The Unfolded Protein Response and Cellular Stress, Part C

1. Auflage 2011
ISBN: 978-0-12-385929-7
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 491, 464 Seiten, Web PDF

Reihe: Methods in Enzymology

This volume provides descriptions of the occurrence of the UPR, methods used to assess it, pharmacological tools and other methodological approaches to analyze its impact on cellular regulation. The authors explain how these methods are able to provide important biological insights - This volume provides descriptions of the occurrence of the UPR, methods used to assess it, pharmacological tools and other methodological approaches to analyze its impact on cellular regulation - The authors explain how these methods are able to provide important biological insights

Autoren/Hrsg.

Inhaltsverzeichnis

1;Front Cover;1
2;Methods in Enzymology: The Unfolded Protein Response and Cellular Stress, Part C;4
3;Copyright Page;5
4;Contents;6
5;Contributors;14
6;Preface;20
7;Volume in Series;22
8;Section 1: New Approaches to Studying UPR and Cell Stress;52
8.1;Chapter 1: CFTR Expression Regulation by the Unfolded Protein Response;54
8.1.1;1. Introduction;55
8.1.2;2. Methods;57
8.1.3;Acknowledgments;73
8.1.4;References;73
8.2;Chapter 2: GRP78/BiP: Modulation ofGRP78/BiP in Altering Sensitivityto Chemotherapy;76
8.2.1;1. Introduction;77
8.2.2;2. Measurement of ER Stress In Vitro and In Vivo;78
8.2.3;3. Conclusion;87
8.2.4;References;87
8.3;Chapter 3: Targeting the Unfolded Protein Response in Cancer Therapy;88
8.3.1;1. Introduction;89
8.3.2;2. The UPR and Cancer;89
8.3.3;3. Targeting the UPR;91
8.3.4;4. Combination of EGF-SubA with Other UPR-Targeting Drugs;101
8.3.5;Acknowledgments;105
8.3.6;References;105
8.4;Chapter 4: Large-Scale Analysis of UPR-Mediated Apoptosis in Human Cells ;108
8.4.1;1. Introduction;109
8.4.2;2. Monitoring Proliferation and Caspase Activation Following UPR Activation;111
8.4.3;3. Monitoring the Expression of UPR and Cell Death Target Genes;112
8.4.4;4. DNA Fragmentation Analysis;119
8.4.5;Acknowledgments;120
8.4.6;References;120
8.5;Chapter 5: Quantitative Analysis of Amino Acid Oxidation Markers by Tandem Mass Spectrometry;124
8.5.1;1. Introduction;126
8.5.2;2. Experimental Procedures;127
8.5.3;3. Results;133
8.5.4;4. Conclusions;137
8.5.5;Acknowledgments;137
8.5.6;References;138
8.6;Chapter 6: Animal Models in the Study of the Unfolded Protein Response;142
8.6.1;1. Introduction;143
8.6.2;2. Activating Transcription Factor 6;144
8.6.3;3. IRE1/X-Box-Binding Protein-1;145
8.6.4;4. PKR-Like ER Kinase;148
8.6.5;5. eIF2a;149
8.6.6;6. ATF4;150
8.6.7;7. CHOP;151
8.6.8;8. GADD34;152
8.6.9;9. P58IPK;153
8.6.10;10. Transgenic Mouse Models for Monitoring ER Stress;153
8.6.11;11. UPR and Lipid Metabolism;154
8.6.12;12. UPR, Hypoxia, and Cancer;155
8.6.13;13. UPR and Inflammatory-Mediated Demyelination;156
8.6.14;14. Future Challenges;156
8.6.15;References;157
8.7;Chapter 7: Measurement of Fluoride-Induced Endoplasmic Reticulum Stress Using Gaussia Luciferase;162
8.7.1;1. Introduction;163
8.7.2;2. Properties of Gaussia Luciferase;165
8.7.3;3. Materials;166
8.7.4;4. Procedure;169
8.7.5;5. Conclusions;174
8.7.6;References;175
8.8;Chapter 8: Analysis of Nelfinavir-Induced Endoplasmic Reticulum Stress;178
8.8.1;1. Introduction;179
8.8.2;2. Obtaining Nelfinavir;180
8.8.3;3. Using Nelfinavir;180
8.8.4;4. Analysis of Nelfinavir-Induced ER Stress;181
8.8.5;5. Immunoblot Analysis;185
8.8.6;6. RT-PCR Analysis;186
8.8.7;7. Conclusions;192
8.8.8;Acknowledgment;193
8.8.9;References;193
8.9;Chapter 9: Using Temporal Genetic Switches to Synchronize the Unfolded Protein Response in Cell Populations In Vivo;194
8.9.1;1. Introduction;195
8.9.2;2. Variable Functions of CHOP in the PERK Signaling Pathway ;197
8.9.3;3. Mutations in the PLP1 Gene: A Model UPR Disease;198
8.9.4;4. Problems with Current Paradigms Used to Characterize the UPR;200
8.9.5;5. A Novel In Vivo Genetic Switch Solves Many of These Problems;201
8.9.6;6. Generalizing GST to Study Other UPR Diseases;208
8.9.7;Acknowledgments;208
8.9.8;References;209
8.10;Chapter 10: Glycoprotein Maturation and the UPR;214
8.10.1;1. Introduction;214
8.10.2;2. N-glycosylation;216
8.10.3;3. O-glycosylation;226
8.10.4;Acknowledgment;232
8.10.5;References;232
8.11;Chapter 11: Monitoring and Manipulating Mammalian Unfolded Protein Response;234
8.11.1;1. Introduction;235
