Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 23 of 23
Full-Text Articles in Life Sciences
Deconvoluting Cell-Type Specific 3'Utr Isoform Expression In The Adult And Developing Cerebellum, Saša Jereb
Deconvoluting Cell-Type Specific 3'Utr Isoform Expression In The Adult And Developing Cerebellum, Saša Jereb
Student Theses and Dissertations
Alternative polyadenylation has been implicated in the regulation of mRNA translation and stability, as well as mRNA and protein localization. However, it is unclear to what extent alternative polyadenylation regulates these processes uniquely in specific cell types. Using a newly developed technique, termed conditionally-tagged poly(A) binding protein-mediated mRNA 3’ end retrieval by crosslinking immunoprecipitation (cTag-PAPERCLIP), we discovered significant differences in alternative polyadenylation between granule and Purkinje cells in the mouse cerebellum, as well as between proliferating and adult granule cells. Interestingly, among transcripts that differed in alternative polyadenylation in both these comparisons, many were involved in key neuronal functions. We …
Specification Of Stem Cells And Niche During Hair Follicle Morphogenesis, Tamara Ouspenskaia
Specification Of Stem Cells And Niche During Hair Follicle Morphogenesis, Tamara Ouspenskaia
Student Theses and Dissertations
Adult stem cell (SC) behavior is tightly coordinated by the signals received from the “niche” - the microenvironment that the SCs reside in. Little is known about the role of the niche in SC specification during organ morphogenesis. In particular, the question of whether the niche exists prior to SC specification or whether it is recruited after SC establishment in a developing tissue remains largely unanswered. In addition, the signals responsible for the specification and regulation of SCs during morphogenesis remain unexplored. To answer these questions, I focused my analysis on the earliest stages of hair follicle (HF) morphogenesis. Using …
A Comparative Study Of Sensory Neuron Synaptic Activity And The Role Of Presynaptic Diversity, Specificity, And Regulation In Caenorhabitis Elegans, Donovan Ventimiglia
A Comparative Study Of Sensory Neuron Synaptic Activity And The Role Of Presynaptic Diversity, Specificity, And Regulation In Caenorhabitis Elegans, Donovan Ventimiglia
Student Theses and Dissertations
Chemical synapses are complex structures that have a diversity of specific activities that shape nervous system computation. To understand how this diversity contributes to specific circuit functions, we sought to characterize synaptic release in the stereotyped and defined neural circuitry of C. elegans. Here we use pHluorin imaging (Vglut-pH) to monitor presynaptic glutamate release from single chemosensory neurons in intact animals and characterize the dynamics of endo- and exocytosis from two types of glutamatergic neurons, AWCON and ASH. In Chapter 1, we describe the optimization of Vglut-pH, we introduce a reagent for measuring synaptic calcium influx by tethering GCaMP …
Isopeptide And Ester Bond Ubiquitination Regulate Degradation Of The Human Dopamine Receptor 4, Jennifer C. Peeler
Isopeptide And Ester Bond Ubiquitination Regulate Degradation Of The Human Dopamine Receptor 4, Jennifer C. Peeler
Student Theses and Dissertations
The human dopamine receptor 4 (hD4R) is a seven-transmembrane helical G protein-coupled receptor (GPCR) found in neural synaptic membranes. The neurotransmitter dopamine binds to and activates the hD4R, which is involved in central nervous system pathways that modulate cognition and circadian rhythms. The hD4R is the primary dopaminergic receptor for the atypical anti-psychotic drug clozapine, which is used to treat schizophrenia and other cognitive disorders. The hD4R gene is unique among the superfamily of GPCR-encoding genes because within the human population, it contains a variable number of tandem repeat (VNTR) exon polymorphism. Because of the VNTRs, the length of the …
Density-Dependent Foraging In Caenorhabditis Elegans, Joshua Greene
Density-Dependent Foraging In Caenorhabditis Elegans, Joshua Greene
Student Theses and Dissertations
Game theory has long predicted that the density of competitors and their behaviors should affect foraging, and moreover suggests that multiple strategies can evolve and co-exist within a single species. I show that both of these predictions are met by foraging Caenorhabditis elegans. In Chapter 2, I show that animals alter their foraging behavior in response to population density, that certain pheromones induce this behavioral change, and that different wild isolates vary in response to the potent ascaroside icas#9. I use QTL mapping to find a major locus responsible for this variation, and map it to an icas#9 receptor, srx-43. …
Single Molecule Ligand Binding Studies On Ccr5 By Fluorescence Cross-Correlation Spectroscopy, Carlos Rico
Single Molecule Ligand Binding Studies On Ccr5 By Fluorescence Cross-Correlation Spectroscopy, Carlos Rico
Student Theses and Dissertations
