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Bioadhesives are essential for tissue adhesion and regeneration. Optimal bioadhesive should possess elasticity, robust adhesion capabilities in wet environments, and a cytocompatible scaffold for cell regeneration. Current options like cyanoacrylates and fibrin glues fail in these aspects due to cell toxicity and poor moisture adhesion, prompting the need for new materials that reconcile cytocompatibility with robust adhesion. These limitations by available commercial bioadhesives, demand the development of new adhesive biomaterials that combine cytocompatibility with strong adhesion. Marine organisms such as mussels secrete proteins that adhere effectively even underwater, but the adhesion mechanisms remain partly elusive. These proteins' adhesion strength is largely attributed to catechol side chains of L-Dopa, which can form various surface interactions, including hydrogen bonding and metal coordination. Commercial use of natural adhesive proteins is time- and labor-demanding, and uneconomical, as it takes thousands of mussel specimens to extract just one gram of adhesive proteins. In addition, low expression yield, low purification yield, and high levels of post-purification insolubility, restrict the production of recombinant foot protein types in Escherichia coli. To overcome these issues and inspired by intrinsically disordered domains of tropoelastin, the soluble precursor of elastin, elastin-like polypeptides (ELPs) consist of repeated sequences of the pentapeptide motif “VPGXG” (with “X” representing any amino acids except proline), emerge as promising synthetic alternatives. These stimuli-responsive adhesives exhibit a reversible phase transition regulated by temperature, making them suitable for applications such as drug delivery and wound healing. Their lower critical solution temperature (LCST) can be genetically adjusted to just below human body temperature, offering versatility for medical use. The bioadhesive efficacy of ELPs is linked to Dopa, cruc

Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50% and MGEs by over 65%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus)

Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50% and MGEs by over 65%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus)

An integrated model was developed to simulate airborne transmission of infectious animal viral diseases. Computational fluid dynamics (CFD), viral infectivity decay, and dose-response models were integrated to simulate physical and biological processes in the aerosol transmission pathway of animal disease. In the first part of this study, a CFD model was developed and validated for simulating movement of bioaerosols of porcine reproductive and respiratory syndrome virus (PRRSV) in laboratory conditions where air flowed from a source to a recipient chamber. The model performed well (normalized mean square error NMSE <0.25) at simulating steady-state PRRSV bioaerosol concentrations, but differences were greater (NMSE >0.25) during the transient stage of airflow. In the second part of this study, a series of dose-response models were performed for five infectious animal viruses on various transmission routes. The transmissibility of animal viruses varied with the transmission route, and aerosol transmission required lower doses to cause infection than intranasal and oral transmission for PRRSV. The CFD model was coupled with aerosol transmission dose-response models for PRRSV. The coupled models predicted probability of infection (82% to 100%), which was in good agreement with observed rates in two experimental studies (84% and 90%). In the third part of this study, an integrated model consisting of CFD, infectivity decay, and dose-response was developed to simulate the aerosol transmission of PRRSV between a source and a recipient building in field conditions, based on an experimental study reported in the literature. CFD was used to model the PRRSV aerosol movement towards and within the recipient building, and the infectivity decay and dose-response models were used to predict the probability of infection upon exposure to the calculated aerosol dose of PRRSV. The integrated model predicted that the aerosol transmission event occurred in the recipient building on a d

Clostridium thermocellum is one of the most promising candidates for consolidated bioprocessing of lignocellulosic biomass to biofuels and chemicals but its low product yield and the presence of unexpected minor fermentation products, such as amino acids, has restricted industrial scale production. Few reports have compared the physiological effects of end-product accumulation and the behavior of C. thermocellum in a natural, consortium setting. This may provide a more detailed understanding of the complex metabolism of C. thermocellum, aiding future engineering efforts to increase product yield. In this study, we grew C. thermocellum in co-culture with Methanothermobacter marburgensis, a hydrogenotrophic methanogen, on cellulose in batch culture at 60 oC to investigate the physiological effects of continuous H2 removal on C. thermocellum. When grown in co-culture, minimal H2 concentration and continuous CH4 production was detected, indicating continuous H2 and CO2 consumption by M. marburgensis. C. thermocellum growth rate did not change significantly, but a faster rate of cellulose hydrolysis was observed. Major end-product profile of C. thermocellum changed with the most notable difference being an increase in acetate, and a decrease in formate and ethanol. Changes in alternate end-products, such as amino acids and TCA cycle intermediates, were also observed. The metabolic shift to H2 and acetate in response to continuous H2 removal was accompanied by changes in the expression of [FeFe] H2ases of C. thermocellum: (a) 10-fold decrease in Cthe_0430, (b) 2-fold decrease in Cthe_0342, (c) 1.5-fold decrease in Cthe_3003. We demonstrated that growth with a naturally occurring hydrogenotrophic partner, such as methanogens, alter the metabolic patterns and H2ase gene expression in C. thermocellum. Low H2 partial pressure required to overcome thermodynamic barriers for the oxidation of reducing equivalents was achieved by continuous H2 removal via methanogen consumption.

Hemostasis is an important issue in-clinic treatments for acute wounds. Existing hemostatic materials may not fully meet the demands in emergency situations in terms of hospitals and battlefields which calls for the development of cost-effective hemostatic materials for clinical applications. Cellulose as a natural polymer is abundant in nature and has been widely used in different applications, like food, cosmetics, and hemostatic applications. Cellulose-based materials can absorb water from blood upon contact with wounds, which helps to stop bleeding. In this work, cellulose-based aerogels and hydrogels were prepared and their potential applications as hemostatic materials were explored. Aerogels with ultra-high porosity and large surface area can absorb water from blood and form barriers in the trauma site to stop bleeding. In this thesis, an aerogel with lightweight, injectability, antibacterial ability, water-induced shape memory behavior, and excellent compressibility was developed from carboxymethylated nanocellulose fibers (NCFs), alginate and zinc chloride. The obtained NCFs-alginate aerogels have dual networks which are the physical network of NCFs formed by freeze-drying and physical crosslinking between alginate and zinc ions. Here, zinc chloride endowed the aerogels with the antibacterial ability to prevent infection and reduce the probability of complications due to microorganisms. The NCFs-alginate aerogels with high water absorption can absorb water when contacting blood to stop bleeding. Meanwhile, in the presence of NCFs and alginate, the aerogels can promote wound healing quickly. Besides, injectability and rapid water-induced shape recovery ability (4s) allowed the NCFs-alginate aerogels to be used for penetrating wounds. Carboxymethylated cellulose (CMC) is an important derivation of cellulose and has been widely used in biomedical applications. A facile and environmentally friendly method for preparing self-healing hydrogels using CMC, polyviny

Fossil-fuel-based insulation materials such as polyvinyl chloride (PVC), low-density polyethylene (LDPE), cross-linked polyethylene (XLPE) and ethylene-vinyl acetate (EVA) have dominated the electrical insulation industry at present. Increased use of these polymers have caused a serious threat to environment causing, environmental pollution, global warming, and climate changes worldwide. Biopolymers offers a solution to these problems, since they are fully renewable from bio-sources such as biomass, agricultural by-products, and biological waste. In order to utilize biopolymers as an electrical insulation material, they should match or exceed electrical, mechanical, and thermal properties of their fossil-fuel-based counterparts. Four bio-polymers namely polyhydroxy butyrate (PHB), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), poly (lactic acid) (PLA), cellulose acetate (CA) and three fossil-fuel-based synthetic polymers polycaprolactone (PCL), polybutylene succinate (PBS), poly (butylene adipate-co-terephthalate) (PBAT) are selected based on their popularity in research and commercial availability. Although commercial manufacturing of these four synthetic polymers is from fossil-fuel-based sources, they can be synthesised from bio-sources as well. Samples of six of these selected polymers, PHB, PHBV, PCL, PBS, and PBAT are obtained collaborating with the Biosystems Engineering department for the electrical measurements. These samples are thin films, prepared from spin-casting process. Electrical properties such as complex dielectric constant, volume resistivity and AC electrical breakdown strength of these samples are measured, while thermal and mechanical properties are summarized from literature. Using experimental measurements and the literature data, properties of these selected polymers are compared with conventional polymers such as PVC, LDPE, XLPE and EVA. Few biopolymers are shortlisted as possible candidate materials for electrical insulation applica

