Applied Bioengineering

Toshiomi Yoshida is Professor Emeritus of Osaka University (Japan). He received his doctorate degree at the same university in 1968, after studying fermentation technology. From 1972 to 1973, he visited the University of Pennsylvania (USA) for a research stay. In the further course of his career, he became Associate Professor at Osaka University in 1978, Full Professor in 1988 and held several positions within the university until his retirement in 2003. From 1995 to 1999, he was Director of the International Center for Biotechnology. After his retirement, Toshiomi Yoshida was appointed as Director of the Bangkok Liaison Office of the Japan Society for the Promotion of Science, a position he hold until 2007. From 2007 to 2012, he was Director General of the Research Institute of Environmental, Agriculture and Fisheries of the Osaka Prefectural Government. In between 2009 and 2013, Toshiomi Yoshida served as the first President of the Asian Federation of Biotechnology.

• List of Contributors XIX1 Introduction 1Toshiomi Yoshida1.1 Introduction 11.2 Enzyme Technology 21.3 Microbial Process Engineering 21.4 Plant Cell Culture 51.5 Animal Cell Culture 51.6 Environmental Bioengineering 61.7 Composition of the Volume 7References 7Part I Enzyme Technology 112 Enzyme Technology: History and Current Trends 13Klaus Buchholz and Uwe T. Bornscheuer2.1 The Early Period up to 1890 132.2 The Period from 1890 to 1940 162.3 A New Biocatalyst Concept – Immobilized Enzymes 192.4 Expanding Enzyme Application after the 1950s 242.5 Recombinant Technology –A New Era in Biocatalysis and Enzyme Technology 272.6 Current Strategies for Biocatalyst Search and Tailor Design 322.7 Summary and Conclusions 39Acknowledgment 40Abbreviations 40References 403 Molecular Engineering of Enzymes 47Maria Elena Ortiz-Soto and Jürgen Seibel3.1 Introduction 473.2 Protein Engineering: An Expanding Toolbox 483.3 High-Throughput Screening Systems 563.4 Engineered Enzymes for Improved Stability and Asymmetric Catalysis 583.5 De Novo Design of Catalysts: Novel Activities within Common Scaffolds 653.6 Conclusions 69References 694 Biocatalytic Process Development 81John M.Woodley4.1 A Structured Approach to Biocatalytic Process Development 834.2 Process Metrics 834.3 Technologies for Implementation of Biocatalytic Processes 874.4 Industrial Development Examples 914.5 Future Outlook 954.6 Concluding Remarks 96References 965 Development of Enzymatic Reactions in Miniaturized Reactors 99Takeshi Honda, Hiroshi Yamaguchi, and Masaya Miyazaki5.1 Introduction 995.2 Fundamental Techniques for Enzyme Immobilization 1005.3 Novel Techniques for Enzyme Immobilization 1505.4 Conclusions and Future Perspectives 155Abbreviations 156References 157Part II Microbial Process Engineering 1676 Bioreactor Development and Process Analytical Technology 169Toshiomi Yoshida6.1 Introduction 1696.2 Bioreactor Development 1706.3 Monitoring and Process Analytical Technology 1966.4 Conclusion 203Abbreviations 204References 2047 Omics-Integrated Approach for Metabolic State Analysis of Microbial Processes 213Hiroshi Shimizu, Chikara Furusawa, Takashi Hirasawa, Katsunori Yoshikawa, Yoshihiro Toya, Tomokazu Shirai, and Fumio Matsuda7.1 General Introduction 2137.2 Transcriptome Analysis of Microbial Status in Bioprocesses 2147.3 Analysis of Metabolic State Based on Simulation in a Genome-Scale Model 2197.4 13C-Based Metabolic Flux Analysis of Microbial Processes 2237.5 Comprehensive Phenotypic Analysis of Genes Associated with Stress Tolerance 2277.6 Multi-Omics Analysis and Data Integration 2307.7 Future Aspects for Developing the Field 231Acknowledgments 233References 2338 Control of Microbial Processes 237Kazuyuki Shimizu, Hiroshi Shimizu, and Toshiomi Yoshida8.1 Introduction 2378.2 Monitoring 2388.3 Bioprocess Control 2428.4 Recent Trends in Monitoring and Control Technologies 2508.5 Concluding Remarks 253Abbreviations 254References 254Part III Plant Cell Culture and Engineering 2599 Contained Molecular Farming Using Plant Cell and Tissue Cultures 261Stefan Schillberg, Nicole Raven, Rainer Fischer, Richard M. Twyman, and Andreas Schiermeyer9.1 Molecular Farming –Whole Plants and Cell/Tissue