green Fluorescent Protein (EGFP) and mCherry. In this thesis, we aim to improve optical properties and metal binding properties of green EGFP-based sensor CatchER and mCherry based red sensors by site-directed mutagenesis and protein engineering, various spectroscopic methods and cell imaging. The green EGFP-based sensor CatchER, with a Ca2+ binding pocket charge of -5, displays the greatest affinity for Ca2+ and has the greatest fluorescence intensity change with Ca2+ when compared to its variants with a less negative binding pocket charge. In addition, we have also designed several SR/ER targeting CatchER variants using Ryanodine receptor and Calnexin transmembrane domains. These constructs were shown to display a strong presence in the SR/ER lumen and further designed for a new luminal orientation. Further, we have shown that the optical properties of two red calcium sensors can be significantly improved by modifying the local environment of the chromophore.

Compressed and supercritical fluids, such as pressurized CO2, ethane, orpropane, provide a versatile and environmentally acceptable alternative to conventionalliquid organic solvents in bioprocessing applications – specifically in the areas ofproduct extraction, protein purification, microbial sterilization, and enzymatic and wholecellbiocatalysis. While their advantages have been well demonstrated, the effects ofcompressed and supercritical fluids on whole cells are largely unknown.Metabolic and structural perturbations of whole cells by compressed andsupercritical fluid solvents were examined. These perturbations exist as cell metabolismand membrane structure are influenced by pressure and the presence of a solventphase. Continuous cultures of Clostridium thermocellum (a model ethanol-producingthermophilic bacterium) were conducted under elevated hydrostatic and hyperbaricpressure to elucidate pressure- and solvent-effects on metabolism and growth.Fluorescence anisotropy was employed to study liposome fluidization due to thepresence of compressed and supercritical fluids and their partitioning/accumulation inthe phospholipid bilayer.Under elevated hydrostatic pressure (7.0 and 13.9 MPa; 333 K), significantchanges in product selectivity (towards ethanol) and growth were observed in C.thermocellum in conjunction with reduced maximum theoretical growth yields andincreased maintenance requirements. Similarly, metabolism and growth were greatlyinfluenced under hyperbaric pressure (1.8 and 7.0 MPa N2, ethane, and propane; 333K); however, severe inhibition was observed in the presence of supercritical ethane andliquid propane. These changes were attributed to mass-action effects on metabolicpathways, alterations in membrane fluidity, and the dominant role of phase toxicityassociated with compressed and supercritical fluids.Fluorescence anisotropy revealed fluidization and melting point depression ofdipalmitoylphosphatidylcholine liposomes in the presence of CO2, ethane, and propane(1.8 to 20.7 MPa; 295 to 333 K). The accumulation of these fluids within the bilayerupon pressurization and the ordering effects of pressure influenced liposome fluidity, themelting temperature, and the gel-fluid phase transition region. These resultsdemonstrate the disordering effects of compressed and supercritical fluids on biologicalmembranes and the ability to manipulate liposomes.

Detection, identification and separation of polycyclic aromatic compounds in environmental samples are of extreme importance since many of these compounds are well known for their potential carcinogenic and/or mutagenic activities. Selective quenching of molecular fluorescence can be utilized effectively to analyze mixtures containing different polycyclic aromatic hydrocarbons. Molecularly organized assemblies are used widely in detection and separation of these compounds mainly because of less toxicity and enhanced solubilization capabilities associated with these media. Feasibility of using nitromethane and the alkylpyridinium cation as selective fluorescence quenching agents for discriminating between alternant versus nonalternant polycyclic aromatic hydrocarbons (PAHs) is critically examined in several molecularly organized micellar solvent media. Fluorescence quenching is used to probe the structural features in mixed micelles containing the various combinations of anionic, cationic, nonionic and zwitterionic surfactants. Experimental results provide valuable information regarding molecular interactions between the dissimilar surfactants.

