Life Sciences Commons^™

Notch-Mediated Regulation Of Atrial Arrhythmogenesis, Catherine Lipovsky

Arts & Sciences Electronic Theses and Dissertations

Abnormalities in electrical impulse generation and/or propagation that affect the heartճ normal rhythm are extremely common. Clinically, cardiac arrhythmias are prevalent worldwide, yet the molecular mechanisms underlying their pathology remain largely unknown. Current treatments for arrhythmias primarily target symptoms rather than the underlying cause and these treatments have limited efficacy. The most common risk factor for developing an arrhythmia is a previous cardiac injury; however, the mechanisms underlying this are not well described. My thesis work has demonstrated that the Notch signaling pathway, which is crucial for cardiac patterning and development and is normally quiescent in adult cardiomyocytes (CMs), is …

Elucidating The Effect Of Myopathy-Causing Mutations And Second-Site Suppressors On Client Processing By J-Domain Proteins, Melanie Y. Pullen

Arts & Sciences Electronic Theses and Dissertations

Defects in protein quality control may lead to protein misfolding and aggregation often associated with protein conformational disorders such as Alzheimerճ Disease and Limb Girdle Muscular Dystrophy, among others. Molecular chaperones protect against protein misfolding and aggregation. A chaperone of interest is the ubiquitously expressed type II Hsp40 co-chaperone DNAJB6, which assists in protein folding and disaggregation. Mutations within the DNAJB6 G/F domain have been associated with the dominantly inherited disease Limb-Girdle Muscular Dystrophy type 1D (LGMD1D), now referred to as LGMDD1. Our collaborators recently discovered novel LGMDD1-associated mutations in the J-domain of DNAJB6. In the enclosed body of work, …

Nonsense Mediated Rna Decay Promotes Survival Of Cells With Defective Splicing, Abigael Jeruto Cheruiyot

Arts & Sciences Electronic Theses and Dissertations

Nonsense mediated RNA decay (NMD) is an RNA surveillance pathway present in all eukaryotes that detects and degrades nonsense mRNAs, which contain pre-mature translation termination codons. Nonsense mRNAs are prevalent when pre-mRNA splicing is altered or defective. Interestingly, defective pre-mRNA splicing is emerging as a major driver of cancer development, including development of myelodysplastic syndrome (MDS), leukemia, and some solid tumors. Moreover, pre-mRNA splicing is also thought to enhance NMD in human cells, although itճ still unclear whether and how splicing or splicing factors promote NMD. The role of NMD in regulating mis-spliced mRNA and the link between NMD and …

The Role Of Apolipoprotein E In Alzheimer Disease: From Therapy To Mechanism, Tien-Phat Vuong Huynh

Arts & Sciences Electronic Theses and Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disorder associated with irreversible damage to the brain, which manifests in cognitive dysfunction, memory loss, and eventual death. The pathological hallmarks of AD are amyloid plaques, which are cerebral aggregates consisting of fibrils of the amyloid β-protein (Aβ), and filamentous lesions of the microtubule-associated protein tau known as neurofibrillary tangles. In the early 1990s, the apolipoprotein E (apoE) was found to co-localize with amyloid plaques. The ε4 allele of the APOE gene was sequentially identified as the strongest genetic risk factor for AD, increasing the risk by 4 – 12-fold, whereas the ε2 allele …

Development Of An In Vitro Culture System For Cryptosporidium Parvum, Georgia Wilke

Arts & Sciences Electronic Theses and Dissertations

Cryptosporidium is a genus of protozoan parasites that causes diarrheal disease in humans and other animals. There are two major species that cause disease in humans: C. parvum, which infects both humans and animals, and C. hominis, which primarily infects humans. A recent study investigating the etiologies of pediatric diarrheal illness in Africa and South Asia found that Cryptosporidium is the 2nd most prevalent cause of diarrhea in infants and may be a contributing factor to chronic malnutrition. This discovery has led to renewed interest in studying this parasite and a reexamination of the barriers to studying Cryptosporidium. The main …

An Evolving Epigenome That Determines Tissue And Cell Specificity, Renee Louise Sears

