Autophagy: B Autophagy in mammalian systems
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier
2009
|
| Schriftenreihe: | Methods in enzymology
452 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XLIX, 508 S., [6] Bl. Ill., graph. Darst. |
| ISBN: | 9780123745477 |
Internformat
MARC
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| 020 | |a 9780123745477 |9 978-0-12-374547-7 | ||
| 035 | |a (OCoLC)551947213 | ||
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| 041 | 0 | |a eng | |
| 049 | |a DE-12 |a DE-19 |a DE-20 |a DE-91G |a DE-355 | ||
| 245 | 1 | 0 | |a Autophagy |n B |p Autophagy in mammalian systems |c ed. by Daniel J. Klionsky |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier |c 2009 | |
| 300 | |a XLIX, 508 S., [6] Bl. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in enzymology |v 452 | |
| 490 | 0 | |a Methods in enzymology |v ... | |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-017321006 | ||
Datensatz im Suchindex
| _version_ | 1804138827656200192 |
|---|---|
| adam_text | Contents
Contributors
xiii
Preface
xxi
Volumes in Series
xxiii
1.
Monitoring Autophagy in Mammalian Cultured Cells through the
Dynamics of LC3
1
Shunsuke Kimura, Naonobu Fujita, Takeshi Noda, and Tamotsu Yoshimori
1.
Introduction
2
2.
Estimation of Autophagy Induction by LC3
Puncta
Formation
4
3.
The tfLC3 Assay
7
4.
Determination of LC3 Turnover by Western Blotting
9
5.
Concluding Remarks
10
References
11
2.
Methods for Monitoring Autophagy Using
Transgenic Mice
13
Noboru Mizushima
1.
Introduction
14
2.
Genetic Features of GFP-LC3 Mice
15
3.
Mouse Maintenance
16
4.
Genotyping of GFP-LC3 Mice
17
5.
Sample Preparation
18
6.
Fluoresence Microscopy
19
7.
Precautions
20
References
21
3.
Using Photoactivatable Proteins to Monitor
Autophagosome Lifetime
25
Dale W. Hailey and Jennifer Lippincott-Schwartz
1.
Introduction
26
2.
Photoactivatable Fluorescent Protein Labeling
27
3.
Experimental Example: Setting up a Sample and
Optimizing Photoactivation
32
4.
Photobleaching
35
5.
Carrying Out the Photochase Assay
36
v¡
Contents
6.
Pulse-Labeling Induced Autophagosomes
38
7.
Determining the Half-Life of Pulse-Labeled Autophagosomes
40
8.
Controls
42
9.
Conclusions
43
References
44
4.
Assaying of Autophagic Protein Degradation
47
Chantai
Bauvy, Alfred J.
Meijer,
and Patrice Codogno
1.
Introduction
48
2.
Assaying the Degradation of Long-Lived Proteins in
Cultured Cell Lines
48
3.
Assay of the Degradation of Long-Lived Protein in Isolated
Rat Hepatocytes
50
4.
Other Methods for Measuring Autophagic Flux
57
5.
Pitfalls
58
References
59
5.
Sequestration Assays for Mammalian Autophagy
63
Per
O. Seglen,
Anders 0verbye, and Frank Saetre
1.
Introduction
64
2.
Membrane-lmpermeant Autophagy Probes: Introduction into
Cytosol by Reversible Electropermeabilization (Electroporation)
of the Plasma Membrane
67
3.
Damage-Induced Cell Permeabilization
69
4.
Electrodisruption: A Simple Method for the Separation
of Sedimentable from Soluble Cell Components
70
5.
Electroinjected Sugars as Autophagic Sequestration Probes
71
6.
Cytosolic Proteins as Autophagic Sequestration Probes
74
7.
Autophagic Fragment Generation: An Autophagic
Cargo Assay Applicable to Whole Cells
77
8.
Concluding Remarks
79
References
80
6.
Assays to Assess Autophagy Induction and Fusion of Autophagic
Vacuoles
with a Degradative Compartment, Using
Monodansylcadaverine (MDC) and DQ-BSA
85
Cristina Lourdes Vázquez
and
María
Isabel Colombo
1.
Overview
86
2.
Assessing Autophagy Induction by Fluorescence
Microscopy and Fluorometry
86
3.
