This paper describes a new technique for analyzing fire debris using nuclear magnetic resonance (NMR) spectroscopy. Petroleum distillates, which are commonly used accelerants, were weathered, burned, and steamdistilled. These, as well as virgin samples of the accelerants, were analyzed by gas chromatography and nuclear magnetic resonance spectroscopy. In addition, solvent studies and detectibility limit studies were conducted. The use of NMR is described as a valuable adjunct to the existing methods of analysis.

CTG repeat is one of the most common triplet repeat sequences that have been found to form slipped-strand structures leading to self-expansion during DNA replication. The lengthening of these repeats causes the onset of neurodegenerative diseases such as myotonic dystrophy. Through designing a series of CTG repeat sequences with high hairpin populations, systematic analysis of imino and methyl proton spectra study has been carried out to investigate the length and structural roles of CTG repeats in affecting the propensity of hairpin formation. Direct NMR evidence has been obtained to support three types of hairpin structures in sequences containing one to ten CTG repeats. The differences in loop structures and extent of interactions observed in the hairpins account for the differences in hairpin formation propensity and explain how slippage occurs that lead to triplet repeat expansion. / DNA has been found to adopt unusual structures leading to different types of mutations, which can ultimately cause genetic diseases and cancers. In this thesis, investigations on (i) structural role of CTG repeats in trinucleotide repeat expansion, (ii) primer-template structures in strand slippage during low fidelity replication and (iii) sequence effect of nucleotide downstream of thymine templates on primer-template structures have been carried out using NMR spectroscopy. / In addition, NMR structural investigations have also been carried out to determine solution structures of primer-template models. NMR evidence confirms misalignment can occur in primer-templates upon misincorporation of dNTP opposite a template sequence, leading to bulge formation in the primer-template. Depending on the template sequence, further incorporation of dNTP can bring about either realignment or further stabilization of the primer-template structure. Consequently, either mismatch or deletion errors will occur, leading to base substitution or frameshift mutation. These results imply that DNA sequences do not only play a passive role to store genetic information in the replication process, they also play an active structural role in governing the types of mutation during low-fidelity DNA replication. / Some of the results in this thesis have been reported in the following peer-reviewed journals: (1) Chi, L. M. and Lam, S. L. (2005) Structural roles of CTG repeats in slippage expansion during DNA replication. Nucleic Acids Res, 33, 1604-1617. (2) Chi, L. M. and Lam, S. L. (2006) NMR investigation of DNA primer-template models: structural insights into dislocation mutagenesis in DNA replication. FEBS Lett. , 580, 6496-6500. (3) Chi, L. M. and Lam, S. L. (2007) NMR investigation of primer-template models: structural effect of sequence downstream of a thymine template on mutagenesis in DNA replication. Biochemistry, 46, 9292-9300. / Chi, Lai Man. / "August 2007." / Adviser: Lam Sik Lok. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0877. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (p. 102-112). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

No description available.

In this thesis the synthesis and full characterization of a new bulky diphosphine, tetrakis-(2,6-diisopropylphenyl)diphosphine, are described. This compound displays facile oxidation and a thorough investigation of its redox properties has been studied by combining solution electrochemical techniques such as cyclic voltammetry (CV) and rotating disk electrode (RDE) voltammetry, with spectroscopic methods such as electron paramagnetic resonance (EPR) and Simultaneous Electrochemical Electron Paramagnetic Resonance (SEEPR) spectroscopy over a wide temperature range. Density functional theory (DFT) calculations were carried out to aid in structural characterization of the radical cation that is produced and to provide computed hyperfine splitting (HFS) constants for comparison with experimental results. For comparison to this species with bulky aromatic substituents, similar studies were conducted that have identified the previously unreported radical cation of tetrakis-tert-butyldiphosphine with a bulky aliphatic substituent that provides even higher steric pressure than the 2,6-diisopropylphenyl group. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. Further CV and EPR (SEEPR) studies are reported that led to the identification of radical cations of tris(2,6-diisopropylphenyl)arsine and bis(2,4,6-triisopropylphenyl)(2,6-diisopropylphenyl)phosphine. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. / xix, 172 leaves : ill (some col.) ; 29 cm

Thesis (M.Sc.). / Written for the Dept. of Chemistry. Title from title page of PDF (viewed 2009/06/23). Includes bibliographical references.

