Master of Science / Department of Grain Science and Industry / Bhadriraju Subramanyam / Organic, hard red winter wheat of 11% moisture was tempered with distilled water to moisture levels of 16 and 18% and held for 8, 16, and 24 h. At each moisture and holding time wheat was unexposed (control) or exposed to infrared radiation for 1, 1.5, and 2 min using a bench-top flameless catalytic infrared emitter. The mean external grain temperatures for 16% mc wheat measured with thermocouples during infrared exposure of 1, 1.5, and 2 min ranged from 77.4-83.1, 93.7-101.2, and 91.2-98.3°C, respectively; corresponding mean internal temperatures were 67.3-76.4, 80.0-85.6, and 81.3-93.2°C. Minor differences in kernel moisture, hardness, and weight were observed among treatments. Tempered wheat after infrared exposure among treatments lost 1.5-2% moisture. Infrared exposure of wheat reduced initial bacterial loads (6.7×10[superscript]4 CFU/g) by 98.7% and fungal loads (4.3×10[superscript]3 CFU/g) by 97.8% when compared with those on untreated wheat. Wheat tempered to 18% and exposed for 2 min to infrared radiation lost 2% moisture, and this wheat when milled had a yield of 73.5%. The color of flour from infrared- exposed wheat was slightly dark (color change, ΔE = 0.31) when compared with untreated flour. Differential scanning calorimetry showed that flours from infrared exposed wheat had lower enthalpy (3.0 J/g) than those unexposed to infrared (3.3 J/g). These flours were adversely affected because they had longer mixing times (7-15 min) at all infrared exposures due to the presence of insoluble polymeric proteins (up to 60%). Microbial loads in flour from wheat tempered to 18% and exposed for 1-2 min had 0.6-2.4 log reduction compared to flour from untreated wheat. Wheat tempered to 18% moisture with electrolyzed-oxidizing (EO) water reduced bacterial and fungal loads up to 66%. EO water tempered wheat exposed for 1, 1.5, and 2 min to infrared radiation showed microbial reductions of 99.5% when compared with control wheat. Infrared treatment of tempered wheat cannot be recommended as it adversely affected flour functionality. The use of EO water for tempering as opposed to potable water that is generally used in mills slightly enhances microbial safety of hard red winter wheat.

