Note: Front Cover -- PCR STRATEGIES -- Copyright Page -- CONTENTS -- Contributors -- Foreword -- Preface -- Part One: KEY CONCEPTS FOR PCR -- Chapter 1. The Use of Cosolvents to Enhance Amplification by the Polymerase Chain Reaction -- Chapter 2. DNA Polymerase Fidelity: Misinsertions and Mismatched Extensions -- Chapter 3. Extraction of Nucleic Acids: Sample Preparation from Paraffin-Embedded Tissues -- Chapter 4. Thermostable DNA Polymerases -- Chapter 5. Amplification of RNA: High-Temperature Reverse Transcription and DNA Amplification with Thermus thermophilus DNA Polymerase -- Chapter 6. Nucleic Acid Hybridization and Unconventional Bases -- Chapter 7. Practical Considerations for the Design of Quantitative PCR Assays -- Part Two: ANALYSIS OF PCR PRODUCTS -- Chapter 8. Carrier Detection of Cystic Fibrosis Mutations Using PCR-Amplified DNA and a Mismatch-Binding Protein, MutS -- Chapter 9. Single-Stranded Conformational Polymorphisms -- Chapter 10. Analysis of PCR Products by Covalent Reverse Dot Blot Hybridization -- Chapter 11. High-Performance Liquid Chromatography Analysis of PCR Products -- Chapter 12. Heteroduplex Mobility Assays for Phylogenetic Analysis -- Chapter 13. PCR Amplification of VNTRs -- Part Three: RESEARCH APPLICATIONS -- Chapter 14. Site-Specific Mutagenesis Using the Polymerase Chain Reaction -- Chapter 15. Exact Quantification of DNA-RNA Copy Numbers by PCR-TGGE -- Chapter 16. The in Situ PCR: Amplication and Detection of DNA in a Cellular Context -- Chapter 17. Y Chromosome-Specific PCR: Maternal Blood -- Chapter 18. Genomic Subtraction -- Chapter 19. DNA Amplification-Restricted Transcription Translation (DARTT): Analysis of in Vitro and in Situ Protein Functions and Intermolecular Assembly -- Chapter 20. DNA and RNA Fingerprinting Using Arbitrarily Primed PCR. , Chapter 21. PCR-Based Screening of Yeast Artificial Chromosome Libraries -- Chapter 22. Oligonucleotide Ligands That Discriminate between Theophylline and Caffeine -- Chapter 23. Generation of Single-Chain Antibody Fragments by PCR -- Chapter 24. Longer PCR Amplifications -- Chapter 25. Direct Analysis of Specific Bonds from Arbitrarily Primed PCR Reactions -- Part Four: ALTERNATIVE AMPLIFICATION STRATEGIES -- Chapter 26. Detection of Leber's Hereditary Optic Neuropathy by Nonradioactive Ligase Chain Reaction -- Chapter 27. Detection of Listeria monocytogenes by PCR-Coupled Ligase Chain Reaction -- Index.

Note: Front Cover -- Methods in Cell Biology -- Copyright Page -- Contents -- Contributors -- Preface -- Dedication Page -- Section 1: Solution Methods -- Chapter 1: Binding: A Polemic and Rough Guide -- I. Introduction -- II. Binding Constants Provide an Entry into Thermodynamics -- III. General Properties of Binding Isotherms -- IV. Thermodynamics from Thermal Denaturation Methods -- V. Completing the Thermodynamic Profile -- VI. Thermodynamics in the Real World: Some Useful Strategies -- VII. Ligand-Receptor Binding in the Absence of an Optical Signal -- VIII. Toward High-Throughput Thermodynamics -- IX. Summary -- Acknowledgments -- References -- Suggested Reading -- Chapter 2: Linked Equilibria in Regulation of Transcription Initiation -- I. Introduction -- II. Multiple Levels of Linkage in Transcription Regulation -- III. A Road Map for Quantitative Studies of Assembly of Gene Regulatory Complexes -- IV. Measurements of Binding Interactions in Transcription Regulation -- A. Determine the Assembly State of the Protein(s) of Interest -- B. Small Ligand Binding -- C. Analysis of Binding Data -- D. Tools for Measuring Protein-Protein Interactions -- E. Protein-DNA Interactions -- V. Case Studies of Multiple Linked Equilibria in Transcription Regulatory Systems -- A. CRP and CytR: Combinatorial Control of Transcription in E. coli -- B. The Progesterone Receptor: A Nuclear Hormone Receptor -- References -- Chapter 3: Biosensor-Surface Plasmon Resonance Methods for Quantitative Analysis of Biomolecular Interactions -- I. Introduction -- II. Rationale: Biomolecular Interactions with SPR Detection -- III. Materials and Methods -- A. Instrument Preparation -- B. Sensor-Chip Surface Preparation -- C. Sample Preparations -- D. Data Collection and Processing -- IV. Results and Data Analysis -- A. Equilibrium Analysis -- B. Kinetic Analysis -- V. Summary. , Acknowledgments -- References -- Chapter 4: Isothermal Titration Calorimetry: Experimental Design, Data Analysis, and Probing Macromolecule/Ligand Binding and Kinetic Interactions -- I. Introduction -- II. Calorimetry Theory and Operation -- A. Heat Change Measurement and Theory -- B. Variations in Ligand/Macromolecule Mixing Techniques -- C. Commercial Availability -- III. Thermodynamic ITC Experiments -- A. Preface and Review of Basic Thermodynamics -- B. Planning the Thermodynamic ITC Experiment -- C. Running the Thermodynamic ITC Experiment -- D. Analyzing Thermodynamic Data -- E. Models -- F. Error Analysis/Monte Carlo -- G. Summary -- IV. Kinetic ITC Experiments -- A. Reaction Rate Versus Heat Rate -- B. Planning the Experiment -- C. Running the Kinetic ITC Experiment -- D. Analyzing the Kinetic ITC Data -- E. Models -- F. Summary -- V. Conclusions -- Acknowledgments -- References -- Chapter 5: Differential Scanning Calorimetry -- I. Introduction -- II. DSC Instrumentation -- III. Experimental Protocols and Preliminary Data Treatment -- IV. Modeling DNA Unfolding -- A. Freire-Biltonen Deconvolution -- B. Cooperative DNA Unfolding -- C. Melting Oligomeric Hairpins -- V. Summary -- Acknowledgments -- References -- Chapter 6: Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium -- I. Introduction -- A. Types of Problems That Can be Addressed -- II. Basic Theory -- A. Sedimentation Velocity -- B. Sedimentation Equilibrium -- III. Dilute Solution Measurements -- IV. Concentrated and Complex Solutions -- V. Instrumentation