Methods in plant biochemistry and molecular biology (gnv64)

METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY Edited by William V Dashek Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY Edited by William V Dashek Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business First published 1997 by CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 Reissued 2018 by CRC Press © 1997 by CRC Press, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S Government works This book contains information obtained from authentic and highly regarded sources Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint Except as permitted under U.S Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright com/) or contact the Copyright Clearance Center, Inc (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400 CCC is a not-for-profit organization that provides licenses and registration for a variety of users For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe Library of Congress Cataloging-in-Publication Data Plant biochemistry and molecular biology / edited by William V Dashek p.   cm Includes bibliographical references and index ISBN 0-8493-9480-5 Botanical chemistry—Laboratory manuals.  Plant molecular biology—laboratory manuals I Dashek, William V QK861.P53 1995 581.19’2—dc20 96-41196 A Library of Congress record exists under LC control number: 96041196 Publisher’s Note The publisher has gone to great lengths to ensure the quality of this reprint but points out that some imperfections in the original copies may be apparent Disclaimer The publisher has made every effort to trace copyright holders and welcomes correspondence from those they have been unable to contact ISBN 13: 978-1-315-89538-3 (hbk) ISBN 13: 978-1-351-07448-3 (ebk) Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Dedication Dr Dashek wishes to dedicate this manual to his children, Kristin Ann Simpson and Karin Ann Dashek, who patiently dealt with his need for years of scholarship He also thanks the following for his intellectual development: Dr W G Rosen, Dr Wm F Millington, Dr D T A Lamport, Dr J G Varner, Dr L Margulis, and Dr M W Schein Dr Dashek extends his gratitude to Ms Kim Chancey of the University of Georgia for her patience and thoughtful clerical assistance Dr Dashek is grateful to Terry L Highley, Project Director, Biodeterioration of Wood, U.S Department of Agriculture - Forest Service, Forest Products Laboratory, for the use of facilities and his encouragement He also expresses his appreciation to Ms K K Nelson of the Forest Products Laboratory for graphics Finally, this volume is dedicated to the late Dr J E Varner, who invented methods to advance our knowledge of plant biochemistry Acknowledgments The staff at CRC Press has been crucial in bringing this project to fruition My thanks go out to Paul Petralia, Senior Acquisitions Editor, for signing this project; to Cindy Carelli, Editorial Assistant, for her excellent organizational and follow-up skills; and to Carrie Unger, Project Editor, for bringing together the final product in a well-edited, well-presented format Index A Abies balsamea, ABP (auxin-binding proteins), 116, 119-129 Abscis1c acid (ABA), 154, 166, 178-179, 183, 353 Absorption spectroscopy, 255-256, 259-260, 266, 316 ACC ( 1-aminocyclopropane-1-carbox ylie acid), 154-155, 157-160, 166, 168-174 ACC oxidase, 154-155, 159-160, 434 ACC synthase, 154-155, 159-160 Acer rubrum, 192 Acer saccharinum, 192 Acer saccharum, 192 Acetate pathway, 190, 192 Acetic acid, 108, 110 Acetyl bromide, 206 207 Aciftuorfen (AF), 236 237 ACP (acyl carrier proteins), 338-344 Actin, 75 Acyl-ACP synthetase, 339-340 Acyl carrier proteins (ACP), 338-344 Adenine (A; Ade), 97-99, 135, 148 Adenosine (Ado), 136 Adenosine-5'-monophosphate (AMP), 137, 142-147 S-Adenosylmethionine (AdoMet; SAM), 154, 160, 166, 174 Ado (adenosine), 136 Adrenic acid, 90 Adsorption chromatography, 91, 267-269 AF (aciftuorfen), 236 237 Affinity chromatography, 53, 55 Agarose gel electrophoresis, 104, 378-381, 391 Agglutmation assays, 78, 80 Agrobacterium tumefaciens, 362-373, 401 407, 426 433 AIDS, 75 ALA (5-aminolevulinic acid), 230 233, 235-238 Aldohexoses, 43 Aldopentoses, 41 Aldoses, 29-30, 43 Alfalfa, 102, 282, 284, 379 Algae, 245-246, 260 Alkaloids, 185-188 Alkylaryl ether, 200 201, 208-209 Allose, 30 Almond, 315 Alternative terminal oxidase (AOX), 290 293, 297, 299-302 Althaea rosea, 182 Altrose, 30 Amberlite XAD resins, 268-269 1-Aminocyclopropane-1-carboxylic acid (ACC), 154-155, 157-160, 166, 168-174 5-Aminolevu1inic acid (ALA), 230 233, 235-238 Amino sugars, 32, 43 Ammonium sulfate fractionation, 53, 55, 127 AMP (adenosine-5'-monophosphate), 137, 142-147 Amylase, 317-318 Amylopectin, 34 Amylose, 34 Anion exchange chromatography, 56, 112, 252, 341-346 See also Diethylaminoethyl cellulose anion exchanger (DEAE) p-Anisidine HCl, 43 Antheraxanthin, 255 Anthocyanins, 218-221 Antibodies against cytokinin, 136, 140 ethylene detection using, 160 lignin analysis using, 203-204 monoclonal See Monoclonal antibodies overview of, 74-76 polyclonal See Polyclonal antibodies transgenic protein detection using, 373-374 Antigens, 74-76 443 444 Methods in Plant Biochemistry and Molecular Biology Antimycin A, 290, 301 Antirrhinum, 219, 416 Antirrhinum majus, 219 Antisense RNA delivery of, 427-429 ethylene analysis using, 160 overv1ew of, 424-425 plant transformation and, 424-425, 429-436 preparation of, 425-427 Antrodia