Genetics and Genomics Commons^™

Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang

Capstones

As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.

https://lucy-huang-9tge.squarespace.com/

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 …

Nuclear Genome Size Diversity Of Marine Invertebrate Taxa Using Flow Cytometric Analysis, Kyle Roebuck

HCNSO Student Theses and Dissertations

Genomic analysis provides a substantial amount of information on evolutionary history, novel genes, transcriptomic expression and regulation in response to environmental stimuli, how efficiently organisms utilize their genome, and directional genome evolution. Genome size analysis serves as the first step in the sequencing process, because sequencing and annotation costs are directly correlated with genome size. Invertebrates represent the vast majority of faunal diversity on the planet, and, to a greater extent, the marine environment, although they are vastly understudied when compared to vertebrate genomes. Flow cytometry is a widely used, reliable, and accurate means of estimating genome sizes and has …

Transcriptome-Based Gene Networks For Systems-Level Analysis Of Plant Gene Functions, Chirag Gupta

Graduate Theses and Dissertations

Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of

cellular activities with increasing breadth and depth. However, we know very little about how the

genome functions and what the identified genes do. The lack of functional annotations of genes

greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant

biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant

Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some

aspects of their functions assigned. Therefore, there is an …

Characterization Of Plant-Spider Mite Interactions And Establishment Of Tools For Spider Mite Functional Genetic Studies, Nicolas Bensoussan

Electronic Thesis and Dissertation Repository

The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is one of the most polyphagous herbivores feeding on cell contents of over 1100 plant species including more than 150 crops. However, despite its important pest status and a growing understanding of the molecular basis of its interactions with plant hosts, knowledge of the way mites interface with the plant while feeding and the plant damage directly inflicted by mites is lacking. Likewise, while the use of the reverse genetic tools in plants facilitated our understanding of the establishment of defense mechanisms against spider mite herbivory, such tools are lacking for …

Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin

Electronic Thesis and Dissertation Repository

The two-spotted spider mite (TSSM), Tetranychus urticae (Koch), is one of the most damaging agricultural pests in the world. It feeds on over 150 crops, causing considerable yield losses in greenhouses and agricultural fields. Currently, using synthetic acaricides is the main method to control TSSM. However, it can develop resistance to acaricides with repeated exposure, and typically resistance can occur within two to four years. To understand the underlying mechanisms of spider mite adaptation to acaricides is an essential part of resistance management strategy. The resistance ratio of the pyridaben-selected strain compared with the pre-selection strain was estimated at greater …

The Effect Of Diet On Midgut And Resulting Changes In Infectiousness Of Acmnpv Baculovirus In Trichoplusia Ni, Elizabeth Chen

Electronic Thesis and Dissertation Repository

The cabbage looper, Trichoplusia ni, a global generalist lepidopteran pest, has developed resistance to many synthetic and biological insecticides, requiring effective and environmentally acceptable alternatives. One possibility is the Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). This baculovirus is highly infectious for T. ni, with potential as a biocontrol agent, however, its effectiveness is strongly influenced by dietary context. In this study, microscopy and transcriptomics were used to examine how the efficacy of this virus was affected when T. ni larvae were raised on different diets. Larvae raised on potato host plants had lower chitinase and chitin deacetylase transcript levels …

Exploring Biological Heterogeneity And Its Consequences At Tissue And Cellular Scales Through Mathematical And Computational Modeling, Romica Kerketta

Biomedical Sciences ETDs

This dissertation explores the effects of heterogeneity across different biological scales in cancer as well as normal cells. At the tissue scale, we investigated the variability present in the tumor microenvironment and its effect on patient chemotherapeutic outcomes using a mathematical model of drug transport. We found that parameters such as tumor blood perfusion and radius of blood vessel had an impact on the tumor cytotoxicity. This indicated that the physical microenvironment of the tumor is an important regulator of the tumor response to chemotherapy. At the cellular scale, we investigated the heterogeneity present on the membrane landscape of ErbB2 …

The Role Of T-Box Proteins In Vertebrate Germ Layer Formation And Patterning, Sushma Teegala

Dissertations, Theses, and Capstone Projects

All of the tissues in triploblastic organisms, with the exception of the germ cells, arise from the three germ layers, ectoderm, mesoderm and the endoderm. The identification of the genes that underlie the differentiation of these layers is crucial to our understanding of development. T-box family proteins are DNA-binding transcriptional regulators that play important roles during germ layer formation in the early vertebrate embryo. Well-characterized members of this family, including the transcriptional activators Brachyury and VegT, are essential for the proper formation of mesoderm and endoderm, respectively. To date, T-box proteins have not been shown to play a role in …

