The Relationship Between Gene Network Structure and Expression Variation Among Individuals and Species
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Transcriptomic and Epigenomic Characterization of the Developing Bat Wing
ARTICLES OPEN Transcriptomic and epigenomic characterization of the developing bat wing Walter L Eckalbar1,2,9, Stephen A Schlebusch3,9, Mandy K Mason3, Zoe Gill3, Ash V Parker3, Betty M Booker1,2, Sierra Nishizaki1,2, Christiane Muswamba-Nday3, Elizabeth Terhune4,5, Kimberly A Nevonen4, Nadja Makki1,2, Tara Friedrich2,6, Julia E VanderMeer1,2, Katherine S Pollard2,6,7, Lucia Carbone4,8, Jeff D Wall2,7, Nicola Illing3 & Nadav Ahituv1,2 Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation. The order Chiroptera, commonly known as bats, is the only group of To characterize the genetic differences that underlie divergence in mammals to have evolved the capability of flight. -
Genetic and Molecular Control of Vertebrate Limb Development and Morphological Diversity
Genetic and Molecular Control of Vertebrate Limb Development and Morphological Diversity Lee Niswander HHMI/ U Colorado Health Sciences Center [email protected] Limb Development Chick Pro: experimental embryology, rapid functional analysis Con: relative lack of genetics Mouse Pro: genetics, genetic manipulation Con: in utero development Bat Pro: evo-devo studies, experimental embryology Con: relative lack of genetics relatively difficult to obtain Diversity of Diversity of Vertebrate Limbs Vertebrate Limbs A s= stylopod s Pr D z= zeugopod z a a= autopod P Modified from: Ridley M. Evolution, 2nd ed. A-P= Anterior-Posterior Blackwell Science 1996 Pr-D= Proximal-Distal P. Martin Int. J. Dev. Biol 1990 The thickened ectoderm at the distal rim of the limb bud is termed the apical ectodermal ridge. Laying down of the cartilage condensations E11.5 Martin, 1990 E12.5 Khokha et al. 2003 s z a Specification Elaboration of Patterning s z a 3 QuickTime™ and a 4 TIFF (LZW) decompressor 2 3 4 are needed to see this picture. 2 5 5 a z ssor ? ture. s pg pg S Z A Plzf/Gli3 dKO Barna et al. Fgf4/Fgf8 dKO Hoxa11/d11 dKO Sun et al. Nature (2002) Davis et al. Nature (1995) 1 Maria Barna AC D H Sin3A N-CoR/ SMRT POZ Zn+ Zn+ Zn+ Zn+ Zn+ Zn+ Zn+ Zn+ Zn+ PLZF (also known as ZFP 145) PLZF translocated to the Retinoic Acid Receptor Alpha (RARα)gene is associated with acute promyelocytic leukemia (APL) PLZF is a sequence specific DNA binding transcriptional repressor belonging to the POK (POZ and Kruppel) family of proteins that can remodel chromatin to a heterochromatic state. -
Biological Sciences
A Comprehensive Book on Environmentalism Table of Contents Chapter 1 - Introduction to Environmentalism Chapter 2 - Environmental Movement Chapter 3 - Conservation Movement Chapter 4 - Green Politics Chapter 5 - Environmental Movement in the United States Chapter 6 - Environmental Movement in New Zealand & Australia Chapter 7 - Free-Market Environmentalism Chapter 8 - Evangelical Environmentalism Chapter 9 -WT Timeline of History of Environmentalism _____________________ WORLD TECHNOLOGIES _____________________ A Comprehensive Book on Enzymes Table of Contents Chapter 1 - Introduction to Enzyme Chapter 2 - Cofactors Chapter 3 - Enzyme Kinetics Chapter 4 - Enzyme Inhibitor Chapter 5 - Enzymes Assay and Substrate WT _____________________ WORLD TECHNOLOGIES _____________________ A Comprehensive Introduction to Bioenergy Table of Contents Chapter 1 - Bioenergy Chapter 2 - Biomass Chapter 3 - Bioconversion of Biomass to Mixed Alcohol Fuels Chapter 4 - Thermal Depolymerization Chapter 5 - Wood Fuel Chapter 6 - Biomass Heating System Chapter 7 - Vegetable Oil Fuel Chapter 8 - Methanol Fuel Chapter 9 - Cellulosic Ethanol Chapter 10 - Butanol Fuel Chapter 11 - Algae Fuel Chapter 12 - Waste-to-energy and Renewable Fuels Chapter 13 WT- Food vs. Fuel _____________________ WORLD TECHNOLOGIES _____________________ A Comprehensive Introduction to Botany Table of Contents Chapter 1 - Botany Chapter 2 - History of Botany Chapter 3 - Paleobotany Chapter 4 - Flora Chapter 5 - Adventitiousness and Ampelography Chapter 6 - Chimera (Plant) and Evergreen Chapter -
University of Cape Town Faculty of Science Department of Molecular and Cell Biology
The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the Universityof of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University University of Cape Town Faculty of Science Department of Molecular and Cell Biology Limbs gone batty: Town The role of the anterior-posterior patterning signal, Sonic Hedgehog, in the Cape development of the unique bat limb. of Oorit Hockman Supervisors: Prof. Nicola II ling (MCI3) and Prof. David Jacobs (Zoology) University Research report Submitted in fulfillment of the requirements for the degree of Master of Science (Molecular Bio~gy) December 2007 "Twinkle, twinkle, little batl How I wonder what you're at! Up above the world you fly, Like a teatray in the sky." Town Cape of -The Mad Halter lewis Carroll's Alice's Adventures in Wonderland. University Table of Contents List of Figures and Tables IV Abbreviations vi Acknowledgements vii Abstract viii Chapter 1: Hypotheses for the molecular mechanisms of bat limb development 1.1. Introduction 1 1.2. The unique bat limb 1 1.3. Ecological hypotheses for bat wing development 3 1.4. The morphological development of the bat limb 3 1.5. The molecular mechanisms of limb development Town 5 1.5.1. Sonic Hedgehog and the patterning of the anterior-posterior axis 6 1.5.2. Activation and maintenance of the Sonic Hedgehog signal 8 1.5.3. -
Evolution and Development of Cetacean Appendages Across the Cetartiodactylan Land-To-Sea Transition
