This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

In the human gut, bacterial fermentation of dietary fibers and proteins produces metabolites, primarily as short-chain fatty acids (SCFA), that are highly beneficial for host health. However, unlike dietary fiber, bacterial fermentation of protein additionally generates potentially toxic substances such as ammonia, hydrogen sulfide, amines, and indoles. It is believed that most gut bacteria favor utilization of dietary fiber over that of protein for energy. Therefore, when fermentable dietary fiber is readily available to colonic bacteria, protein fermentation, and its subsequent potentially toxic metabolites, remains relatively low. Dietary intake primarily determines the quantity of dietary fiber and protein substrate available to the gut microbiota and the resulting profile of metabolites produced. Increased protein consumption is associated with deleterious health outcomes such as higher risk of colorectal cancer and type II diabetes. Conversely, diets following US dietary recommendations are high in fiber, which promote a healthy microbiome and are protective against disease. Diets following the recommendation are also moderate in protein intake so that, ultimately, far more fiber than protein is available for colonic bacterial fermentation. On the contrary, dietary fiber intake is chronically low in a standard Western diet, while protein consumption is above dietary recommendations, which results in nearly equal amounts of dietary fiber and protein available for gut microbial fermentation. Furthermore, the popularity of high-protein diets for athletes, as well as that of high-protein low-carbohydrate diets for weight loss, may flip fiber and protein substrate proportions upside down, resulting in more protein than fiber available in the gut for fermentation. The objective of this study was to elucidate how substrate ratios in protein-fiber mixtures affect protein fermentation and metabolites, as well as examine the degree to which fiber source may influence these outcomes. Each dietary fiber source [fructooligosaccharides (FOS), apple pectin (Pectin), a wheat bran and raw potato starch mixture (WB+PS), and an even mixture of the three aforementioned fibers (Even Mix)] and protein were combined in three ratios and provided as substrate for in vitro fecal fermentation to understand how low, medium, and high fiber inclusion levels influence fermentation outcomes. They were compared to 100% protein and fiber (each different fiber) controls. Branched-chain fatty acids (BCFAs), metabolites produced exclusively from protein fermentation, were used as a measure of protein fermentation; the data were normalized based on the initial quantity of protein within the substrate. In protein-fiber substrate mixtures, only FOS and Even Mix inhibited BCFAs (mM/g protein basis) and only when they made up at least half of the substrate. Unexpectedly, the rate of protein fermentation was increased when the protein-fiber substrate contained 25% WB+PS fiber, possibly due to the starch component of the fiber. There was evidence that when pH drops during fermentation, as was the case for protein-FOS mixtures, it played a significant role in suppressing protein fermentation. Ammonia production was not largely affected by increasing the proportion of dietary fiber. A significant reduction did not occur until FOS made up at least 50% of the protein-fiber substrate; for Pectin, WB+PS, and Even Mix fibers, 75% inclusion was required for a significant decrease in ammonia. Interestingly, protein was butyrogenic. Protein as the sole substrate produced more butyrate than either Pectin or Even Mix as the sole substrates, and in fact, addition of Pectin to protein significantly reduced butyrate concentrations. However, the possible benefits of butyrate produced via protein fermentation needs to be tempered by the production of potentially toxic compounds and the association between protein fermentation and colorectal cancer. Overall, the thesis findings showed protein fermentation to be relatively stable and not easily influenced by increasing the availability of dietary fiber, and no clear evidence of microbial preference for carbohydrates over protein was found.

