Life Sciences Commons^™

The Effect Of Dietary Fat On Obesity, Gene Expression, And Dna Methylation In Two Generations Of Mice, Madeline Rose Keleher

Arts & Sciences Electronic Theses and Dissertations

As obesity rates continue rising nationally and globally, it is crucial to understand how a high-fat diet disrupts the regulation of the genome and leads to adverse health effects. Uncovering the underlying gene expression and DNA methylation changes induced by an individual’s high-fat diet and a maternal high-fat diet can pinpoint new targets for epigenetic therapies and reveal the physiological and behavioral changes in obesity. The goal of this dissertation is to gain deeper insight into the DNA methylation and gene expression changes that occur in response to a high-fat diet.

I studied the response to dietary fat within two …

Mechanisms And Regulation Of Resection In Dna Damage Response, Sharad C. Paudyal

Arts & Sciences Electronic Theses and Dissertations

Deoxyribonucleic acid (DNA) encodes genetic information essential for cell survival and function. However, it is constantly under assault from endogenous and exogenous damaging agents that not only threaten our own survival but also affect the faithful transmission of genetic information to our offspring. Double-strand breaks (DSBs) are one of the most hazardous forms of DNA damage, which if unrepaired or improperly repaired could lead to plethora of systemic human diseases including cancer. To deal with this problem, cells have evolved with a mechanism called DNA damage response (DDR) to detect, signal, and repair the breaks by inducing multiple cellular events. …

Designing Epigenome Editing Tools To Understand The Functional Role Of Dna Methylation Changes In Cancer, James Mcdonald

Arts & Sciences Electronic Theses and Dissertations

DNA methylation is known to silence gene expression in the context of imprinting, X-chromosome inactivation, and retrotransposon silencing. However, the role of DNA methylation in silencing gene expression outside of these contexts is not fully understood. This is especially true in diseases such as cancer, where normal DNA methylation patterns are significantly altered. In breast cancer as well as nearly all cancer types, most of the genome loses DNA methylation while small regions of the genome gain methylation. DNA methylation generally correlates with decreased gene expression when present at a gene promoter. Therefore, these regions of hypo- and hyper-methylation may …

Effects Of Nucleosome Structure On Dna Photoproduct Formation And Deamination, Kesai Wang

Arts & Sciences Electronic Theses and Dissertations

Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites, and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggest that DNA bending causes the modulation of photoproduct formation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we had developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been …

Sequence Determinants Of The Individual And Collective Behaviour Of Intrinsically Disordered Proteins, Alexander S. Holehouse

Arts & Sciences Electronic Theses and Dissertations

Intrinsically disordered proteins and protein regions (IDPs) represent around thirty percent of the eukaryotic proteome. IDPs do not fold into a set three dimensional structure, but instead exist in an ensemble of inter-converting states. Despite being disordered, IDPs are decidedly not random; well-defined - albeit transient - local and long-range interactions give rise to an ensemble with distinct statistical biases over many length-scales. Among a variety of cellular roles, IDPs drive and modulate the formation of phase separated intracellular condensates, non-stoichiometric assemblies of protein and nucleic acid that serve many functions. In this work, we have explored how the amino …

Determining The Molecular Mechanisms Of Huntington’S Disease Through Multi-Scale Modeling, Kiersten Ruff

Arts & Sciences Electronic Theses and Dissertations

Huntington’s disease (HD) is associated with a mutational CAG repeat expansion within exon 1 of the huntingtin (Htt) gene. Post-transcriptional processing leads to the generation of N-terminal Htt protein fragments (Htt-NTFs), including those that encompass exon 1 (Httex1). Within Httex1, the CAG-repeat encoded polyglutamine (polyQ) tract is flanked N-terminally by a 17-residue amphipathic stretch (N17) and C-terminally by a 50-residue proline rich (PR) domain. Htt-NTFs, including Httex1, are among the smallest fragments that recapitulate HD pathology in mouse models. However, the direct link between Htt-NTFs with polyQ expansions and neurodegeneration that leads to HD remains unresolved. Despite being a monogenic …

The Solid & The Shifting: Darwinian Time, Evolutionary Form And The Greek Ideal 
In The Early Works Of Virginia Woolf, Joseph Monroe Kreutziger