carbonica, 15 AOX (alternative terminal oxidase), 290-293, 297, 299-302 Apigenin, 222-225 Apple, 155 Apricot, 315 Arabidopsis, 124, 127,427,429,431-434,436 Arabinans, 33, 35-36 Arabinogalactans, 33, 35 Arabinose, 30, 42, 316 Arabinoxylans, 33 Arachidic acid, 90 Arachidonic acid, 90 Armillaria mellea, 79 Ascorbic acid, 283 Asparagus, 33 Aspartate aminotransferase, 52 Aspergillus niger, 66-67, 320 Atherosclerosis, 222 Atropa belladonna, 187 Atropine, 186-187 Autoradiography of auxin-binding proteins, 121, 129 of cytokmins, 149 DNA manipulation and, 328, 372, 410-411 high resolution, of lipids, 338, 344 microautoradiography, 129 RFLP and, 378, 384-385 Auxin-binding proteins (ABP), 116, 119-129 Auxins, 116-124, 126-127, 154-155, 166, 353 4-Azido-2-chlorophenoxyacetic acid, 116-117 5-Azido-3-ch1orophenoxyacetic acid, 116-117 4-Azidoindole-3-acetic acid, 116-117 6-Azidoindole-3-acetic acid, 116-118 5-Azidoindole-3-acetic acid (5-N)AA), 116-129 5-Azidonaphtha1ene-1-acetic acid, 116, 118 B BA (benzyladenine), 140, 148-150, 166 Balsam fir 3-4 Barley, 250 Basidiomata, 14-20 Basidiosporogenesis, 13-20 BCA protein technique, 58, 63, 77 Beans, 399-400,408,414-416 Behenic acid, 90 Benzyladenine (BA), 140, 148-150, 166 Berberine, 186 Binary plasmids, 362-365 Bioassays cell growth, 276-277 of cytokinin, 137 electrode-based, 277 of elicitin, 272-277 laser microprobe, 281 leaf panel infiltration, 272, 274-276 Biomimetic dye-ligand assay, 65, 68 Bio-Rad protem assays, 62, 64 Bio-Rad resins, 55-57, 59, 61 Biotin, 283-284 Biphenyl, 200-201 Bisabolene, 183 Bjerkandera adusta, 24-25 Block samples, preparation of, 5-6 Blotting analyses dot, 78, 82 immunoblot, 434 northern, 148, 435 slot, 148 southern, 372, 378, 381, 407, 435 western, 77, 82-83, 254 Bradford technique, 58, 62 Bradyrhizobium japonicum, 124 Brassica napus, 344 Brassica oleracea, 167-168 Brassinosteroids, 154, 353 Bromphenol blue, 253 Brown-rot fungi See also Postia placenta detection of, 77-78, 84-85, 312, 320 lignin degradation by, 355 oxalate decarboxylene and, 63 production of, 13-14 Burnett's clonal selection and expansion theory, 75 sec-Butanol, 257-258 c Cabbage, 283 Cactorin, 270, 275 Cadinene, 183 Caffeic acid, 218-221, 223 Callose, 33 Callus growth assay, 147-148 Calonyction aculeatum, 182 Campesterol, 90 Camphor, 180 Camptotheca acummata, 187 CaMV (cauliflower mosaic virus), 363, 425 Canavalia aculeatum, 181 Canavalia gladiata, 181 Capillary electrophoresis, 111 Index Capsicein, 270 Carbohydrates, 29-46 Carbohydrolases, 309-320 Carbon column chromatography, 44 Carbon dioxide (C0 ) enrichment of air, 217, 222-225 Carbonic anhydrase, 52 Carboxymethylcellulose (CMC), 311-312 Carboxymethyl (CM) cation exchange, 252 Cardiolipin (CL), 338 Cardiovascular disease, 222 Carene, 180 Carnations, 166 [~-]Carotene, 255-256, 258 Carotenoids, 177, 244, 255-257, 259-260 Carotol, 183 Carpogenesis, 13-20 Carrot, 429 Carvone, 180 Caryophyllene, 183 Catalase, 52 Catechin, 190, 192 Cation exchange, 56, 65, 252 Cauliflower mosaic virus (CaMV), 363, 425 CBL (column boundary layer), 190-192, 195 CD (circular dichroism), 259-261 eDNA libraries, 349-352, 392-394, 400, 416, 418-419 Celite, 44 Cell fractionation, Cell growth bioassays, 276-277 Cell plates, 6, l Cells, structure of, 3-10 Cellulases, 310-313, 320, 414 Cellulose, 31, 33, 39, 107, 307, 310 Cell walls, 6, 9, 31-32, 40, 305-307, 313 Centoleic acid, 90 Ceratocystis coerulescens, 24 Cervonic acid, 90 Chalcone synthase, 220, 426, 434 Chaperonin, 400, 436 Chelidonic acid, 108 Chemotaxonomy, 208 Chickpeas, 154 Chitinase, 317 Chlamydomonas, 258 Chlide (chlorophyllide), 230-234, 237-238 Chloramine T method, 272-273 Chloramphenicol acetyltransferase, 424 Chlorophyll, 177, 229-238, 244, 249-251 Chlorophyll a (Chl a), 230, 232, 234, 244 245, 253, 255-260 Chlorophyll b (Chi b), 230, 232, 234, 245, 255-260 Chlorophyll c (Chl c), 244, 247, 253, 255-258 Chlorophylhde (Chlide), 230-234, 237-238 Chloroplasts, 245, 301, 338-339, 341, 344 345 445 Cholesterol, 89 Cholinesterase, 51 Chonodedron, 187 Chromatm, 6-7, Chromatofocusing, 339 Chromatography adsorption, 91, 267-269 affinity, 53, 55 anion exchange, 56, 112, 252, 341-346 carbon column, 44 droplet countercurrent, 194 extrusion column, 44 gas (GC) See Gas chromatography; Gas chromatography/mass spectrometry gel See Gel chromatography high-pressure liquid (HPLC) See High-pressure liquid chromatography hydrophobic interaction, 53, 56, 60 hydroxyapatite, 53, 56 immunoaffinity (lAC), 138, 140-142 ion exchange See Ion exchange chromatography liquid chromatography/mass spectrometry (LC/MS), 138 paper, 42-43, 109, 179, 187, 194, 233 PVPP, 139-140 silicic acid, 91, 338 thin-layer (TLC) See Thin-layer chromatography Chrysanthemum, 429 Chrysophytes, 245 Chymotrypsin, 52 CIE (crossed immunoelectrophoresis), 80-81, 254 Cinchora officinalis, 187 Cinnamic acid, 192 Cinnamomin, 270 Circular dichroism (CD), 259-261 Citramalate, 110 Citric acid, 108-110 Citrus aurantium, 217, 222, 224 225 Citrus reticulata, 182 Citrus sines is, 109 CL (cardiolipm), 338 Clematis, 174 Cloning of genes, 378, 424-425 Clupanodonic acid, 90 Clyoxylic acid, 108 CMC (carboxymethylcellulose), 311-312 erne (critical micelle concentration), 248 CoA (coenzyme A), 284, 344-345 Cobalamin, 284 Cocaine, 187 Codeine, 186 Coenzymes, 281, 284, 344-345 Coffee, 315 Colchicine, 186-187 446 Methods in Plant Biochemistry and Molecular Biology Colchium autumnole, 187 Colloidal gold techmque, 63, 84-86 Colorimetry of