The Role of the Metaphorical in Scientific Process Jun Xu A
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(Bsc Zoology and Microbiology) Concept of Introns and Exons
Unit-5 Molecular Biology (BSc Zoology and Microbiology) Concept of introns and exons Most of the portion of a gene in higher eukaryotes consists of noncoding DNA that interrupts the relatively short segments of coding DNA. The coding sequences are called exons. The noncoding sequences are called introns. Intron: An intron is a portion of a gene that does not code for amino acids An intron is any nucleotide sequence within a gene which is represented in the primary transcript of the gene, but not present in the final processed form. In other words, Introns are noncoding regions of an RNA transcript which are eliminated by splicing before translation. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are very large chunks of RNA within a messenger RNA molecule that interfere with the code of the exons. And these introns get removed from the RNA molecule to leave a string of exons attached to each other so that the appropriate amino acids can be encoded for. Introns are rare in genes of prokaryotes. #Look carefully at the diagram above, we have already discussed about the modification and processing of eukaryotic RNA. In which 5’ guanine cap and 3’poly A tail is added. So at that time, noncoding regions i.e. introns are removed. We hv done ths already. Ok Exon: The coding sequences are called Exon. An exon is the portion of a gene that codes for amino acids. In the cells of plants and animals, most gene sequences are broken up by one or more DNA sequences called introns. -
158273436.Pdf
4. , .;z.. ", ,:,. - 21sk , 44 "00,4 'WM 4 44 44 4 COLD SPRING HARBOR LABORATORY OF QUANTITATIVE BIOLOGY ESTABLISHED JULY 1, 1963 ANNUAL REPORT 1967 COLD SPRING HARBOR, LONG ISLAND, NEW YORK COLD SPRING HARBOR LABORATORY OF QUANTITATIVE BIOLOGY COLD SPRING HARBOR, LONG ISLAND,NEW YORK OFFICERS OF THE CORPORATION Chairman: Dr. H. Bentley Glass Secretary: Dr. Harry G. Albaum 1st Vice-Chairman: Mr. Walter H. Page Treasurer: Mr. Richard B. McAdoo 2nd Vice-Chairman: Assistant Secretary-Treasurer Dr. James D. Watson Mr. John B. Philips Laboratory Director: Dr. John Cairns BOARD OF TRUSTEES AND PARTICIPATING INSTITUTIONS Rockefeller University Albert Einstein College of Medicine Dr. Norton Zinder Dr. Harry Eagle Long Island Biological Association Duke University Mr. Walter H. Page Dr. Samson Gross Princeton University Brooklyn College of the City University of Dr. Arthur B. Pardee New York Dr. Harry G. Albaum New York University Medical Center The Public Health Research Institute of New York University of the City of New York, Inc. Dr. Alan W. Bernheimer Dr. Paul Margolin Sloan-Kettering Institute for Cancer Research Dr. Leo Wade INDIVIDUAL TRUSTEES Dr. H. Bentley Glass Mr. Richard B. McAdoo Dr. I. C. Gunsalus Dr. Lewis Sarett Dr. Alexander Hollaender Mr. Dudley W. Stoddard Dr. James D. Watson TABLE OF CONTENTS Board of Trustees 2 Director's Report 5-7 Year-round Research Activities 8-15 32nd Cold Spring Harbor Symposium "Antibodies" 16-17 Phycomyces Workshop 18-19 Summer Post-Graduate Training Courses 20-22 Undergraduate Research Participation -
Series DOI 10.1007/S12038-012-9186-6
Series DOI 10.1007/s12038-012-9186-6 What history tells us XXVII. A new life for allostery MICHEL MORANGE Centre Cavaillès, CIRPHLES USR 3308, Ecole normale supérieure, 29 rue d’Ulm, 75230 Paris Cedex 05, France (Fax, 33-144-323941; Email, [email protected]) 1. Introduction 2003), and on the extension of Darwinism to the molecular level (Kupiec 2009). The number of articles published on allostery has rapidly increased in recent years. Since the 1960s, the word ‘allostery’ 2. The origin of the allosteric model has always had different meanings. On the one hand, allostery simply describes the conformational changes of proteins (and The roots of allostery were in the discovery by H Edwin other macromolecules) following the binding of ligands. On Umbarger of the end-product inhibition of the first enzymes the other hand, allostery may explicitly refer to the theory of metabolic pathways (Umbarger 1956). Arthur Pardee and proposed by Jacques Monod, Jeffries Wyman and Jean-Pierre Jean-Pierre Changeux simultaneously confirmed these early Changeux in 1965 – also known as the MWC model, or model observations, and discovered the possibility of desensitizing of the concerted transition (Monod et al. 1965). In this model, proteins to the action of their regulators without altering their the allosteric change in conformation of proteins is not catalytic activities (Changeux 2003). More than the difference directly induced by the interaction of the proteins with their in chemical structures between the substrates and regulators, effectors, but results from the displacement of equilibrium desensitization was the main argument suggesting the exis- between conformational states. -
