Oilseeds may be processed to yield a number of potentially valuable compounds and fractions including oil, protein and small molecules. However, energy costs associated with industrial processing of oilseeds can be significant. For example, processes that use water to dissolve and separate materials are burdened with the costs associated with concentrating value-added products from dilute solutions. The ethanol industry produces large amounts of an aqueous solution called thin stillage that has little value and is used in animal feed. Thin stillage contains some of the necessary salts used in protein extraction but has a low pH. Protein extraction and protein isolate production is commonly conducted at higher pH. Waste alkali from biodiesel production has a high pH and can be used to adjust the pH of thin stillage to improve its ability to extract protein from oilseed meal. By combining the properties of the waste products of both the ethanol and the biodiesel industries, a complementary process is possible that may have greater economic potential than current practices in industry.<p> In this study, processes for protein extraction from mustard (<i>Brassica juncea</i> (L.) Czern.) meal using thin stillage from ethanol production and glycerol from biodiesel production were studied. The osmotic potential of thin stillage used in this research was lower than that of water, whereas both the density and the viscosity were higher. The pH was typically 3.7-3.8, and the total Kjeldahl nitrogen was approximately 0.080.10 %, w/w. Organic compounds identified in thin stillage were isopropanol, ethanol, lactic acid, 1,3-propanediol, acetic acid, succinic acid, glycerophosphorylcholine, betaine, glycerol and phenethyl alcohol. In addition, yeasts, bacteria and fungi were also found. Moreover, the salt types and their concentrations in thin stillage were predictable. The salt types present in thin stillage were CaCl2, NaCl, K2SO4, NaNO3, Mg(OH)2, Na2SO4 and KOH. A model thin stillage synthesized for the purposes of this research had components and chemical and physical properties comparable to those of thin stillage from ethanol production. Protein was extracted from ground, defatted meal using thin stillage at different pHs and salt concentrations. The results showed that pH and salt content affected protein extraction efficiency. However, no differences were found in the efficiency of extraction, SDS-PAGE profile, digestibility, lysine availability or amino acid composition of protein extracted with thin stillage, model thin stillage or sodium chloride solution. Moreover, extracted protein did not display significant hydrolysis. The results from peptide sequencing showed that napin and cruciferin were the most prevalent proteins in the extracted fractions. When increasing the scale of the extraction, the efficiency of protein extraction and the percentage of protein in the extracted protein were decreased. Protein recovery achieved with the complementary protocol was higher than that reported for a published protocol. Allyl isothiocyanate was found in protein extracts.

Microfluidic chips have gained wide applications in various fields, including medicine, environmental sciences and forensic investigations. They are used for the separation of proteins, blood, bacterial cell suspensions, antibody solutions, and drugs. Microfluidic chips display significant advantages, which include faster analysis time, reduced amounts of samples and reagents volumes, flexibility in design and increased separation efficiency. Whole column imaging detection (WCID) exhibits significant advantages compared to other detection methods that are widely used for detecting analytes after the separation of these analytes using isoelectric focusing. With these other methods, there is a need to mobilize the focused sample bands past the detector after separation but with WCID, there is no need for mobilization step. The aim of this research is further development of WCID by characterizing microfluidic chips fabricated for the detection system, to enhance its detection so that high efficiency can be obtained. The chips were fabricated using soft lithography technology at the Microfluidic laboratory, University of Waterloo and they were used to perform isoelectric focusing of various proteins in our laboratory. The fabricated chips with straight channel design were used to carry out isoelectric focusing of some proteins and the results obtained were compared with the results obtained using commercial cartridges. The chips with tapered channel design were used to carry out isoelectric focusing of proteins in which thermally generated pH gradient principle was employed. The samples after separation were sprayed into a mass spectrometer using nano-electrospray interface to obtain their molecular masses. Compatible cartridges for nano-electrospray mass spectrometer were developed and these cartridges were used to carry out capillary isoelectric focusing of low molecular pI markers and proteins. These cartridges were also connected to the nano-electrospray mass spectrometer to obtain the mass to charge ratios of some proteins. The fabricated microfluidic chips with straight channel design were also used to investigate the interaction between drugs and protein.

