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Essential oils are natural products used to flavor food and beverages. With the increase in nutrition conscious consumers, manufacturers of food additives and food products are faced with the challenge of making healthy alternatives. In particular, food products going to market with label claims stating reductions in sugar and salt, organic certified, organic compliant, and all natural; moreover the ingredients used in flavors must meet these label claims as well. More often than not, the challenge in using ingredients that follow these requirements is the pricing, the sourcing and the variability among those sources. Variability is common in the ingredients coming from nature such as fruits and plants because the area of cultivation can vary by the soil at the sight of planting and/or the climate in the region. Pricing is also problematic in naturally grown ingredients because it is a matter of supply and demand. Stock could be depleted from natural disasters, disease carrying pest(s), pests that consume the crop, and/or other causes for scarce supply of crop(s). Essential oils are natural byproducts of fruit, peels, and leaves from plants that contribute to flavor formulae for a large variety of food products. Because the essential oils are a crop based commodity, every variety has inherent differences based on the growing conditions and their ripening stages [1]. Nevertheless, each type of oil has marker chemicals that make up the majority of its composition; these marker chemicals have the tendency to degrade over time based on their interaction with light, oxygen exposure, and temperature. For companies that manufacture flavorings, understanding the variability among sources of essential oils as well as the possible degradants of essential oils is valuable information to obtain because it is possible the variants and degradants will negatively impact the flavor profile. Flavor is without question the most important attribute of the food we consume and by default stability of said flavor(s) need to be understood [30]. The content in this dissertation involves the stability analysis of a common essential oil, Oil Mandarin Italian Select, from Citrus Reticulata Blanco. It has known off notes that form from unknown causes. Most common is the plastic note that has formed in carbonated products like soda. Studying this particular essential oil in various conditions is intended to shed light on what those degradants are and under which conditions they form to give mandarin oil an off-note when applied to high acid and carbonated beverage applications. Once the note is reproduced, a correlation between analytical data and sensory interpretation of the oil will be developed. Mandarin essential oil being in the Citrus genus is traditionally analyzed via gas chromatography (GC) because of the high quantities of volatile constituents that give an oil high aroma activity. The volatile fraction of mandarin oil to be studied includes stability of methyl-N-methylanthranilate (MNMA), a major component giving mandarin its distinct grapey character, as well as gamma terpinene, thymol, sinensal, alpha pinene, beta pinene, myrcene, para cymene, alpha terpineol, and beta caryophyllene. Each of these ten compounds contributes to the unique flavor profile of mandarin oils when compared to orange and tangerine essential oils [1]. It was the common knowledge that para cymene can be perceived as rancid in aroma and the many interconversions the terpenes make that cause para cymene formation in Citrus oils, which made monitoring the changes of this chemical in the three stability environments crucial. Attention is being paid to para-cymene, as a specific marker of degradation in Citrus. The data obtained from the applied stability studies were challenging to understand as the marker chemicals are volatile and sensitive to chemical change. In this work the chemical changes and trends were analyzed under various storage conditions. Significant statistical analyses were employed to help define criteria of usability. The analyses were required because of natural variants and apparent inconsistencies of the data. Dixon Q Test and the Z Test were applied to determine outliers. Additionally, the Bland Altman method was applied to compare storage conditions and to determine if this statistical approach could be used to define significant changes in the marker chemical stability. The Bland Altman plots suggest that each component met the statistical limits of agreement, meaning the samplings were not significantly changing, statistically speaking. A final approach to assess the analytical data of the mandarin oil for significant change was the mass balance of each marker chemical from week 0 to week 24. Instrumental fluctuations have an acceptable range of +/- 20% in the industry; hence, a significant change criterion for a chemical in the mass balance must be one that exceeded +/- 20%. Unlike classical statistic methods, the mass balance was indicative that significant change had occurred to the compounds in the three studies. Upon sensory analysis of the oil samples, display of plastic note, oxidation, and overall loss of characteristic mandarin notes, the mass balance was found to correlate best to the significant change detected by sensory evaluation of the oil samplings. Due to the inadequate number of validated methods on Citrus essential oil research and the absence of large groupings of terpenes validated in a unified methodology, reconciliation of mass balance is an underutilized method of assessment in the literature. As a final assessment of the GC method validated, a product containing the selected mandarin oil was analyzed to evaluate the ability of the method to separate the oil components within a significantly more complicated matrix than the initial samples. The method was successful though not all marker chemicals were detected due to their low formulation concentration being below the level of detection of the method. This should not be seen as a failure of the method. For the major components of the essential oil studied, the method was quantitatively successful, meeting industry requirements. / Chemistry

