UPSTREAM INDUSTRIAL BIOTECHNOLOGY -- CONTENTS -- PREFACE -- CONTRIBUTORS -- PART I INTRODUCTION -- PART II INDUSTRIAL CELL GROWTH AND GENE EXPRESSION SYSTEMS -- 1 Animal Cells, Suspension Culture -- 1.1 INTRODUCTION -- 1.2 TYPES USED FOR LARGE-SCALE PRODUCTION IN SUSPENSION CULTURE -- 1.3 SUSPENSION CULTURE REACTORS -- 1.4 OPERATING MODES FOR REACTORS -- 1.5 PROCESS MONITORING AND CONTROL -- 1.6 CULTURE MEDIA FOR SUSPENSION CULTURE -- 1.7 CONCLUSIONS -- REFERENCES -- 2 Baculovirus Expression Systems -- 2.1 INTRODUCTION -- 2.2 BACULOVIRUS STRUCTURE AND REPLICATION -- 2.3 PRODUCTION OF RECOMBINANT BACULOVIRUSES -- 2.4 BACULOVIRUS TRANSFER VECTORS -- 2.5 MODIFYING THE BACULOVIRUS GENOME TO IMPROVE PROTEIN PRODUCTION -- 2.6 INSECT CELL CULTURE -- 2.7 BACULOVIRUSES FOR GENE EXPRESSION IN MAMMALIAN CELLS -- 2.8 CONCLUSION -- REFERENCES -- 3 Baculovirus Kinetics, Insect Culture -- 3.1 HISTORY AND CHALLENGE -- 3.2 BACULOVIRUS -- 3.3 CELL YIELD CONCEPT -- 3.4 KINETIC MODEL OF VIRAL INFECTION: SYNCHRONOUS INFECTION -- 3.5 KINETIC MODEL OF VIRAL INFECTION: ASYNCHRONOUS INFECTION -- REFERENCES -- 4 Cell Culture, Aseptic Techniques -- 4.1 INTRODUCTION -- 4.2 ASEPTIC TECHNIQUE: GENERAL CONSIDERATIONS -- 4.3 ASEPTIC TECHNIQUE: BASIC PROCEDURES -- 4.4 HEPA FILTRATION -- 4.5 HOODS AND CABINETS EMPLOYING HEPA FILTRATION -- 4.6 WORKING WITHIN UNIDIRECTIONAL AIRFLOW CABINETS AND MICROBIOLOGICAL SAFETY CABINETS -- 4.7 TESTING OF CLASS I AND CLASS II MICROBIOLOGICAL SAFETY CABINETS -- 4.8 CLEANROOMS FOR CELL CULTURE USE -- REFERENCES -- 5 Cell Cycle in Bioprocesses -- 5.1 INTRODUCTION -- 5.2 THE CELL CYCLE -- 5.3 METHODS FOR DESCRIBING THE CELLCYCLE -- 5.4 IMPORTANCE OF THE CELL CYCLE IN PROCESS BIOTECHNOLOGY -- REFERENCES -- 6 Cell Growth and Protein Expression Kinetics -- 6.1 INTRODUCTION -- 6.2 BATCH CULTURE KINETICS -- 6.3 CONTINUOUS CULTURE KINETICS.

