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El. knyga: Biophysical Tools for Biologists: In Vivo Techniques

Volume editor H. William Detrich III (Professor of Biochemistry and Marine Biology at Northeastern University), Volume editor John J. Correia (University of Mississippi Medical Center, Jackson, USA)

Formatas: PDF+DRM
Serija: Methods in Cell Biology
Išleidimo metai: 19-Jan-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780080919782

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Formatas: PDF+DRM
Serija: Methods in Cell Biology
Išleidimo metai: 19-Jan-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780080919782

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Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vivo and their applications to cellular biology. The volume covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval.

* Describes techniques in the context of important biological problems
* Delineates critical steps and potential pitfalls for each method

Daugiau informacijos

Single-source reference that details state-of-the-art biophysical techniques

Contributors

Preface

xix

SECTION I Fluorescence Methods

In Vivo Applications of Fluorescence Correlation Spectroscopy

Huimin Chen

Elaine R. Farkas

Watt W. Webb

Introduction

(8)

PCS Technology

(4)

Applications of In Vivo PCS

(9)

Future Directions for In Vivo FCS

(3)

Conclusions

(10)

References

(10)

Molecular Sensors Based on Fluorescence Resonance Energy Transfer to Visualize Cellular Dynamics

Bharath Ananthanarayanan

Qiang Ni

Jin Zhang

Introduction

(1)

Basic Principles of FRET-Based Molecular Sensors

(7)

Methods

(7)

A Case Study of P13K/Akt Signaling Pathway

(2)

Discussion and Conclusion

(6)

References

(6)

A Fluorescent Window Into Protein Folding and Aggregation in Cells

Zoya Ignatova

Lila M. Gierasch

Introduction

(1)

Rationale

(1)

Methods

(7)

Summary

(4)

References

(3)

Combining Microfluidics and Quantitative Fluorescence Microscopy to Examine Pancreatic Islet Molecular Physiology

Jonathan V. Rocheleau

David W. Piston

Introduction

(1)

Rationale

(6)

Methods and Materials

(9)

Discussion

(8)

References

(7)

SECTION II Microscopic Methods

Imaging in Depth: Controversies and Opportunities

Don O'Malley

Introduction

(2)

Basic Imaging Methodologies

(2)

Forays Deeper into Depth

100

(18)

Discussion: Terms of Resolution

118

(2)

Summary

120

(10)

References

120

(10)

Principles and Practice in Electron Tomography

Bruce F. McEwen

Christian Renken

Michael Marko

Carmen Mannella

Introduction

130

(1)

Specimen Preparation

131

(7)

Data Collection for Electron Tomography

138

(6)

Computation of an Electron Tomographic Reconstruction

144

(7)

Interpretation of Electron Tomographic Reconstructions

151

(10)

Summary and Future Directions

161

(9)

References

162

(8)

Total Internal Reflection Fluorescence Microscopy

Daniel Axelrod

Introduction

170

(1)

Rationale

171

(4)

Theoretical Principles

175

(11)

Combinations of TIRF with Other Techniques

186

(10)

Optical Configurations and Setup

196

(12)

General Experimental Considerations

208

(4)

Summary: TIRF Versus Other Optical Section Microscopies

212

(12)

References

213

(11)

Spatiotemporal Dynamics in Bacterial Cells: Real-Time Studies with Single-Event Resolution

Ido Golding

Edward C. Cox

Introduction

224

(1)

Studying Cellular Dynamics with Single-Event Resolution

225

(2)

Methods

227

(21)

Summary and General Lessons for Following Discrete Events

248

(6)

References

249

(5)

Counting Proteins in Living Cells by Quantitative Fluorescence Microscopy with Internal Standards

Jian-Qiu Wu

Chad D. McCormick

Thomas D. Pollard

Introduction

254

(3)

Experimental Methods

257

(10)

Data Analysis

267

(2)

Conclusions

269

(7)

References

272

(4)

Infrared and Raman Microscopy in Cell Biology

Christian Matthaus

Benjamin Bird

Milos Miljkovic

Tatyana Chernenko

Melissa Romeo

Max Diem

Introduction

276

(2)

Methods

278

(10)

Results and Discussion

288

(19)

Conclusions

307

(3)

References

307

(3)

Imaging Fluorescent Mice In Vivo Using Confocal Microscopy

Stephen G. Turney

Jeff W. Lichtman

Introduction

310

(1)

Rationale

310

(11)

Methods and Materials

321

(4)

Discussion and Summary

325

(5)

References

326

(4)

Nanoscale Biological Fluorescence Imaging: Breaking the Diffraction Barrier

Travis J. Gould

Samuel T. Hess

Introduction

330

(5)

Theory and Rationale

335

(3)

Methods

338

(7)

Materials

345

(2)

Discussion

347

(9)

Summary

356

(6)

References

356

(6)

SECTION III Methods at the In Vitro/In Vivo Interface

Imaging of Cells and Tissues with Mass Spectrometry: Adding Chemical Information to Imaging

Tyler A. Zimmerman

Eric B. Monroe

Kevin R. Tucker

Stanislav S. Rubakhin

Jonathan V. Swedler

Introduction

362

(2)

Instrumentation

364

(8)

Sample Preparation for MSI

372

(10)

Image Acquisition and Data Analysis

382

(2)

Specialized Methods

384

(1)

Summary and Future Directions

385

(7)

References

386

(6)

Electron Microscopy of Hydrated Samples

Winston Timp

Paul Matsudaira

Introduction

392

(1)