carbohydrates, 41-42 of carbohydrolases, 317-319 microplate assay, 318-319 of nucleic actds, 102, 104 of organic acids, 111 of proteins, 58, 61 Column boundary layer (CBL), 190-192, 195 Compartmentalization, 190-193, 196 Competition assay, 411-412 Complete plus yeast extract medium (CYM), 14 Conductometric titration, Ill Confocal laser microscopy, Comferyl alcohol, 200 202 Conjugated ACC, 158-160 Coomassie Blue, 253-254, 434 Copper block, 36 Coproporphyrin III (Copro III), 232, 234, 237 Coproporphyrinogen III (Coprogen III), 230 232 Com, 283, 313 Cotton, 312 p-Coumaryl alcohol, 200 201 COX (cytochrome oxidase), 290-292, 297, 299-300 CP/MAS NMR (cross polarization/magic angle spmning NMR), 211 Crataegus oxyacantha, 217, 222-224 Critical micelle concentration (cmc), 248 Cross-Bevan reaction, 202 Crossed immunoelectrophoresis (CIE), 80 81, 254 Cross polarization/magic angle spinning (CP/MAS) NMR, 211 Cryptogein, 270, 272, 274-275 Cucumber, 157, 236 Cup-plate assay, 320 Cupric oxide (CuO) oxidation of lignin, 207-208 Cyanide, 290, 301 Cylindrotheca, 258 Cylindrotheca fusiformis, 251, 253 CYM (complete plus yeast extract medium), 14 Cytisine, 186 Cytisus scoparius, 181 Cytochrome c, 120, 290 Cytochrome oxidase (COX), 290 292,297,299-300 Cytochrome pathway, 290 292, 300 302 Cytokinins, 127, 134-150, 154, 353 Cytosine (C), 97-99, 373 D DAD (diode array detection), 218, 220, 222 DAG (diacylglycerol), 341 Dahlia, 33 Dandehon, 282 Daucic acid, 108 DEAE (dtethylaminoethyl cellulose anion exchanger), 58, 144, 252, 339-340, 342, 345 Decapitation assay, 274 Decolorization of wood sapstain, 23-26 Dehydroascorbic acid, 283 Dehydrogenation polymers (DHP), 203-204 Densitometry, scanning laser, 149-150 Deoxycholate (DOC), 248-250 6-Deoxyhexose, 41-42 Deoxynucleotide triphosphates, 349 2-Deoxypentose, 41 Detergent solubilizatwn, 123-125, 244-245, 248-249, 259 Dextranase, 318 DGDG (digalactosyldiacylglycerol), 337, 341 DHP (dehydrogenation polymers), 203-204 DHZ (dihydrozeatin), 137, 140, 145-146 DHZR (dihydrozeatin ribostde), 140 Diacylglycerol (DAG), 341 Diadinoxanthin, 255, 258 Diaion HP-2MG resin, 268-269 Dtalysis, 53, 55 Dianthus, 166 Diarylpropane, 200-201 Diatoms, 245, 247-248, 250, 255 Diatoxanthin, 255, 258 2,4-Dichlorophenoxyacetic aetd, 116-117 Dictyosomes, Dideoxynucleoside, 105 Diethylaminoethyl cellulose anion exchanger (DEAE), 58, 144, 252, 339-340, 342, 345 Differential oxygen isotope discrimination, 290 Differential precipitation, 144 Differential pulse polarography, Ill Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, 210 Digalactosyldiacylglycerol (DGDG), 337, 341 Digitonm (DIG), 248 Dihydrozeatin (DHZ), 137, 140, 145-146 Dihydrozeatin riboside (DHZR; dZR), 140 Dinitrosalicylic acid (DNS) procedure, 310-311 Dinoflagellates, 245 Dinoxanthin, 255 Diode array detection (DAD), 218, 220, 222 4,6-Dioxoheptanoate, 231, 236-237 Diphenylamine colonmetry, 104 Dipheny1 ether, 200-201 2,2'-Dipyridy1 (DP), 231, 235-237 Distal necrosis assay, 270, 274-275 Distended vesicles, 6, DM (dodecylmaltoside), 249, 251 DNA amplification of, 387-394 447 Index antisense, 424-429, 436 assay of, 100-105, 379 binding proteins, 408-411, 415 eDNA, 349~352 fingerprinting, 378 footprinting, 390, 394, 416 hybndization of, 384 libraries, 349~352, 392~394, 400, 416, 418-419 overview of, 97~101 probes, 138, 392, 410-411 recombinant, 267 smgle-stranded, 349 transformation of, 362~365, 372, 427-433 DNA polymerase, 349, 389, 394 DNS procedure (dinitrosalicylic acid procedure), 310-311 DOC (deoxycholate), 248~250 Docosapentaenoic acid, 90 Dodecylmaltoside (DM), 249, 251 Dot blot immunoassay, 78, 82 DP (2,2'-Dipyridyl), 231, 235~237 Dragendorffs reagent, 188 Dreschslerin, 270 Droplet countercurrent chromatography, 194 Dunaliella salina, 246 Dyed-particle capture immunoassay, 86 Dye-labeled substrate assay, 312, 315~317, 319 dZR (dihydrozeatin riboside), 140 E Eadie-Hofstee plots, 52~53 Elaidic acid, 90 Electrode-based bioassays, 277 Electrodes, 277, 292~297, 301~302 Electron energy system imaging, Electron microscopy, 3-4, 83, 203 Electrophoresis agarose gel, 104, 378~381, 391 capillary, Ill crossed immunoelectrophoresis (CIE), 80-81, 254 FACE, 45-46 gel See Gel electrophoresis LDS-PAGE, 249~251, 253 mobility-shift assay (EMSA), 408-412, 416 rocket-immunoelectrophoresis (RIE), 254 SDS-PAGE See Sodium dodecyl sulfate polyacrylamide gel electrophoresis Electroporation, 415, 424, 427-429 Elicitins, 266-277 ELISA (enzyme-linked immunosorbent assay), 77~78, 81~82, 135~136, 168~169, 434 Ellagic acid, 191 Embedding medium (Spurrs's), 4~5 Emetine, 186-187 EMSA (electrophoresis mobility-shift assay), 408-412, 416 Endoglucanases, 126, 312~313 Endoplasmic reticulum (ER) auxins and, 126, 129 lipids m, 337, 341, 344 phaseolin and, 400 structure of, 6, Endopolysaccharidase, 311 Enzymatic methods, 111, 353 Enzyme-linked immunosorbent assay (ELISA), 77~78, 81~82, 135~136, 168~169, 434 Enzymes antisense technology and, 434 assay of, 49~53, Ill classification of, 49~50 inhibitors of, 53~54, 231, 236~237 kinetics of, 49~53 purification of, 53~67 Epimerases, 305 ER See Endoplasmic reticulum Erucic acid, 90 Erythrose, 30 Escherichia coli acyl carrier proteins from, 338~340 coenzymes m, 344, 346 DNA transfer from, 362~365, 389 elicitins from, 267 gene expression in, 400, 415, 418 RFLP probe libraries and, 382 ribosomes of, 324 Ethylene, 154 161, 166~170, 353,434 Ethylene-forming enzyme, 154 155, 159~160, 434 Exoglucanases, 312~313 