EVOLUTION AND DEVELOPMENT OF CETACEAN APPENDAGES A dissertation submitted to Kent State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Lisa Noelle Cooper December, 2009 Dissertation written by Lisa Noelle Cooper B.S., Montana State University, 1999 M.S., San Diego State University, 2004 Ph.D., Kent State University, 2009 Approved by _____________________________________, Chair, Doctoral Dissertation Committee J.G.M. Thewissen _____________________________________, Members, Doctoral Dissertation Committee Walter E. Horton, Jr. _____________________________________, Christopher Vinyard _____________________________________, Jeff Wenstrup Accepted by _____________________________________, Director, School of Biomedical Sciences Robert V. Dorman _____________________________________, Dean, College of Arts and Sciences Timothy Moerland ii TABLE OF CONTENTS LIST OF FIGURES ........................................................................................................................... v LIST OF TABLELS ......................................................................................................................... vii ACKNOWLEDGEMENTS .............................................................................................................. viii Chapters Page I INTRODUCTION ................................................................................................................ 1 The Eocene Raoellid Indohyus ........................................................................................ -
The Evolution and Development of Chiropteran Flight
University of New Hampshire University of New Hampshire Scholars' Repository Honors Theses and Capstones Student Scholarship Spring 2020 The Evolution and Development of Chiropteran Flight Emmaline Willis University of New Hampshire Follow this and additional works at: https://scholars.unh.edu/honors Part of the Developmental Biology Commons, Evolution Commons, Other Ecology and Evolutionary Biology Commons, and the Zoology Commons Recommended Citation Willis, Emmaline, "The Evolution and Development of Chiropteran Flight" (2020). Honors Theses and Capstones. 538. https://scholars.unh.edu/honors/538 This Senior Honors Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Honors Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. Willis 1 Emmaline Willis Zool Thesis Advisor- Bolker 9/25/19 The Evolution and Development of Chiropteran Flight Intro Flying is thought of as a reserved skill used by very few animals throughout history. These animals may be the birds outside your window, the pterodactyl in a children’s book, or the insects buzzing about on a hot day. There are also thousands of bats flapping around in the dark all around the world. Exploring the sky, bats are the only mammal capable of true powered flight (Gunnel and Simmons 2005). Bats are an extraordinarily diverse group of mammals. Chiroptera, the order name for this group of mammals, has over one thousand species (Hill, 2018). In fact, the number may be closer to 1,400 species (K. -
Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the Hoxd 2 Locus 3 4 5 Betty M
bioRxiv preprint doi: https://doi.org/10.1101/034017; this version posted December 9, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD 2 Locus 3 4 5 Betty M. Booker1,2¶, Tara Friedrich2,3¶, Mandy K. Mason4, Julia E. VanderMeer1,2, Jingjing 6 Zhao1,2,5, Walter L. Eckalbar1,2, Malcolm Logan7,8, Nicola Illing4, Katherine S. Pollard2,3,6*&, Nadav 7 Ahituv1,2,*& 8 9 1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 10 San Francisco, CA, USA 11 12 2Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA 13 14 3Gladstone Institutes, San Francisco, CA, USA 15 16 4Department of Molecular and Cell Biology, University of Cape Town, South Africa 17 18 5Key Laboratory of Advanced Control and Optimization for Chemical Processes of the Ministry 19 of Education, East China University of Science and Technology, Shanghai, China. 20 21 6Division of Biostatistics, University of California San Francisco, San Francisco, CA, USA 22 23 7Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, 24 London, United Kingdom 25 26 8Randall Division of Cell and Molecular Biophysics, King’s College London, Guys Campus, 27 London, United Kingdom 28 29 30 31 ¶These authors contributed equally to this work. 32 &These authors also contributed equally to this work. -
Morphometric Analyses of Embryonic Mouse Limbs Deficient In
MORPHOMETRIC ANALYSES OF EMBRYONIC MOUSE LIMBS DEFICIENT IN ECTODERMAL SMAD4 SIGNALING A thesis submitted to Kent State University in partial fulfillment of requirements for the degree in Master of Science By Kimberly Novak May 2012 Thesis written by Kimberly Novak Bachelor of Biology, Kent State University, 2010 M.S., Kent State University, 2012 Approved by ________________________ Dr. Y. Chen, Advisor ________________________James L. Blank, Chair, Department of Biological Sciences ________________________Dr. J. Stalvey, Dean, College of Arts and Science ii Table of Contents Table of Figures ...................................................................................................................... vi List of Tables...........................................................................................................................vii Abbreviations Used .............................................................................................................viii Acknowledgements .................................................................................................................x Introduction.............................................................................................................................. 1 Limb Development Background...................................................................................................1 The Apical Ectodermal Ridge, Proximal/Distal Patterning, and FGF8............................4 The Zone of Polarizing Activity, Anterior/Posterior patterning, and SHH....................6 -
