Biology Commons^™

The Role Of Dnmt3a In Acute Myeloid Leukemia Pathogenesis, Christopher Browning Cole

Arts & Sciences Graduate Student Theses and Dissertations

Loss of function mutations in the DNA methyltransferase DNMT3A are highly recurrent in acute myeloid leukemia (AML). DNMT3A and the highly homologous gene DNMT3B encode the two methyltransferases that are primarily responsible for mediating de novo methylation of specific DNA sequences during cellular differentiation. DNMT3A mutations are mutually exclusive of several translocations that create oncogenic fusion genes (PML-RARA, RUNX1-RUNX1T1, CBFB-MYH11, and MLL-X), suggesting that these fusions may require functional DNMT3A to initiate leukemogenesis. Using bone marrow cells from a constitutive Dnmt3a null mouse, we show that loss of Dnmt3a caused a striking loss of DNA methylation throughout the genome of …

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

Arts & Sciences Graduate Student 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 …

Refining Associations Between Targeted Genes And The Development Of Substance Use Disorders, Emily Olfson

Arts & Sciences Graduate Student Theses and Dissertations

Recent genome-wide association studies (GWAS) provide strong evidence for the contribution of a few specific genes to alcohol and nicotine dependence. Chapter 2 explores numerous previously identified candidate genes for alcohol dependence using a publicly available GWAS. I found that many candidate loci do not replicate, highlighting the utility of GWAS for focusing on disease associated genes. Chapters 3-5 dissect associations between three genome-wide significant genes and substance use disorders. Chapter 3 focuses on a functional variant in alcohol dehydrogenase (ADH) 1B. Through examining 1,550 adolescent drinkers in the Collaborative Study on the Genetics of Alcoholism (COGA), I extended adult …

Application Of Genomic Technologies To Study Infertility, Nicholas Rui Yuan Ho

Arts & Sciences Graduate Student Theses and Dissertations

An estimated one in eight couples in the United States are diagnosed with infertility. There is a significant genetic contribution to infertility, with estimates of heritability ranging from 0.2 to 0.5. We know surprisingly little about the genetic causes, with only slightly more than a hundred genes known to cause human infertility. I have been translating recent advances in genomics to study infertility in a more efficient manner, in order to improve our knowledge of the genetic causes. By using high throughput genomics and proteomics datasets from other groups, I was able to feed that into a machine learning algorithm …

Granulocyte-Colony Stimulating Factor Reprograms The Bone Marrow Microenvironment To Suppress B Lymphopoiesis, Ryan Brent Day

Arts & Sciences Graduate Student Theses and Dissertations

The production of hematopoietic cells in the bone marrow is tightly and dynamically regulated in response to environmental stimuli. In response to infection, the bone marrow increases granulopoiesis at the expense of lymphopoiesis. The mechanisms mediating this shift are poorly understood. We show that treatment with granulocyte-colony stimulating factor (G-CSF), which is often induced during infection, results in marked decline of B lymphocytes at multiple stages of bone marrow B cell development. Transgenic mouse models show that G-CSF acts in a non-cell intrinsic fashion through cells of the monocyte-macrophage lineage to suppress B lymphopoiesis by downregulating important B trophic factors …

A Novel Ultrashort Pulsed Laser Method For Pathogen Inactivation, Shaw-Wei David Tsen

Arts & Sciences Graduate Student Theses and Dissertations

Emerging viral pathogens represent a constant and prominent threat to human health worldwide. There is a dire need to develop new pathogen inactivation techniques that can be used to safeguard the blood supply and to generate inactivated vaccines against these emerging viruses. Unfortunately, current techniques are inadequate because they introduce toxic/carcinogenic chemicals or alter the structure of the products, leading to loss of safety and efficacy. We have developed a novel, chemical-free ultrashort pulsed laser treatment system capable of inactivating a broad spectrum of both enveloped and non-enveloped viruses. We found that ultrashort pulsed laser treatment targets the vibrational modes …

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

Arts & Sciences Graduate Student 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 …

The Murine Accessory Olfactory Bulb As A Model Chemosensory System: Experimental And Computational Analysis Of Chemosensory Representations, Gary Francis Hammen

