Life Sciences Commons^™

Escherichia Coli Iron Acquisition Paradigms And Host Responses In The Human Urinary Milieu, Robin Reid Shields-Cutler

Arts & Sciences Electronic Theses and Dissertations

Urinary tract infections (UTIs) are some of the most common bacterial infections worldwide and are increasingly complicated by high antibiotic resistance and recurrence rates. Explanations for the marked individual differences in UTI susceptibility remain incomplete. In this thesis we show that urinary colonization by uropathogenic E. coli (UPEC) is influenced by urine composition and the activity of an important innate immune protein, siderocalin (SCN; also called lipocalin 2 or neutrophil gelatinase-associated lipocalin/NGAL). During UTI, host factors limit the availability of iron, an essential nutrient for the invading pathogen. In response, UPEC modify the urinary environment with metal binding siderophores, some …

Peripheral And Central Mechanisms Of Temporal Pattern Recognition, Christa Ann Baker

Arts & Sciences Electronic Theses and Dissertations

Encoding information into the timing patterns of action potentials, or spikes, is a strategy used broadly in neural circuits. This type of coding scheme requires downstream neurons to be sensitive to the temporal patterns of presynaptic inputs. Indeed, neurons with temporal filtering properties have been found in a wide range of sensory pathways. However, how such response properties arise was previously not well understood. The goal of my dissertation research has been to elucidate how temporal filtering by single neurons contributes to the behavioral ability to recognize timing patterns in communication signals.

I have addressed this question using mormyrid weakly …

A Gnotobiotic Mouse Model For Studying The Effect Of Human Gut Community Ecology On A Pathobiont, Bacteroides Fragilis, Vitas Wagner

Arts & Sciences Electronic Theses and Dissertations

ABSTRACT OF THE DISSERTATION

A Gnotobiotic Mouse Model for Studying the Effect of Human Gut Community Ecology on a Pathobiont, Bacteroides fragilis

by

Vitas Wagner

Doctor of Philosophy in Biology and Biomedical Sciences

Evolution, Ecology, and Population Biology

Washington University in St. Louis, 2015

Professor Jeffrey I. Gordon, Chair

Childhood undernutrition represents a pressing global health challenge. Epidemiologic studies have shown that undernutrition is not due to food insecurity alone, but rather represents a complex set of interactions between intra- and intergenerational factors. The gut microbiota has been implicated as one such factor. This thesis tested the hypothesis that enteropathogen …

Programming The Myocardium: The Notch-Wnt Axis, Benjamin S. Gillers

Arts & Sciences Electronic Theses and Dissertations

Heart related deaths are the number one cause of death in the United States. While heart failure and other mechanical issues are common, arrhythmias account for the majority of these deaths. By understanding the genetic architecture that patterns the normal cardiac conduction system, we can further deepen our understanding of how arrhythmias arise and develop targeted therapies to treat this deadly class of disease. I have found that canonical Wnt signaling is necessary for development of the atrioventricular junction. Furthermore, absence of myocardial Wnt signaling leads to tricuspid atresia. Overexpression of Wnt signaling leads to development of ectopic atrioventricular junction …

Flap Endonuclease 1 Promotes Telomere Replication And Stability By Distinct Mechanisms On The Leading And Lagging Strands, Daniel Cole Teasley

Arts & Sciences Electronic Theses and Dissertations

High fidelity DNA replication is essential for genomic stability and cell survival; this fact is underscored by the redundancy present in DNA replication and repair pathways. The complexity of these pathways is most evident at challenging DNA templates, such as those with repetitive sequence and transcribed loci. Among these challenging templates are telomeres, which are terminal, highly repetitive sequences that maintain genomic stability by preventing aberrant end-to-end chromosome fusions. In the absence of accurate, complete telomere replication, genomic instability results, ultimately leading to cell death or transformation. Here, we describe two unique roles in telomere stability for the DNA replication …

Neural Basis Of Functional Connectivity Mri, Jingfeng Li

Arts & Sciences Electronic Theses and Dissertations

The brain is hierarchically organized across a range of scales. While studies based on electrophysiology and anatomy have been fruitful on the micron to millimeter scale, findings based on functional connectivity MRI (fcMRI) suggest that a higher level of brain organization has been largely overlooked. These findings show that the brain is organized into networks, and each network extends across multiple brain areas. This large-scale, across-area brain organization is functionally relevant and stable across subjects, primate species, and levels of consciousness.

