Biology Commons^™

Environmental Stimuli And Intragenerational Epigenetics, Nicholas J. Napier

Student Scholarship

Epigenetics is the study of any change in gene expression that is not mediated by DNA sequence. The effects of environmental stimuli on epigenetic changes have been studied extensively in recent years. Multiple reviews have provided comprehensive summations of the effects of environmental stimuli on transgenerational epigenetic changes, but few reviews have focused upon environment-induced intragenerational epigenetic changes. This review will summarize current knowledge of the intragenerational epigenetic changes that are induced by two groups of well-studied environmental stimuli: nutritional deficiencies and carcinogens. This survey of intragenerational epigenetic changes will focus upon the mechanisms behind them, the disorders associated with …

Saponin-Permeabilization Is Not A Viable Alternative To Isolated Mitochondria For Assessing Oxidative Metabolism In Hibernation, Katherine E. Mathers, James F. Staples

Biology Publications

Saponin permeabilization of tissue slices is increasingly popular for characterizing mitochondrial function largely because it is fast, easy, requires little tissue and leaves much of the cell intact. This technique is well described for mammalian muscle and brain, but not for liver. We sought to evaluate how saponin permeabilization reflects aspects of liver energy metabolism typically assessed in isolated mitochondria. We studied the ground squirrel (Ictidomys tridecemlineatus Mitchell), a hibernating mammal that shows profound and acute whole-animal metabolic suppression in the transition from winter euthermia to torpor. This reversible metabolic suppression is also reflected in the metabolism of isolated liver …

Recbcd Is Required To Complete Chromosomal Replication: Implications For Double- Strand Break Frequencies And Repair Mechanisms, Justin Courcelle, Brian M. Wendel, Dena D. Livingstone, Charmain T. Courcelle

Biology Faculty Publications and Presentations

Several aspects of the mechanism of homologous double strand break repair remain unclear. Although intensive efforts have focused on how recombination reactions initiate, far less is known about the molecular events that follow. Based upon biochemical studies, current models propose that RecBCD processes double strand ends and loads RecA to initiate recombinational repair. However, recent studies have shown that RecBCD plays a critical role in completing replication events on the chromosome through a mechanism that does not involve RecA or recombination. Here, we examine several studies, both early and recent, that suggest RecBCD also operates late in the recombination process- …

Aversive Stimuli Drive Drug Seeking In A State Of Low Dopamine Tone, Robert C. Twining, Daniel S. Wheeler, Amanda L. Ebben, Andre J. Jacobsen, Mykel A. Robble, John R. Mantsch, Robert A. Wheeler

Biological Sciences Faculty Research and Publications

Background

Stressors negatively impact emotional state and drive drug seeking, in part, by modulating the activity of the mesolimbic dopamine system. Unfortunately, the rapid regulation of dopamine signaling by the aversive stimuli that cause drug seeking is not well characterized. In a series of experiments, we scrutinized the subsecond regulation of dopamine signaling by the aversive stimulus, quinine, and tested its ability to cause cocaine seeking. Additionally, we examined the midbrain regulation of both dopamine signaling and cocaine seeking by the stress-sensitive peptide, corticotropin releasing factor (CRF).

Methods

Combining fast-scan cyclic voltammetry with behavioral pharmacology, we examined the effect of …

The Role Of Myc And Ap-1 Transcription Factors In The Development And Function Of The Dendritic Cell Lineage, Wumesh K.C.

Arts & Sciences Graduate Student Theses and Dissertations

Dendritic cells (DCs) orchestrate immune responses to foreign and self proteins by capturing, processing and presenting antigens to naïve CD4+ and CD8+ T cells in specialized regions of lymphoid organs. Consequently, DCs function in many disparate infectious settings, during which their activation can result in both pathogenic and protective responses. The diverse properties of DCs manifest through the actions of a limited set of lineage-specifying DNA-binding proteins called transcription factors (TFs). The precise molecular program controlled by these developmentally important TFs (such as Irf8 and Batf3) is largely unknown because most studies to date have been largely descriptive. We have …

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 Graduate Student 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 …

Assessing Vascular Inflammation With Bioluminescence Imaging, Reece Joseph Goiffon

Arts & Sciences Graduate Student 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 Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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, …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

Regulation Of Host And Viral Rna Expression During Gammaherpesvirus Infection, Susan Priscilla Canny

Arts & Sciences Graduate Student Theses and Dissertations

Gammaherpesviruses are oncogenic viruses that establish latent infection and can periodically reactivate. Replication, reactivation from latency and gammaherpesvirus-mediated pathology are regulated by viral and host factors. Long-standing interests in the field include understanding viral gene expression and regulation during lytic and latent infection and the effects of chronic viral infection on the host. Murine gammaherpesvirus 68 (MHV68) is used to model features of human gammaherpesvirus biology.In this dissertation, I investigated: (1) the function of antisense viral transcripts; (2) Stat1 regulation of MHV68 gene 50 promoters; and (3) the effect of chronic infection on host gene expression. Our laboratory identified extensive …