The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers

Electronic Theses and Dissertations

Primordial germ cells (PGCs) are hypothesized to deposit hematopoietic stem cells (HSCs) along their migration route through the embryo during the early stages of embryogenesis. PGCs also undergo global chromatin remodeling, including the erasure and reestablishment of genomic imprints, during this migration. While PGCs do not spontaneously form teratomas, their malignant development into germ cell tumors (GCTs) in vivo is often accompanied by the retention of hypomethylation at the IGF2-H19 imprinting control differentially methylated region (DMR). Previous studies in bimaternal embryos determined that proper genomic imprinting at two paternally imprinted loci was necessary for their growth and development: Igf2-H19 and …

Chaperoning Ef Hands That Shape Calcium Response: Ncald, Hpca And S100b, Jingyi Zhang

Graduate School of Biomedical Sciences Theses and Dissertations

All organisms have an internal clock with a defined period between repetitions of activities. The period for circadian clock in human is 24.5 hours, while in mouse and rat, it is 23.5 hours. However, all organisms are forced to be in synchronization with their environment. A major environmental force that resets the internal clock to 24 hours is light. This phenomenon is defined as “light entrainment” or “phase-setting”. It is unclear how this entrainment process occurs. Studies from this laboratory indicate a role for two neuronal calcium sensor proteins: Neurocalcin  (NCALD) and S100B. For these two genes, mRNA as …

Molecular Mechanisms Of Dna Replication Initiation In Hpvs With Genetic Variations Leading To Cellular Carcinogenesis, Gulden Yilmaz

Graduate School of Biomedical Sciences Theses and Dissertations

Human papillomaviruses are a vast family of double-stranded DNA viruses containing non-carcinogenic and carcinogenic types, whose crucial differences remain unknown, except for the difference in the frequency of DNA replication. The human papillomavirus (HPV) E2 protein regulates the initiation of viral DNA replication and transcription. Its recognition and binding to four 12 bp palindromic sequences in the viral origin is essential for its function. Little is known about the DNA binding mechanism of the E2 protein found in HPV types that have low risk for oncogenicity (low-risk) as well as the roles of various elements of the individual binding sites. …

Mitochondrial Regulation Of Yeast Ampk During Energy Stress, Aishwarya Shevade

Theses and Dissertations

In eukaryotes, members of the conserved AMP-activated protein kinase (AMPK) family play a pivotal role in sensing and responding to energy stress. Mammalian AMPK becomes activated when the AMP:ATP ratio is too high, and functions to prevent unnecessary ATP spending and to increase ATP production. Due to their role in ATP production through aerobic respiration, mitochondria are known to play an indirect role in the negative control of AMPK. The conserved voltage-dependent anion channel (VDAC) proteins, also known as mitochondrial porins, mediate the passage of small metabolites between the mitochondria and cytoplasm, including the release of ATP. One would therefore …

Optimizing A Method For Simultaneous Recovery Of Proteins And Dna From Fingerprints, Steven Kranes

Student Theses

DNA testing on touched objects is a valuable tool in forensic investigations, but DNA is usually present in low amounts, causing poor STR typing results. For touch DNA evidence, there is a clear need for additional individualization, especially for highly probative samples. This could be achieved by testing genetically variable proteins. The goal of this project was to develop a DNA/protein co-extraction method to facilitate DNA and protein testing on the same evidence item. Existing DNA extraction methods were carefully adjusted to allow for downstream mass spectrometry analysis. Initial experiments on saliva and fingerprints placed on glass suggested that trypsin …

Functional Characteristics Of Four Novel Lone Atrial Fibrillation-Linked Connexin40 Mutants, Mahmoud Noureldin

Electronic Thesis and Dissertation Repository

Atrial fibrillation (AF) is the most common form of cardiac arrhythmia. Recently, four novel heterozygous Cx40 mutations, K107R, L223M, Q236H, and I257L were identified in 4 of 310 unrelated AF patients. To study possible alterations associated with these mutants, we studied their localization and function using gap junction (GJ)-deficient model cells. Cell pairs expressing Q236H alone or together with wildtype Cx43 showed a significantly lower coupling conductance. Impaired GJ function and dominant negative action on Cx43 of this mutant are consistent with previous findings on the majority of AF-linked Cx40 mutants. The remaining three novel AF-linked mutants did not show …

Cellular/Molecular Analysis Of Interspecies Sterile Male Hybrids In Drosophila, Rachelle L. Kanippayoor

Electronic Thesis and Dissertation Repository

Over time, genetic differences can accumulate between populations that are geographically separated. This genetic divergence can lead to the evolution of reproductive isolating mechanisms that reduce gene flow between the populations and, upon secondary contact, result in distinct species. The process of speciation is, thus, what accounts for the multitude of species that contribute to the rich biodiversity on Earth. Interspecies hybrid sterility is a postzygotic isolating mechanism that affects the development of hybrids, rendering them sterile. A notable trend, known as Haldane's Rule, describes that heterogametic individual (e.g. males in Drosophila) are more susceptible to sterility than homogametic …