and Optical Systems -- A. Absorbance -- B. Interference -- C. Fluorescence -- D. High Concentrations and High Concentration Gradients -- VI. Sample Requirements -- VII. Sample Preparation -- VIII. Sedimentation Velocity -- A. Instrument Operation and Data Collection -- B. Data Analysis. , IX. Sedimentation Equilibrium -- A. Instrument Operation and Data Collection -- B. Monitoring Approach to Equilibrium -- C. Data Analysis -- X. Discussion and Summary -- Acknowledgment -- References -- Chapter 7: Determination of Membrane Protein Molecular Weights and Association Equilibrium Constants Using Sedimentation Equilibrium and Sedimentation Velocity -- I. Introduction -- II. Rationale -- A. Why Use AUC? -- B. General Considerations for Sedimentation Equilibrium Experiments of Membrane Proteins -- C. Special Considerations for Sedimentation Equilibrium Experiments in the Presence of Detergent Micelles -- III. Materials and Methods -- A. Expression and Purification of Membrane Proteins Used in This Study -- B. Determination of the Density-Matching Point for C14SB -- C. Sedimentation Equilibrium Experiments on Membrane Protein Samples Dispersed in C14SB -- D. Sedimentation Velocity Experiments on OmpF -- E. Viscosity Measurements -- F. Density Measurements -- IV. Results -- A. Analysis of OMPLA Dimerization Energetics -- B. Analysis of OmpF Trimer Stability in C14SB -- C. Sedimentation Velocity Experiments on OmpF -- V. Discussion -- VI. Summary -- Acknowledgments -- References -- Chapter 8: Basic Aspects of Absorption and Fluorescence Spectroscopy and Resonance Energy Transfer Methods -- I. Introduction -- II. Absorption Spectroscopy -- A. Absorption Spectrophotometers -- B. Measuring Absorption Spectrum -- C. Common Applications -- D. Microplate Reader Spectrophotometers -- III. Fluorescence Spectroscopy -- A. Introduction to Fluorescence -- B. Fluorophores -- C. Fluorescence Instrumentation -- D. Absorption Versus Fluorescence -- E. Measuring Emission and Excitation Spectra -- F. Common Experimental Problems and Their Solutions -- G. Fluorescence Quenching -- H. Environmental Effects on Fluorescence. , I. Fluorescence Resonance Energy Transfer -- IV. Summary -- Acknowledgments -- References -- Suggested Reading -- Chapter 9: Applications of Fluorescence Anisotropy to the Study of Protein-DNA Interactions -- I. Introduction and General Background -- A. Fluorescence Anisotropy in a Nutshell -- B. Anisotropy and Polarization -- II. Advantages and Disadvantages of Anisotropy in Monitoring DNA Binding -- III. Equipment -- IV. Experimental Design and Performance -- A. Reagents -- B. Polarizer Calibration and G-Factor -- C. Sample Compartment Control -- D. Excitation and Emission Parameters -- E. Data Collection -- F. Data Analysis -- G. Other Controls -- H. Competition Experiments -- V. Other Applications of Fluorescence Anisotropy to the Study of Protein-DNA Interactions -- References -- Chapter 10: Circular Dichroism and Its Application to the Study of Biomolecules -- I. Introduction -- II. Instrumentation and Sample Preparation -- A. Instrumentation -- B. Instrument Care and Calibration -- C. Sample Preparation -- D. Determination of Sample Concentration -- III. Data Collection -- A. Wavelength Range -- B. Scanning Speed and Time Constant (or Response Time) -- C. Spectral Bandwidth -- D. Temperature Control -- IV. Data Processing and Spectral Characteristics -- A. Data Processing -- B. Spectral Characteristics -- V. Applications -- A. Secondary Structure Content of Proteins -- B. Detecting Altered Conformation -- C. CD in the Study of Protein Stability -- D. Determination of Equilibrium Dissociation Constants -- VI. Summary -- Acknowledgments -- References -- Chapter 11: Protein Folding and Stability Using Denaturants -- I. Introduction -- II. Rationale -- III. Methods -- A. General Features of Chemical Denaturation -- B. Equilibration and Reversibility -- C. Automated Titrations -- D. Modeling the Unfolding Reaction. , E. Calculating Folding Energies Within Transition Regions -- F. Modeling the Effects of Denaturant on Folding Energies -- G. Analyzing Denaturation Curves to Extract Thermodynamic Parameters -- H. Spectroscopic Tests of the Two-State Model -- IV. Materials -- A. Preparation of Denaturant Solutions -- B. Determination of Concentrations of Denaturant Solutions -- V. Discussion -- A. Baselines, Parameter Correlation, and Influence on Stability Estimates -- B. The Physical Interpretation of m-Values -- C. Identification of Domain Boundaries -- D. Assessing the Effects of Missense Mutations on Structure and Stability -- E. Identification of Interdomain Interactions -- VI. Summary -- Acknowledgments -- References -- Chapter 12: Hydrodynamic Modeling: The Solution Conformation of Macromolecules and Their Complexes -- I. Introduction -- II. Background to HBM -- II. Model Construction -- A. AtoB -- B. PDB2AT, PDB2AM and MAP2GRID -- C. MAKEPIXB (and HYDROPIX) -- D. SOMO and ASAB1 -- IV. Model Visualization -- A. RasMol and RAZ -- B. VisualBeads -- V. Hydration -- VI. Hydrodynamic Calculations -- A. HYDRO -- B. HYDROPRO -- C. SOLPRO -- D. HYDROSUB -- E. HYDROMIC -- F. SUPCW/SUPCWIN -- G. HYDRONMR (and Fast-HYDRONMR) -- H. How Do Differently Constructed Models and Different Computations Compare? -- VII. Advanced Hydrodynamic Calculations -- A. MULTIHYDRO, MONTEHYDRO and Rayuela -- B. BROWNRIG and BROWNFLEX -- Concluding Comments -- Acknowledgments -- References -- Chapter 13: X-Ray and Neutron Scattering Data and Their Constrained Molecular Modeling -- I. Introduction -- II. Rationale -- A. Complementary Structural Approaches -- B. Properties of X-Ray Scattering -- C. Properties of Neutron Scattering -- III. X-R.ay and Neutron Facilities -- A. High-Flux Sources -- B. X-Ray Instrumentation -- C. Neutron Reactor Instrumentation. , D. Spallation Neutron Instrumentation.

