Brief Contents
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Characterisation of Streptococcus Pneumoniae Opacity Phase Variation
Characterisation of Streptococcus pneumoniae Opacity Phase Variation Melissa Hui Chieh Chai, BBiomedSc (Hon), MSc A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy from the University of Adelaide February 2016 Research Centre for Infectious Diseases Department of Molecular and Cellular Biology The University of Adelaide Adelaide, S.A., Australia Table of Contents Chapter 1: INTRODUCTION ........................................................................... 1 1.1 The Pneumococcus ....................................................................................................... 1 1.1.1 Burden of Disease .................................................................................................. 1 1.1.2 Antimicrobial resistance ........................................................................................ 3 1.2 Pneumococcal Vaccines ............................................................................................... 4 1.3 Pathogenesis of Pneumococcal Disease ....................................................................... 7 1.3.1 Pneumococcal colonisation.................................................................................... 7 1.3.2 Progression to disease .......................................................................................... 10 1.4 S. pneumoniae Virulence Factors ............................................................................... 11 1.4.1 Pneumococcal capsule ........................................................................................ -
Mechanism of Nucleotide Flipping by Human Alkyladenine DNA Glycosylase
Mechanism of Nucleotide Flipping by Human Alkyladenine DNA Glycosylase by Jenna M. Hendershot A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2014 Doctoral Committee: Associate Professor Patrick J. O’Brien, Chair Professor Hashim M. Al-Hashimi, Duke University Professor Carol A. Fierke Associate Professor Bruce A. Palfey Associate Professor Raymond C. Trievel © Jenna M. Hendershot 2014 Table of Contents List of Figures.………………….…………………………………………………………………………………………… iii List of Tables.……………………………………………………………………………………………………………….. vi List of Appendices.…….....…………………………………………………………………………………………….. vii List of Abbreviations..………………………………………………………………………………………………….. viii Abstract...…………………………………………………………………………………………………………………….. xi Chapter (1) Introduction…………………………………………………………………………………………………. 1 (2) Substitution of Active Site Tyrosines with Tryptophan Alters the Free Energy for Nucleotide Flipping by Human Alkyladenine DNA Glycosylase.………..……. 18 (3) Critical Role of DNA Intercalation in Enzyme-Catalyzed Nucleotide Flipping… 58 (4) Evidence for Early Intercalation during the Search for DNA Damage by Human Alkyladenine DNA Glycosylase………………………………..………………………. 94 (5) Structure/Function Analysis of Intercalation and Nucleotide Flipping in Human Alkyladenine DNA Glycosylase….…………………………………………………….. 124 (6) Conclusions and Future Directions……….………………………………………………………. 155 ii List of Figures Figure 1.1: Nucleotide flipping……………………………………………………………………………………… -
Characterization of the Relationship Between Measles Virus Fusion
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2006-05-17 Characterization of the Relationship Between Measles Virus Fusion, Receptor Binding, and the Virus-Specific Interaction Between the Hemagglutinin and Fusion Glycoproteins: a Dissertation Elizabeth Ann Corey University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Amino Acids, Peptides, and Proteins Commons, Cells Commons, Chemical Actions and Uses Commons, Lipids Commons, and the Virus Diseases Commons Repository Citation Corey EA. (2006). Characterization of the Relationship Between Measles Virus Fusion, Receptor Binding, and the Virus-Specific Interaction Between the Hemagglutinin and Fusion Glycoproteins: a Dissertation. GSBS Dissertations and Theses. https://doi.org/10.13028/hg2y-0r35. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/221 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. CHARACTERIZATION OF THE RELATIONSHIP BETWEEN MEASLES VIRUS FUSION , RECEPTOR BINDING , AND THE VIRUS-SPECIFIC INTERACTION BETWEEN THE HEMAGGLUTININ AND FUSION GL YCOPROTEINS A Dissertation Presented Elizabeth Anne Corey Submitted to the Faculty of the University of Massachusetts Graduate -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Max Perutz (1914–2002)
