MOLECULAR BIOLOGY Different Facets MOLECULAR BIOLOGY Different Facets Anjali Priyadarshini, PhD Prerna Pandey, PhD Apple Academic Press Inc. Apple Academic Press Inc. 3333 Mistwell Crescent 9 Spinnaker Way Oakville, ON L6L 0A2 Canada Waretown, NJ 08758 USA © 2018 by Apple Academic Press, Inc. Exclusive worldwide distribution by CRC Press, a member of Taylor & Francis Group No claim to original U.S. Government works International Standard Book Number-13: 978-1-77188-641-3 (Hardcover) International Standard Book Number-13: 978-1-315-09927-9 (eBook) All rights reserved. No part of this work may be reprinted or reproduced or utilized in any form or by any electric, mechanical or other means, now known or hereafter invented, including pho- tocopying and recording, or in any information storage or retrieval system, without permission in writing from the publisher or its distributor, except in the case of brief excerpts or quotations for use in reviews or critical articles. 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Library and Archives Canada Cataloguing in Publication Priyadarshini, Anjali, author Molecular biology : different facets / Anjali Priyadarshini, PhD, Prerna Pandey, PhD. Includes bibliographical references and index. Issued in print and electronic formats. ISBN 978-1-77188-641-3 (hardcover).--ISBN 978-1-315-09927-9 (PDF) 1. Molecular biology. I. Pandey, Prerna, author II. Title. QH506.P75 2018 572.8 C2018-901454-7 C2018-901455-5 Library of Congress Cataloging-in-Publication Data Names: Priyadarshini, Anjali, author. | Pandey, Prerna, author. Title: Molecular biology : different facets / Anjali Priyadarshini, Prerna Pandey. Description: Toronto ; New Jersey : Apple Academic Press, 2018. | Includes bibliographical references and index. Identifiers: LCCN 2018008546 (print) | LCCN 2018009409 (ebook) | ISBN 9781315099279 (ebook) | ISBN 9781771886413 (hardcover : alk. paper) Subjects: | MESH: Biochemical Phenomena | Genetic Phenomena | Genetic Techniques | Molecular Biology Classification: LCC QH390 (ebook) | LCC QH390 (print) | NLM QU 34 | DDC 572.8/38--dc23 LC record available at https://lccn.loc.gov/2018008546 Apple Academic Press also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic format. For information about Apple Academic Press products, visit our website at www.appleacademicpress.com and the CRC Press website at www.crcpress.com ABOUT THE AUTHORS Anjali Priyadarshini, PhD Anjali Priyadarshini, PhD, is an Assistant Professor at Delhi University, India. Dr. Priyadarshini is a Council of Scientific and Industrial Research (CSIR) Government of India awardee. Her field of research and interest includes biotechnology and nanotechnology. Dr. Priyadarshini has published papers in peer-reviewed journals in the biomedical field. Prerna Pandey, PhD Prerna Pandey, PhD, is a biotechnologist with several years of wet lab research experience. She has worked at the International Center for Genetic Engineering and Biotechnology, New Delhi, India. Her PhD research involved isolation and molecular characterization of Geminiviruses, genome sequencing, gene annotation, and gene silencing using the RNA interference technology. She has also worked at Transasia Biomedicals and Advance Enzyme Technologies as a scientist. Dr. Pandey has published papers in peer-reviewed journals in the field and has submitted a number of annotated Geminiviral genome sequences to GenBank, including two novel ones. She has also completed editing and proofreading courses from the Society for Editors and Proofreaders (SfEP) and now works as a free- lance scientific writer and editor. Author Details: Dr. Anjali Priyadarshini, MSc, PhD Recipient of CSIR: JRF, SRF. Address: 74 B, Ayodhya Enclave, Sector 13 Rohini, New Delhi 85, India. Affiliation: Assistant Professor, SRM University, Sonipat, Haryana, India. E-mail: [email protected]; [email protected] Dr. Prerna Pandey, MSc, PhD Address: B 1403, Jasper, Hiranandani Estate, Thane 400607, Maharashtra, India. Affiliation: Freelance scientific writer and editor. Phone: +919167932133. E-mail: [email protected]; [email protected] CONTENTS List of Abbreviations .................................................................................... ix Preface .......................................................................................................xiii Introduction ..................................................................................................xv 1. Cell ................................................................................................................ 