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bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted March 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. Title: Evolution of the D. melanogaster chromatin landscape and its associated proteins Authors and affiliations: Elise Parey(1, 2) and Anton Crombach*(1,3) (1) Center for Interdisciplinary Research in Biology (CIRB), Collè!e de France, C#RS, IN$ERM, P$& Uni(ersit) Paris, 75005 Paris, France (2) (c-rrent address) Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, P$& Uni(ersit) Paris, 75005 Paris, France (3) (current address) Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France Author for Correspondence (*): Anton Crombach, Center for Interdisciplinary Research in Biology (CIRB), Collè!e de France, CNRS, I#$ERM, P$& Uni(ersit) Paris, 75005 Paris, "rance, anton.crombach@colle!e0de-france.fr Keywords: phylogenomics, chromatin-associated proteins, chromatin types, histone modi1cations, centromere dri(e, D. melanogaster. 1 of 46 bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted March 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. Abstract (221w, max 250w) In the nucleus of eukaryotic cells, !enomic 3#A associates 4ith numerous protein comple5es and RNAs, forming the chromatin landscape. -
SCRIPPS DISCOVERS FALL 2010 Selective Inhibition of BMK1 Suppresses Tumor Growth
SC RIPPS DISC OVERS Accelerating Discoveries, Saving Lives A Newsletter for Philanthropists Published Quarterly by The Scripps Research Institute WINTER 2010 | VOL 7 | NO 1 California-Florida RESEARCH UPDATE Scripps Research Scientists Develop Molecular Test Providing a New Pathway for Identifying Obesity and Diabetes Drugs cientists at The Scripps Research Institute The Worm Institute for Research and Medicine have designed a new molecular test that at Scripps Research. Swill allow researchers to look for potential Janda and Amanda Garner, Ph.D., a research drugs targeting a human metabolic enzyme believed associate in his laboratory, described the new to stimulate the appetite and play a role in diabetes. approach—which may also prove useful for The new test, which the scientists call a simple investigating other enzymes involved in a assay, will allow researchers to look through variety of diseases—in an advance, online Early hundreds of thousands of compounds for those that Edition of the journal Angewandte Chemie on have potential to block the action of an enzyme September 15, 2010. known as ghrelin O-acyltransferase (GOAT). If Even though GOAT was only discovered drugs can be found that safely suppress the action recently, in 2008, scientists had speculated for of GOAT, they may help people who have clinical years that it had to exist. After all, its target (ghrelin, problems with appetite, obesity, and diabetes. or the “G” in the acronym GOAT) had been Professor Kim Janda “There hasn’t been a simple screen until now,” known for more than a decade. says Kim D. Janda, Ph.D., a professor in the Ghrelin, a small peptide hormone that is Departments of Chemistry and Immunology mainly produced in the stomach, signals hunger, and Microbial Science, member of The Skaggs typically before meals. -
Evolution of the D. Melanogaster Chromatin Landscape and Its Associated Proteins
bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted January 15, 2019. 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-NC-ND 4.0 International license. Title: Evolution of the D. melanogaster chromatin landscape and its associated proteins Authors and affiliations: Elise Parey(1, 2) and Anton Crombach*(1,3,4) (1) Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, 75005 Paris, France (2) (current address) Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France (3) (current address) Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France (4) Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, 69621 Villeurbanne, France Author for Correspondence (*): Anton Crombach, Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France, [email protected] 1 of 49 bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted January 15, 2019. 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-NC-ND 4.0 International license. Abstract (240w, max 250w) In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin- associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. -
IISER Pune Annual Report 2015-16 Chairperson Pune, India Prof
