<p>It is well known that colonic microbiota is influenced by both intrinsic and extrinsic factors; out of all these, diet plays a major role. The traditional human diet has typically been high in overall dietary fiber intake, due its inherent presence in plant-derived foods. However, over the years, dietary patterns have transitioned into a low-fiber Westernized diet. This diet is increasingly implicated in colonic diseases. Dietary fiber consumption is known to increase microbial diversity, yet the mechanisms are still unclear. This is partially true because dietary fiber as a category is composed of a wide variety of structures, which may have divergent effects on the gut microbiome. The food industry has extracted, isolated, refined and purified non-digestible carbohydrates and, in some cases, modified them for improved function, which may influence their interaction with the gut microbiome. This study was developed in two phases: we first hypothesized that glucans produced by different processes were structurally distinct and that these fine structural differences in glucans would govern microbial responses to the polymers. To test this hypothesis, we first determined the structural characteristics of the glucans by gas chromatography and mass spectrometry, which revealed substantial structural differences among the glucans with respect to size and linkage patterns, consequently categorizing the glucans by structure (i.e., mixed linkage α-glucans, resistant maltodextrins, and polydextroses). The second study involved the <i>in vitro </i>fecal fermentation of these commercially available soluble glucans which are uniformly composed of glucose linked into different structural arrangements. We further hypothesized that each glucan would select for different microbiota and that there would be glucan-specific general responses across microbiomes. We were able to identify a variety of idiosyncratic metabolic patterns as well as differential organisms selecting for specific glucan structures. Although there were associations with glucan classes at the family level (e.g., <i>Bacteriodaceae </i>and <i>Lachnospiraceae </i>were discriminants of the resistant maltodextrins and polydextroses respectively), associations with glucans across individual species within these families varied. These findings suggest that microbiome responses to structurally distinct glucans depend upon both fine glucan structure and community context, and community metabolic phenotypes emerge from the interaction of the two. These findings are relevant to the food industry as they may enable optimization of synthesis to generate chemical structures that select for specific organisms and/or improve overall gut health.</p>

<p>This dissertation investigates two major structure-function relationships important to food science: vitamin stability and water-solid interactions. Thiamine, vitamin B₁, is an essential micronutrient in the human diet. While thiamine is found naturally and as a fortification supplement in many foods, it is chemically unstable on exposure to heat and some co-formulated ingredients, with degradation exacerbated in prolonged shelf-life products. The instability of thiamine is a concern for the development of dietary deficiencies, which are prevalent even in developed countries; however, thiamine stability is not widely studied in the food or pharmaceutical industries. Thiamine is commercially available in two salt forms: thiamine mononitrate (TMN) and thiamine chloride hydrochloride (TClHCl). This study focused on documenting the storage stability of thiamine in solution, considering the effects of which commercially available salt form of the vitamin was used, vitamin concentration, pH, and ions present in solution by monitoring chemical stability and degradation kinetics over a 6-month to 1-year period following storage at 25-80ºC, and expanded these studies into food systems (bread doughs). The results from these studies, including the reaction kinetics of thiamine degradation, the degradation pathway, and the sensory impacts of the degradation products formed, especially as affected by pH and food matrix, can be used to improve thiamine stability and delivery in foods.</p><p></p><p>The studies of water-solid interactions in this dissertation covered two topics: 1) the effects of formulating a variety of food-relevant additives on the crystallization tendency of amorphous sucrose; and 2) the effects of formulation on the moisture sorption behaviors and physical stability of spices, herbs, and seasoning blends. Sucrose lyophiles were co-formulated with a variety of additives and stored at 11-40% relative humidity (RH). The structural compatibility of sucrose with the additive, and related intermolecular interactions, dictated the tendency of the additive to either delay, prevent, or accelerate sucrose crystallization. Spices, herbs, and seasoning blends were exposed to increasing RH (23-75%) and temperature (20-50ºC) to determine the effect of storage and formulation on a variety of physical properties. In general, as complexity of blends increased, physical stability decreased. While this dissertation covers a wide variety of food chemistry and food materials science topics, including vitamin chemical stability, amorphous sucrose physical stability, and moisture sorption behaviors of spices, herbs, and seasoning blends, the findings provide valuable information on the chemical and physical stability of ingredient systems and how the structure-function relationships of the systems can be controlled for optimal ingredient functionality.</p><p></p>

