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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
