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Oleaginous yeasts are able to produce a high percentage of their weight as lipids, which can be used as the starting material for biodiesel production, producing a fuel with many of the same properties as petroleum-based diesel. The objective of this research was to compare three oleaginous yeast species, Rhodosporidium babjevae, Rhodosporidium diobovatum, and Yarrowia lipolytica to determine which species would be the best candidate for larger-scale production. Following the comparison work, it was determined that R. diobovatum was the best candidate for scale-up. Subsequent experiments used batch cultures in bioreactors at a volume of 3.5 L, followed by a 25x fold increase to 90 L production. The results of this scale-up showed that the high levels of production and growth continued in a reactor system. As such, R. diobovatum could be a possible organism to use in the production of lipids from waste glycerol for biodiesel production. / October 2015

Consolidated bioprocessing is a one-step process that allows the direct microbial conversion of cellulosic substrates to ethanol and hydrogen. The fermentation was initially performed in batch cultures, in a pH and temperature controlled reactor using Clostridium thermocellum ATCC 27405. With an objective of increasing the production of ethanol and hydrogen, various types of fed-batch fermentations were investigated: variable volume (VV) fed-batch, fixed volume (FV) fed-batch, and semi-continuous fermentation. Semi-continuous processes were carried out at low (10-15 g/L) and high (20-25 g/L) cellulose concentrations. The maximum ethanol production obtained in batch, VV, FV, semi-continuous with low concentrations and high concentrations were 554 mmol, 336 mmol, 477 mmol, 695 mmol and 741 mmol respectively. In the same order, the total hydrogen production was 288 mmol, 364 mmol, 231 mmol, 434 mmol, and 387 mmol. Overall, the semi-continuous fermentation showed more promise in terms of large-scale deployment compared to batch, VV, and FV fed-batch. / October 2015

<p>The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.</p><p>Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.</p><p>In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.</p><p>&#8232;For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of <italic>Escherichia coli</italic> K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 <underline>+</underline> 13.2 and 38.2 <underline>+</underline> 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.</p><p>Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of <italic>E. coli</italic> K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h<super>-1</super>, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 10<super>8</super> PFU/mL and 10<super>8</super> CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.</p><p>In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.</p><p>Finally, for an industrial application, the use of phages to inhibit invasive <italic>Lactobacilli</italic> in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of <italic>Lactobacillus plantarum</italic> during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.</p><p>In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.</p> / Dissertation

Thesis (DTech (Chemistry))--Cape Peninsula University of Technology, 2005 / A 2-factorial experiment, involving 3 levels of phosphorus (0, 40, and 80 kg P.ha-I ) as main treatment and 4 cropping systems (mono crop, maize/cowpea inter-row, maize/cowpea intra-row, and maize/cowpea intra-hole cropping) as sub-treatment was conducted in the field for 2 consecutive years in 2003 and 2004 to assess i) the effects of exogenous P supply and cropping system on the concentrations of plant-available nutrients in the rhizosphere of cowpea and maize; ii) the effect of exogenous P supply on tissue concentrations of minerals in nodulated cowpea and maize in mixed plant cultures iii) the effects of exogenous P supply and cropping system on plant growth and N2 fixation, and iv) the effects of exogenous P supply and cropping system on phosphatase activity and microbial biomass in the rhizosphere of cowpea and maize. At harvest, it was found that applying 40 or 80 kg P.ha-I significantly increased cowpea grain yields by 59-65% in 2003 and 44-55% in 2004. With maize, the increases in grain yield were 2037% in 2003 and 48-55% in 2004 relative to zero-P control. In both cropping seasons, the number of pod-bearing peduncles per plant, the number of pods per plant, the number of seeds per pod, and seed yield per cowpea plant were significantly increased with the application of exogenous P. In contrast, these parameters were all significantly depressed by mixed culture relative to mono crop cowpea. Intercropping maize with cowpea produced higher total yields per unit land area than the sole crop counterpart.

