TY  - BOOK
AU  - Yoshida,Toshiomi
AU  - Lee,Sang Yup
AU  - Nielsen,Jens
AU  - Stephanopoulos,Gregory
TI  - Applied Bioengineering: Innovations and Future Directions
T2  - Advanced Biotechnology Series
SN  - 9783527800605
AV  - TP248.3.A675 2017 
PY  - 2017///
CY  - Newark
PB  - John Wiley & Sons, Incorporated
KW  - Biochemical engineering
KW  - Electronic books
N1  - Cover -- Title Page -- Copyright -- Contents -- List of Contributors -- Chapter 1 Introduction -- 1.1 Introduction -- 1.2 Enzyme Technology -- 1.3 Microbial Process Engineering -- 1.3.1 Bioreactor Development -- 1.3.2 Measurement and Monitoring -- 1.3.3 Modeling and Control -- 1.3.4 Solid-State Fermentation -- 1.4 Plant Cell Culture -- 1.5 Animal Cell Culture -- 1.6 Environmental Bioengineering -- 1.7 Composition of the Volume -- References -- Part I Enzyme Technology -- Chapter 2 Enzyme Technology: History and Current Trends -- 2.1 The Early Period up to 1890 -- 2.1.1 Observations and Empirical Results -- 2.1.2 Theoretical Approaches -- 2.2 The Period from 1890 to 1940 -- 2.2.1 Scientific Progress -- 2.2.2 Theoretical Developments -- 2.2.3 Technological Developments -- 2.3 A New Biocatalyst Concept - Immobilized Enzymes -- 2.3.1 Fundamental Research -- 2.3.2 Examples of Industrial Development: The Case of Penicillin Amidase (PA) - Penicillin Hydrolysis and Derivatives -- 2.3.3 Examples of Industrial Development: The Case of Sugar Isomerization -- 2.4 Expanding Enzyme Application after the 1950s -- 2.5 Recombinant Technology - A New Era in Biocatalysis and Enzyme Technology -- 2.5.1 New Enzymes - A Key to Genetic Engineering -- 2.5.2 Analytical and Diagnostic Enzymes -- 2.5.3 Expanding Market of Industrial Enzymes -- 2.6 Current Strategies for Biocatalyst Search and Tailor Design -- 2.6.1 Enzyme Discovery from the Metagenome or Protein Databases -- 2.6.2 Protein Engineering of Enzymes -- 2.6.3 Enzyme Cascade Reactions -- 2.6.4 Metabolic Engineering -- 2.7 Summary and Conclusions -- Acknowledgment -- Abbreviations -- References -- Chapter 3 Molecular Engineering of Enzymes -- 3.1 Introduction -- 3.2 Protein Engineering: An Expanding Toolbox -- 3.2.1 From Sequence to Fold and Function; 3.2.2 Improving Enzyme Properties by Rational Design and Directed Evolution -- 3.2.3 Designing Smart Libraries -- 3.2.4 In Vivo Continuous Directed Evolution -- 3.2.5 Diversification of Enzyme Functionalities by Recombination -- 3.3 High-Throughput Screening Systems -- 3.4 Engineered Enzymes for Improved Stability and Asymmetric Catalysis -- 3.4.1 Stability -- 3.4.1.1 Cellulases -- 3.4.1.2 Lipases -- 3.4.2 Asymmetric Biocatalysis -- 3.5 De Novo Design of Catalysts: Novel Activities within Common Scaffolds -- 3.6 Conclusions -- References -- Chapter 4 Biocatalytic Process Development -- 4.1 A Structured Approach to Biocatalytic Process Development -- 4.2 Process Metrics -- 4.2.1 Reaction Yield -- 4.2.2 Productivity -- 4.2.3 Biocatalyst Yield -- 4.2.4 Product Concentration -- 4.3 Technologies for Implementation of Biocatalytic Processes -- 4.3.1 Biocatalyst Engineering -- 4.3.1.1 Protein and Genetic Engineering -- 4.3.1.2 Biocatalyst Immobilization -- 4.3.2 Reaction Engineering -- 4.3.2.1 Reactant Supply -- 4.3.2.2 Product Removal -- 4.3.2.3 Two-Phase