Research Methods in Biomineralization Science - 1st Edition - ISBN: 9780124166172, 9780124166554

Research Methods in Biomineralization Science, Volume 532

1st Edition

Serial Volume Editors: Jim De Yoreo
Hardcover ISBN: 9780124166172
eBook ISBN: 9780124166554
Imprint: Academic Press
Published Date: 15th September 2013
Page Count: 704
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Table of Contents

Series Page

Contributors

Preface

Methods in Enzymology

Section I: Investigating Solution Chemistry, Structure, and Nucleation

Chapter One. Development of Accurate Force Fields for the Simulation of Biomineralization

Abstract

1 Introduction

2 Force Field Selection and Refinement

3 The Mineral–Aqueous Interface

4 Organics in Geochemical Systems

5 Summary

Acknowledgments

References

Chapter Two. The Integration of Ion Potentiometric Measurements with Chemical, Structural, and Morphological Analysis to Follow Mineralization Reactions in Solution

Abstract

1 Introduction

2 Ion Potentiometric Measurements

3 Combination of Ion Potentiometric Measurements with other Analysis Techniques

4 Comparison with Standard Analyses

5 Summary

References

Chapter Three. Investigating the Early Stages of Mineral Precipitation by Potentiometric Titration and Analytical Ultracentrifugation

Abstract

1 Introduction

2 Equipment

3 Experimental Procedures

4 Data Evaluation

5 Conclusions and Outlook

References

Chapter Four. Replica Exchange Methods in Biomineral Simulations

Abstract

1 Introduction

2 Monte Carlo Sampling

3 Replica Exchange MD

4 Application of REMD to Early Stage Mineralization

5 Summary

References

Chapter Five. SAXS in Inorganic and Bioinspired Research

Abstract

1 Introduction

2 General Considerations: How Does SAXS/WAXS Work and When It Is Applicable?

3 What Happens in a Solution When Ions Meet and How Do We Quantify it?

4 SAXS Data Processing and Interpretation

5 Case Studies

6 Outlook

Acknowledgments

References

Chapter Six. In Situ Solution Study of Calcium Phosphate Crystallization Kinetics

Abstract

1 Introduction

2 Solution Preparation and Experimental Considerations

3 In Situ Experiments

4 Data Handling/Processing

5 Summary

References

Section II: Probing Structure and Dynamics at Surfaces and Interfaces

Chapter Seven. Design, Fabrication, and Applications of In Situ Fluid Cell TEM

Abstract

1 Introduction

2 Fluid Cell Design

3 Cell Fabrication and Assembly

4 TEM Operation

5 Effects of the Electron Beam on Reactions in the Fluid Cell

6 Conclusions

Acknowledgments

References

Chapter Eight. X-ray Absorption Spectroscopy for the Structural Investigation of Self-Assembled-Monolayer-Directed Mineralization

Abstract

1 Introduction

2 Theory

3 Experimental

4 Analysis

Acknowledgments

References

Chapter Nine. Cryo-TEM Analysis of Collagen Fibrillar Structure

Abstract

1 Introduction

2 Sample Preparation for Cryo-TEM

3 Image Acquisition and Processing

4 Image Averaging

5 Summary and Outlook

Acknowledgments

References

Section III: Biomimetic Crystallization Techniques in vitro

Chapter Ten. Preparation of Organothiol Self-Assembled Monolayers for Use in Templated Crystallization

Abstract

1 Introduction

2 Crystallization Approaches Using SAMs as Templates

3 Preparation

4 Why Good SAMs Go Bad

5 SAM Preparation Procedure

6 Summary

Acknowledgments

References

Chapter Eleven. Experimental Techniques for the Growth and Characterization of Silica Biomorphs and Silica Gardens

Abstract

1 Introduction

2 Silica Biomorphs

3 Chemical Gardens

4 Conclusions and Outlook

Acknowledgments

References

Chapter Twelve. Precipitation in Liposomes as a Model for Intracellular Biomineralization

Abstract

1 Introduction

2 Model Systems for Studying the Influence of Confinement on Biomineralization

3 Preparation of Liposomes

4 Precipitation Inside Liposomes

5 Characterization Methods

6 Conclusions

Acknowledgments

References

Chapter Thirteen. Polymer-Mediated Growth of Crystals and Mesocrystals

Abstract

1 Introduction

2 Insoluble Polymers

3 Soluble Polymers

4 Conclusion

References

Chapter Fourteen. Phage Display for the Discovery of Hydroxyapatite-Associated Peptides