This thesis describes the use of functional nucleic acid (FNA) superstructures entrapped within monolithic macroporous sol–gel-derived silica for solid-phase flow-based sensing of small molecules and macromolecular proteins. The work described herein overcomes a long-standing issue with entrapment of biomolecule into sol–gel-derived materials; the mesoporous pore morphology required to retain entrapped biomolecules prevents detection of large analytes as these can’t access the entrapped species. It is shown that large DNA superstructures can be produced through rolling circle amplification of a functional nucleic acid, resulting in concatemeric FNA species with dameters of several microns. Such species can be entrapped within macroporous sol-gel derived materials with micron-sized pores with minimal leaching, thus allowing for detection of a wide range of molecules, including biomolecules. Optimal materials for entrapment of FNA superstructures was achieved using a high-throughput material screening method, which minimized biomolecule leaching while maintaining FNA activity. Using an optimized material, concatemeric aptamer superstructures were entrapped within macroporous monolithic columns for flow-based detection of small molecules and proteins, extending the range of analytes that can be analyzed using biohybrid monolithic columns. Preliminary studies on the formation and properties of a DNAzyme superstructure for detection of E. coli detection were also performed, which provided valuable information on factors that must be controlled to allow reproducible fluorescence-based detection of E. coli using the crude intracellular matrix as the target. / Thesis / Master of Science (MSc)

Oncolytic viruses (OVs) are a class of cancer therapy that is currently undergoing clinical trials on its way to full regulatory approval. At present, the downstream processing of OVs relies on a combination of chromatography and membrane-based processes to remove process-related (e.g. host-cell proteins and nucleic acids) and product-related impurities (e.g. aggregated virus particles). This thesis explores various methods that can potentially be used to address the challenges associated with downstream processing during the production of OVs. To this end, the Rhabdoviral vector, which is currently undergoing clinical trials (phase I/II) for use in treating advanced or metastatic solid tumors, was selected as a promising oncolytic virus. One potential improvement in the downstream process that was investigated was the use of monolithic column chromatography for Rhabdovirus purification. Two monolithic anion-exchange columns (2 and 6 µm pore size) and one hydrophobic interaction column (6 µm pore size) were used to examine how column pore size affects virus recovery and contaminant removal. This investigation ultimately inspired the development of a purification process based on monolithic hydrophobic interaction column chromatography. Furthermore, this work is also the first to investigate how additives, namely glycerol, impact the hydrophobic interaction chromatography of virus particles. The developed process could be readily implemented for the scaled-up purification of the Rhabdoviral vector. Another challenge associated with the downstream processing of OVs is membrane fouling, which is characterized by a dramatic rise in transmembrane pressure (TMP) and low virus recovery. Indeed, membrane fouling poses a significant challenge, as some recent studies have reported that it can result in viral vector titer losses of over 80%. One critical use of membranes in downstream processing is for the sterile filtration of OVs, which is a required final step that is conducted right before vialing and involves passing the virus particles through a validated sterile filter. One of the main objectives of this thesis was to develop a fundamental understanding of the sterile filtration process and to optimize it in order to achieve higher throughput and lower losses, which are both essential to the large-scale production of OVs. To this end, a dead-end sterile filtration setup was designed, and various commercially available filters were evaluated to examine how membrane morphology affects fouling and product recovery. The results of these tests showed that double-layered composite filters enabled higher virus recovery and filtration capacity compared to single-layered sterile filters. Another cause of membrane fouling is the aggregation of virus particles, which is mediated by various interactions in the solution. To study this, the above-described setup was re-designed to create an effective procedure that utilizes minimal volumes of virus solution, while also enabling the rapid assessment of microscale filtration performance and a comprehensive understanding of virus-virus and virus-membrane interactions. This setup was used to study how different additives, including various proteins (bovine serum albumin and α-lactalbumin) and polymers (polyethylene glycol and polyvinylpyrrolidone), affect the microfiltration of the Rhabdoviral vector and, consequently, the TMP profile. Furthermore, the correlation between the membrane fouling rate (via TMP profiles) and virus recovery was also investigated. This investigation revealed that proteins significantly increase virus transmission and that polymers are incapable of mimicking the effects of the proteins. To explain this phenomenon, a theory based on the biophysical structure of proteins, mainly heterogenicity in charge distribution, was proposed. Moreover, membrane surface modification tests were conducted using bovine serum albumin, with the results indicating that this approach has considerable potential for enhancing virus transmission. Due to the similarities between the test setup and actual downstream processing unit operations, the results from this part of the thesis could be easily and accurately applied to process optimization. / Thesis / Candidate in Philosophy / There is considerable interest in the development of oncolytic viruses for cancer immunotherapy. Indeed, at the time of this thesis’ writing, a Canadian team of researchers is conducting the world’s first clinical trial using a combination of two viruses to kill cancer cells and stimulate an immune response. The process of manufacturing oncolytic viruses is generally divided into two major steps: upstream processing and downstream processing. While upstream processing focuses on virus propagation, downstream processing aims at removing process-related and product-related impurities. However, research into downstream process design and optimization has largely been neglected in favour of a focus on upstream processing, aimed at increasing bioreactor yields and achieving high viral titers. Consequently, downstream processing has become the main bottleneck in virus manufacturing processes, accounting for as much as 70% production costs. This thesis aims to identify and develop a fundamental understanding of the main challenges associated with the downstream processing of oncolytic viruses and to investigate methods for addressing them. Specifically, the present work focuses on the purification and final sterile filtration steps in the manufacturing of oncolytic Rhabdoviral vectors.

