Cell biology: a laboratory handbook. - 3rd ed. Vol.4 / ed. by Celis J. - Amsterdam; Boston: Elsevier Academic Press., 2006. - xliv, 584 p. - ISBN 10 0-12-164734-X; ISBN 13 978-0-12-1644734-6  Место хранения:   040 | Институт биофизики СО РАН | Красноярск | Библиотека

Оглавление / Contents

Contents of other Volumes ...................................... xi Contributors ................................................ xxiii Preface ....................................................... xiv PART A. TRANSFER OF MACROMOLECULES Section 1. Proteins 1. Impact-Mediated Cytoplasmic Loading of Macromolecules into Adherent Cells .......................................... 5 MARK S.F. CLARKE, DANIEL L. FEEBACK, AND CHARLES R. VANDERBURG 2. A Peptide Carrier for the Delivery of Biologically Active Proteins into Mammalian Cells: Application to the Delivery of Antibodies and Therapeutic Proteins ............. 13 MAY С. MORRIS, JULIEN DEPOLLIER, FREDERIC HEITZ, AND GILLES DIVITA 3. Selective Permeabilization of the Cell-Surface Membrane by Streptolysin О ........................................... 19 J0RGEN WESCHE AND SJUR OLSNES Section 2. Genes 4. New Cationic Liposomes for GeneTtransfer .................... 25 NANCY SMYTH TEMPLETON 5. Cationic Polymers for Gene Delivery: Formation of Polycation-DNA Complexes and in vitro Transfection .......... 29 YONG WOO СНО, JAE HYUN JEONG, CHEOL-HEE AHN, JONG-DUK KIM, AND KINAM PARK 6. Electroporation of Living Embryos ........................... 35 TAKAYOSHI INOUE, KRISTEN CORREIA, AND ROBB KRUMLAUF Section 3. Somatic Cell Nuclear Transfer 7. Somatic Cell Nuclear Transplantation ........................ 45 KEITH H.S. CAMPBELL, RAMIRO ALBERIO, CHRIS DENNING, AND JOON-HEE LEE PART B. EXPRESSION SYSTEMS Section 4. Expression Systems 8. Expression of cDNA in Yeast ................................. 57 CATERINA HOLZ AND CHRISTINE LANG 9. Semliki Forest Virus Expression System ...................... 63 MARIA EKSTROM, HENRIK GAROFF, AND HELENA ANDERSSON 10.Transient Expression of cDNAs in COS-1 Cells: Protein Analysis by Two-Dimensional Gel Electrophoresis ............. 69 PAVEL GROMOV, JULIO E. CELIS, AND PEDER S. MADSEN 11.High-Throughput Purification of Proteins from Escherichia coli ............................................ 73 PASCAL BRAUN AND JOSHUA LABAER PART C. GENE EXPRESSION PROFILING Section 5. Differential Gene Expression 12.Microarrays for Gene Expression Profiling: Fabrication of Oligonucleotide Microarrays, Isolation of RNA, Fluorescent Labeling of RNA, Hybridization, and Scanning .................................................... 83 MOGENS KRUH0FFER, NILS E. MAGNUSSON, MADS ААВОЕ, LARS DYRSKJ0T, AND TORBEN F. 0RNTOFT 13.ArrayExpress: A Public Repository for Microarray Data ....... 95 HELEN PARKINSON, SUSANNA-ASSUNTA SANSONE, UGIS SARKAN, PHILIPPE ROCCA-SERRA, AND ALVIS BRAZMA 14.Serial Analysis of Gene Expression (SAGE): Detailed Protocol for Generating SAGE Catalogs of Mammalian Cell Transcriptomes ........................................ 103 SERGEY V. ANISIMOV, KIRILL V. TARAScV, AND KENNETH R. BOHELER 15.Representational Difference Analysis: A Methodology to Study Differential Gene Expression ...................... 113 MARCUS FROHME AND JORG D. HOHEISEL 16.Single Cell Gene Expression Profiling: Multiplexed Expression Fluorescence in situ Hybridization: Application to the Analysis of Cultured Cells .............. 121 JEFFREY M. LEVSKY, STEVEN A. BRAUT, AND ROBERT H. SINGER PART D. PROTEINS Section 6. Protein Determination and Analysis 17.Protein Determination ...................................... 