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Part 1 Fundamentals and principles1

1 Public perception of biotechnology JOHN E．SMITH3

1.1 Introduction3

1.2 Public awareness of genetic engineering4

1.3 Regulatory requirements-safety of genetically engineered foods7

List of contributors9

Contents9

1.4 Labelling-how far should it go?10

1.5 Policy making11

1.6 Areas of significant public concern12

Preface13

1.7 Conclusions16

1.8 Further reading16

2.1 Introduction17

2 Biochemistry and physiology of growth and metabolism COLIN RATLEDGE17

2.2 Metabolism18

2.3 Catabolic pathways21

2.4 Gluconeogenesis29

2.5 Energy production in aerobic micro-organisms29

2.6 Anaerobic metabolism32

2.7 Biosynthesis35

2.8 Control of metabolic processes38

2.9 Efficiency of microbial growth43

2.10 Further reading44

3 Stoichiometry and kinetics of microbial growth from a thermodynamic perspective J．J．HEIJNEN45

Nomenclature45

3.1 Introduction45

3.2 Stoichiometry calculations46

3.3 Stoichiometry predictions based on Gibbs energy dissipation52

3.4 Growth kinetics from a thermodynamic point of view56

3.5 Further reading57

4 Genome management and analysis:prokaryotes COLIN R．HARWOOD and ANIL WIPAT59

4.1 Introduction59

4.2 Bacterial chromosomes and natural gene transfer59

4.3 What is genetic engineering and what is it used for?65

4.4 The basic tools of genetic engineering66

4.5 Cloning vectors and libraries76

4.6 Analysis of genomes/proteomes81

4.7 Analysis of gene expression83

4.8 Engineering genes and optimising products87

4.9 Production of heterologous products89

4.10 In silico analysis of bacterial genomes92

4.11 Further reading93

Glossary95

5 Genetic engineering:yeasts and filamentous fungi DAVID B．ARCHER DONALD A．MACKENZIE and DAVID J．JEENES95

5.1 Introduction97

5.2 Introducing DNA into fungi(fungal transformation)100

5.3 Gene cloning107

5.4 Gene structure,organisation and expression116

5.5 Special methodologies119

5.6 Biotechnological applications of fungi120

5.7 Further reading126

6 Microbial process kinetics JENS NIELSEN127

Nomenclature127

6.1 Introduction128

6.2 Kinetic modelling of cell growth130

6.3 Mass balances for ideal bioreactors141

6.4 Further reading149

Nomenclature151

7 Bioreactor design YUSUF CHISTI and MURRAY MOO-YOUNG151

7.1 Introduction152

7.2 Bioreactor configurations153

7.3 Bioreactor design features158

7.4 Design for sterile operation159

7.5 Photobioreactors162

7.6 Heat transfer164

7.7 Shear effects in culture168

7.8 Further reading171

8 Mass transfer HENK J．NOORMAN173

Nomenclature173

8.1 Introduction174

8.2 The mass transfer steps175

8.3 Mass transfer equations177

8.4 Determining the volumetric mass transfer coefficients183

8.5 The effect of scale on mass transfer185

8.6 Further reading186

9 Downstream processing in biotechnology RAJNI HATTI-KAUL and BO MATTIASSON187

9.1 Introduction187

9.2 Downstream processing:a multistage operation187

9.3 Solid-liquid separation188

9.4 Release of intracellular components193

9.5 Concentration of biological products195

9.6 Purification by chromatography204

9.7 Product formulation207

9.8 Monitoring of downstream processing209

9.9 Process integration210

9.10 Further reading211

10 Measurement and control A L？BBERT and R．SIMUTIS213

Nomenclature213

10.1 Introduction214

10.2 Structure of process models215

10.3 Kinetic rate expressions216

10.4 Advanced modelling considerations222

10.5 Process supervision and control228

10.6 Open-loop control230

10.7 Closed-loop control231

10.8 Conclusion236

10.9 Further reading238

11 Process economics BJ？RN KRISTIANSENRAJNI239

11.1 Introduction239

11.2 The starting point240

11.3 Cost estimates240

11.4 Process design242

11.5 Design exercise244

11.7 Operating costs estimates247

11.6 Capital costs estimates247

11.8 The costs case-to build or not to build250

11.9 Further reading252

Part Ⅱ Practical applications253

12 The business of biotechnology WILLIAM BAINS and CHRIS EVANS255

12.1 Introduction255

12.2 What is biotechnology used for?255

12.3 Biotechnology companies,their care and nurturing260

12.4 Investment in biotechnology268

12.5 Who needs management?275

12.6 Patents and biotechnology278