6.4 FED-BATCH AND PERFUSION CULTURES -- 6.5 CONCLUSIONS -- NOMENCLATURE -- REFERENCES -- 7 Cell Viability Measurement -- 7.1 INTRODUCTION -- 7.2 PERMEABILITY ASSAYS -- 7.3 FUNCTIONAL ASSAYS -- 7.4 FLOW CYTOMETRY -- 7.5 PHYSICAL METHODS -- REFERENCES -- 8 Contamination Detection in Animal Cell Culture -- 8.1 INTRODUCTION -- 8.2 HISTORICAL PERSPECTIVES -- 8.3 REGULATORY ISSUES -- 8.4 MANUFACTURING AND SAFETY TESTING STANDARDS -- 8.5 EXAMPLES OF VIRAL CONTAMINANTS -- 8.6 DETECTION OF VIRAL CONTAMINANTS IN CELL LINES -- 8.7 TESTING RAW MATERIALS -- 8.8 DETECTION OF MYCOPLASMAS -- 8.9 BACTERIA AND FUNGI -- 8.10 OXYGEN UPTAKE RATE -- 8.11 ENDOTOXIN DETECTION -- 8.12 STATISTICAL ANALYSIS -- 8.13 DETECTION OF PRIONS -- 8.14 SUMMARY -- REFERENCES -- 9 Culture Collections and Biological Resource Centers (BRCs) -- 9.1 INTRODUCTION -- 9.2 CULTURE COLLECTION FUNDING -- 9.3 OPERATION -- 9.4 QUALITY MANAGEMENT -- 9.5 SERVICES -- 9.6 SUMMARY -- REFERENCES -- FURTHER READING -- 10 Culture Preservation -- 10.1 INTRODUCTION -- 10.2 CULTURE AND PRESERVATION OF BACTERIA -- 10.3 CULTURE AND PRESERVATION OF FUNGI AND YEAST -- 10.4 CULTURE AND PRESERVATION OF CELL CULTURES -- REFERENCES -- 11 Expression and Secretion of Heterologous Proteins, Bacillus and Other Gram-Positive Bacteria -- 11.1 INTRODUCTION -- 11.2 MAJOR INDUSTRIAL STRAINS -- 11.3 BACILLUS MEGATERIUM -- 11.4 PROTOCOLS FOR BACILLUS MEGATERIUM -- REFERENCES -- 12 Gene Expression in Human Cells -- 12.1 BACKGROUND -- 12.2 THE SAFETY AND REGULATORY ASPECTS OF USING HUMAN CELL LINES FOR GENE EXPRESSION -- 12.3 GENE EXPRESSION IN HUMAN CELL LINES -- 12.4 SCALE-UP OF RECOMBINANT HUMAN CELL LINES CULTIVATION -- 12.5 CONCLUDING REMARKS -- REFERENCES -- 13 Gene expression in Pichia and other methylotroph yeast -- 13.1 INTRODUCTION -- 13.2 BACKGROUND -- 13.3 STRATEGIES FOR OPTIMIZATION OF PROTEIN EXPRESSION.

13.4 FERMENTATION PROCESS -- 13.5 CONCLUSIONS AND FUTURE PERSPECTIVES -- 13.6 MEDIA COMPOSITIONS -- 13.7 GLOSSARY OF P. PASTORIS STRAINS -- REFERENCES -- 14 Gene Expression in Recombinant Animal Cells and Transgenic Animals -- 14.1 INTRODUCTION -- 14.2 OVERVIEW -- 14.3 PLASMID EXPRESSION VECTORS FOR ANIMAL CELLS -- 14.4 OTHER DIRECT TRANSFER VECTORS -- 14.5 DIRECT DNA TRANSFER -- 14.6 TRANSFECTION METHODS -- 14.7 VIRAL EXPRESSION VECTORS -- 14.8 EXPRESSION PARAMETERS AND OPTIMIZATION-VECTOR AND INSERT SEQUENCES -- 14.9 EXPRESSION PARAMETEROPTIMIZATION-CONSEQUENCES OF TRANSGENE INTEGRATION -- 14.10 RECOMBINATION-BASED METHODOLOGY AND GENE INHIBITION STRATEGY -- 14.11 THE PRODUCTION OF TRANSGENIC MAMMALS FROM MANIPULATED CELLS -- 14.12 USES FOR TRANSGENIC ANIMALS -- 14.13 NUCLEAR TRANSFER TECHNOLOGY -- REFERENCES -- 15 Inoculum Expansion Methods, Animal Cell Lines -- 15.1 INTRODUCTION -- 15.2 INOCULUM EXPANSION PROCESSES -- 15.3 IMPACT OF