<p>  </p> <p>School-based agricultural education programs use laboratories to develop cognitive, psychomotor, and procedural skills (Phipps et al., 2008). It is important to help preservice teachers develop the ability to design instruction to cultivate skills that are taught in laboratory settings. Shulman (1986) authored a term called Pedagogical Content Knowledge (PCK), which is a teacher’s knowledge of teaching. Animal science dissection was the topic chosen for this study, as PCK is topic-specific (Chan & Hume, 2018). There are many interpretations of PCK. The Refined Consensus Model (RCM) of PCK in Science Education (Carlson et al., 2019) was the conceptual model used in this study, as it is the most recent PCK model, and was developed by experts in science education from multiple countries. This model asserts that PCK is comprised of three realms: Collective PCK (cPCK), Personal PCK (pPCK), and Enacted PCK (ePCK). The first purpose of this study was to describe preservice agriculture teachers' Professional Knowledge Bases (which informs pPCK), before and after instruction, on the topic of animal science dissection in a Laboratory Practices in Agricultural Education (LPAE) course. The second purpose was to describe preservice agriculture teachers' cPCK, after instruction, on animal science dissection in an LPAE course. Content Representations (CoRes), a common tool used for PCK research, were used identify evidence of the Professional Knowledge Bases (PKBs) in preservice agriculture teachers’ instructional planning. Results from this study showed elevated descriptions of Professional Knowledge Bases, and participants collectively gained new ideas and collaboration skills. Overall LPAE dissection experience appeared to push the depth of student thinking and ability to make connections with future learning. Future research recommendations include using the RCM of PCK (Carlson et al., 2019) and CoRes in agricultural education; more PCK research, specifically exploring the development of Curricular Knowledge, on preservice teachers in agricultural education; and PCK research on other topics in agricultural education. It is recommended to not only include PCK development in teacher preparation programs but also have more than one exposure to PCK development.</p>

The cell wall provides a complex and rigid structure to the plant for support, protection from environmental factors, and transport. It is mainly composed of polysaccharides, proteins, and lignin. Arabinoxylan (AX), pectin (P), and cellulose (C) are the main components of cereal cell walls and are particularly concentrated in the bran portion of the grain. Cereal arabinoxylans create networks in plant cell walls in which other cell wall polysaccharides are imbedded forming complex matrices. These networks give an insolubility profile to plant cell wall. A previous study in our lab showed that soluble crosslinked arabinoxylan with relatively high residual ferulic acid from corn bran provided advantageous <i>in vitro </i>human fecal fermentation products and promoted butyrogenic gut bacteria. In the present work, arabinoxylan was isolated from corn bran with a mild sodium hydroxide concentration to keep most of its ferulic acid content. Highly ferulated corn bran arabinoxylan was crosslinked to create an insoluble network to mimic the cereal grain cell wall matrices. Firstly, arabinoxylan film (Cax-F), pectin film (P-F), the film produced by embedding pectin into arabinoxylan networks (CaxP-F), and cellulose embedding arabinoxylan matrices (CaxC-F), and embedding the mixture of cellulose and pectin into arabinoxylan networks (CaxCP-F) were fabricated into simulated plant cell wall materials. Water solubility of films in terms of monosaccharide content was examined and revealed that Cax-F was insoluble, and P-F was partially insoluble, and nanosized pectin and cellulose were partially entrapped inside the crosslinked-arabinoxylan matrices. In a further study, these films were used in an <i>in vitro </i>human fecal fermentation assay to understand how gut microbiota access and utilize the different simulated plant cell walls to highlight the role of each plant cell wall component during colonic fermentation. <i>In vitro </i>fecal samples, obtained from three healthy donors were used to ferment the films (Cax-F, P-F, CaxP-F, CaxC-F, and CaxCP-F) and controls (free form of cell wall components -Cax, P and C). The fabricated films that were compositionally similar to cell walls were fermented more slowly than the free polysaccharides (Cax and P). Besides, CaxP-F produced the highest short chain fatty acids (SCFA) amount among the films after 24 hour <i>in vitro </i>fecal fermentation. Regarding specific SCFA, butyrate molar ratio of all films was significantly higher than the free, soluble Cax and P. 16S rRNA gene sequencing explained the differences of the butyrate proportion derived from specific butyrogenic bacteria. Particularly, some bacteria, especially in a butyrogenic genera from Clostridium cluster XIVa, were increased in arabinoxylan films forms compared to the native free arabinoxylan polysaccharide. However, no changes were observed between P and P-F in terms of both end products (SCFA) and microbiota compositions. Moreover, CaxP-F promoted the butyrogenic bacteria in fecal samples compared with pectin alone, arabinoxylan alone, and the arabinoxylan film. Differences in matrix insolubility of the film, which was high for the covalently linked arabinoxylan films, but low for the non-covalent ionic-linked pectin film, appears to play an important role in targeting Clostridial bacterial groups. Overall, the cell wall-like films were useful to understand which bacteria degrade them related to their physical form and location of the fiber polymers. This study showed how fabricated model plant cell wall films influence specificity and competitiveness of some gut bacteria and suggest that fabricated materials using natural fibers might be used for targeted support of certain gut bacteria and bacterial groups.