Arts & Sciences Graduate Student Theses and Dissertations

A common challenge across sensory processing modalities is forming meaningful associations between the neural responses and the outside world. These neural representations of the world must then be integrated across different sensory systems contributing to each individuals perceptual experience. While there has been considerable study of sensory representations in the visual system of humans and multiple model organisms, other sensory domains, including olfaction, are less well understood. In this thesis, I set out to better understand the sensory representations of the mouse accessory olfactory system (AOS), a part of the olfactory system. The mouse AOS, our model chemosensory system, comprises …

Discrete But Variable Structure Of Animal Societies Leads To The False Perception Of A Social Continuum, Dustin R. Rubenstein, Carlos A. Botero, Eileen A. Lacey

Biology Faculty Research

Animal societies are typically divided into those in which reproduction within a group is monopolized by a single female versus those in which it is shared among multiple females. It remains controversial, however, whether these two forms of social structure represent distinct evolutionary outcomes or endpoints along a continuum of reproductive options. To address this issue and to determine whether vertebrates and insects exhibit the same patterns of variation in social structure, we examined the demographic and reproductive structures of 293 species of wasps, ants, birds and mammals. Using phylogenetically informed comparative analyses, we found strong evidence indicating that not …

Tree-Mycorrhizal Associations Detected Remotely From Canopy Spectral Properties, Joshua B. Fisher, Sean Sweeney, Edward R. Brzostek, Tom P. Evans, Daniel J. Johnson, Jonathan A. Myers, Norman A. Bourg, Amy T. Wolf, Robert W. Howe, Richard P. Philllips

Biology Faculty Research

A central challenge in global ecology is the identification of key functional processes in ecosystems that scale, but do not require, data for individual species across landscapes. Given that nearly all tree species form symbiotic relationships with one of two types of mycorrhizal fungi – arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi – and that AM- and ECM-dominated forests often have distinct nutrient economies, the detection and mapping of mycorrhizae over large areas could provide valuable insights about fundamental ecosystem processes such as nutrient cycling, species interactions, and overall forest productivity. We explored remotely sensed tree canopy spectral properties to …

Sex Ratio And Gamete Size Across Eastern North America In Dictyostelium Discoideum, A Social Amoeba With Three Sexes, Tracy Edwards Douglas, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Theory indicates that numbers of mating types should tend towards infinity or remain at two. The social amoeba, Dictyostelium discoideum, however, has three mating types. It is therefore a mystery how this species has broken the threshold of two mating types, but has not increased towards a much higher number. Frequency-dependent selection on rare types in combination with isogamy, a form of reproduction involving gametes similar in size, could explain the evolution of multiple mating types in this system. Other factors, such as drift, may be preventing the evolution of more than three. We first looked for evidence of …

The Coursesource Bioinformatics Learning Framework, Sarah C.R. Elgin, Anne Rosenwald, Mark A. Pauley, Lonnie Welch, Robin Wright, Jessamina Blum

Biology Faculty Research

No abstract provided.

Fine-Scale Spatial Ecology Drives Kin Selection Relatedness Among Cooperating Amoebae, Jeff Smith, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Cooperation among microbes is important for traits as diverse as antibiotic resistance, pathogen virulence, and sporulation. The evolutionary stability of cooperation against “cheater” mutants depends critically on the extent to which microbes interact with genetically similar individuals. The causes of this genetic social structure in natural microbial systems, however, are unknown. Here, we show that social structure among cooperative Dictyostelium amoebae is driven by the population ecology of colonization, growth, and dispersal acting at spatial scales as small as fruiting bodies themselves. Despite the fact that amoebae disperse while grazing, all it takes to create substantial genetic clonality within multicellular …

Kin Discrimination In Dictyostelium Social Amoebae, Joan E. Strassmann

Biology Faculty Research

Presentation delivered at the symposium Evidence of Taxa, Clone, and Kin Discrimination in Protists: Ecological and Evolutionary Implications, VII European Congress of Protistology, University of Seville, 5–10 September 2015, Seville Spain.

Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile multicellular body in which, about 20% of participants ultimately die to form a stalk. This benefits the remaining individuals that become hardy spores at the top of the stalk, together making up the fruiting body. In studied species with stalked migration, P. violaceum, D. purpureum, and …

A Parallel G Quadruplex-Binding Protein Regulates The Boundaries Of Dna Elimination Events Of Tetrahymena Thermophila, Christine M. Carle, Hani S. Zaher, Douglas L. Chalker

Biology Faculty Research

Guanine (G)-rich DNA readily forms four-stranded quadruplexes in vitro, but evidence for their participation in genome regulation is limited. We have identified a quadruplex-binding protein, Lia3, that controls the boundaries of germline-limited, internal eliminated sequences (IESs) of Tetrahymena thermophila. Differentiation of this ciliate’s somatic genome requires excision of thousands of IESs, targeted for removal by small-RNA-directed heterochromatin formation. In cells lacking LIA3 (ΔLIA3), the excision of IESs bounded by specific G-rich polypurine tracts was impaired and imprecise, whereas the removal of IESs without such controlling sequences was unaffected. We found that oligonucleotides containing these polypurine tracts formed …

Crystal Structure Of Deinococcus Phytochrome In The Photoactivated State Reveals A Cascade Of Structural Rearrangements During Photoconversion, E Sethe Burgie, Junrui Zhang, Richard D. Vierstra

Biology Faculty Research

Phytochromes are photochromic photoreceptors responsible for a myriad of red/far-red light-dependent processes in plants and microorganisms. Interconversion is initially driven by photoreversible isomerization of bilin, but how this alteration directs the photostate-dependent changes within the protein to actuate signaling is poorly understood. Here, we describe the structure of the Deinococcus phytochrome photosensory module in its near complete far-red light-absorbing Pfr state. In addition to confirming the 180° rotation of the D-pyrrole ring, the dimeric structure clearly identifies downstream rearrangements that trigger large-scale conformational differences between the dark-adapted and photoactivated states. Mutational analyses verified the importance of residues surrounding the bilin …

When Does Intraspecific Trait Variation Contribute To Functional Beta-Diversity?, Marko J. Spasojevic, Benjamin L. Turner, Jonathan A. Myers

Biology Faculty Research

Summary

1. Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional-trait composition of communities (functional Β-diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales.
2. We examined how ITV contributes to functional Β-diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across …

Insights From A Convocation: Integrating Discovery-Based Research Into The Undergraduate Curriculum, Sarah C.R. Elgin, Gita Bangera, Sean M. Decatur, Erin L. Dolan, Laura Guertin, Wendy C. Newstetter, Elvyra F. San Juan, Mary A. Smith, Gabriela C. Weaver, Susan R. Wessler, Kerry A. Brenner, Jay B. Labov

Biology Faculty Research

The National Academies of Sciences, Engineering, and Medicine organized a convocation in 2015 to explore and elucidate opportunities, barriers, and realities of course-based undergraduate research experiences, known as CUREs, as a potentially integral component of undergraduate science, technology, engineering, and mathematics education. This paper summarizes the convocation and resulting report.

Rna Sequencing Analysis Of The Msl2msl3, Crl, And Ggps1 Mutants Indicates That Diverse Sources Of Plastid Dysfunction Do Not Alter Leaf Morphology Through A Common Signaling Pathway, Darron R. Luesse, Margaret E. Wilson, Elizabeth S. Haswell

Biology Faculty Research

Determining whether individual genes function in the same or in different pathways is an important aspect of genetic analysis. As an alternative to the construction of higher-order mutants, we used contemporary expression profiling methods to perform pathway analysis on several Arabidopsis thaliana mutants, including the mscS-like (msl)2msl3 double mutant. MSL2 and MSL3 are implicated in plastid ion homeostasis, and msl2msl3 double mutants exhibit leaves with a lobed periphery, a rumpled surface, and disturbed mesophyll cell organization. Similar developmental phenotypes are also observed in other mutants with defects in a range of other chloroplast or mitochondrial functions, including …

Ubiquitin Goes Green, Zhihua Hua, Richard D. Vierstra

Biology Faculty Research

Chloroplasts depend on the nucleus for much of their proteome. Consequently, strong transcriptional coordination exists between the genomes, which is attuned to the developmental and physiological needs of the organelle. Recent studies highlight that the post-translational modifier ubiquitin adds another layer to plastid homeostasis and even helps eliminate damaged chloroplasts.

