Cognitive theories claim that phobias involve unconscious processing and that anxious individuals search the environment for threatening stimuli and therefore detect them more rapidly. However, evidence for this is mixed and suggests that anxious individuals do not detect threat more accurately but are more liberal to report that they detected threat even if there was no actual threat (response bias). In this study, 55 women performed a detection task with pictures of snakes, spiders, and guns. The pictures were backward masked to reduce their visibility. Participants also filled in questionnaires that assessed their fear and disgust. As found in previous studies, detection performance did not correlate with fear. However, inconsistent with previous results, disgust sensitivity correlated with lower detection performance of snakes, and response biases varied with fear of spiders or snakes. These findings provide mixed support for notions of relationships between fear and disgust in threat detection.

Celiac disease (CD) is an immune-mediated enteropathy caused by permanent intolerance to dietary gliadin in wheat gluten and related prolamines in barley and rye. The pathogenesis of CD is still unknown and several different environmental factors have been associated with CD, such as dysbiosis of the microflora. In this translational study we investigated the immune status and the interplay of T-cells and Tregs in the mucosa of children with CD and controls, as well as the immune status in treated CD patients, provoked by either dietary oats, CD associated bacteria or gluten. The major findings in the studies were: First, indicators of extrathymic T-cells maturation (ETCM), i.e., the RAG1 enzyme required for recombination of the T cell receptor (TCR) genes and the preTα-surrogate chain in the immature TCR, were both expressed at lower levels in CD patients compared to controls. In addition, IELs expressing RAG1 were less abundant in CD patients compared to controls. The levels of these two indicators stayed low in treated CD patients as well, suggesting that impaired capacity of ETCM is an inherent feature of CD patients. Second, IL-17A, a cytokine involved in both inflammation and anti-bacterial responses was increased in active CD. The major cellular source was CD8+IELs. Furthermore, ex vivo challenge of biopsies from treated CD patients with gluten and with CD-associated bacteria induced an IL-17A response. The CD-associated bacteria also influenced the magnitude of the IL-17A response to gluten. Third, we investigated the effect of dietary oats on local immune status in the intestinal mucosa by comparing CD patients receiving GFD with and without oats. 22 different mRNAs for immunity effector molecules and tight junction proteins were analyzed. We found that expression of two down-regulatory cytokines, two activating NK-receptors and the tight-junction protein claudin-4 normalized in patients on a standard GFD while they did not normalize in patients on a GFD with oats. Fourth, we analyzed the expression level of mRNAs for chemokines, cytotoxic effector molecules, NK-receptors and their ligands in IELs and epithelial cells. Expression levels of several of these genes follow disease activity, suggesting massive recruitment of immune cells by both cell types accompanied by increased IEL-mediated cytotoxicity in the epithelium of inflamed mucosa. In this thesis we have identified three potential risk factors for development of CD: 1) an inherent lower level of ETCM in the small intestinal mucosa than in controls. This could lead to decreased generation of regulatory T cells and less capacity to tolerate gluten and adapt to the local milieu in the mucosa. 2) Dysbiosis of the resident microbiota with increased IL-17A production that could promote local inflammation and immune cell infiltration as well as antibacterial reactions. 3) Dietary oats may provoke a local immune response in a sub-population of CD patients. These patients should probably avoid oats in their GFD but larger studies are needed.

Two key proteins, LexA and RecA, are involved in regulation of the SOS expression system in bacteria. LexA and RecA act as the transcriptional repressor and inducer of the SOS operon, respectively. LexA downregulates the expression of at least 43 unlinked genes and activated RecA interacts with the repressor LexA and therefore, LexA undergoes self-cleavage. The ability of the LexA protein to dimerize is critical for its ability to repress SOS-regulated genes in vivo, as the N-terminal domain (NTD) alone has a lower DNA-binding affinity without the C-terminal domain (CTD) and the components for the dimerization of LexA are located in the CTD. Two antiparallel β-strands (termed β-11) in the CTD at the dimer interface of LexA are involved in the dimerization. LexA interacts with the active form of RecA in vivo during the SOS response. It was determined experimentally that monomeric and non-cleavable LexA binds more tightly to RecA and is resistant to self-cleavage. Therefore, we reasoned that if we can produce such LexA mutants we would be able to stabilize the LexA and active RecA complex for crystallization. Therefore, in this experiment, we attempted to make a non-cleavable and predominantly monomeric LexA that interacts intimately with RecA. We produced four single mutations at the dimer interface of the non-cleavable and NTD-truncated mutant of LexA (∆68LexAK156A) in order to weaken the interactions at the interface. The predominant forms of LexA mutants and the affinities of interaction between the mutant LexA proteins and RecA were examined. ∆68LexAK156AR197P mutant was found as predominantly monomeric at a concentration of 33.3 μM both by gel filtration chromatography and dynamic light scattering (DLS) experiments. It also bound RecA more tightly than wild-type LexA. Another mutant, ∆68LexAK156AI196Y, was also found as predominantly monomeric at a concentration of 33.3 μM by DLS. Both these proteins were subjected to crystallization with wild-type RecA protein. We were able to produce some predominantly monomeric LexA with good binding affinity for RecA; however, we were unsuccessful in co-crystallization.

