cytometry third edition, part b - gbv · cytometry, third edition, part a part i principles of...
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Methods in Cell Biology
VOLUME 64CytometryThird Edition, Part B
Zbigniew Darzynkiewicz
Harry A. Crissman
J. Paul Robinson
Contents of Volume 63
xi i
Contributors
x v
Preface to the Third Edition
xix
Preface to the Second Edition
xxiii
Preface to the First Edition
xxvi i
PART VII Cytogenetics and Molecular Genetics
30 . Sorting of Plant Chromosomes
Jaroslav Doleel, Martin A . Lysdk, Marie Kubaldkovd, Hana Simkovit, Jiff Mat-as ,and Sergio Lucretti
I. Introduction
3
II. Application
5
III. Materials
6
IV. Procedures
1 2
V. Critical Aspects of the Procedures
1 8
VI. Instruments
2 1
VII. Results
2 1
VIII. Conclusions and Perspectives
2 6
References
2 8
31 . Quantitative DNA Fiber Mapping
Heinz-Ulli G . Weier
I. Introduction
3 3
II. Materials
3 5
III. Protocols
3 8
IV. Critical Aspects of the Procedure
4 6
V. Results and Discussion
4 7
References
5 2
32 . Primed in Situ Labelin g
Johnny Hindkjaer, Lars Bolund, and Steen Kelvra a
I. Introduction
5 5II. Applications
5 6
III. Materials
5 6
IV. Protocols
58
V. Critical Aspects of the Procedures
66
References
67
33 . Measurements of Telomere Length on Individual Chromosomes b y
Image Cytometry
Steven S. S . Poon and Peter M. Lansdorp
I. Introduction
7 0
II. Background
7 2
III. Methods
7 7
IV. Results
88
V. Discussion
92References
94
34 . Detection of Chromosome Translocation Products in Single Interphas e
Cell Nucle i
Jingly Fung, Santiago Munne, and Heinz-Ulli G . Weier
I. Introduction
9 8II. Materials
9 9
III. Protocols
10 2
IV. Results and Discussion
108
V. Critical Aspects of the Procedure
11 1
VI. Applications
11 2
References
11 3
PART VIII Cell Function and Differentiatio n
35 . Analysis of Mitochondria by Flow Cytometry
Martin Poot and Robert H . Pierce
I. Introduction
11 8
II. Materials and Methods
12 1
III. Critical Aspects
12 5
References
12 6
36 . Analysis of RNA Synthesis by Cytometry
Peter ostrup Jensen, Jacob Larsen, and Jergen K. Larsen
I. Introduction
12 9
II. Background
13 0
III. Methods for Analysis of 5'-Bromouridine Incorporation and
13 1
DNA Conten t
IV. Results of Labeling RNA with 5 ' -Bromouridine
134
V. Applications
13 6
References
137
37 . Flow Cytometry of Erythropoiesis in Culture : Bivariate Profiles of Feta l
and Adult Hemoglobin
Ralph M. Böhmer
I. Introduction
13 9II. Details of the Method
14 1III. Sample Experiments
143IV. Problems and Limitations
14 9References
15 1
38 . Flow Cytometric Analysis of Human Hemopoietic Progenito r
Differentiation by Assessing Cell Division Rate and Phenotypic Profil e
Luca Pierelli, Giovanni Scambia, and Andrea Fattoross i
I. Introduction
15 3II. Background
15 5III. Critical Aspects of Methodology
15 6IV. Functionally Distinct Circulating Hemopoietic Progenitor Subsets Can Be
15 7Assessed during Cytokine-Driven Differentiatio n
V. Concluding Remarks
16 7References
16 9
PART IX Experimental Oncology
39 . Cytometry of Antitumor Drug-Intracellular Target Interactions
Paul J. Smith and Marie Wiltshire
I. Introduction
17 3II. General Classification of Cytotoxic Anticancer Agents
17 4III. Establishment of Quality Control Parameters
17 8IV. Drug-DNA Interactions
18 3V. Conclusions
18 8References
19 0
40 . Monitoring of Cellular Resistance to Cancer Chemotherapy: Dru g
Retention and Efflux
Awtar Krisha n
I. Introduction and Background
19 3II. Applications
19 6III. Cell Lines, Efflux, Multiple Drug Resistance Drugs, and Blockers
19 6IV. Staining Protocols
19 7V. Critical Aspects
19 8VI. Controls, Standards, and Instruments
19 9VII. Results and Conclusions
20 1References
206
41 . Resistance of Tumor Cells to Chemo- and Radiotherapy Modulated b ythe Three-Dimensional Architecture of Solid Tumors and Spheroid s
Ralph E . Durand and Peggy L. Olive
I. Introduction and Historical Perspective
21 1
II. Background
21 3
III. Methods
21 5
IV. Results and Discussion
21 7
V. Conclusions and Future Directions
22 7
References
22 8
42 . Analysis of DNA Damage in Individual Cell s
Peggy L . Olive, Ralph E. Durand, Judit P. Bandth, and Peter" Johnston
I. Introduction
23 5
II. The Development of the Single Cell Gel Electrophoresis/Comet Assay