Functional Consequences Of Cantu Syndrome Associated Mutations In The Atp Sensitive Potassium Channel, Paige Cooper

Arts & Sciences Graduate Student Theses and Dissertations

ATP-sensitive potassium (KATP) channels are composed of inward-rectifying potassium channel pore-forming subunits (Kir6.1 and Kir6.2, encoded by KCNJ8 and KCNJ11, respectively) and regulatory sulfonylurea receptor subunits (SUR1 and SUR2, encoded by ABCC8 and ABCC9, respectively). These channels couple metabolism to excitability in multiple tissues. Mutations in ABCC9 have been linked to Cantú syndrome (CS), a multi-organ disease characterized by congenital hypertrichosis, distinct facial features, osteochondrodysplasia, and cardiac defects. Additionally, two ABCC9 mutation-negative patients, exhibiting clinical hallmarks of CS, have been identified as having KCNJ8 mutations. This body of work is focused on determining the functional consequences and molecular mechanisms of …

Human Immunodeficiency Virus Type 1 Envelope Protein Interaction With Host Cell Coreceptor C-X-C Chemokine Receptor Type 4, Jie Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Human Immunodeficiency Virus Type 1 (HIV-1) envelope protein is the sole determinant for viral entry and tropism. The ability of HIV-1 to infect susceptible host cells depends on the ability of its envelope protein to engage host cell receptor CD4 and coreceptor C-C Chemokine Receptor Type 5 (CCR5) and/or C-X-C Chemokine Receptor Type 4 (CXCR4). Most naturally occurring infections start with a single CCR5-tropic virion. In approximately 50% of HIV-1 Clade B infected patients, the viral population spontaneous develops the ability to utilize CXCR4 at a late disease stage, and this coreceptor shift corresponds to a poor prognosis for the …

Ion Selectivity And Allostery In The Nak Channel, Joshua B. Brettmann

Arts & Sciences Graduate Student Theses and Dissertations

Ion channels require proper ion selectivity and regulated gating in order to perform their cellular functions. Bacterial ion channels serve as excellent model systems to study structure/function relationships concerning the fundamental processes of ion selectivity and gating. NaK, a non-selective cation channel from Bacillus cereus, has the conserved pore structure of K+ channels. However, its non-canonical selectivity filter structure leads to non-selectivity between Na+ and K+. Full selectivity is restored with two mutations that lead to the restoration of a Kcsa-like selectivity filter structure. Many mutations can be made to the selectivity filter of NaK without loss of protein stability …

Lysosomal Rnaset2 Is Required For Metabolic Stress-Mediated Ros Generation And Cell Death, George Caputa

Arts & Sciences Graduate Student Theses and Dissertations

Ectopic lipid deposition in non-adipose tissues is a hallmark of metabolic diseases, such as obesity and diabetes, and associated with cell dysfunction, cell death, and organ dysfunction. However, the molecular mechanisms linking excess free fatty acid to cell death are poorly understood. In order to identify genes critical for lipotoxicity, our lab performed a genetic screen in Chinese hamster ovary cells and isolated mutants that were resistant to lipotoxic death. In one of the lines, mutant 2B1, an allele encoding RNASET2, a ribonuclease of the T2 family, was disrupted by proviral insertion. We found that RNASET2 is induced during lipotoxicity …

Characterizing The Role Of Sialylated Milk Glycans And The Infant Gut Microbiota In Growth And Metabolism, Mark Richard Charbonneau

Arts & Sciences Graduate Student Theses and Dissertations

Undernutrition is a pressing and pervasive global health problem. The pathogenesis of this disease remains unclear, but epidemiologic studies indicate that it is not due to food insecurity alone. Moreover, current therapeutic interventions have limited efficacy in preventing or ameliorating the long-term sequelae of undernutrition, including stunting and cognitive deficits. Recent culture-independent studies have demonstrated that the normal postnatal pattern of gut microbiota development is disrupted in children with undernutrition, leading to the proposal that perturbations in gut microbiota development impairs healthy growth of the host. Human breast milk contains a diverse repertoire of free and conjugated human milk oligosaccharides …