Note: Front Cover -- Methods in Cell Biology -- Copyright Page -- Dedication Page -- Contents -- Contributors -- Preface -- Section I: Fluorescence Methods -- Chapter 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 -- Acknowledgments -- References -- Chapter 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 -- Acknowledgments -- References -- Chapter 3: A Fluorescent Window Into Protein Folding and Aggregation in Cells -- I. Introduction -- II. Rationale -- III. Methods -- IV. Summary -- Acknowledgments -- References -- Chapter 4: Combining Microfluidics and Quantitative Fluorescence Microscopy to Examine Pancreatic Islet Molecular Physiology -- I. Introduction -- II. Rationale -- III. Methods and Materials -- IV. Discussion -- Ackowledgments -- References -- Section II: Microscopic Methods -- Chapter 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 -- Acknowledgments -- References -- Chapter 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 -- Acknowledgments -- References -- Chapter 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 -- Acknowledgments -- References -- Chapter 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 -- Acknowledgments -- References -- Chapter 9: Counting Proteins in Living Cells by Quantitative Fluorescence Microscopy with Internal Standards -- I. Introduction -- II. Experimental Methods -- III. Data Analysis -- IV. Conclusions -- Acknowledgments -- References -- Chapter 10: Infrared and Raman Microscopy in Cell Biology -- I. Introduction -- II. Methods -- III. Results and Discussion -- IV. Conclusions -- Acknowledgment -- References -- Chapter 11: Imaging Fluorescent Mice In Vivo Using Confocal Microscopy -- I. Introduction -- II. Rationale -- III. Methods and Materials -- IV. Discussion and Summary -- References -- Chapter 12: Nanoscale Biological Fluorescence Imaging: Breaking the Diffraction Barrier -- I. Introduction -- II. Theory and Rationale -- III. Methods -- IV. Materials -- V. Discussion -- VI. Summary -- Acknowledgments -- References -- Section III: Methods at the In Vitro/In Vivo Interface -- Chapter 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 -- Acknowledgments -- References -- Chapter 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 -- Chapter 15: Live-Cell Single-Molecule Force Spectroscopy -- I. Introduction -- II. Materials and Instrumentation -- III. Procedures -- IV. Pearls and Pitfalls -- V. Concluding Remarks -- References -- Chapter 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 -- Acknowledgements -- References -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Acknowledgments -- References -- Chapter 20: Automated Spatial Mapping of Microtubule Catastrophe Rates in Fission Yeast -- I. Introduction -- II. Methods -- III. Results -- IV. Discussion -- Acknowledgments -- References -- Section V: Techniques for Protein Activity and Protein-Protein Interactions. , Chapter 21: Quantitative Fluorescence Lifetime Imaging in Cells as a Tool to Design Computational Models of Ran-Regulated Reaction Networks -- Abbreviations -- 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 -- References -- Chapter 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 -- Chapter 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 Glossary of Terms -- References -- Chapter 24: Computational Modeling of Self-Organized Spindle Formation -- I. Introduction -- II. Rationale -- III. Methods -- IV. Materials -- V. Discussion and Summary -- Acknowledgments -- VI. Appendix A: Geometry of Dynamic Degrees of Freedom -- VII. Appendix B: Langevin Calculation Algorithm -- References -- Index -- Volumes in Series -- Color Plate Section.

