CLAIRE KOMIVES, PHD, is a Professor in the Chemical and Materials Engineering Department at San Jose State University. Her research interests focus on the development of low cost snake antivenom compounds.

WEICHANG ZHOU, PHD, is Chief Technology Officer, Biologics Development & Manufacturing at WuXi Biologics. He has previously worked at Genzyme Corporation and Merck Research Laboratories.

List of Contributors xi

Part I Case Study 1

1 Bacillus and the Story of Protein Secretion and Production 3
Giulia Barbieri, Anthony Calabria, Gopal Chotani, and Eugenio Ferrari

1.1 Bacillus as a Production Host: Introduction and Historical Account 3

1.2 The Building of a Production Strain: Genetic Tools for B. subtilis Manipulation 5

1.2.1 Promoters 5

1.2.2 Vectors for Building a Production Strain 6

1.2.3 B. subtilis Competent Cell Transformation 7

1.2.4 Protoplasts-Mediated Manipulations 9

1.2.5 Genetics by Electroporation 9

1.3 B. subtilis Secretion Systemand Heterologous Protein Production 9

1.3.1 Bacillus Fermentation and Recovery of Industrial Enzyme 11

1.3.2 Fermentation Stoichiometry 12

1.3.3 Fermentor Kinetics and Outputs 14

1.3.4 Downstream Processing 17

1.4 Summary 21

References 21

2 New Expression Systems for GPCRs 29
Dimitra Gialama, Fragiskos N. Kolisis, and Georgios Skretas

2.1 Introduction 29

2.2 Recombinant GPCR Production – Traditional Approaches for Achieving High-Level Production 39

2.3 Engineered Expression Systems for GPCR Production 42

2.3.1 Bacteria 42

2.3.2 Yeasts 48

2.3.3 Insect Cells 51

2.3.4 Mammalian Cells 54

2.3.5 Transgenic Animals 54

2.3.6 Cell-Free Systems 56

2.4 Conclusion 57

References 58

3 Glycosylation 71
Maureen Spearman, Erika Lattová, Hélène Perreault, andMichael Butler

3.1 Introduction 71

3.2 Types of Glycosylation 72

3.2.1 N-linked Glycans 72

3.2.2 O-linked Glycans 74

3.3 Factors Affecting Glycosylation 76

3.3.1 Nutrient Depletion 76

3.3.2 Fed-batch Cultures and Supplements 79

3.3.3 Specific Culture Supplements 80

3.3.4 Ammonia 82

3.3.5 pH 82

3.3.6 Oxygen 83

3.3.7 Host Cell Systems 83

3.3.8 Other Factors 85

3.4 Modification of Glycosylation 86

3.4.1 siRNA and Gene Knockout/Knockin 86

3.4.2 Glycoprotein Processing Inhibitors and In Vitro Modification of Glycans 88

3.5 Glycosylation Analysis 89

3.5.1 Release of Glycans from Glycoproteins 90

3.5.2 Derivatization of Glycans 91

3.6 Methods of Analysis 91

3.6.1 Lectin Arrays 91

3.6.2 Liquid Chromatography 93

3.6.2.1 HILIC Analysis 93

3.6.2.2 Reversed Phase (RP) and Porous Graphitic Carbon (PGC) Chromatography 95

3.6.2.3 Weak Anion Exchange (WAX) HPLC Analysis 96

3.6.2.4 High pH Anion Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD) 96

3.6.3 Capillary Electrophoresis (CE) 97

3.6.4 Fluorophore-assisted Carbohydrate Electrophoresis (FACE) and CGE-LIF 99

3.6.5 Mass Spectrometry (MS) 100

3.6.5.1 Ionization 100

3.6.5.2 Derivatization Techniques Used for MS Analysis of Glycans 102

3.6.5.3 Fragmentation of Carbohydrates 103

3.7 Conclusion 109

References 109

Part II Bioreactors 131

4 Bioreactors for StemCell and Mammalian Cell Cultivation 133
Ana Fernandes-Platzgummer, Sara M. Badenes, Cláudia L. da Silva, and JoaquimM. S. Cabral

