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Discovery And Characterization Of A Novel Class Of Metabolic Regulators In The Malaria Parasite Plasmodium Falciparum, Ann Marie Guggisberg

Arts & Sciences Electronic Theses and Dissertations

The malaria parasite, Plasmodium falciparum, infects hundreds of millions of people per year and causes hundreds of thousands of deaths. Within the host red blood cell, the parasite relies on glycolysis for energy and synthesis of essential biomolecules. One such anabolic fate of glucose is the synthesis of isoprenoids, a broad and essential class of compounds that participate in a variety of cellular functions. In the face of ever-evolving drug resistance, new inhibitors and better understanding of parasite metabolism are required. The antibiotic fosmidomycin (FSM) targets the methylerythritol phosphate pathway for isoprenoid synthesis and is a well-validated inhibitor of P. …

Genetic Mechanisms For The Maintenance Of Behavioral Mating Barriers In Drosophila, Kathleen M. Mortland

Arts & Sciences Electronic Theses and Dissertations

One of the most successful and diverse systems involved in the maintenance of behavioral barriers between closely related animal species is pheromonal communication. In the fruit fly, contact chemosensation input is especially important during sexual decision-making as it allows for the sensing of sex and species-specific non-volatile cuticular hydrocarbons (CHCs), which function as insect pheromones. However, how pheromonal systems support the maintenance of mating barriers is puzzling since any change in either pheromone ligands or their cognate receptors would carry a fitness cost, which should be eliminated by stabilizing selection. To resolve this evolutionary conundrum I hypothesized that pleiotropic genes …

Epigenomics Of Cell Fate In Development And Disease, Rebecca Faith Lowdon

Arts & Sciences Electronic Theses and Dissertations

Epigenetic features at regulatory elements provide instructive cues for transcriptional regulation during development. However, the particular epigenetic alterations necessary for proper cell fate acquisition and differentiation are not well understood. This dissertation explores the epigenetic dynamics of regulatory elements during development and uses epigenome annotations to document inappropriate transcriptional regulation in disease. First, I summarize my contributions to developing a new algorithm for detecting differential DNA methylation, M&M. I report the application of the M&M algorithm to identify distinct classes of DNA methylation dynamics in surface ectoderm (SE) progenitor cells and SE-derived lineages: epigenome alterations, and differential DNA methylation in …

Patterns Of Fecal Progestagens, Estrogens, And Androgens Associated With Reproduction In Blue-Throated Piping Guans (Pipile Cumanensis), Leslie Ann Sterling, Helen Clawitter, Corinne P. Kozlowski, Michael Macek, Anne Tieber

Undergraduate Research Symposium Posters

While fecal hormone analyses are routinely employed to monitor reproduction in mammals, few studies have used these techniques for monitoring reproductive events in birds. This study describes the endocrine patterns associated with reproduction in the blue-throated piping guan (Pipile cumanensis), a less threatened relative of the critically endangered Trinidad piping guan (P. pipile). Fecal samples were collected approximately once a week for 3 years from seven female guans and six male guans at the Saint Louis Zoo. Concentrations of fecal progestagens, estrogens, and androgens were quantified using commercially available enzyme immunoassays. Baseline progestagen concentrations for females …

New Tools For Viscoelastic Spectral Analysis, With Application To The Mechanics Of Cells And Collagen Across Hierarchies, Behzad Babaei

McKelvey School of Engineering Theses & Dissertations

Viscoelastic relaxation spectra are essential for predicting and interpreting the mechanical responses of materials and structures. For biological tissues, these spectra must usually be estimated from viscoelastic relaxation tests. Interpreting viscoelastic relaxation tests is challenging because the inverse problem is expensive computationally. We present here (1) an efficient algorithm and (2) a quasi-linear model that enable rapid identification of the viscoelastic relaxation spectra of both linear and nonlinear materials. We then apply these methods to develop fundamental insight into the mechanics of collagenous and fibrotic tissues.

The first algorithm, which we term the discrete spectral approach, is fast enough to …

Neural Representation Of Vocalizations In Noise In The Primary Auditory Cortex Of Marmoset Monkeys, Ruiye Ni

McKelvey School of Engineering Theses & Dissertations

Robust auditory perception plays a pivotal function in processing behaviorally relevant sounds, particularly when there are auditory distractions from the environment. The neuronal coding enabling this ability, however, is still not well understood. In this study we recorded single-unit activity from the primary auditory cortex of alert common marmoset monkeys (Callithrix jacchus) while delivering conspecific vocalizations degraded by two different background noises: broadband white noise (WGN) and vocalization babble (Babble).