Fenn, Dickson. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 74-81). / Abstract also in Chinese. / Title Page --- p.i / Thesis Committee --- p.ii / Acknowledgement --- p.iii / Table of Contents --- p.v / List of Tables --- p.ix / List of Figures --- p.x / List of Abbreviations and Symbols --- p.xv / Abstract --- p.xvii / Chapter 1.Chapter One: --- Introduction --- p.1 / Chapter 1.1 --- Oxidation and Hyperoxidation of Guanine --- p.1 / Chapter 1.2. --- DNA Replication --- p.2 / Chapter 1.3 --- Mutagenesis --- p.3 / Chapter 1.4 --- Literature Survey on Spiroiminodihydantoin (Sp) --- p.4 / Chapter 1.5 --- Purpose of This Work --- p.5 / Chapter 1.6 --- DNA Structure --- p.6 / Chapter 1.6.1 --- Nomenclature --- p.6 / Chapter 1.6.2 --- Torsion Angles --- p.6 / Chapter 1.6.3 --- Sugar Pucker Conformation --- p.7 / Chapter 1.6.4 --- Secondary Structures of DNA --- p.8 / Chapter 2.Chapter Two: --- Materials and Methodology --- p.10 / Chapter 2.1 --- Sample Design --- p.10 / Chapter 2.2 --- Sample Preparation --- p.11 / Chapter 2.2.1 --- DNA Synthesis and Purification --- p.11 / Chapter 2.2.2 --- HPLC Separation --- p.11 / Chapter 2.2.3 --- NMR Samples Preparation --- p.12 / Chapter 2.3 --- NMR Analysis --- p.12 / Chapter 2.3.1 --- Resonance Assignment --- p.14 / Chapter 2.3.1.1 --- Proton --- p.14 / Chapter 2.3.1.2 --- Phosphorous --- p.16 / Chapter 2.3.2 --- Sugar Pucker Conformation --- p.17 / Chapter 2.3.3 --- Backbone Conformation --- p.18 / Chapter 2.4 --- UV Melting Analysis --- p.19 / Chapter 3.Chapter Three: --- "HPLC, NMR and UV Results" --- p.21 / Chapter 3.1 --- HPLC Separation of Sp Diastereoisomers --- p.21 / Chapter 3.2 --- NMR Resonance Assignments --- p.24 / Chapter 3.2.1 --- 5'-GG Sample --- p.24 / Chapter 3.2.2 --- 5'-G(oG) Sample --- p.26 / Chapter 3.2.3 --- 5'-G(Sp) Sample --- p.29 / Chapter 3.2.4 --- 5'-T(oG) Sample --- p.31 / Chapter 3.2.5 --- 5'-T(Sp) Sample --- p.34 / Chapter 3.3 --- Sugar Pucker Conformation --- p.38 / Chapter 3.4 --- Backbone Conformation --- p.41 / Chapter 3.5 --- UV Melting --- p.43 / Chapter 4.Chapter Four: --- Effect of Spiroiminodihydantoin and 7-hydro-8-oxoguanine on Primer-Template Structures --- p.44 / Chapter 4.1 --- Overview --- p.42 / Chapter 4.2 --- NMR Investigations of the Primer-Template Models --- p.45 / Chapter 4.2.1 --- Incorporation of a dCTP Opposite a 5'-GG Template --- p.45 / Chapter 4.2.2 --- Incorporation of a dCTP Opposite a 5'-G(oG) Template --- p.46 / Chapter 4.2.3 --- Incorporation of a dCTP Opposite a 5'-G(Sp) Template --- p.48 / Chapter 4.2.4 --- Incorporation of a dATP Opposite a 5'-T(oG) Template --- p.50 / Chapter 4.2.5 --- Incorporation of a dATP Opposite a 5'-T(Sp) Template --- p.51 / Chapter 4.3 --- Effect of Sp and oG on Primer-Template Structures --- p.52 / Chapter 4.3.1 --- Misaligned Structure with a Sp-Bulge --- p.52 / Chapter 4.3.2 --- C·oG Base Pair in 5'-G(oG) --- p.54 / Chapter 4.3.3 --- Biological Implications --- p.54 / Chapter 5. --- Chapter Five: Preliminary Structural Calculations on Primer- Template Structures --- p.56 / Chapter 5.1 --- Experimental Restraints Extraction --- p.56 / Chapter 5.2 --- Experimental Restraints Distribution --- p.58 / Chapter 5.3 --- Structural Calculations --- p.60 / Chapter 5.4 --- Structural Results --- p.62 / Chapter 5.4.1 --- 5'-GG --- p.63 / Chapter 5.4.2 --- 5'-G(oG) --- p.64 / Chapter 5.4.3 --- 5'-T(oG) --- p.65 / Chapter 5.4.4 --- 5'-T(SpR) with 5'-T(Spl) Restraints --- p.66 / Chapter 5.4.5 --- 5'-T(SpR) with 5'-T(Sp2) Restraints --- p.67 / Chapter 5.4.6 --- 5'-T(SpS) with 5'-T(Spl) Restraints --- p.68 / Chapter 5.4.7 --- 5'-T(SpS) with 5'-T(Sp2) Restraints --- p.69 / Chapter 5.6 --- Structural Analysis --- p.70 / Chapter 6. --- Chapter Six: Conclusions and Future Work --- p.72 / Appendix --- p.73 / References --- p.74

Symbiosis is commonly present in marine invertebrates. Many corals and sponges have symbiotic algae or bacteria. In the previous studies of the sponge Cinachyra australiensis, 85% of the bacteria associated with the sponge have high similarity (88.65%) with the symbiotic chemoautotrophic sulfur-oxidizing bacteria of the deep-sea hydrothermal vent mussel, Solemya reidi. This study aims to investigate the localization of the chemoautotrophic sulfur-oxidizing bacteria associated with Cinachyra australiensis. The Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) large-subunit genes for autotrophic organisms were amplified by polymerase chain reaction from the sponge samples. The phylogenetic relationship of the RubisCO large subunit genes was analyzed. A total of 26 clones were selected and sequenced. They could be divided into two groups. One (9 clones) belongs to form I type IB (cynobacteria and green algae). The other (17 clones) belongs to form II type IA (chemoautotrophic symbiotic bacteria). The location of the sulfur-oxidizing chemoautotrophic bacteria was shown to be intracellular symbiosis within the mesoglial cells by fluorescence in situ hybridization.

