Note: Front Cover -- Cytometry, 4th Edition: New Developments -- Copyright Page -- Contents -- Contributors -- Preface -- Preface to the Third Edition -- Preface to the Second Edition -- Preface to the First Edition -- Part I: Instrumentation/Fluorochromes -- Chapter 1. Optimization of Emission Optics for Multicolor Flow Cytometry -- I. Introduction -- II. Fluorochromes -- III. Hardware Components Affecting Light Collection -- IV. Maximizing Signal Intensities -- V. Maximizing Signal Collection Quality -- VI. Emission Collection Optimization -- VII. Testing Emission Optics -- References -- Chapter 2. Two-Photon Tissue Cytometry -- I. Introduction -- II. Technical Development of Two-Photon Tissue Cytometry -- III. Experimental Demonstration of Two-Photon Tissue Cytometry -- IV. Future Outlook -- V. Conclusion -- References -- Chapter 3. Confocal Microscopy: Quantitative Analytical Capabilities -- I. Introduction -- II. Cartesian Coordinates, Distance, Size, Shape, and Volume in Confocal Microscopy -- III. Measurements of Fluorescence Intensity in Confocal Microscopy -- IV. Time Resolution in Confocal Microscopy -- V. Confocal Techniques Based on Measurements of Fluorescence Intensity vs Time -- VI. Spectrally Resolved Confocal Microscopy -- VII. Conclusion -- References -- Chapter 4. Surface-Plasmon-Coupled Emission. New Technology for Studying Molecular Processes -- I. Introduction -- II. Overview of Surface Plasmon Resonance -- III. Surface-Plasmon-Coupled Emission -- IV. Experimental Studies of Surface-Plasmon-Coupled Emission -- V. Practical Applications -- VI. Conclusion -- References -- Chapter 5. Cytometry of Fluorescence Resonance Energy Transfer -- I. Introduction -- II. Theory of FRET -- III. Measuring FRET -- IV. Applications -- V. Perspectives -- VI. Conclusions -- References -- Chapter 6. The Rainbow of Fluorescent Proteins. , I. The Fluorescent Proteins -- II. Flow Analysis Using Fluorescent Proteins -- III. Flow Sorting Using Fluorescent Proteins -- IV. Conclusion -- References -- Chapter 7. Labeling Cellular Targets with Semiconductor Quantum Dot Conjugates -- I. Introduction -- II. Selection of QDs and Their Conjugates -- III. Labeling of Fixed Cells for Fluorescence Microscopy -- IV. Measurements on Living Cells Using QD Conjugates -- V. Conclusion -- References -- Chapter 8. Next-Generation Laser Scanning Cytometry -- I. Introduction -- II. LSC-Hybrid Technology -- III. Description of the LSC Platform -- IV. Selected Applications -- V. Utility of Solid-Phase Imaging Cytometry in Life Science Research and Drug Discovery -- References -- Part II: General Techniques -- Chapter 9. Biohazard Sorting -- I. Introduction -- II. Critical Aspects of the Procedure -- III. Applications and Future Directions -- References -- Chapter 10. Guidelines for the Presentation of Flow Cytometric Data -- I. Introduction -- II. General Principles of Graphical Presentation -- III. Statistics -- IV. Subset Analysis -- V. Conclusion -- References -- Chapter 11. Mechanism of Antitumor Drug Action Assessed by Cytometry -- I. Introduction -- II. Choice of a Model System -- III. Drug Dose and Length of Exposure -- IV. Single-Parameter DNA Histogram Analysis -- V. Multiparameter Approaches -- VI. Data Presentation -- VII. Summary and Future Directions -- References -- Chapter 12. Cytometric Methods to Detect Apoptosis -- I. Introduction -- II. Physical and Molecular Features of Cells Dying by Apoptosis or Necrosis -- III. Different Time-Windows for Detection of Apoptosis: Possible Source of Error in Measurement of Incidence of Apoptosis -- IV. Light-Scattering Properties of Cells Dying by Apoptosis -- V. Mitochondrial Transmembrane Potential -- VI. Activation of Caspases -- VII. Annexin V Binding. , VIII. DNA Fragmentation -- IX. Susceptibility of DNA to Denaturation -- X. Activation of ''Tissue'' Transglutaminase -- XI. Measuring Incidence of Apoptosis: Which Method to Choose? -- References -- Chapter 13. Real-Time Analysis of Apoptosis In Vivo -- I. Introduction -- II. In Vivo Membrane Markers -- III. A New Generation of Caspase Markers -- IV. Conclusion -- References -- Chapter 14. Detection of DNA Damage in Individual Cells by Analysis of Histone H2AX Phosphorylation -- I. Introduction -- II. Considerations in the Use of yH2AX as a Measure of Double-Stranded Breaks -- III. Methods of Analysis -- IV. Typical Results -- V. Possible Applications -- VI. Conclusion -- References -- Chapter 15. Cytometry of Freshwater Phytoplankton -- I. Introduction -- II. Background -- III. Methods -- IV. Results -- V. Limitations and Applications -- Future Directions -- References -- Chapter 16. Multiplexed Microsphere Assays for Protein and DNA Binding Reactions -- I. Introduction -- II. Technology and Instrumentation -- III. Methods -- IV. Results -- V. Software -- VI. Critical Aspects of the Methodology -- VII. Comparison with Other Methods -- VIII. Future Directions -- References -- Part III: Immunology/T-Cell Responses -- Chapter 17. Flow Cytometry Applications of MHC Tetramers -- I. Introduction -- II. Materials and Methods -- III. Analyzing Tetramer Data -- IV. Combining Tetramer Staining with Functional Assays -- V. Conclusion -- References -- Chapter 18. Use of Peptides and Peptide Libraries as T-Cell Stimulants in Flow Cytometric Studies -- I. Introduction -- II. Background -- III. Results/Discussion of the Literature -- IV. Technical Considerations -- V. Specific Applications -- VI. Potential Clinical Use -- VII. Protocols -- References -- Chapter 19. Flow Cytometric Analysis of Human Antigen-Specific T-Cell Proliferation. , I. Introduction and Background -- II. Methods -- III. Results -- IV. Critical Aspects of the Methodology -- V. Pitfalls and Misinterpretation of the Data -- VI. Future Directions -- References -- Chapter 20. Detection of T-Cell Degranulation: CD107a and b -- I. Introduction: Methods to Assess CD8+ T-Cell Function -- II. Materials and Methods -- III. Results -- IV. Critical Aspects -- V. Applications -- References -- Chapter 21. T-Cell Responses to Cancer -- I. Introduction -- II. Methods to Identify and Enumerate TAA-Specific T Cells -- III. Important Considerations -- IV. Methods to Further Analyze In Vivo Biology of Antitumor T Cells -- V. Novel Issues and Methods -- VI. Conclusion -- References -- Part IV: Multi-Color Immunophenotyping -- Chapter 22. Multicolor Flow Cytometric Analysis in SIV-Infected Rhesus Macaque -- I. Introduction -- II. Methods -- III. Flow Cytometry Instrumentation and Software -- IV. Instrument Setup -- V. Critical Aspects of the Technology -- VI. Application of 10-Color Analysis to SIV Infection -- VII. Conclusion -- References -- Chapter 23. Multicolor Immunophenotyping: Human Immune System Hematopoiesis -- I. Introduction -- II. Methodology -- III. Normal Immunophenotypic Patterns of Maturation -- IV. Abnormal Immunophenotypic Patterns of Maturation -- References -- Chapter 24. Multicolor Immunophenotyping: Human Mature Immune System -- I. Introduction -- II. Choice of Markers -- III. Staining Panels: Matching Fluorochrome with Cell Marker -- IV. Conclusion -- References -- Chapter 25. Differential Diagnosis of T-Cell Lymphoproliferative Disorders by Flow Cytometry Multicolor Immunophenotyping. Correlation with Morphology -- I. Introduction -- II. Materials -- III. Methods -- IV. Identification of Abnormal T-Cell Population by Flow Cytometry -- V. Precursor T Lymphoblastic Lymphoma/Leukemia. , VI. Peripheral (Mature/Post-thymic) Lymphoma Versus Precursor T-Lymphoblastic Lymphoma/Leukemia -- VII. Thymocytes from Thymic Hyperplasia/Thymoma Versus Precursor T-Lymphoblastic Lymphoma/Leukemia -- VIII. Mature T-Cell Lymphoproliferative Disorders -- IX. CD117 Expression in T-Cell Lymphoproliferations -- X. Blastic NK Cell Lymphoma (DC-2 Acute Leukemia) -- XI. Conclusion -- References -- Chapter 26. Isolation and Immunophenotyping of Human and Rhesus Macaque Dendritic Cells -- I. Introduction -- II. In Vitro Differentiation of Monocyte-Derived Dendritic Cells -- III. Detection and Sorting Procedures of Subsets of Dendritic Cells -- IV. Culture and Activation of Dendritic Cells -- References -- Chapter 27. B-Cell Immunophenotyping -- I. Introduction -- II. Immunophenotyping of B-Cell Developmental Stages in the Bone Marrow -- III. Peripheral B-Cell Populations -- IV. Antigen-Induced B-Cell Subsets -- V. Antigen-Specific B Cells -- References -- Part V: Other Topics in Immunology -- Chapter 28. Flow Cytometry Immunophenotypic Characteristics of Monocytic Population in Acute Monocytic Leukemia (AML-M5), Acute Myelomonocytic Leukemia (AML-M4), and Chronic Myelomonocytic Leukemia (CMML) -- I. Introduction -- II. Materials -- III. Methods -- IV. Acute Monocytic Leukemia -- V. Chronic Myelomonocytic Leukemia -- VI. Acute Myelomonocytic Leukemia -- VII. Differential Diagnosis -- VIII. Conclusion -- References -- Chapter 29. Phagocyte Function -- I. Introduction -- II. Background -- III. Methods -- IV. Results -- V. Pitfalls and Misinterpretation of the Data -- VI. Comparison with Other Methods -- VII. Applications and Biomedical Information -- VIII. Future Directions -- References -- Chapter 30. Neutralizing Antibody Quantification by Flow Cytometry -- I. Introduction -- II. Background -- III. Results -- IV. Discussion and Key Points -- References. , Part VI: Cytogenetics.

Note: Front Cover -- Essential Cytometry Methods -- Copyright Page -- Contents -- Contributors -- Preface -- Part I: Fluorochromes/General Techniques -- Chapter 1: Principles of Confocal Microscopy -- I. Brief History of Microscope Development -- II. Development of Confocal Microscopy -- III. Image Formation in Confocal Microscopy -- IV. Useful Fluorescent Probes for Confocal Microscopy -- V. Applications of Confocal Microscopy -- VI. Conclusions -- References -- Chapter 2: Protein Labeling with Fluorescent Probes -- I. Update -- II. Introduction -- III. Labeling of Proteins with Organic Fluorescent Dyes -- IV. Labeling of Antibodies with Zenon Probes -- V. Labeling of Proteins with Phycobiliproteins -- VI. Conclusion -- References -- Chapter 3: Cytometry of Fluorescence Resonance Energy Transfer -- I. Introduction -- II. Theory of FRET -- III. Measuring FRET -- IV. Applications -- V. Perspectives -- VI. Conclusions -- Acknowledgments -- References -- Chapter 4: The Rainbow of Fluorescent Proteins -- I. Update -- II. The Fluorescent Proteins -- III. Flow Analysis Using Fluorescent Proteins -- IV. Flow Sorting Using Fluorescent Proteins -- V. Conclusion -- Acknowledgments -- References -- Chapter 5: Labeling Cellular Targets with Semiconductor Quantum Dot Conjugates -- I. Introduction -- II. Selection of QDs and their Conjugates -- III. Labeling of Fixed Cells for Fluorescence Microscopy -- IV. Measurements in Living Cells Using QD Conjugates -- V. Conclusion -- Acknowledgment -- References -- Chapter 6: High-Gradient Magnetic Cell Sorting -- I. Update -- II. Introduction -- III. Application -- IV. Materials -- V. MACS: Staining and Sorting -- VI. Critical Aspects of the Procedure -- VII. Controls -- VIII. Instruments -- IX. Results -- Acknowledgment -- References -- Chapter 7: Multiplexed Microsphere