Cultures 2619.2 Plant Cell and Tissue Culture Platforms 2639.3 Comparison ofWhole Plants and In Vitro Culture Platforms 2659.4 Technical Advances on the Road to Commercialization 2679.5 Regulatory and Industry Barriers on the Road to Commercialization 2719.6 Outlook 273Acknowledgments 275References 27510 Bioprocess Engineering of Plant Cell Suspension Cultures 283Gregory R. Andrews and Susan C. Roberts10.1 Introduction 28310.2 Culture Development and Maintenance 28610.3 Choice of Culture System 28810.4 Engineering Considerations 29110.5 Bioprocess Parameters 29410.6 Operational Modes 29610.7 Bioreactors for Plant Cell Suspensions 29710.8 Downstream Processing 30310.9 Yield Improvement Strategies 30610.10 Case Studies 31010.11 Conclusion 315References 31611 The Role of Bacteria in Phytoremediation 327Zhaoyu Kong and Bernard R. Glick11.1 The Problem 32711.2 Defining Phytoremediation and Its Components 32911.3 Role of Bacteria in Phytoremediation 33011.4 Examples of Phytoremediation in Action 34211.5 Summary and Perspectives 343References 344Part IV Animal Cell Cultures 35512 Cell Line Development for Biomanufacturing Processes 357Mugdha Gadgil andWei-Shou Hu12.1 Introduction 35712.2 Host Cell 35912.3 Vector Components 36012.4 Transfection 36512.5 Integration of Foreign DNA into Host Chromosome 36612.6 Amplification 36912.7 Single-Cell Cloning 37012.8 Selecting the Production Clone 37312.9 Clone Stability 37612.10 Conclusion 376Acknowledgments 377References 37713 Medium Design, Culture Management, and the PAT Initiative 383Ziomara P. Gerdtzen13.1 Historical Perspective on Culture Medium 38313.2 Cell Growth Environment 38413.3 Media Types 38613.4 Medium Components 38713.5 High MolecularWeight and Complex Supplements 40013.6 Medium for Industrial Production 40713.7 Conclusions 411References 412Further Reading/Resources 41614 Advanced Bioprocess Engineering: Fed-Batch and Perfusion Processes 417Sarika Mehra, Vikas Chandrawanshi, and Kamal Prashad14.1 Primary Modes of Bioreactor Operation 41714.2 Fed-Batch Mode of Operation 41914.3 Perfusion Mode of Bioreactor Operation 43514.4 Use of Disposables in Cell Culture Bioprocesses 44714.5 Analytical Methods to Monitor Key Metabolites and Parameters 45014.6 Concluding Remarks 453Nomenclature 455References 456Further Reading/Resources 468Part V Environmental Bioengineering 46915 Treatment of Industrial and Municipal Wastewater: An Overview about Basic and Advanced Concepts 471Jyoti K. Kumar, Parag R. Gogate, and Aniruddha B. Pandit15.1 Types ofWastewater 47115.2 Biological Treatment 47115.3 Wastewater Regulations 47315.4 Biological Treatment Processes 47315.5 Aerobic Techniques 47515.6 Anaerobic Techniques 48815.7 Aerobic–Anaerobic Processes 49515.8 Modified Biological Processes 49615.9 Overall Conclusions 511List of Acronyms/Abbreviations 512List of Variables and Coefficients 513References 51416 Treatment of SolidWaste 521Michael Nelles, Gert Morscheck, Astrid Lemke, and Ayman El Naas16.1 Biological Treatment of Source Segregated Bio-Waste 52216.2 Mechanical–Biological Treatment of Mixed Municipal Solid Waste 53816.3 Biological Treatment of AgriculturalWaste 54216.4 Conclusion 542References 54217 Energy Recovery from Organic Waste 545Yutaka Nakashimada and Naomichi Nishio17.1 Advantage of Methane Fermentation for Energy Recovery from Organic Matter 54517.2 Basic Knowledge of Methane Fermentation of OrganicWastes 54617.3 Conventional Methane Fermentation Process 54917.4 Advanced Methane Fermentation Processes 55117.5 Hydrogen Production from OrganicWastes 55517.6 Upgrading of Biogas from OrganicWastes Based on Biological Syngas Platform 56117.7 Conclusions 564References 56518 Microbial Removal and Recovery of Metals from Wastewater 573Michihiko Ike,Mitsuo Yamashita, and Masashi Kuroda18.1 Microbial Reactions Available for Metal Removal/Recovery 57418.2 Selenium Recovery by Pseudomonas stutzeri NT-I 58318.3 Future Prospects 58718.4 Conclusions 590References 59019 Sustainable Use of Phosphorus Through Bio-Based Recycling 597Hisao Ohtake19.1 Introduction 59719.2 Microbiological Basis 59819.3 Bio-Based P Recycling 60019.4 Other Options for P Recycling 60419.5 Conclusions 607References 609Index 613