Note: cover page -- Series editors -- Title page -- copyright page -- Contents -- Contributors -- Preface -- SECTION I -- CHAPTER 1 -- I. Introduction -- II. Protocols -- III. Buffer Compositions -- IV. Concluding Comments -- Acknowledgments -- References -- CHAPTER 2 -- Abstract -- I. Why Tubulin from Nonneural Sources? -- II. General Principles of Tubulin Purification -- III. Specific Properties of Distinct Nonneural Sources -- IV. Genetic Manipulation of Tubulin Genes -- V. Isolation of Tubulin: Theme and Variation -- VI. Protocol Notes -- VII. Summary -- Acknowledgments -- References -- CHAPTER 3 -- Abstract -- I. Introduction -- II. The Characterization of AA2, a Pan-specific Anti-beta-tubulinMonoclonal Antibody That Reacts with All Vertebrate beta-Tubulin Isotypes (Gene Products) -- III. The Characterization of Isotype-Specific beta-TubulinMonoclonal and Polyclonal Antibodies -- IV. The Characterization of Antibodies That Recognizethe Glutamyl Side Chain of Glutamylated Proteins -- V. Summary -- References -- CHAPTER 4 -- Abstract -- I. Introduction and Rationale -- II. Methods and Materials -- III. Results and Discussion -- IV. Summary -- References -- CHAPTER 5 -- I. Introduction -- II. Rationale -- III. Methods -- IV. Materials -- V. Discussion -- VI. Summary -- Acknowledgments -- References -- CHAPTER 6 -- Abstract -- I. Introduction -- II. Methods -- III. Results and Discussion -- IV. Conclusion -- Acknowledgments -- References -- CHAPTER 7 -- Abstract -- I. Introduction -- II. Methods -- III. Summary -- Acknowledgments -- References -- SECTION II -- CHAPTER 8 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Discussion -- V. Summary -- Acknowledgments -- References -- CHAPTER 9 -- Abstract -- I. Introduction to AFM Imaging of Biomolecules -- II. Rationale -- III. AFM Principle and Operation Mode. , IV. Practical Aspects of Microtubules Adsorption on Surface and AFM Imaging -- V. AFM Imaging in Air of Microtubule -- VI. AFM Imaging in Air of Tubulin or Microtubule:Protein Interactions -- VII. Conclusion -- References -- CHAPTER 10 -- Abstract -- I. Introduction -- II. Mathematical and Computational Modeling: A Primer -- III. Using Modeling to Understand Microtubule Dynamics -- IV. Conclusions -- References -- CHAPTER 11 -- Abstract -- I. Introduction -- II. Method -- III. Summary and Conclusion -- Acknowledgments -- References -- CHAPTER 12 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Materials -- V. Discussion -- VI. Summary -- Acknowledgments -- References -- CHAPTER 13 -- Abstract -- I. Introduction -- II. Single-Molecule TIRF Microscopy -- III. List of Reagents -- IV. Choice of Fluorophore/Protein Labeling -- V. (Anti-)blinking/Photo-Toxicity/Photo-Bleaching Cocktails -- VI. Preparation of GMPCPP-Stabilized Microtubules -- VII. Glass Treatment and Sample Chamber Preparation -- VIII. Binding of Microtubules and Passivation of Surfaces -- IX. Dynamic Microtubule Assays -- References -- CHAPTER 14 -- Abstract -- I. Introduction -- II. Setup of Gliding Motility Assays -- III. Analysis of Microtubule and Quantum Dot Movements -- IV. Future Directions -- Acknowledgments -- Reagents -- References -- SECTION III -- CHAPTER 15 -- Abstract -- I. Introduction -- II. Materials and Methods -- III. Results and Discussion -- IV. Summary -- References -- CHAPTER 16 -- Abstract -- I. Introduction -- II. Methods -- III. Materials -- Acknowledgments -- References -- CHAPTER 17 -- Abstract -- I. Introduction -- II. Colchicine Binding to Tubulin -- III. Vinblastine Binding to Tubulin -- IV. Taxol Binding to Microtubules -- V. Determination of Binding Constants Using Extrinsic Fluorescent Probes -- VI. Conclusion -- Acknowledgments. , References -- CHAPTER 18 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Summary -- References -- CHAPTER 19 -- Abstract -- I. Introduction -- II. Materials -- III. Methods -- IV. Applications and Discussion -- V. Summary -- Acknowledgments -- References -- CHAPTER 20 -- Abstract -- I. Introduction -- II. Rationale -- III. Structural Studies of the Tubulin-Vinca Domain Ligand Interactions -- IV. Fluorescence Is Useful to Monitor Binding of Vinca Domain Ligands to Tubulin in Solution -- V. Effects of Vinca Domain Ligands on Tubulin Biochemical Properties -- VI. Discussion -- Acknowledgments -- References -- CHAPTER 21 -- Abstract -- I. Introduction and Rationale -- II. Methods -- III. Discussion -- Acknowledgments -- References -- SECTION IV -- CHAPTER 22 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Application to Tubulin/Microtubules Interactions -- V. Conclusion -- VI. Appendix I. Materials -- References -- CHAPTER 23 -- Abstract -- I. Introduction -- II. Rationale -- III. Materials and Methods -- IV. Discussion -- V. Concluding Remarks -- Acknowledgments -- References -- CHAPTER 24 -- Abstract -- I. Introduction and Rationale -- II. Methods -- III. Materials -- IV. Summary -- Acknowledgments -- References -- CHAPTER 25 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Fluorescent Labeling for FPM -- V. Discussion and Future Directions -- Acknowledgments -- References -- CHAPTER 26 -- Abstract -- I. Introduction -- II. TIRF Optics -- III. Labeling Molecules -- IV. Examples and Protocols -- V. Conclusions and Outlook -- Acknowledgments -- References -- CHAPTER 27 -- Abstract -- I. Introduction -- II. Rationale -- III. Methods -- IV. Discussion -- Acknowledgments -- References -- CHAPTER 28 -- Abstract -- I. Introduction -- II. Rationale -- III. Materials -- IV. Methods. , V. Surface Chemistry on Glass -- VI. Fluorescence Microscopy Assays -- VII. Discussion -- VIII. Conclusion -- Acknowledgments -- References -- SECTION V -- CHAPTER 29 -- Abstract -- I. Introduction to Cytoskeletal Filament Dynamics -- II. Single-Molecule Lifetime Measurements -- III. Theoretical Foundations -- IV. Results and Conclusion -- References -- CHAPTER 30 -- Abstract -- I. Introduction -- II. Rationale -- III. Materials -- IV. Methods -- V. Discussion -- VI. Summary -- Acknowledgments -- References -- CHAPTER 31 -- Abstract -- I. Introduction -- II. Materials -- III. Methods -- IV. Results -- V. Conclusion -- Acknowledgments -- References -- CHAPTER 32 -- Abstract -- I. Introduction -- II. Methods -- III. Conclusion -- References -- CHAPTER 33 -- Abstract -- I. Introduction -- II. Rationale -- III. Materials and Methods -- IV. Summary and Discussion -- Acknowledgments -- References -- INDEX -- VOLUMES IN SERIES.