Assays (MMAs) for Protein and DNA Binding Reactions. , I. Update -- II. Introduction -- III. Technology and Instrumentation -- IV. Methods -- V. Results -- VI. Software -- VII. Critical Aspects of the Methodology -- VIII. Comparison with Other Methods -- IX. Future Directions -- Acknowledgment -- References -- Chapter 8: Biohazard Sorting -- I. Recent Developments -- II. Introduction -- III. Critical Aspects of the Procedure -- IV. Applications and Future Directions -- Acknowledgment -- References -- Chapter 9: Guidelines for the Presentation of Flow Cytometric Data -- I. Introduction -- II. General Principles of Graphical Presentation -- III. Statistics -- IV. Subset Analysis -- V. Conclusion -- References -- Part II: Cellular DNA Content Analysis -- Chapter 10: Detergent and Proteolytic Enzyme-Based Techniques for Nuclear Isolation and DNA Content Analysis -- I. Introduction -- II. Basic Principles of the Methods -- III. Applications -- IV. Materials -- V. Methods -- VI. Results -- Acknowledgments -- References -- Chapter 11: DNA Content and Cell Cycle Analysis by the Propidium Iodide-Hypotonic Citrate Method -- I. Introduction -- II. Application -- III. Materials -- IV. Staining Procedure -- V. Caution -- VI. Instrument Setup -- VII. Comments -- VIII. Results -- References -- Chapter 12: DNA Analysis from Paraffin-Embedded Blocks -- I. Introduction -- II. Application -- III. Methods -- IV. Critical Aspects of Technique -- V. Alternative Methods for Sample Preparation -- Acknowledgment -- References -- Chapter 13: Flow Cytometry and Sorting of Plant Protoplasts and Cells -- I. Update -- II. Introduction -- III. Application -- IV. Materials -- V. Procedures -- VI. Critical Aspects of the Procedures -- VII. Controls and Standards -- VIII. Instruments -- IX. Results -- Acknowledgments -- References -- Chapter 14: DNA Content Histogram and Cell-Cycle Analysis -- I. Introduction. , II. DNA Content Histogram Basic Principles -- III. Cell-Cycle Analysis of DNA Content Histograms -- IV. Critical Aspects of DNA Content and Cell-Cycle Analysis -- V. Interpretation of DNA Content and Cell-Cycle Histograms -- VI. Conclusion -- References -- Chapter 15: Simultaneous Analysis of Cellular RNA and DNA Content -- I. Update -- II. Introduction -- III. Applications -- IV. Materials -- V Staining Procedures Employing AO -- VI. Staining RNA and DNA with PY and Hoechst 33342 -- VII. Critical Aspects of the Procedures -- VIII. Controls and Standards -- IX. Instruments -- X. Results -- XI Comparison of the Methods -- References -- Part III: Cell proliferation and the Death Assays -- Chapter 16: Immunochemical Quantitation of Bromodeoxyuridine: Application to Cell-Cycle Kinetics -- I. Update -- II. Introduction -- III. Applications -- IV. Materials -- V. Procedures -- VI. Critical Aspects of the Procedure -- VII. Controls and Standards -- VIII. Instruments -- IX. Results -- X. Summary -- References -- Chapter 17: Cell-Cycle Kinetics Estimated by Analysis of Bromodeoxyuridine Incorporation -- I. Introduction -- II. Applications -- III. Materials -- IV. Methods -- V. Critical Aspects of the Procedure -- References -- Chapter 18: Flow Cytometric Analysis of Cell Division History Using Dilution of Carboxyfluorescein Diacetate Succinimidyl Ester, a Stably . -- I. Introduction and Background -- II. Reagents and Solutions -- III. Preparation and Labeling of Cells -- IV. Gathering of Information Concurrent with Division -- V. Analysis of Data -- VI. Application of Carboxyfluorescein Diacetate Succinimidyl Ester to In Vitro Culture of Lymphocytes -- VII. Monitoring Lymphocyte Responses In Vivo -- VIII. Antigen Receptor Transgenic Models -- References. , Chapter 19: Antibodies Against the Ki-67 