by Hon-chiu Leung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1991. / Bibliography: leaves 122-126. / Abstract --- p.i / Acknowledgement --- p.iv / Dedication --- p.v / Table of Contents --- p.vi / Introduction --- p.1 / Literature Review --- p.4 / Chapter 1) --- Ethanol production in bacteria / Chapter 1.1) --- Zymomonas mobilis --- p.4 / Chapter 1.2) --- Clostridium species --- p.7 / Chapter 1.3) --- "Enterobacter, Klebsiella, Serritia and Erwinia sp" --- p.9 / Chapter 1.4) --- Escherichia coli and Salmonella typhimurium --- p.10 / Chapter 2) --- Pyruvate decarboxylase of Z. mobilis / Chapter 2.1) --- Enzyme properties --- p.13 / Chapter 2.2) --- Cloning and expression of pdc gene --- p.15 / Chapter 3) --- Alcohol dehydrogenase (adh) gene / Chapter 3.1) --- "Cloning, chararterization and expression of adh genes" --- p.17 / Chapter 4) --- Gene transfer systems in Vibrio species --- p.21 / Chapter 5) --- Rationale and objectives of this study --- p.22 / Chapter Part I) --- Ethanol Production in terrestrial enteric bacteria / Chapter A) --- Introduction --- p.24 / Chapter B) --- Materials and Methods / Chapter 1) --- Bacterial strains and plasmids --- p.25 / Chapter 2) --- Media --- p.26 / Chapter 3) --- Solutions --- p.27 / Chapter 4) --- Isolation of plasmids / Chapter 4.1) --- Small Scale Isolation of plasmids --- p.30 / Chapter 4.2) --- Large Scale Isolation of plasmids --- p.32 / Chapter 5) --- Construction of a broad-host-range plasmid harbouring Zymomonas mobilis genes --- p.35 / Chapter 6) --- Transformation --- p.35 / Chapter 7) --- High Performance Liquid Chromatography of Organic Acids --- p.36 / Chapter 8) --- Maintenace of plasmids harbouring the genes of Zymomonas mobilis genes --- p.38 / Chapter 9) --- Ethanol tolerance of S. typhimurium strains --- p.38 / Chapter C) --- Results / Chapter 1) --- Construction of Salmonella typhimurium strains harbouring Z. mobilis genes --- p.39 / Chapter 2) --- Fermentative end products in culture medium --- p.48 / Chapter 3) --- Growth of hosts and transformants --- p.61 / Chapter 4) --- Ethanol tolerance of S. typhimurium strains --- p.65 / Chapter 5) --- Maintenance of plasmids --- p.67 / Chapter 6) --- Construction of broad-host-range plasmid harbouring Z. mobilis genes --- p.69 / Chapter D) --- Discussions / Chapter 1) --- Comparison of ethanol production in Escherichia coli and Salmonella typhimurium --- p.72 / Chapter 2) --- Ethanol tolerance of S. typhimurium strains --- p.74 / Chapter 3) --- Maintenance of plasmids --- p.76 / Chapter 4) --- Construction of broad-host-range plasmids harbouring Z. mobilis genes --- p.78 / Chapter Part II) --- Ethanol Production in marine enteric bacteria / Chapter A) --- Introduction --- p.79 / Chapter B) --- Materials and Methods / Chapter 1) --- Bacterial strains and plasmids --- p.80 / Chapter 2) --- Media --- p.80 / Chapter 3) --- Solutions --- p.80 / Chapter 4) --- Routine Identification Processes --- p.81 / Chapter 5) --- Systematic studies by Arbitrarily- Primed Polymerase Chain Reaction --- p.86 / Chapter 6) --- Optimal growth conditions --- p.88 / Chapter 7) --- Isolation of broad-host-range plasmid pIOl ( 64kb) --- p.89 / Chapter 8) --- Transformation of Vibrio sp. strain 60 --- p.90 / Chapter 9) --- Production of ethanol using different carbon sources in fermentation --- p.91 / Chapter C) --- Results / Chapter 