PERSONAL NEWS NEWS Max Perutz (1914–2002) Max Perutz died on 6 February 2002. He Nobel Prize for Chemistry in 1962 with structure is more relevant now than ever won the Nobel Prize for Chemistry in his colleague and his first student John as we turn attention to the smallest 1962 after determining the molecular Kendrew for their work on the structure building blocks of life to make sense of structure of haemoglobin, the red protein of haemoglobin (Perutz) and myoglobin the human genome and mechanisms of in blood that carries oxygen from the (Kendrew). He was one of the greatest disease.’ lungs to the body tissues. Perutz attemp- ambassadors of science, scientific method Perutz described his work thus: ted to understand the riddle of life in the and philosophy. Apart from being a great ‘Between September 1936 and May 1937 structure of proteins and peptides. He scientist, he was a very kindly and Zwicky took 300 or more photographs in founded one of Britain’s most successful tolerant person who loved young people which he scanned between 5000 and research institutes, the Medical Research and was passionately committed towards 10,000 nebular images for new stars. Council Laboratory of Molecular Bio- societal problems, social justice and This led him to the discovery of one logy (LMB) in Cambridge. intellectual honesty. His passion was to supernova, revealing the final dramatic Max Perutz was born in Vienna in communicate science to the public and moment in the death of a star. Zwicky 1914. He came from a family of textile he continuously lectured to scientists could say, like Ferdinand in The Tempest manufacturers and went to the Theresium both young and old, in schools, colleges, when he had to hew wood: School, named after Empress Maria universities and research institutes. -
Hugh Huxley (1924-2013) Biophysicist Who Established the Mechanism of Muscle Contraction
COMMENT OBITUARY Hugh Huxley (1924-2013) Biophysicist who established the mechanism of muscle contraction. n a career spanning more than 65 years, salt solutions that extract myosin removed how calcium ions regulated cross-bridge Hugh Huxley achieved his lifelong only the optically dense A-bands (another interaction. In 1970, using intense X-ray ambition of understanding how eureka moment). Their 1953 Nature paper, synchrotron radiation, Huxley began time- Imuscles contract. together with earlier X-ray work, provided resolved studies of cross-bridge movement. Huxley, who died on 25 July after a heart the key evidence for the ‘sliding filament’ Huxley’s move in 1988 to Brandeis Univer- attack, was born in 1924 in Cheshire, UK, model of muscle contraction. sity in Waltham, Massachusetts, as director and studied physics at Christ’s College at the of the Rosenstiel Basic Medical Sciences University of Cambridge, UK. His education Research Center, gave him access to even was interrupted by service in the Royal Air more powerful X-ray sources, particularly Force from 1943 to 1947, testing height-to- at Argonne National Laboratory in Illinois. surface (H2S) radar — a ground-scanning Improved detectors with high-sensitivity system used by bomber aircraft. There, charge-coupled devices (used in digital he learned the importance of doing work cameras) enabled him to collect in milli- himself, and experimenting with electrical seconds data that would have taken hours ADDIS/PHOTOFUSION PETE and mechanical devices became a lifetime when he started out. With the atomic struc- passion. Huxley was able to fix a wildly tures of actin and the myosin cross-bridge, inaccurate version of H2S developed for east along with other evidence, he wrote in the Asia by switching from a voltage-controlled European Journal of Biochemistry in 2004 that display system, in which overheating was a he finally had direct evidence for the type of problem, to a current-controlled system. -
3-Methyladenine DNA Glycosylases: Structure, Function, and Biological Importance Michael D