dm{f©H$ à{VdoXZ Annual Report 2015-16 ¼ããäÌãÓ¾ã ãä¶ã¹ã¥ã †Ìãâ Êãà¾ã „ÞÞã¦ã½ã ½ãÖ¦Ìã ‡ãŠñ †‡ãŠ †ñÔãñ Ìãõ—ãããä¶ã‡ãŠ ÔãâÔ©ãã¶ã ‡ãŠãè Ô©ãã¹ã¶ãã ãä•ãÔã½ãò ‚㦾ãã£ãìãä¶ã‡ãŠ ‚ã¶ãìÔãâ£ãã¶ã Ôããä֦㠂㣾ãã¹ã¶ã †Ìãâ ãäÍãàã¥ã ‡ãŠã ¹ãî¥ãùã Ôãñ †‡ãŠãè‡ãŠÀ¥ã Öãñý ãä•ã—ããÔãã ¦ã©ãã ÀÞã¶ã㦽ã‡ãЦãã Ôãñ ¾ãì§ãŠ ÔãÌããó§ã½ã Ôã½ãã‡ãŠÊã¶ã㦽ã‡ãŠ ‚㣾ãã¹ã¶ã ‡ãñŠ ½ã㣾ã½ã Ôãñ ½ããõãäÊã‡ãŠ ãäÌã—ãã¶ã ‡ãŠãñ ÀãñÞã‡ãŠ ºã¶ãã¶ããý ÊãÞããèÊãñ †Ìãâ Ôããè½ããÀãäÖ¦ã / ‚ãÔããè½ã ¹ã㟿ã‰ãŠ½ã ¦ã©ãã ‚ã¶ãìÔãâ£ãã¶ã ¹ããäÀ¾ããñ•ã¶ãã‚ããò ‡ãñŠ ½ã㣾ã½ã Ôãñ œãñ›ãè ‚ãã¾ãì ½ãò Öãè ‚ã¶ãìÔãâ£ãã¶ã àãñ¨ã ½ãò ¹ãÆÌãñÍãý Vision & Mission Establish scientific institution of the highest caliber where teaching and education are totally integrated with state-of-the- art research Make learning of basic sciences exciting through excellent integrative teaching driven by curiosity and creativity Entry into research at an early age through a flexible borderless curriculum and research projects Annual Report 2015-16 Governance Correct Citation Board of Governors IISER Pune Annual Report 2015-16 Chairperson Pune, India Prof. T.V. Ramakrishnan (till 03/12/2015) Emeritus Professor of Physics, DAE Homi Bhabha Professor, Department of Physics, Indian Institute of Science, Bengaluru Published by Dr. K. Venkataramanan (from 04/12/2015) Director and President (Engineering and Construction Projects), Dr. -
Commencement Program
Sunday, the Sixteenth of May, Two Thousand and Ten ten o’clock in the morning ~ wallace wade stadium Duke University Commencement ~ 2010 One Hundred Fifty-Eighth Commencement Notes on Academic Dress Academic dress had its origin in the Middle Ages. When the European universities were taking form in the thirteenth and fourteenth centuries, scholars were also clerics, and they adopted Mace and Chain of Office robes similar to those of their monastic orders. Caps were a necessity in drafty buildings, and Again at commencement, ceremonial use is copes or capes with hoods attached were made of two important insignia given to Duke needed for warmth. As the control of universities University in memory of Benjamin N. Duke. gradually passed from the church, academic Both the mace and chain of office are the gifts costume began to take on brighter hues and to of anonymous donors and of the Mary Duke employ varied patterns in cut and color of gown Biddle Foundation. They were designed and and type of headdress. executed by Professor Kurt J. Matzdorf of New The use of academic costume in the United Paltz, New York, and were dedicated and first States has been continuous since Colonial times, used at the inaugural ceremonies of President but a clear protocol did not emerge until an Sanford in 1970. intercollegiate commission in 1893 recommended The Mace, the symbol of authority of the a uniform code. In this country, the design of a University, is made of sterling silver throughout. gown varies with the degree held. The bachelor’s Significance of Colors It is thirty-seven inches long and weighs about gown is relatively simple with long pointed Colors indicating fields of eight pounds. -
The Drosophila Speciation Factor HMR Localizes to Genomic Insulator Sites
Aus dem Biomedizinischen Centrum der Ludwig-Maximilians-Universität München Medizinische Fakultät Lehrstuhl für Molekularbiologie Vorstand: Prof. Dr. rer. nat. Peter B. Becker The Drosophila speciation factor HMR localizes to genomic insulator sites Dissertation zum Erwerb des Doktorgrades der Naturwissenschaften an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München vorgelegt von Thomas Andreas Gerland aus München Jahr 2017 Gedruckt mit Genehmigung der Medizinischen Fakultät der Ludwig-Maximilians-Universität München Betreuer: Prof. Dr. rer. nat. Axel Imhof Zweitgutachter: Prof. Dr. André Brändli Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 14.11.2017 Eidesstattliche Versicherung Gerland, Thomas Andreas Ich erkläre hiermit an Eides statt, dass ich die vorliegende Dissertation mit dem Thema “The Drosophila speciation factor HMR localizes to genomic insulator sites” selbständig verfasst, mich außer der angegebenen keiner weiteren Hilfsmittel bedient und alle Erkenntnisse, die aus dem Schrifttum ganz oder annähernd übernommen sind, als solche kenntlich gemacht und nach ihrer Herkunft unter Bezeichnung der Fundstelle einzeln nachgewiesen habe. Ich erkläre des Weiteren, dass die hier vorgelegte Dissertation nicht in gleicher oder in ähnlicher Form bei einer anderen Stelle zur Erlangung eines akademischen Grades eingereicht wurde. _________________________________ _________________________________ Ort, Datum Unterschrift Doktorandin/Doktorand Wesentliche Teile dieser Arbeit sind veröffentlicht in: PLoS ONE, 2017 February 16, doi:10.1371/journal.pone.0171798 The Drosophila speciation factor HMR localizes to genomic insulator sites Gerland T. A., Sun B., Smialowski P., Lukacs A., Thomae A. W., Imhof A. Mitwirkungen: Bioinformatische und statistische Datenanalyse durchgeführt in Zusammenarbeit mit Bo Sun, Dr. Pawel Smialowski und Dr. Tobias Straub Next Generation Sequencing durchgeführt in Zusammenarbeit mit Dr. -