Arts & Sciences Electronic Theses and Dissertations

ABSTRACT OF THE DISSERTATION

“The Solid & the Shifting”: Evolutionary Form, Darwinian Time, and the Greek Ideal in the Early Works of Virginia Woolf

By

Joseph Kreutziger

Doctor of Philosophy in English and American Literature

Washington University in St. Louis, 2017

Professors Melanie Micir, Robert Milder, Steven Meyer, Vincent Sherry, Zoe Stamatopoulou

_____________________________________________________________________

“Now is life very solid or very shifting?” Virginia Woolf asks in her diary of 1931, a question she claims haunts her in its contradictions. This dynamism between the solid and the shifting aspects of life and temporality is fundamental to an analysis of Woolf’s writing process. …

Neurogenetics Of The Externalizing Spectrum, Caitlin E. Carey

Arts & Sciences Electronic Theses and Dissertations

Externalizing spectrum disorders, which include attention-deficit/hyperactivity disorder, oppositional defiant disorder, conduct disorder, alcohol and substance use disorders, and antisocial personality disorder, are characterized by behavioral disinhibition and are thought to be manifestations of a common heritable liability factor throughout the lifespan. However, relatively little is known about their underlying etiology. Here, I probe genetic and neural risk mechanisms for externalizing psychopathology in three complementary studies. First, I report an indirect association between genetic risk for childhood attention-deficit/hyperactivity disorder (ADHD) and problem drinking in young adulthood, mediated by heightened reward-related neural activity within the ventral striatum, among 404 college students. I …

Exploring Host-Virus Interactions In Caenorhabditis Nematodes, Kevin Chen

Arts & Sciences Electronic Theses and Dissertations

Caenorhabditis elegans is a powerful model organism that has elucidated many biological questions in the fields of genetics, development, and neurobiology. In addition, C. elegans has been used in the past decade to investigate host-pathogen interactions with bacteria and fungi. The recent identification of nematode viruses that naturally infect C. elegans and Caenorhabditis briggsae provides a unique opportunity to define host-virus interactions in these model hosts.

This dissertation first explored the transcriptional response of C. elegans and C. briggsae to virus infection by RNA-seq. I identified a total of 320 differentially expressed genes (DEGs) in C. elegans following Orsay virus …

Understanding The Relationship Between Hosts And Their Microbiome, Boahemaa Adu-Oppong

Arts & Sciences Electronic Theses and Dissertations

Microbes are bountiful and associated with every animal and plant kingdom. Furthermore, microbes can alter host phenotype, development, health and functioning. However, this is not a one-way interaction, hosts can structure microbial communities by changing the environment to be suitable for certain microbial species. Several studies have characterized microbial communities associated with hosts to answer two2 main questions in ecology: who’s there, and what are they doing? However, two questions from the field of community ecology are often ignored (1) what forces are structuring the microbial communities (how was the community formed) and (2) how stable are these communities. Vellend …

Characterization And Function Of Islet Antigen Presenting Cells During Nod Diabetes, Stephen Thomas Ferris

Arts & Sciences Electronic Theses and Dissertations

Here we characterized the initial antigen presenting cells (APCs) within the islet of Langerhans to ascertain their identity and functional role as it pertains to autoimmune diabetes. The activation of the adaptive immune system is induced by the innate immune system, and more specifically APCs. Therefore, it is crucial to identify the APCs that are initiating T1D in order to elucidate the break in tolerance and intervene in order to inhibit progression. We have found that there is a resident macrophage that is present in all strains of mice. This islet macrophage has a distinct transcriptional profile that is unique …

Nuclear Export Factor 3 Regulates The Localization Of Small Nucleolar Rnas, Melissa Wanling Li

Arts & Sciences Electronic Theses and Dissertations

Metabolic diseases, such as obesity and diabetes, are associated with excess levels of lipids, which can lead to organelle dysfunction, cell death and eventually organ dysfunction. This process, termed lipotoxicity, is still not completely understood. In a genetic screen used to identify genes critical for lipotoxicity, the Schaffer lab has identified small nucleolar RNAs (snoRNAs) within the ribosomal protein L13a (Rpl13a) locus that mediate the cellular response to lipotoxic and general metabolic stress. These snoRNAs are non-canonical in that they accumulate in the cytosol after metabolic stresses like lipotoxicity and oxidative stress, suggesting that cells have specific mechanisms for regulating …

