This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

Dissertation (PhD)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Yeast species differ remarkably in their ability to degrade extracellular dicarboxylic acids and to utilise them as their only source of carbon. The fission yeast Schizosaccharomyces pombe effectively degrades L-malate, but only in the presence of an assimilable carbon source. In contrast, the yeast Saccharomyces cerevisiae is unable to effectively degrade L-malate, which is ascribed to the slow uptake of L-malate by diffusion. In contrast, the yeast Candida utilis can utilise L-malate as the only source of carbon and energy, but this is subject to substrate induction and catabolite repression. Very little research has been done on a molecular level in C. utilis and only a few of its genes have been studied. In this study, we have shown that the yeast C. utilis effectively degraded extracellular L-malate and fumarate, but in the presence of glucose or other assimilable carbon sources, the transport and degradation of these dicarboxylic acids was repressed. The transport of both dicarboxylic acids was shown to be strongly inducible by either L-malate or fumarate and kinetic studies suggest that the same transporter protein transports the two dicarboxylic acids. In contrast, S. pombe effectively degraded extracellular L-malate, but not fumarate, only in the presence of glucose or other assimilable carbon sources. The S. pombe malate transporter was unable to transport fumarate, although fumarate inhibited the uptake of L-malate. In order to clone the C. utilis dicarboxylic acid transporter, a cDNA library from C. utilis was constructed using a number of strategies to ensure representativeness and high transformation frequencies. The cDNA library was transformed in a S. cerevisiae strain carrying a plasmid containing the S. pombe malic enzyme gene (mae2) to allow screening for a malate-degrading S. cerevisiae clone. However, no positive clones that would indicate the successful cloning of the C. utilis malate transporter were obtained. The C. utilis malic enzyme gene, CuME, was subsequently isolated from the cDNA library based on conserved sequence homologies with the genes of S. cerevisiae and S. pombe, and characterised on a molecular and biochemical level. Sequence analysis revealed an open reading frame of 1926 bp, encoding a 641 amino acid polypeptide with a predicted molecular weight of 70.2 kDa. The optimum temperature for the C. utilis malic enzyme was 52°C and the enzyme was stable at 50°C for 2 hours. The inferred amino acid sequence showed significant homology with the malic enzymes of S. pombe and S. cerevisiae. Expression of the CuME gene is subject to glucose repression and substrate induction, as was observed for the dicarboxylic acid transporter from C. utilis. The CuME gene was successfully coexpressed with the S. pombe malate permease gene (mae1), resulting in a recombinant strain of S. cerevisiae able to effectively degrade L-malate. / AFRIKAANSE OPSOMMING: Daar is ’n merkwaardige verskil in die vermoë van verskillende gisspesies om ektrasellulêre dikarboksielsure af te breek en dit as enigste bron van koolstof te benut. Die splitsingsgis Schizosaccharomyces pombe kan L-malaat effektief afbreek, maar slegs in die teenwoordigheid van ’n ander benutbare koolstofbron. In teenstelling hiermee is dit vir die gis Saccharomyces cerevisiae onmoontlik om L-malaat effektief af te breek en te benut, wat hoofsaaklik toegeskryf kan word aan die stadige opname van L-malaat deur middel van diffusie. Die gis Candida utilis kan egter L-malaat as die enigste bron van koolstof en energie benut, maar dit is onderhewig aan substraat-induksie en kataboliet onderdrukking. Baie min navorsing op molekulêre vlak is tot hede in C. utilis uitgevoer en slegs ’n paar gene in hierdie gis is al bestudeer. In hierdie studie het ons aangetoon dat die gis C. utilis L-malaat en fumaraat effektief afbreek, maar dat glukose of ander benutbare koolstofbronne die opname en afbraak van hierdie dikarboksielsure onderdruk. Die opname van beide dikarboksielsure is sterk induseerbaar deur L-malaat óf fumaraat, terwyl kinetiese studies toon dat beide dikarboksielsure deur dieselfde transporter-proteïen vervoer word. In teenstelling hiermee kan S. pombe ekstrasellulêre L-malaat, maar nie fumaraat nie, in die teenwoordigheid van glukose of ’n ander benutbare koolstofbron effektief afbreek. Die S. pombe L-malaat transporter was nie in staat om fumaraat te vervoer nie, alhoewel fumaraat die opname van L-malaat onderdruk het. Ten einde die dikarboksielsuur transporter van C. utilis te kloneer, is verskeie strategieë gevolg ten einde ’n cDNA-biblioteek van C. utilis te konstrueer wat verteenwoordiging en hoë transformasie-frekwensies kan verseker. Die cDNA-biblioteek is getransformeer in ’n S. cerevisiae ras wat die S. pombe malaatensiem geen (mae2) bevat om die sifting van ’n S. cerevisiae kloon wat malaat effektief kan afbreek, moontlik te maak. Geen positiewe klone wat dui op die klonering van die C. utilis malaat transporter kon egter gevind word nie. Die C. utilis malaatensiem geen, CuME, is vervolgens van uit die cDNA biblioteek geïsoleer deur van gekonserveerde DNA-homologie met S. cerevisiae en S. pombe gebruik te maak, en op molekulêre en biochemiese vlak gekarakteriseer. DNA-volgordebepaling het ’n oopleesraam van 1926 bp onthul, wat kodeer vir ’n 641 aminosuur polipeptied met ’n verwagte molekulêre gewig van 70.2 kDa. Die optimale temperatuur van die C. utilis malaatensiem was 52°C en die ensiem was vir 2 ure stabiel by 50°C. Die afgeleide aminosuurvolgorde het beduidende homologie met die malaatensieme van S. pombe en S. cerevisiae getoon. Die CuME geen is suksesvol saam met die S. pombe malaat permease geen (mae1) uitgedruk om ’n rekombinante S. cerevisiae ras te genereer wat in staat is om L-malaat effektief af te breek.