Abstract

1 Introduction

2 Methods

3 Summary

References

Section IV: Protein Structure, Interactions and Function

Chapter Fifteen. Quantitatively and Kinetically Identifying Binding Motifs of Amelogenin Proteins to Mineral Crystals Through Biochemical and Spectroscopic Assays

Abstract

1 Introduction

2 Strategy and Rationale

3 Experimental Components and Considerations

4 Experimental Approaches

5 Data Handling and Processing

6 Summary

Acknowledgments

References

Chapter Sixteen. Using the RosettaSurface Algorithm to Predict Protein Structure at Mineral Surfaces

Abstract

1 Introduction

2 Algorithm Evolution and Prior Results

3 Computational Methods

4 Protocol Capture

5 Future Challenges

Acknowledgments

References

Chapter Seventeen. Investigating Protein Function in Biomineralized Tissues Using Molecular Biology Techniques

Abstract

1 Introduction

2 Discovery of Proteins Involved in Biomineralization

3 Analysis of Function

Acknowledgments

References

Section V: Mapping Biomineral Morphology and Ultrastructure

Chapter Eighteen. Imaging the Nanostructure of Bone and Dentin Through Small- and Wide-Angle X-Ray Scattering

Abstract

1 Introduction

2 Experimental Setup

3 Overview of Parameters

4 Treatment of SAXS Data from Mineralized Tissue

5 Treatment of WAXD Data from Mineralized Tissues

6 Analysis Tools

7 Combination of Scanning SAXS/WAXD with Other Methods

8 Conclusions

References

Chapter Nineteen. Synchrotron X-Ray Nanomechanical Imaging of Mineralized Fiber Composites

Abstract

1 Introduction

2 Molecular and Nanoscale Strains and Stresses in a Prototypical Biomineralized Composite

3 Relation between X-Ray Spectra and Nanomechanics

4 Sample Preparation for In Situ Mechanical Testing with Synchrotron X-Rays

5 Mechanical Tester Design

6 Synchrotron Setup

7 In Situ Experimental Procedure

8 Data Analysis

9 Case Studies

10 Model Interpretation

11 Summary

Acknowledgments

References

Section VI: Mapping Mineral Chemistry

Chapter Twenty. Application of Total X-Ray Scattering Methods and Pair Distribution Function Analysis for Study of Structure of Biominerals

Abstract

1 Introduction

2 Total Scattering Methodology

3 The PDF

4 Extracting Information from the PDF

5 PDF Studies of Biominerals

6 Summary

Links

Acknowledgments

References

Chapter Twenty-One. X-Ray Microdiffraction of Biominerals

Abstract

1 Introduction

2 Elements of X-Ray (Micro)Diffraction

3 Synchrotron, X-Ray Focusing Optics, and Area Detectors

4 Sample Preparation

5 Powder X-Ray Microdiffraction

6 White-Beam X-Ray Microdiffraction

7 Microbeam Small-Angle X-Ray Scattering

8 Future Developments

References

Chapter Twenty-Two. FTIR and Raman Studies of Structure and Bonding in Mineral and Organic–Mineral Composites

Abstract

1 Introduction

2 FTIR and Raman Spectroscopies Overview

3 The Raman Effect

4 Measuring Biomimetic Crystals and Biominerals

5 Future Directions

Acknowledgments

References

Chapter Twenty-Three. A Mixed Flow Reactor Method to Synthesize Amorphous Calcium Carbonate Under Controlled Chemical Conditions

Abstract

1 Introduction

2 Method

3 Characterization

4 Results

References

Author Index

Subject Index


Description

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in biomineralization science, and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure.

Key Features

  • Continues the legacy of this premier serial with quality chapters authored by leaders in the field
  • Covers research methods in biomineralization science
  • Contains sections on such topics as and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.


Details

No. of pages:
704
Language:
English
Copyright:
© Academic Press 2013
Published:
Imprint:
Academic Press
eBook ISBN:
9780124166554
Hardcover ISBN:
9780124166172

About the Serial Volume Editors

Jim De Yoreo Serial Volume Editor