Extrusion column chromatography, 44 F FACE (fiuorophore-assisted carbohydrate electrophoresis), 45-46 Famesol, 183 Fatty acid methyl esters (FAMES), 336-339, 344 Fatty acids, 89~90, 336~346 Fenchone, 180 Feverfew, 222 Filter paper assay, 343, 346 Filters, nitrocellulose, 418-419 Fiscus, 317 FITC (fluorescein isothiocyanate), 79 Fixation of tissue samples, Flammulina velutipes, 17, 66-67 Flavones, 218, 220-221 Flavonoids, 217~225 Flavonols, 218, 220-221 Florigen, 167~168 448 Methods in Plant Biochemistry and Molecular Biology Flower ptgments, 218-220 Fluorescein isothiocyanate (FITC), 79 Fluorescence spectroscopy, 187, 234, 255-256, 259-260 Fluorescent labeling, 45 Fluorography, 328 Folic acid, 283-284 Falin reagent, 193-194 Formic acid, 108, 110-111 Fourier-transform infrared spectroscopy (FTIR), 210 Fraser fir, Free-hydroxyl radical-generating systems, 24 26 Freeze-thaw transformation, 402-403, 405 French press, 246, 338 Freund's complete adjuvant, 75-76 Fructans, 31, 33 Fructofuranose, 31 Fructose, 31 FTIR (Fourier-transform infrared spectroscopy), 210 Fucose, 42 Fucoxanthm, 251, 253, 255, 258 Fumarase, 52 Fumaric acid, 108 Fungal glucan, 65 Fungal sapstain, 23-26 Furanose, 36 Furfural, 41 G Gabaculine, 231, 235-237 GACC ([y-]glutamylACC), 154, 159-160 Gadoleic acid, 90 GA (gibberellins), 166, 174, 178-179, 181-182, 353 Gaillardia grandifiora, 166 Galactans, 33 Galactoglucomannans, 33 Galactolipids, 89 Galactosamine, 32 Galactose, 30, 42, 316 Galactosidase, 52 Galacturonans, 33 Galacturonic acid, 32, 316 Gallic acid, 191-192 Gas chromatography (GC) of alkaloids, 185 of carbohydrates, 43-44 of cytokinins, 137 electron capture detection (GC/ECD), 179 flame ionization detection (GC/FID), 155-159, 336 of lignins, 208 of lipids, 91, 336 mass spectrometry See Gas chromatography/ mass spectrometry of organic acids, 109-111 of plant hormones, 353 of terpenoids, 179 Gas chromatography/mass spectrometry (GC/MS) of ACC, 158 of alkaloids, 185, 187 of cytokinins, 135, 137-138, 145-147 of IAA, 169 of lignins, 209-210 of lipids, 91, 337 of organic acids, 109 of plant hormones, 353 pyrolysis, 209-210 of terpenoids, 179 Gas liquid chromatography (GLC) See Gas chromatography G-box, 411-413,414-417 GC See Gas chromatography GC/ECD (gas chromatography/electron capture detection), 179 GC/FID (gas chromatography/flame ionization detector), 155-159, 336 GC/MS See Gas chromatography/mass spectrometry Gel chromatography of elicitins, 267 of fatty acids, 342 of organic acids, 111 of pigment-protein complexes, 249, 252 protein purification by, 53, 55, 82 Gel diffusion techniques, 78-79 Gel electrophoresis electrophoresis mobility-shift assay (EMSA), 408-412, 416 of elicitins, 268, 270 271 LDS-PAGE, 249-251, 253 of nucleic acids, 102, 105 ofRFLP, 378 SDS-PAGE See Sodium dodecyl sulfate polyacrylamide gel electrophoresis Gel filtration See Gel chromatography Gene induction by cytokinin, 148-150 Gene isolation, 392-393 Gene "knock-outs," 424 Geraniol, 180 Gibberella fujikuroi, 181-182 Gibberellic acid, 166 Gibberellins (GA), 166, 174, 178-179, 181-182, 353 Glass fiber disc assay, 343 Glassy carbon electrode, 293-294, 296 GLC (gas liquid chromatography) See Gas chromatography Globulins, 400 Gloeophyllum trabeum, 16, 320 Index 449 Glucagon, 345 317 Glucans, 33, 305, 317 Glucan synthetase, 305-306 Glucomannans, 33, 307 Glucosamme, 32 Glucose, 30, 316, 318 Glucose-6-phosphate, 32 Glucosidase, 127 0-Giucosyl dihydrozeatin (OGDHZ), 136 0-Giucosyl dihydrozeatin riboside (OGDHZR), 136 0-Glucosyl zeatin (OGZ), 137 0-Glucosyl zeatin riboside (OGZR), 134, 141 0-Glucosyl zeatin transferase (OGZTase), 137 Glucuronic acid, 32 [~-]Glucuronidase (GUS), 363, 373, 411, 414-415, 425 Glucuronomannans, 33 Glutamic acid, 230 231, 236 [y-]Glutamy!ACC (GACC), 154, 159-160 Glutaraldehyde fixation, Glutarate, 110 Glutathione-S-transferase (GST), 124-126 Glyceraldehyde, 30 Glycolic acid, 108 Glycoproteins, 32-33 Glycosidases, 318 Glycosidic linkage, 31, 41 Glyoxylic acid, 109 Golgi body, 7, 400 Gondoic acid, 90 Grafting procedures, 371 Grapefruit, 154 Green gel LDS-PAGE, 249-251, 253 GST (glutathione-S-transferase ), 124-126 Guaiacyl (G-type) lignin, 200 202 Guanine (G), 97-99 Gulose, 30 Gums, 33 GUS ([~-]glucuronidase), 363, 373, 411, 414-415, 425 Gymnosperm buds, 3-4, [~-]1,3-Giucanase, H Halogenation reactions, 209 Hawthorn berry, 217, 222-224 Headaches, 222 Helianthus annuus, 362, 365, 368-371 Hemicellulases, 310, 313-315 Hemicellulose, 31, 33, 39, 307, 310 Hemocytometers, 14 Heptose, 41 Heptulose, 31 Herbal medicines, 221-222 Hershberg apparatus, 36 Heterobasidwm annosum, 79 Hevea brasiliensis, 178 Hexokinase, 52 Hexoses, 41-42 Hexuloses, 43 Hexuronic acids, 41-43 High-pressure liquid chromatography (HPLC) of alkaloids, 185 of chlorophylls, 232-235 of cytokinins, 135, 137-138, 143, 146 diode array detection (DAD), 218, 220, 222 of elicitins, 266-269 of flavonoids, 217-225 ion exchange, 339 of lignins, 208 of lipids, 91, 339 of organic acids, 109-111 of phenolics, 194-195 of pigments, 255-259 of plant hormones, 353 protein purification by, 53 reverse-phase, 128, 218, 233-234, 259, 267-269, 339 of terpenoids, 179 Histological analysis, 195-196 HIV mfection, 75 Hormones, 116, 154, 353, 430 HPLC See High-pressure liquid chromatography Hybridization techniques, 148, 362, 365, 372-373, 384, 393 Hybridomas, 76-77 Hydrolases, 50 Hydrophobic interaction chromatography, 53, 56, 60 Hydroxyapatite chromatography, 53, 56 