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Retrospective Theses and Dissertations

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Relatedness Of Haemophilus Parasuis Strains And Their Proteins' Possible Roles As Virulence Factors, Emilie Susanna Noel Zehr Jan 2008

Relatedness Of Haemophilus Parasuis Strains And Their Proteins' Possible Roles As Virulence Factors, Emilie Susanna Noel Zehr

Retrospective Theses and Dissertations

Haemophilus parasuis, the causative agent of Glasser's disease, is considered to be a remerging pathogen of swine in high-health status herds. Several molecular typing methods have been suggested as alternatives to serotyping, which failed to identify up to 30% of field isolates. This study compared random amplification of polymorphic DNA (RAPD) profiles and protein profiles of H. parasuis reference strains and field isolates as methods for identifying and grouping virulent and avirulent isolates. DNA and protein profiles of 15 reference strains and 31 field isolates of H. parasuis, analyzed with two computer-based similarity analyses, revealed unique and reproducible DNA ...


Mechanisms Of Bes1-Regulated Gene Expression Downstream Of Brassinosteroid Signaling In Arabidopsis Thaliana, Xiaofei Yu Jan 2008

Mechanisms Of Bes1-Regulated Gene Expression Downstream Of Brassinosteroid Signaling In Arabidopsis Thaliana, Xiaofei Yu

Retrospective Theses and Dissertations

Brassinosteroids (BRs), the plant steroid hormones, play an important role in mediating plant responses to developmental and environmental cues. BRs signal through a membrane receptor BRI1 and a GSK3 kinase BIN2 to control the activity of BES1/BZR1 family transcription factors. To understand how BES1 regulates gene expression, I looked into both trans-acting protein factors and cis-acting DNA elements that affect BES1 functions, by yeast genetic screen and chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip), respectively. We identified 1609 BES1 direct target genes and discovered conserved DNA motifs in BES1 binding regions. We also showed that BES1 target genes were ...


Use Of Fourier Transform Infrared (Ftir) Spectroscopy To Determine The Health-Promoting Index (Hpi) Of Cow's Milk, Wendy Leanne Thomas Jan 2008

Use Of Fourier Transform Infrared (Ftir) Spectroscopy To Determine The Health-Promoting Index (Hpi) Of Cow's Milk, Wendy Leanne Thomas

Retrospective Theses and Dissertations

Fourier transform infrared (FTIR) spectroscopy steadily has been gaining popularity for the analysis of milk components including total fat, protein, lactose, and ketones. To date, there have been few descriptions of the use of FTIR spectroscopy for the determination of milk fatty acid composition.;The first objective of this thesis was to develop a method utilizing FTIR spectroscopy for prediction of the health-promoting index (HPI) of milk. The HPI is known to affect the relative softness of butter (Bobe et al., 2003); so, this model could be used to predict which cows' milk could be designated for generation of niche ...


Development Of An Rna Aptamer To Pd173955n Through Selex, Samir Mehanovic Jan 2008

Development Of An Rna Aptamer To Pd173955n Through Selex, Samir Mehanovic

Retrospective Theses and Dissertations

With all the technology available to us, the causes of cancers are still puzzling researchers all over the world. Everyday different approaches are being tested to help cure various cancers. With the development of molecular biology, we are able to understand cancer more at molecular level, which helps us look at different methods to treat cancer patients.;The molecular basis for leukemia cancers are understood to a level where we are able to design treatments that specifically target proteins responsible for the disease. One of those proteins is the Bcr-Abl tyrosine kinase which is mostly responsible for chronic myelogenous leukemia ...


A Negative Regulator Of Ribosomal Rna Processing Specifies R-Gene-Independent Cell Death In Barley - Powdery Mildew Interactions, Liu Xi Jan 2008

A Negative Regulator Of Ribosomal Rna Processing Specifies R-Gene-Independent Cell Death In Barley - Powdery Mildew Interactions, Liu Xi

Retrospective Theses and Dissertations

Programmed Cell Death (PCD) plays a pivotal role in plant development and defense. Pathogen dependent cell-death mutants were used to investigate the complex regulatory pathways between PCD and R-gene mediated resistance. Time-course expression profiles of Blumeria graminis f. sp. hordei (Bgh) challenged C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Contrasts were made to identify genes associated with the cell death phenotype as opposed to R-gene mediated resistance. One hundred eighty-two genes were found in the intersection of these contrasts at a ...


