Comprehensive biotechnology Vol. 1/ principles and practices in industry agriculture medicine and the environment Moo-Young,Murray

General Preface

Nomenclature Guidelines

Permission Acknowledgments

1.01. Introduction

1.02. Amino Acid Metabolism

Glossary

1.02.1. Introduction

1.02.2. General Properties, Classification, and Structure of Amino Acids

1.02.3. Biosynthesis of Amino Acids

1.02.4. Catabolism of Amino Acids

1.02.5. Important Biomolecules Synthesized from Amino Acids

1.03. Enzyme Biocatalysis

Glossary

1.03.1. Introduction to Enzymes

1.03.2. Enzyme Kinetics

1.03.3. Enzyme Engineering

1.03.4. Enzyme Production

1.03.5. Immobilized Enzymes

1.03.6. Enzyme Applications

1.03.7. Conclusions

1.04. Immobilized Biocatalysts

1.04.1. Introduction: Definitions and Scope

1.04.2. Applications of Immobilized Enzymes

1.04.3. Methods of Enzyme Immobilization

1.04.4. Properties of Immobilized Enzymes

1.04.5. Evaluation of Enzyme Immobilization

1.04.6. Heterogeneous Biocatalysis

1.04.7. Future Prospects for Immobilized Biocatalysts

1.05. Lipids, Fatty Acids

Glossary

1.05.1. Introduction

1.05.2. Structure of Fatty Acids

1.05.3. Nomenclature

1.05.4. Form in the Cell

1.05.5. What Do Lipids Do?

1.05.6. Biosynthesis of Fatty Acids and Lipids

1.05.7. Biochemistry of Lipid Accumulation

1.06. DNA Cloning in Plasmid Vectors

Glossary

1.06.1. Introduction

1.06.2. Cloning Vectors: Replication Origins and Partition Regions

1.06.3. Cloning Vectors: Selection Markers

1.06.4. Preparing DNA Fragments for Ligation

1.06.5. Ligation Systems

1.06.6. Methods of Bacterial and Yeast Transformation

1.06.7. Exploitation of Bacteriophage Packaging for DNA Cloning in Plasmid Vectors

1.06.8. Screening of Plasmid Clones in Bacteria for the Desired Recombinant Plasmids

1.06.9. Vector-Implemented Systems for the Direct Selection of Recombinant Plasmids

1.06.10. Direct Selection of Recombinant Plasmids Involving Restriction Enzyme Digestion of the Ligation Mixture

1.06.11. Particular Features of Oligonucleotides’ Cloning

1.06.12. Particular Features of Cloning of PCR Amplicons

1.06.13. Introduction of Deletions into Plasmids

1.06.14. Instability of Recombinant Plasmids

1.06.15. DNA Cloning Using Site-Specific Recombination

1.06.16. DNA Cloning Using Homologous (General) Recombination

1.06.17. Employment of Transposons for In Vivo Cloning and Manipulation of Large Plasmids

1.06.18. Conclusion

1.07. Structure and Biosynthesis of Glycoprotein Carbohydrates

Glossary

Acknowledgments

1.07.1. Introduction

1.07.2. Monosaccharide Structure

1.07.3. Oligosaccharide Structure

1.07.4. Biosynthesis of Glycoproteins

1.07.5. Glycosylation of Therapeutic Glycoproteins

1.08. Nucleotide Metabolism

Glossary

1.08.1. Introduction

1.08.2. Synthesis of Phosphoribosyl Diphosphate (PRPP)

1.08.3. Purine Biosynthesis

1.08.4. Pyrimidine Biosynthesis

1.08.5. Nucleoside Triphosphate Formation

1.08.6. Deoxyribonucleotide Biosynthesis

1.08.7. Nucleotide Salvage

1.08.8. Purine and Pyrimidine Catabolism

1.08.9. Regulation of Gene Expression in Bacterial Nucleotide Synthesis

1.08.10. Exploitation of the Knowledge of Nucleotide Metabolism in Biotechnology

1.09. Organic Acids

Glossary

1.09.1. Introduction

1.09.2. Citric Acid

1.09.3. Gluconic Acid

1.09.4. Lactic Acid

1.09.5. Itaconic Acid

1.09.6. Other Acids

1.10. Peptides and Glycopeptides

Glossary

1.10.1. Introduction

1.10.2. Peptide Hormones

1.10.3. Neuropeptides

1.10.4. Antibacterial Peptides

1.10.5. Glycosylation Is a Common and Important Post-Translational Modification of Peptides

1.10.6. Common Glycosidic Linkages

1.10.7. Peptide Synthesis

1.10.8. Glycopeptide Synthesis