<div> <div> <div> <p>As a major part of the dietary fiber classification, plant polysaccharides often have chemically complex structures which may differ by genera and species, and perhaps even by genotype and growing environment. Arabinoxylans from cereal cell walls are known to differently impact human gut microbiota composition and fermentation metabolites due to variability in chemical structure, though specificities of structure to these functions are not known at the level of genotype ́ environment. In the first study, corn bran arabinoxylan (CAX) extracted from 4 genotypes ́ 3 growing years at the Purdue Agronomy Farm was compared in human fecal fermentations to test the hypotheses that, 1) CAXs extracted from brans from different corn genotypes and grown over different years (environments) show distinct structures, and 2) these cause differences in gut microbiota response and fermentation metabolites. Monosaccharides and linkage analysis revealed that CAXs had different structures and the differences were genotype-specific, but not significantly due to environment. PCA analysis revealed that both short chain fatty acid production and the microbial community shifted also in a genotype-specific way. Thus, small structural changes, in terms of sugar and linkage compositions, cause significant changes in fermentation response showing very high specificity of structure to gut microbiota function. </p> <p>Insoluble fermentable cell wall matrix fibers have been shown to support beneficial butyrogenic Clostridia, but have restricted use in food products due to their insoluble character.</p></div></div> </div> <div> <div> <div> <p>In the second study, a soluble fiber matrix was developed that exhibited a similar fermentation effect as fermentable insoluble fiber matrices. Low arabinose/xylose ratio CAX was extracted with two concentrations of sodium hydroxide to give soluble polymers with relatively low and high residual ferulic acid (CAX-LFA and CAX-HFA). After laccase treatment to make diferulate crosslinks, soluble matrices were formed with average size of 3.5 to 4.5 mer. In vitro human fecal fermentation of CAX-LFA, CAX-HFA, soluble crosslinked ~3.5 mer CAX-LFA (SCCAX- LFA), and ~4.5 mer SCCAX-HFA revealed that the SCCAX matrices had slower fermentation property and higher butyrate proportion in SCCAX-HFA. 16S rRNA gene sequencing showed that SCCAX-HFA promoted OTUs associated with butyrate production including Unassigned Ruminococcaceae, Unassigned Blautia, Fecalibacterium prausnitzii, and Unassigned Clostridium. This is the first work showing the fabrication of soluble crosslinked fiber matrices that favors growth of butyrogenic bacteria. </p> <p>Moreover, these same SCCAXs exhibited an interesting gel forming property on simple pH reduction, which is similar in gelling property to low acyl gellan gum, though is differently readily soluble in water. Both of the SCCAXs formed gels at pH 2, with SCCAX-HFA forming the stronger gel. Gels showed shear-thinning behavior and a thermal and pH reversible property. A gel forming mechanism was proposed involving noncovalent crosslinking including hydrogen bonds and hydrophobic interaction among the SCCAX complexes. This mechanism was supported by structural characterization of SCCAX complexes using a Zeta-sizer and FT-IR spectroscopy. SCCAX-HFA could be used in low sugar gels and has the above property of promoting butyrogenic bacteria in the gut. </p> <p>In conclusion, gut microbiota responds differentially to CAXs with various fine structures. This probably due to dietary fiber-gut microbiota relationships have been evolved over time to be highly specific. Forming soluble fiber matrices could be a good strategy to promote butyrogenic bacteria and improve gut health, in a readily usable form in beverages.</p></div></div></div>

