Applied Bioengineering Innovations and Future Directions

List of Contributors XIX

1 Introduction 1
Toshiomi Yoshida

1.1 Introduction 1

1.2 Enzyme Technology 2

1.3 Microbial Process Engineering 2

1.4 Plant Cell Culture 5

1.5 Animal Cell Culture 5

1.6 Environmental Bioengineering 6

1.7 Composition of the Volume 7

References 7

Part I Enzyme Technology 11

2 Enzyme Technology: History and Current Trends 13
Klaus Buchholz and Uwe T. Bornscheuer

2.1 The Early Period up to 1890 13

2.2 The Period from 1890 to 1940 16

2.3 A New Biocatalyst Concept – Immobilized Enzymes 19

2.4 Expanding Enzyme Application after the 1950s 24

2.5 Recombinant Technology –A New Era in Biocatalysis and Enzyme Technology 27

2.6 Current Strategies for Biocatalyst Search and Tailor Design 32

2.7 Summary and Conclusions 39

Acknowledgment 40

Abbreviations 40

References 40

3 Molecular Engineering of Enzymes 47
Maria Elena Ortiz-Soto and Jürgen Seibel

3.1 Introduction 47

3.2 Protein Engineering: An Expanding Toolbox 48

3.3 High-Throughput Screening Systems 56

3.4 Engineered Enzymes for Improved Stability and Asymmetric Catalysis 58

3.5 De Novo Design of Catalysts: Novel Activities within Common Scaffolds 65

3.6 Conclusions 69

References 69

4 Biocatalytic Process Development 81
John M.Woodley

4.1 A Structured Approach to Biocatalytic Process Development 83

4.2 Process Metrics 83

4.3 Technologies for Implementation of Biocatalytic Processes 87

4.4 Industrial Development Examples 91

4.5 Future Outlook 95

4.6 Concluding Remarks 96

References 96

5 Development of Enzymatic Reactions in Miniaturized Reactors 99
Takeshi Honda, Hiroshi Yamaguchi, and Masaya Miyazaki

5.1 Introduction 99

5.2 Fundamental Techniques for Enzyme Immobilization 100

5.3 Novel Techniques for Enzyme Immobilization 150

5.4 Conclusions and Future Perspectives 155

Abbreviations 156

References 157

Part II Microbial Process Engineering 167

6 Bioreactor Development and Process Analytical Technology 169
Toshiomi Yoshida

6.1 Introduction 169

6.2 Bioreactor Development 170

6.3 Monitoring and Process Analytical Technology 196

6.4 Conclusion 203

Abbreviations 204

References 204

7 Omics-Integrated Approach for Metabolic State Analysis of Microbial Processes 213
Hiroshi Shimizu, Chikara Furusawa, Takashi Hirasawa, Katsunori Yoshikawa, Yoshihiro Toya, Tomokazu Shirai, and Fumio Matsuda

7.1 General Introduction 213

7.2 Transcriptome Analysis of Microbial Status in Bioprocesses 214

7.3 Analysis of Metabolic State Based on Simulation in a Genome-Scale Model 219

7.4 13C-Based Metabolic Flux Analysis of Microbial Processes 223

7.5 Comprehensive Phenotypic Analysis of Genes Associated with Stress Tolerance 227

7.6 Multi-Omics Analysis and Data Integration 230

7.7 Future Aspects for Developing the Field 231

Acknowledgments 233

References 233

8 Control of Microbial Processes 237
Kazuyuki Shimizu, Hiroshi Shimizu, and Toshiomi Yoshida

8.1 Introduction 237

8.2 Monitoring 238

8.3 Bioprocess Control 242

8.4 Recent Trends in Monitoring and Control Technologies 250

8.5 Concluding Remarks 253

Abbreviations 254

References 254

Part III Plant Cell Culture and Engineering 259

9 Contained Molecular Farming Using Plant Cell and Tissue Cultures 261
Stefan Schillberg, Nicole Raven, Rainer Fischer, Richard M. Twyman, and Andreas Schiermeyer