Note: Intro -- Contents -- Series Foreword -- Preface -- Introduction -- 1. Atmosphere, Oceans, and Rivers -- Atmosphere Composition -- Ozone Depletion -- Changes in Solar Radiation -- Long-Term (Tens of Thousands of Years) Cycles -- The Last Ice Age and the Consequences of Its End -- Short-Term (Hundreds of Years) Variations -- Climate of the Last 2,000 Years -- Present Global Warming -- Evidence for Global Warming -- Causes of Global Warming -- Reducing the Rate of Global Warming -- Consequences of Global Warming -- Climatic Effects of Volcanoes -- Toba -- Krakatoa, 535 AD -- Tambora -- Laki, Iceland -- Mount Billy Mitchell, Solomon Islands -- Huaynaputina, Peru -- Possible Future Eruptions of Yellowstone and Long Valley -- Wind -- Hurricane Katrina -- Ocean Currents -- El Nino -- Rivers -- The Missouri River and the Lewis and Clark Expedition -- Atchafalaya and Mississippi Rivers -- Chamizal and the U.S.-Mexico border -- Nile River and Its Floods -- Route Across the Great Basin -- Canals -- The Suez Canal -- Panama Canal -- 2. Tectonics -- Solid Earth -- Isostasy -- Plate Tectonics -- Earth's Heat -- Structures and Processes -- Hot Spots and Mantle Plumes -- Effect of Tectonics on Human History -- Volcanic Eruptions -- Earthquakes -- Tsunamis -- Living in Rifts -- Living on Small Islands -- 3. Evolution, Creationism, and the Long History of the Earth -- Creationism -- Uniformitarianism -- Evolution -- Conflict Between Creationism and Evolution in the 20th and 21st Centuries -- Paleontologic Record -- Cyanobacteria -- Algae -- Oldest Animals -- Oldest Vertebrates -- Oldest Land Plant -- Permian-Triassic Extinction -- Oldest Mammal -- Cretaceous-Tertiary Extinction -- Pleistocene Megafauna Extinction -- Relative Time and the Geologic Time Scale -- Radiometric Dating and the Absolute Time Scale -- Radiometric Dating Using Heavy Isotopes. , Radiometric Dating Using the K-Ar System -- Radiometric Dating Using Carbon-14 (Radiocarbon Dating) -- Measured Ages -- Continents and Supercontinents -- Formation of Continents -- History of Supercontinents -- The Supercontinent Cycle -- 4. Resources and the Environment -- Energy Resources -- United States Energy Production and Consumption -- World Energy Production and Consumption -- Fossil Fuel -- Nuclear Energy -- Nuclear Hazards -- Renewable Resources -- Rock and Mineral Resources -- Base Metals -- Iron and Iron Alloy (Ferro-Alloy) Metals -- Nonmetals -- History of Tools -- Fertilizer -- Precious Metals and Gems -- Food -- Nutritional Requirements -- Sources of Food -- Food Supply and Population Growth -- Water -- Wireless Communication and the Internet -- Silk Road -- Development of Modern Communication -- Units and Abbreviations -- Glossary -- A -- B -- C -- D -- E -- F -- G -- H -- I -- L -- M -- N -- O -- P -- R -- S -- T -- U -- V -- W -- Selected Bibliography -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- U -- V -- W -- Y -- Z.

Note: Intro -- RNA INTERFERENCE -- CONTENTS -- CONTRIBUTORS -- PREFACE -- FOREWORD -- I BIOLOGY OF RNA INTERFERENCE -- 1 RNA INTERFERENCE: WHAT IS IT? -- 2 NUCLEIC ACIDS AS REGULATORY MOLECULES -- 3 USE OF SIRNA OLIGONUCLEOTIDES TO STUDY GENE FUNCTION -- 4 GENOME SCANNING BY RNA INTERFERENCE -- II DEVELOPMENT OF SIRNA FOR THERAPEUTIC APPLICATIONS -- 5 DISCOVERY OF NEW SIRNA DELIVERY AGENTS -- 6 SIRNA DELIVERY VEHICLES -- 7 INTERFERON, CYTOKINE INDUCTION, AND OTHER POTENTIAL IN VIVO TOXICITIES -- 8 APPLICATION OF RNA INTERFERENCE TO VIRAL DISEASES -- INDEX -- Color Plate.