This dissertation addresses the neural origin of MRI functional connectivity. fcMRI relies on temporal correlation in at-rest blood oxygen …

Host Immune Signals Regulate Blood-Brain Barrier Function During Central Nervous System Infection And Autoimmunity, Brian Daniels

Arts & Sciences Electronic Theses and Dissertations

A major hallmark of neuroinflammatory diseases is the breakdown of the blood-brain barrier (BBB). This barrier between the hematogenous circulation and the parenchyma of the central nervous system (CNS) is a multicellular interface made up of endothelial cells joined by tight and adherens junctions (TJs and AJs), along with pericytes and the endfeet projections of astroglia. Together, these cells tightly restrict the movement of solutes and cells from the circulation into the CNS in a manner crucial for proper CNS homeostasis. Regulation of BBB function occurs dynamically during neuroinflammatory diseases such as infection and CNS autoimmunity, resulting in both protective …

Spatial And Epigenetic Regulation Of T-Cell Receptor Beta Gene Assembly, Kinjal Majumder

Arts & Sciences Electronic Theses and Dissertations

The adaptive immune system endows mammals with a sophisticated mechanism to recognize foreign proteins via surface antigen receptors that are expressed on the surface of all lymphocytes. This defense network is generated by V(D)J recombination, a set of sequentially controlled DNA cleavage and repair events that assembles functional antigen receptor genes from distally located Variable (V), Diversity (D) and Joining (J) gene segments. However, the recombination process must be stringently regulated to prevent formation of chromosomal translocations, which can lead to tumors. The process of V(D)J recombination is controlled at the levels of tissue, stage and allele specificity by a …

Β-Lactamase Gene Exchange Within The Enterobacteriaceae, Mitchell William Pesesky

Arts & Sciences Electronic Theses and Dissertations

Antibiotic resistance represents a grave threat to modern medicine’s control over infectious disease. Pathogens of the Enterobacteriaceae have proven particularly problematic as they can cause a wide variety of infections, and they can be, in some cases, resistant to all antibiotics recommended for use against them. A major part of the threat posed by the Enterobacteriaceae is their ability to exchange resistance genes by horizontal gene transfer (HGT). HGT has allowed some Enterobacteriaceae to quickly accumulate resistance against diverse antibiotics, and then to spread their resistance gene collection to other pathogenic strains. I explore three aspects of how HGT has …

Evolutionary Developmental Leaf Morphology Of The Plant Family Araceae, Claudia Liliana Henriquez

Arts & Sciences Electronic Theses and Dissertations

Studying the evolutionary developmental morphology of leaves using next-generation phylogenetics, a candidate gene approach and comparative developmental studies in the plant family Araceae is the overarching theme of the dissertation.

The plant family Araceae is an ancient lineage from the Early Cretaceous and belongs to the monocotyledons. Members of Araceae display striking variation in leaf development; such variation contradicts traditional models of monocot leaf development. Additionally, dissected leaves, which are rare in monocots, seem to have evolved independently multiple times in Araceae by various developmental mechanisms.

Despite extensive efforts to elucidate the evolutionary history of Araceae, phylogenetic ambiguity in the …

Functional Identification And Characterization Of Cis-Regulatory Elements, Christopher Michael Fiore

Arts & Sciences Electronic Theses and Dissertations

Transcription is regulated through interactions between regulatory proteins, such as transcription factors (TFs), and DNA sequence. It is known that TFs act combinatorially in some cases to regulate transcription, but in which situations and to what degree is unclear.

I first studied the contribution of TF binding sites to expression in mouse embryonic stem (ES) cells by using synthetic cis-regulatory elements (CREs). The synthetic CREs were comprised of combinations of binding sites for the pluripotency TFs Oct4, Sox2, Klf4, and Esrrb. A statistical thermodynamic model explained 72% of the variation in expression driven by these CREs. The high predictive power …

A Novel Cholesterol-Independent Mode Of Binding Promotes Cytolysin-Mediated Translocation And Pore Formation By Streptolysin O, Cara Mozola Forsberg

Arts & Sciences Electronic Theses and Dissertations

Effector translocation is a common strategy used by bacteria to promote pathogenesis via disruption of the immune response, prevention of phagocytosis, or induction of toxicity in the infected cell. The Gram-positive bacterium Streptococcus pyogenes utilizes a unique effector translocation system termed cytolysin-mediated translocation (CMT) to introduce the NAD+ glycohydrolase SPN into host cells during infection, resulting in cytotoxicity. Host cell membrane recognition by the cholesterol-dependent cytolysin (CDC) Streptolysin O (SLO) is a requisite step in this process, but the canonical cholesterol-dependent pore-forming activity of SLO is unnecessary, indicating that SLO is a bifunctional toxin. SLO exhibits extensive homology to other …