Submitted in partial compliance with the requirements of the Master's Degree in Technology: Homoeopathy, Durban University of Technology, 2010. / The aim of this study was to compare the Nuclear Magnetic Resonance (NMR) spectra of homoeopathic potencies prepared according to the orthodox Hahnemannian method with those produced with Radionic instrumentation. Methodology The chemical shift values and relative integration values for the H2O, CH2, CH3 and OH peaks of the 6C, 12C and 30C potencies of Hahnemannian and Radionic Natrum muriaticum were compared. The orthodox Hahnemannian method of preparing potencies involves dilution of the crude substance followed by the dilution and succussion at each subsequent deconcentration (potency) level. The Hahnemannian potencies were prepared according to the German Homoeopathic Pharmacopoeia (GHP) and the potencies diluted using a 1:100 ratio and succussed ten times at each potency level. The Radionic group of potencies were prepared using the ‘Magnetogeometric Potency Simulator’ (a Radionic apparatus). NMR testing took place at the Chemistry Department at the University of KwaZulu Natal, Pietermaritzburg using a Bruker Avance lll NMR spectrometer 500MHz.The samples were dispensed into boro-silicate glass NMR tubes with a co-axial tube containing Dimethyl sulfoxide-d6 (DMSO-d6) which was used as a frequency lock around the tube. Three samples were drawn from each group, including the controls, and analysed using the NMR spectrometer. The NMR spectrometer information was received and the chemical shift and relative integration values of H2O, OH, CH2 and CH3 peaks on the NMR spectra recorded. All the data was entered into a Microsoft Excel© 2000 spreadsheet and then from there transferred into SPSS© software package for statistical analysis. The Kruskal-Wallis test was used to make a comparison between the eight unpaired groups. If a significant difference occurred between the groups iii individual comparisons between groups were made using the non-parametric Mann-Whitney test. The significant value was set at α= 0.05. Results The results of this study revealed significant differences between the Hahnemannian and Radionic samples. The chemical shift values of the parallel potencies showed significant differences for the H2O, CH2 and CH3 peaks. A significant difference for the OH peaks was observed between the 30C potencies. The relative integration values showed a significant difference for the OH and CH3 peaks between the parallel 12C and 30C potencies but not between the parallel 6C potencies. Conclusion From studying the results it can be concluded that the respective manufacture methods resulted in the NMR spectra of the parallel potencies being significantly different (exhibiting distinctive physico-chemical properties) thus confirming the hypotheses of the study. The standardisation of the process of preparing homoeopathic remedies is important as different methods produce potencies with distinct physico-chemical identities. Further studies into different methods should be researched in order to control and standardise the production of potencies.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2010. / Please refer to full text for abstract

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: See full text for abstract / AFRIKAANSE OPSOMMING: Sien volteks vir opsomming