The G protein-coupled receptor (GPCR) C-C chemokine receptor 5 (CCR5) is the major co-receptor for HIV-1. CCR5 binds to the viral glycoprotein gp120 allowing HIV particles to infect T cells. Currently, maraviroc is the only Food and Drug Administration (FDA) approved entry inhibitor for HIV-1 but resistance to maraviroc has been reported indicating the need for novel entry inhibitors. Recently, four peptides derived from RANTES (Regulated on Activation, Normal T cell Expressed and Secreted), the endogenous ligand of CCR5, were shown to induce different CCR5 signaling pathways and efficiently block viral entry. The peptide analogues are 5P12, which blocks HIV-1 …
Compromising The 20s Proteasome Activates A Quality Control Pathway To Mitigate Proteotoxic Stress, Irit Shachrai
Compromising The 20s Proteasome Activates A Quality Control Pathway To Mitigate Proteotoxic Stress, Irit Shachrai
Student Theses and Dissertations
The regulation of the ubiquitin-proteasome system (UPS) has been the subject of a vast body of work because of its implication in normal development and a wide range of diseases. The UPS controls the degradation of a large number of cellular proteins and thereby regulates essential cellular processes critical for cellular adaptation and more. Amongst the main processes are removal of mis-folded and potentially toxic proteins, cell’s loss of protein quality control is often associated with muscle atrophy and neurodegenerative diseases. The proteasome is subject to tight regulation, as many different proteins govern its transcription, assembly, stability and activity. Consequently, …
Investigating Differentiation: A Role For Organelle Inheritance In Epidermal Growth, Amma Asare
Investigating Differentiation: A Role For Organelle Inheritance In Epidermal Growth, Amma Asare
Student Theses and Dissertations
Balanced growth and differentiation is essential to tissue morphogenesis and homeostasis. How imbalances arise in disease states such as cancers is poorly understood. Loss of differentiation is associated with poorer prognosis in human patients and increasing malignancy in animal models. Here we explore this intersection between growth and differentiation in the context of epidermal development, where populations of stem cells are maintained in careful equilibrium and induced to proliferate and differentiate in response to stimuli such as injury or cyclical growth signals. During development, a naïve epidermis undergoes rapid proliferation and differentiation to form skin containing hair follicles, neurons, immune …
Transcriptional Governance Of Hair Follicle Stem Cell Quiescence And Niche Maintenance In Long-Term Tissue Regeneration, Kenneth Lay
Student Theses and Dissertations
Adult stem cells are endowed with the remarkable ability to maintain, regenerate and repair tissues throughout the lifetime of the organism. Whether parsimonious utilization of adult stem cells is necessary to preserve their long-term potential has not been fully explored. I investigated this issue using the adult murine hair follicle stem cell (HFSC) as my paradigm. HFSCs reside in their niche called the bulge, and mostly remain in a quiescent state, becoming mobilized only transiently to fuel cyclical bouts of hair follicle regeneration. By ablating a key HFSC transcription factor, Forkhead Box C1 (FOXC1), I discovered that hair follicles underwent …
Separate Roles Of Fan1 And Fanconi Anemia Proteins In Dna Interstrand Crosslink Repair And Human Disease, Supawat Thongthip
Separate Roles Of Fan1 And Fanconi Anemia Proteins In Dna Interstrand Crosslink Repair And Human Disease, Supawat Thongthip
Student Theses and Dissertations
DNA interstrand crosslink (ICL) repair is vital for cellular proliferation and survival. Defects in the repair of DNA crosslinks have been associated with congenital abnormalities, bone marrow and kidney failure, liver dysfunction, and cancer. DNA nucleases play a significant role during the repair of ICLs and they function at multiple repair steps. Here, we assessed the contributions of FANCD2/FANCI-Associated Nuclease 1 (FAN1) to the repair of ICL lesions and studied the consequences of its deficiency, which results in rare chronic kidney disease - Karyomegalic Interstitial Nephritis (KIN). FAN1 is a highly conserved nuclease from yeast to humans. It was first …
Home Sweet Home: Epigenetic Paths Of Stem Cells In And Out Of Their Niche, Rene C. Adam
Home Sweet Home: Epigenetic Paths Of Stem Cells In And Out Of Their Niche, Rene C. Adam
Student Theses and Dissertations
Adult stem cells reside in niches, which control their long-term ability to selfrenew and produce the differentiated cell lineages necessary to regenerate and repair their tissues. Following injury, culture or transplantation, stem cells outside their niche often acquire broader plasticity in fates. In my graduate work, I showed that super-enhancers underlie the identity, lineage commitment and plasticity of adult stem cells in vivo. My chosen model is the hair follicle, where its stem cells (HFSCs), niche and master regulators are well-characterized. By mapping global chromatin domains of HFSCs in their native niche, and of committed progenitors, I discovered that super-enhancers …
Ir Laser-Induced Gene Expression For Tracking Development Of Single Embryonic Neurons And Glia In C. Elegans, Anupriya Singhal