Systems -- 4.4 Industrial Development Examples -- 4.4.1 Development of a Biocatalytic Route to Atorvastatin (Developed by Codexis Inc., USA) -- 4.4.2 Development of a Biocatalytic Route to Sitagliptin (Developed by Codexis Inc., USA and Merck and Co., USA) -- 4.5 Future Outlook -- 4.6 Concluding Remarks -- References -- Chapter 5 Development of Enzymatic Reactions in Miniaturized Reactors -- 5.1 Introduction -- 5.2 Fundamental Techniques for Enzyme Immobilization -- 5.2.1 Enzyme Immobilization by Adsorption -- 5.2.1.1 Monoliths and Particles -- 5.2.1.2 Synthetic Polymer Membranes and Papers -- 5.2.1.3 Adsorption to Channel Walls -- 5.2.2 Enzyme Immobilization by Entrapment -- 5.2.2.1 Silica-Based Matrices -- 5.2.2.2 Non-Silica-based Matrices -- 5.2.3 Enzyme Immobilization by Affinity Labeling; 5.2.3.1 His-Tag/Ni-NTA System -- 5.2.3.2 GST-Tag/Glutathione System -- 5.2.3.3 Avidin/Biotin System -- 5.2.3.4 DNA Hybridization System -- 5.2.3.5 Other Techniques Using Nucleotides for Enzyme Immobilization -- 5.2.4 Enzyme Immobilization by Covalent Linking -- 5.2.4.1 Immobilization to Solid Supports -- 5.2.4.2 Direct Immobilization to a Channel Wall -- 5.2.4.3 Enzyme Polymerization -- 5.2.5 Enzyme Immobilization by Other Techniques Using Organisms -- 5.2.6 Application of Immobilized Enzymes in Microfluidics -- 5.3 Novel Techniques for Enzyme Immobilization -- 5.3.1 Polyketone Polymer: Enzyme Immobilization by Hydrogen Bonds -- 5.3.2 Thermoresponsive Hydrogels -- 5.3.3 Immobilization Methods Using Azide Chemistry -- 5.3.3.1 Staudinger Ligation -- 5.3.3.2 Click Chemistry -- 5.3.4 Graphene-Based Nanomaterial as an Immobilization Support -- 5.3.5 Immobilization Methods Using Proteins Modified with Solid-Support-Binding Modules -- 5.4 Conclusions and Future Perspectives -- Abbreviations -- References -- Part II Microbial Process Engineering -- Chapter 6 Bioreactor Development and Process Analytical Technology -- 6.1 Introduction -- 6.2 Bioreactor Development -- 6.2.1 Parallel Bioreactor Systems for High-Throughput Processing -- 6.2.1.1 Microtiter Plate Systems -- 6.2.1.2 Stirred-Tank Reactor Systems -- 6.2.1.3 Microfluidic Microbioreactor Systems -- 6.2.1.4 Bubble Column Systems -- 6.2.1.5 Comparison of Various Parallel-Use Micro-/Mini-Bioreactor System -- 6.2.2 Single-Use Disposable Bioreactor Systems -- 6.2.2.1 Features of Single-Use Bioreactors -- 6.2.2.2 Sensors and Monitoring -- 6.2.2.3 Single-Use Bioreactors in Practical Use -- 6.3 Monitoring and Process Analytical Technology -- 6.3.1 Monitoring and State Recognition -- 6.3.1.1 Sensors for Monitoring Bioprocesses -- 6.3.1.2 Spectrometry -- 6.3.2 Process Analytical Technology (PAT); 6.3.2.1 PAT Tools -- 6.3.2.2 PAT Implementations -- 6.4 Conclusion -- Abbreviations -- References -- Chapter 7 Omics-Integrated Approach for Metabolic State Analysis of Microbial Processes -- 7.1 General Introduction -- 7.2 Transcriptome Analysis of Microbial Status in Bioprocesses -- 7.2.1 Introduction -- 7.2.2 Microbial Response to Stress Environments and Identification of Genes Conferring Stress Tolerance in Bioprocesses -- 7.2.3 Transcriptome Analysis of the Ethanol-Stress-Tolerant Strain Obtained by Evolution Engineering -- 7.3 Analysis of Metabolic State Based on