131 MARTIN GUTTENBERGER 18.Phosphopeptide Mapping: A Basic Protocol ................... 139 JILL MEISENHELDER AND PETER VAN DER GEER 19.Coupling of Fluorescent Tags to Proteins ................... 145 MARKUS GRUBINGER AND MARIO GIMONA 20.Radioiodination of Proteins and Peptides ................... 149 MARTIN ВEНE, MARTIN GOTTHARDT, AND THOMAS M. BEHR Section 7. Sample Fractionation for Proteomics 21.Free-Flow Electrophoresis .................................. 157 PETER J.A. WEBER, GERHARD WEBER, AND CHRISTOPH ECKERSKORN Section 8. Gel Electrophoresis 22.Gel-Based Proteomics: High-Resolution Two-Dimensional Gel Electrophoresis of Proteins. Isoelectric Focusing and Nonequilibrium pH Gradient Electrophoresis ............. 165 JULIO E. CELIS, SIGNE TRENTEM0LLE, AND PAVEL GROMOV 23.High-Resolution Two-Dimensional Electrophoresis with Immobilized pH Gradients for Proteome Analysis ............. 175 ANGELIKA GORG AND WALTER WEISS 24.Two-Dimensional Difference Gel Electrophoresis: Application for the Analysis of Differential Protein Expression in Multiple Biological Samples .................. 189 JOHN F. TIMMS 25.Affinity Electrophoresis for Studies of Biospecific Interactions: High-Resolution Two-Dimensional Affinity Electrophoresis for Separation of Hapten-Specific Polyclonal Antibodies into Monoclonal Antibodies in Murine Blood Plasma ........................................ 197 KAZUYUKI NAKAMURA, MASANORI FUJJMOTO, YASUHIRO KURAMITSU, AND KAZUSUKE ТАKEO 26.Image Analysis and Quantitation ............................ 207 PATRICIA M. PALAGI, DANIEL WALTHER, GERARD BOUCI SONJA VOORDIJK, AND RON D. APPEL Section 9. Detection of Troteins in Gels 27.Protein Detection in Gels by Silver Staining: A Procedure Corjipatible with Mass Spectrometry ............ 219 IRINA GROMOVA AND JULIO E. CELIS 28.Fluorescence Detection of Proteins in Gels Using SYPRO Dyes ....................................................... 225 WAYNE F. PATTON 29.Autoradiography and Fluorography: Film-Based Techniques for Imaging Radioactivity in Flat Samples .................. 235 ERIC QUEMENEUR Section 10.Gel Profiling of Posttranslationally Modified Proteins 30.Two-Dimensional Gel Profiling of Posttranslationally Modified Proteins by in vivo Isotope Labeling .............. 243 PAVEL GROMOV AND JULIO E. CELIS Section 11.Protein/Protein and Protein/Small Molecule Interactions 31.Immunoprecipitation of Proteins under Nondenaturing Conditions ................................................. 253 JIRI LUKAS, JIRI BARTEK, AND KLAUS HANSEN 32.Nondenaturing Poly aery lamide Gel Electrophoresis as a Method for Studying Protein Interactions: Applications in the Analysis of Mitochondrial Oxidative Phosphorylation Complexes .................................. 259 JOEL SMET, BART DEVREESE, JOZEF VAN BEEUMEN, AND RUDY N.A. VAN COSTER 33.Affinity Purification with Natural Immobilized Ligands ..... 265 NISHA PHILIP AND TIMOTHY A. HAYSTEAD 34.Analysis of Protein-Protein Interactions by Chemical Cross-Linking .............................................. 269 ANDREAS S. REICHERT, DEJANA MOKRANJAC, WALTER NEUPERT, AND KAI HELL 35.Peroxisomal Targeting as a Tool to Assess Protein- Protein Interactions ....................................... 275 TRINE NILSEN, CAMILLA SKIPLE SKJERPEN, AND SJUR OLSNES 36.Biomolecular Interaction Analysis Mass Spectrometry ........ 279 DOBRIN NEDELKOV AND RANDALL W. NELSON 37.Blot Overlays with 32P-Labeled GST-Ras Fusion Proteins: Application to Mapping Protein-Protein Interaction Sites ... 285 ZHUO-SHEN ZHAO AND EDWARD MANSER 38.Ligand Blot Overlay Assay: Detection of Ca+2- and Small GTP-Binding Proteins ....................................... 