Dna Replication Challenges: Telomeres And R Loops, Shankar Parajuli

Arts & Sciences Electronic Theses and Dissertations

Faithful DNA replication and repair are essential for maintaining genome stability and preventing various diseases including cancer. Both processes are executed by numerous redundant mechanisms to ensure that these processes are uninterrupted even when a primary mechanism fails. Despite this, they are not immune to challenges and failures leading to DNA damage and genome instability. These problems are more evident at the difficult-to-replicate regions of the genome such as the telomeres that cap and protect linear chromosome ends. Additionally, topological structures such as RNA:DNA hybrids, commonly referred to as R loops, can also present severe challenges to the DNA replication …

Brain Enriched Micrornas Open The Neurogenic Potential Of Adult Human Fibroblasts, Daniel Gene Abernathy

Arts & Sciences Electronic Theses and Dissertations

The seemingly limitless capacities of mammals to sense, respond, and manipulate their environments stems from their structurally and functionally diverse nervous systems. Establishing these complex behaviors requires the integration of many biological phenomena including, morphogenetic gradients, cell-cell signaling, transcriptional networks, cell migration and epigenetic gene regulation. As mammalian development progresses, these pathways coordinate the production of highly specialized neuronal and glial cells, that connect and communicate with another in an even more complex manner. While evolution has shaped a multitude of pathways to produce numerous favorable traits, it has also created an intricate system vulnerable to disease. The loss of …

Investigation Of The Contribution Of Type 1 Pili In Enterotoxigenic Escherichia Coli (Etec) Pathogen-Host Interactions, Alaullah Sheikh

Arts & Sciences Electronic Theses and Dissertations

Enterotoxigenic Escherichia coli (ETEC) are one of the leading causes of death due to diarrhea in children living in developing countries. ETEC are also the leading cause of diarrhea in travelers to developing countries lacking sanitation and safe drinking water. Unfortunately, there is no broadly protective vaccine available against these important pathogens. In order to cause infection, ETEC colonize the intestinal epithelium and secrete toxins, including heat-labile toxin (LT) and/or heat-stable toxin (ST). Efficient delivery of these toxins to the cognate receptors on target intestinal cells requires direct ETEC-host interactions. Earlier studies demonstrated that ETEC facilitate interactions with host by …

The Role Of Vip Scn Neurons In Circadian Physiology And Behavior, Cristina Mazuski

Arts & Sciences Electronic Theses and Dissertations

Located in the ventral hypothalamus, the suprachiasmatic nucleus (SCN) is necessary for entraining daily rhythms in physiology and behavior to environmental cues. Though the 20,000 neurons of the SCN uniformly express GABA, they differ greatly in neuropeptide content. One anatomically and functionally distinct class of neuropeptidergic SCN neurons is vasoactive intestinal polypeptide (VIP). Expressed by approximately 10% of SCN neurons, VIP is necessary for synchronizing single-cell SCN rhythms to produce coherent output and sufficient for entrainment. However, little is known about the firing activity of these neurons releases VIP and results in circadian entrainment. We utilized multielectrode array technology and …

Identification And Characterization Of An Interferon Stimulated Gene That Restricts Alphavirus Infection And Pathogenesis, Subhajit Poddar

Arts & Sciences Electronic Theses and Dissertations

Viral infection of host cells induces the Type I interferon (IFN) response, which is

characterized by the production of hundreds of IFN-stimulated genes (ISGs). Altogether, these

ISGs function to induce an antiviral state, hindering or blocking various steps of the viral

lifecycle. Many individual ISGs have potent and broad antiviral functions. However elimination

of a single ISG does not completely abrogate protection, suggesting that other ISGs, although

moderate or moderate when considered alone, must work cooperatively to provide optimal

antiviral activity.

