Genetics Commons^™

The Role Of Trm9 In Stress Responses, Ashish Ravindra Patil

Legacy Theses & Dissertations (2009 - 2024)

Cells need to respond appropriately to environmental changes in order to maintain homeostasis. The cellular response to an environmental stress is regulated at transcriptional, translational and post translational levels. The tRNA, which acts as an adaptor molecule between the mRNA and the protein, plays an important role in the translational regulation of cellular responses to stress and is one of the most heavily modified biomolecules. In Saccharomyces cerevisiae , the wobble uracil of the tRNA(3'-UCU-5') Arg, tRNA(3'-UUC-5') Glu and certain other specific tRNAs are modified to 5-methoxycarbonylmethyluridine (mcm5U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) residues by the tRNA methyltransferase 9 (Trm9). Modifications at …

A Novel Gene Silencing Vector For Plant Genomics And Biotechnology, Dustin Hoover, Scott Nicholson, Vibha Srivastava

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Gene silencing is a process of suppressing activity of specific genes by producing “interfering” RNA encoded by foreign genes. This process serves as the principle of genetic modification in plants and animals, which is an important tool in genomics and biotechnology, allowing scientists to manipulate organisms to better meet human demands. New approaches of gene silencing may enable improvements on current practices of genetic modification, and broaden the application and impact of gene silencing in biotechnology. Recently, a novel vector design consisting of the transcription of short gene fragments lacking transcription termination signals was demonstrated to be effective in partial …

Electro-Gene Transfer To Skin Using A Noninvasive Multielectrode Array, Siqi Guo, Amy Donate, Gaurav Basu, Cathryn Lundberg, Loree Heller, Richard Heller

Bioelectrics Publications

Because of its large surface area and easy access for both delivery and monitoring, the skin is an attractive target for gene therapy for cutaneous diseases, vaccinations and several metabolic disorders. The critical factors for DNA delivery to the skin by electroporation (EP) are effective expression levels and minimal or no tissue damage. Here, we evaluated the non-invasive multielectrode array (MEA) for gene electrotransfer. For these studies we utilized a guinea pig model, which has been shown to have a similar thickness and structure to human skin. Our results demonstrate significantly increased gene expression 2 to 3 logs above injection …

Field Introgression Of Diabrotica Barberi And Diabrotica Longicornis (Coleoptera: Chrysomelidae) Based On Genetic And Morphological Characters, Laura A. Campbell, Thomas L. Clark, Pete L. Clark, Lance Meinke, John E. Foster

Department of Entomology: Faculty Publications

Diabrotica barberi Smith & Lawrence and Diabrotica longicornis (Say) (Coleoptera: Chrysomelidae) are considered to be sister species, and it has been proposed that the two species may hybridize under field conditions. The objective of this study was to examine genetic and morphological characters of D. barberi and D. longicornis for evidence of field introgression. Both species were collected from sympatric and allopatric areas. Amplified fragment length polymorphisms and morphological characters (color and head capsule width) were used to examine variation within and among populations of D. barberi and D. longicornis. Relatively little of the overall …

Mendelian Breeding Units Versus Standard Sampling Strategies: Mitochondrial Dna Variation In Southwest Sardinia, Daria Sanna, Joseph G. Lorenz

All Faculty Scholarship for the College of the Sciences

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and …

Loss Of Bloom Syndrome Protein Causes Destabilization Of Genomic Architecture And Is Complemented By Ectopic Expression Of Escherichia Coli Recg In Human Cells, Michael Wayne Killen

University of Kentucky Doctoral Dissertations

Genomic instability driven by non-allelic homologous recombination (NAHR) provides a realistic mechanism that could account for the numerous chromosomal abnormalities that are hallmarks of cancer. We recently demonstrated that this type of instability could be assayed by analyzing the copy number variation of the human ribosomal RNA gene clusters (rDNA). Further, we found that gene cluster instability (GCI) was present in greater than 50% of the human cancer samples that were tested. Here, data is presented that confirms this phenomenon in the human GAGE gene cluster of those cancer patients. This adds credence to the hypothesis that NAHR could be …

Axogial Communication Mediated By Soluble Neuregulin-1 And Bdnf, Zhenzhong Ma

Wayne State University Dissertations

During peripheral nervous system development, successful communication between axons and glial cells including Schwann cells in peripheral nervous system and oligodendrocytes in central nervous system, is required for the proper functions of both neurons and glia. Three types of alternatively-spliced proteins belonging to the neuregulin1 (NRG1) gene family of growth and differentiation factors are essential for Schwann cell survival and peripheral nerve development. While membrane-bound NRG1 forms (type III) has been strongly implicated in the regulation of myelination process at late stage of Schwann cell development, little is known about the role of soluble, heparin-binding forms of NRG1 (type I/II) …