23 6
III. Comet Preparation and Analysis
23 8
IV. Types of Damage Detected by the Comet Assay
242
V. Using DNA Damage to Predict Cell Survival in Complex Systems
244
VI. Future Directions
246
References
247
43 . Cytometric Methods to Analyze Ionizing-Radiation Effect s
William D . Wright, Isabelle Lagroye, Peng Zhang, Robert S. Malyapa ,
and Joseph L. Roti Rot i
I. Introduction
25 1
II. Applications
252
III. Methods for Measuring DNA Damage on a Cell-by-Cell Basis
253
IV. Summary
267
References
267
44 . Cytometric Methods to Analyze Thermal Effect s
Robert P . VanderWaal, Ryuji Higashikubo, Mai Xu, Douglas R . Spitz,William D . Wright, and Joseph L . Roti Roti
I. Introduction
26 9
II. Application
27 0
III. Methods to Measure Nuclear and Nuclear Matrix Protein Content
27 1
IV. Identification of Altered DNA Replication Patterns Following Heat Shock
27 6
V. Nuclear Localization of hsp70
27 8
VI. Prooxidant Measurement
28 0
VII. Results
28 1
References
285
PART X Clinical Oncology
45 . Multiparameter Data Acquisition and Analysis of Leukocytes by
Flow Cytometry
Carleton C . Stewart and Sigrid' . Stewart
I. Introduction
28 9II. Correlated List Mode Data
29 0III. Verification of Instrument Performance
29 3IV. Optical Filtration and Spectral Compensation
29 5V. Multiparameter Data Analysis
30 8VI. Summary
31 1References
31 1
46 . Immunophenotyping of Hematological Malignancies by Lase r
Scanning Cytometry
Richard J. Clatch
I. Immunophenotyping of Leukemia and Lymphoma: General Considerations
31 3II. Description of Laser Scanning Cytometry
31 6III. Immunophenotyping by Laser Scanning Cytometry
31 6IV. Extensions of the Method
32 7V. Conclusions
34 0References
34 0
47 . Immunophenotyping of Acute Leukemia : Utility of CD45 for Blas t
Cell Identification
J-P. Vial and F . Lacombe
I. Introduction
344II. Background
344III. Methods
34 5IV. Results and Comparison with Other Methods
34 8V. Critical Aspects of the Methodology
35 2VI. Pitfalls and Misinterpretation of the Data
35 3VII. Future Directions
35 5References
35 7
48 . Cell Proliferation Markers in Human Solid Tumors : Assessing Their
Impact in Clinical Oncology
Maria Grazia Daidone, Aurora Costa, and Rosella Silvestrin i
I. Introduction
35 9II. Proliferation Markers
36 1III. Biological Studies
365IV. Clinical Studies
36 6V. Conclusions on First Generation Translational Studies with
37 7Proliferation MarkersReferences
378
49 . Detection of Minimal Residual Diseas e
Andrzej Deptala and Sharon P . Mayer
I . Introduction
38 5IL Tissue Sources to Detect Minimal Residual Disease
38 7III. Methods to Detect Minimal Residual Disease
38 8IV. Technical Problems
41 4V. Concluding Remarks
41 6
References
41 6
50 . Analysis of Human Tumors by Laser Scanning Cytometr y
Wojciech Gorczyca, Andrzej Deptala, Elzbieta Bedner, Xun Li, Myron R. Melarned,
and Zbigniew Darzynkiewicz
I . Introduction
42 2
11 . Analysis of Cellular DNA Content by Laser Scanning Cytometry
423
III. Analysis of Apoptosis by Laser Scanning Cytometry
425
IV. Analysis of Proliferation Associated Antigens by Laser Scanning Cytometry
43 0
V. Analysis of Estrogen Receptors by Laser Scanning Cytometry
43 5
VI. Analysis of Transcription Factors by Laser Scanning Cytometry
437
VII. Measurement of Nucleoli Using Laser Scanning Cytometry Fluorescence in
43 8
Situ Hybridization ProtocolReferences
44 1
51 . Laser Cytometry of Human Tissues and Tumors : Proliferation and
Therapeutic Applications
David A . Rew
I. Introduction
44 6
II. Ploidy and Proliferation in Surgical Oncology
447
III. Cytometric Studies of Proliferation
44 8IV. The Halogenated Pyrimidines in Cell Proliferation Research
44 9
V. Clinical Studies of Cell Production Rates with Thymidine Analogs
45 2
VI. Further Applications of Cytometry in Clinical Oncology
47 4
VII. Conclusions
47 8
References
47 8
52 . Prediction and Precise Diagnosis of Diseases by Data Pattern Analysis i n
Multiparameter Flow Cytometry: Melanoma, Juvenile Asthma, and
Human Immunodeficiency Virus Infection
Günter Valet, Hanna Kahle, Friedrich Otto, Edeltraut Bräutigam, and Luc Kestens
I. Introduction
48 8
II. Material and Methods
48 9
III. Results
49 3
IV. Discussion
50 6References
507
PART XI Microorganisms and Infectious Disease s