1) --- Identification of Vibrio sp. strain 60 --- p.92 / Chapter 2) --- Optimal growth conditions --- p.101 / Chapter 3) --- Isolation of high molecular weight plasmid --- p.105 / Chapter 4) --- Ethanol production from different carbon sources --- p.107 / Chapter 5) --- Ethanol tolerance of Vibrio sp. strain 60 --- p.109 / Chapter 6) --- Salt tolerance of Vibrio sp. strain 60 --- p.111 / Chapter 7) --- Transformation of Vibrio sp. strain 60 --- p.113 / Chapter D) --- Discussions / Chapter 1) --- Strain identification by arbitrarily-primed PCR --- p.116 / Chapter 2) --- Isolation of high molecular weight plasmid --- p.118 / Chapter 3) --- Ethanol production of Vibrio sp. strain60 --- p.120 / References --- p.122

腐乳是中國傳統的黃豆發酵類製品，口感柔滑，風味獨特，與西方的芝士相似。多個世紀以來一直是中國的特色配菜和開胃小吃。以往對腐乳的研究只限於使用水蒸氣蒸餾法，溶劑抽提法，超臨界萃取法以及頂空萃取法提取其揮發性化合物，但它們卻有準備時間長、可能產生製造物、較低靈敏度、使用有機溶劑或需要精密的設備等的缺點。而固相微萃取方法(SPME)是集取樣、提取、濃縮三個步驟為一的提取方法。這是一個簡單、快速、溫和而且有相對靈敏度較高的方法。因此，這項研究的主要目標是開發一個快速的頂空固相微萃取方法，並配合氣相色譜-質譜聯用方法來提取和鑒定巿面上白腐乳的揮發性物質，並研究白腐乳整個發酵週期的理化的變化。 / 第一部份的研究首先對固相微萃取塗層(萃取頭)，提取溫度，提取時間，鹽濃度和水含量等參數進行優化。優化條件的結果如下:(1)樣本對鹽溶液(NaCl溶液(25%飽和濃度))的比例為1:2(w/v)，(2)用Divinylbenzene/Carboxen/ Polydimethylsiloxane 塗層的萃取頭，(3)在55°C的水浴進行30分鐘提取。 / 第二部份的研究是用氣相色譜-質譜聯用方法分析利用以上的方法提取的三種商業白腐乳的揮發性化合物。結果在三個樣品中共檢測出131揮發性化合物。樣品A、B和C，分別檢測出112、112和118種成份，他們均屬於不同的官能團。三種腐乳共有76種相同的化合物。其中包括11種由Chung等人於2005年確定的重要香味化合物。而醇類和酯類化合物的含量最為豐富。另外，許多酯類，醛類和芳香烴化合物都是首次在腐乳中發現的。總括而言，該部份實驗成功開發了一種廉價且溫和的提取技術，讓我們可以簡單及快速地從檢定出腐乳中多種揮發性化合物。 / 研究的最後部份是針對商業白腐乳在發酵(腐乳坯期)和老化(後加入紅酒和鹽水)時，揮發性化合物的種類及濃度和理化參數的變化進行了研究。結果顯示，主要的化學成分的濃度是在發酵及熟成過程中増加，同時新的化合物亦不斷地形成。由腐乳坯階段至36小時、60天、120天和180天的發酵期，分別有37、58、69、83和86種化合物形成。其中酯類及吡嗪佔大多數，其濃度亦不斷地增加。而且，大部份的重要香味化合物的濃度亦顯著地增加。另外，許多在黃酒和芝麻油檢測出來的揮發物也可以從腐乳中找到的。理化分析的結果顯示，水分含量沒有顯著變化，但蛋白質的含量在熟化期的首四個月顯著下降。相反，灰含量則在四個月顯著地增加。此研究為腐乳發酵和熟化過程中的揮發性成分和化學成分的變化提供了更多的資料，然而要進一步了解腐乳發酵對味道和口感的影響則需要更多感官測試方面的研究。 / Sufu is a traditional Chinese fermented product with a soft creamy cheese-like texture and a unique flavour. It has been widely consumed in China as an appetizer for centuries. Previous investigations on its volatile compounds using simultaneous steam distillation and solvent extraction (SDE), supercritical fluid extraction (SFE) or headspace extraction may suffer from drawbacks such as artifact formation, the use of organic solvents and the need for sophisticated equipment. An alternative Solid-phase Microextraction (SPME) method integrates sampling, extraction, concentration into a single step method. However, this technique is highly sensitive to experimental conditions, careful optimization would be required to ensure a good extraction performance. / Our primary objective in this study was to develop a quick volatile profiling method using the Headspace - Solid-phase Microextraction - Gas Chromatography/Mass Spectrometry (HS-SPME-GC/MS) for subsequent studies on commercial products and their changes throughout the fermentation and ageing periods. Parameters including stationary phase (fiber coating), extraction temperatures, exposure times, concentration of salt and water content were optimized. / The optimal conditions found using the Divinylbenzene/Carboxen/ Polydimethylsiloxane (DVB/CAR/PDMS) fiber for sufu sample are (1) sample to 25% of (saturated) NaCl solution is 1:2 (w/v), (2) 30 min of extraction time at 55°C water bath. / The developed method was applied to study the volatile profile of three commercial brands