Monitoring the Formation of an Autolysosome
92
4.
Concluding Remarks
94
Acknowledgments
94
References
94
Contents
vii
7.
The GST-BHMT Assay and Related Assays for Autophagy
97
Patrick B. Dennis and Carol A. Mercer
1.
Introduction
98
2.
Measurement of Macroautophagy Using the GST-BHMT Assay
100
3.
Measurement of Autophagy Using a Linker-Specific
Cleavage Site (LSCS)
107
4.
Measurement of Reticulophagy and Mitophagy Using
LSCS-Based Reporters
110
5.
Concluding Remarks
114
Acknowledgments
116
References
116
8.
Monitoring Starvation-Induced Reactive Oxygen
Species Formation
119
Ruth Scherz-Shouval and Zvulun Elazar
1.
Introduction
120
2.
Detection of
ROS
in Living Cells Using Fluorescent Dyes
121
3.
Interfering with
ROS
Formation: The Use of Antioxidants to
Inhibit Autophagy
126
4.
Concluding Remarks
128
Acknowledgments
128
References
129
9.
Flow Cytometric Analysis of Autophagy in Living
Mammalian Cells
131
Elena Shvets and Zvulun Elazar
1.
Introduction
132
2.
Qualitative Analysis of LC3 Levels in Cells
133
3.
Establishing Flow Cytometry and FACS Analysis to Quantify
GFP-LC3 Levels During
Amino
Acid Deprivation
134
4.
Quantification of Decline in GFP-LC3 Using Flow Cytometry and
FACS Analysis
137
5.
Using FACS to Quantify Autophagy in Response to
Specific Treatments
138
6.
Concluding Remarks
139
Acknowledgments
140
References
140
10.
Monitoring Autophagy by Electron Microscopy in
Mammalian Cells
143
Päivi Ylä-Anttila,
Helena Vihinen, Eija Jokitalo, and Eeva-Liisa Eskelinen
1.
Introduction
144
2.
Methods
146
viii Contents
3.
Results and Discussion
155
4.
Concluding Remarks
162
Acknowledgments
163
References
163
11.
Monitoring
Mammatian
Target of Rapamycin (mTOR) Activity
165
Tsuneo Ikenoue, Sungki Hong, and Ken Inoki
1.
Introduction
166
2.
Methods
168
3.
Concluding Remarks
177
Acknowledgment
178
References
178
12.
Monitoring Autophagic Degradation of P62/SQSTM1
181
Geir Bj0rk0y, Trond Lamark, Serhiy
Pankiv, Aud 0vervatn,
Andreas Brech, and Terje Johansen
1.
Introduction
182
2.
Monitoring Autophagy-Mediated Degradation of
Endogenous P62/SQSTM1
183
3.
Monitoring the Autophagic Degradation of
p62/SQSTMl
by Live Cell Imaging
192
4.
Concluding Remarks
194
Acknowledgments
195
References
195
13.
Cytosolic LC3 Ratio as a Quantitative Index of Macroautophagy
199
Motoni
Kad
owaki
and
Md. Razaul
Karim
1.
Introduction
200
2.
Measurement of Proteolysis
201
3.
Measurement of the Cytosolic LC3 Ratio
203
4.
Concluding Remarks
211
References
211
14.
Method for Monitoring Pexophagy in Mammalian Cells
215
Junji Ezaki, Masaaki Komatsu, Sadaki Yokota, Takashi Ueno,
and Eiki
Kominami
1.
Introduction
216
2.
Experimental Models for the Study of Pexophagy in Mammals
216
3.
Monitoring Degradation of Excess Peroxisomes
217
Contents
¡χ
4.
Concluding Remarks
223
Acknowledgment
225
References
225
15.
Mitophagy in Mammalian Cells: The Reticulocyte Model
227
Ji Zhang, Mondira Kundu, and Paui A. Ney
1.
Introduction
228
2.
Reticulocyte Production and Maturation
229
3.
Methods
230
4.
Mouse Models of Mitophagy
239
5.
Conclusions
240
Acknowledgments
241
References
241
16.
Assessing Mammalian Autophagy by WIPI-l/Atgie
Puncta
Formation
247
Tassula Proikas-Cezanne and Simon G. Pfisterer
1.