Ir Laser-Induced Gene Expression For Tracking Development Of Single Embryonic Neurons And Glia In C. Elegans, Anupriya Singhal
Student Theses and Dissertations
The assembly of neural circuits requires a complex choreography of developmental events: neurons must be generated, extend neurites at the correct time and location, and then integrate extracellular information, like long-range guidance cues or cellular contacts, with an internal developmental program to make correct wiring decisions. Visualizing neural-circuit assembly in vivo can provide insight into how these events are coordinated. The C. elegans embryo, which contains only 222 neurons and 56 glia, is an attractive setting to study nervous system development comprehensively in an intact, living organism. However, methods to label and track optically-resolvable neurites or manipulate single neurons through …
The Apoptotic And Wallerian Degeneration Pathways Regulate Disease Onset And Progression In The Sod-1g93a Transgenic Mouse Model Of Als, Deanna Belsky
The Apoptotic And Wallerian Degeneration Pathways Regulate Disease Onset And Progression In The Sod-1g93a Transgenic Mouse Model Of Als, Deanna Belsky
Student Theses and Dissertations
Amyotrophic Lateral Sclerosis is a neurodegenerative disorder characterized by progressive muscle denervation, motor axon degeneration and the death of motor neurons. The molecular mechanisms that mediate axon degeneration in ALS remain unknown, but motor neuron cell body death occurs through apoptosis. Genetic deletion of the pro-apoptotic gene Bax delays muscle denervation, prolongs disease onset, prevents motor neuron cell death and improves survival in an ALS mouse model. However, the timing and extent of axon degeneration in these mice is unaffected. Here, we examine the role of Sarm1, a component of the Wallerian degeneration pathway, and its interaction with the classical …
Lysin Based Antimicrobial Peptides Against Acinetobacter Baumannii, Mya Thandar
Lysin Based Antimicrobial Peptides Against Acinetobacter Baumannii, Mya Thandar
Student Theses and Dissertations
Acinetobacter baumannii is a Gram-negative bacterial pathogen responsible for a range of nosocomial infections. The recent rise and spread of multidrug resistant A. baumannii clones has fueled a search for alternative therapies, including bacteriophage endolysins with potent antibacterial activities. A common feature of these lysins is the presence of a highly positively charged C-terminal domain with a likely role in promoting outer membrane penetration. In the current study, we show that the C-terminal amino acids 108-138 of phage lysin PlyF307, named P307, alone was sufficient to kill A. baumannii (>3-logs). Furthermore, P307 could be engineered for improved activity, the …
The Physics Of Rodent Ultrasonic Vocalizations, Matthew Dornfeld
The Physics Of Rodent Ultrasonic Vocalizations, Matthew Dornfeld
Student Theses and Dissertations
Although much work has been done on the physics of vocalizations caused by the vibrating motion of vocal folds, relatively little work has been done on the physics of ultrasonic vocalizations (USVs). There are two orders of mammals known to make these kind of vocalizations: cetaceans and rodents. Of these two the mechanism behind the rodent calls are better understood. Thus, this thesis investigates the physics of rodent USVs with the hope that findings will help elucidate the mechanisms behind cetacean USVs. Chapter 1 discusses the anatomical background of rodent vocal tracts, evolutionary pressures that shaped the development of USVs, …
Light Sheet Microscopy And Image Analysis Of Neural Development And Programmed Cell Death In C. Elegans Embryos, Peter Insley
Light Sheet Microscopy And Image Analysis Of Neural Development And Programmed Cell Death In C. Elegans Embryos, Peter Insley
Student Theses and Dissertations
The positioning of neuronal cell bodies and neurites is critical for intact functioning of the nervous system. Mapping the positions of the soma and neurites in the brains of developing embryos as important central nervous system structures are being created may yield novel insight into the role of distinct cell groups in creating these structures. New developments in microscopy have made this an excellent time to study neural development in the C. elegans embryo. In the past decade, implementations of highly light efficient methods such as single plane illumination microscopy have rendered it possible to follow development of embryonic structures …
High Throughput Detection Of Pseudouridine: Caveats, Conundrums, And A Case For Open Science, Maryam Zaringhalam
High Throughput Detection Of Pseudouridine: Caveats, Conundrums, And A Case For Open Science, Maryam Zaringhalam
Student Theses and Dissertations
The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs ,owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded …
A Neuronal Circuit Architecture For Angular Integration In Drosophila, Jonathan Green
A Neuronal Circuit Architecture For Angular Integration In Drosophila, Jonathan Green
Student Theses and Dissertations