The Locations And Signaling Of H-Ras On Endosomes And Plasma Membrane, Xing Wang Jan 2008

The Locations And Signaling Of H-Ras On Endosomes And Plasma Membrane, Xing Wang

Retrospective Theses and Dissertations

No abstract provided.


Functional Analysis Of Paralogous Genes In Acetyl Coenzyme A Metabolism, Joel D. Schmidt Jan 2008

Functional Analysis Of Paralogous Genes In Acetyl Coenzyme A Metabolism, Joel D. Schmidt

Retrospective Theses and Dissertations

No abstract provided.


Functional Analysis Of The C-Terminal Domain In The Drosophila Jil-1 Histone H3 Kinase, Xiaomin Bao Jan 2008

Functional Analysis Of The C-Terminal Domain In The Drosophila Jil-1 Histone H3 Kinase, Xiaomin Bao

Retrospective Theses and Dissertations

Epigenetic regulation is an important process utilized by biological systems to control gene expression and organize development, with histone modification enzymes among the most important components in this regulatory network. The predominant interphase H3 Serine10 kinase in Drosophila is JIL-1, which plays an important role in regulating chromosome structure and modulating gene expression. The full-length JIL-1 protein is composed of four domains including a N-terminal domain (NTD), two kinase domains (KDI and KDII), and a unique C-terminal domain (CTD). In order to study the biological importance of these individual domains, a domain analysis research approach was taken and different functions ...


Characterization Of Barley Yellow Dwarf Virus Subgenomic Rnas, Jacquelyn R. Jackson Jan 2008

Characterization Of Barley Yellow Dwarf Virus Subgenomic Rnas, Jacquelyn R. Jackson

Retrospective Theses and Dissertations

Transcription of subgenomic RNAs (sgRNAs) is a common strategy used by many positive strand RNA viruses of plants and animals to regulate viral gene expression. Barley yellow dwarf virus (BYDV) produces three nested 3'-coterminal subgenomic RNAs in infected cells. SgRNA1 serves as the messenger for the structural and movement proteins. sgRNA2 encodes a small open reading frame (ORF6), that appears not to be translated. The role of sgRNA3 is unknown, as it encodes no ORFs. Neither sgRNA2 nor sgRNA3 is needed for BYDV RNA replication in oat protoplasts. However, sgRNA2 does function as a riboregulator of viral translation in ...


Biochemical And Genetic Analyses Of Physical Associations Among Zea Mays Starch Biosynthetic Enzymes, Tracie Ann Hennen-Bierwagen Jan 2008

Biochemical And Genetic Analyses Of Physical Associations Among Zea Mays Starch Biosynthetic Enzymes, Tracie Ann Hennen-Bierwagen

Retrospective Theses and Dissertations

Mutations affecting specific starch biosynthetic enzymes commonly have pleiotropic effects on other enzymes in the same metabolic pathway. Such genetic evidence indicates functional relationships between components of the starch biosynthetic system including starch synthases (SS), starch branching enzymes (BE), and starch debranching enzymes (DBE), however, the molecular explanation for these functional interactions is not known. One possibility is that specific SSs, BEs, and/or DBEs associate physically with each other in multisubunit complexes. To test this hypothesis, this study sought to identify stable associations between SSI, SSIIa, SSIII, SBEI, SBEIIa, and SBEIIb from maize amyloplasts. Three separate detection methods, yeast ...