The Role Of Tmem178 In Regulation Of Osteo-Immune Activation And Inflammatory Bone Loss, Corinne Elaine Decker

Arts & Sciences Electronic Theses and Dissertations

Pathological bone loss in human disease such as arthritis is largely due to excessive osteoclast recruitment as a consequence of localized inflammation. Innate immune cells, namely neutrophils and macrophages, infiltrate the joint space and release pro-inflammatory cytokines as well as proteases to drive local tissue damage and inflammation. Importantly, IL-1 and TNF-a in particular act on the synovial fibroblasts as well as directly on osteoclast precursors to potently augment osteoclast differentiation and thus bone resorption. Current therapeutics to treat pathological bone loss are widely unsuccessful at targeting both the resorptive and inflammatory components of disease. We have previously demonstrated that …

Neural Mechanisms Of Working Memory Cortical Networks, Charalampos Papadimitriou

Arts & Sciences Electronic Theses and Dissertations

This dissertation is aimed at understanding the cortical networks that maintain working memory information. By leveraging patterns of information degradation in spatial working memory encoding we reveal new neural mechanisms that support working memory function and challenge existing models of working memory circuits.

First we examine how interference from previous memoranda influences memory of a currently remembered location. We find that memory for a currently remembered location is biased toward the previously memorized location. This interference is graded, not all-or-none. Interference is strongest when the previous and current targets are close and activate overlapping populations of neurons. Contrary to the …

Characterizing And Modeling Antibiotic Resistance Dynamics In Diverse Microbial Communities, Molly Krisann Gibson

Arts & Sciences Electronic Theses and Dissertations

Complex microbial communities colonize every habitat investigated to date, including soil, animals, water, and humans, as well as the structures we live in. It has been hypothesized that there is network of exchange allowing both bacterial organisms and functions to seamlessly move between and within these environments. These microbial communities often serve essential and beneficial functions for the host organism or environment. This is particularly evident in the human gut, where microbial communities consistently provide a set of services to its human host, including protecting against enteric pathogens, liberating nutrients from food, and signaling immune system regulation. However, these communities …

Essential Roles Of Stat3 In Zebrafish Development, Yinzi Liu

Arts & Sciences Electronic Theses and Dissertations

Vertebrate gastrulation is a fundamental morphogenetic process during which germ layers are formed, patterned and shaped into a body plan with organ rudiments. Among the conserved gastrulation movements, convergence and extension (C&E) occur concurrently to narrow the germ layers mediolaterally and elongate them along the anteroposterior embryonic axis. C&E are largely driven by cell migration and cell intercalation, while cell proliferation has been considered dispensable and even incompatible with gastrulation movements and morphogenesis. Signal transducer and activator of transcription 3 (Stat3) has been implicated by antisense morpholino loss-of-function study in regulation of zebrafish C&E movements in part by promoting non …

Dissection Of Affective Catecholamine Circuits Using Traditional And Wireless Optogenetics, Jordan Gary Mccall

Arts & Sciences Electronic Theses and Dissertations

Parsing the complexity of the mammalian brain has challenged neuroscientists for thousands of years. In the early 21st century, advances in materials science and neuroscience have enabled unprecedented control of neural circuitry. In particular, cell-type selective manipulations, such as those with optogenetics and chemogenetics, routinely provide answers to previously intractable neurobiological questions in the intact, behaving animal.

In this two-part dissertation, I first introduce new minimally invasive, wireless technology to perturb neural activity in the ventral tegmental area dopaminergic system of freely moving animals. I report a series of novel devices for studying and perturbing intact neural systems through optogenetics, …

Melittin-Derived Peptides For Sirna Delivery: Mechanisms Of Efficient Cytoplasmic Release, Kirk Kohwa Hou

Arts & Sciences Electronic Theses and Dissertations

The development of small molecules as therapeutic agents for targeted disease treatment is unable to keep up with the rapid expansion of databases cataloguing disease-causing proteins enabled by high throughput analysis of patient samples. As an alternative, the use of small interfering RNA (siRNA) provides a simple means of efficiently and specifically silencing the expression of these pathogenic proteins without the need for screening and development required of small molecules. Unfortunately, the delivery of siRNA is not trivial, and existing technology is characterized by either poor siRNA transfection efficiency or induction of cytotoxicity. Detailed work by many groups has supported …

The Roles Of Mist1 And Rab26 In Zymogenic (Chief) Cell Differentiation And Subcellular Organization, Ramon Jin

Arts & Sciences Electronic Theses and Dissertations

Little is known about how differentiating cells reorganize their cellular structure to perform specialized physiological functions. Specifically, exocrine cells like pancreatic acinar and zymogenic chief cells have a highly developed secretory architecture that is rapidly established upon differentiation. What is known in these cells is that the evolutionarily conserved transcription factor MIST1 is required for final maturation. We hypothesized that MIST1 directly regulates specific subcellular components that facilitate functional maturation of secretory cells.