The Human WIPI Protein Family
248
2.
WIPI-1 Puncta-Formation Assay
250
3.
Indirect Immunofluorescence to Visualize Endogenous
WIPI-1 by Confocal Microscopy
251
4.
Direct Fluorescence of Transiently Expressed GFP-WIPI-1
255
5.
Generation of Stable GFP-WIPI-1 Cell Lines
256
6.
Live-Cell Imaging of GFP-WIPI-1
257
7.
WIPI-1 Protein-Lipid Overlay Assay
258
8.
Concluding Remarks
259
Acknowledgments
259
References
259
17.
Correlative Light and Electron Microscopy
261
Minoo
Razi
and Sharon A. Tooze
1.
Introduction
262
2.
CLEM
263
3.
Cell Culture
264
4.
Light Microscopy
266
5.
Electron Microscopy
268
6.
Results, Interpretation, and Presentation
271
7.
Tomography and CLEM
273
8.
Cryoimmunogold EM and CLEM—the Future?
273
9.
Conclusions
274
References
274
Contents
18. Semiconductor Nanocrystals
¡η
Autophagy Research:
Methodology Improvement at Nanosized Scale
277
Oleksandr Seleverstov, James M. Phang, and
Olga
Zabirnyk
1.
Introduction
278
2.
Autophagy Probing in Living Cells Using Different-Sized
Fluorescent NP
279
3.
Application of Nanotechnology-Based Products for Other
Methods in Autophagy Research. The Perspectives
285
4.
Conclusion and Future Perspectives
290
Acknowledgments
292
References
293
19.
Methods to Monitor Chaperone-Mediated Autophagy
297
Susmita Kaushik and Ana Maria Cuervo
1.
Introduction
298
2.
Experimental Models for the Study of CMA
300
3.
Properties of CMA Substrates
301
4.
Methods to Measure CMA
303
5.
Measurement of Protein Degradation Rates
303
6.
Measurement of Levels of Key CMA Components
308
7.
Analysis of the Subcellular Location of CMA-Active Lysosomes
312
8.
In Vitro Assay to Measure
Translocation
of CMA Substrates
315
9.
Concluding Remarks
320
Acknowledgments
321
References
321
20.
Methods to Monitor Autophagy of Salmonella
enterica
serovar Typhimurium
325
Cheryl L. Birmingham and John H. Brumell
1.
Introduction
326
2.
Characteristics of Autophagy of S. Typhimurium
330
3.
S. Typhimurium Infection and Autophagy
334
4.
Controls for Autophagy of Bacteria
337
5.
Concluding Remarks
339
References
339
21.
Monitoring Autophagy during Mycobacterium
tuberculosis Infection
345
Marisa
Ponpuak, Monica
A. Delgado,
Rasha A. Elmaoued,
and Vojo
Deretic
1.
Introduction
346
2.
Methods
347
Contents xi
Acknowledgments
359
References
359
22.
Streptococcus-, Shigella-, and Listeria-lnduced Autophagy
363
Michinaga Ogawa, Ichiro Nakagawa, Yuko Yoshikawa,
Torsten Hain,
Trinad
Chakraborty, and Chihiro Sasakawa
1.
Introduction
364
2.
GAS Infection and Autophagy
365
3.
Shigella Infection and Autophagy
371
4. Listeria
Infection and Autophagy
376
5.
Concluding Remarks
379
Acknowledgments
379
References
379
23.
Kinetic Analysis of Autophagosome Formation and
Turnover in Primary Mouse
Macrophages
383
Michele
S.
Swanson, Brenda
G.
Byrne, and Jean-Francois Dubuisson
1.
Introduction
384
2.
Monitoring Flux Through the Autophagy Pathway
386
3.
Assessing the Impact of Infection on the Autophagy Pathway
388
4.
LC3 Localization in Primary Mouse
Macrophages
390
5.
Isolation of Bone Marrow-Derived
Macrophages
393
6.
Conclusion
400
References
400
24.
Monitoring Macroautophagy by Major Histocompatibility
Complex Class II Presentation of Targeted Antigens
403
Monique Gannagé
and Christian
Münz
1.
Introduction
404
2.