Arts & Sciences Electronic Theses and Dissertations

Understanding the mechanisms driving phenotypic variation is a major goal of biology that unifies classical genetics with the emerging fields of genomics and epigenomics. Human and mouse share over 90% of genes and global tissue-specific patterns of expression are maintained between the species. Thus, it is hypothesized that gene expression is influenced through distinctive regulation among species in order to account for the unmistakable phenotypic divergence. DNA methylation, histone modifications, open chromatin patterns, transcription factor binding, and other epigenetic factors are all associated with shaping, maintaining, and repressing regulatory regions which in turn coordinate gene expression. It is vital to …

Understanding The Physiology Of Extracellular Electron Uptake In Purple Nonsulfur Bacteria, Michael Singh Guzman

Arts & Sciences Electronic Theses and Dissertations

Microbially catalyzed oxidation-reduction reactions drive nutrient cycling and energy flux on Earth. Photoautotrophs, which include the cyanobacteria (oxygenic) and purple and green sulfur bacteria (anoxygenic), transform light energy into chemical energy and are responsible for substantial global primary productivity. Anoxygenic phototrophs, in particular, play a crucial role in biogeochemical cycling in anoxic illuminated environments because of their ability to oxidize an array of inorganic compounds for CO2 fixation. Electron donors include molecular hydrogen, nitrite, and reduced sulfur compounds. Recent evidence has also suggested that solid-phase conductive substances (SPCSs), including rust (mixed-valent iron minerals) and their proxies (poised electrodes), can serve …

Expression And Function Of Snornas In Acute Myeloid Leukemia, Wayne Alsworth Warner

Arts & Sciences Electronic Theses and Dissertations

Small nucleolar RNAs (snoRNAs) are non-coding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. These modifications are critical for a variety of cellular processes, including ribosomal biogenesis and splicing of RNAs. Recent studies have suggested an expanded role for snoRNAs beyond ribosomal biogenesis and splicing, including, regulation of chromatin structure, metabolism, and neoplastic transformation. The contribution of snoRNAs to the regulation of normal and malignant hematopoiesis is largely unknown. The lack of a method to accurately and comprehensively assess snoRNA expression has limited research in this area. In particular, array-based methods …

Secretory Iga Enhances Gut B Cells Priming And Systemic Igg Responses Towards Commensals, You Zhou

Arts & Sciences Electronic Theses and Dissertations

IgA is the primary antibody response at mucosal surfaces and is reported to inhibit adaptive immune responses against gut bacteria. Here, we utilize an in vitro system to expand and screen IgA memory B cells for their ability to recognize gut bacteria in the context of secretory IgA (sIgA) deficiency in polymeric Ig receptor (Pigr–/–) mice. Contrary to the prevailing hypothesis that IgA provides an immune exclusionary function, we found that mice lacking sIgA showed decreased anti-bacterial IgA specificities as assessed using flow cytometry. IgA B cell responses against certain taxa such as those of order Bacteriodales showed greater dependence …

Multi-Omic Understanding Of The Evolution Of Xenobiotic Tolerance In Bacterial Isolates And Communities, Tayte Paul Campbell

Arts & Sciences Electronic Theses and Dissertations

Xenobiotic compounds are any chemicals that are released into an environment by human action and that occur at concentrations higher than found naturally. Xenobiotics, including aromatic compounds and antibiotics, are recalcitrant to degradation because they are often toxic or mutagenic. Despite this toxicity, bacteria account for a large portion of xenobiotic degradation in the environment. Bacteria are able to adapt to these foreign chemicals, gaining increased levels of tolerance and increased rates of xenobiotic degradation. On the strain level, increased tolerance can be caused by mutations in individual cells or through the acquisition of genes from other cells. At the …

Genomic Signatures Of Conflict And Cooperation In Plants And Social Amoebae, Katherine Sylvia Geist

Arts & Sciences Electronic Theses and Dissertations

Arms races involve bouts of reciprocal co-adaptation to a social environment. We have a strong sense for how arms races drive the evolution of genes in purely antagonistic contexts, such as host-pathogen or predator-prey. In these systems, conflict that produces arms races between two parties results in positive selection – the fixation of adaptive alleles between species – for both parties. However, we do not have an equal sense for how arms races during cooperative enterprises shape genic evolution. If we assume that arms races affect genic evolution similarly regardless of context – antagonistic or cooperative – then we would …