<p>  </p> <p>The world has experienced an unprecedented change in the systems responsible for food production, distribution, and commercialization with concurrent changes in diets. In developed and developing countries, the shift in consumption patterns has moved towards a Western diet pattern which has been linked to negative health outcomes including obesity, diabetes and associated non-communicable diseases. Traditional African diets have previously been associated with protective effects against the development of the above-mentioned conditions. Yet, the underlying reasons for this is not clear. One dietary factor that may contribute to its protective effect is the principal available carbohydrate, starch, which in traditional African staples is considered to contain slowly digestible carbohydrates (SDCs) and some amount of resistant starch (RS). We reported that traditional African staple starchy foods (sorghum and millet) had markedly slower gastric emptying than introduced modern starchy foods (rice, pasta and potatoes). This response was attributed to activation of enteroendocrine cells of the small intestine (L-cells) with potential to trigger physiological, hormonal, and neurological processes that affect digestion time and perception of hunger; effect known as the ileal brake. Moreover, at least in mice models, consumption of SDCs has shown to have beneficial effects on the rate and type of fuel (e.g. carbohydrate vs fat) used for metabolic processes.</p> <p>The first thesis study compared the effect of diets (cohorts in the USA and Kenya) on gastric half-emptying time and metabolic fuel utilization in healthy adults. Our findings showed that gastric emptying time was not different between cohorts and that diet did not influence gastric emptying time; however, calculated respiratory exchange ratio (RER) (which is a measure of metabolic fuel utilization at the cellular level, e.g. carbohydrate vs fat) and metabolic flexibility (which is the ability to switch between metabolic fuel sources upon demand or need) was higher for the Kenyan cohort. Multivariant models were developed and corrected for multicollinearity of some diet variables. Carbohydrate and protein in multivariate model 1; total fiber, added sugars and starch in multivariate model 2; and diet quality (measured as the Healthy Eating Index based on 2015-2020 dietary guidelines, or HEI-2015) in multivariate model 3, were significantly and independently correlated with RER and metabolic flexibility.   </p> <p>The second study assessed if slow gastric emptying and improve metabolic fuel utilization could be induced through SDC supplementation. The objective of this study was to determine if continual consumption of SDC for 21 days delayed the rate of gastric emptying, moderated postprandial glycemic response, decreased hunger, and/or improved metabolic fuel utilization in subjects with low diet quality (HEI-2015<65). Our results indicated that supplementation with SDC did not slow gastric emptying time or acute measures of metabolic fuel utilization; however, continuous consumption of SDC had a modest but significant effect on improving metabolic flexibility and decreasing hunger scores. </p> <p>The last two chapters of this thesis focused on the use of a low-cost, high-pressure, high temperature extruder suitable for processing in Africa of whole grain pearl millet (<em>Pennisetum glaucum</em>). In Africa, emerging, entrepreneurial companies are increasingly gaining share of local markets by manufacturing and distributing high-quality locally sourced processed foods made with indigenous grains. Whole pearl millet is particularly susceptible to development of rancidity. The objective of our third study was to assess the use of the extruder on the stability and sensory attributes of whole grain pearl millet extruded flours to be used for instant thin and thick porridges. Findings showed that extrusion fully gelatinized the starch in pearl millet and prevented hydrolytic rancidity in the instant flour products. However, extrusion cooking did not stop oxidative rancidity. We concluded that while extrusion cooking is a versatile technology for whole grain processing, refinement of extrusion conditions used in the experiment and the evaluation of other unit operations (e.g. steeping, germination) in combination with extrusion cooking may improve the sensory properties of final products.</p> <p>Finally, extrusion cooking has been showed to promote the formation of beneficial amylose-lipid complexes (ALCs). The objective of the last study was to evaluate the formation of ALCs in whole grain pearl millet extruded flours, characterize their composition, and assess their ability to slowly digest <em>in vitro</em>. Extrusion promoted the formation ALCs and these flours exhibited a slow enzymatic digestion <em>in vitro</em>. The findings from this thesis provide insights into the role of diets and metabolic fuel utilization, and improvement of processed pearl millet foods in Africa.</p>

