Fundamental bioengineering / edited by John Villadsen. -- Weinheim, Germany : Wiley-VCH, c2016. – (58.2/F981)

Contents

List of Contributors  xiii

About the Series Editors  xv

1  Introduction and Overview  1

Part One  Fundamentals of Bioengineering  3

2  Experimentally Determined Rates of Bio-Reactions

2.0  Summary  5

2.1  Introduction  5

2.2  Mass Balances for a CSTR Operating at Steady State Operation of the Steady-State CSTR  13

References  16

3  Redox Balances and Consistency Check of Experiments  17

Summary  17

3.1  Black-Box Stoichiometry Obtained in a CSTR Operated at Steady State  17

3.2  Calculation of Stoichiometric Coefficients by Means of a Redox Balance  20

3.3  Applications of the Redox Balance  23

3.4  Composition of the Biomass X  28

3.5  Combination of Black-Box Models  30

3.6  Application of Carbon and Redox Balances in Bio-Remediation Processes  34

References  38

4  Primary Metabolic Pathways and Metabolic Flux Analysis  39

Summary  39

4.0  Introduction  39

4.1  Glycolysis  43

4.2  Fermentative Metabolism: Regenerating the NAD+ Lost in Glycolysis  47

4.3  The TCA Cycle: Conversion of Pyruvate to NADH + FADH2, to Precursors or Metabolic Products  50

4.4  NADPH and Biomass Precursors Produced in the PP Pathway  56

4.5  Oxidative Phosphorylation: Production of ATP from NADH (FADH2) in Aerobic Fermentation  57

4.6  Summary of the Biochemistry of Primary Metabolic Pathways  59

4.7  Metabolic Flux Analysis Discussed in Terms of Substrate to Product Pathways  61

4.8  Metabolic Flux Analysis Discussed in Terms of Individual Pathway Rates in the Network  88

4.9  Propagation of Experimental Errors in MFA  94

4.10  Conclusions  96

References  96

5  A Primer to 13C Metabolic Flux Analysis  97

5.1  Introduction  97

5.2  Input and Output Data of 13C MFA  99

5.3  A Brief History of lSC MFA  101

5.4  An Illustrative Toy Example  102

5.5  The Atom Transition Network  104

5.6  Isotopomers and Isotopomer Fractions  104

5.7  The Isotopomer Transition Network  105

5.8  Isotopomer Labeling Balances  107

5.9  Simulating an Isotope Labeling Experiment  109

5.10  Isotopic Steady State  110

5.11  Flux Identifiability  112

5.12  Measurement Models  113

5.13  Statistical Considerations  114

5.14  Experimental Design  115

5.15  Exchange Fluxes  116

5.16  Multidimensional Flux Identifiability  118

5.17  Multidimensional Flux Estimation  120

5.18  The General Parameter Fitting Procedure  121

5.19  Multidimensional Statistics  123

5.20  Multidimensional Experimental Design  124

5.21  The Isotopically Nonstationary Case  127

5.22  Some Final Remarks on Network Specification  130

5.23  Algorithms and Software Frameworks for 13C MFA  132

Glossary  135

References  137

6  Genome-Scale Models  143

Summary  143

6.1  Introduction  143

6.2  Reconstruction Process of Genome-Scale Models  144

6.3  Genome-Scale Model Prediction  147

6.4  Genome-Scale Models of Prokaryotes  152

6.5  Genome-Scale Models of Eukaryotes  159

6.6  Integration of Polyomic Data into Genome-Scale Models  169

Acknowledgment  172

References  173

7  Kinetics of Bio-Reactions  183

Summary  183

7.1  Simple Models for Enzymatic Reactions and for Cell Reactions with Unstructured      Biomass  184

7.2  Variants of Michaelis-Menten and Monod kinetics  189

7.3  Summary of Enzyme Kinetics and the Kinetics for Cell Reactions  201

7.4  Cell Reactions with Unsteady State Kinetics  203

7.5  Cybernetic Modeling of Cellular Kinetics  211

7.6  Bioreactions with Diffusion Resistance  213

7.7  Sequences of Enzymatic Reactions: Optimal Allocation of Enzyme Levels  221

References  230

8  Application of Dynamic Models for Optimal Redesign of Cell Factories  233

Summary  233

8.1  Introduction  233

8.2  Kinetics of Pathway Reactions: the Need to Measure in a Very Narrow Time Window  235

8.3  Tools for In Vivo Diagnosis of Pathway Reactions  245

8.4  Examples: The Pentose-Phosphate Shunt and Kinetics of Phosphofructokinase  247

8.5  Additional Approaches for Dynamic Modeling Large Metabolic Networks  256

8.6  Dynamic Models Used for Redesigning Cell Factories. Examples: Optimal Ethanol Production in Yeast and Optimal Production of Tryptophan in E. Coli  268