53 . Flow Cytometric Analysis of Microorganism s
S . A . Sincock and J. Paul Robinso n
I. Introduction
51 1II. Experimental Approaches
51 4III. Applications in Medical and Food Microbiology
52 6IV. Conclusion
53 1
References
53 2
54 . Staining and Measurement of DNA in Bacteri a
Harald B . Steen
I. Introduction
53 9II. Basic Considerations
54 0III. Experimental Methods
54 3IV. Standards and Controls
54 8
References
55 0
55 . Flow Cytometric Monitoring of Bacterial Susceptibility to Antibiotic s
Mette Walberg and Harald B . Stee n
I. Introduction
553II. Fluorescent Dyes
55 4III. Uptake of Fluorescent Dyes
55 5IV. Effects of Antibiotics
55 8V. Assessment of Drug Effects
55 8VI. Applications of Flow Cytometry to Medical Microbiology
563
References
563
56 . Flow Cytometry for Evaluation and Investigation of Human
Immunodeficiency Virus Infectio n
Thomas W. Mc Closkey
I. Introduction
56 7II. Application of Flow Cytometry to Monitor HIV Infection
56 8III. Application of Flow Cytometry to Investigate HIV Disease
58 2IV. Conclusions
58 4
References
58 4
Index
593
Volumes in Series
609
Contents of Volume 63Cytometry, Third Edition, Part A
PART I Principles of Cytometry and General Method s
1. A Brief History of Flow Cytometry and Sortin g
Myron R . Melame d
2. Principles of Flow Cytometry : An Overvie w
Alice L. Giva n
3. Laser Scanning Cytometry
Louis A . Kamentsk y
4. Principles of Confocal Microscopy
J. Paul Robinson
5. Optical Measurements in Cytometry : Light Scattering, Extinction ,
Absorption, and Fluorescence
Howard M. Shapiro
6. Flow Cytometric Fluorescence Lifetime Measurements
Harry A . Crissman and John A . Steinkamp
7. Principles of Data Acquisition and Display
Howard M . Shapiro
8. Time as a Flow Cytometric Parameter
Larry Seamer and Larry A . Sklar
9. Protein Labeling with Fluorescent Probe s
Kevin L. Holmes and Larry M. Lantz
PART II Cell Preparation
10. Preparation of Cells from Bloo d
J. Philip McCoy, Jr .
11. Cell Preparation for the Identification of Leukocyte s
Carleton C . Stewart and Sigrid J. Stewart
12. Strategies for Cell Permeabilization and Fixation in Detecting Surfac eand Intracellular Antigen s
Steven K. Koester and Wade E. Bolto n
PART III Standardization, Quality Assuranc e
13. Stoichiometry of Immunocytochemical Staining Reaction s
James IN. Jacobberger
14. Standardization and Quantitation in Flow Cytometr yRobert A . Hoffman
PART IV Cell Proliferation
15. Methods to Identify Mitotic Cells by Flow Cytometry
Gloria Juan, Frank Traganos, and Zbigniew Darzynkiewicz
16. Cell Cycle Kinetics Estimated by Analysis o fBromodeoxyuridine Incorporation
Nicholas H. A . Terry and R . Allen White
17. Flow Cytometric Analysis of Cell Division History Using Dilution o fCarboxyfluorescein Diacetate Succinimidyl Ester, a Stably Integrate dFluorescent Prob e
A. Bruce Lyons, Jhagvaral Hasbold, and Philip D . Hodgkin
18. Antibodies against the Ki-67 Protein : Assessment of the Growth Fractionand Tools for Cell Cycle Analysi s
Elmar Endl, Christiane Hollmann, and Johannes Gerdes
19. Detection of Proliferating Cell Nuclear Antigen
Jargen K. Larsen, Göran Landberg, and Göran Roos
20. Lymphocyte Activation Associated Antigens
Andrea Fattorossi, Alessandra Battaglia, and Cristiano Ferlini
PART V Cell Death/Apoptosi s
21. Analysis of Mitochondria during Cell Deat h
Andrea Cossarizza and Stefano Salviol i
22. Cytometry of Caspases
Steven K. Koester and Wade E . Bolto n
23. Analysis of Apoptosis in Plant Cells
Iona E . Wei r
24. Difficulties and Pitfalls in Analysis of Apoptosi s
Zbigniew Darzynkiewicz, Elzbieta Bedner, and Frank Tragano s
PART VI Cell-Cell, Cell-Environment Interactions
25. Analysis of Cell Migratio n
Nicole Dodge Zantek and Michael S . Kinch
26. Three-Dimensional Extracellular Matrix Substrates for Cell Cultur e
Sherry L . Voytik-Harbin
27. Three-Dimensional Imaging of Extracellular Matrix and Extracellular
Matrix-Cell Interaction s
Sherry L . Voytik-Harbin, Bartlomiej Rajwa, and J . Paul Robinson
28. Cytometric Analysis of Cell Contact and Adhesio n
Michael S . Kinch
29. Invadopodia : Unique Methods for Measurement of Extracellular Matrix
Degradation in Vitro
Emma T. Bowden, Peter J. Coopman, and Susette C . Mueller