<p>Hermetic storage systems have gained global popularity for their ability to minimize stored product losses by depleting oxygen. However, relying solely on insects to deplete oxygen in hermetic storage, when this process takes longer, can result in (further) damage to stored commodities. This study was conducted to investigate: (i) the potential of four different germinating seeds (soybean, rice, cowpea, and corn) in scavenging oxygen within hermetic storage systems; (ii) the impact of container volume and the number of germinating seeds on oxygen depletion; and (iii) the effects of germinating seeds on insect mortality and grain quality. Among the crops tested, cowpea, during their fourth, fifth, and sixth germination stages (T4, T5, and T6), depleted oxygen below 5% within 12 hours. The fourth stage of cowpea (T4) was identified as a potential oxygen scavenger due to its shorter germination time and ease of handling. Moreover, increasing the number of germinating seeds resulted in a faster initial rate of oxygen depletion in all-sized jars. Doubling both the volume of the jars and the number of germinating seeds had a similar rate of oxygen depletion. Additionally, an equation was derived to predict the required number of germinating seeds based on data from different numbers of seed and container volume combinations. Relative humidity levels increased to approximately 90% when empty jars were used but remained consistent at 40% when the jars were filled with grains. Furthermore, using 10, 20, and 30 germinating cowpea seeds with stored grains and insects, oxygen levels were reduced below 5% at different time intervals. Complete adult mortality of <em>C. maculatus</em> was achieved within 3-5 days of exposure, depending upon the number of germinating seeds. 20 and 30 seeds achieved complete mortality within 72 hours, while 10 seeds required 120 hours. As the number of germinating seeds increased, egg counts decreased, and moisture content significantly increased in the treatment involving 30 seeds. Furthermore, no adult emerged after 96 and 120 hours of exposure to normoxia for the 30 and 20 seed treatments, respectively. However, in the 10 seeds treatment, a small percentage of adults (0.29%) did emerge even after 120 hours of exposure.</p>

<p>The data in this dissertation describes changes in metabolic flux in bovine cell culture and bovine hepatic models. </p>

<p>Germination testing and seedling vigor for Kentucky bluegrass germination. Analyzing growth from Kentucky bluegrass cultivars. </p>

<p dir="ltr">Stocking density, space availability, and lameness are important aspects affecting broiler chicken behavior and welfare. Stocking density refers to the weight of broiler chickens per a set area of space typically measured as kg/m2. Space availability is the amount of space per individual broiler chicken typically measured as m2/bird. Stocking density and space availability can contribute to lameness and other aspects of welfare such as footpad dermatitis, hock burn, and feather cleanliness. The behavior of broiler chickens can also be modified by stocking density, space availability, and lameness. All of these aspects are typically related to a change in activity levels which could be used as an indicator of animal welfare. To date, the majority of research that has examined the walking ability of broiler chickens has assessed how stocking density influences the development of gait problems when applied during the grower phase. However, not all broilers develop gait problems at the same point in time and it is unknown whether broilers that initially have sound gait develop gait problems at a similar rate to broilers that are initially classified as having affected gait. Further, the influence of stocking density on the progression of gait abnormalities of broilers with sound and poor gait is unknown. Finally, since space becomes more and more limited as broiler chickens increase in body weight and age, it is unknown how the provision of space during the finisher phase, when broiler chickens are gaining weight rapidly, can influence their walking ability and welfare outcomes. Stocking density is calculated based on projected final weights of broiler chickens from the time they are placed on a commercial farm, and that projected stocking density remains the same from the chick placement date. As stocking densities are increased, there is also an increase in the prevalence of lameness. Age is also known to be related to walking ability, and as broiler chickens age, there is an increase in the prevalence of lameness. While it is known that increasing stocking density and aging are both contributing factors to broiler chicken lameness, there is no previous research on if reducing stocking density at a later age can help alleviate the prevalence of lameness. To address this knowledge gap, two studies were conducted. In the first study, 784 mixed-sex Ross 708 broiler chickens in commercial barns were placed into of four treatment groups. · SOUND: Consisted of broiler chickens that were considered to have sound gait (scores of 0 and 1) and the broilers were housed at farm stocking density (6lb/ft2, 29.29 kg/m2), · AFFECTED: Consisted of broiler chickens that were considered to have affected gait (scores of 2 or higher) and were housed at farm stocking density (6lb/ft2, 29.29 kg/m2) · MIXED-F: Consisted of 50% of broiler chickens that were considered to have sound gait and 50% that were considered to have affected gait and were housed at farm stocking density (6lb/ft2, 29.29 kg/m2) · MIXED-L: Consisted of 50% of broiler chickens that were considered to have sound