We show that MIST1 binds to conserved CATATG E-boxes to activate transcription of 6 genes, including the small GTPases RAB26 and RAB3D. We next demonstrate that RAB26 …

Assessing Vascular Inflammation With Bioluminescence Imaging, Reece Joseph Goiffon

Arts & Sciences Electronic Theses and Dissertations

Cardiovascular disease (CVD) is the leading cause of morbidity, mortality, and health care costs in the developed world and is often undiagnosed until clinical presentation with a major adverse cardiovascular event (MACE). Plasma myeloperoxidase (MPO) content is an emerging biomarker for risk, progression, and prognosis at different stages of CVD. Enzyme-linked immunosorbent assays (ELISAs) are currently used to measure clinical plasma MPO concentration, but ELISAs are costly and time-intensive. Luminol is a chemiluminescent compound with specificity for MPO activity in vivo, but is not sensitive enough for use as a bioluminescence reporter of plasma MPO oxidation. The luminol derivative L-012 …

Excessive Complement Activation Due To Genetic Haploinsufficiency Of Regulators In Multiple Human Diseases, Michael Triebwasser

Arts & Sciences Electronic Theses and Dissertations

The complement system is an ancient and powerful form of innate immunity. The alternative pathway (AP), a positive feedback loop, is at the core of the complement system. Activating components and regulators of the AP are genetically implicated in atypical hemolytic uremic syndrome (aHUS) and age-related macular degeneration (AMD). aHUS features kidney failure, and often affects young children, but may occur throughout life and can be precipitated by pregnancy. aHUS associated variants are extremely rare and are considered highly penetrant. At the opposite end of the spectrum, AMD affects the retina leading to loss of central vision with a late …

Functional Consequences Of Cd4+ T Cell Receptor Ligation In The Immune Response To Listeria Monocytogenes, Stephen Phillip Persaud

Arts & Sciences Electronic Theses and Dissertations

Interactions between the ab T cell receptor (TCR) and peptide-bound MHC molecules (pMHC) are highly specific and sensitive despite low affinities. The basis of TCR ligand specificity and its functional manifestations during protective immune responses are incompletely understood. To study this, we have generated two TCR transgenic mice called LLO56 and LLO118, which bear CD4+ T cells that recognize the same dominant epitope from the virulence factor Listeriolysin O (LLO) of Listeria monocytogenes. These TCRs were cloned from Listeria-infected B6 mice, and thus represent two solutions to recognizing the same pathogen-derived pMHC. LLO118 T cells expanded better than LLO56 during …

Genetic And Cellular Studies Of The Podocyte In Focal Segmental Glomerulosclerosis, Haiyang Yu

Arts & Sciences Electronic Theses and Dissertations

The podocyte forms the outer layer of the filtration barrier in the glomerulus to prevent albumin leakage. Podocyte damage leads to focal segmental glomerulosclerosis (FSGS), a leading cause of chronic kidney disease. The cause of the majority of FSGS cases is unknown and referred to as sporadic FSGS. Genetic studies have identified genes as monogenic causes of FSGS in patients with a strong family history, but these cases account for only a small proportion of the FSGS population. Whether genetic susceptibility contributes to sporadic FSGS and which cellular process in the podocyte initiates the pathogenesis of FSGS are important questions …

Guanine Nucleotide Synthesis And The Enteric Nervous System, Jonathan Ian Lake

Arts & Sciences Electronic Theses and Dissertations

There are currently no prevention strategies for Hirschsprung disease (HSCR), a potentially lethal birth defect caused by the failure of the enteric nervous system (ENS) to develop completely, resulting in an aganglionic segment of intestine. HSCR can result from one or a combination of partially-penetrant mutations in genes affecting the enteric neural crest-derived cells (ENCDCs) that colonize the intestine to form the ENS. While the genetics of HSCR and ENS development has been extensively studied, little is known about environmental risk factors for HSCR. To investigate maternal medication exposure as a possible HSCR risk factor, we conducted a chemical screen …

How Gains And Losses Influence The Brain And Behavior: Relations To Age, Risk For Depression, And Individual Differences, Katherine R. Luking