9.1 Molecular Farming –Whole Plants and Cell/Tissue Cultures 261

9.2 Plant Cell and Tissue Culture Platforms 263

9.3 Comparison ofWhole Plants and In Vitro Culture Platforms 265

9.4 Technical Advances on the Road to Commercialization 267

9.5 Regulatory and Industry Barriers on the Road to Commercialization 271

9.6 Outlook 273

Acknowledgments 275

References 275

10 Bioprocess Engineering of Plant Cell Suspension Cultures 283
Gregory R. Andrews and Susan C. Roberts

10.1 Introduction 283

10.2 Culture Development and Maintenance 286

10.3 Choice of Culture System 288

10.4 Engineering Considerations 291

10.5 Bioprocess Parameters 294

10.6 Operational Modes 296

10.7 Bioreactors for Plant Cell Suspensions 297

10.8 Downstream Processing 303

10.9 Yield Improvement Strategies 306

10.10 Case Studies 310

10.11 Conclusion 315

References 316

11 The Role of Bacteria in Phytoremediation 327
Zhaoyu Kong and Bernard R. Glick

11.1 The Problem 327

11.2 Defining Phytoremediation and Its Components 329

11.3 Role of Bacteria in Phytoremediation 330

11.4 Examples of Phytoremediation in Action 342

11.5 Summary and Perspectives 343

References 344

Part IV Animal Cell Cultures 355

12 Cell Line Development for Biomanufacturing Processes 357
Mugdha Gadgil andWei-Shou Hu

12.1 Introduction 357

12.2 Host Cell 359

12.3 Vector Components 360

12.4 Transfection 365

12.5 Integration of Foreign DNA into Host Chromosome 366

12.6 Amplification 369

12.7 Single-Cell Cloning 370

12.8 Selecting the Production Clone 373

12.9 Clone Stability 376

12.10 Conclusion 376

Acknowledgments 377

References 377

13 Medium Design, Culture Management, and the PAT Initiative 383
Ziomara P. Gerdtzen

13.1 Historical Perspective on Culture Medium 383

13.2 Cell Growth Environment 384

13.3 Media Types 386

13.4 Medium Components 387

13.5 High MolecularWeight and Complex Supplements 400

13.6 Medium for Industrial Production 407

13.7 Conclusions 411

References 412

Further Reading/Resources 416

14 Advanced Bioprocess Engineering: Fed-Batch and Perfusion Processes 417
Sarika Mehra, Vikas Chandrawanshi, and Kamal Prashad

14.1 Primary Modes of Bioreactor Operation 417

14.2 Fed-Batch Mode of Operation 419

14.3 Perfusion Mode of Bioreactor Operation 435

14.4 Use of Disposables in Cell Culture Bioprocesses 447

14.5 Analytical Methods to Monitor Key Metabolites and Parameters 450

14.6 Concluding Remarks 453

Nomenclature 455

References 456

Further Reading/Resources 468

Part V Environmental Bioengineering 469

15 Treatment of Industrial and Municipal Wastewater: An Overview about Basic and Advanced Concepts 471
Jyoti K. Kumar, Parag R. Gogate, and Aniruddha B. Pandit

15.1 Types ofWastewater 471

15.2 Biological Treatment 471

15.3 Wastewater Regulations 473

15.4 Biological Treatment Processes 473

15.5 Aerobic Techniques 475

15.6 Anaerobic Techniques 488

15.7 Aerobic–Anaerobic Processes 495

15.8 Modified Biological Processes 496

15.9 Overall Conclusions 511

List of Acronyms/Abbreviations 512

List of Variables and Coefficients 513

References 514

16 Treatment of SolidWaste 521
Michael Nelles, Gert Morscheck, Astrid Lemke, and Ayman El Naas

16.1 Biological Treatment of Source Segregated Bio-Waste 522

16.2 Mechanical–Biological Treatment of Mixed Municipal Solid Waste 538

16.3 Biological Treatment of AgriculturalWaste 542

16.4 Conclusion 542

References 542

17 Energy Recovery from Organic Waste 545
Yutaka Nakashimada and Naomichi Nishio

17.1 Advantage of Methane Fermentation for Energy Recovery from Organic Matter 545

17.2 Basic Knowledge of Methane Fermentation of OrganicWastes 546

17.3 Conventional Methane Fermentation Process 549

17.4 Advanced Methane Fermentation Processes 551

17.5 Hydrogen Production from OrganicWastes 555

17.6 Upgrading of Biogas from OrganicWastes Based on Biological Syngas Platform 561

17.7 Conclusions 564

References 565

18 Microbial Removal and Recovery of Metals from Wastewater 573
Michihiko Ike,Mitsuo Yamashita, and Masashi Kuroda

18.1 Microbial Reactions Available for Metal Removal/Recovery 574

18.2 Selenium Recovery by Pseudomonas stutzeri NT-I 583

18.3 Future Prospects 587

18.4 Conclusions 590

References 590

19 Sustainable Use of Phosphorus Through Bio-Based Recycling 597
Hisao Ohtake

19.1 Introduction 597

19.2 Microbiological Basis 598

19.3 Bio-Based P Recycling 600

19.4 Other Options for P Recycling 604

19.5 Conclusions 607

References 609

Index 613

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