CELL BANKS ON INOCULUM EXPANSION -- 15.4 CURRENT TRENDS IN INOCULUM EXPANSION -- 15.5 TECHNOLOGY TRANSFER -- 15.6 CONCLUSION -- 15.7 PRODUCT WEBSITES -- REFERENCES -- FURTHER READING -- 16 Insect Cell Culture -- 16.1 INTRODUCTION -- 16.2 INSECT CELL LINES -- 16.3 VIRUSES -- 16.4 BACULOVIRUS GENE EXPRESSION -- 16.5 CONSTRUCTION OF RECOMBINANT BACULOVIRUSES -- 16.6 POSTTRANSLATIONAL PROCESSING -- 16.7 APPLICATIONS -- 16.8 LARGE-SCALE PROCESSING: CELL CULTURE OR LARVAL PRODUCTION -- 16.9 CONCLUSION -- REFERENCES -- 17 Kinetics of Microbial Growth -- 17.1 INTRODUCTION -- 17.2 GROWTH STOICHIOMETRY -- 17.3 KINETICS OF CHEMICAL AND ENZYME REACTIONS -- 17.4 SIMPLE MODELS OF MICROBIAL AND CELL GROWTH -- 17.5 STRUCTURED MODELS -- 17.6 POPULATION DYNAMICS (MUTATIONS, AUTOSELECTION, PLASMID TRANSFER) -- 17.7 MICROBIAL GROWTH IN VARIOUS CULTIVATION SYSTEMS -- REFERENCES -- 18 Microalgae, Mass Culture Methods -- 18.1 INTRODUCTION.

18.2 BIOREACTORS FOR MICROALGAE MASS CULTURES -- 18.3 MAJOR FACTORS GOVERNING THE PRODUCTION OF MICROALGAE -- 18.5 PHOTOSYNTHETIC EFFICIENCY IN MICROALGAL MASS CULTURES -- 18.6 OPERATIONAL CONSIDERATIONS -- 18.7 CONCLUDING REMARKS -- NOMENCLATURE -- REFERENCES -- 19 Microbial Growth Measurement -- 19.1 INTRODUCTION -- 19.2 DIRECT PARTICLE COUNTS -- 19.3 COLONY COUNTS EQUAL VIABLE COUNTS -- 19.4 DIRECT BIOMASS MEASUREMENTS -- 19.5 BIOMASS BY LIGHT SCATTERING -- 19.6 SAMPLING -- REFERENCES -- 20 Microbial Media Composition -- 20.1 INTRODUCTION -- 20.2 ESSENTIAL NUTRITIONAL REQUIREMENTS -- 20.3 PHYSICAL PARAMETERS -- 20.4 MEDIA DESIGN AND COMPOSITION -- 20.5 MEDIA STERILIZATION -- 20.6 MEDIA STORAGE -- REFERENCES -- 21 Microscopic Characterization of Cells -- 21.1 INTRODUCTION AND PERSPECTIVE -- 21.2 DEVELOPMENTS AND MILESTONES IN MICROSCOPY -- 21.3 LIGHT MICROSCOPY -- 21.4 LASER TWEEZERS AND SCISSORS -- 21.5 SCANNING-PROBE NEAR-FIELD MICROSCOPES -- 21.6 VIDEO MICROSCOPY AND IMAGE PROCESSING -- 21.7 ELECTRON MICROSCOPES -- 21.8 SUMMARY -- 21.9 WEB SITES -- REFERENCES -- 22 Mycoplasma Contamination of Cell Cultures -- 22.1 BIOLOGY AND NOMENCLATURE OF MYCOPLASMAS -- 22.2 MYCOPLASMA CONTAMINATION OF CELL CULTURES -- 22.3 DETECTION OF MYCOPLASMA CONTAMINATION -- 22.4 ELIMINATION OF MYCOPLASMA CONTAMINATION -- 22.5 WORKING PROTOCOLS FOR DETECTION, ELIMINATION, AND PREVENTION OF MYCOPLASMA CONTAMINATION -- REFERENCES -- 23 Protein Glycosylation: Analysis, Characterization, and Engineering -- 23.1 INTRODUCTION -- 23.2 OVERVIEW OF PROTEIN GLYCOSYLATION -- 23.3 EFFECTS OF GLYCOSYLATION ON PROTEINS -- 23.4 TECHNIQUES FOR ANALYZING GLYCOPROTEINS, GLYCOPEPTIDES, AND THEIR ATTACHED GLYCANS -- 23.5 GLYCOSYLATION OF RECOMBINANT PROTEIN THERAPEUTICS -- 23.6 CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- 24 Secretion of Heterologous Proteins, Gram Positive Bacteria.