Discovery of the Secrets of Life Timeline
Discovery of the Secrets of Life Timeline: A Chronological Selection of Discoveries, Publications and Historical Notes Pertaining to the Development of Molecular Biology. Copyright 2010 Jeremy M. Norman. Date Discovery or Publication References Crystals of plant and animal products do not typically occur naturally. F. Lesk, Protein L. Hünefeld accidentally observes the first protein crystals— those of Structure, 36;Tanford 1840 hemoglobin—in a sample of dried menstrual blood pressed between glass & Reynolds, Nature’s plates. Hunefeld, Der Chemismus in der thierischen Organisation, Robots, 22.; Judson, Leipzig: Brockhaus, 1840, 158-63. 489 In his dissertation Louis Pasteur begins a series of “investigations into the relation between optical activity, crystalline structure, and chemical composition in organic compounds, particularly tartaric and paratartaric acids. This work focused attention on the relationship between optical activity and life, and provided much inspiration and several of the most 1847 HFN 1652; Lesk 36 important techniques for an entirely new approach to the study of chemical structure and composition. In essence, Pasteur opened the way to a consideration of the disposition of atoms in space.” (DSB) Pasteur, Thèses de Physique et de Chimie, Presentées à la Faculté des Sciences de Paris. Paris: Bachelier, 1847. Otto Funcke (1828-1879) publishes illustrations of crystalline 1853 hemoglobin of horse, humans and other species in his Atlas der G-M 684 physiologischen Chemie, Leizpig: W. Englemann, 1853. Charles Darwin and Alfred Russel Wallace publish the first exposition of the theory of natural selection. Darwin and Wallace, “On the Tendency of 1858 Species to Form Varieties, and on the Perpetuation of Varieties and G-M 219 Species by Natural Means of Selection,” J. -
Profile of Masayori Inouye PROFILE
PROFILE Profile of Masayori Inouye PROFILE Jennifer Viegas, Science Writer Masayori Inouye, a distinguished professor at the Rutgers Robert Wood Johnson Medical School, has cut a wide swath in biochemistry and molecular biology. His wide-ranging accomplishments include the determination of genetic codons in a protein and thus, for the first time, a partial DNA sequence of a gene, elucidation of the mechanism of biogenesis and assembly of membrane proteins, and creation of a protein-synthesizing bioreactor, among others. Many of his findings hold promise for application in bio- technology and clinical medicine. Inouye, who was elected to the National Academy of Sciences in 2019, is now trying to determine how genetic codons ’ Masayori Inouye. Image credit: Colin Germain (Rutgers University, first evolved. Inouye s Inaugural Article (1) presents Piscataway, NJ). his hypothesis that primordial proteins consisted of seven amino acids, which he is using to synthesize an enzyme that may have been fundamental to the First Partial DNA Sequence origin of life. During his postdoctoral stint, Inouye collaborated with Tsugita and phage geneticist George Streisinger to determine the codons of a gene, T4 phage lysozyme Education and World War II (2, 3). The approach involved comparing the amino Inouye was born in Port Arthur, Manchuria, which is acid sequences of several double frameshift mutants “ now known as the Lüshunkou District of Dalian, China. with those of the wild-type lysozyme. Inouye says, I His father, who held a PhD in organic chemistry, along established a method for large-scale purification by ” with his mother, moved to Port Arthur from Japan as designing and building a 600-liter culture tank. -
Chapter 19: RNA Splicing and Processing
Chapter 19: RNA Splicing and Processing Chapter Opener: © Laguna Design/Getty Images. CHAPTER OUTLINE 19.1 Introduction 19.2 The 5′ End of Eukaryotic mRNA Is Capped 19.3 Nuclear Splice Sites Are Short Sequences 19.4 Splice Sites Are Read in Pairs 19.5 Pre-mRNA Splicing Proceeds Through a Lariat 19.6 snRNAs Are Required for Splicing 19.7 Commitment of Pre-mRNA to the Splicing Pathway booksmedicos.org 19.8 The Spliceosome Assembly Pathway 19.9 An Alternative Spliceosome Uses Different snRNPs to Process the Minor Class of Introns 19.10 Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns 19.11 Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression 19.12 Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes 19.13 Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers 19.14 trans-Splicing Reactions Use Small RNAs 19.15 The 3′ Ends of mRNAs Are Generated by Cleavage and Polyadenylation 19.16 3′ mRNA End Processing Is Critical for Termination of Transcription 19.17 The 3′ End Formation of Histone mRNA Requires U7 snRNA 19.18 tRNA Splicing Involves Cutting and Rejoining in Separate Reactions 19.19 The Unfolded Protein Response Is Related to tRNA Splicing 19.20 Production of rRNA Requires Cleavage Events and Involves Small RNAs 19.1 Introduction booksmedicos.org RNA is a central player in gene expression. It was first characterized as an intermediate in protein synthesis, but since then many other RNAs that play structural or functional roles at various stages of gene expression have been discovered. -