Compostos orgânicos podem ser liberados dos materiais resinosos, mesmo após sua polimerização, como resultado da presença de monômeros residuais e do processo de degradação do próprio material, podendo ocasionar efeitos citotóxicos, genotóxicos e alergênicos. O objetivo do presente estudo, in vitro, foi avaliar a liberação de compostos orgânicos de dois materiais resinosos, recentemente lançados no mercado, que apresentam inovações em suas formulações (resinas Kalore TM - GC FUJI e FiltekTM Silorane - 3M ESPE), variando a fonte de luz polimerizadora (halógena ou LED), a solução de imersão (água ou saliva artificial) e o pH da solução de imersão (7 ou 4,5). Foram confeccionados 56 corpos de prova da resina Kalore TM e 56 da resina FiltekTM Silorane, sendo 28 polimerizados com luz halógena e 28 com luz LED. Após aleatorização, 7 corpos de prova de cada resina foram armazenados em água com pH neutro, 7 em água com pH ácido, 7 em saliva com pH neutro e 7 em saliva com pH ácido. A leitura dos espectros das soluções foi realizada por meio da espectroscopia de fluorescência após 1, 3, 24, 48, 72, 168, 216, 312, 432, 504 e 672 horas. Após 672 horas, ainda verificou-se a liberação de compostos orgânicos das resinas KaloreTM e FiltekTM Silorane em todas as condições avaliadas. A liberação de compostos orgânicos foi menor nos grupos experimentais polimerizados pela luz LED. A quantidade de compostos orgânicos liberados foi menor nas amostras imersas em saliva. A resina KaloreTM liberou uma quantidade maior de compostos orgânicos em pH neutro, independente do meio de imersão. A resina FiltekTMSilorane liberou uma quantidade maior de compostos orgânicos em pH ácido, quando imersas em água, e uma maior quantidade de compostos orgânicos em pH neutro, quando imersas em saliva. A resina FiltekTMSilorane liberou mais de um componente orgânico. A espectrometria de fluorescência permitiu avaliar a liberação de compostos orgânicos das resinas KaloreTM e FiltekTM Silorane. / Organic compounds may be released from the resin materials, even after polymerization, as a result of the presence of residual monomers and degradation of the material itself, which may cause cytotoxic, genotoxic and allergenics effects. The purpose of this study, in vitro, was to evaluate the release of organic compounds from two resin materials, recently launched on the market, that present innovations in their formulations (resins KaloreTM - GC FUJI and FiltekTM Silorane - 3M ESPE), varying the source curing light (LED or halogen), the immersion solution (water or artificial saliva) and the pH of the immersion solution (7 or 4.5). Were prepared 56 specimens resin KaloreTM and 56 resin FiltekTM Silorane, 28 polymerized with halogen light and 28 with LED light. After randomization, 7 samples of each resin were immersed in water at neutral pH, 7 in water at acid pH, 7 in the saliva at a neutral pH, and 7 in the saliva at acid pH. The reading of the spectra of the solutions was performed by fluorescence spectroscopy at 1, 3, 24, 48, 72, 168, 216, 312, 432, 504 and 672 hours. After 672 hours, there was still release of organic resins KaloreTM and FiltekTM Silorane under all conditions evaluated. The release of organic compounds was lower in the experimental groups polymerized by LED light. The amount of organic compounds released was lower in samples immersed in saliva. The resin KaloreTM released more organic compounds at neutral pH in both immersion media. The resin FiltekTMSilorane immersed in water released more organic compounds at acid pH, but when the resin was immersed in saliva the release of organic compounds was higher at neutral pH. The resin FiltekTMSilorane released more that one organic component. The fluorescence spectrometry allowed us to evaluate the release of organic compounds resins KaloreTM and FiltekTMSilorane.

by Kwong Tsz-kin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1993. / Includes bibliographical references (leaves 90-96). / Chapter I. --- Abstract --- p.i / Chapter II. --- Acknowledgment --- p.ii / Chapter III. --- Table of contents --- p.iii / Chapter IV. --- List of Tables and Figures 、 --- p.iv / Chapter Chapter 1. --- Introduction --- p.1 / Chapter 1.1. --- General introduction / Chapter 1.2. --- Review of analytical methods for aluminium analysis / Chapter 1.3. --- Spectrofluorimetric determination of aluminium / Chapter 1.4. --- Project aim / Chapter Chapter 2. --- Experimental --- p.14 / Chapter 2.1. --- Apparatus / Chapter 2.2. --- Reagents & Material / Chapter 2.3. --- Procedure / Chapter 2.4. --- Treatment of data / Chapter Chapter 3. --- Results and discussion --- p.24 / Chapter 3.1. --- Optimization of experimental conditions / Chapter 3.2. --- Analytical Parameters / Chapter 3.3. --- Analytical results / Chapter Chapter 4. --- Conclusion --- p.89 / Chapter Chapter 5. --- References --- p.90 / Appendix --- p.97