Review articles 3-Methyladenine DNA glycosylases: structure, function, and biological importance Michael D. Wyatt,1 James M. Allan,1 Albert Y. Lau,2 Tom E. Ellenberger,2 and Leona D. Samson1* Summary The genome continuously suffers damage due to its reactivity with chemical and physical agents. Finding such damage in genomes (that can be several million to several billion nucleotide base pairs in size) is a seemingly daunting task. 3-Methyladenine DNA glycosylases can initiate the base excision repair (BER) of an extraordinarily wide range of substrate bases. The advantage of such broad substrate recognition is that these enzymes provide resistance to a wide variety of DNA damaging agents; however, under certain circumstances, the eclectic nature of these enzymes can confer some biological disadvantages. Solving the X-ray crystal struc- tures of two 3-methyladenine DNA glycosylases, and creating cells and animals altered for this activity, contributes to our understanding of their enzyme mechanism and how such enzymes influence the biological response of organisms to several different types of DNA damage. BioEssays 21:668–676, 1999. 1999 John Wiley & Sons, Inc. Introduction ately interpreted by DNA-processing enzymes. Unfortunately, DNA carries life’s genetic information encoded in the arrange- these bases are also chemically reactive, and the inevitable ment of bases along the length of the DNA molecule. Each base modifications produce a variety of biological outcomes, DNA base has a distinct chemical structure that is appropri- depending on how a cell recognizes and responds to the modification. Cellular DNA repair mechanisms target these inappropriate DNA structures, and play a vital role in maintain- 1Department of Cancer Cell Biology, Harvard School of Public Health, ing genomic integrity. -
Francis Crick Personal Papers
http://oac.cdlib.org/findaid/ark:/13030/kt1k40250c No online items Francis Crick Personal Papers Special Collections & Archives, UC San Diego Special Collections & Archives, UC San Diego Copyright 2007, 2016 9500 Gilman Drive La Jolla 92093-0175 [email protected] URL: http://libraries.ucsd.edu/collections/sca/index.html Francis Crick Personal Papers MSS 0660 1 Descriptive Summary Languages: English Contributing Institution: Special Collections & Archives, UC San Diego 9500 Gilman Drive La Jolla 92093-0175 Title: Francis Crick Personal Papers Creator: Crick, Francis Identifier/Call Number: MSS 0660 Physical Description: 14.6 Linear feet(32 archives boxes, 4 card file boxes, 2 oversize folders, 4 map case folders, and digital files) Physical Description: 2.04 Gigabytes Date (inclusive): 1935-2007 Abstract: Personal papers of British scientist and Nobel Prize winner Francis Harry Compton Crick, who co-discovered the helical structure of DNA with James D. Watson. The papers document Crick's family, social and personal life from 1938 until his death in 2004, and include letters from friends and professional colleagues, family members and organizations. The papers also contain photographs of Crick and his circle; notebooks and numerous appointment books (1946-2004); writings of Crick and others; film and television projects; miscellaneous certificates and awards; materials relating to his wife, Odile Crick; and collected memorabilia. Scope and Content of Collection Personal papers of Francis Crick, the British molecular biologist, biophysicist, neuroscientist, and Nobel Prize winner who co-discovered the helical structure of DNA with James D. Watson. The papers provide a glimpse of his social life and relationships with family, friends and colleagues. -
The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily
Clemson University TigerPrints All Dissertations Dissertations December 2017 The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily Jing Li Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Recommended Citation Li, Jing, "The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily" (2017). All Dissertations. 2546. https://tigerprints.clemson.edu/all_dissertations/2546 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. THE EVOLUTIONARY DIVERSITY OF URACIL DNA GLYCOSYLASE SUPERFAMILY A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Biochemistry and Molecular Biology by Jing Li December 2017 Accepted by: Dr. Weiguo Cao, Committee Chair Dr. Alex Feltus Dr. Cheryl Ingram-Smith Dr. Jeremy Tzeng ABSTRACT Uracil DNA glycosylase (UDG) is a crucial member in the base excision (BER) pathway that is able to specially recognize and cleave the deaminated DNA bases, including uracil (U), hypoxanthine (inosine, I), xanthine (X) and oxanine (O). Currently, based on the sequence similarity of 3 functional motifs, the UDG superfamily is divided into 6 families. Each family has evolved distinct substrate specificity and properties. In this thesis, I broadened the UDG superfamily by characterization of three new groups of enzymes. In chapter 2, we identified a new subgroup of enzyme in family 3 SMUG1 from Listeria Innocua. This newly found SMUG1-like enzyme has distinct catalytic residues and exhibits strong preference on single-stranded DNA substrates. -