Pharmaceuticals and personal care products (PPCPs) are widely used, resulting in trace amounts being detected in the aquatic environment. This presence is of human health and ecological concern and it is necessary to determine the best methods to eliminate them from our waters. The oxidation of PPCPs by permanganate was evaluated using a spectrophotometer to monitor permanganate reduction. Thirty-nine compounds were chosen to represent numerous classifications, including beta blockers, cephalosporins, fluoroquinolones, macrolides, non-steroidal anti-inflammatory drugs, phenol structures, polypeptides, sulfonamides, tetracyclines, and triazines. The reactivity of each compound was determined by measuring the absorbance of permanganate over time as it reacted with an excess of the compound. The absorbance data was fit to a pseudo-first-order reaction model that accounted for the growth of manganese dioxide colloids. The most reactive groups that reduced permanganate within minutes at pH 7.0 were the cephalosporins, phenol structures, and tetracyclines. The majority of the remaining pharmaceuticals and personal care products were moderately or weakly reactive (reducing permanganate within hours). Caffeine, carbadox, monensin, simetone, and tri(2-carboxyethyl)phosphine were poorly reactive (reducing permanganate over days). Metoprolol was the only selected compound that was determined to be potentially non-reactive (no reaction after 1 day). Polarizability and refractive index of the organic compounds showed significant positive correlations (R-squared > 0.50) with the first-order reaction rates for non-steroidal anti-inflammatory drugs and the phenol structures group. The half-life of each PPCP was determined based on a typical dosage of permanganate used for pre-oxidation. Eleven of the thirty-nine PPCPs had a half-life of less than thirty minutes (a typical contact time), indicating that oxidation by permanganate may be a viable option. There are many opportunities for further research in this area, including investigating more PPCPs, physicochemical property correlations, and the impact of water quality conditions

M. Tech. Metallurgical Engineering. / Investigate the dissolution behaviour of sphalerite minerals in sulphuric acid using ferric ions as oxidants. The specific objectives are to study the following: 1. the mineralogical characteristics of sphalerite ores ; 2. mineralogical effects on dissolution kinetics in sulphuric acid and 3. Effect of ferric ion concentration on the dissolution kinetics of sphalerite ores in sulphuric acid. Mineralogy is a critical area in mineral processing and has to be considered during process design stage, and during each processing stage. The type and concentration of oxidizing agent depend on the mineralogical composition of the ore. Many researchers investigations and test-works have been reported on leaching of sphalerite using both ferric sulphate and ferric chloride (Al-Harahsheh and Kingman, 2007; Rath et al., 1981). However, little or no studies have been reported on the combined oxidants.

Boreal peatlands are important ecosystems to the global carbon cycle. Although they cover only 3% of the earth's land surface area, boreal peatlands store roughly one third of the world's soil carbon. Peatlands also comprise a large natural source of methane emitted to the atmosphere. Some methane in peatlands is oxidized before escaping to the atmosphere by aerobic methane oxidizing bacteria. With changing climate conditions, the fate of the stored carbon and emitted methane from these systems is uncertain. One important step toward better understanding the effects of climate change on carbon cycling in peatlands is to ascertain the microorganisms actively involved in carbon cycling. To investigate the active aerobic methane oxidizing bacteria in a boreal peat bog, a combination of microcosm experiments, DNA-stable isotope probing, and next generation sequencing technologies were employed. Studies were conducted on samples from the S1 peat bog in the Marcell Experimental Forest (MEF). Potential rates of methane oxidation were determined to be in the range of 13.85 to 17.26 μmol CH₄ g dwt⁻¹ d⁻¹. After incubating with ¹³C-CH₄, DNA was extracted from these samples, separated into heavy and light fractions with cesium chloride gradient formation by ultracentrifugation and needle fractionation, and fractions were fingerprinted with automated ribosomal intergenic spacer analysis (ARISA) and further interrogated with qPCR. Based on ARISA, distinct banding patterns were observed in heavy fractions in comparison to the light fractions indicating an incorporation of ¹³C into the DNA of active methane oxidizers. This was further supported by a relative enrichment in the functional gene pmoA, which encodes a subunit of the particulate methane monooxygenase, in heavy fractions from samples incubated for fourteen days. Within heavy fractions for samples incubated for 8 and 14 days, the relative abundance of methanotrophs increased to 37% and 25%, respectively, from an in situ abundance of approximately 4%. Phylogenetic analysis revealed that the methanotrophic community was composed of both Alpha and Gammaproteobacterial methanotrophs of the genera Methylocystis, Methylomonas, and Methylovulum. Both Methylocystis and Methylomonas have been detected in peatlands before, however, none of the phylotypes in this study were closely related to any known cultivated members of these groups. These data are the first to implicate Methylovulum as an active methane oxidizer in peatlands, though this organism has been detected in another cold aquatic ecosystem with consistent methane emissions. The Methylovulum sequences from this study, like Methylocystis and Methylomonas, were not closely related to the only cultivated member of this genus. While Methylocystis was dominant in ¹³C-enriched fractions with a relative abundance of 30% of the microbial community after an eight-day incubation, Methylomonas became dominant with a relative abundance of approximately 16% after fourteen days of incubation. The relative abundance of Methylovulum was maintained at 2% in ¹³C- enriched fractions after eight and fourteen days.