gait and 50% that were considered to have affected gait and were housed at half of the farm stocking density (3lb/ft2, 14.65 kg/m2) Broiler chickens were randomly selected at 33 days of age from each of four commercial barns for welfare assessments, which included gait scoring to assess walking ability, as well as the assessment of footpad dermatitis and hock burn. Broilers were then assigned to one of two gait categories based on their gait scores. Broilers were either considered to have sound gait meaning they had no or unidentifiable abnormalities, or affected gait meaning there were identifiable abnormalities. To separate treatment groups, custom-built pens (4 ft x 12 ft, 1.22 m x 3.66 m) were constructed. At 37 days of age welfare assessments were conducted again, and then the broiler chickens were placed back into the flock (Chapter 2). The behavior of the broiler chickens was recorded from the evening of day 33 to the morning of day 37 and video was analyzed using scan sampling. The proportion of broiler chickens performing target behaviors was recorded every 10 minutes in the morning (6:00 – 8:00) and evening (19:00 – 21:30). Better gait scores were observed at 37 days of age in broiler chickens in the MIXED-L group and broiler chickens in the SOUND group. The presence of hock burn was lower in broiler chickens in the SOUND group. Cleanliness scores were better for broiler chickens in the MIXED-L group and in broiler chickens in the SOUND. Stocking density impacted the proportion of broilers performing eating, drinking, sitting, and walking (P < 0.05). Walking ability impacted the proportion of broiler chickens standing, walking, and sitting (P < 0.05). To continue investigating the implementation of housing changes later in the broiler chickens’ life, a second study was conducted using 705 mixed-sex Ross 708 broiler chickens. At 7 d, broiler chickens were randomly assigned to 1 of 16 pens (46-47 birds/pen). At 28 d, half of the pens doubled in size after welfare assessments were completed (measuring 8 ft x 10 ft, 3.05 m x 2.44 m, DOUBLE), while the other half remained at the original dimensions (8 ft x 5 ft, 2.44 m x 1.5 m, SINGLE). The DOUBLE pens had an expected stocking density of 15.2 - 15.5 kg/m2 (3.11 - 3.17 lb/ft2) and an estimated space availability of 0.15 to 0.16 m2/bird while the SINGLE pens had an estimated stocking density of 30.4 - 31.1 kg/m2 (6.23-6.37 lb/ft2) and an estimated space availability of 0.07-0.08 m2/bird. Welfare assessments consisting of scoring gait, feather cleanliness and for the presence of FPD and hock burn were conducted at 22 d, 28 d, and 38 d (Chapter 4). At 38 d, broiler chickens in SINGLE pens were less likely to have a score of 0 for FPD (Wald c2 = 15.45, P < 0.0001), hock burn (Wald c2 = 7.26, P = 0.0071), and feather cleanliness (Wald c2 = 11.77, P = 0.0006) than broiler chickens in DOUBLE pens. However, broiler chickens in SINGLE pens were more likely to have a gait score of 0 compared to broiler chickens in DOUBLE pens (Wald c2 = 11.34, P = 0.0008). Broiler chicken behavior was recorded at 23-26 d (Period 1: before space increase), 28-31 d (Period 2: time of space increase), and 36-37 d (Period 3: after space increase). Behavior data were collected using focal sampling for two broiler chickens per each of the 16 pens in the morning, afternoon, and evening (Chapter 5). Broiler chickens housed in double pens had an increased frequency of leg extensions compared to broiler chickens housed in single pens (P < 0.05). Period had a significant impact on the frequency of eating, sitting, and walking and the durations of sitting, environmental pecking, standing, and walking (P < 0.05). Time of day had a significant impact on the frequency of eating, sitting, walking, preening, and leg extensions and the durations of sitting, eating, preening, and standing (P < 0.05). The interaction of age and time of day had a significant impact on the frequency of drinking and leg extensions and the durations of sitting, eating, and walking (P < 0.05). The interaction of age and treatment had a significant impact on the frequency of eating and walking and the duration of preening (P < 0.05). In conclusion, broiler chickens housed in DOUBLE pens did not exhibit a difference in behaviors compared to those in SINGLE pens, other than broilers in the DOUBLE pens performing leg extensions more often. While the first study indicated that having more space available per broiler chicken led to better walking ability, the second study showed the opposite to be true as those with more space had reduced walking ability. This indicates that changing the stocking density through manipulating space in the finisher phase may impact welfare, but further investigation is needed. Future research should first examine the effects of adding space in the finisher phase with 3 treatment groups. While the two discussed here would remain the same, the third group should start with broilers in a pen that is already the size of the DOUBLE pens and remains that way for the entire project. This will ensure that increasing space during the finisher period is beneficial rather than the additional space availability in general accounting for the differences in treatments. All treatment groups should also get fresh bedding with the pen increase to ensure the welfare measurement results are due to the changes in space availability rather than the provision of fresh litter.</p>