No / In this work, parameters of the steric mass-formalism SMA are optimally ascertained for a reliable determination of the adsorption isotherms of beta-lactoglobulin A and B under non-isocratic conditions. For this purpose, static batch experiments are used in contrast to the protocols based on different experimental steps, which use a chromatographic column. It is shown that parameters can already be determined for a small number of experiments by using a systematic procedure based on optimal model-based experimental design and an efficient NLP-solver. The in different works observed anti-Langmuir shape of the isotherm for small concentrations of beta-lactoglobulin A was corroborated. Moreover, we also found indications for a porosity variation with changing protein concentrations.

Preventing flavor fade requires an understanding of the relationship between carbonyl amine and lipid oxidation reactions. The polyunsaturated fatty acid content of lipids in peanuts makes them more susceptible to lipid oxidation. The major by-products of the oxidation reaction are nonanal, hexanal, octanal, and decanal. These chemicals are associated with cardboardy, painty, and oxidized flavors associated with flavor fade. The carbonyl-amine reaction yields a variety of pyrazines with positive flavor attributes. Initial flavor notes were explored through sensory work, Gas Chromatography-Olfactometry, and chemical analysis. The fresh roasted volatiles produced from roasted peanuts and the aldehydes resulting from oxidation were also evaluated using GC-FID to quantify and identify the pyrazines and hexanal over a 21 day storage period. Electronic Nose was used to determine differences between storage periods. Gas chromatography-Olfactometry identified potent pyrazines contributing to fresh roasted peanutty aroma in fresh peanuts. Using GC-FID a significant decrease (p<.05) in 2-ethylpyrazine and 2,3-diethylpyrazine concentration was found over a 21-day period. No significant difference (p>0.05) was noted in the other pyrazines evaluated. A significant increase (p<0.05) was noted in the hexanal concentration over a 21-day period. The peroxide values and sensory analysis correlated directly with the GC-FID results with a significant increase (p<0.05) in peroxide value at Day 14 and Day 21, and a significant decrease (p<0.05) in fresh roasted peanuty flavor from days 0-21 and a significant increase (p<.05) in painty, cardboardy and bitter from days 7-21. The electronic nose successfully separated Day 0 and Day 21 samples from Day 7 and 14, which were also separated, but with minimal overlap. / Ph. D.