Noise effects on single-unit neural representation of target vocalizations were quantified by measuring the response similarity elicited by natural vocalizations as a function of signal-to-noise ratio (SNR). Four consistent response …

Actin-Based Feedback Circuits In Cell Migration And Endocytosis, Xinxin Wang

Arts & Sciences Electronic Theses and Dissertations

In this thesis, we study the switch and pulse functions of actin during two important cellular processes, cell migration and endocytosis. Actin is an abundant protein that can polymerize to form a dendritic network. The actin network can exert force to push or bend the cell membrane. During cell migration, the actin network behaves like a switch, assembling mostly at one end or at the other end. The end with the majority of the actin network is the leading edge, following which the cell can persistently move in the same direction. The other end, with the minority of the actin …

Perceiving Oldness In Parietal Cortex: Fmri Characterization Of A Parietal Memory Network, Adrian Gilmore

Arts & Sciences Electronic Theses and Dissertations

The manner in which the human brain recognizes certain stimuli as novel or familiar is a matter of ongoing investigation. The overarching goal of this dissertation is to improve our understanding of how this may be accomplished. More specifically, work contained herein focuses on a recently described "parietal memory network" (PMN; Gilmore et al., 2015) that shows opposite patterns of activity when perceiving novel or familiar stimuli: deactivating in response to novelty, and activating in response to familiarity. Critically, our understanding of this network is based on explicit memory tasks, in which subjects are deliberately instructed to learn or remember …

Regulation Of Transcription And Stress Response By Card In Mycobacteria, Ashley Louise Garner

Arts & Sciences Electronic Theses and Dissertations

Mycobacterium tuberculosis, the causative agent of Tuberculosis, infects over one third of the world's population. To control this epidemic, we must develop new chemotherapeutic strategies for treatment, which requires further insight into the physiology of this bacterium. Previous studies have identified CarD as a transcriptional regulator essential during both acute and persistent infection. Depletion of CarD sensitizes strains to a diverse panel of stresses and deregulates several hundred genes and ribosomal RNA (rRNA) which suggested that CarD may be a transcriptional regulator. Chromatin immunoprecipitation sequencing experiments showed that CarD was localized to promoters throughout the genome, suggesting that CarD regulates …

Mechanisms Of Extracellular Vesicle Biogenesis, Charles Eldon Jackson

Arts & Sciences Electronic Theses and Dissertations

Extracellular vesicles (EVs) are important mediators of intercellular communication. Different types of EVs are released from cells by either fusion of late endsomal multivesicular bodies with the plasma membrane (exosomes) or direct budding from the plasma membrane (ectosomes). Topologically equivalent processes including intralumenal vesicle formation for degradation in the endosomal pathway and virus budding from the plasma membrane depend on the ATPase VPS4 and its Endosomal Sorting Complex Required for Transport (ESCRT)-III substrates for membrane fission and release. Whether this machinery is generally required for EV biogenesis has, however, been the subject of debate. Studies of the EV proteome from …

Use Of Proteomics To Probe Dynamic Changes In Cyanobacteria, Amelia Yen Nguyen

Arts & Sciences Electronic Theses and Dissertations

Cyanobacteria are unicellular photosynthetic microorganisms that capture and convert light energy to chemical energy, which is the precursor for feed, fuel, and food. These oxygenic phototrophs appear blue-green in color due to the blue bilin pigments in their phycobilisomes and green chlorophyll pigments in their photosystems. They also have diverse morphologies, and thrive in terrestrial, marine water, fresh water, as well as extreme environments. Cyanobacteria have developed a number of protective mechanisms and adaptive responses that allow the photosynthetic process to operate optimally under diverse and extreme conditions. Prolonged deprivation of essential nutrients, such as nitrogen and sulfur, commonly found …

The Role Of Epidermal Enhancer 923 In The Chromatin Architecture And Transcriptional Regulation Of The Epidermal Differentiation Complex, Inez Oh