Clostridium thermocellum is one of the most promising candidates for consolidated bioprocessing of lignocellulosic biomass to biofuels and chemicals but its low product yield and the presence of unexpected minor fermentation products, such as amino acids, has restricted industrial scale production. Few reports have compared the physiological effects of end-product accumulation and the behavior of C. thermocellum in a natural, consortium setting. This may provide a more detailed understanding of the complex metabolism of C. thermocellum, aiding future engineering efforts to increase product yield. In this study, we grew C. thermocellum in co-culture with Methanothermobacter marburgensis, a hydrogenotrophic methanogen, on cellulose in batch culture at 60 oC to investigate the physiological effects of continuous H2 removal on C. thermocellum. When grown in co-culture, minimal H2 concentration and continuous CH4 production was detected, indicating continuous H2 and CO2 consumption by M. marburgensis. C. thermocellum growth rate did not change significantly, but a faster rate of cellulose hydrolysis was observed. Major end-product profile of C. thermocellum changed with the most notable difference being an increase in acetate, and a decrease in formate and ethanol. Changes in alternate end-products, such as amino acids and TCA cycle intermediates, were also observed. The metabolic shift to H2 and acetate in response to continuous H2 removal was accompanied by changes in the expression of [FeFe] H2ases of C. thermocellum: (a) 10-fold decrease in Cthe_0430, (b) 2-fold decrease in Cthe_0342, (c) 1.5-fold decrease in Cthe_3003. We demonstrated that growth with a naturally occurring hydrogenotrophic partner, such as methanogens, alter the metabolic patterns and H2ase gene expression in C. thermocellum. Low H2 partial pressure required to overcome thermodynamic barriers for the oxidation of reducing equivalents was achieved by continuous H2 removal via methanogen consumption.

Fossil-fuel-based insulation materials such as polyvinyl chloride (PVC), low-density polyethylene (LDPE), cross-linked polyethylene (XLPE) and ethylene-vinyl acetate (EVA) have dominated the electrical insulation industry at present. Increased use of these polymers have caused a serious threat to environment causing, environmental pollution, global warming, and climate changes worldwide. Biopolymers offers a solution to these problems, since they are fully renewable from bio-sources such as biomass, agricultural by-products, and biological waste. In order to utilize biopolymers as an electrical insulation material, they should match or exceed electrical, mechanical, and thermal properties of their fossil-fuel-based counterparts. Four bio-polymers namely polyhydroxy butyrate (PHB), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), poly (lactic acid) (PLA), cellulose acetate (CA) and three fossil-fuel-based synthetic polymers polycaprolactone (PCL), polybutylene succinate (PBS), poly (butylene adipate-co-terephthalate) (PBAT) are selected based on their popularity in research and commercial availability. Although commercial manufacturing of these four synthetic polymers is from fossil-fuel-based sources, they can be synthesised from bio-sources as well. Samples of six of these selected polymers, PHB, PHBV, PCL, PBS, and PBAT are obtained collaborating with the Biosystems Engineering department for the electrical measurements. These samples are thin films, prepared from spin-casting process. Electrical properties such as complex dielectric constant, volume resistivity and AC electrical breakdown strength of these samples are measured, while thermal and mechanical properties are summarized from literature. Using experimental measurements and the literature data, properties of these selected polymers are compared with conventional polymers such as PVC, LDPE, XLPE and EVA. Few biopolymers are shortlisted as possible candidate materials for electrical insulation applica

An integrated model was developed to simulate airborne transmission of infectious animal viral diseases. Computational fluid dynamics (CFD), viral infectivity decay, and dose-response models were integrated to simulate physical and biological processes in the aerosol transmission pathway of animal disease. In the first part of this study, a CFD model was developed and validated for simulating movement of bioaerosols of porcine reproductive and respiratory syndrome virus (PRRSV) in laboratory conditions where air flowed from a source to a recipient chamber. The model performed well (normalized mean square error NMSE <0.25) at simulating steady-state PRRSV bioaerosol concentrations, but differences were greater (NMSE >0.25) during the transient stage of airflow. In the second part of this study, a series of dose-response models were performed for five infectious animal viruses on various transmission routes. The transmissibility of animal viruses varied with the transmission route, and aerosol transmission required lower doses to cause infection than intranasal and oral transmission for PRRSV. The CFD model was coupled with aerosol transmission dose-response models for PRRSV. The coupled models predicted probability of infection (82% to 100%), which was in good agreement with observed rates in two experimental studies (84% and 90%). In the third part of this study, an integrated model consisting of CFD, infectivity decay, and dose-response was developed to simulate the aerosol transmission of PRRSV between a source and a recipient building in field conditions, based on an experimental study reported in the literature. CFD was used to model the PRRSV aerosol movement towards and within the recipient building, and the infectivity decay and dose-response models were used to predict the probability of infection upon exposure to the calculated aerosol dose of PRRSV. The integrated model predicted that the aerosol transmission event occurred in the recipient building on a d

Degradation of extracellular Polyhydroxyalkanoates (PHAs) in the environment depends on the secretion of specific extracellular PHA depolymerases and lipases. Compared to extracellular scl-PHA degrading enzymes, extracellular enzymes that can degrade mcl-PHAs are poorly investigated. In this project, Proteobacteria members that produce extracellular mcl-PHAs depolymerases/ lipases were screened on mcl-PHA agar plates. Then, genes involved in the production and regulation of mcl-PHA depolymerases/lipases were identified using transposon mutagenesis, insertional mutagenesis, and bioinformatics prediction tools. Once the genes were identified, the mcl-PHA depolymerase/lipase encoding genes were cloned and characterized. Burkholderia thailandensis E264, Stenotrophomonas maltophilia K279a, S. maltophilia D457, and S. maltophilia NCPPB1683 were found to produce extracellular mcl-PHA depolymerases/lipases. In Pseudomonas chlororaphis PA23, transposon mutagenesis showed that disruption of certain metabolic pathways positively affects mcl-PHA depolymerase/lipase production. Transposon mutagenesis of B. cepacia ATCC 25416 indicated that disruption of the APZ15_13320 gene negatively affected the production of pigmented metabolites and positively affected mcl-PHA depolymerase/lipase production. A novel S. maltophilia strain that can produce mcl-PHA depolymerase/lipase was discovered during the screening process as a contaminant strain of the T. caryophylli DSMZ16666. Using whole-genome sequencing and bioinformatics, a putative extracellular mcl-PHA depolymerase/lipase known as fig|40323.255.peg.2780 was identified in the novel S. maltophilia HT01 strain. The in-silico prediction of a putative extracellular mcl-PHA depolymerase/lipase in S. maltophilia K279a resulted in twenty-five protein-coding sequences. Five of the twenty-five putative depolymerase/lipases were cloned in E. coli. The E. coli clones expressing these genes were screened for degradation of polyhydroxyoctanaoate

Oleaginous red yeasts are capable of producing an array of useful bioproducts including triacylglycerides (TAGs) for biodiesel and carotenoids for nutraceuticals. The previously under-characterized oleaginous red yeast, Rhodotorula diobovata, was the focus of this research. This study first examines the effect of aeration on R. diobovata grown under nitrogen-limiting conditions. Results showed a link between nitrogen-limitation and the onset of TAG synthesis, and a link between oxygen-limitation and the onset of carotenoid synthesis. To understand the molecular basis of these results, and R. diobovata’s productivity under varying culture conditions, the genome was sequenced, assembled, annotated and compared with other oleaginous yeasts in relation to their TAG and carotenoid biosynthesis. Amino acid sequence alignments of key proteins in the de novo fatty acid and carotenoid biosynthesis pathways revealed core differences between R. diobovata and other oleaginous non-carotenogenic yeasts such as Yarrowia lipolytica and Lipomyces starkeyi. A dot-plot analysis of the nucleotide sequences of key genes in the de novo fatty acid and carotenoid biosynthesis pathways revealed multiple inversions and frame shifts between the phenotypically similar R. graminis WP1 and R. diobovata. The availability of the annotated genome allowed for a robust proteomic investigation of R. diobovata conditions across growth phases under nitrogen- and oxygen- limiting conditions. Nitrogen- and oxygen-limitation across growth phases resulted in elevated levels of NADPH supplying proteins and downregulation of acetyl-CoA supplying proteins, which resulted in an overall reduction of fatty acid synthesis. The carotenoid biosynthetic pathways were however upregulated resulting in increased concentrations of carotenoids. This implies that the flux of acetyl-CoA favoured isoprenoid biosynthesis over fatty acid biosynthesis under nitrogen- and oxygen- limiting conditions across growth curve. Overall