The Recycling Gtpase, Rab-10, Regulates Autophagy Flux In Caenorhabditis Elegans, Nicholas J. Palmisano

Dissertations, Theses, and Capstone Projects

Autophagy and endocytosis are two cellular pathways that are vital to cell growth and homeostasis. Autophagy is a dynamic and catabolic process involving the formation of a double-membrane vesicle called the autophagosome, which engulfs long-lived proteins and damaged organelles. Endocytosis involves the uptake of extracellular material into the cell through the formation of intracellular vesicles termed endosomes. Although both endocytosis and autophagy are interconnected processes, the extent to which endocytic proteins and/or compartments contribute to autophagy, and how these endocytic components do so, is still unknown. To improve our understanding of the connections that exist between autophagy and endocytosis, we …

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 …

Characterization Of Neuronal Specific Responses To Induced Misfolded Protein Stress In Caenorhabditis Elegans, Claire Gormley

Senior Honors Projects, 2010-2019

Abstract

Misfolded protein stress has been associated with many types of disease,

including neurodegenerative disorders like Alzheimer’s, Parkinson’s and Huntington’s

disease. When a cell accumulates misfolded proteins in the endoplasmic reticulum,

misfolded protein stress occurs and the unfolded protein response (UPR) is triggered to

induce mechanisms that will allow the cell to either survive or undergo cell death. The

nascent polypeptide associated complex (NAC) is a co-translational chaperone and α/β

heterodimer that manages protein folding and localization, and protects against misfolded

protein stress; changes in NAC function have been linked to both neurodegeneration and

cancer. In these studies, I depleted …

Characterization Of E-Cadherin Regulation In Response To Zeb1 Inhibition In Endometrial Cancer Cell Lines, Chidozie Paul Chukwu

Graduate School of Biomedical Sciences Theses and Dissertations

Epithelial to mesenchymal transition (EMT) is the process in which cells lose their epithelial structure during gastrulation. This process also affects the migration and movement of tumor cells and promotes invasion and metastases of endometrial carcinomas. Down-regulation of E-cadherin (CDH1) by transcription factors is the key target of EMT modulators and is achieved mainly by ZEB1 (zinc finger E-box binding homeobox 1). Current research looking at restoration of E-cadherin expression in vitro involves the use of small molecules such as histone deacetylase (HDAC) inhibitors and DNA methyltransferase inhibitors. Trichostatin A (TSA) and small interfering ribonucleic acid (siRNA) are tools that …

The Role Of The Expansion Segment 7 Of 25s Rrna During Oxidative Stress In Saccharomyces Cerevisiae, Ethan Gardner

Graduate School of Biomedical Sciences Theses and Dissertations

Translation is an essential process for protein expression in both eukaryotes and prokaryotes. Like any cellular process, translational factors are prone to damage when the cell is under stress. One common stressor that nearly all cells may experience is abnormal levels of reactive oxygen species (ROS). Damage caused by ROS has been associated with disease ranging from neurodegenerative impairments, to the aging process of cells. These oxygen radicals are capable of damaging a litany of molecules including nucleic acids, and molecular factors involved in translation. It has been shown that tRNA can be cleaved upon ROS-induced stress and these fragments …

Proteomic Identification Of Histone Post-Translational Modifications Induced By Dna Double-Strand Breaks And Novel Proteins Involved In The Dna Damage Response, Pingping Wang

Dissertations & Theses (Open Access)

Inaccurate repair of DNA double-strand breaks (DSBs) can lead to DNA mutation and chromosome rearrangements, causing human diseases such as cancer. Although we know the basic mechanisms of DSB repair, the added complexities in the chromatin context are unclear. This is partially due to the lack of unbiased systems for identifying proteins and post-translational modifications (PTMs) involved in DSB repair. In this work, we established a novel method, termed DSB-ChAP-MS (Double Strand Break-Chromatin Affinity Purification with Mass Spectrometry), for the affinity purification of a sequence-specific single copy endogenous chromosomal locus containing a DSB, followed by the proteomic identification of enriched …

Understanding The Mechanism Of Genomic Instability During Replicative Aging In Budding Yeast, Sangita Pal

Dissertations & Theses (Open Access)

Aging brings a gradual decline in molecular fidelity and biological functionality, resulting in age related phenotypes and diseases. Despite continued efforts to uncover the conserved aging pathways among eukaryotes, exact molecular causes of aging are still poorly understood. One of the most important hallmarks of aging is increased genomic instability. However, there remains much ambiguity as to the cause. I am studying the replicative life span (RLS) of the genetically tractable model organism Saccharomyces cerevisiae, or budding yeast using the innovative “mother enrichment program” as the method to isolate unparalleled numbers of aged yeast cells to investigate the molecular changes …