Arts & Sciences Electronic Theses and Dissertations

The epidermis covers the surface of the skin and provides a functional barrier across the entire body. Epidermal cells or keratinocytes proliferate in the innermost basal layer and migrate upwards into the suprabasal spinous and granular layers as they differentiate, and finally into the terminally differentiated outermost stratum corneum. Keratinocytes undergoing terminal differentiation are marked by tissue-specific concomitant expression of genes encoded in the Epidermal Differentiation Complex (EDC) locus. The EDC genes are organized into four gene families - S100, Sprr, Lce, and Flg-like, which are coordinately expressed upon activation of the terminal differentiation program in keratinocytes. The molecular mechanisms …

Functions Of The Dna Polymerase Delta Replicase In Lagging Strand Replication, Joseph L. Stodola

Arts & Sciences Electronic Theses and Dissertations

The work described in this dissertation focuses on several aspects of DNA replication in the model organism Saccharomyces cerevisiae, with particular attention paid to the function of the replicative DNA polymerase delta (Pol ), and its functions in Okazaki fragment synthesis and maturation. The first major theme of this dissertation is investigating the role that metal binding motifs play in the structure and function of Pol and other budding yeast polymerases. First, I discuss the role that two metal binding motifs within the catalytic subunit of Pol play in creating the multi-subunit polymerase complex and in promoting crucial interactions with …

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

McKelvey School of Engineering Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess …

Revelation Of Yin-Yang Balance In Microbial Cell Factories By Data Mining, Flux Modeling, And Metabolic Engineering, Gang Wu

McKelvey School of Engineering Theses & Dissertations

The long-held assumption of never-ending rapid growth in biotechnology and especially in synthetic biology has been recently questioned, due to lack of substantial return of investment. One of the main reasons for failures in synthetic biology and metabolic engineering is the metabolic burdens that result in resource losses. Metabolic burden is defined as the portion of a host cells resources either energy molecules (e.g., NADH, NADPH and ATP) or carbon building blocks (e.g., amino acids) that is used to maintain the engineered components (e.g., pathways). As a result, the effectiveness of synthetic biology tools heavily dependents on cell capability to …

Mechanism Of Calcium-Dependent Chloride Channel Activation By The Secreted Regulator Clca1, Zeynep Yurtsever

Arts & Sciences Electronic Theses and Dissertations

The calcium-activated chloride channel regulator (CLCA) proteins are key signaling molecules, which are implicated in various diseases through their tissue-specific expression. Human CLCA1 protein, overexpressed in airway epithelia under pathophysiological conditions, is centrally involved in the manifestation of IL-13-driven mucus cell metaplasia (MCM), a hallmark feature of asthma and chronic obstructive pulmonary disease (COPD), for which there are currently no available therapeutics. Elucidating the poorly understood molecular basis of CLCA1 function is thus required to design specific inhibitors of CLCA1 activity to treat MCM in asthma and COPD.

Originally misannotated as ion channels, CLCA proteins are secreted soluble proteins that …

Development And Application Of Comparative Gene Co-Expression Network Methods In Brachypodium Distachyon, Henry David Priest

Arts & Sciences Electronic Theses and Dissertations

Gene discovery and characterization is a long and labor-intensive process. Gene co-expression network analysis is a long-standing powerful approach that can strongly enrich signals within gene expression datasets to predict genes critical for many cellular functions. Leveraging this approach with a large number of transcriptome datasets does not yield a concomitant increase in network granularity. Independently generated datasets that describe gene expression in various tissues, developmental stages, times of day, and environments can carry conflicting co-expression signals. The gene expression responses of the model C3 grass Brachypodium distachyon to abiotic stress is characterized by a co-expression-based analysis, identifying 22 modules …

Understanding The Interactions Of Developing Thymocytes And Antigen Presenting Cells In The Thymic Medulla, Justin Shaun Arnold Perry

Arts & Sciences Electronic Theses and Dissertations

Various thymic APC subsets have been invoked in deletional tolerance and Treg cell induction, but previous studies either assessed total T cell numbers or used TCR transgenic lines, obscuring roles that individual thymic APC subsets might serve for particular antigen-specific T cell populations. Utilizing T cell receptor sequencing, we found that medullary thymic epithelial cells (mTECs) and bone marrow-derived (BM) APCs delete or select unique conventional and Treg cell TCR repertoires, demonstrating distinct roles for these APCs. We show that BM APCs and mTECs each contribute to Aire-dependent T cell tolerance development, albeit through either cooperative or autologous antigen presentation …

Development Of Steady-State And Dynamic Flux Models For Broad-Scope Microbial Metabolism Analysis, Lian He

McKelvey School of Engineering Theses & Dissertations

Flux analysis techniques, including flux balance analysis (FBA) and 13C-metabolic flux analysis (MFA), can characterize carbon and energy flows through a cells metabolic network. By employing both 13C-labeling experiments and nonlinear programming, 13C-MFA provides a rigorous way of examining cell flux distributions in the central metabolism. FBA, on the other hand, gives a holistic review of optimal fluxomes on the genome scale. In this dissertation, flux analysis techniques were constructed to investigate the microbial metabolisms.

