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Department of Biology, Report to the President 2016-2017
Department of Biology Academic year 2016–2017 was exciting and productive for the Department of Biology. The department is considered one of the best biological science departments in the world. Our superb faculty members are leaders in biological research and education. Some of the news regarding our faculty, research, and educational programs is highlighted below. Faculty Count and Departures During AY2017, the Department of Biology had 56 faculty members: 44 full professors, eight associate professors, and four assistant professors. Research homes are distributed among Building 68, the Broad Institute, the Koch Institute for Integrative Cancer Research, the Picower Institute for Learning and Memory, and the Whitehead Institute for Biomedical Research. In addition to 56 primary faculty members, there were six faculty members with secondary appointments in Biology. These joint faculty members provide important connections to other departments, including Brain and Cognitive Sciences, Chemistry, Biological Engineering, and Civil and Environmental Engineering. We are saddened by the loss of Professor Susan Lindquist, who passed away in October 2016. Hidde Ploegh (Whitehead Institute) moved to Children’s Hospital in January 2017. Professor William (Chip) Quinn (Biology/Brain and Cognitive Sciences) retired in July 2016. Faculty Awards Department of Biology faculty members are widely recognized for their contributions to the field. Among our core faculty are three Nobel Laureates, 30 members of the National Academy of Sciences, 28 members of the American Academy of Arts and Sciences, 14 fellows of the American Association for the Advancement of Science, four recipients of the National Science Foundation National Medal of Science, and 15 Howard Hughes Medical Institute (HHMI) investigators. -
Discovery of DNA Structure and Function: Watson and Crick By: Leslie A
01/08/2018 Discovery of DNA Double Helix: Watson and Crick | Learn Science at Scitable NUCLEIC ACID STRUCTURE AND FUNCTION | Lead Editor: Bob Moss Discovery of DNA Structure and Function: Watson and Crick By: Leslie A. Pray, Ph.D. © 2008 Nature Education Citation: Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100 The landmark ideas of Watson and Crick relied heavily on the work of other scientists. What did the duo actually discover? Aa Aa Aa Many people believe that American biologist James Watson and English physicist Francis Crick discovered DNA in the 1950s. In reality, this is not the case. Rather, DNA was first identified in the late 1860s by Swiss chemist Friedrich Miescher. Then, in the decades following Miescher's discovery, other scientists--notably, Phoebus Levene and Erwin Chargaff--carried out a series of research efforts that revealed additional details about the DNA molecule, including its primary chemical components and the ways in which they joined with one another. Without the scientific foundation provided by these pioneers, Watson and Crick may never have reached their groundbreaking conclusion of 1953: that the DNA molecule exists in the form of a three-dimensional double helix. The First Piece of the Puzzle: Miescher Discovers DNA Although few people realize it, 1869 was a landmark year in genetic research, because it was the year in which Swiss physiological chemist Friedrich Miescher first identified what he called "nuclein" inside the nuclei of human white blood cells. (The term "nuclein" was later changed to "nucleic acid" and eventually to "deoxyribonucleic acid," or "DNA.") Miescher's plan was to isolate and characterize not the nuclein (which nobody at that time realized existed) but instead the protein components of leukocytes (white blood cells). -
Biochemistrystanford00kornrich.Pdf
University of California Berkeley Regional Oral History Office University of California The Bancroft Library Berkeley, California Program in the History of the Biosciences and Biotechnology Arthur Kornberg, M.D. BIOCHEMISTRY AT STANFORD, BIOTECHNOLOGY AT DNAX With an Introduction by Joshua Lederberg Interviews Conducted by Sally Smith Hughes, Ph.D. in 1997 Copyright 1998 by The Regents of the University of California Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the Nation. Oral history is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well- informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is indexed, bound with photographs and illustrative materials, and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. ************************************ All uses of this manuscript are covered by a legal agreement between The Regents of the University of California and Arthur Kornberg, M.D., dated June 18, 1997. The manuscript is thereby made available for research purposes. All literary rights in the manuscript, including the right to publish, are reserved to The Bancroft Library of the University of California, Berkeley. -
1 History for Canonical and Non-Canonical Structures of Nucleic Acids