Bruce N. Ames
Oral History Center University of California The Bancroft Library Berkeley, California Bruce N. Ames Bruce N. Ames: The Marriage of Biochemistry and Genetics at Caltech, the NIH, UC Berkeley, and CHORI, 1954–2018 University History Interviews conducted by Paul Burnett in 2019 and 2020 Copyright © 2021 by The Regents of the University of California Oral History Center, The Bancroft Library, University of California, Berkeley ii Since 1953 the Oral History Center of The Bancroft Library, formerly 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 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 recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is 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 Bruce N. Ames dated January 20, 2021. The manuscript is thereby made available for research purposes. -
The Role of Histone Modifications in the Regulation of Alternative Splicing During Epithelial-To-Mesenchymal Transition Alexandre Segelle
The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition Alexandre Segelle To cite this version: Alexandre Segelle. The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTT017. tel-03137009 HAL Id: tel-03137009 https://tel.archives-ouvertes.fr/tel-03137009 Submitted on 10 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Biologie Moléculaire et Cellulaire École doctorale Sciences Chimiques et Biologiques pour la Santé (ED CBS2 168) Unité de recherche UMR9002 CNRS-UM – Institut de Génétique Humaine (IGH) The role of histone modifications in the regulation of alternative splicing during the epithelial-to-mesenchymal transition Présentée par Alexandre Segelle Le 28 Septembre 2020 Sous la direction de Reini Fernandez de Luco Devant le jury composé de Anne-Marie MARTINEZ, -
Sequential Splicing of a Group II Twintron in the Marine Cyanobacterium Trichodesmium Received: 02 July 2015 Accepted: 20 October 2015 Ulrike Pfreundt & Wolfgang R
www.nature.com/scientificreports OPEN Sequential splicing of a group II twintron in the marine cyanobacterium Trichodesmium Received: 02 July 2015 Accepted: 20 October 2015 Ulrike Pfreundt & Wolfgang R. Hess Published: 18 November 2015 The marine cyanobacterium Trichodesmium is unusual in its genomic architecture as 40% of the genome is occupied by non-coding DNA. Although the majority of it is transcribed into RNA, it is not well understood why such a large non-coding genome fraction is maintained. Mobile genetic elements can contribute to genome expansion. Many bacteria harbor introns whereas twintrons, introns-in-introns, are rare and not known to interrupt protein-coding genes in bacteria. Here we show the sequential in vivo splicing of a 5400 nt long group II twintron interrupting a highly conserved gene that is associated with RNase HI in some cyanobacteria, but free-standing in others, including Trichodesmium erythraeum. We show that twintron splicing results in a putatively functional mRNA. The full genetic arrangement was found conserved in two geospatially distinct metagenomic datasets supporting its functional relevance. We further show that splicing of the inner intron yields the free intron as a true circle. This reaction requires the spliced exon reopening (SER) reaction to provide a free 5′ exon. The fact that Trichodesmium harbors a functional twintron fits in well with the high intron load of these genomes, and suggests peculiarities in its genetic machinery permitting such arrangements. The diazotrophic Trichodesmium is a tropical marine cyanobacterium of global importance1. Trichodesmium is unusual in its genomic architecture, characterized by the presence of a large non-coding fraction, encompassing about 40% of the total genome length, compared to the cyanobacterial aver- age of only 15%2,3. -
Understanding Pre-Mrna Dynamics in Single Spliceosome Complexes