Zinc oxide is used in the swine industry as an antibiotic-alternative, to protect piglets against Escherichia coli infections during the post-weaning period. The global overuse of zinc oxide in piglet feed is currently a major concern in the swine industry. The post-weaning period is a markedly sensitive period for piglets that is often characterized by illness, commonly diarrhea caused by enterotoxigenic E. coli (ETEC F4). There are several issues around the use of high doses of zinc oxide, of which environmental pollution is a major consideration. As a response to this concern, this research focuses on a targeted zinc oxide delivery approach by encapsulating zinc oxide in a physiologically active material. This preserves the antimicrobial activity of zinc oxide, while reducing overuse, and the mitigating the negative environmental impacts. Three zinc oxide encapsulated delivery vehicles were fabricated: ZnO-HET (whey protein, sodium alginate, and zinc oxide in a heterogenous mix); ZnO-SW (whey protein and sodium alginate shell encapsulating a zinc oxide core); and ZnO-L100 (commercial EUDRAGIT® L100 shell encapsulating a zinc oxide core). The zinc oxide release profiles were assessed under in vitro conditions, and in extracted digestive fluids. In both situations, ZnO-L100 demonstrated the most effective targeted delivery of zinc oxide to the intestinal environment, which is the area where ETEC F4 would physiologically colonize and infect in the post-weaning piglet. ZnO-L100 delivered at least 20% more zinc oxide to the intestinal environment compared to ZnO-HET and ZnO-SW (p < 0.05). As a result of this potential, it was of interest to investigate the antibacterial ability of ZnO-L100. Using the WST-8 microbial viability assay method, we demonstrated that ZnO-L100 had ETEC F4 antibacterial activity within 30 minutes and sustained antibacterial activity beyond 150 minutes. Overall, the ZnO-L100 product was able to demonstrate a responsive release profile favourabl

Immune cell migration plays an essential role in immune surveillance and homeostasis maintenance. Misguided migratory responses of immune cells contribute to various pathological issues. Understand ing the mechanisms of immune cell migration is crucial and its investigation requires a suitable approach. Although various methods for cell migration study have been established, most of them lacking configuration of the complex microenvironment in vitro which makes the development of a suitable approach of vital importance. Organ-on-chip (OoC) approach can provide a better platform due to its ability to simulate the key features of certain tissues or organs. In this thesis, we developed different OoC related approaches to study disease-oriented immune cell migration. Specifically, we employed clinical samples in microfluidic device to simulate the microenvironment of chronic obstructive pulmonary disease (COPD), and demonstrated the usage of this approach to quantitatively investigate the complex migratory responses of T cells in COPD. Our results showed an inhibitory effect of the COPD sputum on T cell motility and chemotaxis, which may suggest a possible stopping mechanism to facilitate T cell accumulati on in the airway in COPD. We also mimicked the tumor microenvironment in vitro using primary murine natural killer (NK) cells and mouse tumor cell line (i.e., 4T1) in our microfluidic device, and demonstrated it as a proof of principle approach to study di rectional NK cell migration and NK cancer cell interactions in real-time. Furthermore, we developed a mimicked skin-on-chip (SoC) model that configured the key features of human skin and relevant chemical fields during cutaneous inflammation, and demonstrated its feasibility as a versatile tool for investigating T cell migration and screening potential drugs for targeting chemotactic signaling. Collectively, studies in this thesis bridge organ-specific applications with disease-oriented immune cell migration, and ad

Degradation of extracellular Polyhydroxyalkanoates (PHAs) in the environment depends on the secretion of specific extracellular PHA depolymerases and lipases. Compared to extracellular scl-PHA degrading enzymes, extracellular enzymes that can degrade mcl-PHAs are poorly investigated. In this project, Proteobacteria members that produce extracellular mcl-PHAs depolymerases/ lipases were screened on mcl-PHA agar plates. Then, genes involved in the production and regulation of mcl-PHA depolymerases/lipases were identified using transposon mutagenesis, insertional mutagenesis, and bioinformatics prediction tools. Once the genes were identified, the mcl-PHA depolymerase/lipase encoding genes were cloned and characterized. Burkholderia thailandensis E264, Stenotrophomonas maltophilia K279a, S. maltophilia D457, and S. maltophilia NCPPB1683 were found to produce extracellular mcl-PHA depolymerases/lipases. In Pseudomonas chlororaphis PA23, transposon mutagenesis showed that disruption of certain metabolic pathways positively affects mcl-PHA depolymerase/lipase production. Transposon mutagenesis of B. cepacia ATCC 25416 indicated that disruption of the APZ15_13320 gene negatively affected the production of pigmented metabolites and positively affected mcl-PHA depolymerase/lipase production. A novel S. maltophilia strain that can produce mcl-PHA depolymerase/lipase was discovered during the screening process as a contaminant strain of the T. caryophylli DSMZ16666. Using whole-genome sequencing and bioinformatics, a putative extracellular mcl-PHA depolymerase/lipase known as fig|40323.255.peg.2780 was identified in the novel S. maltophilia HT01 strain. The in-silico prediction of a putative extracellular mcl-PHA depolymerase/lipase in S. maltophilia K279a resulted in twenty-five protein-coding sequences. Five of the twenty-five putative depolymerase/lipases were cloned in E. coli. The E. coli clones expressing these genes were screened for degradation of polyhydroxyoctanaoate

Oleaginous red yeasts are capable of producing an array of useful bioproducts including triacylglycerides (TAGs) for biodiesel and carotenoids for nutraceuticals. The previously under-characterized oleaginous red yeast, Rhodotorula diobovata, was the focus of this research. This study first examines the effect of aeration on R. diobovata grown under nitrogen-limiting conditions. Results showed a link between nitrogen-limitation and the onset of TAG synthesis, and a link between oxygen-limitation and the onset of carotenoid synthesis. To understand the molecular basis of these results, and R. diobovata’s productivity under varying culture conditions, the genome was sequenced, assembled, annotated and compared with other oleaginous yeasts in relation to their TAG and carotenoid biosynthesis. Amino acid sequence alignments of key proteins in the de novo fatty acid and carotenoid biosynthesis pathways revealed core differences between R. diobovata and other oleaginous non-carotenogenic yeasts such as Yarrowia lipolytica and Lipomyces starkeyi. A dot-plot analysis of the nucleotide sequences of key genes in the de novo fatty acid and carotenoid biosynthesis pathways revealed multiple inversions and frame shifts between the phenotypically similar R. graminis WP1 and R. diobovata. The availability of the annotated genome allowed for a robust proteomic investigation of R. diobovata conditions across growth phases under nitrogen- and oxygen- limiting conditions. Nitrogen- and oxygen-limitation across growth phases resulted in elevated levels of NADPH supplying proteins and downregulation of acetyl-CoA supplying proteins, which resulted in an overall reduction of fatty acid synthesis. The carotenoid biosynthetic pathways were however upregulated resulting in increased concentrations of carotenoids. This implies that the flux of acetyl-CoA favoured isoprenoid biosynthesis over fatty acid biosynthesis under nitrogen- and oxygen- limiting conditions across growth curve. Overall

Zinc oxide is used in the swine industry as an antibiotic-alternative, to protect piglets against Escherichia coli infections during the post-weaning period. The global overuse of zinc oxide in piglet feed is currently a major concern in the swine industry. The post-weaning period is a markedly sensitive period for piglets that is often characterized by illness, commonly diarrhea caused by enterotoxigenic E. coli (ETEC F4). There are several issues around the use of high doses of zinc oxide, of which environmental pollution is a major consideration. As a response to this concern, this research focuses on a targeted zinc oxide delivery approach by encapsulating zinc oxide in a physiologically active material. This preserves the antimicrobial activity of zinc oxide, while reducing overuse, and the mitigating the negative environmental impacts. Three zinc oxide encapsulated delivery vehicles were fabricated: ZnO-HET (whey protein, sodium alginate, and zinc oxide in a heterogenous mix); ZnO-SW (whey protein and sodium alginate shell encapsulating a zinc oxide core); and ZnO-L100 (commercial EUDRAGIT® L100 shell encapsulating a zinc oxide core). The zinc oxide release profiles were assessed under in vitro conditions, and in extracted digestive fluids. In both situations, ZnO-L100 demonstrated the most effective targeted delivery of zinc oxide to the intestinal environment, which is the area where ETEC F4 would physiologically colonize and infect in the post-weaning piglet. ZnO-L100 delivered at least 20% more zinc oxide to the intestinal environment compared to ZnO-HET and ZnO-SW (p < 0.05). As a result of this potential, it was of interest to investigate the antibacterial ability of ZnO-L100. Using the WST-8 microbial viability assay method, we demonstrated that ZnO-L100 had ETEC F4 antibacterial activity within 30 minutes and sustained antibacterial activity beyond 150 minutes. Overall, the ZnO-L100 product was able to demonstrate a responsive release profile favourabl