Structure, Function, and Evolution of a Signal-Regulated Enhancer
Structure, Function, and Evolution of a Signal-Regulated Enhancer by Christina Ione Swanson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cell and Developmental Biology) in the University of Michigan 2010 Doctoral Committee: Assistant Professor Scott E. Barolo, Chair Professor J. Douglas Engel Associate Professor Kenneth M. Cadigan Associate Professor Billy Tsai Assistant Professor Patricia J. Wittkopp To my family, for your truly unconditional love and support. And to Mike - the best thing that happened to me in grad school. ii TABLE OF CONTENTS DEDICATION .................................................................................................................. ii LIST OF FIGURES ............................................................................................................ v CHAPTER I: INTRODUCTION ....................................................................................... 1 What do enhancers look like? ................................................................................ 2 Mechanisms of enhancer function ......................................................................... 3 Enhancer structure and organization ...................................................................... 6 Unanswered questions in the field ....................................................................... 10 The D-Pax2 sparkling enhancer .......................................................................... 12 CHAPTER II: STRUCTURAL RULES -
Millennium Development Holes
www.nature.com/nature Vol 446 | Issue no. 7134 | 22 March 2007 Millennium development holes The political commitment to helping the developing world is failing to deliver on its promises. The problem is made worse by the questionable evaluation of progress. n 2000, 189 world leaders committed to eight Millennium Devel- few developing countries have any data for around 1990, the baseline opment Goals (MDGs), ranging from halving extreme poverty and year. It is impossible to estimate progress for most of the indicators Ihunger, and rolling back killer diseases such as AIDS and malaria, over less than five years, and sparse poverty data can only be reliably to providing universal primary education. The deadline of 2015 to compared over decades. To pretend that progress towards the 2015 achieve all these ambitious goals is now rapidly approaching. goals can be accurately and continually measured is false. As a rallying cry that has pushed development up the inter national Significant efforts are now being made to improve data collection. political agenda, the goals have been an indisputable success. They Meanwhile, UN agencies fill in the missing data points using ‘model- have also, for better or worse, conferred power and legitimacy on ling’ — in practice, a recipe for potentially misleading extrapolation interests within the international aid machine, in particular the and political tampering. United Nations (UN) and the World Bank. Indeed, the lack of data makes it impossible not only to track But the goals are ultimately political promises, and as such they progress, but also to assess the effectiveness of measures taken. -
Handbook of Child Psychology and Developmental Science
HANDBOOK OF CHILD PSYCHOLOGY AND DEVELOPMENTAL SCIENCE Seventh Edition Volume 2 Cognitive Processes Volume Editors LYNN S. LIBEN ULRICH MÜLLER Editor-in-Chief RICHARD M. LERNER Cover design: Wiley This book is printed on acid-free paper. Copyright © 2015 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, pho- tocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The adviceandstrategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. -
Special Supplement to the Bulletin of the American Meteorological Society Vol
J. Blunden, D. S. Arndt, and M. O. Baringer, Eds. Associate Eds. H. J. Diamond, A. J. Dolman, R. L. Fogt, B. D. Hall, M. Jeffries, J. M. Levy, J. M. Renwick, J. Richter-Menge, P. W. Thorne, L. A. Vincent, and K. M. Willett Special Supplement to the Bulletin of the American Meteorological Society Vol. 92, No. 6, June 2011 STATE OF THE CLIMATE IN 2010 STATE OF THE CLIMATE IN 2010 JUNE 2011 | S1 HOW TO CITE THIS DOCUMENT __________________________________________________________________________________________ Citing the complete report: Blunden, J., D. S. Arndt, and M. O. Baringer, Eds., 2011: State of the Climate in 2010. Bull. Amer. Meteor. Soc., 92 (6), S1 –S266. Citing a chapter (example): Fogt, R. L., Ed., 2011: Antarctica [in “State of the Climate in 2010”]. Bull. Amer. Meteor. Soc., 