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Methods in cell biology. v. 89, Biophysical tools for biologists. v.2, In vivo techniques / edited by John J. Correia, H. William Detrich, III. — Amsterdam : Elsevier, c2008. – (58.1574/M592/v.89)

Contents

    CONTENTS
    
    SECTION I Fluorescence Methods
    1. In Vivo Applications of Fluorescence Correlation Spectroscopy
    I. Introduction
    II. FCS Technology
    III. Applications of In Vivo FCS
    IV. Future Directions for In Vivo FCS
    V. Conclusions
    References
    2. Molecular Sensors Based on Fluorescence Resonance Energy Transfer to Visualize Cellular Dynamics
    I. Introduction
    II. Basic Principles of FRET-Based Molecular Sensors
    III. Methods
    IV. A Case Study of PI3K/Akt Signaling Pathway
    V. Discussion and Conclusion
    References
    3. A Fluorescent Window Into Protein Folding and Aggregation in Cells
    I. Introduction
    II. Rationale
    III. Methods
    IV. Summary
    References
    4. Combining Microfluidics and Quantitative Fluorescence Microscopy to Examine Pancreatic Islet Molecular Physiology
    I. Introduction
    II. Rationale
    III. Methods and Materials
    IV. Discussion
    References
    SECTION II Microscopic Methods
    5. Imaging in Depth: Controversies and Opportunities
    I. Introduction
    II. Basic Imaging Methodologies
    III. Forays Deeper into Depth
    IV. Discussion: Terms of Resolution
    V. Summary
    References
    6. Principles and Practice in Electron Tomography
    I. Introduction
    II. Specimen Preparation
    III. Data Collection for Electron Tomography
    IV. Computation of an Electron Tomographic Reconstruction
    V. Interpretation of Electron Tomographic Reconstructions
    VI. Summary and Future Directions
    References
    7. Total Internal Reflection Fluorescence Microscopy
    I. Introduction
    II. Rationale
    III. Theoretical Principles
    IV. Combinations of TIRF with Other Techniques
    V. Optical Configurations and Setup
    VI. General Experimental Considerations
    VII. Summary: TIRF Versus Other Optical Section Microscopies
    References
    8. Spatiotemporal Dynamics in Bacterial Cells: Real-Time Studies with Single-Event Resolution
    I. Introduction
    II. Studying Cellular Dynamics with Single-Event Resolution
    III. Methods
    IV. Summary and General Lessons for Following Discrete Events
    References
    9. Counting Proteins in Living Cells by Quantitative Fluorescence Microscopy with Internal Standards
    I. Introduction
    II. Experimental Methods
    III. Data Analysis
    IV. Conclusions
    References
    10. Infrared and Raman Microscopy in Cell Biology
    I. Introduction
    II. Methods
    III. Results and Discussion
    IV. Conclusions
    References
    11. Imaging Fluorescent Mice In Vivo Using Confocal Microscopy
    I. Introduction
    II. Rationale
    III. Methods and Materials
    IV. Discussion and Summary
    References
    12. Nanoscale Biological Fluorescence Imaging: Breaking the Diffraction Barrier
    I. Introduction
    II. Theory and Rationale
    III. Methods
    IV. Materials
    V. Discussion
    VI. Summary
    References
    SECTION III Methods at the In Vitro/In Vivo Interface
    13. Imaging of Cells and Tissues with Mass Spectrometry: Adding Chemical Information to Imaging
    I. Introduction
    II. Instrumentation
    III. Sample Preparation for MSI
    IV. Image Acquisition and Data Analysis
    V. Specialized Methods
    VI. Summary and Future Directions
    References
    14. Electron Microscopy of Hydrated Samples
    I. Introduction
    II. Basic SEM
    III. Environmental SEM
    IV. Wet SEM
    V. Summary
    References
    SECTION IV Methods for Diffusion, Viscosity, Force and Displacement
    15. Live-Cell Single-Molecule Force Spectroscopy
    I. Introduction
    II. Materials and Instrumentation
    III. Procedures
    IV. Pearls and Pitfalls
    V. Concluding Remarks
    References
    16. Magnetic Manipulation for Force Measurements in Cell Biology
    I. Introduction
    II. Sample Preparation
    III. Video and Laser-Based Magnetic Systems
    IV. Calibration of Pole Tips
    V. Pole Configurations
    VI. Modes of Magnet Controls
    VII. Cell Experiments with Magnetics
    VIII. Driven Bead Rheology of Biologic Fluids
    IX. Conclusions
    References
    17. Application of Laser Tweezers to Studies of Membrane-Cytoskeleton Adhesion
    I. Introduction
    II. Materials and Methods
    III. Tether Force Measurements of the Adhesion Energy Between the Plasma Membrane and the Cortical Cytoskeleton
    IV. Concluding Remarks
    References
    18. Sensing Cytoskeletal Mechanics by Ballistic Intracellular Nanorheology (BIN) Coupled with Cell Transfection
    I. Introduction
    II. Materials and Instrumentation
    III. Procedures
    IV. Pearls and Pitfalls
    V. Concluding Remarks
    References
    19. Mechanical Response of Cytoskeletal Networks
    I. Introduction
    II. Rheology
    III. Cross-Linked F-Actin Networks
    IV. Effects of Microtubules in Composite F-Actin Networks
    V. Intermediate Filament Networks
    VI. Conclusions and Outlook
    References
    20. Automated Spatial Mapping of Microtubule Catastrophe Rates in Fission Yeast
    I. Introduction
    II. Methods
    III. Results
    IV. Discussion
    References
    SECTION V Techniques for Protein Activity and Protein-Protein Interactions
    21. Quantitative Fluorescence Lifetime Imaging in Cells as a Tool to Design Computational Models of Ran-Regulated Reaction Networks
    I. Quantitative Imaging and Systems Modeling as a Tool in Cell Biology--The Rationale and Strategy
    II. Quantitative Detection of Biochemical Interactions by FLIM
    III. Technical Considerations for FLIM in Live Cells
    IV. Analysis of the Mitotic RanGTP Gradient Function by FLIM and Computational Modeling
    V. Materials and Methods
    22. Quantitation of Protein-Protein Interactions: Confocal FRET Microscopy
    I. Introduction
    II. Rationale
    III. Material and Methods
    IV. Results and Discussion
    V. Summary
    References
    SECTION VI Computational Modeling
    23. Stochastic Modeling Methods in Cell Biology
    I. Introduction
    II. Stochastic Methods in Signaling and Genetic Networks
    III. Molecular Motors and the Inclusion of Biomolecular Structure in Stochastic Models
    IV. Cytoskeleton and Cytoskeletal Network Structures
    V. Procedures
    VI. Discussion and Concluding Remarks
    VII. Appendix
    References
    24. Computational Modeling of Self-Organized Spindle Formation
    I. Introduction
    II. Rationale
    III. Methods
    IV. Materials
    V. Discussion and Summary
    VI. Appendix A
    VII. Appendix B
    References