Immune cell migration plays an essential role in immune surveillance and homeostasis maintenance. Misguided migratory responses of immune cells contribute to various pathological issues. Understand ing the mechanisms of immune cell migration is crucial and its investigation requires a suitable approach. Although various methods for cell migration study have been established, most of them lacking configuration of the complex microenvironment in vitro which makes the development of a suitable approach of vital importance. Organ-on-chip (OoC) approach can provide a better platform due to its ability to simulate the key features of certain tissues or organs. In this thesis, we developed different OoC related approaches to study disease-oriented immune cell migration. Specifically, we employed clinical samples in microfluidic device to simulate the microenvironment of chronic obstructive pulmonary disease (COPD), and demonstrated the usage of this approach to quantitatively investigate the complex migratory responses of T cells in COPD. Our results showed an inhibitory effect of the COPD sputum on T cell motility and chemotaxis, which may suggest a possible stopping mechanism to facilitate T cell accumulati on in the airway in COPD. We also mimicked the tumor microenvironment in vitro using primary murine natural killer (NK) cells and mouse tumor cell line (i.e., 4T1) in our microfluidic device, and demonstrated it as a proof of principle approach to study di rectional NK cell migration and NK cancer cell interactions in real-time. Furthermore, we developed a mimicked skin-on-chip (SoC) model that configured the key features of human skin and relevant chemical fields during cutaneous inflammation, and demonstrated its feasibility as a versatile tool for investigating T cell migration and screening potential drugs for targeting chemotactic signaling. Collectively, studies in this thesis bridge organ-specific applications with disease-oriented immune cell migration, and ad

The main objectives of this study were to numerically model negative air ionization for removal of bioaerosols and, to experimentally determine the effects of air ionization on the concentrations and the infectivity of aerosolized virus in enclosed spaces without ventilation. The Finite Volume Method (FVM) was used to simulate the physical processes of bioaerosol removal from air. A commercial software package (ANSYS FLUENT) was used to implement the FVM model. The transport of bioaerosols were modeled as a discrete phase using the Lagrangian approach under discrete random walk. The ions were modelled as unipolar (negatively charged) with a constant generation rate into the confined space. Experiments were conducted using a commercial ionizer in a chamber to validate the model and to quantify the effects of ionization on viral infectivity and virion (viral particles) concentrations. The model predictions of bioaerosol removal were within 22% of the measured values. The results showed that at a steady-state ion concentration of 2.4 E13 ions/m³ , ionization significantly reduced the concentrations of bioaerosols over time. The reduction of bioaerosol concentrations led to a one log10 reduction in virion concentrations over 90 s of ionization. Furthermore, at a steady-state ion concentration of 2.4 E13 ions/m³, ionization began to cause a significant reduction in viral infectivity at 30 s of ionization until a two log10 reduction in viral infectivity was achieved at 90 s. However, at a steady state ion concentration of 3.0 E10 ions/m³, ionization did not produce any significant effect on the viral infectivity. In conclusion, ionization is an effective technology for the purification of air in enclosed spaces when a critical ion threshold is present. The model presented in this study can be used as a tool to predict the spread and removal of bioaerosols in enclosed spaces.

Among different types of thermoplastics, polyhydroxyalkanoates (PHAs) with different physical/mechanical and thermal properties are well known, as they are biodegradable, biocompatible, and non-toxic. However, the main drawback of PHA biosynthesis in large scale is the high cost of production. It is known that PHA production can be considerably increased under oxygen-limited conditions. In this study, growth and synthesis of medium chain length PHAs (mcl-PHAs) by Pseudomonas putida LS46 cultured with octanoic acid under oxygen-limited conditions in the batch mode was modeled. Four models including the Monod model incorporated Leudeking–Piret (MLP), the Moser model incorporated Leudeking–Piret (Moser-LP), the Logistic model incorporated Leudeking–Piret (LLP), and the Modified Logistic model incorporated Leudeking–Piret (MLLP) were investigated. Kinetic parameters of each model were calibrated by using the multi-objective optimization algorithm, Pareto Archived Dynamically Dimensioned Search (PA-DDS) by minimizing the sum of absolute error (SAE) for PHA production and growth simultaneously. Among the four models, MLP and Moser-LP models adequately represented the experimental data for oxygen limited conditions. In addition, the MLP and Moser-LP models could not adequately simulate PHA production under oxygen excess conditions. For growth, under oxygen excess conditions, this deviation was not very significant.

Thin-layer drying characteristics of fresh and partially field-dried buckwheat hay were studied at 30 to 180 °C drying temperatures, 12.5 to 60% relative humidities and 0.2 m s-1 constant airflow. The hay was harvested three different times with a 10 to 12 days interval between the harvesting times. Three-fourth of the harvested hay was sun-dried on the field for 4 days (referred to as partially field-dried hay). The drying behaviour of different parts of the hay (flowers, leaves and stems) was tested separately. During drying, the hay samples’ mass was measured at intervals of 60 to 900 s. These measurements were used to characterize the drying behaviour of fresh or partially field-dried hay, which include: mass ratios, drying constants, effective water diffusivities and activation energies. Non-linear regression analysis was conducted using semi-theoretical or empirical models. A constant-rate period of drying for different parts of both fresh and partial field-dried hay was not observed. These distinctive parts required varying drying times to reach their EMC. The order of the drying time from fastest to slowest, is: flowers, leaves, then stems. Partially field-dried and/or later harvested hay needed less drying time. Because of its highest R2 and the lowest MSE, the logarithmic model was the best fit model for all of the tested drying and harvest conditions. Optimum harvesting time was about 70 days after sowing. The hay’s effective moisture diffusivity ranged between 10-12 to 10-9 m2 s-1; the activation energy of the hay ranged between 19.63 to 37.42 kJ mol-1. The determined drying characteristics of fresh and field-dried hay would be useful in designing of commercial drying system for buckwheat hay.

Thin-layer drying characteristics of fresh and partially field-dried buckwheat hay were studied at 30 to 180 °C drying temperatures, 12.5 to 60% relative humidities and 0.2 m s-1 constant airflow. The hay was harvested three different times with a 10 to 12 days interval between the harvesting times. Three-fourth of the harvested hay was sun-dried on the field for 4 days (referred to as partially field-dried hay). The drying behaviour of different parts of the hay (flowers, leaves and stems) was tested separately. During drying, the hay samples’ mass was measured at intervals of 60 to 900 s. These measurements were used to characterize the drying behaviour of fresh or partially field-dried hay, which include: mass ratios, drying constants, effective water diffusivities and activation energies. Non-linear regression analysis was conducted using semi-theoretical or empirical models. A constant-rate period of drying for different parts of both fresh and partial field-dried hay was not observed. These distinctive parts required varying drying times to reach their EMC. The order of the drying time from fastest to slowest, is: flowers, leaves, then stems. Partially field-dried and/or later harvested hay needed less drying time. Because of its highest R2 and the lowest MSE, the logarithmic model was the best fit model for all of the tested drying and harvest conditions. Optimum harvesting time was about 70 days after sowing. The hay’s effective moisture diffusivity ranged between 10-12 to 10-9 m2 s-1; the activation energy of the hay ranged between 19.63 to 37.42 kJ mol-1. The determined drying characteristics of fresh and field-dried hay would be useful in designing of commercial drying system for buckwheat hay.

The main objectives of this study were to numerically model negative air ionization for removal of bioaerosols and, to experimentally determine the effects of air ionization on the concentrations and the infectivity of aerosolized virus in enclosed spaces without ventilation. The Finite Volume Method (FVM) was used to simulate the physical processes of bioaerosol removal from air. A commercial software package (ANSYS FLUENT) was used to implement the FVM model. The transport of bioaerosols were modeled as a discrete phase using the Lagrangian approach under discrete random walk. The ions were modelled as unipolar (negatively charged) with a constant generation rate into the confined space. Experiments were conducted using a commercial ionizer in a chamber to validate the model and to quantify the effects of ionization on viral infectivity and virion (viral particles) concentrations. The model predictions of bioaerosol removal were within 22% of the measured values. The results showed that at a steady-state ion concentration of 2.4 E13 ions/m³ , ionization significantly reduced the concentrations of bioaerosols over time. The reduction of bioaerosol concentrations led to a one log10 reduction in virion concentrations over 90 s of ionization. Furthermore, at a steady-state ion concentration of 2.4 E13 ions/m³, ionization began to cause a significant reduction in viral infectivity at 30 s of ionization until a two log10 reduction in viral infectivity was achieved at 90 s. However, at a steady state ion concentration of 3.0 E10 ions/m³, ionization did not produce any significant effect on the viral infectivity. In conclusion, ionization is an effective technology for the purification of air in enclosed spaces when a critical ion threshold is present. The model presented in this study can be used as a tool to predict the spread and removal of bioaerosols in enclosed spaces.