Microfluidic chips have gained wide applications in various fields, including medicine, environmental sciences and forensic investigations. They are used for the separation of proteins, blood, bacterial cell suspensions, antibody solutions, and drugs. Microfluidic chips display significant advantages, which include faster analysis time, reduced amounts of samples and reagents volumes, flexibility in design and increased separation efficiency. Whole column imaging detection (WCID) exhibits significant advantages compared to other detection methods that are widely used for detecting analytes after the separation of these analytes using isoelectric focusing. With these other methods, there is a need to mobilize the focused sample bands past the detector after separation but with WCID, there is no need for mobilization step. The aim of this research is further development of WCID by characterizing microfluidic chips fabricated for the detection system, to enhance its detection so that high efficiency can be obtained. The chips were fabricated using soft lithography technology at the Microfluidic laboratory, University of Waterloo and they were used to perform isoelectric focusing of various proteins in our laboratory. The fabricated chips with straight channel design were used to carry out isoelectric focusing of some proteins and the results obtained were compared with the results obtained using commercial cartridges. The chips with tapered channel design were used to carry out isoelectric focusing of proteins in which thermally generated pH gradient principle was employed. The samples after separation were sprayed into a mass spectrometer using nano-electrospray interface to obtain their molecular masses. Compatible cartridges for nano-electrospray mass spectrometer were developed and these cartridges were used to carry out capillary isoelectric focusing of low molecular pI markers and proteins. These cartridges were also connected to the nano-electrospray mass spectrometer to obtain the mass to charge ratios of some proteins. The fabricated microfluidic chips with straight channel design were also used to investigate the interaction between drugs and protein.

Oilseeds may be processed to yield a number of potentially valuable compounds and fractions including oil, protein and small molecules. However, energy costs associated with industrial processing of oilseeds can be significant. For example, processes that use water to dissolve and separate materials are burdened with the costs associated with concentrating value-added products from dilute solutions. The ethanol industry produces large amounts of an aqueous solution called thin stillage that has little value and is used in animal feed. Thin stillage contains some of the necessary salts used in protein extraction but has a low pH. Protein extraction and protein isolate production is commonly conducted at higher pH. Waste alkali from biodiesel production has a high pH and can be used to adjust the pH of thin stillage to improve its ability to extract protein from oilseed meal. By combining the properties of the waste products of both the ethanol and the biodiesel industries, a complementary process is possible that may have greater economic potential than current practices in industry.<p> In this study, processes for protein extraction from mustard (<i>Brassica juncea</i> (L.) Czern.) meal using thin stillage from ethanol production and glycerol from biodiesel production were studied. The osmotic potential of thin stillage used in this research was lower than that of water, whereas both the density and the viscosity were higher. The pH was typically 3.7-3.8, and the total Kjeldahl nitrogen was approximately 0.080.10 %, w/w. Organic compounds identified in thin stillage were isopropanol, ethanol, lactic acid, 1,3-propanediol, acetic acid, succinic acid, glycerophosphorylcholine, betaine, glycerol and phenethyl alcohol. In addition, yeasts, bacteria and fungi were also found. Moreover, the salt types and their concentrations in thin stillage were predictable. The salt types present in thin stillage were CaCl2, NaCl, K2SO4, NaNO3, Mg(OH)2, Na2SO4 and KOH. A model thin stillage synthesized for the purposes of this research had components and chemical and physical properties comparable to those of thin stillage from ethanol production. Protein was extracted from ground, defatted meal using thin stillage at different pHs and salt concentrations. The results showed that pH and salt content affected protein extraction efficiency. However, no differences were found in the efficiency of extraction, SDS-PAGE profile, digestibility, lysine availability or amino acid composition of protein extracted with thin stillage, model thin stillage or sodium chloride solution. Moreover, extracted protein did not display significant hydrolysis. The results from peptide sequencing showed that napin and cruciferin were the most prevalent proteins in the extracted fractions. When increasing the scale of the extraction, the efficiency of protein extraction and the percentage of protein in the extracted protein were decreased. Protein recovery achieved with the complementary protocol was higher than that reported for a published protocol. Allyl isothiocyanate was found in protein extracts.