8.7  Target Identification for Drug Development  280

References  285

9  Chemical Thermodynamics Applied in Bioengineering  293

Summary  293

9.0  Introduction  293

9.1  Chemical Equilibrium and Thermodynamic State Functions  296

9.2  Thermodynamic Properties Obtained from Galvanic Cells  305

9.3  Conversion of Free Energy Harbored in NADH and FADH2 to ATP in Oxidative Phosphorylation  310

9.4  Calculation of Heat of Reaction Q=(-AHc) and of (-AGc) Based on Redox Balances  312

References  317

Part Two  Bioreactors  319

10  Design of Ideal Bioreactors  321

Summary  321

10.0  Introduction  321

10.1  The Design Basis for a Once-Through Steady-State CSTR  322

10.2  Combination of Several Steady-State CSTRs in Parallel or in Series  329

10.3  Recirculation of Biomass in a Single Steady-State CSTR  332

10.4  A Steady-State CSTR with Uptake of Substrates from a Gas Phase  338

10.5  Fed-Batch Operation of a Stirred Tank Reactor in the Bio-Industry  340

10.6  Loop Reactors: a Modern Version of Airlift Reactors  349

References  355

Mixing and Mass Transfer in Industrial Bioreactors  357

Summary  357

11.0  Introduction  357

11.1  Definitions of Mixing Processes  358

11.2  The Power Input P Delivered by Mechanical Stirring  362

11.3  Mixing and Mass Transfer in Industrial Reactors  367

11.4  Conclusions  372

References  376

Part Three  Downstream Processing  379

12  Product Recovery from the Cultures  381

Summary  381

12.0  Introduction  381

12.1  Steps in Downstream Processing and Product Recovery  383

12.2  Baker's Yeast  383

12.3  Xanthan Gum  384

12.4  Penicillin  385

12.5  R-A Interferon  386

12.6  Insulin  390

12.7  Conclusions  391

References  391

13  Purification of Bio-Products  393

Summary  393

13.1  Methods and Types of Separations in Chromatography  394

13.2  Materials Used in Chromatographic Separations  396

13.3  Chromatographic Theory  398

13.4  Practical Considerations in Column Chromatographic Applications  399

13.5  Scale-Up  401

13.6  Industrial Applications  402

13.7  Some Alternatives to Column Chromatographic Techniques  403

13.8  Electrodialysis  403

13.9  Electrophoresis  404

13.10  Conclusions  407

References  407

Part Four  Process Development, Management and Control  409

14  Real-Time Measurement and Monitoring of Bioprocesses  411

Summary  411

14.1  Introduction  411

14.2  Variables that should be Known  414

14.3  Variables Easily Accessible and Standard  415

14.4  Variables Requiring More Monitoring Effort and Not Yet Standard  422

14.5  Data Evaluation  433

References  434

15  Control of Bioprocesses  439

Summary  439

15.1  Introduction  439

15.2  Bioprocess Control  440

15.3  Principles and Basic Algorithms in Process Control  450

References  460

16  Scale-Up and Scale-Down  463

Summary  463

16.1  Introduction  463

16.2  Description of the Large Scale  465

16.3  Scale Down  480

16.4  Investigations at Lab Scale  485

16.5  Scale Up  491

16.6  Outlook  494

References  495

17  Commercial Development of Fermentation Processes  499

Summary  499

17.1  Introduction  499

17.2  Basic Principles of Developing New Fermentation Processes  501

17.3  Techno-economic Analysis: the Link Between Science, Engineering, and Economy  506

17.4  From Fermentation Process Development to the Market  528

17.5  The Industrial Angle and Opportunities in the Chemical Industry  537

17.6  Evaluation of Business Opportunities  540

17.7  Concluding Remarks and Outlook  542

Acknowledgment  543

References  543

Index  547