1 1 History for Canonical and Non-canonical Structures of Nucleic Acids The main points of the learning: Understand canonical and non-canonical structures of nucleic acids and think of historical scientists in the research field of nucleic acids. 1.1 Introduction This book is to interpret the non-canonical structures and their stabilities of nucleic acids from the viewpoint of the chemistry and study their biological significances. There is more than 60 years’ history after the discovery of the double helix DNA structure by James Dewey Watson and Francis Harry Compton Crick in 1953, and chemical biology of nucleic acids is facing a new aspect today. Through this book, I expect that readers understand how the uncommon structure of nucleic acids became one of the common structures that fascinate us now. In this chapter, I introduce the history of nucleic acid structures and the perspective of research for non-canonical nucleic acid structures (see also Chapter 15). 1.2 History of Duplex The opening of the history of genetics was mainly done by three researchers. Charles Robert Darwin, who was a scientist of natural science, pioneered genetics. The proposition of genetic concept is indicated in his book On the Origin of Species published in 1859. He indicated the theory of biological evolution, which is the basic scientific hypothesis of natural diversity. In other words, he proposed biological evolution, which changed among individuals by adapting to the environment and be passed on to the next generation. However, that was still a primitive idea for the genetic concept. After that, Gregor Johann Mendel, who was a priest in Brno, Czech Republic, confirmed the mechanism of gene evolution by using “factor” inherited from parent to children using pea plant in 1865. -
DNA: the Timeline and Evidence of Discovery
1/19/2017 DNA: The Timeline and Evidence of Discovery Interactive Click and Learn (Ann Brokaw Rocky River High School) Introduction For almost a century, many scientists paved the way to the ultimate discovery of DNA and its double helix structure. Without the work of these pioneering scientists, Watson and Crick may never have made their ground-breaking double helix model, published in 1953. The knowledge of how genetic material is stored and copied in this molecule gave rise to a new way of looking at and manipulating biological processes, called molecular biology. The breakthrough changed the face of biology and our lives forever. Watch The Double Helix short film (approximately 15 minutes) – hyperlinked here. 1 1/19/2017 1865 The Garden Pea 1865 The Garden Pea In 1865, Gregor Mendel established the foundation of genetics by unraveling the basic principles of heredity, though his work would not be recognized as “revolutionary” until after his death. By studying the common garden pea plant, Mendel demonstrated the inheritance of “discrete units” and introduced the idea that the inheritance of these units from generation to generation follows particular patterns. These patterns are now referred to as the “Laws of Mendelian Inheritance.” 2 1/19/2017 1869 The Isolation of “Nuclein” 1869 Isolated Nuclein Friedrich Miescher, a Swiss researcher, noticed an unknown precipitate in his work with white blood cells. Upon isolating the material, he noted that it resisted protein-digesting enzymes. Why is it important that the material was not digested by the enzymes? Further work led him to the discovery that the substance contained carbon, hydrogen, nitrogen and large amounts of phosphorus with no sulfur. -
Structure of DNA &
Structure Of DNA & RNA By Himanshu Dev VMMC & SJH DNA DNA Deoxyribonucleic acid DNA - a polymer of deoxyribo- nucleotides. Usually double stranded. And have double-helix structure. found in chromosomes, mitochondria and chloroplasts. It acts as the genetic material in most of the organisms. Carries the genetic information A Few Key Events Led to the Discovery of the Structure of DNA DNA as an acidic substance present in nucleus was first identified by Friedrich Meischer in 1868. He named it as ‘Nuclein’. Friedrich Meischer In 1953 , James Watson and Francis Crick, described a very simple but famous Double Helix model for the structure of DNA. FRANCIS CRICK AND JAMES WATSON The scientific framework for their breakthrough was provided by other scientists including Linus Pauling Rosalind Franklin and Maurice Wilkins Erwin Chargaff Rosalind Franklin She worked in same laboratory as Maurice Wilkins. She study X-ray diffraction to study wet fibers of DNA. X-ray diffraction of wet DNA fibers The diffraction pattern is interpreted X Ray (using mathematical theory) Crystallography This can ultimately provide Rosalind information concerning the structure Franklin’s photo of the molecule She made marked advances in X-ray diffraction techniques with DNA The diffraction pattern she obtained suggested several structural features of DNA Helical More than one strand 10 base pairs per complete turn Rosalind Franklin Maurice Wilkins DNA Structure DNA structure is often divided into four different levels primary, secondary, tertiary -
Reflections on the Historiography of Molecular Biology