Understanding Pre-mRNA Dynamics in Single Spliceosome Complexes by Ramya Krishnan A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Chemistry) in the University of Michigan 2013 Doctoral Committee: Professor Nils G. Walter, Chair Professor Hashim M. Al-Hashimi Professor Carol A. Fierke Assistant Professor Aaron C. Goldstrohm © Ramya Krishnan 2013 To amma, appa, Chikki, Girish and Abhi ii Acknowledgements First, I would like to thank my advisor, Dr. Nils Walter for taking me into his group and giving me the independence to pursue the science I wanted to. My days spent doing experiments have been fun alongside Mario Blanco and Matt Kahlscheuer, whom I have to thank for being great colleagues with a solid team spirit. I am honored to have worked in close collaboration with two great scientists in the field, Drs. John Abelson and Christine Guthrie. I would like to thank them for the insightful and encouraging discussions. For my time spent as a GSI, and for being a source of constant encouragement and support, I want to extend my wholehearted gratitude to Dr. Kathleen Nolta. Finally I would like to thank my friends in the Walter lab for maintaining a congenial environment, full of fun and life. Of course, none of this would be possible without the unconditional love and support from mom, dad and my sister. My mom has always encouraged me to excel in whatever I did, and my dad has set an example for the confident person I am today. I know this will make them proud. -
What Mad Pursuit BOOKS in the ALFRED P
What Mad Pursuit BOOKS IN THE ALFRED P. SLOAN FOUNDATION SERIES Disturbing the Universe by Freeman Dyson Advice to a Young Scientist by Peter Medawar The Youngest Science by Lewis Thomas Haphazard Reality by Hendrik B. G. Casimir In Search of Mind by Jerome Bruner A Slot Machine, a Broken Test Tube by S. E. Luria Enigmas of Chance by Mark Kac Rabi: Scientist and Citizen by John Rigden Alvarez: Adventures of a Physicist by Luis W. Alvarez Making Weapons, Talking Peace by Herbert F. York The Statue Within by François Jacob In Praise of Imperfection by Rita Levi-Montalcini Memoirs of an Unregulated Economist by George J. Stigler Astronomer by Chance by Bernard Lovell THIS BOOK IS PUBLISHED AS PART OF AN ALFRED P. SLOAN FOUNDATION PROGRAM What Mad Pursuit A Personal View of Scientific Discovery FRANCIS CRICK Library of Congress Cataloging-in-Publication Data Crick, Francis, 1916– What mad pursuit. (Alfred P. Sloan Foundation series) Includes index. 1. Crick, Francis, 1916– 2. Biologists—England—Biography. 3. Physicists—England—Biography. I. Title. II. Series. QH31.C85A3 1988 574.19’1’0924 [B] 88–47693 ISBN 0–465–09137–7 (cloth) ISBN-10: 0-465-09138-5 ISBN-13: 978-0-465-09138-6 (paper) eBook ISBN: 9780786725847 Published by BasicBooks, A Member of the Perseus Books Group Copyright © 1988 by Francis Crick Printed in the United States of America Designed by Vincent Torre Experience is the name everyone gives to their mistakes. —OSCAR WILDE Preface to the Series THE ALFRED P. SLOAN FOUNDATION has for many years had an interest in encouraging public understanding of science. -
Chapter 15 the Chromosomal Basis of Inheritance
CHAPTER 15 THE CHROMOSOMAL BASIS OF INHERITANCE OUTLINE I. Relating Mendelism to Chromosomes A. Mendelian inheritance has its physical basis in the behavior of chromosomes during sexual life cycles B. Morgan traced a gene to a specific chromosome: science as a process C. Linked genes tend to be inherited together because they are located on the same chromosome D. Independent assortment of chromosomes and crossing over produce genetic recombinants E. Geneticists can use recombination data to map a chromosome’s genetic loci II. Sex Chromosomes A. The chromosomal basis of sex varies with the organism B. Sex-linked genes have unique patterns of inheritance III. Errors and Exceptions to Chromosomal Inheritance A. Alterations of chromosome number or structure cause some genetic disorders B. The phenotypic effects of some genes depend on whether they were inherited from the mother or father C. Extranuclear genes exhibit a non-Mendelian pattern of inheritance OBJECTIVES After reading this chapter and attending lecture, the student should be able to: 1. Explain how the observations of cytologists and geneticists provided the basis for the chromosome theory of inheritance. 2. Describe the contributions that Thomas Hunt Morgan, Walter Sutton, and A.H. Sturtevant made to current understanding of chromosomal inheritance. 3. Explain why Drosophila melanogaster is a good experimental organism. 4. Define linkage and explain why linkage interferes with independent assortment. 5. Distinguish between parental and recombinant phenotypes. 6. Explain how crossing over can unlink genes. 7. Map a linear sequence of genes on a chromosome using given recombination frequencies from experimental crosses. 8. Explain what additional information cytological maps provide over crossover maps.