<p> Despite the continuous breeding efforts towards improving yield, seed quality, and yield-related traits, there is still little understanding of several aspects of soybean breeding; however, crop breeding is ever-evolving, and plant breeding technologies offer immense potential for accelerating genetic improvement in soybeans. This thesis explores different frameworks to further characterize tradeoffs among seed quality traits, soybean maturity's genetic architecture, and selections for yield. We explored the interactions of carbohydrate traits with other seed traits, flowering, and maturity using data from a large panel of <em>G. max </em>accessions from the USDA soybean germplasm collection. We found a negative correlation between sucrose and protein and a negative correlation between protein and oil, representing a significant challenge for improving seed quality. In contrast to other well-documented correlations, such as protein and oil, correlations between raffinose and oil content seem more specific to populations and environments and are unlikely to generalize to the whole specie; however, the correlations of sucrose with protein and seed size appears to be more stable. In addition, we performed a genome-wide association analysis (GWA) to detect novel QTLs for flowering (R1) time, maturity (R8) time, and reproductive length (RL) using a soybean panel with the same genotype for major <em>E </em>genes (<em>e1-as/E2/E3). </em>While major maturity <em>E</em> genes are known to have pleiotropic effects on R1 and R8, we found two QTLs associated with R8 and RL that do not control R1, suggesting minor-effect, trait-specific loci are also involved in controlling R1 and R8. In addition, w<em>e identified six genes that may play essential roles in regulating R1, R8, and RL; however, further validation of the QTLs and f</em>ine mapping and map-based cloning studies of the candidate genes are necessary before they can be used in breeding programs. Lastly, we conducted a selection experiment in progeny row (PR) populations of four breeding programs to compare the agronomic performance of lines selected by breeders using their usual selection methods to lines selected through prediction of yield performance using new sources of data and information. Our results suggest that aerial average canopy coverage (ACC) used as a secondary trait in combination with field spatial variation adjustment is an efficient high throughput methodology to effectively select high-yielding lines from non-replicated experiments at the PR stage. </p>

<p>  </p> <p>Food system STEM projects have the capacity to motivate high school students in urban schools. This study explored food as a context to engage students because everyone interacts with food on a daily basis and has had cultural experiences related to food. An integrated STEM approach in combination with a systems thinking approach challenged students to make transdisciplinary connections, view problems from different perspectives, analyze complex relationships, and develop 21st-century and career skills (Hilimire et al., 2014; Nanayakkara et al., 2017). The purpose of this study was to describe and explain the relevance students perceive in Ag+STEM content by measuring high school students' self-efficacy, intrinsic value, attainment value, cost value, and utility value after participating in a food system STEM project. The study was informed by Eccles and Wigfield’s (2020) Situated Expectancy Value Theory. The convenience sample of this study was comprised of high school students from metropolitan area schools. High school students completed a food system STEM project with a food system context. Quantitative data was collected using the developed Food System Motivation questionnaire. Data were collected through a retrospective pre-test and a post-test. Descriptive statistics were used to analyze the data including means and standard deviations. Relationships were explored by calculating correlations.</p> <p>There were four conclusions from this study. First, high school students were somewhat interested, felt it was important to do well, and agreed there were costs regarding participation in the food system STEM project. Second, high school students reported higher personal and local utility value motivation after completing the food system STEM project. Third, high school students were somewhat self-efficacious in completing the project tasks and completing the project tasks informed by their cultural identity and experiences. Fourth, intrinsic value and attainment value motivation (independent variables) were related to personal and local utility value motivation and project and cultural self-efficacy motivation (dependent variables). Implications for practice and recommendations for future research were discussed.</p>