Nutritional And Hormonal Modulation Of Diabetes-Perturbed Folate, Homocysteine, And Methyl Group Metabolism, Kristin M. Nieman Jan 2008

Nutritional And Hormonal Modulation Of Diabetes-Perturbed Folate, Homocysteine, And Methyl Group Metabolism, Kristin M. Nieman

Retrospective Theses and Dissertations

Folate, homocysteine, and methyl group metabolism mutually function to provide methyl groups for numerous biosynthetic- and modification-type reactions necessary for optimal health. Methyl groups from these pathways are utilized in the production of important compounds such as nucleic acids, protein, and phospholipids. Thus it is vital to understand the factors that both disrupt and maintain their delicate balance to prevent disease. Disruption of these metabolic pathways is associated with several pathologies including carcinogenesis, birth defects, and vascular disease. Moreover, the disruption of these metabolic pathways may be a link between chronic disease and complications of that disease. Both nutritional and ...


Post-Orbital Color Pattern Variation And The Evolution Of A Radiation Of Turtles (Graptemys), Erin M. Myers Jan 2008

Post-Orbital Color Pattern Variation And The Evolution Of A Radiation Of Turtles (Graptemys), Erin M. Myers

Retrospective Theses and Dissertations

One of the most studied areas in the field of evolutionary biology is the formation and maintenance of new species, as well as variation in the rate and extent to which taxa radiate. A range of evolutionary processes, from ecological adaptation to sexual selection and reinforcement, can lead species formation. However, the generation of new species likely results from several isolating mechanisms acting in concert. The map turtle complex (genus: Graptemys) is an excellent model system for exploring the nature of speciation given its exceptional species richness and morphological diversity, particularly in facial coloration patterns. This research utilizes an integrative ...


Phylogenetic Placement And Population Genetic Analysis Of The Endangered Winged Mapleleaf, Quadrula Fragosa, Amanda Heather Hemmingsen Jan 2008

Phylogenetic Placement And Population Genetic Analysis Of The Endangered Winged Mapleleaf, Quadrula Fragosa, Amanda Heather Hemmingsen

Retrospective Theses and Dissertations

The endangered winged mapleleaf, Quadrula fragosa once occurred in the Mississippi, Tennessee, Ohio, and Cumberland River basins in the United States. While the range of this species was thought to have been reduced to a single population in the St. Croix River (Minnesota/Wisconsin), individuals morphologically similar to Q. fragosa were recently recorded in Missouri, Arkansas, and Oklahoma. We employed a phylogenetic analysis of mitochondrial ND1 gene sequences. Our results indicate that Q. fragosa is a separate species and that the southern populations are genetically Q. fragosa. In addition, we developed and utilized 12 microsatellite loci to quantify genetic variation ...


Dissection Of The Mitotic And Nuclear Functions Of Chromator, A Nuclear-Derived Spindle Matrix Component In Drosophila, Yun Ding Jan 2008

Dissection Of The Mitotic And Nuclear Functions Of Chromator, A Nuclear-Derived Spindle Matrix Component In Drosophila, Yun Ding

Retrospective Theses and Dissertations

A spindle matrix has long been proposed to serve as a stationary or elastic molecular matrix substrate for the organization and activities of microtubules and motors, based on the consideration of a mechanical and functional support for the stabilization of microtubule spindle during force generation from mitotic motors. Recently, the identification of four Drosophila proteins, Skeletor, Megator, EAST and Chromator has provided molecular evidence for the existence of this macromolecular matrix structure during mitosis. All of these four proteins have been shown to interact with each other within a protein complex and redistribute from the nucleus at interphase to form ...


Understanding The Biological Activity Of Hypericum Species Through Metabolomics Studies, Matthew Lee Hillwig Jan 2008

Understanding The Biological Activity Of Hypericum Species Through Metabolomics Studies, Matthew Lee Hillwig

Retrospective Theses and Dissertations

The Hypericum genus contains plants which biosynthesize various polyketides with various known and unknown biological and medicinal activities. However, many Hypericum species have not been chemically or biochemically characterized. These species represent an opportunity for understanding chemical ecology and for new drug discovery research. Acyl-phloroglucinols are of particular interest since they are the most diverse class of specialized metabolites in Hypericum. We used analytical methods such as HPLC, LC-MS and 2-D NMR to screen Hypericum species for metabolite diversity. One species, H. gentianoides, was investigated further based on its historical use by Native Americans and its unique metabolite fingerprint. This ...