<p dir="ltr">This thesis explores the intricate mechanisms governing paracellular permeability, a process vital for maintaining homeostasis and barrier integrity in epithelial and endothelial tissues. Central to this exploration are tight junctions (TJs), multi-protein complexes that regulate substance movement between cells. The thesis begins with a comprehensive literature review synthesizing current research on how bacterial and viral proteins can enhance paracellular permeability or modulate TJs, highlighting their significance in both scientific and medical fields.</p><p dir="ltr">A focal point of the thesis is the detailed study of the <i>Listeria</i> adhesion protein (LAP), an epithelial TJ modulator (TJM). LAP’s interaction with the epithelial receptor, Hsp60, facilitates the translocation of <i>Listeria monocytogenes </i>across the epithelial barrier, presenting a novel approach for drug delivery. Addressing the limitations of current TJMs, such as poor bioavailability and toxic side effects, the thesis provides an in-depth analysis of LAP as an alternative biologics’ delivery vehicle. Utilizing a multidisciplinary research approach, the study reveals the cryo-EM structure of LAP at 2.9 Å resolution, elucidating its multimeric formation and interaction with Hsp60 through electrostatic forces, as supported by computational modeling.</p><p dir="ltr">The functional efficacy of LAP is further established through experiments demonstrating its capability to transport drug analogs across epithelial cell monolayers comparably to established TJMs. Moreover, <i>in vivo</i> studies using a mouse oral gavage model show that LAP significantly enhances the blood levels of peptide drugs without triggering inflammatory responses or harming tight junction architecture. This thesis ultimately positions the LAP-Hsp60 complex as a promising TJM candidate, offering an innovative means for enhancing oral drug delivery and maintaining epithelial barrier integrity.</p>

<p>  </p> <p>The research in this dissertation explored the impact of different sugar reducing agents [SRAs: sugars, sugar alcohols, oligosaccharides (OS), and polymers] on the thermal properties of starch (gelatinization, pasting, and retrogradation) and the baking performance of a model baked goods system (wire-cut cookies). The overconsumption of added sugar and underconsumption of dietary fiber have been linked to increased developmental risks for obesity and related diseases, including cardiovascular disease, diabetes, and colorectal cancer. Some SRAs, such as non-digestible oligosaccharides (OS), are considered soluble dietary fiber and could help offset the health detriments from excess sugar and low fiber intake, while also providing similar functionality (texture and structure) to that of sucrose in baked goods systems that rely on the control of phase and state changes in starch. The gelatinization temperature (Tgel) of wheat starch in the presence of SRA solutions at various concentrations (10% to 60% w/w) was measured using differential scanning calorimetry (DSC), and was best explained by SRA plasticization properties [solvent effective volume fraction (<em>feff,w</em>)], solution viscosity, and size (based on the previously proposed starch granule size limit of 1,000 g/mol). The paste viscosity parameters of starch in SRA solutions were measured with a routine rapid visco analyzer (RVA); and were increased in monosaccharide solutions and decreased in 6-carbon sugar alcohol and OS solutions as solution concentration was increased. Differences in starch paste response variables were explained by SRAs either promoting or restricting amylose leaching during heating. The recrystallization of amylopectin over time was promoted in monosaccharide solutions (glucose, fructose, allulose) and in many OS solutions, and was explained in terms of SRA hydrogen bonding interactions with water and/or starch chains. The appearance attributes of wire-cut cookies containing OS were similar to a sucrose control formulation; however, differences were found in cookie texture attributes which were linked to OS effects on solution viscosity and moisture retention during baking. Cookies made with allulose and erythritol were the least similar to the sucrose control across all quality attributes, and therefore these two SRAs would not be recommended as sugar replacers in low-moisture baked goods. The findings from this dissertation could be helpful to food researchers and product developers seeking to reduce or replace added sugars in starch-containing food systems with healthier alternatives.</p>