Hydroxybenzaldehyde, 207 p-Hydroxyphenyl (H-type) lignin, 200-201 Hydroxypyruvate reductase, 138 Hyoscyamus muticus, 120 121, 125-126 Hypertension, 222 Hypoxanthine, 98 5-N3IAA (5-Azidoindo1e-3-acetic ac1d), 116-129 IAA (indo1e-3-acetic acid), 116-117, 121-124, 126-127, 168-174,432 lAC (immunoaffinity chromatography), 138, 140 142 Idose, 30 IEF (isoe1ectric focusing), 53, 60, 125, 328 IgG, 64, 75, 77 IgM, 75 Immunization, 75-76 Immunoaffinity chromatography (lAC), 138, 140-142 Immunoassays, 74-86, 135, 138, 179, 185, 254 450 Methods in Plant Biochemistry and Molecular Biology Immunoblotting, 434 Immunodiffusion, 78-79 Immunoelectron microscopy, Immunoelectrophoresis, 80-81, 254 Immunofluorescence, 78-79 Immunoglobulins, 76-77 Immunogold labeling, 83-86 Immuno-polymerase chain reaction (Immuno-PCR), 391-392 Immunoprecipitation, 327-328 lmmunoscreening, 351 Indole-3-acetic acid (IAA), 116 117, 121-124, 126 127, 168-174,432 Indole-3-carboxylic acid, 121 Infestin, 270 Infrared (IR) spectroscopy, 35-38,91, 179, 185, 187, 210 Inheritance of transgenes, 374 See also Plant transformation Insulin, 345 Introgression, 378 Inulin, 33 in vivo spectrophotometry, 233 Iodination of e1icitin See Radiolabeling Ion exchange chromatography anion, 56, 112, 252, 341-346 of auxins, 120 cation, 56, 65, 252 of cytokinins, 144 diethylaminoethyl cellulose anion exchanger (DEAE), 58, 144, 252, 339-340, 342, 345 of elicitins, 267 of lipids, 91, 339, 341-343, 346 of organic acids, 111-112 of pigment-protein complexes, 249, 252 protein purification by, 53, 56, 65 resins for, 56, 58-59 theory of, 60 iP (N ([8]2-Isopentenyl)adenine), 140, 143-145 [7G]iP (N6 ([8]2-Isopentenyl adenine-7 -glucoside)), 136 [9R]iP (N 6([8]2-Isopentenyl)adenosine), 136 [9R-5'P] iP (N ( [ 8]2-Isopenteny!)adenosine-5'monophosphate), 136, 145, 147 Ipomoea nil, 158, 166 174 Ipomoea purpurea, 217-221 [8]2-iPP ([8]2-Isopentyl pyrophosphate), 142-144, 146-147 iPR (isopentenyl adenosine), 140-141 Iridoids, 178-179 IR (mfrared) spectroscopy, 35-38,91, 179, 185, 187, 210 Isocitric acid, 108 Isoelectric focusing (SDS-PAGE/IEF), 53, 60, 125, 328 Isoelectric points of elicitins, 270 lsomerases, 50 lsopentane, 177 N6 ([8]2-Isopentenyl)adenine (iP), 140, 143-145 N ([8]2-Isopentenyl ademne-7-glucoside) ([7G]iP), 136 N ([8]2-Isopentenyl)adenosine ([9R]iP), 136 N6 ( [ 8F-Isopenteny I)adenosine-5'-monophosphate ([9R-5'P]iP), 136, 145, 147 Isopentenyl adenosine (iPR), 140-141 [8]2-Isopentyl pyrophosphate ([8]2-iPP), 142-144, 146 147 Isoprenoids, 177-178 Isoquinoline, 186 J Jasmonates, 353 Jerusalem artichoke, 33 Junction fragments, 373 K Ketoglutaric acid, 108 Ketoses, 29, 31, 43 Kinetin, 140 Klason lignin, 205-206, 208 Km (Michaelis-Menten kinetics constant), 50-54, 66 Kofler block, 36 Kreb's cycle, 109 Kuhn-Roth method, 40 L Lactic acid, 108 Lanosterol, 90 Laser microprobe bioassay, 281 LC/MS (liquid chromatography/mass spectrometry), 138 LCR (ligation chain reaction), 390, 392, 394 LDS (lithium dodecyl sulfate), 249, 254 LDS-PAGE (lithium dodecyl sulfate-polyacrylamide gel electrophoresis), 249-251, 253 Leaf panel infiltration bioassay, 272, 274 276 Legumes, 147-148 Lemna gibba, 167 Lemna paucicostata, 168 Lettuce, romaine, 251, 25 Leucoanthocyanins, 191-192 Levans, 33 Levu1inate, 231, 236 Ligase, 50, 392 Ligation chain reaction (LCR) 390, 392, 394 Light-harvesting complexes (LHC), 244, 249, 252-253, 255 Lignin characterization of, 207-211 degradation of, 79, 355-356 451 Index detection of, 39, 200-204 fluorescence, 200-201 Klason, 205-206, 208 overview of, 190, 200 quantitation of, 204-207 soluble, 206-207 Ligninase, 355 Lignoceric acid, 90 Lilium, 174 Limonene, 180 Lineweaver-Burk plots, 50, 52-54 Linoleic acid, 90 Linolenic acid, 90 Lipids, plant, 89-94, 336-338, 341-344, 346 Lipoic acid, 284 Lipoxygenase, 155, 160-161 Liquidambar styraciflua, 76 Liquid chromatography/mass spectrometry (LC/MS), 138 Lithium dodecyl sulfate (LDS), 249, 254 Lithium dodecyl sulfate-polyacrylamide gel electrophoresis (LDS-PAGE), 249-251, 253 Locust, 315 Loroxanthin, 255-256, 258 Lowry technique, 58, 61 Lupinus leuteus, 181-182 Lutein, 255-256, 258 Lyases, 50 Lymphocytes, 75 Lysozyme, 120, 316 Lytic enzymes, 317 Lyxose, 30 M Mab See Monoclonal antibodies MACC (malonyl-ACC), 154, 159-160, 166 Maize, 124, 126-129 Maleate, 11 Malic acid, 108-110 Malonate, 108, 110 154, 292, 296, 298 Malonyl-ACC (MACC), 154, 159-160, 166 1-(Malonylamino)-cyclopropane-1-carboxylic acid, 154, 159-160, 166 Malonyl-CoA/ACP transacylase (MCT), 342-343 Malonyl derivatives, 109 Maltose, 318 Manganese-dependent peroxidase (MnP), 356 Mannanase, 315 Mannosamine, 32 Mannose, 30, 42, 316 Mass spectrometry See Gas chromatography/ mass spectrometry Mayer's reagent, 188 MCT (malonyl-CoA/ACP transacylase), 342-343 ME-ACS genes, 155 Mead acid, 90 Megaspermin, 270 Melon, 160 Melting point determination, 35-36 Membrane structure, 89-90 Menthol, 180 Menthone, 180 Methwnine, 399-400 (4-0-Methyl)glucuronoxylans, 33 MGDG (monogalactosyldiacylglycerol), 337, 341 Mg-protoporphyrin IX (Mg-Proto IX), 230-232, 234-236 Mg-protoporphyrin IX monomethyl ester (Mg-Proto IX ME), 230-232, 234-236 Michaelis-Menten kinetics, 50-54, 66 Micrococcus lysodeikticus, 317 Microplate assay, 318-319 Mitochondria lipid synthesis and, 337, 345 respiration in, 290, 292-294, 296-302 structure of, 6, MnP (manganese-dependent peroxidase), 356 Molecular hybridization, 384 Molecular probes, 137 Monoclonal antibodies (Mab) alternative terminal