Antigen Presentation on MHC Class II Molecules After
Macroautophagy
404
3.
Substrates of Endogenous Antigen Processing for MHC Class II
Presentation via Macroautophagy
405
4.
Methods to Measure Antigen Processing for MHC Class II
Presentation After Macroautophagy
407
5.
Concluding Remarks
419
Acknowledgments
419
References
419
25.
Detachment-Induced Autophagy In Three-Dimensional
Epithelial Cell Cultures
423
Jayanta Debnath
1.
Introduction
424
xii
Contents
2.
Monitoring and Manipulating Autophagy In Mammalian
Epithelial Cells
425
3.
Autophagy During Lumen Formation In
3D
Epithelial Cultures
428
4.
Measuring Autophagy In Traditional Anoikis Assays
434
5.
Incubation of Cells With lntegrin Function-Blocking Antibodies
437
6.
Conclusions
437
Acknowledgments
438
References
438
26.
Methods for Inducing and Monitoring Liver Autophagy Relative
to Aging and Antiaging Caloric Restriction in Rats
441
Alessio Donati,
Gabriella
Cavallini, and Ettore Bergamini
1.
Overview
442
2.
Models of Caloric Restriction
442
3.
Methods to Induce and Monitor Liver Autophagy
444
4.
A Minimally Invasive Procedure for the Rapid Evaluation of the
Induced Intensification of Autophagy
448
5.
Autophagic Protein Degradation in Isolated Liver Cells
449
6.
Concluding Remarks
453
References
454
27.
Physiological Autophagy in the Syrian Hamster
Harderian Gland
457
Ignacio Vega-Naredo
and
Ana Coto-Montes
1.
introduction
458
2.
Methods to Detect Autophagy by Morphological Techniques
459
3.
Methods to Detect Autophagy by Biochemical and Molecular
Biology Techniques
465
4.
Measurement of Cell Viability: Ratio of Cathepsins B:D
466
5.
Analysis of the Lysosomal Pathway
467
6.
Western Blot Analysis of Autophagy-Related Proteins
471
7.
Methods to Detect Chaperone-Mediated Autophagy
472
8.
Concluding Remarks
473
Acknowledgments
474
References
474
Author Index
477
Subject Index
499
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| genre_facet | Aufsatzsammlung |
| id | DE-604.BV035400355 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T21:34:23Z |
| institution | BVB |
| isbn | 9780123745477 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017321006 |
| oclc_num | 551947213 |
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| physical | XLIX, 508 S., [6] Bl. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Elsevier |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Autophagy B Autophagy in mammalian systems ed. by Daniel J. Klionsky Amsterdam [u.a.] Elsevier 2009 XLIX, 508 S., [6] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 452 Methods in enzymology ... Wirbeltiere (DE-588)4066376-0 gnd rswk-swf Autophagie Physiologie (DE-588)4441664-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Autophagie Physiologie (DE-588)4441664-7 s Wirbeltiere (DE-588)4066376-0 s b DE-604 Klionsky, Daniel J. Sonstige oth (DE-604)BV035270787 2 Methods in enzymology 452 (DE-604)BV000000938 452 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017321006&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Autophagy Methods in enzymology Wirbeltiere (DE-588)4066376-0 gnd Autophagie Physiologie (DE-588)4441664-7 gnd |
| subject_GND | (DE-588)4066376-0 (DE-588)4441664-7 (DE-588)4143413-4 |
| title | Autophagy |
| title_auth | Autophagy |
| title_exact_search | Autophagy |
| title_full | Autophagy B Autophagy in mammalian systems ed. by Daniel J. Klionsky |
| title_fullStr | Autophagy B Autophagy in mammalian systems ed. by Daniel J. Klionsky |
| title_full_unstemmed | Autophagy B Autophagy in mammalian systems ed. by Daniel J. Klionsky |
| title_short | Autophagy |
| title_sort | autophagy autophagy in mammalian systems |
| topic | Wirbeltiere (DE-588)4066376-0 gnd Autophagie Physiologie (DE-588)4441664-7 gnd |
| topic_facet | Wirbeltiere Autophagie Physiologie Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017321006&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035270787 (DE-604)BV000000938 |
| work_keys_str_mv | AT klionskydanielj autophagyb |