First, an open-source and programming-free platform of 13C-MFA (WUFlux) with a user-friendly interface in MATLAB was developed, which allowed both mass isotopomer distribution (MID) analysis …

Development And Investigation Of Sparse Co-Adaptive Algorithms In Ecog Based Closed-Loop Brain Computer Interface, Piyush Karande

McKelvey School of Engineering Theses & Dissertations

Electrocorticography (ECoG) has gained a lot of momentum and has become a serious contender as a recording modality for the implementation of Brain-Computer Interface (BCI) systems in the last few years. ECoG signals provide the right balance between minimal invasiveness and robust spectral information to accomplish a BCI task. However, all the BCI studies until now have used signals recorded from a large number of implanted electrodes and a larger number of spectral features. The recording and processing of these signals uses a lot of electrical power and thus hinders its use outside the research setting. To translate this research …

Mechanics Of Early Retina And Lens Development In The Embryo, Alina Oltean

McKelvey School of Engineering Theses & Dissertations

Mechanical forces play an essential role in morphogenesis, the shaping of embryonic structures. This research focuses mainly on eye development, a problem that has been studied for decades using a variety of approaches. However, the mechanics of the early stages of eye formation remain incompletely understood.

The embryonic eyes begin as bilateral protrusions called optic vesicles (OVs) that grow outward from the anterior end of the brain tube. The optic vesicles contact and adhere to the overlying surface ectoderm (SE) via extracellular matrix (ECM). Then, both layers thicken in the region of contact to form the retinal and lens placodes, …

The Molecular And Cellular Basis For Cold Sensation, Daniel Brenner

Arts & Sciences Electronic Theses and Dissertations

The ability to sense changes in temperature is crucial to surviving harsh environments. Over the last decade several ion channels that have been proposed to be cold sensitive have been identified, most notably TRPM8 and TRPA1. Although these molecules have been extensively studied in vitro, their exact roles in cold sensation in vivo are still debated. This uncertainty is in large part due to problems with the standard methods of testing cold sensitivity in vivo, which often rely on subjective measures of cold responsiveness. Experiments using these subjective measures have been repeated by different groups and have yielded conflicting results, …

The Resolution Phase Of Nk Cell Proliferation And Ifn Production Following Viral Infection Are Highly Regulated Processes., Leslie Abigail Fogel

Arts & Sciences Electronic Theses and Dissertations

In response to MCMV infection, NK cells undergo three distinct phases of proliferation: the non-specific phase mediated by pro-proliferative cytokines; the specific phase mediated by recognition of an MCMV-encoded protein by an NK cell activating receptor, Ly49H; and the resolution phase, whose mechanism is unknown. MCMV infection of RAG mice, which lack all adaptive immune cells, results in prolonged proliferation of NK cells despite similar viral titers compared to wildtype mice. Interestingly, there are different kinetics for Ly49H+ and Ly49H- NK cells. We have identified several additional markers that may distinguish NK cells that have been specifically activated through their …

A Quantitative Genetic Analysis Of Craniofacial Variation In Baboons, Jessica Lynn Joganic

Arts & Sciences Electronic Theses and Dissertations

This dissertation is an explication of baboon craniofacial variation and its genetic basis. Intraspecific variation is the result of input from and complex interactions among genetic information, functional demands, and developmental processes. The relative effect of each of these on craniofacial variation, as well as the degree of inter-trait covariance, determines whether traits can respond to selection and what that response might look like. Using a sample of pedigreed baboons, I quantify craniofacial variation to address specific questions regarding the distribution and magnitude of phenotypic, genetic, and environmental variation patterns. In addition, I identify regions of the genome containing genetic …