Note: Cover -- Landslides -- Title -- Copyright -- Contents -- Contributors -- Preface -- 1: Landslide hazard and risk -- ABSTRACT -- 1.1 INTRODUCTION -- 1.2 HAZARD AND RISK -- 1.3 EVALUATING HAZARD -- 1.4 FROM HAZARD TO RISK -- 1.5 AN EXAMPLE OF LANDSLIDE RISK EVALUATION -- 1.6 LANDSLIDE RISK IN THE FUTURE -- 1.7 CONCLUSIONS -- REFERENCES -- 2:Landslides in the Earth system -- ABSTRACT -- 2.1 INTRODUCTION -- 2.2 LANDSLIDE DISTRIBUTION AND SIZE -- 2.3 LANDSLIDES AND THE LITHOSPHERE -- 2.4 LANDSLIDES AND THE HYDROSPHERE -- 2.4.1 LANDSLIDES AND THE TERRESTRIAL WATER CYCLE -- 2.4.2 LANDSLIDES AND THE OCEANS -- 2.5 LANDSLIDES AND THE BIOSPHERE -- 2.6 SUMMARY -- ACKNOWLEDGEMENTS -- REFERENCES -- 3: Earthquake ground motion and patterns of seismically induced landsliding -- ABSTRACT -- 3.1 INTRODUCTION -- 3.2 EARTHQUAKES, SEISMIC WAVES, AND GROUND MOTION -- 3.3 LANDSLIDING AND EARTHQUAKE STRONG GROUND MOTION -- 3.4 SPATIAL PATTERNS OF EARTHQUAKE-TRIGGERED LANDSLIDES -- 3.4.1 REGIONAL PATTERNS -- 3.4.2 TOPOGRAPHIC SITE EFFECTS -- 3.5 TEMPORAL PATTERNS OF SEISMICALLY INDUCED LANDSLIDING -- 3.6 EARTHQUAKE EROSION AND MASS BALANCE -- 3.7 CONCLUSIONS AND OUTLOOK -- REFERENCES -- 4: Landslides at stratovolcanoes initiated by volcanic unrest -- ABSTRACT -- 4.1 INTRODUCTION -- 4.2 VOLCANIC LANDSLIDES ASSOCIATED WITH ERUPTIVE ACTIVITY AND UNREST -- 4.2.1 VOLCANIC LANDSLIDES ASSOCIATED WITH PHREATIC ERUPTIONS -- 4.2.2 HOW DO PHREATIC ERUPTIONS INITIATE VOLCANIC LANDSLIDES? -- 4.2.3 VOLCANIC LANDSLIDES ASSOCIATED WITH MAGMATIC INTRUSIONS -- 4.2.4 VOLCANIC LANDSLIDES ASSOCIATED WITH MAGMA EXTRUSION -- 4.2.5 VOLCANIC LANDSLIDES ASSOCIATED WITH EXPLOSIVE CONDUIT PROCESSES -- 4.3 DISCUSSION -- ACKNOWLEDGEMENTS -- REFERENCES -- 5: Mobility of long-runout rock avalanches -- ABSTRACT -- 5.1 INTRODUCTION -- 5.2 MECHANISMS OF LONG RUNOUT. , 5.3 ENVIRONMENTS, MATERIALS AND CHARACTERISTICS OF LONG-RUNOUT ROCK AVALANCHES -- 5.4 IMPLICATIONS -- 5.5 OTHER MECHANISMS -- 5.6 DYNAMIC ROCK FRAGMENTATION -- 5.6.1 OUTLINE -- 5.6.2 THE ENERGETICS OF BREAKING GRAINS -- 5.6.3 SOCOMPA DEBRIS AVALANCHE -- 5.7 DISCUSSION -- 5.8 LOOKING FORWARD -- ACKNOWLEDGEMENTS -- REFERENCES -- 6: Rapid rock-slope failures -- ABSTRACT -- 6.1 INTRODUCTION -- 6.2 OVERVIEW OF ROCK-SLOPE FAILURES AND HAZARD -- 6.3 RECOGNITION OF TYPES OF ROCK-SLOPE FAILURES AND THEIR DEPOSITS -- 6.4 TEMPORAL ROCKSLIDE DISTRIBUTION AND CLIMATE CHANGE -- 6.5 CATASTROPHIC LANDSLIDES AND NEOTECTONICS -- REFERENCES -- 7: Risk assessments for debris flows -- ABSTRACT -- 7.1 INTRODUCTION -- 7.2 DEBRIS-FLOW RISK ASSESSMENT FRAMEWORK -- 7.2.1 CONSULTATION ZONE -- 7.2.2 FREQUENCY-MAGNITUDE ANALYSIS -- 7.2.3 DEBRIS-FLOW HAZARD AND INTENSITY MAPS -- 7.3 DEBRIS-FLOW RISK -- 7.3.1 HAZARD PROBABILITY AND PARTIAL RISK APPROACH -- 7.3.2 QUANTITATIVE ASSESSMENTS FOR DEBRIS-FLOW RISK TO LIFE -- 7.4 CASE STUDIES -- 7.4.1 CASE STUDY 1: DEBRIS-FLOW RISK TO HIGHWAY USERS -- RISK ESTIMATION -- INDIVIDUAL RISK SUMMARIES -- GROUP RISK SUMMARIES -- RESULTS -- 7.4.2 CASE STUDY 2: RISK TO URBAN DEVELOPMENT -- RISK ESTIMATION -- RISK TO INDIVIDUALS -- RISK TO DEVELOPMENT -- 7.5 ERROR SOURCES -- 7.6 CONCLUSIONS -- ACKNOWLEDGEMENT -- REFERENCES -- 8: Landslides in quick clay -- ABSTRACT -- 8.1 INTRODUCTION -- 8.2 WHAT IS QUICK CLAY? -- 8.3 GEOLOGIC SETTINGS -- 8.4 GENERAL MODEL FOR QUICK CLAY DEVELOPMENT -- 8.4.1 MINERALOGY -- 8.4.2 FLOCCULATION -- 8.4.3 CEMENTATION -- 8.4.4 LIQUID LIMIT -- 8.4.5 OTHER FACTORS -- 8.5 DRAINAGE SYSTEM DEVELOPMENT, SUBAERIAL WEATHERING, NODULAR STRUCTURE, AND CUTAN DEVELOPMENT -- 8.6 RANGE OF QUICK CLAY PHYSICAL PARAMETERS -- 8.7 LANDSLIDE TYPES -- 8.8 LANDSLIDE INITIATION -- 8.9 LANDSLIDE DEVELOPMENT -- 8.9.1 STEPWISE LANDSLIDES. , MULTIDIRECTIONAL RETROGRESSION -- 8.9.2 UNINTERRUPTED LANDSLIDES -- FLAKESLIDES -- THE RISSA LANDSLIDE -- ABORTED, TWO-DIMENSIONAL, AND EXCESS RETROGRESSION -- 8.9.3 DEVELOPMENT OF RIBBED LANDSLIDES -- 8.10 HAZARD ASSESSMENT AND PROSPECTIVE METHODS FOR PREVENTION OF QUICK CLAY LANDSLIDES -- REFERENCES -- 9: Controls on the distribution of major types of submarine landslides -- ABSTRACT -- 9.1 INTRODUCTION -- 9.2 SEDIMENT TRANSPORT PROCESSES IN SUBMARINE LANDSLIDES -- 9.3 ARCHITECTURAL TYPES OF SUBMARINE SLIDES -- 9.3.1 INTRODUCTION -- 9.3.2 FRONTALLY EMERGENT AND FRONTALLY CONFINED SLIDES -- 9.3.3 SIMPLE SLUMPS -- 9.3.4 MAJOR RETROGRESSIVE SLUMPS -- 9.3.5 LARGE COMPLEX LANDSLIDES -- 9.3.6 BLOCKY DISAGGREGATED LANDSLIDES -- 9.4 THE CAUSES OF FAILURES -- 9.5 THE GLACIATED EASTERN CANADIAN CONTINENTAL MARGIN -- 9.5.1 DATA AVAILABILITY -- 9.5.2 PROGRADATIONAL AND EROSIONAL CONTINENTAL MARGINS -- 9.5.3 PROGRADATIONAL SMOOTH SLOPES AND SEDIMENT DRIFTS -- 9.5.4 EROSIONAL MARGIN SEGMENTS -- 9.6 DISCUSSION -- 9.7 CONCLUSIONS -- REFERENCES -- 10: Tsunami hazard assessment related to slope failures in coastal waters -- ABSTRACT -- 10.1 INTRODUCTION -- 10.2 COMMON CONDITIONING FACTORS AND TRIGGERS -- 10.3 PROGRESSIVE TSUNAMI HAZARD ASSESSMENT APPROACH -- 10.3.1 PAST ACCOUNTS OF EVENTS -- 10.3.2 GEOLOGIC INVESTIGATIONS -- 10.3.3 GEOTECHNICAL STUDIES -- 10.3.4 FREQUENCY OF TSUNAMIGENIC LANDSLIDES -- 10.3.5 LANDSLIDE-GENERATED TSUNAMI MODELING -- 10.3.6 THINGS WE USUALLY DON'T KNOW -- 10.3.7 SUMMARY OF LANDSLIDE TSUNAMI HAZARD ASSESSMENT APPROACH -- 10.4 CONCLUSIONS -- ACKNOWLEDGEMENTS -- REFERENCES -- 11: Physical impacts of climate change on landslide occurrence and related adaptation -- ABSTRACT -- 11.1 INTRODUCTION -- 11.2 OBSERVED IMPACTS OF CLIMATE CHANGE ON LANDSLIDE ACTIVITY -- 11.2.1 EFFECTS ON SHALLOW LANDSLIDES AND DEBRIS FLOWS. , 11.2.2 EFFECTS ON ROCK-SLOPE FAILURES AND DEBRIS FLOWS IN HIGH MOUNTAINS -- 11.3 PROJECTED IMPACTS OF CLIMATE CHANGE ON LANDSLIDE ACTIVITY -- 11.4 ADAPTATION TO EFFECTS OF CLIMATE CHANGE ON SLOPE STABILITY -- 11.4.1 MODELING PRECIPITATION CHANGE AND ITS EFFECTS ON LANDSLIDE OCCURRENCE -- 11.4.2 ADAPTATION OF A LANDSLIDE EARLY-WARNING SYSTEM TO CHANGING PRECIPITATION -- 11.5 CONCLUSIONS -- ACKNOWLEDGEMENTS -- REFERENCES -- 12: Landslides and geologic environments -- ABSTRACT -- 12.1 INTRODUCTION -- 12.2 THE INFLUENCE OF ROCK TYPE, STRATIGRAPHY, WEATHERING, AND STRUCTURE ON LANDSLIDING -- 12.2.1 GRANITIC ROCKS -- 12.2.2 BASALT -- 12.2.3 SEDIMENTARY ROCKS -- 12.2.4 THE EFFECTS OF FOLDING OF SEDIMENTARY STRATA -- 12.2.5 THE EFFECTS OF STRESS RELIEF FROM FORMATION OF VALLEYS -- 12.2.6 FOLIATED METAMORPHIC ROCKS -- 12.3 SOME FACTORS TO CONSIDER IN THE ANALYSES OF STABILITY OF SLOPES -- 12.3.1 THE MECHANICS OF SLIDING -- 12.3.2 ASSESSMENT OF SHEAR STRENGTH PARAMETERS IN ROCK -- 12.3.3 ASSESSMENT OF PORE PRESSURES IN SLOPES -- REFERENCES -- 13: Numerical modeling of rock-slope instability -- ABSTRACT -- 13.1 INTRODUCTION -- 13.2 KINEMATIC ANALYSIS -- 13.3 ADVANCES IN LIMIT EQUILIBRIUM SLOPE ANALYSIS -- 13.3.1 TWO-DIMENSIONAL LIMIT EQUILIBRIUM APPLICATIONS -- 13.3.2 THREE-DIMENSIONAL LIMIT EQUILIBRIUM APPLICATIONS -- 13.4 CONTINUUM MODELING OF LANDSLIDES -- 13.5 DISCONTINUUM MODELING OF ROCK SLOPES -- 13.6 BRITTLE FRACTURE MODELING -- 13.6.1 FEM/DEM -- 13.6.2 PARTICLE FLOW CODES -- 13.6.3 UDEC DAMAGE MODELS -- 13.6.4 THE SYNTHETIC ROCK MASS (SRM) APPROACH -- 13.7 FUTURE CHALLENGES IN THE NUMERICAL ANALYSIS OF ROCK SLOPES -- 13.7.1 CONSIDERATION OF SPATIAL VARIABILITY IN NUMERICAL MODELING -- 13.7.2 TREATMENT OF UNCERTAINTY