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Biophysical Methods in Cell Biology

1st Edition - January 14, 2015

Editor: Ewa Paluch

Hardback ISBN:

9 7 8 - 0 - 1 2 - 8 0 1 1 0 3 - 4

eBook ISBN:

9 7 8 - 0 - 1 2 - 8 0 1 3 2 6 - 7

This new volume of Methods in Cell Biology looks at methods for analyzing of biophysical methods in cell biology. Chapters cover such topics as AFM, traction force microscopy,… Read more

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This new volume of Methods in Cell Biology looks at methods for analyzing of biophysical methods in cell biology. Chapters cover such topics as AFM, traction force microscopy, digital holographic microscopy, single molecule imaging, video force microscopy and 3D multicolor super-resolution screening

Series Editors
Preface
Chapter 1. Single-molecule imaging of cytoplasmic dynein in vivo
- Introduction
- 1. Visualization of Cytoplasmic Dynein In Vivo
- 2. Image Analysis
- 3. Conclusion
- 4. Methods
Chapter 2. Single-molecule imaging in live cell using gold nanoparticles
- Introduction and Rationale
- 1. Gold Nanoparticle Synthesis and Functionalization
- 2. Photothermal Imaging
- 3. Live Cell Imaging
- Conclusion
Chapter 3. Quantitative measurement of transcription dynamics in living cells
- 1. Visualizing Transcription in Living Cells
- 2. Experimental Protocols
- 3. Cell Segmentation
- 4. Measuring Spot Intensity
- 5. Correcting for Background MS2-GFP Level
- 6. Tracking Algorithms
- 7. Additional Cell Properties
- 8. Summary
Chapter 4. An easy-to-use single-molecule speckle microscopy enabling nanometer-scale flow and wide-range lifetime measurement of cellular actin filaments
- Introduction
- 1. Methods
- 2. Perspectives
Chapter 5. Dissecting microtubule structures by laser ablation
- Introduction
- 1. Theoretical Framework
- 2. Microtubule Organization Measurements
- Discussion and Conclusion
Chapter 6. Quantifying mitochondrial content in living cells
- Introduction
- 1. Basic Protocol (96-Well Glass Bottom Plate)
- 2. Alternate Protocol (CellASIC Microfluidic Flow Chamber)
- 3. Important Considerations for Successful MitoGraph Performance
- 4. Beyond Wild-type Mitochondria in Budding Yeast Imaged with Spinning-Disk Confocal Microscopy
Chapter 7. High-content 3D multicolor super-resolution localization microscopy
- Introduction
- 1. Sample Preparation
- 2. Imaging Acquisition and Image Analysis
- Conclusions and Outlook
Chapter 8. Superresolution measurements in vivo: Imaging Drosophila embryo by photoactivated localization microscopy
- Introduction
- 1. Embryo Preparation
- 2. Sample Mounting
- 3. Optical Setup
- 4. Imaging
- 5. Data Analysis
- 6. Summary and Outlook
Chapter 9. Refractive index measurements of single, spherical cells using digital holographic microscopy
- Introduction
- 1. Setup
- 2. Measurement Preparation
- 3. Data Analysis
- 4. Discussion
- 5. Summary
Chapter 10. Construction, imaging, and analysis of FRET-based tension sensors in living cells
- Introduction
- 1. Design, Production, and Validation of Tension Sensors
- 2. Imaging of FRET-Based Biosensors
- 3. Methods of Analysis of FRET Images
- 4. Summary
Chapter 11. Single-cell mechanics: The parallel plates technique
- Introduction
- 1. Experimental Setup
- 2. Microplates
- 3. Cell Preparation
- 4. Experimental Protocols
- 5. Discussion
Chapter 12. Atomic force microscopy-based force measurements on animal cells and tissues
- Introduction
- 1. Experimental Setup
- 2. Sample Preparation
- 3. AFM and Optical Imaging
- 4. Measuring Cell and Tissue Stiffness
- 5. Measuring Adhesion
- 6. Further Applications