Thin-layer drying characteristics of fresh and partially field-dried buckwheat hay were studied at 30 to 180 °C drying temperatures, 12.5 to 60% relative humidities and 0.2 m s-1 constant airflow. The hay was harvested three different times with a 10 to 12 days interval between the harvesting times. Three-fourth of the harvested hay was sun-dried on the field for 4 days (referred to as partially field-dried hay). The drying behaviour of different parts of the hay (flowers, leaves and stems) was tested separately. During drying, the hay samples’ mass was measured at intervals of 60 to 900 s. These measurements were used to characterize the drying behaviour of fresh or partially field-dried hay, which include: mass ratios, drying constants, effective water diffusivities and activation energies. Non-linear regression analysis was conducted using semi-theoretical or empirical models. A constant-rate period of drying for different parts of both fresh and partial field-dried hay was not observed. These distinctive parts required varying drying times to reach their EMC. The order of the drying time from fastest to slowest, is: flowers, leaves, then stems. Partially field-dried and/or later harvested hay needed less drying time. Because of its highest R2 and the lowest MSE, the logarithmic model was the best fit model for all of the tested drying and harvest conditions. Optimum harvesting time was about 70 days after sowing. The hay’s effective moisture diffusivity ranged between 10-12 to 10-9 m2 s-1; the activation energy of the hay ranged between 19.63 to 37.42 kJ mol-1. The determined drying characteristics of fresh and field-dried hay would be useful in designing of commercial drying system for buckwheat hay.

Thin-layer drying characteristics of fresh and partially field-dried buckwheat hay were studied at 30 to 180 °C drying temperatures, 12.5 to 60% relative humidities and 0.2 m s-1 constant airflow. The hay was harvested three different times with a 10 to 12 days interval between the harvesting times. Three-fourth of the harvested hay was sun-dried on the field for 4 days (referred to as partially field-dried hay). The drying behaviour of different parts of the hay (flowers, leaves and stems) was tested separately. During drying, the hay samples’ mass was measured at intervals of 60 to 900 s. These measurements were used to characterize the drying behaviour of fresh or partially field-dried hay, which include: mass ratios, drying constants, effective water diffusivities and activation energies. Non-linear regression analysis was conducted using semi-theoretical or empirical models. A constant-rate period of drying for different parts of both fresh and partial field-dried hay was not observed. These distinctive parts required varying drying times to reach their EMC. The order of the drying time from fastest to slowest, is: flowers, leaves, then stems. Partially field-dried and/or later harvested hay needed less drying time. Because of its highest R2 and the lowest MSE, the logarithmic model was the best fit model for all of the tested drying and harvest conditions. Optimum harvesting time was about 70 days after sowing. The hay’s effective moisture diffusivity ranged between 10-12 to 10-9 m2 s-1; the activation energy of the hay ranged between 19.63 to 37.42 kJ mol-1. The determined drying characteristics of fresh and field-dried hay would be useful in designing of commercial drying system for buckwheat hay.

Hydrogels have been widely used in the biomedical sector in recent years. However, conventional hydrogels’ disadvantages of poor mechanical performance and lack of efficient self-healing ability limit their practical application. A novel versatile hydrogel with excellent mechanical properties and extraordinary self-healing efficiency was developed by integrating graphene oxide (GO) nanoparticles into a polyacrylic acid (PAA) hydrogel network crosslinked by an organic crosslinker N,N’ methylenebisacrylamide (MBA) and an inorganic crosslinker Ca2+. The resulting PAA-GO-Ca2+ hydrogel, with both covalent and physical dual-crosslinked networks demonstrated remarkable mechanical properties including an ultrahigh strain of 2500% and high toughness (~9.73MJm-3) along with high stiffness (Young’s modulus:~753.667KPa). In addition, the hydrogel also shows super effective self-healing ability (~87.47%, 88.02% and 86.93% healing efficiency in tensile strength, tensile strain, and toughness respectively) which is attributed to the reversible hydrogen bondings existing in abundant hydrogen-containing functional groups and ionic interactions between COO- groups existing in both PAA and GO. To achieve facile fabrication of the developed multifunctional hydrogels for such advanced applications as biosensors, we adjusted the viscosity of the hydrogels by controlling their degree of crosslinking to allow 3D printing. The 3D printed PAA-GO-Ca2+ hydrogels were further treated with HI vapor to reduce GO on the surface of the hydrogels and produce conductive PAA-rGO-Ca2+ hydrogels for different types of wearable biosensors, including sensors to detect different humans activities such as pulse rate, breathing, finger movement, sensors to monitor sweating levels, and ammonia detectors which detect toxic ammonia gas at low concentrations.

This research study evaluated the effect of ceftiofur (CEF), one of the most commonly used antibiotics on dairy farms, on the performance and stability of mesophilic anaerobic digestion of dairy manure, in terms of methane production, organic matter removal (COD, dCOD, TS, and VS) and intermediates (VFAs) profile. Additionally, this study also determined the fate of the antibiotic-resistance gene (ARG) cmy-2, a cephalosporin-resistance marker, in a mesophilic fed-batch anaerobic digester over a 600-day period and assessed how the presence of CEF alters the cmy-2 removal rate in 15-day batch anaerobic digestions. A semi-continuous lab-scale anaerobic digester was set up and operated under mesophilic conditions, with a hydraulic retention time of 30 days and fed with dairy manure from a commercial farm. The sludge of the digester was analyzed for cmy-2 levels and used as inoculum for batch experiments where different CEF concentrations (0.2-250 mg/L) were tested. The results indicated that low CEF concentrations (0.2 – 2 mg/L) do not have any significant effect on either methane production or the stability of the process. CEF concentrations of 10 mg/L can reduce methane productivity by more than 10% in anaerobic digesters operated at HRTs below 20 days. The presence of high CEF levels (50-250 mg/L) can cause a decrease in methane production of up to 60%, although the overall stability of the process is not compromised. The biochemical analyses suggested that hydrolytic microorganisms were the most affected by the presence of the antibiotic, while acetogens seemed to have temporarily slowed down, which was reflected in lower organic matter removal and slightly greater levels of butyrate and valerate accumulation during the anaerobic digestion process, respectively. Methanogens, on the other hand, were not affected, since no acetate or hydrogen accumulation was detected. Regarding the levels of the antibiotic resistance gene cmy-2, this study demonstrated that anaerobic

Metabolic shifts are associated with physico-chemical environment changes during the growth phase of many types of cells. An inability to monitor rapid and/or subtle changes in microbial metabolism may sometimes limit our understanding of microbial physiology. The central focus of this thesis was to better understand changes in microbial metabolism induced by changes in growth conditions (carbon-excess, end-product concentration such as acetate, quick removal of product gases), which may be acquired by continuous monitoring. Clostridium termitidis was chosen as the model organism for this work. A mass spectrometry-based Titration and Off-Gas Analysis (TOGA) system was used as an on-line monitoring tool for headspace gases (H2, CO2, and ethanol) analysis. In addition, GC, HPLC, and spectrophotometry methods were also used for other metabolites analysis as off-line techniques. Several key metabolic shifts were recognized during the early stationary growth phase under carbon-excess condition, compared to carbon-sufficient and carbon-limited conditions. The H2 and CO2 production rates decreased significantly, while the specific rates of ethanol and formate synthesis increased significantly. As a result, the substrate specific yields of H2 were gradually decreased from exponential phase to late stationary phase, whereas the ethanol yields were increased. Decreased CO2 synthesis and increased formate synthesis suggested that carbon flux and reducing equivalent shifted from the pyruvate ferredoxin oxidoreductase (PFOR) pathway to the pyruvate formate lyase (PFL) pathway, resulting in a sudden increase of ethanol synthesis. The addition of exogenous acetate during fermentation, resulted in decreased H2 yields and significantly increased ethanol yields. The substrate specific yields of H2 and CO2 also increased significantly in cultures with a high turbulent growth environment, achieved by a high gas sparging rate (HSR) compared to the cultures with a low turbulent growth en

Positron emission tomography (PET) is a nuclear medicine imaging technique that allows quantitative evaluation of positron emitting radioactive tracers injected into a subject. In both clinical and research settings, the most commonly used radiotracer for PET imaging is the glucose analog [18F]fluorodeoxyglucose (FDG). The central strength and challenge in PET imaging is that the resulting image is of the biodistribution of the radioactively labelled tracer, rather than simply an image of anatomy. This means that biological factors can greatly influence both the appearance and quantification of the PET image, especially for FDG since it is a marker of glucose metabolism. These effective factors include fasting, anesthesia and warming the animal’s body in animal PET imaging. In addition, the animals’ health status must be monitored after imaging. A significant cost in routine small animal PET imaging is the labour associated with the imaging procedures. These animal centre labour costs can be reduced through use of automation and remote monitoring. We see that there is an unmet need for a better approach to animal preparation and monitoring post-procedure and developed a ‘Smart Cage’. This Smart Cage facilitates animal handling for PET imaging by using an automated food removal unit and remote monitoring of the mouse with visible light and night vision camera. We hypothesize that technology of this type can reduce variability in scan results and reduce animal technician costs associated with scanning. Consequently, we designed and constructed the hardware required for the Smart Cage and implemented an initial version of software to control and network the cage.