In order to identify and characterize novel ISGs, an attenuated strain of the alphavirus

chikungunya (CHIKV-181/25) was tested against …

Specificity Determination By Paralogous Winged Helix-Turn-Helix Transcription Factors, Adam Joyce

Arts & Sciences Electronic Theses and Dissertations

Transcription factors (TFs) localize to regulatory regions throughout the genome, where they exert physical or enzymatic control over the transcriptional machinery and regulate expression of target genes. Despite the substantial diversity of TFs found across all kingdoms of life, most belong to a relatively small number of structural families characterized by homologous DNA-binding domains (DBDs). In homologous DBDs, highly-conserved DNA-contacting residues define a characteristic ‘recognition potential’, or the limited sequence space containing high-affinity binding sites. Specificity-determining residues (SDRs) alter DNA binding preferences to further delineate this sequence space between homologous TFs, enabling functional divergence through the recognition of distinct genomic …

Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky

Arts & Sciences Electronic Theses and Dissertations

Biological data, such as molecular abundance measurements and protein

sequences, harbor complex hidden structure that reflects its underlying

biological mechanisms. For example, high-throughput abundance measurements

provide a snapshot the global state of a living cell, while homologous

protein sequences encode the residue-level logic of the proteins' function

and provide a snapshot of the evolutionary trajectory of the protein family.

In this work I describe algorithmic approaches and analysis software I

developed for uncovering hidden structure in both kinds of data.

Clustering is an unsurpervised machine learning technique commonly used

to map the structure of data collected in high-throughput experiments,

such …

Antiviral Nucleoside Inhibitors Of Leishmania Rna Virus 1: Discovery And Mechanism, John Isaac Robinson

Arts & Sciences Electronic Theses and Dissertations

Some Leishmania parasites in the Viannia sub-genus are persistently infected with Leishmania RNA virus 1 (LRV1), a single-segmented double-stranded RNA virus belonging to the family Totiviridae. Infected parasites cause greater pathology and reach higher populations in mouse models of Leishmania infection. In human disease, LRV1+ parasites are correlated with increased frequency of treatment failure and relapse. Efficient methods to detect LRV1 and eliminate it from parasites are required to better understand the role of LRV1 in Leishmania infection. We optimized multiple techniques to measure LRV1 levels in parasites, most notably using flow cytometry to measure the amount of viral capsid …

Mass Spectrometry-Based Structural Proteomics: Methodology And Application Of Fast Photochemical Oxidation Of Proteins (Fpop), Ben Niu

Arts & Sciences Electronic Theses and Dissertations

The dissertation will be solely focused on using mass spectrometry to characterize protein high order structures (HOS), it emphasizes the use of hydroxyl radical footprinting (FPOP) coupled to bottom-up MS approach. A detailed background information about FPOP, and the corresponding method developments as well as applications will be covered.

The first chapter will be a comprehensive review regarding the FPOP. Following this, chapter 2, 3, and 4 will be focused on the method developments. Chapter 2 describes an isotope dilution GC-MS method to quantitate OH radicals in FPOP; chapter 3 describes the incorporation of Leu-enkephalin as reporter peptide for a …

Point Of View: The Sustainable Professor, Elizabeth S. Haswell

Biology Faculty Publications & Presentations

Responsible agricultural practices provide a useful lens through which to consider the lives and careers of researchers.

Life Behind The Wall: Sensing Mechanical Cues In Plants, Olivier Hamant, Elizabeth S. Haswell

Biology Faculty Publications & Presentations

There is increasing evidence that all cells sense mechanical forces in order to perform their functions. In animals, mechanotransduction has been studied during the establishment of cell polarity, fate, and division in single cells, and increasingly is studied in the context of a multicellular tissue. What about plant systems? Our goal in this review is to summarize what is known about the perception of mechanical cues in plants, and to provide a brief comparison with animals.