of plain sufu. In total, 131 volatile compounds were detected in the headspace of the examined samples. Samples A, B and C have totals of 112, 112 and 118 compounds, respectively, and they belong to various chemical groups. Seventy-six compounds were found in common among the commercial samples. These included 11 out of the 14 aroma-impact compounds previously identified by Chung et al., 2005. Quantitatively, alcohols and esters were among the most abundant groups of compound found. Many esters, aldehydes and aromatic hydrocarbons compounds were first reported in this study. The results obtained by SPME were comparable to those obtained by SFE and SDE methods and at the same time it is cheaper and less labor intensive method in terms of the extraction and clean-up steps. In short, the developed HS-SPME method is an inexpensive, simple, rapid and mild extraction technique which allows the detection of a wide range of volatiles from sufu. / In the final part of the study, the changes of volatile profile and the physicochemical parameters of a commercially produced plain sufu were studied throughout its fermentation (pehtze period) and ageing (after wine & brine added) processes. The volatile profiles of the key ingredients, namely, yellow rice wine and sesame seed oil were also studied. In general, all the major chemical groups experienced an increase in concentration during ageing. Many new compounds were formed in the first few months of ageing. A total of 37, 58, 69, 83 and 86 compounds were identified in pehtze stage, days 0 (36 hour since bottling), 60, 120 and 180, respectively. Esters and pyrazines account for most of the quality difference. Their concentrations increased throughout the ageing period. Concentration for most of the aroma-impact compounds increased significantly throughout ageing. Many of the volatiles detected in the yellow rice wine and the sesame oil were found in common with the ageing or matured sufus (6th month). Proximate analysis showed that there were no significant changes in moisture content but a significant decline in both the lipid, protein contents were observed. On the other hand, the ash content was significantly increased in the first four months, but leveled off afterwards. While this study provides some more information to understand the changes in both volatile components and chemical composition during the fermentation and ageing processes, further studies will be needed to explain the flavour and textural changes. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Chiang, Tsz Kei Jackie. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 153-195). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese. / Thesis Committee / Acknowledgements / Abstract --- p.I / 摘要 --- p.IV / Table of Contents --- p.VI / List of Tables --- p.XI / List of Figures --- p.XII / List of Abbreviations --- p.XIV / Chapter Chapter 1 --- Literature Review --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Sufu --- p.3 / Chapter 1.2.1 --- History and Background of Sufu --- p.3 / Chapter 1.2.2 --- Sufu Classification --- p.5 / Chapter 1.2.2.1 --- White Sufu --- p.5 / Chapter 1.2.2.2 --- Red Sufu --- p.5 / Chapter 1.2.2.3 --- Grey Sufu --- p.6 / Chapter 1.2.2.4 --- Other Types --- p.6 / Chapter 1.2.3 --- Manufacturing of Sufu --- p.7 / Chapter 1.2.4 --- Microbes Used in Sufu Fermentation --- p.10 / Chapter 1.2.5 --- Biochemical Changes during Sufu Ageing --- p.10 / Chapter 1.2.5.1 --- Protein Faction --- p.11 / Chapter 1.2.5.2 --- Lipid Fraction --- p.12 / Chapter 1.2.5.3 --- Carbohydrate Fraction --- p.12 / Chapter 1.2.6 --- Flavour Origin of Sufu --- p.13 / Chapter 1.2.7 --- Volatile Components of Sufu --- p.14 / Chapter 1.2.7.1 --- Alcohols --- p.14 / Chapter 1.2.7.2 --- Esters --- p.15 / Chapter 1.2.7.3 --- Aldehydes --- p.16 / Chapter 1.2.7.4 --- Furans --- p.17 / Chapter 1.2.7.5 --- Ketones --- p.17 / Chapter 1.2.7.6 --- Sulphur-containing Compounds --- p.18 / Chapter 1.2.8 --- Aroma-impact Compounds --- p.20 / Chapter 1.2.8.1 --- Aroma-impact Compounds in Sufu --- p.23 / Chapter 1.3 --- Flavor Extraction Techniques --- p.23 / Chapter 1.3.1 --- Headspace Methods --- p.24 / Chapter 1.3.1.1 --- Static Headspace Sampling --- p.25 / Chapter 1.3.1.2 --- Dynamic Headspace Sampling --- p.25 / Chapter 1.3.2 --- Solvent Extraction --- p.26 / Chapter 1.3.3 --- Steam Distillation Techniques --- p.27 / Chapter 1.3.3.1 --- Simultaneous Steam Distillation and Solvent Extraction (SDE) --- p.27 / Chapter 1.3.3.2 --- High-vacuum Distillation Techniques --- p.28 / Chapter 1.3.4 --- Supercritical Fluid Extraction Methods (SFE) --- p.28 / Chapter 1.3.5 --- Solid-phase Extraction (SPE) --- p.30 / Chapter 1.3.6 --- Solid-phase Microextraction (SPME) --- p.31 / Chapter 1.4 --- Objectives --- p.35 / Chapter Chapter 2 --- Optimization of Headspace Solid-phase Microextraction Conditions for the Determination of Volatile Compounds in Sufu --- p.36 / Chapter 2.1 --- Introduction --- p.36 / Chapter 2.2 --- Materials and Methods --- p.40 / Chapter 2.2.1 --- Materials --- p.40 / Chapter 2.2.1.1 --- Commercial Plain Sufu --- p.40 / Chapter 2.2.1.2 --- SPME Accessories --- p.40 / Chapter 2.2.2 --- Sample Preparation --- p.41 / Chapter 2.2.3 --- Optimization of Sample Preparation Method for HS-SPME-GC/MS Analysis --- p.41 / Chapter 2.2.3.1 --- Effect of Ionic Strength (NaCl Concentration) --- p.42 / Chapter 2.2.3.2 --- Optimization of Water Content --- p.42 / Chapter 2.2.4 --- Optimization of the Extraction Conditions for HS-SPME- GC/MS Analysis --- p.42 / Chapter 2.2.4.1 --- HS-SPME Procedures --- p.43 / Chapter 2.2.5 --- Gas Chromatography/Mass Spectrometry (GC/ MS) Conditions --- p.43 / Chapter 2.2.6 --- Identification and Quantification of Selected Volatiles in Sufu --- p.44 / Chapter 2.3 --- Results and Discussions --- p.46 / Chapter 2.3.1 --- Method Development --- p.46 / Chapter 2.3.1.1 --- Choice of Fibers --- p.46 / Chapter 2.3.1.2 --- Effect of Time --- p.48 / Chapter 2.3.1.3 --- Effect of Temperature --- p.49 / Chapter 2.3.1.4 --- Effect of Ionic Strength (NaCl Concentration) --- p.51 / Chapter 2.3.1.5 --- Effect of Water Content --- p.52 / Chapter 2.3.2 --- Application of the HS-SPME-GC/MS Method for the Analysis of Sufu Volatiles --- p.61 / Chapter 2.3.2.1 --- Alcohols --- p.62 / Chapter 2.3.2.2 --- Aldehydes --- p.63 / Chapter 2.3.2.3 --- Aliphatic Hydrocarbons --- p.64 / Chapter 2.3.2.4 --- Aromatic Hydrocarbons --- p.65 / Chapter 2.3.2.5 --- Esters --- p.67 / Chapter 2.3.2.6 --- Furans --- p.69 / Chapter 2.3.2.7 --- Ketones --- p.70 / Chapter 2.3.2.8 --- Pyrazines --- p.71 / Chapter 2.3.2.9 --- Sulphur-containing Compounds --- p.73 / Chapter 2.3.3 --- Comparison of Different Extraction Techniques --- p.74 / Chapter 2.4 --- Conclusion --- p.86 / Chapter Chapter 3 --- Changes in Volatile Constituents and Physicochemical Characteristics of Commercial Plain Sufu throughout the Fermentation and Ageing Process --- p.87 / Chapter 3.1 --- Introduction --- p.87 / Chapter 3.2 --- Materials and Methods --- p.90 / Chapter 3.2.1 --- Sufu Sampling --- p.90 / Chapter 3.2.2 --- Flavour Analysis --- p.90 / Chapter 3.2.2.1 --- Sample Preparation --- p.90 / Chapter 3.2.2.2 --- Solid-phrase Microextraction (SPME) --- p.91 / Chapter 3.2.2.3 --- Gas Chromatography/ Mass Spectrometry (GC/ MS) Conditions --- p.92 / Chapter 3.2.2.4 --- Identification and Quantification of Selected Volatiles in Sufu --- p.93 / Chapter 3.2.3 --- Proximate Analysis --- p.93 / Chapter 3.2.4 --- Statistical Analysis --- p.94 / Chapter 3.3 --- Results and Discussions --- p.95 / Chapter 3.3.1 --- Overall Finding --- p.95 / Chapter 3.3.2 --- Flavour Analysis of Sufu at Different Fermentation and Ageing Stages --- p.97 / Chapter 3.3.2.1 --- Alcohols --- p.97 / Chapter 3.3.2.2 --- Aldehydes --- p.99 / Chapter 3.3.2.3 --- Esters --- p.101 / Chapter 3.3.2.4 --- Furans --- p.104 / Chapter 3.3.2.5 --- Ketones --- p.105 / Chapter 3.3.2.6 --- Pyrazines --- p.107 / Chapter 3.3.2.7 --- Sulphur-containing Compounds --- p.108 / Chapter 3.3.2.8 --- Miscellaneous Compounds --- p.110 / Chapter 3.3.2.9 --- Aroma-impact Compounds --- p.111 / Chapter 3.3.3 --- Potential Volatile Flavour Contributors from the Key Ingredients (Yellow Rice Wine and Sesame Seed Oil) --- p.112 / Chapter 3.3.3.1 --- Volatile Compounds in Yellow Rice Wine --- p.113 / Chapter 3.3.3.2 --- Volatile Compounds in Sesame Seed Oil --- p.114 / Chapter 3.3.4 --- Proximate Composition of Sufu at Different Fermentation and Ageing Stages --- p.115 / Chapter 3.3.5 --- Overall Discussion --- p.144 / Chapter 3.4 --- Conclusion --- p.146 / Chapter Chapter 4 --- OverallConclusion --- p.148 / Chapter 4.1 --- Conclusions and Significance of the Study --- p.148 / Chapter 4.2 --- Future Work --- p.151 / References --- p.153 / Chapter Appendix A --- p.196 / Chapter Appendix B --- p.199

The main aim of this research was to utilise whey as a fermentation substrate for the production of microbial biopolymers.Of the three commercial biopolymer producers tested for biopolymer production in whey, only Pseudodomonas elodea produced significant apparent viscosities of up to 470cP at 2 s-1 on enriched whey broths. In these broths lactose utilisation was poor (14% w/v). A strain of P. elodea that had improved lactose utilising capacity was selected after six serial transfers on whey and lactose rich broths. After screening more than 60 bacterial isolates, a strain of Klebsiella oxytoca that initially produced a broth apparent viscosity of 36 cP at 12 s-1 in whey was isolated from raw milk. Biopolymer production was optimised in the K. oxytoca isolate.Concentrations of over 16 g/1 and broth apparent viscosities greater than 20,000 cP at 0.6 s-1 were obtained after optimisation. The biopolymer produced by the K. oxytoca isolate was shown to contain rhamnose, glucose and cellobiose, a composition not comparable to any reported polysaccharide. Polymer application studies indicated that it had potential to be used as a thickener, stabiliser, and binder. / Doctor of Philosophy (PhD)