Mechanisms Of Nestmate Recognition Cue Production In The European Honey Bee, Apis Mellifera., Cassondra Leigh Vernier

Arts & Sciences Electronic Theses and Dissertations

Social insects are some of the world’s most ecologically successful animal groups, and their complex societies are considered one of the pinnacles of animal evolution. Since these organisms live in colonies composed of many individuals and stored resources, they are a target for intruders, such as parasites, predators and conspecific robbers. Therefore, many social insect species have evolved mechanisms for nest defense, including nestmate recognition, where guarding individuals at the entrance of the colony use cues on incoming individuals to determine whether they are nestmates or intruders. Although nestmate recognition is incredibly important for maintaining colony integrity and fitness, the …

The Role Of Mitofusins In The Osteoclast Lineage, Anna Ballard

Arts & Sciences Electronic Theses and Dissertations

Mitochondria exist in a highly dynamic network in many cell types, and mutations in mitochondrial transmembrane GTPase mitofusin2 (MFN2), a key factor that mediates mitochondrial tethering, cause defects in the nervous system. Intriguingly, the skeleton has been overlooked in patients with such mutations. Because expression of MFN2 and its homolog, mitofusin1 (MFN1) increase with maturation of osteoclasts (OCs), which are rich in mitochondria, we sought to determine the role of mitofusins in the OC lineage. Double knockout of Mfn1 and Mfn2 in OC precursors by Lysozyme-M cre reveals that mitofusin activity is required for OC function and maintenance of bone …

Defining Gastric Epithelial Cell Population Dynamics At Homeostasis And Following Injury, Joseph Ronald Burclaff

Arts & Sciences Electronic Theses and Dissertations

Gastric diseases affect many people around the world, yet surprisingly little is known about the basic dynamics of gastric epithelial cells. Loss of acid-secreting parietal cells has long been observed to precede pre-cancerous gastric metaplasias like Spasmolytic Polypeptide-Expressing Metaplasia (SPEM), yet no signaling component from dying parietal cells has yet been implicated in initiating the metaplastic responses. Also, experiments pulsing 3H-thymidine and or examining intracellular components suggest that gastric mucous neck cells are short-lived transient intermediates between the gastric stem cell and mature zymogenic “chief” cells, yet specifics about this transition remain elusive. Here, we develop a novel mouse line …

A Combinatorial Approach Of Ionomics, Quantitative Trait Locus Mapping, And Transcriptome Analysis To Characterize Element Homeostasis In Maize, Alexandra Asaro

Arts & Sciences Electronic Theses and Dissertations

In plant systems, genetic and biochemical pathways impact uptake of elements from the soil. These environment-sensitive pathways often act in the root tissue to impact element concentrations throughout the plant. In order to characterize element regulation as well as apply ionomics to understand plant adaptation, perspectives are needed from multiple tissues and environments and from approaches that take interactions between elements into account. The work described in this thesis includes multi-environment and multi-tissue experiments that connect variation in genetic sequence, and in gene expression, with variation in element accumulation. The associations found here include those that are sensitive to environment, …

The Role Of The Ascc Complex In The Alkylation Damage Response, Jennifer Soll

Arts & Sciences Electronic Theses and Dissertations

DNA alkylation damage is caused by various agents that are present in the environment as well as cellular metabolism and can be induced by certain chemotherapeutic agents. Thus, the repair of damaged DNA is critical for genomic maintenance. The ALKBH family of proteins plays a central role in the repair of specific alkylated lesions, including 1-methyladenine (1meA) and 3-methylcytosine (3meC). A major outstanding question in the field of alkylation repair is the role of associated protein partners in the function of the human AlkB homologues. Here, I demonstrate that the ALKBH3 associated complex ASCC (comprised of ASCC1, ASCC2, and ASCC3) …

The Splice Is Not Right: Splice-Site-Creating Mutations In Cancer Genomes, Reyka Glencora Jayasinghe

Arts & Sciences Electronic Theses and Dissertations

Accurate interpretation of cancer mutations in individual tumors is a prerequisite for precision medicine. Large-scale sequencing studies, such as The Cancer Genome Atlas (TCGA) project, have worked to address the functional consequences of genomic mutations, with the larger goal of determining the underlying mechanisms of cancer initiation and progression. Many studies have focused on characterizing non-synonymous somatic mutations that alter amino acid sequence, as well as splice disrupting mutations at splice donors and acceptors. Current annotation methods typically classify mutations as disruptors of splicing if they fall on the consensus intronic dinucleotide splice donor, GT, the splice acceptor, AG. Splice …