Hydrogels have been widely used in the biomedical sector in recent years. However, conventional hydrogels’ disadvantages of poor mechanical performance and lack of efficient self-healing ability limit their practical application. A novel versatile hydrogel with excellent mechanical properties and extraordinary self-healing efficiency was developed by integrating graphene oxide (GO) nanoparticles into a polyacrylic acid (PAA) hydrogel network crosslinked by an organic crosslinker N,N’ methylenebisacrylamide (MBA) and an inorganic crosslinker Ca2+. The resulting PAA-GO-Ca2+ hydrogel, with both covalent and physical dual-crosslinked networks demonstrated remarkable mechanical properties including an ultrahigh strain of 2500% and high toughness (~9.73MJm-3) along with high stiffness (Young’s modulus:~753.667KPa). In addition, the hydrogel also shows super effective self-healing ability (~87.47%, 88.02% and 86.93% healing efficiency in tensile strength, tensile strain, and toughness respectively) which is attributed to the reversible hydrogen bondings existing in abundant hydrogen-containing functional groups and ionic interactions between COO- groups existing in both PAA and GO. To achieve facile fabrication of the developed multifunctional hydrogels for such advanced applications as biosensors, we adjusted the viscosity of the hydrogels by controlling their degree of crosslinking to allow 3D printing. The 3D printed PAA-GO-Ca2+ hydrogels were further treated with HI vapor to reduce GO on the surface of the hydrogels and produce conductive PAA-rGO-Ca2+ hydrogels for different types of wearable biosensors, including sensors to detect different humans activities such as pulse rate, breathing, finger movement, sensors to monitor sweating levels, and ammonia detectors which detect toxic ammonia gas at low concentrations.

Positron emission tomography (PET) is a nuclear medicine imaging technique that allows quantitative evaluation of positron emitting radioactive tracers injected into a subject. In both clinical and research settings, the most commonly used radiotracer for PET imaging is the glucose analog [18F]fluorodeoxyglucose (FDG). The central strength and challenge in PET imaging is that the resulting image is of the biodistribution of the radioactively labelled tracer, rather than simply an image of anatomy. This means that biological factors can greatly influence both the appearance and quantification of the PET image, especially for FDG since it is a marker of glucose metabolism. These effective factors include fasting, anesthesia and warming the animal’s body in animal PET imaging. In addition, the animals’ health status must be monitored after imaging. A significant cost in routine small animal PET imaging is the labour associated with the imaging procedures. These animal centre labour costs can be reduced through use of automation and remote monitoring. We see that there is an unmet need for a better approach to animal preparation and monitoring post-procedure and developed a ‘Smart Cage’. This Smart Cage facilitates animal handling for PET imaging by using an automated food removal unit and remote monitoring of the mouse with visible light and night vision camera. We hypothesize that technology of this type can reduce variability in scan results and reduce animal technician costs associated with scanning. Consequently, we designed and constructed the hardware required for the Smart Cage and implemented an initial version of software to control and network the cage.

Metabolic shifts are associated with physico-chemical environment changes during the growth phase of many types of cells. An inability to monitor rapid and/or subtle changes in microbial metabolism may sometimes limit our understanding of microbial physiology. The central focus of this thesis was to better understand changes in microbial metabolism induced by changes in growth conditions (carbon-excess, end-product concentration such as acetate, quick removal of product gases), which may be acquired by continuous monitoring. Clostridium termitidis was chosen as the model organism for this work. A mass spectrometry-based Titration and Off-Gas Analysis (TOGA) system was used as an on-line monitoring tool for headspace gases (H2, CO2, and ethanol) analysis. In addition, GC, HPLC, and spectrophotometry methods were also used for other metabolites analysis as off-line techniques. Several key metabolic shifts were recognized during the early stationary growth phase under carbon-excess condition, compared to carbon-sufficient and carbon-limited conditions. The H2 and CO2 production rates decreased significantly, while the specific rates of ethanol and formate synthesis increased significantly. As a result, the substrate specific yields of H2 were gradually decreased from exponential phase to late stationary phase, whereas the ethanol yields were increased. Decreased CO2 synthesis and increased formate synthesis suggested that carbon flux and reducing equivalent shifted from the pyruvate ferredoxin oxidoreductase (PFOR) pathway to the pyruvate formate lyase (PFL) pathway, resulting in a sudden increase of ethanol synthesis. The addition of exogenous acetate during fermentation, resulted in decreased H2 yields and significantly increased ethanol yields. The substrate specific yields of H2 and CO2 also increased significantly in cultures with a high turbulent growth environment, achieved by a high gas sparging rate (HSR) compared to the cultures with a low turbulent growth en

This research study evaluated the effect of ceftiofur (CEF), one of the most commonly used antibiotics on dairy farms, on the performance and stability of mesophilic anaerobic digestion of dairy manure, in terms of methane production, organic matter removal (COD, dCOD, TS, and VS) and intermediates (VFAs) profile. Additionally, this study also determined the fate of the antibiotic-resistance gene (ARG) cmy-2, a cephalosporin-resistance marker, in a mesophilic fed-batch anaerobic digester over a 600-day period and assessed how the presence of CEF alters the cmy-2 removal rate in 15-day batch anaerobic digestions. A semi-continuous lab-scale anaerobic digester was set up and operated under mesophilic conditions, with a hydraulic retention time of 30 days and fed with dairy manure from a commercial farm. The sludge of the digester was analyzed for cmy-2 levels and used as inoculum for batch experiments where different CEF concentrations (0.2-250 mg/L) were tested. The results indicated that low CEF concentrations (0.2 – 2 mg/L) do not have any significant effect on either methane production or the stability of the process. CEF concentrations of 10 mg/L can reduce methane productivity by more than 10% in anaerobic digesters operated at HRTs below 20 days. The presence of high CEF levels (50-250 mg/L) can cause a decrease in methane production of up to 60%, although the overall stability of the process is not compromised. The biochemical analyses suggested that hydrolytic microorganisms were the most affected by the presence of the antibiotic, while acetogens seemed to have temporarily slowed down, which was reflected in lower organic matter removal and slightly greater levels of butyrate and valerate accumulation during the anaerobic digestion process, respectively. Methanogens, on the other hand, were not affected, since no acetate or hydrogen accumulation was detected. Regarding the levels of the antibiotic resistance gene cmy-2, this study demonstrated that anaerobic

Positron emission tomography (PET) is a nuclear medicine imaging technique that allows quantitative evaluation of positron emitting radioactive tracers injected into a subject. In both clinical and research settings, the most commonly used radiotracer for PET imaging is the glucose analog [18F]fluorodeoxyglucose (FDG). The central strength and challenge in PET imaging is that the resulting image is of the biodistribution of the radioactively labelled tracer, rather than simply an image of anatomy. This means that biological factors can greatly influence both the appearance and quantification of the PET image, especially for FDG since it is a marker of glucose metabolism. These effective factors include fasting, anesthesia and warming the animal’s body in animal PET imaging. In addition, the animals’ health status must be monitored after imaging. A significant cost in routine small animal PET imaging is the labour associated with the imaging procedures. These animal centre labour costs can be reduced through use of automation and remote monitoring. We see that there is an unmet need for a better approach to animal preparation and monitoring post-procedure and developed a ‘Smart Cage’. This Smart Cage facilitates animal handling for PET imaging by using an automated food removal unit and remote monitoring of the mouse with visible light and night vision camera. We hypothesize that technology of this type can reduce variability in scan results and reduce animal technician costs associated with scanning. Consequently, we designed and constructed the hardware required for the Smart Cage and implemented an initial version of software to control and network the cage.