Mass spectrometry (MS) has played a major role in the proteomic analysis of an array of biological samples. Even so, inherent limitations exist such as sample complexity and the dynamic range. In an attempt to overcome these limitations, prefractionation is typically performed followed by reversed phase liquid chromatography coupled with MS. Pre-fractionation can be performed in several formats including chromatographic or electrophoretic based methods. Solution-based isoelectric point (pI) fractionation, specifically isoelectric trapping (IET), provides an attractive alternative for pre-fractionation in bottom-up proteomic studies. A recently developed device, membrane separated wells for isoelectric focusing and trapping (MSWIFT), provides rapid separation on the basis of pI and resulting solutions are MS compatible without the need for extensive sample cleanup. Initial experiments demonstrate fractionation using MSWIFT, of peptide mixtures ranging from standards to a yeast lysate where resulting fractions are analyzed using matrixassisted laser desorption/ionization (MALDI) – MS or further separated using reversed phase liquid chromatography followed by tandem MS (MS/MS) analysis. Identified yeast proteins range in size, pI and copy number illustrating an ability to increase the depth of proteome coverage when using MSWIFT. Extensive studies were also performed using MSWIFT in a multi-stage fractionation platform to improve peptide and protein identifications for the first large-scale proteomic study of the model fungus, Neurospora crassa. A second focus of this work is the development of a new sample preparation method for proteolytic digestion and high-throughput separations using MSWIFT. Histidine is used as a neutral pH, isoelectric, sample buffer for tryptic digestion of proteins and also assists in rapid separations using MSWIFT owing to the low conductivity. Tryptic digests of individual standard proteins and a mixture of standard proteins are used to illustrate these advantages. Finally, the histidine buffer sample preparation method is incorporated into a two-dimensional separation strategy. Tryptic peptides are fractionated using MSWIFT and resulting solutions are further separated using capillary electrophoresis (CE) coupled with MALDI-MS/MS. Performing the two-dimensional strategy allows for increased confidence in peptide and protein assignment owing to experimentally determined in-solution charge states and estimated pI values.

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Proteomics is an increasingly important area of biological research and has gathered much attention over recent years. Major challenges that make a proteomic analysis difficult are sample complexity, diversity and dynamic range. Progress in the area of proteomics relies heavily on new analytical tools for the sensitive, selective, and high-throughput studies of target analytes. It is estimated that there are several hundred thousand proteins in a human cell. In order to be able to analyze such a complex sample, an analytical method must be capable of separating and detecting many different sample peaks. The complexity of such samples indicates that a single separation method will not be able to provide the needed resolution. If two methods that are orthogonal are combined, then the peak capacity of the combined system is the product of the two individual peak capacities. Development of such systems would cater to the current demands of proteomics studies. Matrix assisted laser desorption/ionization (MALDI) mass spectrometry has evolved into a primary analytical tool for proteomics research. MALDI is fast and efficient and has a high tolerance to non-volatile buffers and impurities. The samples for MALDI are typically applied to solid supports after having been subjected to off-line liquid or gel separations. Several methods have been reported involving various chromatographic or electrophoretic separation methods. However, the current methods often require highly sophisticated sample handling systems, which are often expensive and in need of skilled human resources. The current demands of proteomic analyses require fast, efficient and inexpensive methods for separation to fully harness the capability of MALDI mass spectrometry. In this work a microfluidic device has been designed to perform dynamic isoelectric focusing (DIEF) based protein separation with digital sample deposition directly on a MALDI target for offline analysis. DIEF is related to capillary isoelectric focusing which and can facilitate the interface without the loss of the separation resolution. Compared to traditional capillary isoelectric focusing (cIEF) DIEF uses additional high-voltage power supplies to control the pH gradient by manipulating the electric field. The proteins can be focused at a desired sampling position according to their isoelectric point, to be collected for further analysis by MALDI mass spectrometry. DIEF has a peak capacity of over a thousand and offers an ease of interfacing to other techniques making it a preferred separation method for the interface with mass spectrometric techniques such as MALDI. The design of the microfluidic device is based on a digital droplet fractionation. Multiple fractions of the sample solution from DIEF are generated to retain the resolution and to act as an additional separation mode. The microfluidic device is controlled by actuating pneumatic valves built into the device. The DIEF operational parameters were optimized according to the surface functionality and the design of the microfluidic device. A suitable MALDI sample preparation method was found by studying different existing methods. The methods were studied using test proteins prepared in solutions having the additives used in the experiment. A simple mixture of three proteins was used to demonstrate the application of the developed method. The separation between the proteins insulin, hemoglobin and the myoglobin was demonstrated by varying the separation resolution in three experiments.