- Conclusions
Chapter 13. Measuring the elasticity of plant cells with atomic force microscopy
- Introduction
- 1. Sample preparation and mounting
- 2. Atomic force microscopy
- 3. Experimental design
- 4. Discussion
- 5. Notes
Chapter 14. Dual pipette aspiration: A unique tool for studying intercellular adhesion
- Introduction
- 1. Overview of the DPA Setup
- 2. Preparing the Pipettes
- 3. Preparing the Aspiration Assay
- 4. Cell Micromanipulation
- 5. Discussion
- General Conclusions
Chapter 15. Measurement of cell traction forces with ImageJ
- Introduction
- 1. Force Measurement Principle
- 2. Critical Experimental Parameters
- 3. Critical Numerical Parameters
- 4. Preparation of Patterned Polyacrylamide Gels with Fiducial Markers
- 5. Image Acquisition
- 6. Image Analysis, Estimation of Displacement, and Traction Force Fields
- Conclusion
Chapter 16. Micropillar substrates: A tool for studying cell mechanobiology
- Introduction
- 1. Substrate Fabrication
- 2. Substrate Characterization
- 3. Substrate Functionalization
- 4. Cells Seeding and Imaging
- 5. Image Analysis and Evaluation of Traction Force
- 6. Discussion and Perspectives
Chapter 17. Mapping forces and kinematics during collective cell migration
- Introduction
- 1. Experimental Tools to Map Forces and Kinematics during Collective Cell Migration
- 2. Computational Tools to Map Forces and Kinematics during Collective Cell Migration
- General Conclusions
Chapter 18. Practical aspects of the cellular force inference toolkit (CellFIT)
- Introduction
- 1. The Basic Steps in CellFIT
- 2. Working with CellFIT Output
Chapter 19. Quantification of collagen contraction in three-dimensional cell culture
- Introduction
- 1. Method
- 2. Pseudo-speckle Microscopy
- 3. Software
- 4. Data Analysis
- 5. Discussion
- General Conclusion
Chapter 20. Generation of biocompatible droplets for in vivo and in vitro measurement of cell-generated mechanical stresses
- Introduction
- 1. Methods
- 2. Discussion
- Conclusion
Chapter 21. Laser induced wounding of the plasma membrane and methods to study the repair process
- Introduction
- 1. Cell Deposition
- 2. Photodamage and Imaging
- 3. Following Plasma Membrane Damage and Repair
- 4. Image Analysis
- 5. Data Analysis
- 6. Discussion
- General Conclusions
Chapter 22. Electrofusion of giant unilamellar vesicles to cells
- Introduction
- 1. Preparation of GUVs by Electroformation
- 2. Electrofusion of GUVs to Cells
- 3. Discussion
Chapter 23. Measurement and manipulation of cell size parameters in fission yeast
- Introduction
- 1. Measurement of Size Parameters of Single Fission Yeast Cells
- 2. Microchannel Assay for Cell Diameter Manipulation
- Conclusions
Chapter 24. Methods for rectifying cell motions in vitro: breaking symmetry using microfabrication and microfluidics
- Introduction
- 1. Breaking Symmetry with Topography: Fabrication of a Topographical Pattern
- 2. Breaking Symmetry with Chemical Gradient: Preparation of the Fibronectin Gradient
- 3. Cell Migration Experiments
- 4. Discussion
- Conclusions
Chapter 25. Analyzing bacterial movements on surfaces
- Introduction
- 1. Preparing Bacterial Suspension
- 2. Tracking Bacteria on Solid Surfaces
- 3. Tracking Bacteria on Cells
- 4. Discussion Points
- Conclusions
Chapter 26. Advances in single-cell experimental design made possible by automated imaging platforms with feedback through segmentation
- Introduction
- 1. In vitro Experiments where Automation is Important
- 2. Preparation of Cells Described in this Chapter
- 3. Automation Methods
- 4. Discussion
- 5. Outlook
Volumes in Series
Index