The Structure And Mechanism Of Saicar Synthetase, Nathaniel Daum Ginder Jan 2008

The Structure And Mechanism Of Saicar Synthetase, Nathaniel Daum Ginder

Retrospective Theses and Dissertations

SAICAR synthetase catalyzes the eighth step in bacterial de novo purine nucleotide biosynthesis: ATP + L-aspartate + CAIR → ADP + Pi + SAICAR Enzymes involved in nucleotide synthesis are common targets for chemotherapeutic and antimicrobial drugs. They work by reducing the rate of growth of rapidly proliferating cells, thus preventing tumor growth and microbial fecundity. L-Alanosine, an L-aspartate analogue that acts as a substrate for SAICAR synthetase, is a natural product with antiviral and antitumor activities. The product of the reaction is a potent inhibitor of adenylosuccinate synthetase and adenylosuccinate lyase and is responsible for L-alanosine toxicity. L-Alanosine may be effective as a chemotherapeutic ...


Studies Of Intermediates And Regulation In Snare-Mediated Membrane Fusion, Xiaobing Lu Jan 2008

Studies Of Intermediates And Regulation In Snare-Mediated Membrane Fusion, Xiaobing Lu

Retrospective Theses and Dissertations

At the synapse, neurotransmitters are released via Ca2+-triggered exocytotic fusion of synaptic vesicles with the presynaptic plasma membrane. The whole process is controlled by various proteins. SNAREs have been recognized as the key components that drive membrane fusion. In addition, many other proteins, such as Munc18/nSec1, Mun13, synaptotagmin, complexin, etc. are characterized to regulate synaptic transmission temporally and spatially.;The in vitro bulk fluorescence assay was applied to examine the kinetics of membrane fusion of liposomes mediated by recombinant neuronal SNAREs and led to the demonstration of hemifusion as an intermediate in the pathway. In order to monitor ...


Molecular Interactions Of The Mammalian Intermediate Filament Protein Synemin With Cytoskeletal Proteins Present In Adhesion Sites, Ning Sun Jan 2008

Molecular Interactions Of The Mammalian Intermediate Filament Protein Synemin With Cytoskeletal Proteins Present In Adhesion Sites, Ning Sun

Retrospective Theses and Dissertations

The type VI intermediate filament (IF) protein synemin is a very large, unique member of the IF protein superfamily. Synemin associates with the major type III IF protein desmin and/or vimentin forming heteropolymeric intermediate filaments (IFs) within mammalian muscle cells. Previous studies in our lab showed that avian synemin interacts with vinculin and alpha-actinin, both of which are cytoskeletal proteins present in adhesion sites such as the focal adhesions within cells. Thus, synemin may link the heteropolymeric IFs to adhesion sites within mammalian muscle cells or within some non-muscle cells that express synemin. At least two isoforms of synemin ...


Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang Jan 2008

Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang

Retrospective Theses and Dissertations

Because of its appealing simplicity, the elastic network model (ENM) has been widely accepted and applied to study many molecular motion problems, such as the molecular mechanisms of chaperonin GroEL-GroES function, allosteric changes in hemoglobin, ribosome motions, motor-protein motions, and conformational changes in general. In this dissertation, the ENM is employed to study various protein dynamics problems, and its validity is also examined by comparing with experimental data. First, we apply principal component analysis (PCA) to identify the essential protein motions from multiple structures (X-ray, NMR and MD) of the HIV-1 protease. We find significant similarities between the first few ...


Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu Jan 2007

Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu

Retrospective Theses and Dissertations

Porcine Fructose-1,6-bisphosphatase is a homotetramer with four identical subunits. It plays a central role in gluconeogenesis and is tightly regulated by metabolites fructose 2,6-bisphosphate (F26P2) and AMP. Loop 52-72, loop 182-194 and residues 7-11 of the N-terminal segment play important role in the mechanism of catalysis and allosteric inhibition by AMP by retaining a structural hydrophobic region. Disruption of the hydrophobic region will evidently affect the catalysis and regulation of FBPase. Mutation of Thr53 reduced the catalysis activity of FBPase, mutation of Thr194 eliminated inhibition of AMP due to its low affinity to the enzyme, while double mutation ...