Arts & Sciences Electronic Theses and Dissertations

Behavioral and neural response to rewards and punishments has been the subject of a growing literature with particular interest within developmental, psychopathology, and individual difference domains. There is now mounting evidence suggesting that adolescents show heightened response to reward relative to adults, and that adolescents with Major Depressive Disorder (MDD), elevated depressive symptoms, or at high-risk for depression show reduced response to reward. However, it is unclear whether similar relations between response to incentives and development/psychopathology are observed during childhood. Here we examine behavioral, neural (functional magnetic resonance imaging - fMRI), and self-reported responsiveness to gain and loss of rewards …

K-Ras, But Not H-Ras Or N-Ras, Hyperactivation Regulates Brain Neural Stem Cell Proliferation In A Raf/Rb-Dependent Manner, R. Hugh F. Bender

Arts & Sciences Electronic Theses and Dissertations

Neural stem cells (NSCs) give rise to all the major cell types in the brain, including neurons, oligodendrocytes, and astrocytes. However, the intracellular signaling pathways that govern brain NSC proliferation and differentiation have been incompletely characterized to date. Since several neurodevelopmental brain disorders (i.e., Costello syndrome, Noonan syndrome) are caused by germline mutations in the RAS genes, Ras small GTPases are likely critical regulators of brain NSC function. In the mammalian brain, Ras exists as three distinct molecules (H-Ras, K-Ras, and N-Ras), each with different subcellular localizations, downstream signaling effectors, and biological effects. Leveraging a novel series of conditional Ras …

Ketone Body Metabolism Preserves Hepatic Function During Adaptation To Birth And In Overnutrition, David Graham Cotter

Arts & Sciences Electronic Theses and Dissertations

Mammalian ketone body metabolism partially oxidizes hepatic acyl-chains to ketone body intermediates, which can serve as alternative fuels in extrahapetic tissues during carbohydrate restricted states. Ketone body production (ketogenesis) occurs primarily in liver, due to hepatocyte-specific expression of the fate committing ketogenic enzyme, mitochondrial 3-hydroxymethylglutaryl-CoA synthase (HMGCS2). In contrast, the fate committing enzyme of ketone body oxidation, mitochondrial Succinyl-CoA:3-oxoacid CoA Transferase (SCOT), is expressed ubiquitously, except in liver. Here I demonstrate novel roles for ketone body metabolism during a classically ketogenic period, the transition to birth, and in a classically `non-ketogenic' state, overnutrition, using novel genetic mouse models, high-resolution measures …

Molecular And Computational Methods For Cellular State Control, Drew Groves Michael

Arts & Sciences Electronic Theses and Dissertations

The control of cellular state has many promising applications, including stem cell biology and

regenerative medicine, biofuel production, and gene therapy. This dissertation demonstrates a

comprehensive approach to cellular state control at the transcriptional level. We introduce a

novel algorithm, NetSurgeon, which utilizes genome-wide gene regulatory networks to identify

interventions that will force a cell toward a desired expression state. Following extensive in

silico validation, we applied NetSurgeon to S. cerevisiae biofuel production, generating

interventions designed to promote a fermentative state during xylose catabolism. Our selected

interventions successfully promoted a fermentative transcriptional state and generated strains

with higher xylose import …

Molecular Characterization Of A Novel, Highly Protective Combination Monoclonal Antibody Therapy Against Chikungunya Virus, Pankaj Pal

Arts & Sciences Electronic Theses and Dissertations

Chikungunya virus (CHIKV) is an Aedes mosquito-transmitted alphavirus that causes epidemics of a debilitating, often chronic polyarthritis in humans. Over five million people in Africa and Asia have been infected since 2005, and an outbreak occurred recently in Italy demonstrating the potential for a global epidemic. A strong antibody response is elicited during infection and the aim of this thesis was to develop a better understanding of how the humoral immune response can control CHIKV infection. We identified 230 new anti-CHIKV monoclonal antibodies (MAbs) and tested their ability to inhibit infection of strains representing all three CHIKV genotypes (East/Central/South African, …

Molecular Mechanisms Of Plasmodium Red Blood Cell Invasion, Brian Michael Malpede

Arts & Sciences Electronic Theses and Dissertations

The malaria parasite Plasmodium utilizes specialized proteins for adherence to cellular receptors in its mosquito vector and human host. Adherence is critical for parasite development, host cell traversal and invasion, and protection from vector and host immune mechanisms. These vital roles have identified several adhesins as vaccine candidates. A deficiency in current adhesin-based vaccines is induction of antibodies targeting non-conserved, non-functional, and decoy epitopes due to the use of full length proteins or binding domains. To alleviate the elicitation of non-inhibitory antibodies, conserved functional regions of proteins must be identified and exploited. Structural biology provides the tools necessary to achieve …