An earlier approach to restore homeostatic levels of ECM degrading matrix metalloproteases (MMPs) by the Sefton Lab utilized hydroxamate-based MMP inhibitory (MI) beads. While the MI beads delayed ECM degradation in the context of skin wound healing, they caused elevated cell infiltration in a subcutaneous implant model. The primary goal of this project was to further investigate this finding using an air pouch implant model in mice and a different control group – methacrylic acid-based (MAA) beads. Exudate analysis indicated that the MI beads, implanted subcutaneously with gelatin discs, elicited a similar biological response as the MAA beads. Exudates corresponding to both biomaterials had similar cell counts and chemokine levels, which were greater than those corresponding to the control used earlier, poly-methyl methacrylate-based (PMMA) beads. Further, both MI and MAA beads activated infiltrating macrophages in the classical manner, and influenced the activity of an MMP8 catalytic domain in a similar manner.

In order to examine the effects of industry processed pulse powder (navy bean, lentil and chickpea) on postprandial glycaemic response (BG) and subjective appetite (App) before and after a subsequent meal, three randomized, within-subject experiments on healthy young men were conducted. In experiment 1, all navy bean treatments reduced BG at 30 min and navy bean powder suppressed pre-meal App compared to whole wheat flour. In experiment 2, all lentil treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. In experiment 3, all chickpea treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. Therefore, navy bean powder, lentil powder and chickpea powder maintain their low GI and satiating effects, regardless of processing. Pulse powder can be used as a value-added food ingredient to moderate glycaemic response and increase satiety.

An earlier approach to restore homeostatic levels of ECM degrading matrix metalloproteases (MMPs) by the Sefton Lab utilized hydroxamate-based MMP inhibitory (MI) beads. While the MI beads delayed ECM degradation in the context of skin wound healing, they caused elevated cell infiltration in a subcutaneous implant model. The primary goal of this project was to further investigate this finding using an air pouch implant model in mice and a different control group – methacrylic acid-based (MAA) beads. Exudate analysis indicated that the MI beads, implanted subcutaneously with gelatin discs, elicited a similar biological response as the MAA beads. Exudates corresponding to both biomaterials had similar cell counts and chemokine levels, which were greater than those corresponding to the control used earlier, poly-methyl methacrylate-based (PMMA) beads. Further, both MI and MAA beads activated infiltrating macrophages in the classical manner, and influenced the activity of an MMP8 catalytic domain in a similar manner.

In order to examine the effects of industry processed pulse powder (navy bean, lentil and chickpea) on postprandial glycaemic response (BG) and subjective appetite (App) before and after a subsequent meal, three randomized, within-subject experiments on healthy young men were conducted. In experiment 1, all navy bean treatments reduced BG at 30 min and navy bean powder suppressed pre-meal App compared to whole wheat flour. In experiment 2, all lentil treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. In experiment 3, all chickpea treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. Therefore, navy bean powder, lentil powder and chickpea powder maintain their low GI and satiating effects, regardless of processing. Pulse powder can be used as a value-added food ingredient to moderate glycaemic response and increase satiety.

This dissertation estimates the relationship between tax-reporting decision and the change in marginal tax rates, relying on taxpayer's responses (standard labor supply response) as well as reported behavioral responses (compliance). There are still limited studies on elasticity estimates for developing countries. We utilize an applicable theoretical model by using standard labor supply model and summarize a tax avoidance model as the base of our elasticity estimation. The labor supply theoretical model suggests ambiguity of the labor supply decision and the tax avoidance model suggests that the responsiveness of taxpayers in the reporting decision differs across income groups. As previously stated, in developing countries, empirical evidence on reporting decision is still very limited. For our empirical analysis, we estimate reporting income elasticity for microsimulation purposes. We use this elasticity to estimate a dynamic behavior microsimulation model. The elasticity result shows that higher-income groups are more responsive and lower-income groups are less responsive to changes in tax policy. Our empirical analysis continues with estimating differences in taxpayers’ responses to the change in tax policy. We use a modified difference-in-difference model to analyze behavioral responses of taxpayers who are highly affected by the change in marginal tax rate compared to those who are least affected. The result shows that the treatment group, who experienced larger reductions on their marginal tax rate, reported more of their income relative to the control group, whose members are least affected by the change in marginal tax rate. The last part of our empirical analysis examines the distribution of income tax burden across different income groups and examines the government's tax collection from withholding income from some proposed scenarios. We proposed several scenarios and estimated the change in income tax burden compared to that under current income tax law. We also examined the government's revenue loss by calculating the tax differences under current and proposed scenarios. The overall microsimulation results suggest that there is a trade-off between government revenue loss and the distribution of income tax burden.