Small heat shock proteins (hsp) have been implicated in mediation of classic preconditioning in the rabbit. Hsp27 is a terminal substrate of the p38 MAPK cascade. One and 2D gel electrophoresis and immunoblotting of cell fractions was used to determine p38 MAPK and hsp27 phosphorylation levels, respectively, during in vitro ischemia in control, calyculin A (Cal A)-treated (protein phosphatase inhibitor), SB203580-treated (p38MAPK inhibitor) and preconditioned (IPC) isolated adult rabbit cardiomyocytes. The dual phosphorylation of p38 MAPK was increased by early ischemia (30-60 min), after which there was a loss of total cytosolic p38 MAPK. The ischemic increase of p38 MAPK dual phosphorylation was enhanced by IPC. Cal A strongly activated dual phosphorylation of p38 MAPK in oxygenated cells and this was maintained into early ischemia. SB203580 inhibited the dual phosphorylation of p38 MAPK and attenuated the loss of total cytosolic p38 MAPK. In each protocol, ischemia translocated hsp27 from the cytosolic fraction to the cytoskeletal fraction at similar rates and extents. Hsp27 phosphorylation was quantitated as the fraction of diphosphorylated hsp27, based on IEF mobility shifts of hsp27 phosphorylation isoforms. In oxygenated control cells, cytosolic and cytoskeletal hsp27 was highly phosphorylated. After 90 min ischemia, cytoskeletal hsp27 was markedly dephosphorylaled. Cal A slightly increased control cytoskeletal hsp27 phosphorylation. During ischemic incubation, Cal A blocked ischemic dephosphorylation. SB203580 accelerated ischemic hsp27 dephosphorylation and injury. IPC insignificantly decreased the initial rate of ischemic dephosphorylation of hsp27, but not the extent of dephosphorylation in later ischemia. Phosphorylation is regulated by both kinase and phosphatase activities. IPC protection was not correlated with a significant increase in cytosolic or cytoskeletal hsp27 phosphorylation levels during prolonged (> 60-90 min) ischemia.

Mixed solutions of β-lactoglobulin and anionic polysaccharides, specifically pectin, were formed into associative complexes through pH reduction from neutral conditions. Thermal treatment of these associative complexes was investigated as a function of biopolymer composition, heating conditions, pH, and ionic strength. Thermal treatment of β-lactoglobulin-pectin complexes at pH 4.5 – 5.0 was found to create protein-based particulates of consistent and narrow size distribution (diameter ~ 150 – 400 nm). These particulates were relatively stable to further pH adjustment and to high levels of salt (200 NaCl). Particle characteristics were maintained after re-suspending them in aqueous solutions after they have been either frozen or lyophilized. Thermal analysis of β- lactoglobulin-pectin complexes using calorimetry (DSC) and turbidity-temperature scanning indicated that the denaturation of β-lactoglobulin was unaffected by pectin, but protein aggregation was limited by the presence of pectin. Biopolymer particles formed using two different methods were compared: Type 1 – forming β-lactoglobulin nanoparticles by heating, then coating them with pectin; Type 2 – forming particles by heating β-lactoglobulin and pectin together. Type 2 particles had smaller diameters and had better pH and salt stability than Type 1 particles. It was proposed that Type 2 particles had a pectin-saturated surface that limited their aggregation, whereas Type 1 particles had “gaps” in the pectin surface coverage that led to greater aggregation. Finally, the possibility of controlling the size and concentration of biopolymer particles formed by heating β-lactoglobulin-pectin complexes by controlling preparation conditions was studied. Biopolymer particle size and concentration increased with increasing holding time (0 to 30 minutes), decreasing holding temperature (90 to 70 ºC), increasing protein concentration (0 to 2 wt%), increasing pH (4.5 to 5.0), and increasing salt concentration (0 to 50 mol/kg). The influence of these factors on biopolymer particle size was attributed to their impact on protein-polysaccharide interactions, protein denaturation, and protein aggregation kinetics. The knowledge gained from this study will facilitate the rational design of biopolymer particles with specific physicochemical and functional attributes that can be used in the food and other industries, e.g., for encapsulation, texture modification, optical properties modification.