4.1 Overview of (Mammalian and Stem) Cell Culture Engineering 133

4.1.1 Cell Products for Therapeutics 134

4.1.2 Cell as a Product: Stem Cells 136

4.2 Bioprocess Characterization 140

4.2.1 Cell Cultivation Methods 140

4.2.2 Cell Metabolism 141

4.2.3 Culture Medium Design 143

4.2.4 Culture Parameters 144

4.2.5 Culture Modes 145

4.3 Cell Culture Systems 147

4.3.1 Static Culture Systems 147

4.3.2 Roller Bottles 150

4.3.3 Spinner Flask 150

4.3.4 Airlift Bioreactor 151

4.3.5 Fixed/Fluidized-Bed Bioreactor 152

4.3.6 Wave Bioreactor 152

4.3.7 Rotating-Wall Vessel Bioreactor 154

4.3.8 Stirred Tank Bioreactor 155

4.3.8.1 Agitation/Shear Stress 156

4.4 Cell Culture Modeling 157

4.5 Case Studies 159

4.5.1 Antibody Production in Bioreactor Systems 159

4.5.2 mESC Expansion on Microcarriers in a Stirred Tank Bioreactor 161

4.6 Concluding Remarks 162

List of Symbols 163

References 164

5 Model-Based Technologies Enabling Optimal Bioreactor Performance 175
Rimvydas Simutis, Marco Jenzsch, and Andreas Lübbert

5.1 Introduction 175

5.2 Basics 176

5.2.1 Balances 176

5.2.2 Model Identification 177

5.2.3 Model-Based Process Optimization 178

5.3 Examples 180

5.3.1 Model-Based State Estimation 180

5.3.1.1 Static Model Approach 180

5.3.1.2 Dynamic Alternatives 183

5.3.2 Optimizing Open Loop-Controlled Cultivations 184

5.3.2.1 Robust Cultivation Profiles 184

5.3.2.2 Evolutionary Modeling Approach 188

5.3.3 Optimization by Model-Aided Feedback Control 190

5.3.3.1 Improving the Basic Control 190

5.3.3.2 Optimizing the Amount of Soluble Product 190

5.3.4 CO2-Removal in Large-Scale Cell Cultures 194

5.4 Conclusion 197

References 198

6 Monitoring and Control of Bioreactor: Basic Concepts and Recent Advances 201
James Gomes, Viki Chopda, and Anurag S. Rathore

6.1 Introduction 201

6.2 Challenges in Bioprocess Control 202

6.2.1 Process Dynamics and Modeling 202

6.2.2 Limits of Hardware and Software andTheir Integration 203

6.2.3 Regulatory Aspects 204

6.3 Basic Elements of Bioprocess Control 205

6.3.1 Bioprocess Monitoring 205

6.3.2 Parameter Estimators 205

6.3.3 Bioprocess Modeling 206

6.4 Current Practices in Bioprocess Control 208

6.4.1 PID Control 208

6.4.2 Model-Based Control 209

6.4.3 Adaptive Control 211

6.4.4 Nonlinear Control 214

6.5 Intelligent Control Systems 217

6.5.1 Fuzzy Control 217

6.5.2 Neural Control 219

6.5.3 Statistical Process Control 222

6.5.4 Integrated and Plant-Wide Bioprocess Control 224

6.5.5 Metabolic Control 225

6.6 Summary 226

6.7 Future Perspectives 227

Acknowledgments 227

References 227

Part III Host Strain Technologies 239

7 Metabolic Engineering for Biocatalyst Robustness to Organic Inhibitors 241
Liam Royce and Laura R. Jarboe

7.1 Introduction 241

7.2 Mechanisms of Inhibition 243

7.3 Mechanisms of Tolerance 245

7.4 Membrane Engineering 246

7.5 Evolutionary and Metagenomic Strategies for Increasing Tolerance 251

7.6 Reverse Engineering of Improved Strains 254

7.7 Concluding Remarks 255

Acknowledgments 255

References 255

Index 267

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