Engineering Cre Recombinase For Genome Engineering, Chi Zhang

Arts & Sciences Electronic Theses and Dissertations

Cre recombinase recombines its DNA target, loxP sites, without help of accessory proteins or DNA repair systems. The simplicity of Cre-lox system has been widely utilized for genome editing, especially in mouse genetics. The goal of this dissertation is to constructCrerecombinase variants that will operate uponrecombination target sites (RTs) present within the genome, instead of perturbing the genome by inserting wildtype RTs for subsequent genome engineering. In general, the desired RTs native to the genome are asymmetric. However, the loxP sequence is pseudo-palindromic, requiring a homotetrameric formation of Cre recombinase. As a first step, I broke the symmetry of Cre …

Genetic Imputation: Accuracy To Application, Shelina Raynell Ramnarine

Arts & Sciences Electronic Theses and Dissertations

Genotype imputation, the process of inferring genotypes for untyped variants, is used to identify and refine genetic association findings. This body of work focuses on assessing imputation accuracy and uses imputed data to identify genetic contributors to mentholated cigarette preference.

Inaccuracies in imputed data can distort the observed association between variants and a disease. Many statistics are used to assess accuracy; some compare imputed to genotyped data and others are calculated without reference to true genotypes. Prior work has shown that the Imputation Quality Score (IQS), which is based on Cohens kappa statistic and compares imputed genotype probabilities to true …

Modulation Of Human And Malarial Glucose Transporter Activity By Lipids And Small Molecules, Thomas E. Kraft

Arts & Sciences Electronic Theses and Dissertations

Glucose transport is a fundamentally important process for maintenance and regulation of cellular metabolism in all kingdoms of life. Despite their high importance, detailed examination of glucose transport proteins in humans and parasites through biochemical, biophysical and structural properties was greatly hampered by the inability to express, purify and reconstitute sufficient amounts of active transporters. This dissertation describes strategies that led to the first successful expression, purification, stabilization and functional reconstitution of active insulin-responsive GLUT4 transport protein. Furthermore, the work described herein establishes a requirement of anionic and conical lipids for full activity of the mammalian glucose transporters GLUT3 and …

Iron Regulation Of Macrophage Responses To Uropathogenic E. Coli, Nana Kwame Owusu-Boaitey

Arts & Sciences Electronic Theses and Dissertations

Uropathogenic E. coli (UPEC) are the principal cause of urinary tract infections (UTIs), one of the most common infections globally. Given the rising incidence of antibiotic resistance among UPEC strains, there is an increasing need to better understand the host response to UPEC and to develop ways to harness the bladder innate immune response that clears infection. In response to infection, the host attempts to limit the ability of UPEC to access iron, a metal critical to UPEC survival. Innate immune cells known as macrophages are known to regulate iron homeostasis through the production of pro-inflammatory cytokines, though it remains …

Omcp Mediated Cowpox Virulence And Its Dependence On The Immune Receptors Nkg2d And Fcrl5., Michel Muzi Sun

Arts & Sciences Electronic Theses and Dissertations

Viruses with large DNA genomes, such as cowpox virus, encode many open-reading frames involved in the modulation of the host immune system, facilitating escape from immune detection or downregulation of specific aspects of the host immune response. Investigation of virally-encoded immunoevasins has been instrumental in understanding host-pathogen interactions. Here, we focus on the cowpox virus immunoevasin Orthopoxvirus MHC Class I-like Protein (OMCP) and demonstrate for the first time that OMCP facilitates cowpox virus virulence in vivo. We have previously documented that OMCP binds the activating receptor NKG2D on NK cells as well as the orphan receptor FCRL5 on innate B …

Superoxide Dismutase 1: Novel Insights On Disease Models And Tissue Specificity In Amyotrophic Lateral Sclerosis, Matthew James Crisp

Arts & Sciences Electronic Theses and Dissertations

Mutations in superoxide dismutase 1 (SOD1) are known to cause dominantly-inherited amyotrophic lateral sclerosis (ALS), a rapidly-fatal adult-onset neurodegenerative disorder defined by motor neuron loss and progressive paralysis. In the past twenty years, research into the disorder has been driven by the creation of numerous transgenic animal models that have yielded multiple theories on the pathogenesis of the disease. Patients and animal models with SOD1 mutations express the defective protein in every cell, yet the disease only affects tissues in the neuromuscular axis. In this dissertation, I present original work exploring two aspects of SOD1 ALS. The first details the …