Metabolic Pathway Engineering

This book illustrates experimental and computational methodologies used to achieve cost effective biological processes for the production of fuels and biochemicals through multiple approaches to increasing yield, titers, and productivity in a robust host. The volume includes the most recent and cutting-edge aspects of pathway engineering, flux analysis, and metabolic enzyme engineering. Each chapter highlights the complexity and challenges of the problem as well as the methods used to solve this problem or changes needed in current methods. As a part of the highly successful __Methods in Molecular Biology__ series, chapters include the kind of detailed implementation advice that gives researchers a much needed boost. Authoritative and practical, __Metabolic Pathway Engineering__ benefits not only scientists working on more fundamental aspects of this endeavor but also those in the biochemical industry working on strain engineering for robust industrial processes. Front Matter ....Pages i-xi Overview and Future Directions (Yannick J. Bomble, Michael E. Himmel)....Pages 1-3 Genetics of Unstudied Thermophiles for Industry (Daehwan Chung, Nicholas S. Sarai, Michael E. Himmel, Yannick J. Bomble)....Pages 5-19 Methods for Metabolic Engineering of Thermoanaerobacterium saccharolyticum (Shuen Hon, Liang Tian, Tianyong Zheng, Jingxuan Cui, Lee R. Lynd, Daniel G. Olson)....Pages 21-43 Methods for Metabolic Engineering of a Filamentous Trichoderma reesei (Yat-Chen Chou, Arjun Singh, Qi Xu, Michael E. Himmel, Min Zhang)....Pages 45-50 Methods for Algal Protein Isolation and Proteome Analysis (Eric P. Knoshaug, Alida T. Gerritsen, Calvin A. Henard, Michael T. Guarnieri)....Pages 51-59 An Improved Leaf Protoplast System for Highly Efficient Transient Expression in Switchgrass (Panicum virgatum L.) (Chien-Yuan Lin, Hui Wei, Bryon S. Donohoe, Melvin P. Tucker, Michael E. Himmel)....Pages 61-79 Characterizing Intracellular Proteomes for Microbes: An Experimental Approach Using Label-Free Protein Quantitation (Paul E. Abraham, Robert L. Hettich)....Pages 81-87 Bacterial Differential Expression Analysis Methods (Sagar Utturkar, Asela Dassanayake, Shilpa Nagaraju, Steven D. Brown)....Pages 89-112 Measuring Biomass-Derived Products in Biological Conversion and Metabolic Process (Chang Geun Yoo, Yunqiao Pu, Arthur J. Ragauskas)....Pages 113-124 Crystallography of Metabolic Enzymes (Markus Alahuhta, Michael E. Himmel, Yannick J. Bomble, Vladimir V. Lunin)....Pages 125-139 Measuring Metabolic Enzyme Performance (Amanda M. Williams-Rhaesa, Michael W. W. Adams)....Pages 141-147 Gene Editing Technologies for Biofuel Production in Thermophilic Microbes (Sharon Smolinski, Emily Freed, Carrie Eckert)....Pages 149-163 Software and Methods for Computational Flux Balance Analysis (Peter C. St. John, Yannick J. Bomble)....Pages 165-177 Dynamic Flux Analysis: An Experimental Approach of Fluxomics (Wei Xiong, Huaiguang Jiang, PinChing Maness)....Pages 179-196 Network Modeling of Complex Data Sets (Piet Jones, Deborah Weighill, Manesh Shah, Sharlee Climer, Jeremy Schmutz, Avinash Sreedasyam et al.)....Pages 197-215 Connecting Microbial Genotype with Phenotype in the Omics Era (Yongfu Yang, Mengyu Qiu, Qing Yang, Yu Wang, Hui Wei, Shihui Yang)....Pages 217-233 Back Matter ....Pages 235-236 "This book illustrates experimental and computational methodologies used to achieve cost effective biological processes for the production of fuels and biochemicals through multiple approaches to increasing yield, titers, and productivity in a robust host. The volume includes the most recent and cutting-edge aspects of pathway engineering, flux analysis, and metabolic enzyme engineering. Each chapter highlights the complexity and challenges of the problem as well as the methods used to solve this problem or changes needed in current methods. As a part of the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that gives researchers a much needed boost. Authoritative and practical, Metabolic Pathway Engineering benefits not only scientists working on more fundamental aspects of this endeavor but also those in the biochemical industry working on strain engineering for robust industrial processes." -- Prové de l'editor