Environmental Changes Turn On The Sinorhizobium Melitloti Exor-Exos/Chvi (Rsi) Host Invasion Switch, Shari N. Walcott

Dissertations, Theses, and Capstone Projects

The free-living Gram-negative soil bacterium, Sinorhizobium meliloti, must switch into its host-invading form in order to infect the root hairs of the host plant, alfalfa (Medicago sativa), and establish a nitrogen-fixing symbiosis. The activation of the switch is believed to occur inside the infection chamber that is formed by curling of the root hairs. It is not fully understood what signals in the environment of the root hairs trigger and infection chamber S. meliloti to switch into a host-invading form since these signals were not extensively examined until now. This switch can be observed directly, due to …

Differential Activity And Content Of High-Affinity Glutamate Transporters, Content Of Their Regulatory Proteins, And Capacity For Glutamine And Glutathione Synthesis In Tissues Of Finished Versus Growing Steers, Jing Huang

Theses and Dissertations--Animal and Food Sciences

Improvement of feeding regimens for production animals has been hindered by a lack of fundamental knowledge about how the capacity to regulate nutrient absorption across cell membranes affects the function of nutrient metabolizing enzymes. The objective is to determine if the activities and protein content of system X^-_AG glutamate transporter, its regulatory protein (GTRAP3-18 and ARL6IP1), glutamine synthetase (GS) and glutathione (GSH) content, changes in liver (Experiment 1), longissimus dorsi (LM) and subcutaneous adipose tissue (SF) (Experiment 2) as beef steers transitioned from predominantly-lean (growing) to -lipid (finished) tissue accretion phases. In liver (Experiment 1), system X^{- …}

Effects Of Posttranslational Modification Of Transcription Factor Gli-Similar 3 By Sumoylation On Insulin Transcription In Pancreatic Β Cells, Tyler M. Hoard

Murray State Theses and Dissertations

The ability to control blood glucose levels is a fundamental component of vertebrates. In these organisms, blood glucose homeostasis is achieved through a fine-tuned mechanism that largely involves the secretion of hormones from the endocrine pancreas into the bloodstream. These hormones include glucagon, which is secreted by the α cells of the pancreas and initiates the release of glucose into the bloodstream through gluconeogenesis in the liver, and insulin, which is secreted from the β cells and signals the uptake of excess blood glucose by the peripheral tissue. Gli-similar 3 (Glis3) is a transcription factor that has previously been shown …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

Examining The Role Of Grp And Lik1 In Wall Associated Kinase (Wak) Perception Of Pectin In The Plant Cell Wall, Jack Ryan Mitchell

Honors Projects

Wall associated kinases (WAKs) are cell membrane bound receptor kinases that bind pectin and pectin fragments (OGs).The binding of WAKs to pectin sends a growth signal required for cell elongation and plant development. WAKs bind OGs with higher affinity than native pectin and instead activate a stress response. Glycine rich proteins (GRPs) are secreted cell wall proteins of unknown function. Seven GRPs with 65% sequence similarity are coded on a 90kb locus of Arabidopsis chromosome 2. GRP3 and WAK1 have been shown to bind in vitro, but single null mutations have no discernible phenotype, suggesting that the GRPs are redundant. …

The Localization And Function Of Novel Tetrahymena Thermophila Cytoskeletal Genes Bbc29 And Bbc39, Emily K. Moore, Nicole C. Zanolli

Undergraduate Research Symposium Posters

Ciliary function is known to play an important role in many human conditions, including chronic sinus and pulmonary diseases and problems with infertility. Cilia are cytoskeletal structures that protrude from the cell body to facilitate movement. Ciliary structure is conserved throughout eukaryotes, from unicellular to multicellular organisms, including humans. A clear understanding the proteins that compose cilia and how they interact with one another will increase our knowledge about important cytoskeletal elements. Because cilia are difficult to study in multicellular organisms, the unicellular eukaryote Tetrahymena thermophila serves as a useful model for the study of cytoskeletal genes, due to their …

The Role Of The Dosage Compensation Complex As A Pathway For Spiroplasma To Induce Male Lethality In Drosophila Melanogaster, Becky Cheng

CMC Senior Theses

Drosophila melanogaster and many other insects harbor intracellular bacterial symbionts that are transmitted vertically from infected host mothers to their offspring. Many of these bacteria alter host reproductive developmental processes in order to increase their transmission success. For example, Spiroplasma, a spirochete that naturally infects D. melanogaster, selectively kills males during mid-embryogenesis while sparing females. Previous studies suggested that Spiroplasma interacts genetically with the male-specific dosage compensation pathway, which causes ~2-fold up-regulation of most genes located on the male’s single X chromosome so that their expression matches the levels found in females who have two Xs. To further …