The Identification Of Alkaloid Pathway Genes From Non-Model Plant Species In The Amaryllidaceae, Matthew B. Kilgore

Arts & Sciences Graduate Student Theses and Dissertations

Secondary metabolites are often restricted in their distribution to different groups of organisms. For this reason, attempts to study these often useful and interesting products of metabolism require an ability to work in a diversity of non-model species. Methods for gene discovery with low investment and high efficiency are needed to effectively identify the biosynthetic genes in these diverse pathways. During this work, a workflow for efficiently identifying biosynthetic genes was developed and applied to Amaryllidaceae alkaloid biosynthesis. Genes discovered during this work include a norbelladine 4’-O-methyltransferase, a cytochrome P450 capable of phenol-phenol coupling 4’-O-methylnorbelladine to noroxomaritidine, and a short-chain …

Behavioral And Fmri-Based Characterization Of Cognitive Processes Supporting Learning And Retrieval Of Memory For Words In Young Adults, Binyam Nardos

Arts & Sciences Graduate Student Theses and Dissertations

A novel word is rarely defined explicitly during the first encounter. With repeated exposure, a decontextualized meaning of the word is integrated into semantic memory. With the overarching goal of characterizing the functional neuroanatomy of semantic processing in young adults, we employed a contextual word learning paradigm, creating novel synonyms for common animal/artifact nouns that, along with additional real words, served as stimuli for the lexical-decision based functional MRI (fMRI) experiment. Young adults (n=28) were given two types of word learning training administered in multiple sessions spread out over three days. The first type of training provided perceptual form-only training …

Endogenous Protection In Subarachnoid Hemorrhage, Eric Milner

Arts & Sciences Graduate Student Theses and Dissertations

Vasospasm-induced delayed cerebral ischemia (DCI) remains a major source of morbidity in patients with aneurysmal subarachnoid hemorrhage (SAH). Moreover, cognitive dysfunction is the primary driver of poor long-term outcome in SAH survivors; modeling such deficits preclinically is thus key for mechanistic and translational investigation. We hypothesized that activating innate neurovascular protective mechanisms by conditioning may represent a novel therapeutic approach against SAH-induced DCI, short-term, neurological deficits, and long-term neurocognitive deficits; and, secondarily, that the neurovascular protection it provides is mediated by endothelial nitric oxide synthase (eNOS) and hypoxia-inducible factor 1α (HIF-1α).In Experiment 1, wild-type C57BL/6 mice were subjected to hypoxic …

Transcriptional Regulation Of The Endoplasmic Reticulum In Dedicated Secretory Cells, Benjamin David Moore

Arts & Sciences Graduate Student Theses and Dissertations

Differentiating cells express subsets of genes to build the cellular machinery necessary to perform their specific function as they acquire their mature fate. These subsets of genes are regulated by networks of transcription factors as cells progress through their developmental program. In secretory tissue, highly-specialized cells establish a complex secretory apparatus and scale up their cellular architecture to facilitate the production and secretion of large amounts of protein. Here, we identify a network of transcription factors responsible for the development of this cellular machinery in these professional secretory cells, and develop new tools to better study the molecular networks that …

Molecular Mechanisms Of Axon Growth And Regeneration, Dana Watt

Arts & Sciences Graduate Student Theses and Dissertations

Neurons are cells with unique and extremely polarized morphologies. The axon allows communication between the cell soma and the distantly located synaptic terminal and can extend up to one meter in humans. This exceptional cellular structure therefore has specialized biological processes dedicated to its growth, maintenance and regeneration. The structure that carries out axon elongation during development and regeneration is the growth cone, which features a cytoskeletal structure that is both highly dynamic yet consistent in overall organization. The growth cone coordinates a leading edge of dynamic actin with the microtubules of the growing axon, enabling directed outgrowth while maintaining …