oxidase and, 290 IAA analysis using, 169 lignin analysis using, 203 plant diseases and, 74-76, 79, 84-86 Monogalactosyldiacylglycerol (MGDG), 337, 341 Monolignols, 200-201, 207 Monosaccharides, 29-33, 43-44, 46 Monoterpenes, 178, 180 Morning glory, 217-221 Morphine, 186-187 Mucilages, 33 Mungbean, 155 Mutant analysis, 353 Myrcene, 180 Myrothecium verrucaria, 67 Myxothiazol, 290 N Naphthalene-1-acetic acid (NAA), 116, 118, 121, 126, 128, 432 Naphthy1phthalamic acid (NPA), 124 NDP (nucleotide sugars), 305-306 Nelson-Somogyi procedure, 310-311, 319 Neomycin phosphotransferase (NPTII), 402, 427 Neoxanthin, 255-256, 258 Nerolidol, 183 Nervonic acid, 90 Nicotiana plumbaginifolia, 366 452 Methods in Plant Biochemistry and Molecular Biology Nicotiana tabacum alkaloids in, 187 auxins in, 125 cytokinins in, 147 DNA transfer and, 362, 365-367, 427, 429 elicitins in, 266, 273-277 transgenic, 401-407, 434 Nicotine, 186-187 Nicotinic acid, 167, 282, 284 Nicotinic amide, 282 Ninhydrin, 43 Nitrobenzene oxidation of lignin, 207-208 NMR spectroscopy See Nuclear magnetic resonance spectroscopy Nopaline synthase (nos), 426-427 Northern blot analysis, 148, 435 NPA (naphthylphthalamic acid), 124 NPTII (neomycm phosphotransferase), 402, 427 Nuclear magnetic resonance (NMR) spectroscopy of alkaloids, 185, 187 cross polarization/magic angle spinning (CP/MAS), 211 of lignins, 200, 202, 209, 211 of lipids, 91 of nucleic acids, 105 two-dimensional, 211 Nucleic acids, 97-105, 378, 410-412 Nucleotide sequences, 325 Nucleotide sugars (NDP), 305-306 Oats, 158-160 Octadecenoic acid, 337 Octopine synthase (ocs), 426 Octylglucoside (OG), 249 ODC (oxalate decarboxylase), 51, 62-69 ODS (oleoyl-PC desaturase), 339, 344 OGZ (0-Glucosyl zeatin), 137 OGZR (0-Glucosyl zeatin riboside), 134, 141 OGZTase (0-glucosyl zeatin transferase), 137 Oleic acid, 90, 338 Oleoyl-ACP, 340-341 Oleoyl-PC desaturase (ODS), 339, 344 Oleoyl phosphatidylcholine desaturase, 344 Oligosaccharides, 31, 33, 44-46, I 05 Onions, 33 Oranges, 283 Orcinol colorimetry, 104 Osmium tetroxide, Ouchterlony assay, 77-78 Oxalate decarboxylase (ODC), 51, 62-69 Oxalic acid, 107-108, 110 Oxidative phosphorylation, 290 Oxidoreductases, 50 Oxygen electrode, 294-297 Oxygen isotopes, 290 Oxygen uptake measurement, 294-301 OXZTase (0-Xylosyl zeatin transferase), 137 Oysters, 315 p Pab See Polyclonal antibodies PAH (polyaromatic hydrocarbons), 259 PAK (pantothenate kinase), 344-346 Palmitic acid, 90 Palmitoleic acid, 90 Palmitoyl-ACP, 340-341 Pantothenate kinase (PAK), 344-346 Pantothenic acid, 283-284 Papain, 51 Papaver somniferum, 187 Papaya, 317 Paper chromatography, 42-43, 109, 179, 187, 194, 233 Paprika, 283 Parasiticein, 269-270, 272 Parthenolide, 222 Particle capture immunoassay (PCI), 78, 86 PBG (porphobilinogen), 230-232, 236 PChlide (protochlorophyllide), 230-238 PCO (procyanidolic oligomers), 222 PCR See Polymerase chain reaction Peanuts, 102, 379 Peas, 156-159, 250 Pectin, 31, 33, 35, 307, 310 Pectinases, 310-311, 316, 320, 414 Pelletierine, 18 Pentose phosphate pathway (PPP), 191-192 Pentoses, 41-43 Pentuloses, 43 Pepsin, 51 Peridinin, 244-245, 255 Periodate oxidation, 39 Periodic acid, 39, 43 Peroxidases, 355 Petroselenic acid, 90 Petunia, 429, 435 p60 gene, 127 PG (phosphatidylglycerol), 92-93, 337-338 PG (polygalacturonase), 316, 320 pH, enzyme activity and, 49-51, 56, 60 Phanerochaete chrysosporium, 79, 355-356 Pharbitis nil, 167-168, 181, 182-183 Pharmacia ion exchange resins, 55-56, 58, 252 Phaseic acid, 183 Phaseolin, 399-402, 407-409, 411-413, 415-417 Phaseolus, 169 Phaseolus coccineus, 182 Phaseolus lunatus, 147 Phaseolus vulgaris, 147-149, 182, 416 Phenolics, 190-196, 223-225 Index Phenylalamne, 192 Phenylcoumaran, 200-201 PhenylpropanOJds, 218, 355 Pheophytinization, 255 Phloroglucinol test, 202-203 PhL (photoaffinity labeling), 115-129 Phosphatidic acid, 92 Phosphatidylcholine, 92, 337 Phosphatidylethanolamine, 92, 337 Phosphatidylglycerol (PG), 92-93, 337-338 Phosphatidylinositol, 93, 338 Phosphatidylserine, 92, 338 Phospholipids, 89-94 Photoaffinity labeling (PhL), 115-129 Photobleaching herbicides, 232, 235 Photochemistry of auxins, 119-120 Photodiode array absorbance detector, 234 Photometric determinations, 111 Photosystem II (PS II), 244-245, 248-251 Photosystem I (PSI), 25, 244-245, 250-251, 253-254 Phragmoplasts, 6, Phycobilisomes, 244-245, 260 Phylloquinones, 177 Phyllostachys, 182 Phytophthora, 266-268, 270, 272-274 Pichia pastoris, 267 Pigment-protein complexes (PPC), 244-261 Pilocarpine, 187 Pilocarpus pennatifolius, 187 Pinene, 180 Pine needle lipids, 91-94 Pinoresinol, 200-201 Pipecolic acid, 167 Piperidine, 186 Pisum sativum, 156 159, 250 Plant growth regulators, 166 174, 187 Plant transformation, 362-374, 429 436 Plasma membranes (PM), 121-127, 155 Plasmids bacterial, 382, 388, 426 binary, 362-365 control, 363-364 DNA amplification in, 388-389 helper, 364-365 recombinant, 378 Plastoquinone, 177, 284, 301 Platinum electrodes, 296 Pleurotus ostreatus, 18 Plytol, 178 PME (pectin methylesterase), 316 PM (plasma membranes), 121-127, 155 Polar auxin transport, 121-123, 127-129 Polyacrylamide gel electrophoresis (PAGE) See Lithium dodecyl sulfate- polyacrylamide gel electrophoresis; Sodium dodecyl sulfate polyacrylamide gel electrophoresis 453 Poly(A)-mRNA, 349 Polyaromatic hydrocarbons (PAH), 259 Polyclonal antibodies (Pab) cytokinin analysis and, 140 lignin analysis using, 203-204 lipid analysis using, 339 pigment-protein