Genetics Commons^™

Detection Of Genes Influencing Chronic And Mendelian Disease Via Loss-Of-Function Variation, Alexander H. Li

Dissertations and Theses (Open Access)

A typical human exome harbors dozens of loss-of-function (LOF) variants predicted to severely disrupt or abolish gene function. These variants are enriched at the extremely rare end of the allele frequency spectrum (< 0.1%), suggesting purifying selection against these sites. However, most previous population-based sequencing studies have not included analysis of genotype-phenotype relationships with LOF variants. Thus, the contribution of LOF variation to health and disease within the general population remains largely uncharacterized.

Using whole exome sequence from 8,554 participants in the Atherosclerosis Risk in Communities (ARIC) study, we explored the impact of LOF variation on a broad spectrum of human phenotypes. First, we selected 20 common chronic disease risk factor phenotypes and performed gene-based association tests. Analysis of this sample verified two relationships in well-studied genes (PCSK9 and APOC3) and identified eight new loci. Novel relationships included …

Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction …

Topbp1 Governs Hematopoietic Stem/Progenitor Cells Survival In Zebrafish Definitive Hematopoiesis., Lei Gao, Dantong Li, Ke Ma, Wenjuan Zhang, Tao Xu, Wenge Zhu, +12 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

In vertebrate definitive hematopoiesis, nascent hematopoietic stem/progenitor cells (HSPCs) migrate to and reside in proliferative hematopoietic microenvironment for transitory expansion. In this process, well-established DNA damage response pathways are vital to resolve the replication stress, which is deleterious for genome stability and cell survival. However, the detailed mechanism on the response and repair of the replication stress-induced DNA damage during hematopoietic progenitor expansion remains elusive. Here we report that a novel zebrafish mutantcas003 with nonsense mutation in topbp1 gene encoding topoisomerase II β binding protein 1 (TopBP1) exhibits severe definitive hematopoiesis failure. Homozygous topbp1cas003 mutants manifest reduced number of HSPCs …

The Utilization Of Polymerase Chain Reaction, Dna Barcoding And Bioinformatics In Identifying Plant Species, Lindee J. Triplett, Ryan Foo, Ronald W. Strohmeyer (Mentor)

Idaho Conference on Undergraduate Research

Bioinformatics and DNA barcoding is a process used to identify plants, animals, and fungi. DNA barcoding in plants utilizes a key variable region in the genome, the RuBisCo large subunit (RbcL) on Chloroplast DNA. Once the DNA is extracted, Polymerase Chain Reaction (PCR) amplifies that region and that sample is sent off for sequencing. Bioinformatics and DNA barcoding helps taxonomists determine the sequence of the RbcL gene as well as obtain a unique barcode that can be used to identify plants. Several plant species from our local campus were sequenced and identified using the previously described methods.

Population Structure Of Central Stoneroller (Campostoma Anomalum) On The Ozark Plateau In Arkansas And Missouri, Mallory Jane Jeffers

Graduate Theses and Dissertations

Stream fishes on the Ozark Plateau have been influenced both by historic events (i.e. vicariance versus dispersal) and ecological forces (i.e. flow regime). To examine the role of these processes, genetic structure of Central Stoneroller (Campostoma anomalum), an ecologically important omnivorous minnow with a broad distribution and elevated abundance, was evaluated across populations in the White River drainage of the Ozark Plateau in Arkansas and Missouri. Fin clips of five to eight individuals were taken at each of 20 sites (N=138 individuals; average=6.9), selected so as to represent two different flow regimes: intermittently flashy (N=10 sites; N=73 individuals; average=7.3/ site) …

Genetic Variation And Species Distribution Of Subterranean Termites In The Southeastern U.S. Focusing On Family Structure And The Invasive Formosan Subterranean Termite, Mark Allan Janowiecki

Graduate Theses and Dissertations

This work applies molecular genetic tools to distinguish the identity and understand the biology of termites, particularly Reticulitermes Holmgren and Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) in the southeastern U.S. Termites are important economic pests costing billions of dollars annually to Americans but also are important wood decomposers in natural settings. Molecular tools are essential for species identification because of the morphological ambiguities among species. The cryptic nest structure of subterranean termites which prevents adequate sampling makes molecular genetic tools essential to examine an entire colony.

A molecular diagnostic technique was created to differentiate Coptotermes formosanus, an invasive species in the …

Role Of Metabolic Shifts In Protection From Mutation Damage: Characterizing Mitochondrial Membrane Potential In C. Elegans Gas-1 Mutants, Lauren S. Muñoz-Tremblay

PSU McNair Scholars Online Journal

Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via oxidative phosphorylation (OXPHOS) at mitochondrial electron transport chains (ETC). Proper ETC functioning relies on maintenance of the electrochemical gradient essential for energy production, known as mitochondrial membrane potential (ΔψM). The inner mitochondrial membrane is the site of the ETC and is most closely in contact with the enzymatic processes occurring within the mitochondrial matrix. Mutations affecting protein components of the ETC are especially troublesome for organelle health. ETC mutants commonly express altered ΔψM, as well as …

Cell Wall Mutants In Arabidopsis Thaliana, Christy Jane Moore

Theses and Dissertations

Plant cell walls are versatile structures, playing important roles in communication, defense, organization and support. The importance of each of these functions varies by cell type, with specialized cells often utilizing one or two functions more than others. Trichomes, or leaf hairs, and hypocotyl cells for instance, exhibit distinct cell wall characteristics. Trichomes have developed very thick cell walls with several raised structures, known as papillae, on their surfaces. It is believed that these cells function in defense against predators, making it difficult to crawl on the leaf surface, and in protection against ultra violet radiation, through refraction of light …

Mutations That Separate The Functions Of The Proofreading Subunit Of The Escherichia Coli Replicase, Zakiya Whatley, Kenneth N. Kreuzer

Biology Faculty Publications

The dnaQ gene of Escherichia coli encodes the Ɛ subunit of DNA polymerase III, which provides the 3' - 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of Ɛ leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, Ɛ plays a distinct role in replisome disassembly and/or processing of stalled replication …

Genetic Changes To A Transcriptional Silencer Element Confers Phenotypic Diversity Within And Between Drosophila Species, Winslow C. Johnson, Alison J. Ordway, Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz

Biology Faculty Publications

The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raúl Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra Obregon-Tito, Leslie Neal, Cecil M. Lewis, Jr.