The Role Of Apolipoprotein E In Regulating Tau Pathogenesis And Neurodegeneration In A Tauopathy Mouse Model, Yang Shi

Arts & Sciences Electronic Theses and Dissertations

APOE4 is the strongest genetic risk factor for late-onset Alzheimer's disease (AD). APOE4 increases brain amyloid-β (Aβ) pathology relative to other APOE isoforms. However, whether APOE independently influences tau pathology, the other pathological hallmark of AD and other tauopathies, or tau-mediated neurodegeneration, is not clear. By generating P301S tau transgenic mice on either a human APOE knock in (KI) or APOE knockout (KO) background, we show that the presence of human APOE, regardless of APOE isoforms, leads to various degrees of brain atrophy in 9-month old P301S mice, whereas APOE ablation strongly protects against neurodegeneration. In particular, P301S/E4 mice develop …

The Costs Of A Big Brain: How Region Scaling And Energetic Costs Influence Brain Size Evolution In Weakly Electric African Fishes (Mormyridae), Kimberley Varunee Sukhum

Arts & Sciences Electronic Theses and Dissertations

Brains control an organismճ ability to sense, remember, and respond to the frequently changing world. Brains are composed of multiple regions and systems, which are associated with different processes. These regions are homologous across all vertebrates yet vary greatly in size and shape across clades. While regions can function independently, they also interact extensively. These characteristics make it difficult to predict whether regions can change in size independently from other regions in response to selection (mosaic evolution hypothesis), or whether the brain evolves as a single concerted organ (concerted evolution hypothesis). Further, many traits such as cognition, behavioral flexibility, and …

The Role Of Membrane Excitability In Insulin Regulation, Christopher Howard Emfinger

Arts & Sciences Electronic Theses and Dissertations

In mammals, ATP-sensitive K+ (KATP) channels are essential regulators of insulin secretion from pancreatic islet [beta]-cells, illustrated by the finding that gain-of-function mutations in KATP channels (KATP-GOF) cause neonatal diabetes mellitus (NDM). However, variability in symptom severity and effectiveness of treatment is seen in NDM, even for those with the same mutation and in the same family. Short-term treatment of mice expressing KATP-GOF mutations in [beta]-cells (KATP-GOF mice) with the KATP blocker glibenclamide during disease onset results in two outcomes: one subset becomes severely diabetic (non-remitters), whereas the other subset remains below the glucose levels at which significant side effects …

Viral Mhc Class I Evasion Affects Anti-Viral T Cell Development And Responses, Elvin James Lauron

Arts & Sciences Electronic Theses and Dissertations

Cytotoxic CD8+ T cells (CTLs) play a critical role in protective immunity against viruses, a fact underscored by the evolution of viral CTL evasion mechanisms. For instance, many viruses commonly target the major histocompatibility complex class I (MHCI) antigen presentation pathway to prevent CTLs from recognizing infected cells. A striking example of this is cowpox virus (CPXV), which interferes with MHCI antigen presentation through two distinct mechanisms. One mechanism of CPXV-mediated MHCI inhibition is to retain MHCI molecules in the endoplasmic reticulum (ER). The second mechanism is to prevent antigen peptide loading onto MHCI molecules. When combined these mechanisms result …

Multi-Omics Portraits Of Cancer, Kuan-Lin Huang

Arts & Sciences Electronic Theses and Dissertations

Precision oncology demands accurate portrayal of a disease at all molecular levels. However, current large-scale studies of omics are often isolated by data types. I have been developing computational tools to conduct integrative analyses of omics data, identifying unique molecular etiology in each tumor. Particularly, this dissertation presents the following contributions to the computational omics of cancer: (1) uncovering the predisposition landscape in 33 cancers and how germline genome collaborates with somatic alterations in oncogenesis; (2) pioneering methods to combine genomic and proteomic data to identify treatment opportunities; and (3) revealing selective phosphorylation of kinase-substrate pairs. These findings advance our …