complex analysis using, 254 plant diseases and, 74-76, 79, 84, 86 Polygalacturonase (PG), 316, 320 Polymerase chain reaction (PCR) DNA manipulation and, 362, 365, 372-273, 389-394,426,435 immuno-PCR, 391-392 nucleic acid analysis by, 100-102 Polyphenol oxidase, 329, 349 Polysaccharidases, 310-318 Polysaccharides, 31, 33, 39, 305-307, 313 Populus, 192 Porphobilinogen (PBG), 230-232, 236 Porphyrin pathway, 229-238 Postia placenta basidiospore production in, 19 carbohydrolase assays of, 320 enzymes in, 63, 65-67, 84-85 immunochemistry and, 76, 84-85 polysaccharide synthesis in, 306 Potato, 102-103, 292-294, 296-301, 329, 429 PPP (pentose phosphate pathway), 191-192 Prasinoxanthin, 255 Precipitation, differential, 144 Pressure infiltration, 275 Proanthocyandins, 191-192 Procyanidins, 222 Procyanidolic oligomers (PCO), 222 n-Propyl gallate, 290 Protein binding assay, 400, 408 4115 Protoch1orophyllide (PChlide), 230-238 Protoplasts, 411, 413 415, 424 Protoporphyrin IX (Proto IX), 230-232, 234-237 Protoporphyrinogen IX (Protogen IX), 230, 232, 237 Protox inhibitors, 235, 237 Prunus persica, 181 PS II (photosystem II), 244-245, 248-251 PSI (photosystem 1), 25, 244-245, 250-251, 253-254 Purine, 97-98 Putrescine, 166 PVPP chromatography, 139-140 Pyranose, 36 Pyridine, 186 187 Pyridoxal, 282 Pyridoxamine, 282 Pyridoxine (vitamin B6), 282, 284 Pyrimidine, 97-98 Pyrolysis-GC/MS, 209-210 Pythium vexans, 270 454 Methods in Plant Biochemistry and Molecular Biology Q Quaternaryaminoethyl (QAE) anion exchange, 252 Quercitin, 121, 126, 222-225 Quinic acid, I 08 Quinine, 186 187 Quinone electrode, 292-297, 301-302 Quinone pool, 296-300 R Rabbit reticulocyte system, 327, 331-332 Radioimmunoassay (RIA), 135, 179, 185 Radio labeling of chitin, 317 of cytokmins, 142-143, 146-148 of DNA, 351,378,390,410 411,417-418 of elicitms, 272-273 in lignin analysis, 203 of lipids, 337-343, 346 32 P-labeled probes, 383 of plant growth regulators, 171-173 in protein synthesis, 327, 331 Radish, 266 Raman spectroscopy, 36-39, 210 Random primer, 383 Raphanus sativa, 266 Rauwolfia serpentina, 187 Recombinant DNA See DNA Reducing group assay, 314, 318 Relative mobility (Rr) factor, 61-62, 91 Reporter quinone (UQ-2), 292-293, 296 Reserpine, 186 187 Resonance Raman spectroscopy, 10 Resorcinol, 43 Respiration, model of, 291-292, 296-301 Restriction endonucleases, 379-380 Restriction fragment length polymorphisms (RFLP), 378-385 Reticulocyte lysate, 327, 331-332 Reverse transcriptase, 349, 394 RFLP (restnction fragment length polymorphisms), 378-385 R1 (relative mobility factor), 61-62, 91 Rhamnogalacturonans, 33 RIA (radioimmunoassay), 135, 179, 185 Riboflavin (vitamin B2 ), 282, 284 Ribose, 30 Ribosomes, 6, 8, 323-324, 326 Ribulose, 31 Rice, 282, 429 RIE (rocket-immunoelectrophoresis), 254 Ripening and ethylene production, 155 RNA assay of, 103-105, 329-330 DNA-RNA hybrids, 349 fingerprintmg, 394 footprintmg, 394 isolation of, 416 mRNA, 138, 148-150, 326-327, 349 overview of, 97-100 ribosomal (r-RNA), 323 transfer, 326-327 RNase protection assays, 148 Rocket-immunoelectrophoresis (RIE), 254 s Salicyclic acid, 353 Salicylhydroxamic acid (SHAM), 290, 301 SAM (S-Adenosylmethionine), 154, 160, 166, 174 Saponins, 178 Sapstain fungi, 23-25 Sapwood, 190-191 Sauromatum guttatum, 290 Scanned probe microscopy, Scanning electron microscopy (SEM), 4, 83-84 Scanning laser densitometry, 149-150 Scanning tunneling microscopy, Schizophyllum commune, 20, 306 Scintillation autoradiography See Autoradiography Scintillation counting, 144, 173, 339 Sclerotinia sclerotiorum, 66 67 SDS-PAGE See Sodium dodecyl sulfate polyacrylamide gel electrophoresis Sedoheptulose, 31 Selinene, 183 SEM (scanning electron microscopy), 4, 83-84 Senescence, 154 155, 160, 166 Sense genes, 424 Sephadex resins, 55-56, 252, 342-343 Serpula incrassata, 320 Sesquiterpenes, 178-179, 183 SHAM (salicylhydroxamic acid), 290, 301 Shigometer, 78 Shikimic acid, 108, 190-191 Sialic aCJd, 46 Silicic acid chromatography, 91, 338 Silver staining techniques, 61, 271 Sinapyl alcohol, 200-201 Siphonaxanthin, 255 Sitosterol, 90 Size exclusion chromatography See Gel chromatography Slime, fungal, 65 Slot-blotting, 148 Snails, 315 Snapdragons, 219 S Nuclease, 349 455 Index S Nuclease protection assays, 148-150 Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) See also Detergent solubilization of auxins, 121, 124 125 of elicitins, 270 of enzyme activity, 53, 58, 60-61, 434 in immunoassays, 83 of pigment-protein complexes, 246, 252-254 in protein synthesis, 328 second-dimensional, 253 thylakoids, 246 SOD (superox1de dismutase), 126 Solanum bethaultii, 329 Solid probe mass spectrometry, 185 Solvent partitioning, 338 Sonication, 139, 246-247 Sour orange, 217, 222, 224-225 Southern blotting, 372, 378, 381, 407, 435 Soybean, 123, 146-147, 283, 292, 300-301, 313, 342 Spectrofluorometry, 233 Spectroscopy absorption, 255-256, 259-260, 266, 316 DRIFT, 210 fluorescence, 187, 234, 255-256, 259-260 Fourier-transform infrared (FTIR), 210 infrared (IR), 35-38, 91, 179, 185, 187, 210 nuclear magnetic resonance (NMR) See Nuclear magnetic resonance (NMR) spectroscopy Raman, 36-39, 210 ultraviolet (UV) See Ultraviolet spectroscopy vibrational, 209-210 Spermidine, 166 Spinach, 250, 258, 283, 338-339, 345-346 SQDG (sulfoquinovosyldiacylglycerol), 338, 341 Squash, 155 Staining techniques for elicitins, 271 for lignins, 202-203 for pigment-protein complexes, 253-254 for proteins, 61 for transgene