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

Arts & Sciences Graduate Student Theses and Dissertations

The control of cellular state has many promising applications, including stem cell biology andregenerative medicine, biofuel production, and gene therapy. This dissertation demonstrates acomprehensive approach to cellular state control at the transcriptional level. We introduce anovel algorithm, NetSurgeon, which utilizes genome-wide gene regulatory networks to identifyinterventions that will force a cell toward a desired expression state. Following extensive insilico validation, we applied NetSurgeon to S. cerevisiae biofuel production, generatinginterventions designed to promote a fermentative state during xylose catabolism. Our selectedinterventions successfully promoted a fermentative transcriptional state and generated strainswith higher xylose import rates, improved xylose integration and increased ethanol productionrates. …

Single-Chain Rankl Provides Insights Into Rank Receptor Oligomerization And A Novel Approach To Osteoclast Inhibition, Julia Therese Warren

Arts & Sciences Graduate Student Theses and Dissertations

Osteoporosis is a skeletal disease characterized by bone resorption in excess of bone formation. The osteoclast is the sole bone resorbing cell and therefore provides an important avenue for novel therapeutic development. The mature osteoclast is derived from the monocyte/macrophage lineage, and its proper differentiation and function requires the interaction of receptor activator of NF-kB Ligand (RANKL) with its receptor RANK. RANKL exists as a homotrimer, with classical models of receptor activation assuming trimeric clustering of receptor as necessary for signal transduction. We have designed a novel single-chain RANKL (scRANKL) construct to test the assumption that the recruitment of three …

Molecular And Epigenetic Regulation Of Stem Cell Radiosensitivity, Keith Michael Jacobs

Arts & Sciences Graduate Student Theses and Dissertations

Normal tissue injury resulting from ionizing radiation (IR) during cancer radiotherapy has been attributed to reduced regenerative capacity of stem cell compartments. Utilizing multiple in vivo tissue niches and primary culture models, we demonstrate that normal stem cells are highly radiosensitive while their isogenic, directly differentiated progeny are radioresistant. Stem cell dropout is therefore likely responsible for the resulting radiation injury in these niches. This differential radiosensitivity is independent of proliferation status, and increased IR-induced apoptosis in stem cells is more broadly distributed across the cell cycle.We elucidate that stem cells exhibit an attenuated DDR resulting in aberrant cell cycle …

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

Arts & Sciences Graduate Student 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 Effects Of Hpa Axis Genetic Variation And Early Life Stress On Cortisol Levels In Preschool Age Children And On Amygdala And Hippocampus Volumes, Reactivity, And Connectivity At School Age, David Pagliaccio

Arts & Sciences Graduate Student Theses and Dissertations

Internalizing psychopathology has been linked to increased cortisol reactivity and alterations in limbic brain structure and function, yet the mechanisms underlying these alterations are unclear. One key hypothesis is that stress plays a major causal role in these mechanisms. Animal studies find that chronic stress or glucocorticoid administration lead to alterations in hippocampal and amygdala structure and function. Relatedly, life stress is a major risk factors for depression while candidate gene studies have related variation in hypothalamic-pituitary-adrenal (HPA) axis genes to increased prevalence and severity of depression. The present work tested the hypothesis that genetic profile scores combining variance across …

Viral And Innate Immune Factors Controlling Disease Susceptibility During Chikungunya Virus Infection, Anjali Rohatgi

Arts & Sciences Graduate Student Theses and Dissertations

Chikungunya virus (CHIKV) is a re-emerging pathogen that causes a high fever, painful arthritis and a macular rash. The current outbreak began in Kenya in 2004 and spread throughout the Indian Ocean area and Southeast Asia, infecting millions. During this outbreak, more severe disease manifestations, including lethality, were reported for the first time. To understand one possible reason for this change in severity, we explored the impact of genetic changes in the virus on disease pathogenesis. In addition, we dissected the role of type I interferon (IFN) subtypes in CHIKV infection. From these studies, we have gained important insight into …

The Attentional Control Of Reading: Insights From Behavior, Imaging And Development, Sarah Ihnen

Arts & Sciences Graduate Student Theses and Dissertations

The process by which the initially attention-requiring task of transforming scribbles into meaningful concepts eventually becomes facile remains a central riddle of cognitive neuroscience. This body of work represents an effort to provide forward movement in answering the question of how attentional control mediates the process of reading, both by considering different stages of reading competence (development) and by seeking convergence between types of evidence (behavior and imaging).Inspired by a study published by Balota and colleagues in 2000, the paradigm used throughout this work involves comparing a simple speeded reading task vs. a regularize ("sound out") task (Balota et al. …