24.1 PROTEIN SECRETION VIA THE GENERAL EXPORT PATHWAY IN GRAM-POSITIVE BACTERIA -- 24.2 SECRETION OF HETEROLOGOUS PROTEINS IN L. LACTIS -- 24.4 PROTEIN SECRETION IN L. LACTIS -- 24.5 CONCLUSION -- REFERENCES -- 25 Soluble Protein Expression in Bacteria -- 25.1 INTRODUCTION -- 25.2 ALTERING GROWTH CONDITIONS TO INCREASE SOLUBLE EXPRESSION -- 25.3 ALTERING THE HOST STRAIN AND VECTOR TO DIRECT SOLUBLE EXPRESSION -- 25.4 ALTERING THE PROTEIN SEQUENCE FOR SOLUBILITY -- 25.5 GROWTH CONDITIONS AND VARIABLES THAT AFFECT YIELDS OF SOLUBLE PROTEIN -- 25.6 CONCLUSIONS AND OUTLOOK -- REFERENCES -- FURTHER READING -- PART III MEDIA, CELL LINES AND PROCESS DEVELOPMENT -- 26 Animal Cell Culture Media -- 26.1 INTRODUCTION -- 26.2 NUTRIENTS IN CELL CULTURE MEDIA -- 26.3 BASAL MEDIUM DEVELOPMENT -- 26.4 FEED MEDIUM DEVELOPMENT -- 26.5 PRODUCT QUALITY -- 26.6 USE OF APPROPRIATE SMALL-SCALE MODEL AND HIGH THROUGHPUT SYSTEMS -- 26.7 INDUSTRIAL CONSIDERATIONS FOR THE OPTIMIZATION AND IMPLEMENTATION OF BASAL AND FEED MEDIA -- 26.8 CONCLUDING REMARKS -- REFERENCES -- 27 Animal Cell Culture, Effects of Osmolality and Temperature -- 27.1 EFFECT OF OSMOLALITY OF THE CELLULAR MICROENVIRONMENT -- 27.2 EFFECTS OF TEMPERATURE PERTURBATIONS ON CELLULAR PHYSIOLOGY AND PERFORMANCE IN BIOPROCESS SYSTEMS -- 27.3 CONCLUSIONS -- REFERENCES -- 28 Animal Cell Stability -- 28.1 FACTORS THAT AFFECT GENETIC STABILITY OF ENDOGENOUS GENES -- 28.2 GENOTYPIC AND PHENOTYPIC STABILITY OF RECOMBINANT CELL LINES -- 28.3 CONSEQUENCES OF GENETIC INSTABILITY ON RECOMBINANT PROTEIN QUALITY -- 28.4 GENOTYPIC CHARACTERIZATION AND VALIDATION OF GENETIC STABILITY -- REFERENCES -- 29 Animal Cell Types, Hybridomas -- 29.1 INTRODUCTION -- 29.2 ANTIBODY PRODUCTION BY ANIMAL CELLS IN VITRO -- 29.3 NEW METHODS FOR HUMAN ANTIBODY PRODUCTION (IN VITRO IMMUNIZATION, ARTIFICIAL LYMPH NODE SYSTEMS).

29.4 ALTERNATIVES TO ANTIBODIES FOR USE IN HUMAN BEINGS.