Rox1 Function In Dosage Compensation: Structural / Functional Analysis Of A Non-Coding Rna, Ying Kong

Wayne State University Dissertations

roX1 is a long non-coding RNA involved in the chromosome-wide gene regulation that occurs during dosage compensation in Drosophila. Dosage compensation in Drosophila melanogaster occurs by a global two-fold increase of transcription from the single male X chromosome. This essential process compensates for X chromosome monosomy. The male-specific lethal (MSL) complex, containing five proteins, localizes to the male X chromosome and alters chromatin to modify gene expression. roX1 and roX2 RNAs are redundant components of MSL complex that are required for its exclusive X-localization. Recent studies in our lab have revealed a second role of roX RNAs in heterochromatic gene …

Regulation Of The Latency–Reactivation Cycle By Products Encoded By The Bovine Herpesvirus 1 (Bhv-1) Latency-Related Gene, Clinton Jones, Leticia Frizzo Da Silva, Devis Sinani

School of Veterinary and Biomedical Sciences: Faculty Publications

Like other α-herpesvirinae subfamily members, the primary site for bovine herpesvirus 1 (BHV-1) latency is ganglionic sensory neurons. Periodically BHV-1 reactivates from latency, virus is shed, and consequently virus transmission occurs. Transcription from the latency-related (LR) gene is readily detected in neurons of trigeminal ganglia (TG) of calves or rabbits latently infected with BHV-1. Two micro-RNAs and a transcript encompassing a small open reading frame (ORF-E) located within the LR promoter can also be detected in TG of latently infected calves. A BHV-1 mutant that contains stop codons near the beginning of the first open reading frame (ORF2) within the …

Analysis Of The Genetic Structure Of Bithynia Tentaculata Snail Populations In Wisconsin And Minnesota, Sarah J. Whalen

All Graduate Theses, Dissertations, and Other Capstone Projects

In recent years, there have been tens of thousands of waterfowl mortalities in Wisconsin and Minnesota. An invasive species of snail, Bithynia tentaculata, is a host for the trematode parasites (Cyathocotyle bushiensis and Sphaeridiotrema globulus) that have caused these deaths. A microsatellite-enriched genomic library was detected using DNA from a B. tentaculata specimen from Lake Onalaska (Pool 7 of the Upper Mississippi River). Seven polymorphic microsatellite loci were used to genotype snails collected from Lake Butte des Morts, Shawano Lake, and Lake Onalaska in Wisconsin, as well as Lake Winnibigoshish in Minnesota. The genetic diversity of each population was measured …

Population Genetics Of Amphiuma Means And Siren Lacertina In Central Florida, Anna C. Deyle

USF Tampa Graduate Theses and Dissertations

Population structure can be defined as a difference in the frequencies of alleles among populations, and it is often caused by barriers to dispersal. I used mitochondrial DNA sequences to examine the population structure of two large, aquatic salamanders, Amphiuma means (the Two-Toed Amphiuma) and Siren lacertina (the Greater Siren), at two spatial scales in peninsular Florida. Both species appear to have similar life histories, including poor dry land dispersal capabilities, and I hypothesized that they would exhibit significant population structure at both broad and fine scales. Wetland loss and landscape fragmentation are certain to have caused decreases in abundance …

From Dna To Protein: A Study Of Genomic Instability Candidate Genes During Zebrafish Development, Kristine Griffett

USF Tampa Graduate Theses and Dissertations

The zebrafish, Danio rerio, is a type of freshwater minnow often used to model human diseases including cancer, anxiety and aging diseases. The overall biology of zebrafish is strikingly similar to that of humans, allowing these fish to be used for drug discovery and toxicology studies for preclinical trials. In this study, zebrafish embryos were used to identify and characterize several candidate genes within two known regions of genomic instability on chromosome 18 and chromosome 4. This fish that were used in this study had been previously classified as genomic instability (gin) mutants due to increased incidence of somatic mutation …

Efficient Replication Of Over 180 Genetic Associations With Self-Reported Medical Data, Joyce Y. Tung, Chuong B. Do, David A. Hinds, Amy K. Kiefer, J. Michael Macpherson, Arnab B. Chowdry, Uta Francke, Brian Naughton, Joanna Mountain, Anne Wojcicki, Nicholas Eriksson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for obtaining large amounts of medical information from a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we …

Circadian And Homeostatic Regulation Of Sleep In Cast/Eij And C57bl/6j Mice, Peng Jiang

University of Kentucky Doctoral Dissertations

Sleep is essential for mammals and possibly for all animals. Advancing our knowledge of sleep regulation is crucial for the development of interventions in sleep-related health and social problems. With this aim, this study utilizes laboratory mice to explore sleep regulatory mechanisms at behavioral, molecular, and genetic levels.