Hydrogels have been widely used in the biomedical sector in recent years. However, conventional hydrogels’ disadvantages of poor mechanical performance and lack of efficient self-healing ability limit their practical application. A novel versatile hydrogel with excellent mechanical properties and extraordinary self-healing efficiency was developed by integrating graphene oxide (GO) nanoparticles into a polyacrylic acid (PAA) hydrogel network crosslinked by an organic crosslinker N,N’ methylenebisacrylamide (MBA) and an inorganic crosslinker Ca2+. The resulting PAA-GO-Ca2+ hydrogel, with both covalent and physical dual-crosslinked networks demonstrated remarkable mechanical properties including an ultrahigh strain of 2500% and high toughness (~9.73MJm-3) along with high stiffness (Young’s modulus:~753.667KPa). In addition, the hydrogel also shows super effective self-healing ability (~87.47%, 88.02% and 86.93% healing efficiency in tensile strength, tensile strain, and toughness respectively) which is attributed to the reversible hydrogen bondings existing in abundant hydrogen-containing functional groups and ionic interactions between COO- groups existing in both PAA and GO. To achieve facile fabrication of the developed multifunctional hydrogels for such advanced applications as biosensors, we adjusted the viscosity of the hydrogels by controlling their degree of crosslinking to allow 3D printing. The 3D printed PAA-GO-Ca2+ hydrogels were further treated with HI vapor to reduce GO on the surface of the hydrogels and produce conductive PAA-rGO-Ca2+ hydrogels for different types of wearable biosensors, including sensors to detect different humans activities such as pulse rate, breathing, finger movement, sensors to monitor sweating levels, and ammonia detectors which detect toxic ammonia gas at low concentrations.

Positron emission tomography (PET) is a nuclear medicine imaging technique that allows quantitative evaluation of positron emitting radioactive tracers injected into a subject. In both clinical and research settings, the most commonly used radiotracer for PET imaging is the glucose analog [18F]fluorodeoxyglucose (FDG). The central strength and challenge in PET imaging is that the resulting image is of the biodistribution of the radioactively labelled tracer, rather than simply an image of anatomy. This means that biological factors can greatly influence both the appearance and quantification of the PET image, especially for FDG since it is a marker of glucose metabolism. These effective factors include fasting, anesthesia and warming the animal’s body in animal PET imaging. In addition, the animals’ health status must be monitored after imaging. A significant cost in routine small animal PET imaging is the labour associated with the imaging procedures. These animal centre labour costs can be reduced through use of automation and remote monitoring. We see that there is an unmet need for a better approach to animal preparation and monitoring post-procedure and developed a ‘Smart Cage’. This Smart Cage facilitates animal handling for PET imaging by using an automated food removal unit and remote monitoring of the mouse with visible light and night vision camera. We hypothesize that technology of this type can reduce variability in scan results and reduce animal technician costs associated with scanning. Consequently, we designed and constructed the hardware required for the Smart Cage and implemented an initial version of software to control and network the cage.

Bacterial infection is a serious issue in wound healing. Extensive use of biocides in wound dressings have raised concerns like biocide resistance and unwanted harm to normal skin cells. In this thesis, I report a new approach to realize bacteria-triggered release of biocide to the sites of bacterial infections from core-shell polyhydroxyalkanoate (PHA)-based nanofibers prepared by coaxial electrospinning. The hydrophobic PHA-based shell can effectively prevent the biocide from undesirable payload release in physiological environments without pathogens. However, in the presence of pathogens, the PHA-based shell is degraded by pathogens, and the encapsulated biocide is released. The released biocide subsequently can impose targeted antimicrobial effects on the bacteria. Using Pseudomonas aeruginosa as a model bacterium and dodecyltrimethylammonium chloride as a model biocide, we demonstrated that the core-shell PHA-based nanofibers released encapsulated dodecyltrimethylammonium chloride in the presence of Pseudomonas aeruginosa, resulting in targeted inhibition of Pseudomonas aeruginosa growth.

Biofilm formation on medical devices can cause persistent infections. The main feature of biofilms is their self-produced extracellular polymeric substances (EPS) that act as a protective shield to prevent biocide penetration. Iron oxide magnetic nanoparticles (MNPs), synthesized through a simple process, were used as “shield breakers” to damage the biofilm matrix and cause biofilm detachment. The Methicillin-resistant Staphylococcus aureus (MRSA) strain was used to demonstrate the efficacy of MNPs. The highest logarithmic reduction (4.71 log) of S. aureus biofilm was achieved after treatment with 30 mg/mL of 11 nm MNPs under rotating magnetic field for 15 minutes. MNPs caused strong mechanical disruption to the matrix and led to biofilm dispersal. Both alternating and rotating magnetic fields improved the effect of MNPs on biofilm damage. The increased MNPs solution temperature produces by hyperthermic effect in the AC field while the MNPs caused physical damage on biofilms in rotating magnetic field.

Bacterial infection is a serious issue in wound healing. Extensive use of biocides in wound dressings have raised concerns like biocide resistance and unwanted harm to normal skin cells. In this thesis, I report a new approach to realize bacteria-triggered release of biocide to the sites of bacterial infections from core-shell polyhydroxyalkanoate (PHA)-based nanofibers prepared by coaxial electrospinning. The hydrophobic PHA-based shell can effectively prevent the biocide from undesirable payload release in physiological environments without pathogens. However, in the presence of pathogens, the PHA-based shell is degraded by pathogens, and the encapsulated biocide is released. The released biocide subsequently can impose targeted antimicrobial effects on the bacteria. Using Pseudomonas aeruginosa as a model bacterium and dodecyltrimethylammonium chloride as a model biocide, we demonstrated that the core-shell PHA-based nanofibers released encapsulated dodecyltrimethylammonium chloride in the presence of Pseudomonas aeruginosa, resulting in targeted inhibition of Pseudomonas aeruginosa growth.

Bacterial infection is a serious issue in wound healing. Extensive use of biocides in wound dressings have raised concerns like biocide resistance and unwanted harm to normal skin cells. In this thesis, I report a new approach to realize bacteria-triggered release of biocide to the sites of bacterial infections from core-shell polyhydroxyalkanoate (PHA)-based nanofibers prepared by coaxial electrospinning. The hydrophobic PHA-based shell can effectively prevent the biocide from undesirable payload release in physiological environments without pathogens. However, in the presence of pathogens, the PHA-based shell is degraded by pathogens, and the encapsulated biocide is released. The released biocide subsequently can impose targeted antimicrobial effects on the bacteria. Using Pseudomonas aeruginosa as a model bacterium and dodecyltrimethylammonium chloride as a model biocide, we demonstrated that the core-shell PHA-based nanofibers released encapsulated dodecyltrimethylammonium chloride in the presence of Pseudomonas aeruginosa, resulting in targeted inhibition of Pseudomonas aeruginosa growth.

Biofilm formation on medical devices can cause persistent infections. The main feature of biofilms is their self-produced extracellular polymeric substances (EPS) that act as a protective shield to prevent biocide penetration. Iron oxide magnetic nanoparticles (MNPs), synthesized through a simple process, were used as “shield breakers” to damage the biofilm matrix and cause biofilm detachment. The Methicillin-resistant Staphylococcus aureus (MRSA) strain was used to demonstrate the efficacy of MNPs. The highest logarithmic reduction (4.71 log) of S. aureus biofilm was achieved after treatment with 30 mg/mL of 11 nm MNPs under rotating magnetic field for 15 minutes. MNPs caused strong mechanical disruption to the matrix and led to biofilm dispersal. Both alternating and rotating magnetic fields improved the effect of MNPs on biofilm damage. The increased MNPs solution temperature produces by hyperthermic effect in the AC field while the MNPs caused physical damage on biofilms in rotating magnetic field.

Bacterial infection is a serious issue in wound healing. Extensive use of biocides in wound dressings have raised concerns like biocide resistance and unwanted harm to normal skin cells. In this thesis, I report a new approach to realize bacteria-triggered release of biocide to the sites of bacterial infections from core-shell polyhydroxyalkanoate (PHA)-based nanofibers prepared by coaxial electrospinning. The hydrophobic PHA-based shell can effectively prevent the biocide from undesirable payload release in physiological environments without pathogens. However, in the presence of pathogens, the PHA-based shell is degraded by pathogens, and the encapsulated biocide is released. The released biocide subsequently can impose targeted antimicrobial effects on the bacteria. Using Pseudomonas aeruginosa as a model bacterium and dodecyltrimethylammonium chloride as a model biocide, we demonstrated that the core-shell PHA-based nanofibers released encapsulated dodecyltrimethylammonium chloride in the presence of Pseudomonas aeruginosa, resulting in targeted inhibition of Pseudomonas aeruginosa growth.