IN NUMERICAL MODELING -- 13.7.3 IMPROVED MODELING CONSTRAINTS -- 13.8 CONCLUSIONS -- REFERENCES. , 14: Remote sensing techniques and landslides -- ABSTRACT -- 14.1 INTRODUCTION -- 14.2 KEY RECENT TECHNOLOGICAL ADVANCES -- 14.3 PHOTOGRAMMETRY -- 14.4 OPTICAL SATELLITE IMAGERY, INCLUDING THE APPLICATION OF THE GOOGLE EARTH TOOL -- 14.5 RADAR SATELLITE INSTRUMENTATION -- 14.6 AIRBORNE LIDAR -- 14.7 TERRESTRIAL LASER SCANNING (GROUND-BASED LIDAR) -- 14.8 GEOPHYSICAL TECHNIQUES -- 14.8.1 SUBSURFACE ENGINEERING GEOPHYSICAL INVESTIGATION -- 14.8.2 IMAGING OF LANDSLIDES IN THREE DIMENSIONS -- 14.8.3 PERMANENT ARRAYS -- 14.8.4 DATA FUSION -- 14.9 CONCLUSIONS -- REFERENCES -- 15: Engineering geomorphology of landslides -- ABSTRACT -- 15.1 INTRODUCTION -- 15.2 LANDSLIDES: SITUATION AND SITE -- 15.2.1 GEOMORPHOLOGICAL PROCESS-RESPONSE SYSTEMS -- 15.2.2 THE LANDSLIDE GEOMORPHOLOGICAL PROCESS-RESPONSE SYSTEM -- 15.3 ENGINEERING GEOMORPHOLOGICAL INVESTIGATION OF LANDSLIDES -- 15.3.1 THE NATURE AND SCOPE OF THE INVESTIGATION -- 15.3.2 DESK STUDIES AND DIGITAL DATA ANALYSIS -- 15.3.3 FIELD-BASED GEOMORPHOLOGICAL MAPPING -- 15.4 GEOMORPHOLOGICAL CLASSIFICATION OF LANDSLIDES -- 15.5 CONCLUSIONS -- REFERENCES -- 16: Developments in landslide runout prediction -- ABSTRACT -- 16.1 INTRODUCTION -- 16.2 LANDSLIDE RUNOUT MAPPING -- 16.3 EMPIRICAL METHODS -- 16.3.1 VOLUME-FAHRBÖSCHUNG RELATIONSHIPS -- 16.3.2 VOLUME-AREA RELATIONSHIPS -- 16.3.3 OTHER EMPIRICAL METHODS -- 16.4 NUMERICAL MODELS -- 16.4.1 MODEL DEVELOPMENT -- 16.4.2 THE HONG KONG MODEL BENCHMARKING EXERCISES -- 16.4.3 THE CALIBRATION-BASED APPROACH -- 16.4.4 RECENT ADVANCES -- 16.5 CONCLUSIONS -- REFERENCES -- 17: Models of the triggering of landslides during earthquakes -- ABSTRACT -- 17.1 INTRODUCTION -- 17.2 CHARACTERISTICS OF EARTHQUAKE-TRIGGERED LANDSLIDES -- 17.2.1 LANDSLIDE TYPES -- 17.2.2 LANDSLIDE-TRIGGERING CONDITIONS -- 17.2.3 GEOGRAPHIC DISTRIBUTIONS OF EARTHQUAKE-TRIGGERED LANDSLIDES. , 17.3 METHODS FOR ASSESSING THE STABILITY OF SLOPES.

Note: Front cover -- Contents -- Preface -- Acknowledgments -- About the Editors -- Contributors -- Chapter 1. MicroMining: Computational Approaches to microRNA Discovery -- Chapter 2. Animal microRNA Gene Prediction -- Chapter 3. A Suite of Resources for the Study of microRNA Ontology and Function -- Chapter 4. Regulation of Translation and mRNA Stability by Hfq-Binding Small RNAs in Escherichia coli -- Chapter 5. Mechanisms by which microRNAs Regulate Gene Expression in Animal Cells -- Chapter 6. The microRNAs of Caenorhabditis elegans -- Chapter 7. Isolation and Characterization of Small RNAs in Caenorhabditis elegans -- Chapter 8. MicroRNA Tales in Fly Development -- Chapter 9. RNA Interference and microRNAs in Zebra Fish -- Chapter 10. Biogenesis and Function of Plant microRNAs -- Chapter 11. Endogenous Small RNA Pathways in Arabidopsis -- Chapter 12. How to Assay microRNA Expression: A Technology Guide -- Chapter 13. Methods to Quantify microRNA Gene Expression -- Chapter 14. Regulation of Alternative Splicing by microRNAs -- Chapter 15. Recent Progress in Polymerase II-Mediated Intronic microRNA Expression Systems -- Chapter 16. MicroRNA-Based RNA Polymerase II Expression Vectors for RNA Interference in Mammalian Cells -- Chapter 17. Transgenic RNAi: A Fast and Low-Cost Approach to Reverse Genetics in Mammals -- Chapter 18. Symphony of AIDS: A microRNA-Based Therapy -- Chapter 19. MicroRNAs and Cancer: Connecting the Dots* -- Chapter 20. Mammalian Transcriptional Gene Silencing by Small RNAs -- Chapter 21. Regulation of Gene Expression by RNA-Mediated Transcriptional Gene Silencing -- Index -- Back cover.