12.7 Conclusion:jumping the fence279

12.8 Further reading279

13 Amino acids L．EGGELING,W．PFEFFERLE and H．SAHM281

13.1　Introduction281

13.2 Commerical use of amino acids282

13.3 Production methods and tools284

13.4 L-Glutamate285

13.5 L-Lysine289

13.6 L-Threonine294

13.7 L-Phenylalanine296

13.8 L-Tryptophan298

13.9 L-Aspartate300

13.10 Outlook302

13.11 Acknowledgements302

13.12 Further reading302

14 Organic acids CHRISTIAN P．KUBICEK305

14.1 Introduction305

14.2　Citric acid306

14.3　Gluconic acid315

14.4　Lactic acid317

14.5　Other acids319

14.6 Further reading324

15 Microbial polyhydroxyalkanoates,polysaccharides and lipids ALISTAIR J．ANDERSON and JAMES P．WYNN325

15.1 Introduction325

15.2 Microbial polyhydroxyalkanoates325

15.3 Microbial polysaccharides333

15.4 Microbial lipids339

15.5 Further reading348

16 Antibiotics DAVID A．LOWE349

16.1 Introduction349

16.2 Biosynthesis351

16.3 Strain improvement351

16.5 Analysis354

16.6 Culture preservation and aseptic propagation354

16.4 Genetic engineenng354

16.7 Scale-up355

16.8 Fermentation356

16.9 Penicillins361

16.10 Cephalosporins367

16.11 New β-lactam technologies368

16.12 Aminoglycosides370

16.13 Macrolides373

16.14 Economics373

16.15 Good Manufactunng Practices374

16.16 Further reading375

17 Baker's yeast SVEN-OLOF ENFORS377

Nomenclature377

17.1 Introduction378

17.2 Medium for baker's yeast production380

17.3 Aerobic ethanol fornation and consumption381

17.4 The fed-batch technique used to control ethanol production384

17.5 Industrial process control386

17.6 Process outline387

17.7 Further reading389

18 Production of enzymes DAVID A．LOWE391

18.1 Introduction391

18.2 Enzymes from animal and plant sources393

18.3 Enzymes from microbial sources395

18.4 Iarge-scaleproduction396

18.5 Biochemical fundamentals398

18.6 Genetic engineering400

18.7 Recoveryofenzymes402

18.8 Isolation of soluble enzymes403

18.9 Enzyme purification404

18.10 Immobilised enzymes406

18.11 Legislativeand safetyaspects407

18.12 Further reading408

19 Synthesis of chemicals using enzymes409

THORLEIF ANTHONSEN409

19.1 Introduction409

19.2 Hydrolytic enzymes412

19.3 Chiral building blocks for synthesis414

19.4 Reductions and oxidations419

19.5 Use ofenzymes in sugar chemistry422

19.6 Use ofenzymes to make amino acids and peptides426

19.7 Further reading428

20 Recombinant proteins of high value GEORG-B．KRESSE429

20.1 Applications of high-value proteins429

20.2 Analytical enzymes430

20.3 Therapeutic proteins436

20.4 Regulatory aspects of therapeutic proteins446

20.5 Outlook to the future ofprotein therapies446

20.6 Further reading447

21 Mammalian cell culture N．VRIEZEN,J．P．VAN DIJKEN and L．H？GGSTR？M　　449

21.1 Introduction 　449

21.2 Mammalian cell lines and their characteristics 　450

21.3 Commerical products 　452

21.4 Protein glycosylation 　453

21.5　Media for the cultivation ofmammalian cells　455

21.6 Metabolism　458

21.7　Large-scale cultivation of mammalian cells462

21.8 Genetic engineering of mammalian cells468

21.9 Further reading470

22.1 Introduction471

22 Biotransformations JOAQUIM M．S．CABRAL471

22.2 Biocatalyst selection473

22.3 Biocatalyst immobilisation and performance475

22.4 Immobilised enzyme reactors489

22.5 Biocatalysis in non-conventional media491

22.6 Concluding remarks500

22.7 Further reading501

23 Immunochemical applications MIKE CLARK503

Glossary503

23.1 Introduction506

23.2 Antibody structure and functions506

23.3 Antibody protein fragments510

23.4 Antibody affinity512

23.5 Antibody specificity513

23.6 Immunisation and production ofpolyclonal antisera514

23.7 Monoclonal antibodies517

23.8 Antibody engineering518

23.9 Combinatorial and phage display libraries520

23.10 In vitro uses of recombinant and monoclonal antibodies522

23.11 In vivo uses ofrecombinant and monoclonal antibodies526

23.12 Further reading529

24 Environmental applications PHILIPPE VANDEVIVERE and WILLY VERSTRAETE531

24.1 Introduction531

24.2 Treatment of waste water532

24.3 Digestion of organic slurries540

24.4 Treatment of solid wastes542

24.5 Treatment of waste gases545

24.6 Soil remediation549

24.7 Treatment of groundwater554

24.8 Further reading557

Index559