Effects Of Dietary Conjugated Linoleic Acid On European Corn Borer Survival, Growth, Fatty Acid Composition, And Fecundity, Lindsey Gereszek Jan 2007

Effects Of Dietary Conjugated Linoleic Acid On European Corn Borer Survival, Growth, Fatty Acid Composition, And Fecundity, Lindsey Gereszek

Retrospective Theses and Dissertations

No abstract provided.


Characterization Of Rns2, An S-Like Rnase In Arabidopsis Thaliana Suggests Role In Phosphate Recycling, Saralyn Ohanian Jan 2007

Characterization Of Rns2, An S-Like Rnase In Arabidopsis Thaliana Suggests Role In Phosphate Recycling, Saralyn Ohanian

Retrospective Theses and Dissertations

Ribonucleases play important biological roles within all organisms but many have not been well characterized. The family of T2 RNases is well-conserved throughout the kingdoms of life and yet their properties and functions are not well understood. RNS2 is one of five such RNases found in Arabidopsis, and preliminary evidence shows that it may be involved in phosphate recycling and localized to an intracellular compartment. Using rns2 knock-out mutant plants, I showed that RNS2 has an effect on flowering time during times of phosphate starvation. I also showed that RNS2 is localized to the ER, more specifically, to ER-bodies. To ...


Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang Jan 2007

Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang

Retrospective Theses and Dissertations

Membrane fusion is a basic biophysical process involved in cell's physiological activities. The value of studying the exocytosis of mammalian cells and yeast cells lies in that a highly conserved SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein super family mediates this process and is proposed to be the core protein machinery for the membrane. The SNARE proteins located on plasma membrane and vesicle membrane are assembled together to form a trans-SNARE bridging two separate membranes and initiating membrane.;My research centers on how SNARE assembly involved in yeast cells' exocytosis promotes membrane fusion between yeast vesicle and plasma ...


Molecular Basis Of Campylobacter Antibiotic Resistance And Adaptation To The Intestinal Tract Of Chickens, Baoqing Guo Jan 2007

Molecular Basis Of Campylobacter Antibiotic Resistance And Adaptation To The Intestinal Tract Of Chickens, Baoqing Guo

Retrospective Theses and Dissertations

Campylobacter is a major foodborne pathogen causing human enteric infections. Antibiotic treatments are needed for prolonged and severe cases of campylobacteriosis, but Campylobacter is increasingly resistant to antimicrobials, which has rendered antimicrobial therapy less effective. Multiple mechanisms contribute to antibiotic resistance in Campylobacter, but antibiotic efflux mediated by membrane transporters is considered a significant player in conferring intrinsic and acquired resistance to a broad spectrum of antimicrobials. The recently published genomic sequence revealed the presence of multiple genes encoding efflux transporters in C. jejuni, and work conducted in our laboratory identified that CmeABC, a RND (resistance nodulation and cell division ...


Characterization Of Three Spindle Matrix Proteins, Megator, East And Asator, In Drosophila, Hongying Qi Jan 2007

Characterization Of Three Spindle Matrix Proteins, Megator, East And Asator, In Drosophila, Hongying Qi

Retrospective Theses and Dissertations

Two previously identified proteins Skeletor and Chromator provide the molecular evidence for the existence of a spindle matrix complex in Drosophila. The spindle matrix has been proposed to be a macromolecular complex, which plays a role in organization and stabilization of the mitotic spindle as well as in providing structural support for counterbalancing force production.;In this dissertation, I present the identification and characterization of three more putative spindle matrix candidate proteins, Megator, EAST and Asator. Megator, an ortholog of the mammalian TPR protein, contains a large coiled-coil domain at its NH2-terminus and an acidic, non-structural COOH-terminus. Immunohistochemistry studies show ...


Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan Jan 2007

Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan

Retrospective Theses and Dissertations

The roles of three starch branching enzyme isoforms, BE1, BE2 and BE3, in Arabidopsis leaf starch metabolism were investigated by AtBE mutant analysis. We also determined the expression patterns of BEs in Arabidopsis by GUS staining and microarray experiments. The possible correlation of BE gene expression with other genes in the Arabidopsis genome was analyzed to identify putative genes that are functionally correlated with BEs. Motifs in the promoters of the Arabidopsis BE genes were identified to better understand their expression differences. BE2 and BE3 expression levels during a diurnal cycle were evaluated with isoform specific antibodies. Meantime, the in ...


Map Based Candidate Gene Cloning And Functional Analysis Of Genes Involved In Vlcfas Synthesis, Li Fan Jan 2007

Map Based Candidate Gene Cloning And Functional Analysis Of Genes Involved In Vlcfas Synthesis, Li Fan

Retrospective Theses and Dissertations

VLCFAs are biosynthesized by an endoplasmic reticulum associated enzyme system, referred to as fatty acid elongase. Fatty acid elongase generates VLCFAs by elongating 18C fatty acids. The enzymatic machinery of fatty acid elongation is believed to be composed of 3-ketoacyl-CoA synthase, 3-ketoacyl-CoA reductase, 3-hydroxyacyl-CoA dehydratase, and enoyl-CoA reductase. However, the insoluble nature of the fatty acid elongase system has hampered efforts to purify the system and to identify the genes that encode the component proteins. In the current study a candidate gene cloning approach was used to demonstrate that the previously defined gl26 gene of maize encodes a predicted enoyl-CoA ...


Cloning, Expression, Purification, And Characterization Of A Glycoside Hydrolase Family 44 Cellulase From Clostridium Acetobutylicum In Escherichia Coli, Taran Christopher Shilling Jan 2007

Cloning, Expression, Purification, And Characterization Of A Glycoside Hydrolase Family 44 Cellulase From Clostridium Acetobutylicum In Escherichia Coli, Taran Christopher Shilling

Retrospective Theses and Dissertations

Glycoside hydrolase family 44 (GH44) remains one of the smallest and least studied families of cellulases. The cellulosome of Clostridium acetobutylicum ATCC 824 contains the gene CAC0915, which codes for a putative extracellular GH44 catalytic domain with a C-terminal type I dockerin domain. The GH44 catalytic domain was synthesized with codon modifications, ligated into the expression vector pET--22b, and transformed into Escherichia coli BL21 (DE3). Expression during cell growth was induced by isopropyl-beta-D-thiogalactopyranoside and the recombinant protein, produced as a fusion protein containing a C-terminal His6-tag, and isolated from the harvested cells' cytoplasm after sonication. The enzyme has a mass ...


Production Of 3-Hydroxypropionate From Biomass, Netra Rajguru Agarkar Jan 2007

Production Of 3-Hydroxypropionate From Biomass, Netra Rajguru Agarkar

Retrospective Theses and Dissertations

Biorenewable technology is a developing field of science that researches alternative sources for petroleum products like fuels, plastics, paints, etc. The DoE biomass program has identified the 12 top chemicals that can be produced from biomass and further processed to replace many petroleum products; 3-hydroxypropionate (3HP) is a top 12 chemical that can be used to produce plastics, paints, tires, and other consumer products. This thesis describes the attempts to produce 3HP from glucose in E. coli and from syngas in R. rubrum. Malonyl CoA reductase from C. aurantiacus and R. castenholzii was cloned and expressed in E. coli and ...


The Roles Of Lcn2 In The Inflammatory Lung And Liver, Yinghua Liu Jan 2007

The Roles Of Lcn2 In The Inflammatory Lung And Liver, Yinghua Liu

Retrospective Theses and Dissertations

Uterocalin (Lcn2; also called 24p3, SIP24, or siderocalin and abbreviated as Utc) is an acute phase protein, for which the physiological function remains to be determined. Basal Utc expression is highest in the uterus, mammary gland and lung, which are three tissues with direct exposure to the diverse bacterial flora of the external environment. The demonstrated ability to bind siderophores is one means by which Utc can provide protection against pathogenic bacteria. However, its specificity for siderophores limits the ability of Utc to ward off pathogens. Epithelial tissues that interact with the external environment are exposed to many different nonpathogenic ...