Sleep is regulated by the interaction of circadian and homeostatic processes. The circadian clock facilitates sleep to occur at a favorable time of the day. Normal mice, such as the C57BL/6J (B6) strain, sleep mostly during the day and initiate activities at dark onset. Here, I show mice of the CAST/EiJ (CAST) …

Post-Transcriptional Regulation Of Afp And Igm Genes, Lilia M. Turcios

University of Kentucky Doctoral Dissertations

Gene expression can be regulated at multiple steps once transcription is initiated. I have studied two different gene models, the α-Fetoprotein (AFP) and the immunoglobulin heavy chain (IgM) genes, to better understand post-transcriptional gene regulation mechanisms. The AFP gene is highly expressed during fetal liver development and dramatically repressed after birth. There is a mouse strain-specific difference between adult levels of AFP, with BALB/cJ mice expressing 10 to 20-fold higher levels compared to other mouse strains. BALB/cJ mice express low levels of Zhx2 and thus incompletely repress AFP. Despite differences in steady state AFP mRNA levels in the adult liver …

Complexity Through Recombination: From Chemistry To Biology, Niles Lehman, Carolina Diaz Arenas, Wesley A. White, Francis J. Schmidt

Chemistry Faculty Publications and Presentations

Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components of the system can now experience a new response to externally applied selection criteria, such that the evolutionary trajectory of the system is altered. In this work we explore the link between chemical and biological forms of recombination. We estimate how the net system complexity changes, through analysis of RNA-RNA recombination and by mathematical modeling. Our results …

A Study Of Genetic Structuring For Southern California Populations Of The Polychaete Nereis Grubei Using Inter Simple Sequence Repeats, Jignesh Anantray Chandarana

Student Theses and Dissertations

Members of the family Nereididae, including Nereis grubei, have a unique reproductive pattern among polychaetes- they reproduce a single time and possess a short larval period (4-5 days). This limits their potential to transmit their alleles to the next generation. Ocean currents also impact the magnitude and direction of gene flow. This study sampled 252 Nereis grubei from five coastal sites along southern California, two Channel Islands (Santa Cruz and Santa Catalina islands) and one central Mexico population using Inter Simple Sequence Repeats (ISSRs). Genetic diversity as measured by number of loci had a mean of 32, and expected heterozygosity …

Minimum Description Length Measures Of Evidence For Enrichment, Zhenyu Yang, David R. Bickel

COBRA Preprint Series

In order to functionally interpret differentially expressed genes or other discovered features, researchers seek to detect enrichment in the form of overrepresentation of discovered features associated with a biological process. Most enrichment methods treat the p-value as the measure of evidence using a statistical test such as the binomial test, Fisher's exact test or the hypergeometric test. However, the p-value is not interpretable as a measure of evidence apart from adjustments in light of the sample size. As a measure of evidence supporting one hypothesis over the other, the Bayes factor (BF) overcomes this drawback of the p-value but lacks …

Type Ii Protein Arginine Methyltransferase 5 (Prmt5) Is Required For Circadian Pperiod Determination In Arabidopsis Thaliana, Sunghyun Hong, Hae-Ryoung Song, Kerry Lutz, Randall A. Kerstetter, Todd P. Michael, C. Robertson Mcclung

Dartmouth Scholarship

Posttranslational modification is an important element in circadian clock function from cyanobacteria through plants and mammals. For example, a number of key clock components are phosphorylated and thereby marked for subsequent ubiquitination and degradation. Through forward genetic analysis we demonstrate that protein arginine methyltransferase 5 (PRMT5; At4g31120) is a critical determinant of circadian period in Arabidopsis. PRMT5 is coregulated with a set of 1,253 genes that shows alterations in phase of expression in response to entrainment to thermocycles versus photocycles in constant temperature. PRMT5 encodes a type II protein arginine methyltransferase that catalyzes the symmetric dimethylation of arginine residues (Rsme2). …

The Genomic Sequence And Annotation Of Bacteriophage Hk239, Alice Ann Wright

Masters Theses & Specialist Projects

Bacteriophages are viruses that infect bacteria and they are the most numerous biological entities on Earth. Temperate phage can adopt two different lifestyles. In the lytic lifestyle, a phage injects its genome into the host and a controlled developmental program ensues. The phage DNA is replicated, phage genes are expressed and new viral particles are assembled. Ultimately, the host cell lyses and the phage particles are released into the environment. In the lysogenic lifestyle, a phage integrates its genome into the host chromosome, creating a prophage. The cell containing the prophage is known as a lysogen. Most prophage genes are …