Thesis (MTech (Chemistry))--Cape Peninsula University Of Technology, 2015. / Twelve multicomponent crystals of dicarboxylic acids (succinic, adipic and suberic acid) with derivatives of picoline (4-picoline, 2,4-lutidine, 3,4-lutidine and 3,5-lutidine) were analyzed with the aim of finding correlation between their melting points and crystalline structural features. The solvates of SUC•2,4LUT, SUC•3,4LUT, SUC•3,5LUT and ADP•4PIC are already known structures but were remade for completeness and to obtain their accurate melting temperatures. The acids were selected because of their systematically increasing chain lengths and the selection of the picoline derivatives were based on the systematic variation of the positions of the methyl groups around the pyridine moiety. All the formed multicomponent crystals were analyzed with single crystal X-ray diffraction and parallel to the solution crystallizations, grinding experiments were carried out to prepare the aimed inclusion compounds by using much less of the solvent of crystallization. Thermogravimetry was used to confirm the solvent content of the bulk material and differential scanning calorimetry was applied to obtain information about the melting process, such as the onset and the peak temperature of the melting and the concomitant enthalpy change. The melting temperatures revealed that the inclusion formation significantly decreased the melting points of the staring materials and the melting points of the inclusion compounds for the same acid varied significantly. Hirshfeld surfaces of the base-acid-base moieties and the related fingerprint plots were compared both qualitatively and quantitatively. The melting points of the compounds were plotted against the percentage contribution of the various intermolecular interactions.

Soot aerosols are well known to be atmospheric constituents, but the hydrophobic nature of fresh soot likely prohibits them from encouraging cloud development. Soot aged through contact with oxygenated organic compounds may become hydrophilic enough to promote water uptake. In this study, the tandem differential mobility analyzer (TDMA) and differential mobility analyzer?aerosol particle mass analyzer (DMA?APM) were employed to measure the changes in morphology and hygroscopicity of soot aerosol particles upon coating with succinic and glutaric acids. The effective densities, fractal dimensions and dynamic shape factors of fresh and coated soot aerosol particles have been determined. Significant size-dependent increases of soot particle mobility diameter, mass, and effective density (?eff) were observed upon coating of aggregates with succinic acid. These properties were restored back to their initial states once the acid was removed by heating, suggesting no restructuring of the soot core had occurred. Coating of soot with glutaric acid, on the other hand, leads to a strong size shrinking with a diameter growth factor ~0.60, even after the acid has been removed by heating suggesting the strong restructuring of the soot agglomerate. The additional 90% RH cycle can evidently enhance the restructuring process. The extinction and scattering properties at 532 nm of soot particles internally mixed with dicarboxylic acids were investigated experimentally using a cavity ring-down spectrometer and an integrating nephelometer, respectively, and the absorption is derived as the difference between extinction and scattering. It was found that the organic coatings significantly affect the optical and microphysical properties of the soot aggregates. The size-dependent amplification factors of light scattering were as much as 3.8 and 1.7 with glutaric and succinic acids coatings, respectively. Additional measurements with soot particles that are first coated with glutaric acid and then heated to remove the coating show that both scattering and absorption are enhanced by irreversible restructuring of soot aggregates to more compact globules. These results reveal the microphysical state of soot aerosol with incomplete restructuring in the atmosphere, and advance the treatment of atmospheric aged soot aerosol in the Mie theory shell-and-core model.