Hepatitis C virus (HCV) causes a significant health problem worldwide due to the lack of effective vaccines. It has been recognized that a rapid, vigorous, and broadly targeted cell-mediated immune response (Th1-like) is often associated with the clearance of HCV infections. DNA vaccines represent a promising means for HCV vaccination because they tend to induce a Th1-biased cell-mediated response in the host cell. Currently, the delivery of DNA vaccine for HCV in large animals as well as in humans is not as effective as in small animals. Nano delivery systems would be a promising approach to overcome this problem. Carbon nanotubes (CNTs) have been extensively studied for delivering drugs, proteins, peptides, and nucleic acids including plasmid DNA to cells and organs with varying degrees of success, but few of them have been applied to DNA vaccine for HCV.<p> This thesis presents a study of using functionalized CNTs (f-CNTs) to improve the efficacy of plasmid DNA vaccine delivery for HCV. First, CNTs were functionalized via 1,3-dipolar cycloaddition reaction with the appropriate amino acids and aldehydes. NMR and TEM results suggested that the CNTs were successfully functionalized and became soluble in water. Then plasmid DNAs which encode green fluorescence protein reporter gene, luciferase reporter gene, and HCV core protein, respectively, were delivered into human hepatoma cells via calcium phosphate precipitation method, f-CNT delivery system, and a combination of f-CNT and calcium phosphate method, respectively. The result showed that f-CNTs, in combination with the calcium phosphate method, significantly enhanced the gene expression in human hepatoma cells.<p> Consequently, this study concludes that the f-CNT can significantly enhance gene expression in liver cells conferred by a plasmid DNA when combined with calcium phosphate precipitation method. Even though the mechanisms of this enhancement await further investigation, the results of this thesis may have important implications in developing DNA vaccines for infectious diseases in general and for hepatitis C in particular.

Perturbations that derail the proper folding and assembly of proteins in the endoplasmic retriculum (ER) cause misfolded protein accrual in the ER – a toxic condition known as ER stress. The Unfolded Protein Response (UPR) is a signaling system evolved to detect and rectify ER stress. The work I present herein pertains to the most ancient member of the ER stress transducers, IRE1. ER stress stimulates IRE1 to activate a UPR-dedicated transcription factor called XBP1 in metazoans (or HAC1 in yeast) to bolster the productive capacity of the ER and purge misfolded proteins from the ER. To activate XBP1/HAC1, IRE1 cleaves XBP1/HAC1 mRNA twice to eliminate an inhibitory intron using a dormant nuclease function in its cytoplasmic effector region (IRE1cyto). My focus was to understand the mechanism of XBP1/HAC1 activation by IRE1, the regulation of IRE1 function and the manipulation of IRE1 signaling output using chemical tools. To better understand IRE1 mechanism, I determined the crystal structure of IRE1cyto bound to ADP. Structural and mutational analyses uncovered a probable novel IRE1 nuclease active site, allowing a catalytic mechanism of RNA cleavage to be inferred. Further genetic and biophysical experiments revealed that the ordered sequence of events: autophosphorylation, nucleotide binding and dimerization; orchestrates the assembly of the IRE1 nuclease active site to potentiate nuclease function. The flavanol quercetin was identified in a chemical screen as a potent stimulator of IRE1 nuclease output. To understand the mechanism of action of quercetin, I determined the crystal structure of IRE1cyto in complex with quercetin and ADP. Quercetin docked to a novel ligand binding site, termed the Q-site, at the interface of IRE1 dimers. Biophysical and genetic analyses revealed that quercetin engagement of the Q-site promotes IRE1 dimerization, thereby enhancing IRE1 nuclease activity. To gain insight on how IRE1 recognizes RNA, I performed bioinformatic analysis to identify a conserved sequence element in XBP1/HAC1 mRNA (termed XBP1mini) that may compose a higher-order structure recognized by IRE1. I developed an RNA production scheme to generate XBP1mini RNA for structural and biophysical studies. Preliminary X-ray diffraction studies indicate that XBP1mini may indeed adopt an ordered crystallizable tertiary structure.