Human Biology Open Access Pre-Prints

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we utilize ancient DNA extraction methods to investigate the origins of Avondale Burial Place through the use of well-preserved skeletal fragments from 20 individuals …

Mongolians In The Genetic Landscape Of Central Asia: Exploring The Genetic Relations Among Mongolians And Other World Populations, Jane E. Brissenden, Judith R. Kidd, Baigalmaa Evsanaa, Ariunaa Togtokh, Andrew J. Pakstis, Françoise Friedlaender, Kenneth K. Kidd, Janet M. Roscoe

Human Biology Open Access Pre-Prints

Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single …

Divergence Of Vertebrate And Insect Specific Toxin Genes Between Three Species Of Widow Spider, Shannon G. Kahn

Honors College Theses

The Brown widow spider, Latrodectus geometricus, is an introduced species to the southern United States (Brown 2008). The Brown widow is a member of the widow spider genus Latrodectus which includes the southern Black widow (L. mactans) and 29 other venomous species. All species of widow spiders produce venom which is used against both predator and prey. These venoms are composed of several different species-specific toxins, each encoded by a different gene (Graudins 2012). Previous research has shown that positive selection pressures affect the venom of snakes and snails, thus aiding in adaptive potential of the species …

Fisheries Management Paper No 274 - Finfish Resources Of The Peel-Harvey Estuary - Harvest Strategy 2015-2020 (Version 1.0), Department Of Fisheries, Western Australia

Fisheries Management Papers

WEST COAST ESTUARINE MANAGED FISHERY (AREA 2)

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes …

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

Development Of Genetic Goat And Hamster Models Of Atrial Fibrillation And Long Qt Syndrome; And Genetic Hamster Models Of Middle East Respiratory Syndrome, Dane A. Rasmussen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Atrial fibrillation (AF) and long QT syndrome (LQTS) are potentially lethal heart rhythm disorders that can be caused by mutations in the potassium channel gene KCNQ1. Middle East Respiratory Syndrome (MERS) is a viral infection with the potential to replicate the devastating effects of the SARS outbreak in 2003. All three of these diseases are in need of genetic animal models.

To address these needs, my thesis project focused on the development of genetic goat and hamster models of AF and LQTS, and genetic hamster models of MERS. Because of the goat’s similar organ size/physiology and the hamster’s similar lipid …

An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky

Biology Faculty Works

We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to determine whether uncharacterized short mutant lines are GA responsive. These data allow students to place the mutation in the GA signal transduction pathway. During weeks 2 and 3, plants are genotyped for Mendel's "le" mutation using a derived cleaved polymorphic sequences (dCAPS) PCR assay. This laboratory allows students to make a direct connection between …

Overexpression And Gene Profiling Of Asparagine Synthetase In Hybrid Poplar, Kristopher Murray

Renée Crown University Honors Thesis Projects - All

Plants with polysaccharide-rich secondary cell walls have great potential as a source of carbohydrates for bioethanol production. However, the presence of phenolic lignin inhibits the isolation of bioethanol precursors cellulose and hemicellulose from the secondary cell wall. Recent studies have linked nitrogen availability to secondary cell wall development and composition, making nitrogen metabolism genes an interesting target in the improvement of plant cell walls for biofuels production. Plants use a nitrogen assimilation pathway to convert inorganic nitrogen sources into organic sources, included amino acids, which play key roles in metabolism and cell wall development. Asparagine synthetase (AS), a key enzyme …

The Hippo Pathway Effector Yki Downregulates Wg Signaling To Promote Retinal Differentiation In The Drosophila Eye, Erika Lynn Wittkorn, Ankita Sarkar, Kristine Garcia, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

The evolutionarily conserved Hippo signaling pathway is known to regulate cell proliferation and maintain tissue homeostasis during development. We found that activation of Yorkie (Yki), the effector of the Hippo signaling pathway, causes separable effects on growth and differentiation of theDrosophila eye. We present evidence supporting a role for Yki in suppressing eye fate by downregulation of the core retinal determination genes. Other upstream regulators of the Hippo pathway mediate this effect of Yki on retinal differentiation. Here, we show that, in the developing eye, Yki can prevent retinal differentiation by blocking morphogenetic furrow (MF) progression and R8 specification. …

A Phylogenetic Analysis Of Dictyostelium Purpureum Based On Nuclear Rdna Sequences, Mahmoud Suliman

Graduate Theses and Dissertations

Dictyostelids (cellular slime molds) are eukaryotic microorganisms that have both unicellular and multicellular stages during their life cycle. In this study, a molecular phylogenetic analysis was conducted for isolates of one species (Dictyostelium purpureum) based DNA sequences of the ITS, 5.8S and SSU regions of nuclear rDNA. Moreover, a detailed morphological study was carried out using images obtained with both dissecting and compound microscopes. Mating experiments were carried out to assess macrocysts formation between each pair of isolates. The constructed molecular phylogenetic trees indicate that (1) D. purpureum isolates are more closely related to each other than to other species …