While navigating their environment, many animals keep track of their angular heading over time. However, a neuronal-circuit architecture for computing heading remains unknown in any species. In this thesis, I describe a set of neurons in the Drosophila central complex whose wiring and physiology provide a means to shift an angular heading estimate when the fly turns. I show that these clockwise- and counterclockwise-shifting neurons each exist in two subtypes, with spatiotemporal activity profiles that suggest opposing roles for each subtype at the start and end of a turn. Shifting neurons are required for the heading system to properly track …
Apobec1-Mediated Rna Editing In Monocytes Contributes To Genetic Heterogeneity And Modulates Monocyte Activity And Development, Violeta Rayón Estrada
Apobec1-Mediated Rna Editing In Monocytes Contributes To Genetic Heterogeneity And Modulates Monocyte Activity And Development, Violeta Rayón Estrada
Student Theses and Dissertations
Post-transcriptional modifications such as alternative splicing have been shown to add to the complexity needed to compensate for the relatively low number of genes found in higher organisms. Many other modifications recently found in mRNA, which cannot be deduced from what is coded in the genome, such a cytidine to uridine and adenosine to inosine editing, reveal that this complexity is ever expanding. Therefore, the current challenge is to understand what is the function of these modifications. In this thesis, I focus on APOBEC1-mediated RNA editing. In higher eukaryotes RNA editing consists of C to U and A to I …
Pathways Of Nhej At Dysfunctional Telomeres And Their Resolution, Roos Anna Karssemeijer
Pathways Of Nhej At Dysfunctional Telomeres And Their Resolution, Roos Anna Karssemeijer
Student Theses and Dissertations
Shelterin is a multiprotein complex that prevents DNA damage signaling at chromosome ends. In its absence, DNA repair pathways are activated that can promote the fusion of dysfunctional telomeres resulting in chromosomal instability. The work presented here aims to understand how telomeres are protected from these pathogenic repair pathways. The first part of this thesis is focused on the DNA damage response factor 53BP1, a key regulator in double strand break (DSB) repair pathways in mammalian cells. By influencing key regulatory events at and near DNA ends, 53BP1 plays an important role in the decision between non-homologous endjoining (NHEJ) and …
Regulated Recruitment Of The Chromosomal Passenger Complex To Chromatin And Microtubules Promotes Accurate Cell Division, Michael Wheelock
Regulated Recruitment Of The Chromosomal Passenger Complex To Chromatin And Microtubules Promotes Accurate Cell Division, Michael Wheelock
Student Theses and Dissertations
Aurora B, the kinase subunit of the chromosomal passenger complex (CPC), promotes accurate cell division by destabilizing erroneous kinetochoremicrotubule attachments and activating the spindle assembly checkpoint (SAC). Both functions require Aurora B activation, which is promoted by its binding to the C terminus of the CPC subunit INCENP, and by localization to the inner centromere, which requires the N terminus of INCENP. Inner centromere localization also requires phosphorylation of histone 3 threonine 3 (H3T3ph). While H3T3ph is required for CPC localization and the SAC during early mitosis, it must be dephosphorylated at anaphase to facilitate mitotic exit. However, the H3T3 …
Light Stimulation Of Sensory Hair Cells, Julien Azimzadeh
Light Stimulation Of Sensory Hair Cells, Julien Azimzadeh
Student Theses and Dissertations
Hair cells are the mechanosensory detectors that underlie our senses of audition and balance. Their mechanosensitivity arises from direct gating of force-sensitive ion channels by the tension in tip links located at the tops of the stereocilia. The study of hair cells and their mechanically gated channels has heretofore required physical displacement of a hair bundle to open its mechanotransduction channels. The work presented here describes a novel method of hair-bundle stimulation: irradiation with light. The original aim of this study was to elucidate the role of Ca2+ in fast adaptation, a process thought to underlie a hair bundle’s …
Structural And Functional Studies Of Mycobacterial General Transcription Factors Rbpa And Card, Elizabeth Hubin
Structural And Functional Studies Of Mycobacterial General Transcription Factors Rbpa And Card, Elizabeth Hubin
Student Theses and Dissertations
Gene expression in bacteria is highly regulated at the step of transcription initiation. For decades, the vast majority of biochemical and kinetic studies have used Escherichia coli (Eco) RNA polymerase (RNAP) as a model for studying prokaryotic transcription initiation. However, properties of Eco RNAP are not representative of RNAPs from other bacterial species. Transcription in mycobacteria is distinct from Eco by its formation of unstable initiation complexes and its dependence on two transcription factors, RbpA and CarD, which are essential in the pathogen Mycobacteria tuberculosis (Mtb). In this thesis, I report the structural and biochemical characterization of RbpA and describe …