8.11.2;2. Monitoring Mammalian UPR;236
8.11.3;3. Chemical-Genetic Manipulation of Mammalian UPR;240
8.11.4;4. Concluding Remarks;245
8.11.5;Acknowledgments;246
8.11.6;References;246
8.12;Chapter 12: A Screen for Mutants Requiring Activation of the Unfolded Protein Response for Viability;250
8.12.1;1. Introduction;251
8.12.2;2. Screening for Mutants That Require UPR Activation for Viability;253
8.12.3;3. Cloning and Sequencing per Genes;260
8.12.4;4. Monitoring the UPR Activity;263
8.12.5;5. SGA Database;264
8.12.6;6. Media Recipes;265
8.12.7;7. Closing Remarks;265
8.12.8;Acknowledgment;266
8.12.9;References;266
8.13;Chapter 13: Signaling Pathways of Proteostasis Network Unrevealed by Proteomic Approaches on the Understanding of Misfolded Protein Rescue;268
8.13.1;1. Introduction;269
8.13.2;2. 2DE-Based Proteomics Approach Analysis to Study Protein Expression Profile;270
8.13.3;3. Experimental Design;271
8.13.4;4. 2D Gel Electrophoresis;272
8.13.5;5. Protein Identification by MS;274
8.13.6;6. Biochemical Validation;276
8.13.7;7. Data Mining and Publication;277
8.13.8;Acknowledgments;282
8.13.9;References;282
8.14;Chapter 14: Decreased Secretion and Unfolded Protein Response Upregulation;286
8.14.1;1. Introduction;287
8.14.2;2. Heterologous Protein Expression;288
8.14.3;3. Quality Control Mechanisms of the Secretory Pathway;289
8.14.4;4. Endoplasmic Reticulum Export and Trafficking;290
8.14.5;5. Experimental Systems to Evaluate Expression, UPR, and Secretory Processing;290
8.14.6;6. S. cerevisiae Strains Used for Optimal Expression;291
8.14.7;7. Plasmid Design;292
8.14.8;8. Evaluation of Heterologous Protein Expression;294
8.14.9;9. Statistical Analysis of Microarray Results;299
8.14.10;Acknowledgment;308
8.14.11;References;308
8.15;Chapter 15: Measuring Signaling by the Unfolded Protein Response;312
8.15.1;1. Introduction;313
8.15.2;2. Methods to Induce the UPR;317
8.15.3;3. Measuring Signaling by the UPR in S. cerevisiae;317
8.15.4;4. Measuring Signaling by the UPR in Mammalian Cells;327
8.15.5;Acknowledgments;339
8.15.6;References;340
8.16;Chapter 16: Quantitative Measurement of Events in the Mammalian Unfolded Protein Response;344
8.16.1;1. Introduction;345
8.16.2;2. Cell Culture and ER Stress Inducers;346
8.16.3;3. Northern Blots for GRP78/BiP and EDEM;347
8.16.4;4. RT-PCR Analysis of XBP1 mRNA Splicing;350
8.16.5;5. Immunoblotting and Measurement of ATF6;353
8.16.6;6. Measurement of Inhibition of Protein Synthesis;353
8.16.7;7. Measurement of Stimulation of LLO Extension;354
8.16.8;8. Calculations of Transcript Accumulation, Signal Activation, and Correlation;355
8.16.9;9. Conclusion;356
8.16.10;Acknowledgments;357
8.16.11;References;357
8.17;Chapter 17: Regulation of Immunoglobulin Synthesis, Modification, and Trafficking by the Unfolded Protein Response: A Quantitative Approach;360
8.17.1;1. Introduction;361
8.17.2;2. Isolation of Splenic B Cells and Infection Thereof by Retroviruses;363
8.17.3;3. Measurement of Protein Synthesis in Plasma Cells;367
8.17.4;4. Measurement of Ig Mislocalization in Primary B Cells;371
8.17.5;Acknowledgments;375
8.17.6;References;375
8.18;Chapter 18: Use of Chemical Genomics in Assessment of the UPR;378
8.18.1;1. Introduction;379
8.18.2;2. Assessment of the Activation of UPR Transcriptional Program in Cancer Cell;380
8.18.3;3. Gene Expression Signature-Based Identification of UPR Modulators;385
8.18.4;4. Future Perspective of Chemical Genomics in UPR Research;389
8.18.5;Acknowledgments;390
8.18.6;References;390
8.19;Chapter 19: Small GTPase Signaling and the Unfolded Protein Response;394
8.19.1;1. Introduction;395
8.19.2;2. Materials and Methods;397
8.19.3;3. Monitoring the Unfolded Protein Response;399
8.19.4;4. Monitoring Small GTPase Activity;404
8.19.5;5. Pharmacological and Genetic Modulation of UPR and GTPase Signaling;407
8.19.6;Acknowledgments;409
8.19.7;References;409
8.20;Chapter 20: Inhibitors of Advanced Glycation and Endoplasmic Reticulum Stress;412
8.20.1;1. Introduction;413
8.20.2;2. Advanced Glycation and Its Pathophysiology;414
8.20.3;3. Measurement of Advanced Glycation;415
8.20.4;4. Link Between Advanced Glycation and ER Stress;420
8.20.5;5. Effects of Advanced Glycation Inhibitor Against ER Stress;424
8.20.6;6. Conclusion;428
8.20.7;Acknowledgments;428
8.20.8;References;428
8.21;Author Index;432
8.22;Subject Index;450
8.23;Color Plates;460