Thesis (PhD) -- Macquarie University, Division of Environmental and Life Sciences, Dept. of Chemistry and Biomolecular Sciences, 2007. / Bibliography: leaves 295-322.

Nitrification, a key step in biological nitrogen removal processes, is the oxidation of ammonia into nitrate performed by ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) under aerobic condition. Researchers have focused on factors affecting the performance of nitrification for decades, but the inorganic carbon limitation on nitrification had been neglected. However, the increase in nitrogen in wastewater has increased the need to evaluate and improve our understanding of this limitation. In a previous research, the hypothesis that different inorganic carbon concentrations would enrich different AOB populations has been examined. In this study, the focus was on the effect of inorganic carbon concentration on NOB, which has a close relationship with AOB. Two 5L lab–scale continuous–flow stirred tank reactors (CSTR) were operated to evaluate the nitrification performance and microbial ecology of nitrifier populations acclimated under inorganic carbon sufficient (high–IC) and limited (low–IC) conditions for approximately 700 days. During the operation period, both bioreactors were able to maintain satisfactory nitrification efficiency higher than 95% at an influent ammonium concentration of 250 mg–N/L. Nitrate was the major end product and no significant nitrite accumulation was observed. To evaluate the effects of inorganic carbon on NOB community structures, cloning/sequencing and real–time PCR were applied to target and quantify the two common NOB genera, Nitrospira and Nitrobacter, as no molecular probe targeting all known NOB is available presently. The results showed that these two genera were both found in the two reactors. Nitrospira was the dominant NOB population in the high–IC bioreactor, while Nitrobacter was dominant in the low–IC one after one year acclimation. Kinetic analysis revealed that NOB enriched in the two reactors have different kinetic performances. However, IC concentration did not show a significant impact on the nitrite oxidizing kinetics of NOB in the batch tests.

The weathering of shales is a globally important process affecting both natural and built environments. Shales form roughly 70 % of worldwide sedimentary rock deposits and therefore the weathering of these rocks has substantial effects on the geochemical cycling of elements such as carbon, iron and sulfur. Microbes have been shown to play a key role in weathering shales, primarily through the oxidation of the iron and sulfur of embedded pyrite and the resultant production of sulfuric acid. Despite significant interest in the microbial weathering of shales within industrial sectors such as biohydrometallurgy and civil engineering, comparatively few studies have investigated microbial shale weathering in natural environments. Furthermore, the role of microbes in natural shale weathering processes beyond iron oxidation has largely remained unexplored. In this thesis, the weathering capabilities of microbial communities from natural weathered shale was investigated. The North Yorkshire coastline was used as a study location, due to the abundance and diversity of natural cliffs and historic, disused industrial sites. Cliff erosion and recession on the North Yorkshire coastline is a major concern for local authorities and is the focus of current research. The aim of this work has been to evaluate microbial shale weathering processes within these environments, and hypothesise the possible contribution they may have to erosive processes. Phenotypic plate assays inoculated with weathered shale material were used to obtain rock weathering bacterial isolates that tested positive for a specific weathering phenotype, such as iron oxidation or siderophore production. Subsequent 16S rRNA sequencing enabled genera level identification, revealing 15 genera with rock weathering capabilities with several being associated with multiple weathering phenotypes including Aeromonas sp., Pseudomonas sp. and Streptomyces sp. Shale enrichment liquid cultures were incubated with shale rock chips to simulate natural biological weathering conditions, and the concentration of rock-leached elements in the fluid measured. No evidence of microbially-enhanced leaching was found consistently for any element, however the significant reduction in leachate iron concentration under biological conditions indicates that iron precipitation occurred via microbial iron oxidation. Enrichment cultures inoculated with weathered shale and containing organic matter (OM) rich rocks in water or M9 medium, both liquids lacking an organic carbon source, were grown over several months. The cultures yielded microbial isolates that could utilise rock bound OM sources and one bacterial isolate, Variovorax paradoxus, was taken forward for ecophysiological study. The shale rock that the organism was isolated from, along with other OM rich rocks (mudstones and coals), elicited complex responses from V. paradoxus including enhanced growth and motility. Finally, mineral microcosms in vitro and mesocosms in situ investigated microbial colonization and weathering of shale-comprising minerals (albite, calcite, muscovite, pyrite and quartz). Microcosms were established using iron oxidizing enrichment cultures, as based on the results of the simulated rock weathering experiments, while the in situ mesocosms were buried within weathered shale scree within a disused mine level. Levels of colonization significantly varied between minerals within the microcosms (pyrite > albite, muscovite > quartz > calcite). Although differences in mineral colonization were seen in the mesocosms, they did not match those in the microcosms and were not statistically significant. Pyrite incubated in the microcosms became significantly weathered, with extensive pit formation across the mineral surface that is consistent with microbial iron oxidation. In the mesocosms, pit formation was not identified on pyrite surfaces but dark etchings into the pyrite surface were found underneath fungi hyphal growth. The results of this thesis highlights that a range of microbial rock weathering mechanisms are abundant across weathered shale environments. Microbial iron oxidizing activity was a dominant biogeochemical process that altered rock-fluid geochemistry and weathered pyrite surfaces. However, the impact on rock or mineral weathering of other microbial mechanisms was not elucidated by this work. Given the known capabilities of these mechanisms, the conditions under which they are active may not have been met within the experimental setup used. Microbial iron oxidation in shale and shale-derived materials has previously been demonstrated to weaken rock structure through acid production and secondary mineral formation. From the results of this thesis, it is clear that microbial iron oxidation is an active process within some of the weathered shale environments studied, including cliff surfaces. Therefore, it can be hypothesised that microbial activity could play a role in structurally weakening shale rock within cliffs and accelerate their erosion. Future work should attempt to quantify the rate and extent of microbial iron oxidizing activity within shale cliff environments and investigate its contribution to erosive processes.