Developmental, Ecological and Biological Drivers of Macroevolutionary Trajectories of Postcranial Morphological Diversification in Bats
Developmental, ecological and biological drivers of macroevolutionary trajectories of postcranial morphological diversification in bats Camilo López-Aguirre A thesis in fulfillment of the requirements for the degree of Doctor of Philosophy School of Biological, Earth and Environmental Sciences Faculty of Science August 2020 3 4 5 6 7 Table of Contents List of abbreviations............................................................................................... 12 Acknowledgments ................................................................................................. 13 List of figures ......................................................................................................... 16 List of tables .......................................................................................................... 20 Chapter 1: General introduction……………………………………………………………………………. 21 References .................................................................................................................... 24 Chapter 2: Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera)………………………………………………………………..44 Abstract .............................................................................................................................................. 44 Introduction ....................................................................................................................................... 45 Materials and methods ................................................................................................ -
University of Cape Town Rondebosch 7701
Characterization of Transcription Factors and LncRNAs Involved in the Development of the Bat Wing Zoe Gill Department of Molecular and Cellular Biology University of Cape Town Rondebosch 7701 Supervisor: Prof. Nicola Illing University of Cape Town February 2016 This dissertation was conducted in fulfilment of the requirements of a Masters of Science Degree in Molecular and Cellular Biology, MSc, at the University of Cape Town. The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Declaration I, Zoe Gill , know the meaning of plagiarism and declare that all of the work in the document, save for that which is properly acknowledged, is my own. Signature Removed 2 Abstract Mammals have evolved a vast myriad of limb morphologies adapted for a wide range of activities. One of the most remarkable evolutionary adaptations of a mammalian limb is that of the forelimb wing of a bat used for powered flight. This capability evolved ~ 51 Mya from its arboreal ancestor without any fossil record of intermediate forms. To reconstruct how this transition occurred, an Evolutionary Developmental approach can be applied to investigate altered mechanisms present in bat limb development. -
Bat Accelerated Regions Identify BOOKER Acc23nov2015epub26mar2016 GOLD Vor(CC
King’s Research Portal DOI: 10.1371/journal.pgen.1005738 Document Version Publisher's PDF, also known as Version of record Link to publication record in King's Research Portal Citation for published version (APA): Booker, B. M., Friedrich, T., Mason, M. K., VanderMeer, J. E., Zhao, J., Eckalbar, W. L., Logan, M., Illing, N., Pollard, K. S., & Ahituv, N. (2016). Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PL o S Genetics, 12(3), e1005738. https://doi.org/10.1371/journal.pgen.1005738 Citing this paper Please note that where the full-text provided on King's Research Portal is the Author Accepted Manuscript or Post-Print version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version for pagination, volume/issue, and date of publication details. And where the final published version is provided on the Research Portal, if citing you are again advised to check the publisher's website for any subsequent corrections. General rights Copyright and moral rights for the publications made accessible in the Research Portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognize and abide by the legal requirements associated with these rights. •Users may download and print one copy of any publication from the Research Portal for the purpose of private study or research. •You may not further distribute the material or use it for any profit-making activity or commercial gain •You may freely distribute the URL identifying the publication in the Research Portal Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. -
Bat Evolution, Ecology, and Conservation Bat Evolution, Ecology, and Conservation
Rick A. Adams · Scott C. Pedersen Editors Bat Evolution, Ecology, and Conservation Bat Evolution, Ecology, and Conservation Rick A. Adams • Scott C. Pedersen Editors Bat Evolution, Ecology, and Conservation Editors Rick A. Adams Scott C. Pedersen School of Biological Sciences Department of Biology and Microbiology University of Northern Colorado South Dakota State University Greeley , CO , USA Brookings , SD , USA ISBN 978-1-4614-7396-1 ISBN 978-1-4614-7397-8 (eBook) DOI 10.1007/978-1-4614-7397-8 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2013943698 © Springer Science+Business Media New York 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law.