92 (6), S161 –S171. Citing a section (example): Wovrosh, A. J., S. Barreira, and R. L. Fogt, 2011: [Antarctica] Circulation [in “State of the Climate in 2010”]. Bull. Amer. Meteor. Soc., 92 (6), S161 –S163. S2 | JUNE 2011 Editor & Author Affiliations (ALPHABETICAL BY NAME ) Achberger, Christine, Earth Sciences Centre, University of Belward, Alan S., Global Environment Monitoring Unit, IES, EC Gothenburg, Gothenburg, Sweden Joint Research Centre, Ispra, Italy Ackerman, Steven A., CIMSS University of Wisconsin - Madi- Benedetti, Angela, European Centre for Medium-Range son, Madison, Wisconsin Weather Forecasts, Reading, United Kingdom Ahlstrøm, A., Geological Survey of Denmark and Greenland Berrisford, Paul, NCAS-Climate, European Centre for Medi- (GEUS), -
Breakthroughs of 2004 Endeavor VOLUME SEVEN NUMBER THREE Winter 2004/05
VOLUME SEVEN NUMBER THREE Endeavor Breakthroughs of 2004 Endeavor VOLUME SEVEN NUMBER THREE Winter 2004/05 This issue of Endeavor magazine features breakthroughs of 2004 at The Scripps Research Institute. Among many significant scientific milestones this year: the development of potential treatments for certain kinds of blindness that currently have no cure, significant findings on the molecular roots of alcoholism, innovative therapeu- tic strategies for heart attack and stroke, and a new hypothesis on the causes of Alzheimer’s and Parkinson’s diseases. featured page Research Offers New Hope in the Search to Treat Blindness: 6 Martin Friedlander Explores the Potential of Stem Cell Therapy for Restoring Vision Working to Solve the Alzheimer’s and Parkinson’s Puzzles: 10 Jeffery Kelly Proposes a New Explanation for Neurological Disorders Value Added: 14 David Cheresh Conducts Basic Research with Therapeutic Potential At the Roots of Alcoholism: 18 Cindy Ehlers Finds Molecular Answers to an Urgent Social Problem also President’s Introduction 1 Focus on Florida 22 Interview with Harry Orf 24 Financial Highlights 26 Letter from the Development Committee Chair 27 Development Report 29 ENDEAVOR IS A PUBLICATION OF THE SCRIPPS RESEARCH INSTITUTE Year in Review 2004 PRESIDENT’S INTRODUCTION Leadership is about many things: a passionate commitment to pursuing your goals, a vision for the future and an adherence to staying the course, a record of solid performance and achievement, a spirit of innovation and creativity. As an organization, I believe that The Scripps Research Institute has firmly established its leadership position in the international scientific community by remaining true to these basic tenets, by continuing to promulgate a record of outstanding scientific achievements, by attracting extraordinarily talented scientific faculty, staff, students, and board members, and by extending the reach of its capabilities by developing our major new initiative in Florida. -
The Physics of Negative Refraction and Transformation Optics
The Physics of Negative Refraction and Transformation Optics by Wei Hsiung Wee Thesis submitted for the degree of Doctor of Philosophy Condensed Matter Theory Group Department of Physics Imperial College London June 2011 Declaration of Originality This thesis is a result of the author’s own work. All other work contained within are appropriately referenced to the best of the author’s knowledge. Abstract Whilst optics is one of the oldest field in science, there are still aspects of electromag- netism that we are only beginning to uncover. For instance, it was demonstrated that materials with simultaneously negative permittivity and permeability exhibit certain exotic behavior; where familiar physical phenomena, such as refraction, are reversed. As such, these materials came to be known as negative refractive index materials (NRIM) and their collective properties as negative refraction. One of the most important and remarkable property of NRIM is perfect lensing - the ability to transport both supra and sub-wavelength optical information from one surface (ob- ject plane) to another (image plane), forming images with unprecedented resolution, beyond the diffraction limit. Perfect lensing itself is a consequence of deeper sym- metries in electromagnetism, encapsulated in the language of transformation optics - with which we have both a descriptive tool to unify diverse electromagnetic con- figuarations, as well as a prescriptive tool to design media which bends light at will. While, such transformation medium and NRIM have been demonstrably realised using metamaterials, several challenges remain, of which loss is the major challenge. It is therefore under this trinity of concepts: metamaterials, negative refraction and transformation optics that this thesis is presented.