Negative Density Dependence Mediates Biodiversity–Productivity Relationships Across Scales, Joseph A. Lamanna, R Travis Belote, Laura A. Burkle, Christopher P. Catano, Jonathan A. Myers

Biology Faculty Publications & Presentations

Regional species diversity generally increases with primary productivity whereas local diversity–productivity relationships are highly variable. This scale-dependence of the biodiversity–productivity relationship highlights the importance of understanding the mechanisms that govern variation in species composition among local communities, which is known as β-diversity. Hypotheses to explain changes in β-diversity with productivity invoke multiple mechanisms operating at local and regional scales, but the relative importance of these mechanisms is unknown. Here we show that changes in the strength of local density-dependent interactions within and among tree species explain changes in β-diversity across a subcontinental-productivity gradient. Stronger conspecific relative to …

The Tension-Sensitive Ion Transport Activity Of Msl8 Is Critical For Its Function In Pollen Hydration And Germination, Eric S. Hamilton

Biology Faculty Publications & Presentations

All cells respond to osmotic challenges, including those imposed during normal growth and development. Mechanosensitive (MS) ion channels provide a conserved mechanism for regulating osmotic forces by conducting ions in response to increased membrane tension. We previously demonstrated that the MS ion channel MscS-Like 8 (MSL8) is required for pollen to survive multiple osmotic challenges that occur during the normal process of fertilization, and that it can inhibit pollen germination. However, it remained unclear whether these physiological functions required ion flux through a mechanically gated channel provided by MSL8. We introduced two point mutations into the predicted pore-lining domain of …

A Genomics Education Alliance, Sarah C.R. Elgin, Gita Bangera, Vincent Buonaccorsi, Douglas L. Chalker, Elizabeth Dinsdale, Erin L. Dolan, Linnea Fletcher, Arthur G. Hunt, Carolyn Lawrence-Dill, Wilson Leung, Laura Reed, Anne Rosenwald, Sandesh Subramanya, Emily Wiley, Jason Williams

Biology Faculty Publications & Presentations

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene …

Family Living Sets The Stage For Cooperative Breeding And Ecological Resilience In Birds, Michael Griesser, Szymon M. Drobniak, Shinichi Nakagawa, Carlos A. Botero

Biology Faculty Publications & Presentations

Cooperative breeding is an extreme form of cooperation that evolved in a range of lineages, including arthropods, fish, birds, and mammals. Although cooperative breeding in birds is widespread and well-studied, the conditions that favored its evolution are still unclear. Based on phylogenetic comparative analyses on 3,005 bird species, we demonstrate here that family living acted as an essential stepping stone in the evolution of cooperative breeding in the vast majority of species. First, families formed by prolonging parent–offspring associations beyond nutritional independency, and second, retained offspring began helping at the nest. These findings suggest that assessment of the conditions that …

Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut

Undergraduate Research Symposium Posters

A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program …

The Impact Of The Mitochondrial Metabolism Of Induced Pluripotent Stem Cells Upon Differentiation, Stefanie T. Shahan

McKelvey School of Engineering Theses & Dissertations

Induced pluripotent stem cells (iPSCs) can be differentiated into any cell type found in the body. The derivation of a stem cell derived β cell (SC-β) capable of responding to glucose by secreting insulin was hugely significant for diabetes research and opened up the possibility of cell replacement therapy to combat this widespread disease (Pagliuca et al. 2014). The optimization of differentiation procedures such as this could improve yield, function, cost, and efficiency of a stem cell-derived product. Current approaches to improve differentiation are primarily focused on signal transduction pathways, while the metabolic state of the cells has received little …

Sexual Selection, Speciation And Constraints On Geographical Range Overlap In Birds, Christopher Cooney, Joseph A. Tobias, Jason T. Weir, Carlos A. Botero, Nathalie Seddon

Biology Faculty Publications & Presentations

The role of sexual selection as a driver of speciation remains unresolved, not least because we lack a clear empirical understanding of its influence on different phases of the speciation process. Here, using data from 1306 recent avian speciation events, we show that plumage dichromatism (a proxy for sexual selection) does not predict diversification rates, but instead explains the rate at which young lineages achieve geographical range overlap. Importantly, this effect is only significant when range overlap is narrow (< 20%). These findings are consistent with a ‘differential fusion’ model wherein sexual selection reduces rates of fusion among lineages undergoing secondary contact, facilitating parapatry or limited co-existence, whereas more extensive sympatry is contingent on additional factors such as ecological differentiation. Our results provide a more mechanistic explanation for why sexual selection appears to drive early stages of speciation while playing a seemingly limited role in determining broad-scale patterns of diversification.