Basic SEM

392

(4)

Environmental SEM

396

(5)

Wet SEM

401

(3)

Summary

404

(8)

References

406

(6)

SECTION IV Methods for Diffusion, Viscosity, Force and Displacement

Live-Cell Single-Molecule Force Spectroscopy

Terrence M. Dobrowsky

Porntula Panorchan

Konstantinos Konstantopoulos

Denis Wirtz

Introduction

412

(8)

Materials and Instrumentation

420

(1)

Procedures

421

(8)

Pearls and Pitfalls

429

(1)

Concluding Remarks

430

(4)

References

430

(4)

Magnetic Manipulation for Force Measurements in Cell Biology

E. Tim O'Brien

Jeremy Cribb

David Marshburn

Russell M. Taylor II

Richard Superfine

Introduction

434

(2)

Sample Preparation

436

(3)

Video and Laser-Based Magnetic Systems

439

(1)

Calibration of Pole Tips

440

(2)

Pole Configurations

442

(1)

Modes of Magnet Controls

442

(2)

Cell Experiments with Magnetics

444

(2)

Driven Bead Rheology of Biologic Fluids

446

(3)

Conclusions

449

(3)

References

449

(3)

Application of Laser Tweezers to Studies of Membrane-Cytoskeleton Adhesion

Drazen Raucher

Introduction

452

(3)

Materials and Methods

455

(5)

Tether Force Measurements of the Adhesion Energy Between the Plasma Membrane and the Cortical Cytoskeleton

460

(4)

Concluding Remarks

464

(4)

References

465

(3)

Sensing Cytoskeletal Mechanics by Ballistic Intracellular Nanorheology (BIN) Coupled with Cell Transfection

Melissa S. Thompson

Denis Wirtz

Introduction

468

(5)

Materials and Instrumentation

473

(4)

Procedures

477

(7)

Pearls and Pitfalls

484

(1)

Concluding Remarks

485

(3)

References

485

(3)

Mechanical Response of Cytoskeletal Networks

Margaret L. Gardel

Karen E. Kasza

Clifford P. Brangwynne

Jiayu Liu

David A. Weitz

Introduction

488

(1)

Rheology

489

(4)

Cross-Linked F-Actin Networks

493

(11)

Effects of Microtubules in Composite F-Actin Networks

504

(8)

Intermediate Filament Networks

512

(3)

Conclusions and Outlook

515

(7)

References

516

(6)

Automated Spatial Mapping of Microtubule Catastrophe Rates in Fission Yeast

Christian Tischer

Damian Brunner

Marileen Dogterom

Introduction

522

(1)

Methods

523

(11)

Results

534

(1)

Discussion

535

(8)

References

537

(6)

SECTION V Techniques for Protein Activity and Protein-Protein Interactions

Quantitative Fluorescence Lifetime Imaging in Cells as a Tool to Design Computational Models of Ran-Regulated Reaction Networks

Petr Kalab

Arnd Pralle

Quantitative Imaging and Systems Modeling as a Tool in Cell Biology---The Rationale and Strategy

543

(3)

Quantitative Detection of Biochemical Interactions by FLIM

546

(6)

Technical Considerations for FLIM in Live Cells

552

(5)

Analysis of the Mitotic RanGTP Gradient Function by FLIM and Computational Modeling

557

(5)

Materials and Methods

562

(8)

References

565

(5)

Quantitation of Protein---Protein Interactions: Confocal FRET Microscopy

Ammasi Periasamy

Horst Wallrabe

Ye Chen

Margarida Barroso

Introduction

570

(1)

Rationale

571

(1)

Material and Methods

572

(10)

Results and Discussion

582

(13)

Summary

595

(7)

References

595

(7)

SECTION VI Computational Modeling

Stochastic Modeling Methods in Cell Biology

Sean X. Sun

Ganhui Lan

Erdinc Atilgan

Introduction

602

(5)

Stochastic Methods in Signaling and Genetic Networks

607

(2)

Molecular Motors and the Inclusion of Biomolecular Structure in Stochastic Models

609

(4)

Cytoskeleton and Cytoskeletal Network Structures

613

(4)

Procedures

617

(1)

Discussion and Concluding Remarks

618

(1)

Appendix

619

(5)

References

620

(4)

Computational Modeling of Self-Organized Spindle Formation

Stuart C. Schaffner

Jorge V. Jose

Introduction

624

(1)

Rationale

625

(4)

Methods

629

(17)

Materials

646

(1)

Discussion and Summary

647

(1)

Appendix A

647

(1)

Appendix B

648

(5)

References

651

(2)

Index

653

(16)

Volumes in Series

669

Professor of Biochemistry and Marine Biology at Northeastern University, promoted 1996. Joined Northeastern faculty in 1987. Previously a faculty member in Dept. of Biochemistry at the University of Mississippi Medical Center, 1983-1987.Principal Investigator in the U.S. Antarctic Program since 1984. Twelve field seasons "on the ice" since 1981. Research conducted at Palmer Station, Antarctica, and McMurdo Station, Antarctica.Research areas: Biochemical, cellular, and physiological adaptation to low and high temperatures. Structure and function of cytoplasmic microtubules and microtubule-dependent motors from cold-adapted Antarctic fishes. Regulation of tubulin and globin gene expression in zebrafish and Antarctic fishes. Role of microtubules in morphogenesis of the zebrafish embryo. Developmental hemapoiesis in zebrafish and Antarctic fishes. UV-induced DNA damage and repair in Antarctic marine organisms.

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