Reflections on the Historiography of Molecular Biology HORACE FREELAND JUDSON SURELY the time has come to stop applying the word revolution to the rise of new scientific research programmes. Our century has seen many upheavals in scientific ideas--so many and so varied that the notion of scientific revolution has been stretched out of shape and can no longer be made to cover the processes of change characteristic of most sciences these past hundred years. By general consent, two great research pro- grammes arising in this century stand om from the others. The first, of course, was the one in physics that began at the turn of the century with quantum theory and relativity and ran through the working out, by about 1930, of quantum mechanics in its relativistic form. The trans- formation in physics appears to be thoroughly documented. Memoirs and biographies of the physicists have been written. Interviewswith survivors have been recorded and transcribed. The history has been told at every level of detail and difficulty. The second great programme is the one in biology that had its origins in the mid-1930s and that by 1970 had reached, if not a conclusion, a kind of cadence--a pause to regroup. This is the transformation that created molecular biology and latter-day biochemistry. The writing of its history has only recently started and is beset with problems. Accounting for the rise of molecular biology began with brief, partial, fugitive essays by participants. Biographies have been written of two, of the less understood figures in the science, who died even as the field was ripening, Oswald Avery and Rosalind Franklin; other scientists have wri:tten their memoirs. -
Erwin Chargaff 1905–2002
NATIONAL ACADEMY OF SCIENCES ERWIN CHARGAFF 1 9 0 5 – 2 0 0 2 A Biographical Memoir by SEYMOUR S. COHEN with selected bibliography by ROBERT LEHMAN Any opinions expressed in this memoir are those of the authors and do not necessarily reflect the views of the National Academy of Sciences. Biographical Memoir 2010 NATIONAL ACADEMY OF SCIENCES WASHINGTON, D.C. ERWIN CHARGAFF August 11, 1905–June 20, 2002 BY SEYMOUR S . COHEN 1 AND ROBERT LEHMAN N 1944, AS VARIOUS ARMIES WERE planning to invade central IEurope, the recently naturalized U.S. citizen and Columbia University biochemist had learned of the report of O. T. Avery and his colleagues that the deoxyribonucleic acid (DNA) of a specific strain of pneumococcus constituted the genetically specific hereditary determinant of that bacterium. Almost alone among the scientists of the time, Chargaff accepted the unusual Avery report and concluded that genetic differ- ences among DNAs must be reflected in chemical differences among these substances. He was actually the first biochemist to reorganize his laboratory to test this hypothesis, which he went on to prove by 1949. His results and the subsequent work on the nature of DNA and heredity transformed biomedical research and training for the next fifty years at least, and established potentialities for the development of biology, which have created economic entities and opportunities, as well as major ethical and political controversies. Trained as an analytical chemist, Chargaff had never imagined that he would help to solve a major cytological problem. Reprinted with the permission from Proceedings of the American Philosophical Society (vol. -
Chemical Heritage Foundation Boris Magasanik
CHEMICAL HERITAGE FOUNDATION BORIS MAGASANIK Transcript of an interview Conducted by Sondra Schlesinger In three sessions between 1993 and 1995 This interview has been designated as Free Access. One may view, quote from, cite, or reproduce the oral history with the permission of CHF. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Chemical Heritage Foundation Oral History Program to credit CHF using the format below: Boris Magasanik, interview by Sondra Schlesinger, 1993-1995 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0186). Chemical Heritage Foundation Oral History Program 315 Chestnut Street Philadelphia, Pennsylvania 19106 The Chemical Heritage Foundation (CHF) serves the community of the chemical and molecular sciences, and the wider public, by treasuring the past, educating the present, and inspiring the future. CHF maintains a world-class collection of materials that document the history and heritage of the chemical and molecular sciences, technologies, and industries; encourages research in CHF collections; and carries out a program of outreach and interpretation in order to advance an understanding of the role of the chemical and molecular sciences, technologies, and industries in shaping society. BORIS MAGASANIK 1919 Born in Kharkoff, Russia, on December 19 Education 1941 B.S., biochemistry, City College of New York 1948 Ph.D., biochemistry, Columbia University Professional Experience Columbia University 1948-1949 Research Assistant, Department -
Samuel H. Barondes 1