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: In reverse iodine transfer polymerisation (RITP), chain transfer agents (CTAs) are generated in situ from the reaction between 2,2’-azobis(isobutyronitrile) (AIBN) and molecular iodine. This stage of RITP is the inhibition period, which ends when all iodine has been consumed. The evolution of CTAs was studied for the polymerisation reactions of n-butyl acrylate and styrene respectively. RITP of n-butyl acrylate was performed at 70 °C. In situ 1H nuclear magnetic resonance (NMR) experiments were carried out to study the evolution of CTAs during the inhibition period of n-butyl acrylate polymerisation and the structures A-I and A-Mn-I (where A represents the moiety originating from AIBN, M represents the monomer unit and n is the mean number degree of polymerisation) were observed. A polymer with the general structure A-Mm-I is formed. The molecular weight of poly(n-butyl acrylate) (PnBA) was evaluated with size exclusion chromatography (SEC) and NMR. Structural analysis of PnBA was done using NMR spectroscopy and matrix-assisted laser desorption/ionisation time-of-flight (MALDI-ToF) mass spectrometry. Similar conditions to those used for n-butyl acrylate polymerisation were used for RITP of styrene. The evolution of CTAs during the inhibition period of styrene polymerisation was studied using in situ 1H NMR. The inhibition period of styrene polymerised by RITP was much shorter than expected. This is due the consumption of iodine in the reaction between styrene and iodine which reversibly forms 1,2-diiodo-ethyl benzene. The CTAs A-I and A-Mn-I are formed, as well as 1-phenylethyl iodide (1-PEI). The molecular weight of polystyrene (PS) was determined using SEC and NMR and the functionality was evaluated using 1H NMR. The structure of PS was confirmed with 1H NMR and MALDI-ToF mass spectrometry. By increasing the temperature of the reaction, the inhibition period can be shortened. Both polymerisation systems retain control over molecular weight with an increase in temperature, however, n-butyl acrylate is limited due to the possible formation of mid-chain radicals. The formation of an A–Mm–A population (direct combination of the initiator and styrene) in RITP of styrene results in more initiator being consumed than for n-butyl acrylate, despite limited conversion of styrene to polymer. / AFRIKAANSE OPSOMMING: In omgekeerde-jodium-oordrag polimerisasie, is die kettingoordragagente gegenereer in situ van die reaksie tussen 2,2’-azobis(isobutironitriel) (AIBN) en molekulêre jodium. Hierdie fase van RITP is die inhibisie tydperk wat eindig wanneer alle jodium verbruik is. Die evolusie van kettingoordragagente is vir die polimerisasiereaksies van butielakrilaat en stireen onderskeidelik bestudeer. Omgekeerde-jodium-oordrag polimerisasie van butielakrilaat was uitgevoer by 70 °C. In situ 1H kernmagnetieseresonans (KMR) eksperimente is uitgevoer om die evolusie van die kettingoordragagente te bestudeer tydens die inhibisie van butielakrilaat polymerisasie en die strukture A-I en A-Mn-I (waar A die gedeelte voorstel wat afkomstig is van AIBN, M die monomeer-eenheid en n die gemiddelde aantal polymerisasiegraad verteenwoordig) is ge-identifiseer. 'n Polimeer met die algemene struktuur A-Mm-I is gevorm. Die molekulêre gewig van poli(butielakrilaat) (PnBA) was geëvalueer deur grootte-uitsluitings chromatografie en KMR spektroskopie. Strukturele ontleding van PnBA is gedoen deur die KMR spektroskopie en matriks ge-assisteerde laser desorpsie/ionisasie tyd-van-vlug massaspektroskopie. Soortgelyke kondisies as dié wat gebruik word vir butielakrilaat polymerisasie, is gebruik vir omgekeerde-jodium-oordrag polimerisasie van stireen. Die evolusie van die ketting oordrag agente gedurende die inhibisie periode van stireen polymerisasie is deur in situ 1H KMR bestudeer en die inhibisie periode is baie korter as verwag. Dit is as gevolg van die opname van jodium in die reaksie tussen stireen en jodium wat omkeerbare stireen-di-jodied tot gevolg hê. Die ketting oordrag agente A-I en A-Mn-I is gevorm, sowel as 1-feniel-etiel jodied. Die molekulêre massa van polistireen (PS) is bepaal met behulp van grootte-uitsluitings chromatografie en KMR spektroskopie en die funksioneering is geëvalueer met behulp van 1H KMR. Die struktuur van PS is bevestig deur 1H KMR en matriks ge-assisteerde laser desorpsie/ionisasie tyd-vanvlug massaspektroskopie. Deur die verhoging van die temperatuur van die reaksie, kan die inhibisie periode verkort word. Beide polimerisasie sisteme behou beheer oor die molekulêre massa met 'n toename in temperatuur, alhoewel butielakrilaat beperk word as gevolg van die moontlike vorming van middel kettingradikale. Die vorming van die A-Mm-A spesie (direkte kombinering van AIBN en stireen) in omgekeerdejodium- oordrag polimerisasie van stireen veroorsaak dat meer AIBN verbruik word as butielakrilaat, ten spyte van die beperkte omskakeling van stireen tot polimeer.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: This dissertation explores the behaviour and regulation of central carbon metabolism in Escherichia coli K12 W3110 under fermentative microaerobic conditions. To achieve this, an integrative systems modelling approach was adopted, which is introduced in Chapter 1 along with a review of metabolism in E. coli. An open-source software suite NMRPy, developed using the Python programming language, is presented in Chapter 2. NMRPy provides a host functions for basic processing, analysis and visualisation of Nuclear Magnetic Resonance (NMR) spectroscopy data. In addition to this, NMRPy offers specialised functions for the deconvolution of arrayed reaction time series, which proved indispensable to the research presented in this dissertation. NMRPy presents an easy to use, extensible tool for both routine and advanced use. In Chapter 3, a novel methodology is presented which was developed for the effective and comprehensive determination of enzyme kinetic parameters for systems biology