1.10.9. Peptides and Glycopeptides as Models of Proteins and Glycoproteins

1.10.10. Application of Synthetic Peptides and Glycopeptides for the Treatment of Disease

1.10.11. Summary

1.11. Protein Structural Analysis

Glossary

1.11.1. Introduction

1.11.2. Protein X-ray Crystallography

1.11.3. NMR Spectroscopy

1.11.4. Structure Analysis Using Intrinsic Protein Fluorescence

1.11.5. Conclusions

1.12. Secondary Metabolites

Glossary

1.12.1. Introduction

1.12.2. Antibiotics

1.12.3. Other Applications of Secondary Metabolites

1.13. Cell Line Isolation and Design

Glossary

1.13.1. Introduction

1.13.2. Clone Selection and Isolation

1.13.3. Automating Clone Screening

1.13.4. Designer Cell Lines for Bioproduction

1.13.5. Future Perspectives and Conclusions

1.14. Cell Preservation Technology

Glossary

1.14.1. Introduction

1.14.2. Hypothermic Storage

1.14.3. Hypothermic Continuum

1.14.4. Cryopreservation

1.14.5. Modes of Cell Death

1.14.6. Cell Death Continuum

1.14.7. Preservation-Induced Cell Death

1.14.8. Targeted Control of Molecular-Based Death

1.14.9. Concluding Thoughts

1.15. Cytoskeleton and Cell Motility

Glossary

1.15.1. Introduction

1.15.2. Myosins

1.15.3. Cell Migration

1.15.4. Involvement of Unconventional Myosins in Cell Migration and Trafficking

1.16. Design of Culture Media

Glossary

1.16.1. Introduction

1.16.2. Universal Requirements

1.16.3. Specific Requirements

1.16.4. Methods for Media Design

1.16.5. Manufacturing of the Designed Medium

1.16.6. Regulatory Considerations

1.16.7. Quality Control Testing

1.16.8. Security of Supply

1.16.9. Summary

1.17. Protein Folding in the Endoplasmic Reticulum

Glossary

Acknowledgments

1.17.1. Introduction: Protein Folding

1.17.2. The Endoplasmic Reticulum as a Folding, Assembly, and Trafficking Vehicle

1.17.3. Key Chaperones Assisting Folding in the ER

1.17.4. Calnexin and Calreticulin: Glycosylation and Glycoprotein Quality Control

1.17.5. PDI: Redox-Dependent Folding and Disulfide Bond Formation

1.17.6. Glycosylation Glycosylphosphatidylinositol Anchor Addition

1.17.7. Quality Control and ER-Associated Degradation

1.17.8. From the ER to the Golgi

1.17.9. Protein-Folding Status Is Communicated to the Cytosol and Nucleus via the UPR

1.17.10. Transduction of the ER Stress/UPR Signal by Three Proximal Sensors

1.17.11. UPR and Apoptosis

1.17.12. Protein Misfolding, ER Dyshomeostasis, and Human Diseases

1.17.13. Concluding Remarks

1.18. Extremophiles

Glossary

1.18.1. Introduction

1.18.2. The Diversity

1.18.3. High Temperature

1.18.4. Low Temperatures

1.18.5. Low pH

1.18.6. Alkaline pH

1.18.7. Conclusion

1.19. Metabolic Design and Control for Production in Prokaryotes

Glossary

1.19.1. Introduction

1.19.2. Classical Mutagenesis

1.19.3. Protoplast Fusion and Genome Shuffling

1.19.4. Recombinant DNA Technology and First-Generation Metabolic Engineering

1.19.5. Quantitative Approaches for Metabolic Design

1.19.6. Targeted Combinatorial Engineering

1.19.7. Synthetic Biology: Parts, Devices, and Circuits

1.20. Microbial Growth Dynamics

Glossary

1.20.1. Introduction

1.20.2. Kinetic Models of Microbial Growth

1.20.3. Growth Dynamic Variation as Dependent on Internal and External Factors

1.21. Modes of Culture/Animal Cells

Glossary

1.21.1. Introduction

1.21.2. Batch Culture: The Basis for All Cell Culture Systems

1.21.3. Fed-Batch Culture: Dominator of Industrial-Scale Processes

1.21.4. Perfusion Culture: The Most Sophisticated Process

1.21.5. Concluding Remarks on the Selection of Culture Mode

1.22. Modes of Culture/Microbial

Glossary

1.22.1. Introduction

1.22.2. Modes of Microbial Culture