<p>  </p> <p>Food safety researchers and extension workers are focused on educating the different actors of the supply chain, from farm to fork. To accomplish this, researchers identify areas of improvement and investigate the factors that cause or explain food safety behaviors. This thesis is divided into a systematic literature review with a meta-analysis and qualitative synthesis (Ch. 2), then two case studies that use predictive models to find top predictors of food safety behaviors (Ch.3 and 4). The systematic review (Ch.2) investigates online food safety educational programs and their effectiveness, barriers, and recommendations on different subpopulations of students, consumers, and food workers. The findings showed a limited effect on attitudes in the different subpopulations. Several areas for future research and recommendations for educators were identified. The first case study (Ch.3) developed predictive models of different food safety behaviors at ten time points throughout the COVID-19 pandemic. Findings suggest an effect between changes in COVID-19 case numbers and how well attitudes related to COVID-19 can make predictions. Additionally, findings suggest the importance of attitudes when predicting food safety behaviors. Lastly, results identified that the belief that handwashing protects against foodborne illness was more important than the belief that handwashing protects against COVID-19 when predicting handwashing at most time points. These findings can identify insights into consumer behaviors during the pandemic and several possible areas for future research. The second case study (Ch. 4) developed predictive models of consumer flour handling practices and consumer awareness of flour-related recalls and how they are affected by the total number of flour-related recalls for a state where the consumer lives. Findings identified the importance of risk perceptions in predicting consumer flour handling practices. Results also showed that younger consumers were predicted to be more likely to be aware of flour recalls than consumers of older ages. Lastly, results show that the total number of flour-related recalls for a state where the consumer lives do not affect predictions. Findings identify potential challenges to recall communication and areas for future studies.</p>

<p>  </p> <p>The rise of technology as a data source for ecological research and biodiversity conservation has led to a host of new opportunities, and new challenges, for researchers, conservationists, policymakers, and land managers. As these technologies have become more common and more capable, researchers need improved methods and improved theoretical frameworks to integrate these technologies with each other; with social science and policy; and with land-use planning. This thesis proposes several of these conceptual and theoretical frameworks—one for integration of heterogeneous data and another for the integration of ecological data with economic decision-making and policy analysis. It then suggests new methodologies for data quality assurance. Lastly, it demonstrates the applicability of acoustic monitoring in a key land-use context: agriculture in a premium crop that is grown in global biodiversity hotspots. </p>

<p dir="ltr">ABSTRACT</p><p dir="ltr">Bovine Respiratory Disease (BRD) poses a significant challenge in the dairy and beef industry, contributing to high mortality, morbidity, and economic costs. Extensive research has aimed to enhance BRD diagnosis, focusing on various factors such as predisposition, environment, and epidemiology. While diverse methods have been developed for BRD detection, including clinical signs, behavioral changes, lung consolidation assessment via ultrasonography, and molecular techniques for microbiome analysis, accurate diagnosis remain inconsistent. Notably, many studies lack exploration of microbial interactions (fungi, viruses, and bacteria) within BRD-affected animals compared to healthy ones. Moreover, the impact of age, disease, and antibiotic treatment on the microbiome community remains understudied. Thus, additional analysis is crucial to understand the relationships between these factors and BRD development. This dissertation is divided into two parts, each addressing specific conditions. The first part focuses on characterizing the nasopharyngeal (NP) microbiome of dairy calves, pre-weaned and post-transported, and those diagnosed with BRD within the first two weeks of life. The objective is to identify NP microbiome changes as indicators of disease development, considering antibiotic treatment effects on NP alpha and beta diversity. The second part delves into characterizing the fungal and bacterial nasal cavity among BRD-affected and healthy cattle within the same pen. This section, presented in three chapters, explores the bovine nasal mycobiome in beef cattle, as well as the nasal microbiome in both dairy and beef cattle. The overarching goals of these studies are to evaluate differences in the nasal mycobiome or microbiome community between BRD-affected and healthy cattle, focusing on alpha, beta, and community compositions as potential disease indicators. Additionally, the aim is to determine if BRD-affected cattle exhibit higher abundance of BRD-pathobionts (fungi and bacteria) in the nasal cavity compared to healthy pen-mates. In conclusion, findings from this research emphasize the importance of incorporating both mycobiome and microbiome analyses in understanding BRD development. Future studies should consider geographical influences on nasal microbiome structure, highlighting the need for separate investigations in dairy and beef calves due to breed variations. Ultimately, studying mycobiome and microbiome ecology offers insights into microbial transitions from commensal to pathogenic farms in the bovine upper respiratory tract, supporting advancements in BRD prevention or mitigation strategies.</p>