Other Genetics and Genomics Commons^™

48770 (Gmr17e04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48770

• Id - GMR17E04
• Location 2L: 2428913..2432834
• Base pairs – 3921 bp

45833 (Gmr19d09), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45833

• Id - GMR19D09
• Location - 2L:2435128,2438996
• Base pairs – 3868 bp

48784 (Gmr17g08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48784

• Id - GMR 17G08
• Location 2L:2450278,2451074
• Base pairs – 796 bp

45437 (Gmr18b08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45437

• Id - GMR18B08
• Location - 2L:2455899,2457734
• Base pairs – 1835 bp

45442 (Gmr18d08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45442

• Id - GMR 18D08
• Location - 2L:2446783,2449086
• Base pairs – 2303 bp

49283 (Gmr19c03), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 49283

• Id - GMR19C03
• Location - 2L:2440970,2444735
• Base pairs – 3765 bp

Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez

Lawrence University Honors Projects

A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation …

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier and …

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Lewis Honors College Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Biology Faculty Articles

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

Erika Dyck. Facing Eugenics: Reproduction, Sterilization, And The Politics Of Choice, Garland E. Allen

Biology Faculty Research

[Book review of Erika Dyck. Facing Eugenics: Reproduction, Sterilization, and the Politics of Choice. Toronto: University of Toronto Press, 2013.]

Proof-Of-Concept Of Environmental Dna Tools For Atlantic Sturgeon Management, Jameson Hinkle

Theses and Dissertations

Abstract

The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the …

Assessing The Contributions Of Two Stocked Strains On A Minnesota-Wisconsin Border Water, Douglas Zentner

Journal of Earth and Life Science

Stocking has long been used as a management tool in the United States even though many of its effects remain cryptic. Past comparisons between stocked strains were generally based on the survival and growth rates of physically marked individuals. More recently the use of genetic markers to assess contributions of stocked individuals has been employed by fisheries managers. Using 13 microsatellite markers we assessed the contributions of two muskellunge (Esox masquinongy) strains (Wisconsin and Leech) stocked into the St. Louis River Estuary. Ancestry in the adult samples remained relatively constant with differences only observed between the 2008 and …

A Genetic Based Approach To Management And Stocking Of Muskellunge, Douglas Zentner

Journal of Earth and Life Science

Fish stocking has long been used as a management tool among fisheries biologists and continues to be met with popular public opinion. Despite perceived simplicity, the full effects of stocking remain cryptic for many fish populations. Stocking has frequently been used to maintain or establish successful muskellunge (Esox masquinongy) populations. Coupled with other management practices the Minnesota Department of Natural Resources (MNDNR) has established Minnesota as a premier muskellunge fishery. From 1958 to 2012 the MNDNR stocked three strains of muskellunge in Big Mantrap Lake, MN. The first from Shoepack Lake, MN (hereafter Shoepack-strain) was used until the …

The Complexities Of Female Mate Choice And Male Polymorphisms: Elucidating The Role Of Genetics, Age, And Mate-Choice Copying, Kasey D. Fowler-Finn, Laura Sullivan-Beckers, Amy M. Runck, Eileen A. Hebets

Eileen Hebets Publications

Genetic, life history, and environmental factors dictate patterns of variation in sexual traits within and across populations, and thus the action and outcome of sexual selection. This study explores patterns of inheritance, diet, age, and mate-choice copying on the expression of male sexual signals and associated female mate choice in a phenotypically diverse group of Schizocosa wolf spiders. Focal spiders exhibit one of two male phenotypes: ‘ornamented’ males possess large black brushes on their forelegs, and ‘non-ornamented’ males possess no brushes. Using a quantitative genetics breeding design in a mixed population of ornamented/non-ornamented males, we found a strong genetic basis …

The Role Of Angiotensinogen In Atherosclerosis And Obesity, Congqing Wu

Theses and Dissertations--Nutritional Sciences

Angiotensinogen is the only known precursor in the renin-angiotensin system, a hormonal system best known as an essential regulator of blood pressure and fluid homeostasis. Angiotensinogen is sequentially cleaved by renin and angiotensin- converting enzyme to generate angiotensin II. As the major effector peptide, angiotensin II mainly function through angiotensin type 1 receptor.

Angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and more recently renin inhibitors are widely known as the 3 classic renin-angiotensin system inhibitory drugs against hypertension and atherosclerosis. Here, we developed an array of regents to explore the effects of angiotensinogen inhibition. First, we demonstrated that genetic deficiency of …

Homeotic Gene Teashirt (Tsh) Has A Neuroprotective Function In Amyloid-Beta 42 Mediated Neurodegeneration, Michael T. Moran, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is a debilitating age related progressive neurodegenerative disorder characterized by the loss of cognition, and eventual death of the affected individual. One of the major causes of AD is the accumulation of Amyloid-beta 42 (Aβ42) polypeptides formed by the improper cleavage of amyloid precursor protein (APP) in the brain. These plaques disrupt normal cellular processes through oxidative stress and aberrant signaling resulting in the loss of synaptic activity and death of the neurons. However, the detailed genetic mechanism(s) responsible for this neurodegeneration still remain elusive.

Methodology/Principal Findings: We have generated a transgenic Drosophila eye model where …

Aaron Gillette , Eugenics And The Nature Nurture Debate In The Twentieth Century, Garland E. Allen

Biology Faculty Research

Aaron Gillette, Eugenics and the Nature–Nurture Debate in the Twentieth Century, Palgrave Studies in the History of Science and Technology [2007], digital reprint (New York, NY: Palgrave Macmillan, 2010), pp. ix, 239, index, £18.99, paperback, ISBN: 9780230108455. This book treats an important subject – the history of the nature–nurture debate (focused on the US but with references to European players and movements) – and its implications for current theories of evolutionary psychology.

Phylotranscriptomics To Bring The Understudied Into The Fold: Monophyletic Ostracoda, Fossil Placement, And Pancrustacean Phylogeny, Todd H. Oakley, Joanna M. Wolfe, Annie R. Lindgren, Alexander K. Zaharoff

Biology Faculty Publications and Presentations

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We …

Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks

Dissertations and Theses

Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …

Effects Of Reactive Oxygen Species On Life History Traits Of Caenorhabditis Elegans, Samson William Smith

Dissertations and Theses

Evolutionary life history theory predicts that tradeoffs among fitness-related phenotypes will occur as a result of resource limitations and/or physiological constraints. Such tradeoffs are defined as the cost(s) incurred on one component of fitness (e.g., reproduction) by the increased expression of another fitness-related trait (e.g., longevity). Only recently have researchers begun to investigate the mechanistic bases of life history tradeoffs. A recent proposal is that reactive oxygen species (ROS) have a central role in shaping life history traits and tradeoffs. Research on disparate animal taxa has highlighted strong correlations between oxidative stress resistance and fitness-related life history traits, for example. …

The Basis And Implications Of Genetic Counseling In Patient Testing Choice, Yanina Tovpeko

Renée Crown University Honors Thesis Projects - All

Perinatal genetic counseling is a health service provided to patients who carry risk factors for genetic abnormalities for their offspring. There are several non-invasive and invasive tests offered to patients in order to provide genetic information about possible disorders. The non-invasive screens calculate a percentage of risk relative to average population risk. If the non-invasive screens predict an elevated risk, a more invasive test can be offered to obtain definitive results about possible disorders in the pregnancy. The most commonly used invasive test is called amniocentesis and it carries a risk for pregnancy complications. After receiving abnormal results on the …

Dorsal Eye Selector Pannier (Pnr) Suppresses The Eye Fate To Define Dorsal Margin Of The Drosophila Eye, Sarah M. Oros, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Axial patterning is crucial for organogenesis. During Drosophila eye development, dorso-ventral (DV) axis determination is the first lineage restriction event. The eye primordium begins with a default ventral fate, on which the dorsal eye fate is established by expression of the GATA-1 transcription factor pannier (pnr). Earlier, it was suggested that loss of pnr function induces enlargement in the dorsal eye due to ectopic equator formation. Interestingly, we found that in addition to regulating DV patterning, pnr suppresses the eye fate by downregulating the core retinal determination genes eyes absent (eya), sine oculis (so) and dacshund (dac) to define the …