using NMR. In contrast to traditional enzyme kinetic assay methods, this new methodology is less labour-intensive and yields significantly more information per experiment. By fitting kinetic equations to real time NMR data, dynamic changes in substrates, products and allosteric modifiers are quantified and allowed to inform the parameter fitting procedure. These data contain information on cooperative substrate binding, reversibility, product inhibition and allosteric effects. The proposed methodology is applied to the study of the first two enzymes of the glycolytic pathway. In Chapter 4, the construction, parameterisation and validation of a number of kinetic models of glycolysis in E. coli under microaerobic conditions is detailed. To model the lower half of glycolysis, a similar technique was adopted as in Chapter 3, in which models representing the reactions from triosephosphate isomerase to pyruvate kinase were parameterised by fitting them to a collection of 31P NMR reaction time series. This approach extends the methodology to enzyme sub-networks, yielding data that encompass the full complexity of the network regulatory interactions. The verified kinetic models were subjected to scrutiny, the results of which are presented in Chapter 5. The value of the modelling approach is demonstrated by the ease with which cumbersome in vivo experiments can be performed in silico. A structural analysis of the model topology was conducted, elucidating the elementary flux modes of fermentative glycolysis in E. coli, and identifying a futile cycle around PEP carboxylase and PEP carboxykinase. Model steady-state behaviour and control properties were explored in silico under various degrees of ATP demand and oxygen availability and a number of hypotheses are presented, explaining the regulation of free energy in E. coli, and the metabolic responses of E. coli to changing redox demands. Amongst other things, the results demonstrated that the glucose importing phosphoenolpyruvate: phosphotransferase pathway controlled glycolytic flux, and that under microaerobic conditions E. coli is able to regulate redox balance not only by balancing flux between acetate and ethanol, but also by altering the balance of flux between acetate and lactate at the pyruvate formate lyase/lactate dehydrogenase branch point. This study demonstrates the value of an integrated computational and experimental systems approach to exploring biological phenomena. / AFRIKAANSE OPSOMMING: In hierdie proefskrif word die gedrag en regulering van die sentrale koolstofmetabolisme in Escherichia coli K12 W3110 onder fermenterende mikro-a¨erobiese toestande ondersoek. Dit is moontlik gemaak deur ’n ge¨ıntegreerde stelsel-modelleringsbenadering, wat in Hoofstuk 1 bekendgestel word. D´ıe hoofstuk verskaf ook ’n oorsig van die metabolisme in E. coli. ’n Oopbron-kodepakket NMRPy, wat in die programmeringstaal Python ontwikkel is, word in Hoofstuk 2 beskryf. NMRPy verskaf ’n aantal funksies vir die basiese verwerking, analise en visualisering van Kern-Magnetiese Resonansie (KMR) spektroskopiese data, sowel as gespesialiseerde funksies vir die dekonvolusie van opeenvolgende reaksie-tydreekse. Hierdie funksionaliteit was onontbeerlik vir die verdere navorsing in hierdie proefskrif. Hoofstuk 3 beskryf die ontwikkeling van ’n nuwe metodiek vir die omvangryke bepaling van ensiem-kinetiese parameters vir sisteembiologie, deur van KMR gebruik te maak. In teenstelling tot tradisionele ensiem-kinetiese essai-metodes, is hierdie nuwe metodologie minder arbeidsintensief en lewer dit beduidend meer inligting per eksperiment. Deur die kinetiese vergelykings op tydsafhanklike KMR data te pas, word dinamiese veranderinge in substrate, produkte en allosteriese effektors gekwantifiseer en hierdie inligting gebruik in die passingsprosedure. Die data bevat inligting oor ko¨operatiewe substraatbinding, omkeerbaarheid, produkinhibisie en allosteriese effekte. Die voorgestelde metodologie word toegepas op die karakterisering van die eerste twee glikolitiese ensieme. In Hoofstuk 4 word die konstruksie, parameterisering en validering van ’n aantal kinetiese modelle van glikolise in E. coli onder mikro-a¨erobiese toestande uiteengesit. Die waarde van die modelleringsbenadering lˆe in die gemak waarmee omslagtige in vivo eksperimente in silico uitgevoer kan word. Om die onderste helfte van die glikolitiese pad te modelleer word ’n soortgelyke tegniek as in Hoofstuk 3 gebruik. Modelle van die reaksies vanaf triosefosfaat-isomerase tot by pirovaat-kinase is geparameteriseer deur dit op ’n versameling 31P KMR-tydreekse te pas. Hierdie benadering brei bostaande metodologie uit tot ensiem-subnetwerke en genereer data wat die volle kompleksiteit van regulerende interaksies in die netwerk insluit. Die geverifieerde modelle word in Hoofstuk 5 noukeurig ondersoek. ’n Strukturele analise van die modeltopologie word onderneem om die elementˆere fluksie-modes van fermentatiewe glikolise in E. coli te verklaar, sowel as om ’n futiele siklus rondom fosfo¨enolpirovaat karboksilase en fosfo¨enolpirovaat karboksikinase te identifiseer. Die bestendige-toestandsgedrag en kontrole-eienskappe word in silico ondersoek onder toestande van verskeie ATP beladings en suurstofbeskikbaarheid. ’n Aantal hipoteses word voorgelˆe, wat die regulering van vry energie in E. coli, sowel as die metaboliese reaksies van E. coli onder veranderende redoks-vereistes kan verklaar. Onder andere dui die resultate daarop dat die fosfo¨enolpirovaat:fosfotransferase sisteem (wat verantwoordelik is vir glukose-opname in die sel) die glikolitiese fluksie beheer en dat E. coli onder mikro-a¨erobiese toestande die redoksbalans nie net tussen asetaat en etanol kan reguleer nie, maar ook die deur wysiging van die fluksie-balans tussen asetaat en laktaat rondom die pirovaat-formiaat-liase/laktaatdehidrogenase vertakkingspunt. Hierdie studie toon die waarde van ’n ge¨ıntegreerde rekenaarmatige en eksperimentele sisteembenadering om biologiese verskynsels te ondersoek.