The Annotated and Illustrated Double Helix
000_FrontMatter_DH_Double Helix 9/17/12 10:12 AM Page i s 000_FrontMatter_DH_Double Helix 9/17/12 10:12 AM Page ii Cambridge city center, early 1950s. Detail of a map published by W. Heffer & Sons. 000_FrontMatter_DH_Double Helix 9/17/12 10:12 AM Page iii JAMES D. WATSON THE ANNOTATED AND ILLUSTRATED DOUBLE HELIX Edited by Alexander Gann & Jan Witkowski SIMON & SCHUSTER New York London Toronto Sydney New Delhi 000_FrontMatter_DH_Double Helix 9/27/12 3:59 PM Page iv s Simon & Schuster 1230 Avenue of the Americas New York, NY 10020 Copyright © 1968 by James D. Watson Copyright renewed © 1996 by James D. Watson New annotations, illustrations, and appendixes Copyright © 2012 by Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. All rights reserved, including the right to reproduce this book or portions thereof in any form whatsoever. For information address Simon & Schuster Subsidiary Rights Department, 1230 Avenue of the Americas, New York, NY 10020 First Simon & Schuster hardcover edition November 2012 SIMON & SCHUSTER and colophon are registered trademarks of Simon & Schuster, Inc. For information about special discounts for bulk purchases, please contact Simon & Schuster Special Sales at 1-866-506-1949 or [email protected]. The Simon & Schuster Speakers Bureau can bring authors to your live event. For more information or to book an event, contact the Simon & Schuster Speakers Bureau at 1-866-248-3049 or visit our website at www.simonspeakers.com. Designed by Denise Weiss Manufactured in the United States of America 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging-in-Publication Data Watson, James D., date. -
What Makes a Great Lab?
COMMENT 1826 and acquired international renown. It attracted students from all over Europe and earned Liebig a reputation as a ‘chemist breeder’. His lab was an early example of the research and teaching establishments that SOURCE: LMB ARCHIVE LMB SOURCE: made the German universities the envy of many. It began as a single room, with a fire in the middle surrounded by work benches. Liebig’s work on the compositions of chemical substances and their reactions was outstand- ing, and his focus on agricultural, industrial and biological issues gave his research a highly topical flavour. He trained his protégés carefully, espe- cially in qualitative analysis. Students flocked to him, with the result that European chem- istry during the middle of the nineteenth century bore a distinctly Liebigian flavour as his students moved to influential positions elsewhere. The identification of state-of-the- art problems and the training of students to solve them characterize his achievements. Liebig’s initiative was widely adapted in the natural and biomedical sciences throughout Max Perutz, James Watson, John Kendrew and Francis Crick talk to a BBC presenter (centre) about the German university system. their Nobel prizes in 1962. Training was also part of the brief of physiologist Ivan Pavlov (1849–1936), but he brought his own organizational genius to bear on the ‘physiology factory’ that he masterminded in St Petersburg, Russia, What makes famously studying dogs. He adapted aspects of manufacturing to the production of sci- entific knowledge. Pavlov’s staff were among the first to specialize in different tasks: surgi- a great lab? cal, chemical, dog handling. -
Andrew F. Huxley 282
EDITORIAL ADVISORY COMMITTEE Marina Bentivoglio Larry F. Cahill Stanley Finger Duane E. Haines Louise H. Marshall Thomas A. Woolsey Larry R. Squire (Chairperson) The History of Neuroscience in Autobiography VOLUME 4 Edited by Larry R. Squire ELSEVIER ACADEMIC PRESS Amsterdam Boston Heidelberg London New York Oxford Paris San Diego San Francisco Singapore Sydney Tokyo This book is printed on acid-free paper. (~ Copyright 9 byThe 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 "Customer Support" and then "Obtaining Permissions." Academic Press An imprint of Elsevier 525 B Street, Suite 1900, San Diego, California 92101-4495, USA http ://www.academicpress.com Academic Press 84 Theobald's Road, London WC 1X 8RR, UK http://www.academicpress.com Library of Congress Catalog Card Number: 2003 111249 International Standard Book Number: 0-12-660246-8 PRINTED IN THE UNITED STATES OF AMERICA 04 05 06 07 08 9 8 7 6 5 4 3 2 1 Contents Per Andersen 2 Mary Bartlett Bunge 40 Jan Bures 74 Jean Pierre G. Changeux 116 William Maxwell (Max) Cowan 144 John E. Dowling 210 Oleh Hornykiewicz 240 Andrew F.