enzymes, 374 Staphylococcus aureus, 327-328, 333 Starch, 31, 33-34 Stearic acid, 90 Stearoyl-ACP, 340, 425, 434 Sterols, 89, 94 Stigmasterol, 90, 94 Streptococcus, 427 Stress conditions and ethylene, 154, 160 See also Wounding of plants Strychnine, 186-187 Strychnos nux-vomica, 187 Suberin, 190, 200 Substitution mutation analysis, 41 1-413 Succinic ac1d, 108, 110 Sucrose density gradient ultracentnfugation, 249-253, 256, 258, 260, 292, 294 Sugar beets, 316 Sugar phosphates, 32 Sugars acids, 32, 44 chromatographic separation of, 42-44 reducing, 310, 313, 317, 319 Sulfolipids, 89, 338 Sulfoquinovosyldiacylglycerol (SQDG), 338, 341 Sunflowers, 362, 365, 368-371 Superoxide dismutase (SOD), 126 Sweetgum, 76 Synechococcus leopoliensis, 251 Syringa1dehyde, 207 Syringyl (S-type) lignin, 200-202 T Talaromyces flavus, 24-25 Talose, 30 Tanacetum parthenium, 222 Tannins, 191, 202 See also Phenolics Tartaric acid, 108, 110 T-cells, 75 Temperature, enzyme activity and, 49-51, 56 TEM (transmission electron mtcroscopy), 3-4, 83-84 Tentoxin, 235 Terpenoids, 177-183, 185, 187, 336 Terpinolene, 180 Tetrapyrrole, 230, 232, 237 Tetroses, 41 Thebaine, 186 Thermal cycling amplification, 389-393 Thermus aquaticus, 389, 392 Thiamine (vitamin B 1), 282, 284 Thidiazuron, 148-150 Thin-layer chromatography (TLC) of alkaloids, 185, 187 of chlorophylls, 232-233 of ethylene, 159-160 of flavonoids, 222 of lipids, 91, 338, 344 of organic acids, 109, Ill of phenolics, 194 195 photoaffinity labeling and, 119 of pigments, 255-256, 258-259 reverse-phase, 259 of sugars, 42-43 of terpenoids, 179 of vitamins, 281 456 Methods in Plant Biochemistry and Molecular Biology Thioacidolysis, 208-209 Thioglycolic acid, 207 Threonine dehydratase, 52 Threose, 30 Thujone, 180 Thylakoid membranes, 244-249, 251, 253-260 Thymine (T), 97-99 Timnodonic acid, 90 Tissue culture, 366, 432 Tissue ultrastructure, 3-10 TLC See Thin-layer chromatography Tobacco See Nicotiana tabacum Tocopherol quinones, 177 Tomato DNA manipulation in, 101-102, 429, 435 elicitins in, 277 ethylene production in, 155, 158 photoaffinity labeling and, 125 RFLPs in, 379 Topolones, 178 Tosylation, 39 40 Trametes hirsuta, 66-f:J7 Trametes versicolor, 66-67 Transacomtate, 110 Transcriptional regulatory elements, 400 40 I, 408 409,411 412,415 Transferases, 50 Transgenes, 362-363, 371-374, 424 425, 429, 433 435 Transmission electron microscopy (TEM), 4, 83-84 Trichoderma viride, 320 Tncine gels, 270 Triparental mating method, 364-365, 405, 427 428 Trisporic acid, 178 Triton X-100, 249 Triton X-114, 123-125 Tritylation, 40 Tropane, 186-187 Tropolones, 178-179, 187 Trypsin, 51, 128 Tryptophan, 121, 399 Tubocurarine, 187 Tubulin, 75 Turbidity reduction measurement, 317 (I Ubiquinol (UQH ), 290-291 Ubiquinone (UQ), 177, 284, 290-293, 299 Ubiquinone (UQ) pool, 290-293 UG-2 (reporter quinone), 292-293, 296 Ultraviolet (UV) light, 46, 129, 200 Ultraviolet (UV) spectroscopy of alkaloids, 187 of cytokinins, 135, 138 of enzymes, 53, 61 of lipids, 91 microspectroscopy, 203 of nucleic acids, 104 of pigment-protein complexes, 259 UQH (ubiquinol), 290-291 UQ (ubiquinone), 177, 284, 290-293, 299 Uracil (U), 97-98 Uragoya ipecucuanba, 187 Uranyl acetate, Ureides, 136 Uridine diphosphate glucose, 306 Uronic acids, 32, 40 Uroporphyrin III (Uro III), 232, 234, 237 Uroporphyrinogen III (Urogen III), 230-232 UV spectroscopy See Ultraviolet (UV) spectroscopy UV (ultraviolet) light, 46, 129, 200 v Vaccenic acid, 90 Vacuole acids, 109 Vanillin, 207 Veratryl alcohol assay, 355-356 Vibrational spectroscopy, 209-210 Viola, 127 Violaxanthin, 255-256, 258 Viscosimetric methods, 311-312, 314, 316-317 Vitamins, plant, 281-284 Vitexin-4'-rhamnoside, 222 Voltametric measurement of redox state, 290 w Wagner's reagent, 188 Walseth cellulose, 14, 20 Weisner reaction, 202-203 Western blotting, 77, 82-83, 254 Wheat, 157, 283-284, 313 White-rot fungus, 13-14, 24, 63, 79, 355 Wood-deteriorating fungi, 13-14, 62-63, 77-78, 191, 305-307, 318 See also Brown-rot fungi; Postia placenta enzymes in, 62-63, 318 field test kit for, 78 immunoassay in, 77-78 lignin degradation and, 355 overview of, 13-14, 191 po1ysaccharidase in, 305-307, 310 Wounding of plants compartmentalization and, 190-193, 196 ethylene production and, 154-157, 160 metabolism and, 290, 293 phenolics and, 190-192, 194 Index 457 X Xanthine, 98 X-ray diffraction, 105 X-ray microanalysis, Xylanase, 83, 313-315 Xylans, 33 Xyloglucans, 33, 36 Xylose, 30, 42, 316 0-Xylosyl zeatin transferase (OXZTase), 137 Xylulose, 31 y Yeast, 325 Yeda press, 246 z Zeatin, 140-141, 143, 148-150, 353 cis-Zeatin, 136-137, 141 trans-Zeatin, 6-( 4-hydroxy-3-methylbut-trans-2enylamino)purine (Z), 137, 142-147 trans-Zeatin-7 -glucoside ([7G ]Z), 136 trans-Zeatin-9-glucoside ([9G]Z), 136 cis-Zeatin riboside, 141 trans-Zeatin riboside (ZR), 137, 140, 145-147 trans-Zeatin riboside-5'-monophosphate ([9R-5'P]Z), 136 Zeaxanthin, 255 Zucchini, 122-125, 155 ... business METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY Edited by William V Dashek Boca Raton London New York CRC Press is an imprint of the Taylor.. .METHODS IN PLANT BIOCHEMISTRY and MOLECULAR BIOLOGY Edited by William V Dashek Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business METHODS IN. .. registered trademarks, and are used only for identification and explanation without intent to infringe Library of Congress Cataloging -in- Publication Data Plant biochemistry and molecular biology / edited