The Intrinsic Apoptotic Cascade In Hematopoiesis And Susceptibility To Therapy-Related Leukemia, Elise Peterson Lu

Arts & Sciences Graduate Student Theses and Dissertations

Apoptosis and the DNA damage response have been implicated in hematopoietic development and differentiation, as well as in the pathogenesis of myelodysplastic syndrome (MS) and leukemia. However, the specific roles of direct mediators of apoptosis, such as caspases, in hematopoiesis and leukemogenesis have not been elucidated. In order to address this, we studied the effects of loss of Caspase-9, the initiator caspase of the intrinsic apoptotic cascade, and Apaf1, the key component of the apoptosome, on fetal and adult hematopoiesis. We first found that loss of these key regulators has significant effects on the hematopoietic stem and progenitor compartment, with …

Understanding Escherichia Coli Urinary Tract Infection: A Niche Perspective, Drew Joel Schwartz

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, costing greater than $2 billion in healthcare costs and lost wages yearly in America alone. The lifetime risk for a woman exceeds 50% with 25-40% of these suffering recurrent infections. Two of the most important risk factors for recurrent UTI are prior UTIs and sexual intercourse. Over 80% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which binds and invades superficial facet cells lining the bladder surface. UPEC expresses extracellular fibers called type 1 pili with a terminal mannose-binding adhesin, FimH, which interacts with mannosylated uroplakin residues …

The U1a/U2b"/Snf Family Of Rna Binding Proteins: Evolution Of Rna Binding Specificity And Contributions Of Heterotropic Linkage To Snrnp Protein Partitioning, Sandra Gisela Williams

Arts & Sciences Graduate Student Theses and Dissertations

The U1A/U2B"/SNF is a family of RNA binding proteins that is a highly conserved throughout eukaryotes. These proteins are found in the U1 and/or U2 splicing snRNPs (small nuclear ribonucleoprotein particles). In humans, U1A and U2B" specifically bind to the U1 and U2 snRNAs, respectively. The Drosophila genome codes for SNF, an essential protein that localizes to both the U1 and U2 snRNP. While a specific splicing functions for these proteins have not been determined, their conserved snRNP localization suggests an important splicing-related function.The difference in protein number and partitioning between Drosophila and humans suggested that these proteins may use …

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

Arts & Sciences Graduate Student 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 and …

Histone Deacetylase 6 (Hdac6) Promotes The Pro-Survival Activity Of 14-3-3Ζ Via Deacetylation Of Lysines Within The 14-3-3Ζ Binding Pocket, Jeffrey B. Mortenson, Lisa N. Heppler, Courtney J. Banks, Vajira K. Weerasekara, Matthew D. Whited, Stephen R. Piccolo, William E. Johnson, J. Will Thompson, Joshua L. Andersen

Faculty Publications

The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines within the 14-3-3ζ binding pocket and protein-protein interface can be modified by acetylation. The positive charge on two of these lysines, Lys49 and Lys120, is critical for coordinating 14-3-3ζ-phosphoprotein interactions. Through screening, we identified HDAC6 as the Lys49/Lys120 deacetylase. Inhibition of HDAC6 blocks 14-3-3ζ interactions with two well described interacting partners, Bad and AS160, which triggers their dephosphorylation at Ser112 and Thr642, respectively. Expression of an acetylation-refractory K49R/K120R mutant of 14-3-3ζ rescues both the HDAC6 inhibitor-induced loss …

Molecular Mechanism Of Cytokine Production By Human Lung Fibroblast In Response To Pseudomonas Aeruginosa Elastase, Kourtney Bass

Biology Theses

Pathogenicity of Pseudomonas aeruginosa infections can be heavily influenced by the host inflammatory responses. P. aeruginosa secretes several extracellular products such as lipopolysaccharide, exotoxin A, and elastase. This bacterium is widely studied in acute and chronic lung diseases, such as chronic obstructive pulmonary disease (COPD) and Cystic Fibrosis (CF). In order to understand part of the underlying mechanism, we focused on the role of Pseudomonas aeruginosa elastase (PE) in provoking the host inflammatory response in an in vitro model. We hypothesized that PE stimulates cytokine and chemokine production by activating mitogen activated protein kinase (MAPK) cascade through nuclear factor kappa …

Draft Genome Sequences Of Six Different Staphylococcus Epidermidis Clones, Isolated Individually From Preterm Neonates Presenting With Sepsis At Edinburgh's Royal Infirmary, Paul Walsh, M. Bekaert, J. Carroll, T. Manning, B. Kelly, A. O'Driscoll, X. Lu, C. Smith, P. Dickinson, K. Templeton, P. Ghazal, Roy D. Sleator

Department of Biological Sciences Publications

Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.