Enhanced biodenitrification is a technique for remediation of nutrient impacts that uses electron donor amendments to stimulate the microbial community present in natural groundwater aquifers. This study evaluated ethanol as a carbon source to decrease elevated nutrients in groundwater and soil microcosms under cold climate conditions. Initial microcosm nutrient concentrations of ammonia-N, nitrate-N, and nitrite-N were 2010 mg/L, 1690 mg/L, and 118 mg/L, respectively. Ethanol treatments showed that the nitrate-N and nitrite-N concentrations decreased to non-detectable limits in 56 days and ammonia-N decreased by 48% in 231 days. A second experiment examined the effect of vadose zone ethanol injections into nutrient impacted soil columns. The study indicated the ethanol amendments degraded 1.3, 13.9, and 27.2% of nitrate-N concentrations in the three soil columns. However, the vadose zone showed a decrease of 92.4 to 99.4% due to displacement and degradation. Overall biodenitrification shows promise as a cost-effective remedial solution.

Means of improving the quality of CM for poultry, including breeding for low-fiber canola and the use of exogenous enzymes, have been proposed. The objectives of the current study were: (1) To evaluate the chemical and nutritive composition of new yellow-seeded B. napus and B. juncea canola, (2) To investigate the effect of canola type and enzyme supplementation on AMEn and SID of amino acids, and growth performance of broiler chickens, (3) To explore the new carbohydrase enzymes for their ability to depolymerize NSP of CM in vitro, and (4) To evaluate the effect of new enzyme combinations in vivo with broiler chickens. In comparison with the conventional meal, yellow-seeded B. napus and B. juncea contained more crude protein, more sucrose, and less dietary fiber. The AMEn and SID amino acid values for yellow-seeded B. napus, B. juncea canola, and the conventional black-seeded B. napus were 1865, 2092 and 1902 kcal/kg DM, and 82.5, 83.2, and 81.8%, respectively. Enzyme addition resulted in a more pronounced effect on the AMEn content of B. juncea meal. When birds were fed diets containing 15% CM, BWG averaged 2.32, 2.30, 2.19, and 2.31 kg for the SBM-based Control, black and yellow B. napus, and B. juncea meals, respectively. A lower (P<0.05) BWG was observed in birds fed a diet containing 30% of B. juncea meal. In another experiment, enzyme supplementation improved FCR in chicks fed B. juncea meal. In the in vitro enzyme incubation studies, enzyme preparations galactanase/pectinase and cellulase/xylanase showed NSP degradation of more than 40%, and were subsequently used in the broiler chicken experiments. A lower BWG and higher intestinal viscosity were observed in birds fed the enzyme-supplemented diet containing 30% of B. juncea meal. High digesta viscosity could be attributed to the release of water-soluble NSP due to the low dietary enzyme concentration and/or unfavorable gut conditions. No differences in growth performance were observed in broiler chickens fe

One of the major challenges for the pig industry is to control nursery feed costs to maximize profits. The objective of this research was to evaluate potential economic benefits of nutritional strategies for nursery feed costs. The results from 3 experiments show that a simple diet and a fermented wheat diet would be beneficial, directly reducing feed cost and/or increasing nutrient and energy digestibility, respectively, in weaned pigs. The addition of multicarbohydrase in nursery diets would also provide potential economic benefits, improving feed efficiency, nutrient digestibility, and gut health.

I would like to convey my sincerest thanks to my supervisor Dr. John Sorensen for his seemingly unending patience and compassion; without it I would not have finished this program. I have learned a great deal under his guidance. Secondly I owe the Levin, Birouk, and McKenna groups for their collaboration that aided in the overall success of my projects. The Levin group for providing the PHA polymer that I worked with, the Birouk (specifically Carlos Casanova) for testing the combustion properties of my fuel, and the McKenna group (specifically Ewan McRae) for running the RNA assay on my G-quadruplex ligands. I would also like to thank Olds College for running combustion tests on my fuel as well. I would also like to thank the funding I received from Biofuelnet and Dr. Sean McKenna since it kept me alive during my studies. Finally I would like to thank all the people who supported me: my wife Rebecca for putting up with my insanity, my mother Dorothy for always encouraging to pursue higher education, and my friends for being there for me when I always need it.

Enhanced biodenitrification is a technique for remediation of nutrient impacts that uses electron donor amendments to stimulate the microbial community present in natural groundwater aquifers. This study evaluated ethanol as a carbon source to decrease elevated nutrients in groundwater and soil microcosms under cold climate conditions. Initial microcosm nutrient concentrations of ammonia-N, nitrate-N, and nitrite-N were 2010 mg/L, 1690 mg/L, and 118 mg/L, respectively. Ethanol treatments showed that the nitrate-N and nitrite-N concentrations decreased to non-detectable limits in 56 days and ammonia-N decreased by 48% in 231 days. A second experiment examined the effect of vadose zone ethanol injections into nutrient impacted soil columns. The study indicated the ethanol amendments degraded 1.3, 13.9, and 27.2% of nitrate-N concentrations in the three soil columns. However, the vadose zone showed a decrease of 92.4 to 99.4% due to displacement and degradation. Overall biodenitrification shows promise as a cost-effective remedial solution.

Means of improving the quality of CM for poultry, including breeding for low-fiber canola and the use of exogenous enzymes, have been proposed. The objectives of the current study were: (1) To evaluate the chemical and nutritive composition of new yellow-seeded B. napus and B. juncea canola, (2) To investigate the effect of canola type and enzyme supplementation on AMEn and SID of amino acids, and growth performance of broiler chickens, (3) To explore the new carbohydrase enzymes for their ability to depolymerize NSP of CM in vitro, and (4) To evaluate the effect of new enzyme combinations in vivo with broiler chickens. In comparison with the conventional meal, yellow-seeded B. napus and B. juncea contained more crude protein, more sucrose, and less dietary fiber. The AMEn and SID amino acid values for yellow-seeded B. napus, B. juncea canola, and the conventional black-seeded B. napus were 1865, 2092 and 1902 kcal/kg DM, and 82.5, 83.2, and 81.8%, respectively. Enzyme addition resulted in a more pronounced effect on the AMEn content of B. juncea meal. When birds were fed diets containing 15% CM, BWG averaged 2.32, 2.30, 2.19, and 2.31 kg for the SBM-based Control, black and yellow B. napus, and B. juncea meals, respectively. A lower (P<0.05) BWG was observed in birds fed a diet containing 30% of B. juncea meal. In another experiment, enzyme supplementation improved FCR in chicks fed B. juncea meal. In the in vitro enzyme incubation studies, enzyme preparations galactanase/pectinase and cellulase/xylanase showed NSP degradation of more than 40%, and were subsequently used in the broiler chicken experiments. A lower BWG and higher intestinal viscosity were observed in birds fed the enzyme-supplemented diet containing 30% of B. juncea meal. High digesta viscosity could be attributed to the release of water-soluble NSP due to the low dietary enzyme concentration and/or unfavorable gut conditions. No differences in growth performance were observed in broiler chickens fe

One of the major challenges for the pig industry is to control nursery feed costs to maximize profits. The objective of this research was to evaluate potential economic benefits of nutritional strategies for nursery feed costs. The results from 3 experiments show that a simple diet and a fermented wheat diet would be beneficial, directly reducing feed cost and/or increasing nutrient and energy digestibility, respectively, in weaned pigs. The addition of multicarbohydrase in nursery diets would also provide potential economic benefits, improving feed efficiency, nutrient digestibility, and gut health.

I would like to convey my sincerest thanks to my supervisor Dr. John Sorensen for his seemingly unending patience and compassion; without it I would not have finished this program. I have learned a great deal under his guidance. Secondly I owe the Levin, Birouk, and McKenna groups for their collaboration that aided in the overall success of my projects. The Levin group for providing the PHA polymer that I worked with, the Birouk (specifically Carlos Casanova) for testing the combustion properties of my fuel, and the McKenna group (specifically Ewan McRae) for running the RNA assay on my G-quadruplex ligands. I would also like to thank Olds College for running combustion tests on my fuel as well. I would also like to thank the funding I received from Biofuelnet and Dr. Sean McKenna since it kept me alive during my studies. Finally I would like to thank all the people who supported me: my wife Rebecca for putting up with my insanity, my mother Dorothy for always encouraging to pursue higher education, and my friends for being there for me when I always need it.