The purpose of this research was to design a simple, novel interface for on-line coupling of Supercritical Fluid Extraction (SFE) with High Performance Reversed Phase Liquid Chromatography (HP-RPLC), and to explore its ability for quantitative analysis of analytes in different matrices. First, a simple interface was developed via a single one six-port injection valve to connect the SFE and LC systems. A water displacement method was utilized to eliminate decompressed CO2 gas in the solid phase SFE trap and connection tubes. To evalute this novel hyphenated system, spiked polynuclear aromatic hydrocarbons (PAHs) in a sand matrix were used as target analytes with the achievement of quantitative results. Also PAHs in naturally contaminated soil were successfully extracted and quantitatively determined by this hyphenated system. Compared to the EPA method (Soxhlet extraction followed by GC-MS), on-line SFE-LC gave precise (4-10% RSD) and accurate results in a much shorter time. Based on this hyphenated technique, a method for the extraction and analysis of hyperforin in St. John's Wort was developed under air/light free conditions. Hyperforin is a major active constituent in the antidepression herbal medicine-Hypericum Perforatum (St. John's Wort). Hyperforin is very sensitive to oxygen and light. There is no way to date to determine whether any degradation occurs during the sample-processing step in the analytical laboratory. On-line coupling of SFE-LC with UV absorbance/ electrospray ionization mass spectrometry (SFE-LC-UV/ESI-MS) provided an air/light free extraction-separation-detection system, which addressed this issue. Mass spectral data on the extract confirmed the presence of the major degradation compounds of hyperforin (i.e. furohyperforin and two of its analogues). Thus, the degradation process must have occurred during plant drying or storage. The feasibility of quantitative extraction and analysis of hyperforin by on-line SFE-LC was made possible by optimizing the extraction pressure, temperature, and modifier content. High SFE recovery (~90%) relative to liquid-solid extraction was achieved under optimized conditions. We then extended the interface's application to an aqueous sample by using a liquid-fluid extraction vessel. Quantitative extraction and transfer were achieved for the target analytes (progesterone, phenanthrene, and pyrene) spiked in water, as well as in real samples (urine and environmental water). During each extraction, no restrictor plugging was realized. Extraction temperature and pressure were optimized. Different amounts of salt were added to the aqueous matrix to enhance ionic strength and thus extraction efficiency. Methanol and 2-propanol were used as CO2 modifiers. Two modifier modes were compared, e.g. dynamically mixing modifier with the CO2 extraction fluid, and pre-spiking modifier in the extraction vessel. Surprisingly, we found pre-spiking the same amount of modifier in the vessel enhanced the recovery from ~70% to ~100% for progesterone, phenanthrene, and pyrene due to a "co-extraction effect". The last phase of our work explored the disadvantages/limitations of this hyphenated technique through the analysis of more highly polar phenolic compounds in grape seeds. Five types of SFE trapping adsorbent materials were evaluated in an effort to enhance the collection efficiency for the polar components. Pure supercritical CO2 was used first to remove the less polar oil in the seeds. Then methanol-modified CO2 was used to remove the polar components (e.g. phenolic compounds). Catechin and epicatechin (90%) were exhaustively extracted out of the de-oiled seed after 240 minutes with 40% methanol as modifier. Both singly linked (B-type) and doubly linked (A-type) procyanidins were identified by LC-ESI-MS, as well as their galloylated derivatives. Compared to the off-line SFE-LC approach, much less sample was required for extraction in the on-line method, since all the extracted components could be transferred to the LC column. Also, no extract processing/concentration step was needed in the on-line method. However, in the on-line mode, some polar compounds were lost (1) during the collection step (e.g. lower trapping efficiency on a single solid SFE trap when a high percentage modifier was used) and (2) during the water rinsing step (e.g. less retention of polar compounds on C18 trap). Therefore, this hyphenated technique is less desirable for the analysis of highly polar compounds. / Ph. D.

Successful implementation of dietary P management strategies demand improved understanding of P digestion dynamics in ruminants and this is not possible without a reliable and accurate phytate (Pp) quantification method. The objective of the first study was to develop a robust, accurate, and sensitive method to extract and quantify phytate in feeds, ruminant digesta and feces. Clean-up procedures were developed for acid and alkaline extracts of feed, ruminant digesta and feces and clarified extracts were analyzed for Pp using high performance ion chromatography (HPIC). The quantified Pp in acid and alkaline extracts was comparable for feed but alkaline extraction yielded greater estimates of Pp content for digesta and feces than did acid extraction. Extract clean-up procedures successfully removed sample matrix interferences making alkaline extraction compatible with HPIC. The developed method was applied to investigate the disappearance of Pp from the large intestine of dairy heifers. Eight ruminally- and ileally-cannulated crossbred dairy heifers were used and each heifer was infused ileally with 0, 5, 15, or 25 g/d Pp and total fecal collection was conducted. On average 15% of total Pp entering the large intestine was degraded but the amount of infused Pp did not influence the degradability of Pp. Net absorption of P from the large intestine was observed. A feeding trial was conducted to investigate the effect of dietary Pp supply on ruminal and post-ruminal Pp digestion. Six ruminally-and ileally-cannulated crossbred lactating cows were used and dietary treatments were low (0.10% Pp), medium (0.18% Pp), and high (0.29% Pp) Pp, and a high inorganic P (Pi; 0.11% Pp; same total P content as high Pp). Ruminal Pp digestibility increased linearly with dietary Pp. As in the infusion study, net disappearance of Pp from the large intestine was only 16% of total Pp entering the large intestine and not influenced by dietary Pp. Fecal P excretion increased linearly with increasing dietary Pp but was not affected by form of dietary P. In lactating cows Pp digestibility was not affected by dietary Pp and fecal P excretion was regulated by total dietary P rather than by form of dietary P. / Ph. D.