Photocopy of typescript. / Digitized by Kansas Correctional Industries

Understanding the local conformations of DNA at the level of individual nucleic acid bases is important for the study of the mechanism of DNA sequence-dependent behavior. Here we apply linear absorption, circular dichroism (CD), and fluorescence spectroscopy to study the DNA local base conformation using 6-methyl Isoxanthopterin (6-MI) labeled DNA. We interpret excitation–emission peak shift (EES) measurements of the 6-MI, both as a ribonucleotide monophosphate in solution and as a site-specific substituent for guanine in various DNA constructs, by implementing a simple two-state model. We show that the spectroscopic properties of the 6-MI probe in DNA can be used to obtain detailed information about local base conformations and conformational heterogeneity and fluctuations. Based on these findings, we apply a simple theoretical model to calculate CD of 6-MI substituted DNA constructs. We find that our model can be used to extract basesequence- dependent information about the local conformation of the 6-MI probe as modulated by the local base or base-pair environment. We next apply 6-MI to probe the ligand insertion of small molecules to duplex DNA, further extending the potential of 6- MI as a useful reporter of local nucleic acid base conformation. These studies served to establish a new level of sophistication in qualitatively analyzing 6-MI structural behavior in terms of local base stacking and unstacking conformations. v This dissertation contains previously published and unpublished co-authored material.

Han, Fangyuan. / Thesis submitted in: November 2007. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 68-72). / Abstracts in English and Chinese. / Title Page --- p.I / Thesis Committee --- p.II / Acknowledgements --- p.III / Abstract --- p.IV / 摘要 --- p.V / Table of Contents --- p.1 / List of Figures --- p.4 / List of Tables --- p.6 / Chapter Chapter 1 --- Introduction --- p.7 / Chapter Chapter 2 --- Fourier Transform Spectroscopy --- p.10 / Chapter A. --- The Michelson Interferometer and the Interferogram --- p.10 / Chapter B. --- The Link between the Interferogram and the Spectrum: the Fourier Transform --- p.12 / Chapter C. --- "Resolution, Apodization and Spectral Folding" --- p.13 / Chapter D. --- Advantages and Disadvantages of FTIR Spectroscopy --- p.17 / Chapter E. --- Time-resolved FTIR Spectroscopy --- p.18 / Chapter (1) --- Time-resolved Rapid Scan Scheme --- p.18 / Chapter (2) --- Step-scan Scheme --- p.19 / Chapter F. --- Several Considerations in Step-scan Time-resolved Spectroscopy / Chapter Chapter 3 --- Molecular Fluorescence --- p.24 / Chapter A. --- Transitions Between Electronic States --- p.24 / Chapter B. --- Absorption and Vibrational Relaxation --- p.26 / Chapter C. --- Internal Conversion and Fluorescence --- p.26 / Chapter D. --- Intersystem Crossing and Phosphorescence --- p.27 / Chapter E. --- Fluorescence Lifetime and Quantum Yield --- p.29 / Chapter Chapter 4 --- Fourier Transform Spectroscopy of Zinc Phthalocyanine and Derivatives --- p.32 / Chapter A. --- Introduction --- p.32 / Chapter B. --- Apparatus --- p.35 / Chapter (1) --- VERTEX 70 FTIR Spectrometer --- p.35 / Chapter (2) --- Excitation Source --- p.38 / Chapter (3) --- Detectors and the Transient recorder --- p.38 / Chapter (4) --- Samples and Sample Cells --- p.39 / Chapter C. --- Experimental Setup --- p.40 / Chapter (1) --- Absorption Experiments --- p.40 / Chapter (2) --- Emission Experiments --- p.42 / Chapter D. --- Results and Discussion --- p.45 / Chapter (1) --- Absorption and Fluorescence Spectra --- p.45 / Chapter (2) --- Fluorescence Lifetimes and Quantum Yields --- p.51 / Chapter (3) --- Time-resolved Fluorescence Spectra --- p.54 / Chapter E. --- Some Experimental Details --- p.60 / Chapter (1) --- Choice of Windows for Regular Tests of the Instrument Performance --- p.60 / Chapter (2) --- Configurations of the Transient Recorder in OPUS --- p.61 / Chapter (3) --- Configurations of Detectors in OPUS --- p.61 / Chapter (4) --- The Standard Method of Extracting Time Slices --- p.62 / Chapter (5) --- Parameters that Easily Cause Problems --- p.63 / Chapter (6) --- Elimination of Background Noises --- p.64 / Chapter Chapter 5 --- Concluding Remarks --- p.66 / Reference --- p.68