Plant Molecular Biology Manual PDF
Preview Plant Molecular Biology Manual
Springer-Science+Business Media, B.V. Dear Reader We would very much appreciate receiving your suggestions and criticisms for the Plant Molecular Biology Manual, 2 nd Edition. They will prove to be most helpful during our preparations for future supplements. Would you please answer the questions listed below, and send your comments with any further suggestions you may have, to lacco FUpsen at the abovementioned address. Alternatively you may send a fax to + 31 786392334 or e-mail, PLANT MOLECULAR BIOLOGY MANUAL PLANT MOLECULAR BIOLOGY MANUAL Second edition Edited by STANTON B. GELVIN Purdue University, West Lafayette, Indiana, USA ROBBERT A. SCHILPEROORT Leiden University, Leiden, The Netherlands Springer-Science+Business Media, B.V. Supplement 4 ISBN 978-94-011-7655-2 ISBN 978-94-011-4217-5 (eBook) DOI 10.1007/978-94-011-4217-5 Neither Kluwer Academic Publishers nor any person acting on its behalf is responsible for the use which might be made of the information contained herein. Printed on acid-free paper All Rights Reserved © 2000 by Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 2000 Softcover reprint of the hardcover 2nd edition 2000 No part of the material protected by this copyright notice may be reproduced or utilized in any fonn or by any means, electronic or mechanical, including photocopying, recording or by any infonnation storage and retrieval system, without written permission from the copyright owners. Plant Molecular Biology Manual, 2nd Edition Supplement 4, 2000 INSTRUCTIONS FOR SUPPLEMENT 4 Preliminary pages Pages I-XVIll should be replaced by new pages i-xxi. Section E Add after Chapter E2: Chapter E3: AH. Meijer, J. Schouten, P.B.E Ouwerkerk, J.H.C. Hoge/Yeast as versatile tool in transcription factor research Section H Add after Chapter H4: Chapter H5: S. Choi, R.A WingfThe construction of bacterial artificial chromosome (BAC) libraries Section N Insert Chapters NI-N3: Chapter Nl: L.A Lyznik, D. Peterson, Z.-Y. Zhao, X. Guan, B. Bowen, B. Drummond, G. St. Clair, L. Tagliani, C. BaszczynskilGene transfer mediated by site-specific recombination systems Chapter N2: C. Machida, H. Onouchi, E. Semiarti, T. Ishikawa, y. Macbida/Use of the R-RS site-specific recombi- nation system in plants Chapter N3: H. Albert, D.W. Ow/Cre-Iox directed integration of trans genes into the tobacco genome Section 0 Insert Chapter 01: C.J. Staiger, B.C. Gibbon, H. RenIPlant actin isola- tion and characterization Index Replace Contents SECTION A: IN VITRO METHODS OF GENE TRANSFER TO PLANT CELLS 1. PEG-mediated direct gene transfer and electroporation Roland Bilang, Andreas Kloti, Martin Schrott & Ingo Potrykus 2. Gene transfer to plants via particle bombardment Paul Christou ***3. Liposome-mediated transfer of YAC-DNA to tobacco cells Monique Van Wordragen, Roshani Shakya, Ruud Verkerk, Regis Peytavis, Ab Van Karnmen, Pirn Zabel SECTION B: AGROBACTERIUM-MEDIATED GENE TRANFER TO PLANT CELLS 1. Agrobacterium-mediated gene transfer to plant cells: Cointegrate and binary vectors Cindy R. Walkerpeach & J. Velten 2. Specialized vectors for gene tagging and expression studies Csaba Koncz, Norbert Martini, Laszl6 Szabados, Milan Hrouda, Andreas Bachmair & Jeff Schell 3. Agrobacterium molecular genetics Paul J.J. Hooykaas 4. Genetic manipulation of Agrobacterium tumefaciens strains to improve transformation of recalcitrant plant species Stanton B. Gelvin & Chang-Nong Liu 5. Transient expression assays using GUS constructs and ftuorometric detection for analysis of T-DNA transfer Linda A. Castle & Roy O. Morris 6. Agrobacterium inoculation techniques for plant tissues Nancy L. Mathis & Maud A. W. Hinchee ***7. Agrobacterium Germ-Line Transformation: Transformation of Arabidopsis without Tissue Culture Andrew F. Bent & Steven J. Clough *** Included in Supplement 3. x SECTION C: SELECTABLE AND SCREENABLE MARKERS FOR PLANT TRANSFORMATION 1. Antibiotic-resistance markers for plant tranformation M. van Montagu 2. Reporter genes for plants Luis Herrera-Estrella, Patricia Leon, Olof Olsson & Teemu H. Teeri 3. Opines as screenable markers for plant transformation Yves Dessaux & Annik Petit **4. Recombinant aequorin methods for measurement of intracellular calcium in plants H. Knight, A.J. Trewavas & M.R. Knight **5. GUS activity staining - a powerful tool in plant molecular biology Jeong Hee Lee & F. Sch6fil SECTION D: NUCLEIC ACID EXTRACTION FROM PLANT TISSUE 1. Extraction of total cellular DNA from plants, algae and fungi Scott O. Rogers & Arnold 1. Bendich 2. Isolation and characterization of nuclear scaffolds Gerald E. Hall, Jr. & Steven Spiker 3. Isolation of plant mitochondria and mitochondrial nucleic acids Sally A. Mackenzie 4. Isolation of chloroplasts