Dans le but de réduire la consommation en carburant, les émissions de CO2 et les polluants tout en maintenant le haut rendement des moteurs, de nouveaux modes de combustions ont été étudiés et sont d’excellents candidats pour remplacer les moteurs conventionnels. En particulier, le mode HCCI a montré une excellente aptitude pour répondre à ces objectifs. Néanmoins, en dépit de ses avantages, de nombreux challenges sont à surmonter avant de permettre le développement de tels moteurs. Parmi eux, obtenir un contrôle efficace de la totalité de ce processus de combustion sur un large domaine d’utilisation demeure le principal défi. Ces travaux de thèse s’intéressent à l’utilisation des espèces chimiques oxydantes comme un moyen robuste de contrôle de la combustion HCCI. En raison de ces fortes propriétés oxydantes, l’ozone a été la principale molécule étudié. De plus, son intérêt est renforcé par le fait que l’ozone peut être produit au sein d’un véhicule au moyen de petits générateurs, mais cela peut aussi produire des oxydes d’azote. Ces recherches ont été effectuées au moyen d’un banc moteur monocylindre HCCI et couplées avec des simulations de cinétique chimique. Les deux principaux objectifs ont été : (1) Evaluer le potentiel d’utilisation d’un générateur d’ozone pour contrôler la combustion HCCI. L’impact de plusieurs espèces chimiques oxydantes, ozone and NOx, a été étudié sur la combustion de l’isooctane. De plus, un contrôle dynamique a été mis en place avec succès. (2) Comparer l’influence de l’ozone sur la combustion de l’isooctane et de carburants alternatifs. Des carburants à forte teneur en méthane et des alcools ont été étudiés en raison de leur forte résistance à l’autoinflammation et de leur structure chimique. / To reduce the fuel consumption, CO2 emissions and pollutant emissions while keep improving thermal efficiency of engines, alternative combustion modes are being investigated as good candidates to replace spark-ignited and diesel engines. In particular, Homogeneous Charge Compression Ignition (HCCI) engines have proven their potential to meet these requirements. However, despite of these advantages, several challenges remain to be addressed prior to the widespread implementation of HCCI engines. Among them, the control of the overall combustion process in such an engine over the full operating range is still considered as the main challenge to overcome. The present work introduces the use of oxidizing chemical species seeded in the intake system as a robust control technique for HCCI combustion process. In particular, ozone was examined due to its strong oxidizing characteristics. Moreover, ozone can be easily produced on-board a real vehicle from the intake oxygen thanks to small ozone generators, but can also lead to the production of NOx. Investigations were carried out using a single-cylinder HCCI engine and kinetics computation analysis. The two main objectives of this work are: (1) Evaluate the potential of using ozone generator to control the HCCI combustion. Along these lines, the interaction between NOx and ozone was investigated for isooctane as fuel and a real time control of the HCCI combustion was implemented and successfully tested. (2) Compare the influence of ozone on the combustion of isooctane and alternative fuels. Methane-based fuels (methane/propane and methane/hydrogen mixtures) and alcohols (methanol, ethanol, n-butanol) were selected due to their higher resistance to autoignition and their different chemical structure.