To provide a possible alternative for the antimicrobial action of sulfur dioxide in winemaking, and address the issue of stuck fermentations, I studied the efficacy of chicken lysozyme (EC 3.2.1.17) as an antimicrobial in grape juice. Two different forms of lysozyme were used: native lysozyme (NL), that is known to be an effective inhibitor of lactic acid bacteria in wine, and partially unfolded lysozyme (PUL), that has been reported to have antimicrobial activity against both Gram-positive and Gram-negative bacteria. Lactobacillus kunkeei and Acetobacter pasteurianus, two bacteria associated with the induction of stuck fermentations were used in the experiments. Chardonnay and Pinot Noir juices were inoculated with L. kunkeei and two days later with yeast strain EC1118 and then incubated for 10 days. The addition of 250ppm of either NL or PUL reduced populations of L. kunkeei to less than 10 CFU/mL in 24 hours while in inoculated grape juice that did not contain any lysozyme, the bacteria grew to 10⁹ CFU/mL within two days. Grape juices supporting the growth of L. kunkeei developed up to 14 times more volatile acidity (VA) than the control or either of the lysozyme treatments. No differences were observed in the antimicrobial action of NL and PUL or in their effects on the composition of the wine. / Graduation date: 2002

Eight cecally fistulated geldings were used in a randomized 4 x 4 Latin square design to observe the effect varying levels of dietary starch had on cecal environment. The 4 treatment rations contained 2 g starch/kg BW (Diet 2), 4 g/kg BW (Diet 4), 6 g/kg BW (Diet 6), or 8 g/kg BW (Diet 8). The rations were comprised of a commercial pelleted feed to meet 2 g starch/kg BW in each treatment, with ground corn used to fulfill the remaining starch requirements in each diet. Soybean meal was added to ensure diets were iso-nitrogenous, and cottonseed hulls were used to equalize dry matter intake. A 21 day adaptation period was allowed before cecal contents were sampled. Samples were drawn 4 hours after the morning meal and were immediately tested for pH. Samples were used to count total anaerobic bacteria and lactic acid bacteria, as well as determine methane activity, ammonia activity, volatile fatty acids, and in vitro dry matter digestibility (IVDMD). Stoichiometric calculations were performed to give an indirect measure of fermented hexose, methane, and carbon dioxide. Diet did not influence dry matter intake (DMI), however it did have an effect on starch intake (P < 0.0001) and caused a linear increase in starch consumption as the amount of offered starch increased (P < 0.0001). Diet did not influence the pH of the cecum (P > 0.05), although a tendency for a linear decrease (P < 0.06) in pH from 6.92 ? 6.58 occurred when dietary starch increased. Total anaerobic bacteria and lactic acid bacteria were unaffected by treatment diets (P > 0.05). Propionate production was affected by dietary treatment (P < 0.05), causing a quadratic increase (P = 0.04) from 8.26 to 14.13 mM as starch in the diets increased. Diet did not affect the production of acetate, butyrate, or ammonia (P > 0.05). Results found that stoichiometric calculations and IVDMD values were not affected by diet (P > 0.05). These results show that starch intake influenced the production of fermentative by-products, which caused decreases in pH, although there was no observed increase in the bacterial populations of the cecum.