and chloroplast DNA C.A. Price, Nourredine Hadjeb, Lee Newman & Ellen M. Raerdon 5. Isolation of total, poly (A) and poly somal RNA from plant tissues Katharina Pawlowski, Reinhard Kunze, Jacco de Vries & Ton Bisseling ***6. RNA Stability in Chloroplasts JOrg Nickelsen SECTION E: TRANSCRIPTION AND TRANS LAT ION SYSTEMS 1. Assay for gene expression using run-on transcription in isolated nuclei Imre E. Somssich ** Included in Supplement 2. *** Included in Supplement 3. xi 2. Preparation of an in vitro transcription system of plant origin, with methods and templates for assessing its fidelity Yukki Yamaguchi, Fujio Mukumoto, Hidemasa Imasehi & Ken-Ichi Yamazaki ****3. Yeast as versatile tool in transcription factor research A.H. Meijer, J. Schouten, P.B.F. Ouwerkerk, J.H.C. Hoge SECTION F: BLOTTING AND GENE DETECTION SYSTEMS 1. Southern, Northern and Western blot analysis Johan Memelink, Kathleen M.M. Swords, L. Andrew Staehelin & J. Harry C. Hoge 2. Screening of cDNA expression libraries with synthetic oligonucleotides for DNA binding proteins Wolfgang Werr, Barbel Uberlacker & Bethina Klinge 3. Non-radiative nucleic acid detection systems Susan J. Karcher 4. Polymerase chain reaction: gene detection, inverse PCR and genetic engineering 6Jerry L. Slightom, Roger F. Drong & Paula P. Chee **5. RNA differential display M.1. Laskowski **6. Expression analysis of multigene families by RFLP-coupled domain-directed differential display (RC4D) A. Fischer, G. Theissen & H. Saedler SECTION G: IN SITU HYBRIDIZATION AND IMMUNODETECTION 1. RNA in situ hybridization in plants Nicholas B. Duck 2. In situ hybridization to plant metaphase chromosomes using digoxigenin labeled nucleic acid sequences S. Hinnisdaels, I. Farbos, J. Del-Favero, J. Veuskens, M. Jacobs & A. Mouras *3. Light microscopic applications of immunocytochemistry K. Vandenbosch, D.J. Sherrier & D.A. Dreyer * Included in Supplement 1. ** Included in Supplement 2. **** Included in Supplement 4. xii **4. In-cell RT-PCR in a single, detached plant cell Ho-Hyung Woo 9 ***5. Preparation of extended DNA fibres for high resolution mapping by fluorescence in situ hybridization (FISH) Paul Fransz, Hans De Jong & Pim Zabel SECTION H: CLONING AND DETECTION OF DNA SEQUENCES FROM LARGE DNA MOLECULES 1. Methods for generating plant genomic libraries Marjory A. Snaed, Patricia L. Kretz & Jay M. Short 2. Construction of plant yeast artificial chromosome libraries Gregory B. Martin 3. Preparation of high molecular weight plant DNA and analysis by pulsed field gel electrophoresis Raymond A.J.J. van Daelen & Pim Zabel 4. Random amplified polymorphic DNA (RAPD) markers Anton Rafalski, Scott Tingey & John G.K. Williams ****5. The construction of bacterial artificial chromosome (BAC) libraries S. Choi, R.A. Wing SECTION I: PROTEIN-NUCLEIC ACID INTERACTION ANALYSES 1. Gel mobility shift assay Koji Mikarni, Hisabumi Takase & Masaki Iwabuchi 2. Optimization of DNAse I footprinting experiments Susan J. Martino-Catt & Steve A. Key 3. Analysis of plant chromatin and in vivo protein-DNA interactions Robert J. FerI & Anna-Lisa Paul 4. Expression and characterization of recombinant plant trans-acting factors Eric Lam & Lee Meisel SECTION J: SUBCELLULAR TARGETTING OF PROTEINS 1. In vitro import of proteins into chloroplasts Barry D. Bruce, Sharyn Perry, John Froehlich & Kenneth Keegstra ** Included in Supplement 2. *** Included in Supplement 3. **** Included in Supplement 4. xiii 2. In vitro targetting of proteins to mitochondria Marc A. Boutry, Didier Thomas & Fran\(ois Chaumont 3. Targetting of proteins to the vacuole James E. Dombrowski, Luis Gomez, Maarten J. Chrispeels & Natasha V. Raikhel 4. Visualizing protein import into the plant cell nucleus Vitaly Citovsky SECTION K: GENE TAGGING USING TRANSPOSONS 1. Gene tagging by endogenous transposons Wolf-Ekkehard L6nnig & Peter Huijser 2. Heterologous transposon tagging as a tool for the isolation of plant genes Erik A. van der Biezen, Mark J.J. van Haaren, Bert Overduin, H. John J. Nijkamp & Jacques Hille *3. T-DNA tagging in Arabidopsis thaliana: Cloning by gene disruption B. Schulz, M.J. Bennett, B.P. Dilkes & K.A. Feldman SECTION L: VIRAL MEDIA TED GENE TRANSFER * 1. High level gene expression in plants using RNA viruses as transient expression vectors C.M. Kearney, S.N. Chapman, T.H. Turpen & W.O. Dawson *2. Caulimovirus mediated gene transfer 1. Jupin & B. Gronenbom *3. Geminivirus mediated gene transfer D.M. Bisaro & G. Sunter ***4. Tobamovirus Transient Expression Vectors: Tools for Plant Biology and High-Level Expression of Foreign Proteins in Plants Gregory P. Pogue, John A. Lindbo, William O. Dawson, & Thomas H. Turpen * Included in Supplement 1. *** Included in Supplement 3.
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