Simulation in a Genome-Scale Model -- 7.3.1 Introduction -- 7.3.2 Reconstruction of GSMs and Simulation by FBA -- 7.3.3 Using Prediction of Metabolic State for Design of Metabolic Modification -- 7.4 13C-Based Metabolic Flux Analysis of Microbial Processes -- 7.4.1 Introduction -- 7.4.2 Principles of 13C-MFA -- 7.4.3 Examples of 13C-MFA in Microbial Processes -- 7.5 Comprehensive Phenotypic Analysis of Genes Associated with Stress Tolerance -- 7.5.1 Introduction -- 7.5.2 Development of a High-Throughput Culture System -- 7.5.3 Calculation of Specific Growth Rate -- 7.5.4 Results of Comprehensive Analysis of Yeast Cells Under Conditions of High Osmotic Pressure and High Ethanol Concentration -- 7.5.5 Identification of Genes Conferring Desirable Phenotypes Based on Integration with the Microarray Analysis Method -- 7.6 Multi-Omics Analysis and Data Integration -- 7.7 Future Aspects for Developing the Field -- Acknowledgments -- References -- Chapter 8 Control of Microbial Processes -- 8.1 Introduction -- 8.2 Monitoring -- 8.2.1 Online Measurements -- 8.2.2 Filtering, Online Estimation, and Software Sensors -- 8.2.3 Algorithm of Extended Kalman Filter and Its Application to Online Estimation of Specific Rates -- 8.3 Bioprocess Control -- 8.3.1 Control of Fed-Batch Culture; 8.3.2 Online Optimization of Continuous Cultures -- 8.3.3 Cascade Control for Mixed Cultures -- 8.3.4 Supervision and Fault Detection -- 8.4 Recent Trends in Monitoring and Control Technologies -- 8.4.1 Sensor Technologies and Analytical Methods -- 8.4.2 Control Technologies -- 8.5 Concluding Remarks -- Abbreviations -- References -- Part III Plant Cell Culture and Engineering -- Chapter 9 Contained Molecular Farming Using Plant Cell and Tissue Cultures -- 9.1 Molecular Farming - Whole Plants and Cell/Tissue Cultures -- 9.2 Plant Cell and Tissue Culture Platforms -- 9.2.1 Cell Suspension Cultures -- 9.2.2 Tissue Cultures -- 9.2.3 Light-Dependent Expression Platforms -- 9.3 Comparison of Whole Plants and In Vitro Culture Platforms -- 9.4 Technical Advances on the Road to Commercialization -- 9.4.1 Improving the Quantity of Recombinant Proteins Produced in Cell Suspension Cultures -- 9.4.2 Improving the Quality and Consistency of Recombinant Proteins Produced in Cell Suspension Cultures -- 9.5 Regulatory and Industry Barriers on the Road to Commercialization -- 9.6 Outlook -- Acknowledgments -- References -- Chapter 10 Bioprocess Engineering of Plant Cell Suspension Cultures -- 10.1 Introduction -- 10.2 Culture Development and Maintenance -- 10.3 Choice of Culture System -- 10.4 Engineering Considerations -- 10.4.1 Cell Growth and Morphology -- 10.4.2 Gas Requirements -- 10.4.3 Aggregation -- 10.4.4 Medium Rheology -- 10.4.5 Shear Sensitivity -- 10.5 Bioprocess Parameters -- 10.5.1 Medium Composition and Optimization -- 10.5.2 Temperature and pH -- 10.5.3 Agitation -- 10.5.4 Aeration -- 10.6 Operational Modes -- 10.7 Bioreactors for Plant Cell Suspensions -- 10.7.1 Conventional Bioreactors -- 10.7.1.1 Stirred-Tank Reactors -- 10.7.1.2 Pneumatic Bioreactors -- 10.7.2 Disposable Bioreactors -- 10.8 Downstream Processing; 10.8.1 Specialized Metabolite Extraction and Purification
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