1 2. Genes and Genetic Code ........................................................................... 29 3. Molecular Biology of Microorganisms .................................................... 99 4. Plant Molecular Biology ......................................................................... 157 5. Genetic Manipulation by Recombinant DNA Technology .................. 219 6. Molecular Diagnostics............................................................................. 275 Index ................................................................................................................. 311 LIST OF ABBREVIATIONS AAV adeno-associated virus ABA abscisic acid ACC 1-aminocyclopropane-1-carboxylate aCGH array comparative genomic hybridization AD activation domain AdV adenovirus AFLP amplified fragment length polymorphism AOH absence of heterozygosity ARMS amplification refractory mutation system ARS autonomous replicating sequences BAC bacterial artificial chromosome BD DNA-binding domain cAMP cyclic adenosine mono phosphate CAP catabolite activator protein Cas CRISPR-associated Cas9 CRISPR-associated proteins CBF C-repeat binding factors CBLs calcineurin B-like proteins CEN centromeres CIAP calf-intestinal alkaline phosphatase CIPKs CBL-interacting protein kinases CKIs Cdk inhibitors co-IP co-immunoprecipitation CRISPR clustered regularly interspaced short palindromic repeats ddNTPs dideoxynucleotides DGGE denaturing gradient gel electrophoresis DHPLC denaturing high-performance liquid chromatography DNA deoxyribonucleic acid dNTP deoxyribonucleotides DREB dehydration-responsive element-binding proteins dsRNA double-stranded RNA EMS ethyl methanesulfonate ER endoplasmic reticulum x List of Abbreviations EST expressed sequence tag ET ethylene F-SSCP fluorescent SSCP FISH fluorescent in situ hybridization GE genetically engineered GEAC Genetic Engineering Approval Committee GGE gradient gel electrophoresis GINA Genetic Information Non-discrimination Act GM genetically modified gRNA guide RNA GST glutathione S-transferase GWAS genome-wide association studies HAD heteroduplex analyses HBV hepatitis B virus HCN hydrogen cyanide HDR homology-directed repair Hfr high frequency recombination HPV human papilloma virus HR homologous recombination IAA indole-3-acetic acid IF immunofluorescence IHF integration host factor IP immunoprecipitation IRES internal ribosome sites IRGSP International Rice Genome Sequencing Project IS insertion sequence ISO allele-specific oligonucleotide IVF in vitro fertilization IVSP in vitro synthesized protein assay JA jasmonic acid KSI ketosteroid isomerase LOH loss of heterozygosity LVs lentivirus MAPH multiplex amplifiable probe hybridization MAPKs mitogen-activated protein kinases MBP maltose-binding protein MCS multiple cloning site miRNAs microRNA List of Abbreviations xi MLPA multiplex ligation-dependent probe amplification mRNA messenger RNA mRNP mRNA protein NGS next-generation sequencing NHEJ nonhomologous end joining NMPs nucleoside monophosphates NPR nodule promoting rhizobacteria NTPs nucleoside triphosphates OLA oligonucleotide ligation assay PAM protospacer adjacent motif PCR polymerase chain reaction PEG polyethylene glycol PGD pre-implantation genetic diagnosis PGPR plant growth promoting rhizobacteria PHPR plant health promoting rhizobacteria PM personalized medicine PMF plant molecular farming PPi pyrophosphate PPV produced Plum pox virus PR plant resistance pRNA primer RNA PTGS posttranscriptional gene silencing PTM posttranslational modification PTT protein truncation test QTL quantitative trait locus RBS ribosome binding site RCM rolling circle mechanism RFLP restriction fragment length polymorphisms RISC RNA-induced silencing complex RNA ribonucleic acid RNAP RNA polymerase RNP ribonucleoprotein ROS reactive oxygen species rRNA ribosomal RNA SA salicylic acid sgRNA single-guide RNA shRNAs short hairpin RNAs SINEs short interspersed nuclear elements