Biomass Conversion: Methods and Protocols

1. Challenges for Assessing the Performance of Biomass Degrading Biocatalysts

Michael E. Himmel, Stephen R. Decker, and David K. Johnson

Part I: Biomass Feedstock and Cellulose

2. Overview of Computer Modeling of Cellulose

Malin Bergenstråhle-Wohlert, and John W. Brady

3. Imaging Cellulose Using Atomic Force Microscopy

Shi-You Ding and Yu-San Liu

4. Preservation and Preparation of Lignocellulosic Biomass Samples

for Multi-scale Microscopy Analysis

Bryon S. Donohoe, Peter N. Ciesielski, and Todd B. Vinzant

5. Coherent Raman Microscopy Analysis of Plant Cell Walls

Yining Zeng, Michael E. Himmel, and Shi-You Ding

6. Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling

Sivakumar Pattathil, Utku Avci, Jeffrey S. Miller^, and Michael G. Hahn

7. Immunological Approaches To Plant Cell Wall and Biomass Characterization: Immunolocalization of Glycan Epitopes

Utku Avci, Sivakumar Pattathil, and Michael G. Hahn

8. A Method to Evaluate Biomass Accessibility in Wet State Based on Thermoporometry

Bon-Wook Koo and Sunkyu Park

9. Cellulase Processivity

David B. Wilson and Maxim Kostylev

10. A Simple Method for Determining Specificity of Carbohydrate-Binding Modules for Purified and Crude Insoluble Polysaccharide Substrates

Oren Yaniv, Sadanari Jindou, Felix Frolow, Raphael Lamed, and Edward A. Bayer

11. Bacterial Cadherin Domains as Carbohydrate Binding Modules: Determination of Affinity Constants to Insoluble Complex Polysaccharides

Milana Fraiberg, Ilya Borovok, Ronald M. Weiner, Raphael Lamed, and Edward A. Bayer

12. Affinity Electrophoresis as a Method for Determining Substrate-Binding Specificity of Carbohydrate-Active Enzymes for Soluble Polysaccharides

Sarah Moraïs, Raphael Lamed, and Edward A. Bayer

13. Single-Molecule Tracking of Carbohydrate-Binding Modules on Cellulose Using Fluorescence Microscopy

Yu-San Liu, Shi-You Ding, and Michael E. Himmel

14. Bioprospecting Metagenomics for New Glycoside Hydrolases

Jack Gilbert, Luen-Luen Li, Safiyh Taghavi, Sean M. McCorkle, Susannah Tringe, and Daniel van der Lelie

15. Anaerobic High-Throughput Cultivation Method for Isolation

of Thermophiles Using Biomass-Derived Substrates

Scott D. Hamilton-Brehm, Tatiana A. Vishnivetskaya, Steve Allman, Jonathan Mielenz, and James G. Elkins

16. Assessing the Protein Concentration in Commercial Enzyme Preparations

William S. Adney, Nancy Dowe, Edward W. Jennings, Ali Mohagheghi,

John Yarbrough, and James D. McMillan

17. Reducing the Effect of Variable Starch Levels in Biomass Recalcitrance Screening

Stephen R. Decker, Melissa Carlile, Michael J. Selig, Crissa Doeppke, Mark Davis, Robert Sykes, Geoffrey Turner, and Angela Ziebell

18. Analysis of Transgenic Glycoside Hydrolases Expressed in Plants: T. reesei CBH I and A. cellulolyticus EI

Roman Brunecky, John O. Baker , Hui Wei, Larry E. Taylor, Michael E. Himmel, and Stephen R. Decker

Part III: Lignins and HEmicelluloses

19. Structural Characterization of the Heteroxylans

from Poplar and Switchgrass

Koushik Mazumder, Maria J. Peña, Malcolm A. O'Neill, William S. York

20. Laser Microdissection and Genetic Manipulation Technologies to Probe Lignin Heterogeneity and Configuration in Plant Cell Walls

Oliver R. A. Corea, Chanyoung Ki, Claudia L. Cardenas,

Laurence B. Davin, and Norman G. Lewis

21. Lignin-Degrading Enzyme Activities

Yi-ru Chen, Simo Sarkanen and Yun-Yan Wang