289 PAVEL GROMOV AND JULIO E. CELIS 39.Modular Scale Yeast Two-Hybrid Screening ................... 295 CHRISTOPHER M. ARMSTRONG, SIMING L.I, AND MARC VIDAL Section 12. Functional PrOteomics 40.Chromophore-Assisted Laser Inactivation of Proteins by Antibodies Labeled with Malachite Green ................. 307 THOMAS J. DIEFENBACH AND DANIEL G. JAY Section 13. Protein/DNA Interactions 41.Chromatin Immunoprecipitation (ChIP) ....................... 317 VALERIO ORLANDO 42.Gel Mobility Shift Assay ................................... 325 PETER L. MOLLOY 43.DNA Affinity Chromatography of Transcription Factors: The Oligonucleotide Trapping Approach ...................... 335 SUCHAREETA MITRA, ROBERT A. MOXLEY, AND HARRY W. JARRETT Section 14. Protein Degradation 44.Protein Degradation Methods: Chaperone-Mediated Autophagy .................................................. 345 PATRICK F. FINN, NICHOLAS T. MESIRES, AND JAMES FRED DICE 45.Methods in Protein Ubiquitination .......................... 351 AARON CIECHANOVER Section 15. Mass Spectrometry: Protein Identification and Interactions 46.Protein Identification and Sequencing by Mass Spectrometry ............................................... 363 LEONARD J. FOSTER AND MATTHIAS MANN 47.Proteome Specific Sample Preparation Methods for Matrix- Assisted Laser Desorption/Ionization Mass Spectrometry ..... 371 MARTIN R. LARSEN, SABRINA LAUGESEN, AND PETER ROEPSTORFF 48.In-Gel Digestion of Protein Spots for Mass Spectrometry .... 379 KRIS GEVAERT AND JOEL VANDEKERCKHOVE 49.Peptide Sequencing by Tandem Mass Spectrometry ............. 383 JOHN R. YATES III, DAVID SCHIELTZ, ANTONIUS KOLLER, AND JOHN VENABLE 50.Direct Database Searching Using Tandem Mass Spectra of Peptides ................................................ 391 JOHN R. YATES III AND WILLIAM HAYES MCDONALD 51.Identification of Proteins from Organisms with Unsequenced Genomes by Tandem Mass Spectrometry and Sequence-Similarity Database Searching Tools ............... 399 ADAM J. LISKA AND ANDREJ SHEVCHENKO 52.Identification of Protein Phosphorylation Sites by Mass Spectrometry ............................................... 409 RHYS С. ROBERTS AND OLE N. JENSEN 53.Analysis of Carbohydrates/ Glycoproteins by Mass Spectrometry ............................................... 415 MARK SUTTON-SMITH AND ANNE DELL 54.Stable Isotope Labeling by Amino Acids in Cell Culture for Quantitative Proteomics ................................ 427 SHAO-EN ONG, BLAGOY BLAGOEV, IRINA KRATCHMAROVA, LEONARD J. FOSTER, JENS S. ANDERSEN, AND MATTHIAS MANN 55.Site-Specific, Stable Isotopic Labeling of Cysteinyl Peptides in Complex Peptide Mixtures ....................... 437 HUILIN ZHOU, ROSEMARY BOYLE, AND RUEDI AEBERSOLD 56.Protein Hydrogen Exchange Measured by Electrospray Ionization Mass Spectrometry ............................... 443 THOMAS LEE, ANDREW N. HOOFNAGLE, KATHERYN A. RESING, AND NATALIE G. AHN 57.Nongel Based Proteomics: Selective Reversed-Phase Chromatographic Isolation of Methionine-Containing Peptides from Complex Peptide Mixtures ..................... 457 KRIS GEVAERT AND JOEL VANDEKERCKHOVE 58.Mass Spectrometry in Noncovalent Protein Interactions and Protein Assemblies ..................................... 457 LYNDA J. DONALD, HARRY W. DUCKWORTH, AND KENNETH G. STANDING PART E. APPENDIX Section 16. Appendix 59.Bioinformatic Resources for in Silico Proteome Analysis .... 469 MANUELA PRUESS AND ROLF APWEILER List of Suppliers ............................................. 477 Index ......................................................... 533