Protein: Assessment of the Growth Fraction and Tools for Cell Cycle Analysis -- I. Introduction -- II. Application -- III. Materials and Methods -- IV. Critical Aspects -- V. Controls and Standards -- VI. Examples of Results -- References -- Chapter 20: Detection of DNA Damage in Individual Cells by Analysis of Histone H2AX Phosphorylation -- I. Update -- II. Introduction -- III. Considerations in the Use of gammaH2AX as a Measure ofDouble-Stranded Breaks -- IV. Methods of Analysis -- V. Typical Results -- VI. Possible Applications -- VII. Conclusion -- References -- Chapter 21: Assays of Cell Viability -- I. Update -- II. Introduction -- III. Changes in Light Scatter During Cell Death -- IV. Cell Sensitivity to Trypsin and DNase -- V. Fluorescein Diacetate (FDA) Hydrolysis and PI Exclusion -- VI. Rh123 Uptake and PI Exclusion -- VII. PI Exclusion Followed by Counterstaining with Hoechst 33342 -- VIII. Hoechst 33342 Active Uptake and PI Exclusion -- IX. Controlled Extraction of Low MW DNA from Apoptotic Cells -- X. Sensitivity of DNA In Situ to Denaturation -- XI. Detection of DNA Strand Breaks in Apoptotic Cells -- XII. A Selective Procedure for DNA Extraction from Apoptotic Cells Applicable to Gel Electrophoresis and Flow Cytometry... -- XIII. Comparison of the Methods: Confirmation of the Apoptotic Mode of Cell Death -- References -- Chapter 22: Difficulties and Pitfalls in Analysis of Apoptosis -- I. Update -- II. Introduction -- III. AI may not be Correlated with Incidence of Cell Death -- IV. Difficulties in Estimating Frequency of Apoptosis by Analysis of DNA Fragmentation -- V. The Lack of Evidence is not Evidence for the Lack of Apoptosis -- VI. Misclassification of Apoptotic Bodies or Nuclear Fragments as Single Apoptotic Cells -- VII. Apoptosis Versus Necrosis Versus ``Necrotic Stage´´ of Apoptosis. , VIII. Selective Loss of Apoptotic Cells During Sample Preparation -- IX. Live Cells Engulfing Apoptotic Bodies Masquerade as Apoptotic Cells -- X The Problems with Commercial Kits and Reagents -- XI. Cell Morphology is still the Gold Standard for Identification of Apoptotic Cells -- XII. Laser Scanning Cytometry: Have your Cake and Eat it too -- References -- Part IV: Cell Surface Immunophenotyping -- Chapter 23: Cell Preparation for the Identification of Leukocytes -- I. Introduction -- II. Antibodies -- III. Tandem Fluorochromes -- IV. Cell Preparation and Staining Procedures -- V. Titering Antibodies -- VI. Solutions and Reagents -- References -- Chapter 24: Multicolor Immunophenotyping -- I. Update -- II. Introduction -- III. Methodology -- IV. Normal Immunophenotypic Patterns of Maturation -- V. Abnormal Immunophenotypic Patterns of Maturation -- References -- Chapter 25: Differential Diagnosis of T-Cell Lymphoproliferative Disorders by Flow Cytometry Immunophenotyping. Correlation with Morpholog. -- I. Introduction -- II. Materials -- III. Methods -- IV. Identification of Abnormal T-Cell Population by Flow Cytometry -- V. Precursor T-Lymphoblastic Lymphoma/Leukemia (T-ALL) -- VI. Peripheral (Mature/Postthymic) Lymphoma Versus T-ALL -- VII. Thymocytes from Thymic Hyperplasia/Thymoma Versus T-ALL -- VIII. Mature T-Cell Lymphoproliferative Disorders -- IX. Conclusions -- References -- Chapter 26: B Cell Immunophenotyping -- I. Update -- II. Introduction -- III. Immunophenotyping of B Cell Developmental Stages in the Bone Marrow -- IV. Peripheral B Cell Populations -- V. Summary -- VI. Antigen-Induced B Cell Subsets -- VII. Antigen-Specific B Cells -- References -- Part V: Cytogenetics/Chromatin Structure -- Chapter 27: Telomere Length Measurements Using Fluorescence In Situ Hybridization and Flow Cytometry -- I. Introduction -- II. Background. , III. Methods.