Circadian Regulation Of Temozolomide Sensitivity In Glioblastoma, Emily A. Slat

Arts & Sciences Electronic Theses and Dissertations

The safety and efficacy of multiple cancer chemotherapeutics can vary as a function of when during the day they are delivered. This study aimed to improve the treatment of glioblastoma multiforme (GBM), the most common brain cancer, by testing the efficacy of the DNA alkylator Temozolomide (TMZ) on GBM in vitro and in vivo as a function of time of day. We found cell-intrinsic, daily rhythms in susceptibility of GBM tumor cells (mouse astrocytes deficient in NF1 and p53 signaling) to TMZ in vitro. The greatest TMZ-induced DNA damage response, activation of apoptosis and growth inhibition, occurred near the peak …

Regulation Of Epithelial Proliferation And Migration By Apical-Basal Polarity Proteins, Gregory Vincent Schimizzi

Arts & Sciences Electronic Theses and Dissertations

Epithelial cells line all the outside surfaces of the body where they perform essential roles in maintaining homeostasis. In addition, epithelial tissues are implicated in many disease processes and are the most common tissue type to give rise to human cancer. Therefore, a thorough understanding of epithelial development and homeostasis has broad implications for understanding human development, health, and disease. The establishment and maintenance of apical-basal polarity is a defining characteristic and essential feature of functioning epithelia. Proper apical-basal polarity (ABP) is required for epithelial tissues to carry out their functions, which include absorption, secretion, barrier formation, and collective migration. …

Mechanism Of Gene Regulation By Coding Polya Tracks, Laura Lea Arthur

Arts & Sciences Electronic Theses and Dissertations

Regulation of gene expression is essential for cellular development and survival. The great variety and complexity of regulatory mechanisms underscores this fact. Messenger RNA stability and translational efficiency are often key determinants of gene expression. mRNA surveillance pathways, discovered for their role in degradation of aberrant mRNA, are now known to be instrumental in the regulation of physiologically correct mRNA stability. Thus, the study of cis elements in a transcript that can induce mRNA surveillance pathways has become an area of particular interest.

Here I report on the mechanism of gene regulation by coding polyA tracks, defined as a sequence …

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. …

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 …

Factors That Contribute To De Novo Protein Misfolding And Prion Formation In Saccharomyces Cerevisiae, Kathryn Morgan Keefer

Arts & Sciences Electronic Theses and Dissertations

Protein misfolding is a common phenomenon that can have severe consequences on cellular and organismal health. Despite this, the causes of protein misfolding remain poorly understood. Prions are a class of proteins that, when misfolded, can convert other molecules into a heritable, non-native conformation. The yeast Saccharomyces cerevisiae naturally harbors several diverse prion-forming proteins; thus, it is an ideal model with which to investigate the factors that influence misfolding and aggregation.This thesis utilizes the yeast prions [PSI+] and [RNQ+] to investigate two distinct steps of the protein misfolding pathway: interactions with chaperones and their cofactors, and heterologous templating by other …

Metabolic Regulation Of Cd8 T Cell Functions In The Tumor Microenvironment, Jing Qiu

Arts & Sciences Electronic Theses and Dissertations

Failure of T cells to protect against cancer is thought to result from lack of antigen recognition, chronic activation, and/or suppression by other cells. Using a mouse sarcoma model, we show that glucose consumption by tumors metabolically restricts T cells in the tumor microenvironment, leading to their dampened mTOR activity, glycolytic capacity, and IFN-γ production, and thereby allowing tumor progression. We demonstrate that enhancing glycolysis in an antigenic ‘regressor’ tumor is sufficient to override the ability of T cells to respond to a major tumor rejection antigen, allowing progression of tumors that are normally rejected. Checkpoint blockade therapy is used …

The Effects Of The Gut Microbiota On The Host Chromatin Landscape, Nicholas Semenkovich

Arts & Sciences Electronic Theses and Dissertations

The human gut microbiota is home to tens of trillions of microbes belonging to all three domains of life. The structure and expressed functions of this community have myriad effects on host physiology, metabolism, and immune function. My studies focused on a facet of host-microbial interactions and mutualism that has not been explored to a significant degree in part because of the absence of suitable tools: namely, if, when, and how the gut microbiota produces durable effects on host biology through its impact on the epigenome. To address this area, I turned to gnotobiotic mice and developed a variety of …