Rhizobium meliloti mutants defective in C₄-dicarboxylic acid transport (Dct⁻) were previously isolated by Tn5 mutagenesis, and divided into two groups based on complementation of Dct- with cosmid clones. In this work further characterization was carried out on the two loci. Group I mutants were found to be defective in dicarboxylate transport (Dct⁻), nitrate utilization, and symbiotic nitrogen fixation. Subcloning and complementation work confined the Group I mutations to a 3.5 kbp BamHI-EcoRI fragment containing the ntrA gene. Group V mutants were defective in dicarboxylate transport and demonstrated varying levels of nitrogen fixation. Complementation and site-directed Tn5 mutagenesis revealed three transcriptional units, corresponding to dctA, dctB, and dctD, localized within a 6 kbp HindIII fragment. The use of dctA::TnphoA fusions determined the expression of dctA to be ntrA, dctB, and dctD dependent. Dct+ revertants of dctB and dctD mutants were selected which carried second-site mutations responsible for restoring the Dct⁺ phenotype. / Thesis / Master of Science (MS)

Oxidation of organic species, in particular dicarboxylic and humic acids, was investigated in ice. Products were analyzed by Proton Transfer Reaction Mass Spectrometry, ion and gas chromatography, and a Total Organic Carbon analyzer. Photolysis of succinic acid with H2O2, an OH precursor, produced malonic acid and malic acid, illustrating that diacids are subject to photochemical degradation in ice. First-order decay rate constants were an order of magnitude higher at room temperature (~23 °C) than in ice (-20 °C). A smaller difference was observed for malonic acid, a more soluble diacid, suggesting that partial segregation of H2O2 and succinic acid during freezing played an important role in the kinetics. VOCs, likely to be aldehydes and ketones, were produced from ice containing humic acid through heterogeneous ozonolysis and photooxidation which was enhanced by NO3-, an OH precursor. VOCs also formed from ice made from deionized water, likely through oxidation of organic contaminants.

Oxidation of organic species, in particular dicarboxylic and humic acids, was investigated in ice. Products were analyzed by Proton Transfer Reaction Mass Spectrometry, ion and gas chromatography, and a Total Organic Carbon analyzer. Photolysis of succinic acid with H2O2, an OH precursor, produced malonic acid and malic acid, illustrating that diacids are subject to photochemical degradation in ice. First-order decay rate constants were an order of magnitude higher at room temperature (~23 °C) than in ice (-20 °C). A smaller difference was observed for malonic acid, a more soluble diacid, suggesting that partial segregation of H2O2 and succinic acid during freezing played an important role in the kinetics. VOCs, likely to be aldehydes and ketones, were produced from ice containing humic acid through heterogeneous ozonolysis and photooxidation which was enhanced by NO3-, an OH precursor. VOCs also formed from ice made from deionized water, likely through oxidation of organic contaminants.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 4 uppsatser.

- / -

Philosophiae Doctor - PhD / Growth of symbiotic legume hosts is P limited, because of the high energetic requirements associated with N2 fixation. Attempts to overcome P deficiency in soils where legumes are grown involve addition of P-based fertilisers. However, these are produced from fmite, non-renewable resources that could be exhausted in the next 50-80 years. For this and other prudent reasons, viable alternatives are sought that include producing genetically enhanced plants with better P use efficiency (PUE). There exist some inter- and intraspecific genetic variation for associated traits of PUE in various legumes and these will have to be exploited to realize the development of P efficient cultivars. With the advent of sophisticated molecular tools, good progress has been made to understand the molecular response of some common physiological and morphological functions observed under LP. The research aims here were to investigate the energy costs and the alternative metabolic routes associated with C and N metabolism under LP in legumes, which is very scant in literature. We also investigated the recovery responses of nodulated roots upon P alleviation. Consequently, improvement strategies to produce legume varieties for better adaptation in poor P soils are envisaged. We have demonstrated varying degrees of sensitivity between the amide and ureide legume systems being investigated under short-term LP. The species-specific responses were ascribed to differences related to the agro-climatic origins, nodule morphologies and the type of N containing export product of the different legume types. These different responses also underscore possible different regulatory mechanisms under LP. Lupins were probed further, because of its apparent tolerance to P deficiency. Lupin nodules had between 3 to 5-fold higher Pj concentrations compared with soybeans under LP and HP, respectively. The maintenance of Pj levels, as oppose to a decline in the total P pool, is discussed in relation to its role in maintaining N2 fixation in lupins. Under LP, an effective Pj recycling mechanism in nodules is proposed to occur via the induction of the PEPc- MDH-ME route. This route also enhanced the capacity of root nodules to procure high malate concentrations that are used to fuel bacteroid respiration and N2 fixation. Two distinctly different cMDH proteins, one corresponding to HP and another corresponding to LP, were identified. The high malate concentrations reported here are speculated to have arisen through LP-induced cMDH. Metabolically available Pj decline developed gradually as P deficiency progressed. This coincided with a 15% decline in the %Ndfa. Moreover, under prolonged P deficiency the disproportionate synthesis of organic acids, most notably malate, that occurred at the expense of amino acids was proposed to account for this decline. The recovery in response to alleviation from LP involved alterations in the allocation of respiratory costs to growth and nutrient acquisition. Under LP, smaller nodules were formed and nodule metabolism revolved around accentuating PUE. Thus, there is considerable potential for improvement of P efficiency in legumes through manipulation of root: shoot partitioning.