Sepsis is a “life-threatening organ dysfunction caused by a dysregulated host response to infection” that has a widespread impact on human life around the world. It affects more than 1.5 million people, killing at least 250,000 each year in the US alone and affects 90,000 people annually, with estimated mortality rates of up to 30% in Canada. Our understanding of the different biochemical pathways that in the progression of sepsis has improved patient care for sepsis patients. One part of patient care is the use of biomarkers for patient prognosis that draws on the full range of relevant and available information to model the possible outcomes for an individual. Numerous biomarkers have been studied for patient prognosis that includes Procalcitonin (PCT), C-reactive protein (CRP), TNF-α, cfDNA, protein C and PAI 1. Using a panel of multiple biomarkers provided more accuracy in patient prognosis than using individual biomarkers and one such panel that was proposed used cfDNA, protein C, platelet count, creatinine, Glasgow Coma Scale [GCS] score, and lactate. Commercial, low cost POC techniques were available for the measurement of all biomarkers besides cfDNA and protein C. The objective of this doctoral thesis was chosen to develop low cost, microfluidic devices for the measurement of protein C and cfDNA using nonspecific fluorescence dyes that would enable the eventual integration of the systems and improve patient prognosis. The measurement of protein C in plasma required the separation of protein C from interfering proteins in plasma. This was done through the development of a two-stage separation process that included the development of tunable agarose isoelectric gates for separating proteins using their isoelectric point and the miniaturization of immobilized metal affinity chromatography and its extension to Barium for the selective binding of proteins using their chemical affinity. This was performed in a xurographically fabricated chip to reduce costs and enable the use of geometric focusing of the electric field to enable the operation of the device at a lower applied voltage. The challenges faced with cfDNA were different due to the different characteristics of the material and less interference from plasma. The requirement was to measure the total cfDNA content with minimal cost in comparison to currently available techniques. This was achieved through the development of thread microfluidic devices that showed the use of thread for automated aliquoting of samples by controlling length and twists of the thread. Preconcentration and use of external apparatus was avoided by showing that thread could be used to amplify fluorescence response to a range that was sufficient for the measurement of cfDNA in sepsis patients. A portable fluorescence imaging setup was developed for this purpose and was used in demonstration for the measurement of cfDNA in plasma with sufficient resolution. In conclusion, we developed technologies for rapid and low-cost measurement of protein C and cfDNA using xurographic and thread-based microfluidics that may serve as valuable in improving patient prognosis. / Thesis / Doctor of Philosophy (PhD) / Sepsis is a major reason for hospitalization and cause of death in hospitals worldwide. Its treatment is highly time sensitive with each hour of delay in diagnosis causing a significant increase in chances of death. Due to the wide range of symptoms that can be caused by sepsis, its diagnosis uses a scoring method that relies on the expertise of the onsite doctors and nurses increasing their workload. A more objective system for detection requires the measurement of the quantities of different biomarkers in blood. Biomarkers are proteins present in plasma that change in quantity due to the body’s reaction to sepsis. Several of these biomarkers have been identified and studied for their use in both diagnosing the presence of sepsis and in predicting the outcome with the current treatment plan. In this PhD study, we chose two of these biomarkers – circulating free DNA (cfDNA) and protein C and developed low-cost techniques for rapidly measuring their concentration in blood plasma. To do this, we made microfluidic devices with techniques that use low-cost materials such as plastic sheets and threads.The device for the measurement of protein C required separating it from many other proteins in plasma. We showed that a device fabricated from stacked plastic sheets and integrated with agarose gels could be used for the measurement of protein C in plasma with sufficient resolution to help with treating septic patients at a cost of less $5 per device. Similarly, we showed that a device that integrated threads with plastic sheets could be used for measuring the quantity of cfDNA in plasma in a portable format within 15 minutes. Overall, we developed tools for rapid measurement of two biomarkers of sepsis using low cost device that cost under $5 to run and could led to improving the quality of care for sepsis patients.