EDITORIAL ADVISORY COMMITTEE Giovanni Berlucchi Mary B. Bunge Robert E. Burke Larry E Cahill Stanley Finger Bernice Grafstein Russell A. Johnson Ronald W. Oppenheim Thomas A. Woolsey (Chairperson) The History of Neuroscience in" Autob~ograp" by VOLUME 5 Edited by Larry R. Squire AMSTERDAM 9BOSTON 9HEIDELBERG 9LONDON NEW YORK 9OXFORD ~ PARIS 9SAN DIEGO SAN FRANCISCO 9SINGAPORE 9SYDNEY 9TOKYO ELSEVIER Academic Press is an imprint of Elsevier Elsevier Academic Press 30 Corporate Drive, Suite 400, Burlington, Massachusetts 01803, USA 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald's Road, London WC1X 8RR, UK This book is printed on acid-free paper. O Copyright 92006 by the Society for Neuroscience. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permissions may be sought directly from Elsevier's Science & Technology Rights Department in Oxford, UK: phone: (+44) 1865 843830, fax: (+44) 1865 853333, E-mail: [email protected]. You may also complete your request on-line via the Elsevier homepage (http://elsevier.com), by selecting "Support & Contact" then "Copyright and Permission" and then "Obtaining Permissions." Library of Congress Catalog Card Number: 2003 111249 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN 13:978-0-12-370514-3 ISBN 10:0-12-370514-2 For all information on all Elsevier Academic Press publications visit our Web site at www.books.elsevier.com Printed in the United States of America 06 07 08 09 10 11 9 8 7 6 5 4 3 2 1 Working together to grow libraries in developing countries www.elsevier.com ] ww.bookaid.org ] www.sabre.org ER BOOK AID ,~StbFC" " " =LSEVI lnt ..... -
Active Efflux of Tetracycline Encoded by Four Genetically Different
Proc. Natl. Acad. Sci. USA Vol. 77, No. 7, pp. 3974-3977, July 1980 Biochemistry Active efflux of tetracycline encoded by four genetically different tetracycline resistance determinants in Escherichia coli (everted membrane vesicles/tetracycline transport/transposon TnlO/plasmids) LAURA MCMURRY, RICHARD E. PETRUCCI, JR., AND STUART B. LEVY* Department of Molecular Biology and Microbiology and Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts 02111 Communicated by Boris Magasanik, April 21, 1980 ABSTRACT Tetracycline resistance encoded by four ge- at least partly reversed by energy inhibitors (11), which sug- netically different determinants residing on plasmids in Esch- gested that energy was required for the lowered tetracycline erichia coli was shown to be associated in each case with an accumulation. Using everted membrane vesicles, we now energy-dependent decrease in accumulation of the antibiotic containing any one of four ge- in whole cells in which resistance had been induced. The dif- demonstrate that resistant cells ferent class determinants examined were those on plasmids RP1 netically different plasmid-borne tetracycline resistance de- (class A), R222 (class B), R144 (class C), and RAI (class D). This terminants (5) possess an active efflux system for this antibi- decrease in accumulation was attributable to an active efflux, otic. because everted (inside-out) membrane vesicles made from tetracycline-induced E. coli cells containing any one of the four MATERIALS AND METHODS plasmids were shown to concentrate tetracycline by an active Bacterial Strains and Plasmids. The prototroph E. coli strain influx. This active uptake was not seen in inside-out vesicles from P. D. from sensitive cells or uninduced R222-containing cells. -
Transcriptional Repression at a Distance Through Exclusion of Activator Binding in Vivo
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 790–795, February 1997 Biochemistry Transcriptional repression at a distance through exclusion of activator binding in vivo MITSUHIRO SHIMIZU*†,WEISHI LI‡,HEISABURO SHINDO*, AND AARON P. MITCHELL†‡ *School of Pharmacy, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-03, Japan; and ‡Department of Microbiology and Institute of Cancer Research, Columbia University, New York, NY 10032 Communicated by Boris Magasanik, Massachusetts Institute of Technology, Cambridge, MA, December 3, 1996 (received for review October 8, 1996) ABSTRACT The yeast repressor Rme1p acts from distant Repression by Rme1p is unusual in that it is exerted over a binding sites to block transcription of the chromosomal IME1 considerable distance. The Rme1p binding sites lie over 1600 gene. Rme1p can also repress the heterologous CYC1 promoter bp upstream of IME1 RNA start sites and over 600 bp when Rme1p binding sites are placed 250–300 bp upstream of upstream of the IME1 upstream activation sequence (UAS) CYC1 transcriptional activator binding sites (UAS1 and region (refs. 16 and 17; see Fig. 1A). Other yeast repressors UAS2). Here, in vivo footprinting studies indicate that Rme1p generally act over smaller distances in chromosomal promoter acts over this distance by preventing the binding of the CYC1 regions (18–20). Repression depends upon both Rme1p bind- transcriptional activators to UAS1 and UAS2. Inhibition of ing sites and upon flanking chromosomal sequences. A min- activator binding by Rme1p has the same genetic require- imal region for repression has been defined through insertions ments as repression: both depend upon sequences flanking the of IME1 sequences upstream of a CYC1-lacZ reporter gene Rme1p binding sites and upon Rgr1p and Sin4p, two subunits (13).