1.22.3. When the Microbe Itself Is the End Product

1.22.4. Algal Biodiesel: A Case Study in Contemporary Challenges for Microbial Culture

1.22.5. Concluding Remarks

1.23. Photosynthesis and Photoautotrophy

Glossary

1.23.1. Introduction

1.23.2. Energy Absorption, Trapping, Conversion, and Storage

1.23.3. Photostasis and Cellular Energy Imbalance

1.23.4. Photoacclimation Tailors the Photosynthetic Apparatus

1.23.5. Acclimation to Low Temperature Mimics Photoacclimation

1.23.6. Conclusions

1.24. Protein Expression in Insect Cells

Glossary

1.24.1. Historical Background and General Introduction

1.24.2. Baculovirus Biology

1.24.3. The Origins of the BEVS

1.24.4. Baculovirus Recombination in Bacteria: the Development of Bacmids

1.24.5. Hybrid Systems: Bacmid Recombination in Insect Cells

1.24.6. Baculovirus Recombination In Vitro

1.24.7. Nonlytic Systems for Protein Expression in Insect Cells

1.24.8. Insect Cells

1.24.9. Insect Cell Culture

1.24.10. Removing Bottlenecks in the BEVS

1.24.11. Concluding Summary

1.25. Stem Cells

Glossary

1.25.1. Introduction

1.25.2. Human Embryonic Stem Cells

1.25.3. Human-Induced Pluripotent Stem Cells

1.25.4. Neural Stem Cells

1.25.5. Mesenchymal Stem Cells

1.25.6. Hematopoietic Stem Cells

1.26. Structural Organization of Cells – The Cytoskeleton

Glossary

Acknowledgments

1.26.1. Introduction

1.26.2. Molecular and Supramolecular Components

1.26.3. Cytoskeletal Arrays and Their Structural Functions

1.26.4. Motility

1.26.5. Diseases and the Cytoskeleton

1.27. Viruses Produced from Cells

Glossary

1.27.1. Introduction

1.27.2. Cell Culture

1.27.3. Types of Growth Flasks

1.27.4. Parameters of Virus Growth

1.27.5. Virus Purification

1.27.6. Future Perspectives

1.28. Cell Transfection

Glossary

1.28.1. Introduction

1.28.2. Methods of Transfection

1.28.3. Advances in Large-Scale Transfection Technology

1.29. mRNA Translation and Recombinant Gene Expression from Mammalian Cell Expression Systems

1.29.1. Introduction

1.29.2. Translational Machinery

1.29.3. Manipulation of mRNA for Optimal Translational Efficiency

1.29.4. Importance of 5′-UTR and Secondary Structure in 5′-UTR Region of mRNA

1.29.5. mRNA Translation Shutdown

1.29.6. MicroRNAs and Translational Control

1.29.7. In Vitro mRNA Translation Systems

1.29.8. Conclusions and Future Prospects

1.30. Posttranslation Modifications Other Than Glycosylation

Glossary

Acknowledgments

1.30.1. Introduction

1.30.2. Cell Influences on Protein Expression

1.30.3. Induction of Protein Expression

1.30.4. Improving the Protein Folding and Secretory Pathways

1.30.5. Role of Chaperones

1.30.6. Multiple Gene Activators

1.30.7. Cell Clearance of Misfolded Proteins

1.30.8. Protein Aggregation

1.30.9. Analytical Techniques for Protein Aggregate Detection

1.30.10. Asparagine Deamidation

1.30.11. Methionine Oxidation

1.30.12. Surface-Plasmon Resonance

1.30.13. Conclusions

1.31. Engineering Protein Folding and Secretion in Eukaryotic Cell Factories

Glossary

1.31.1. Introduction

1.31.2. Direct Engineering of Recombinant Protein Folding and Assembly

1.31.3. Engineering the Regulation of Protein Folding and Assembly: The Unfolded Protein Response

1.31.4. Glycosylation Engineering for Improved Protein Processing

1.31.5. Engineering of the Secretory Apparatus

1.31.6. Mathematical Modeling of Recombinant Protein Synthesis and Secretion

1.32. Glycomics

Glossary

1.32.1. Introduction

1.32.2. Methods for the Structural Analysis of Glycans

1.32.3. Glycomics in Bioproduction

1.32.4. The Changing Landscape of Regulatory Agencies toward Glycosylation of Biopharmaceuticals

1.32.5. Summary

1.33. Metabolomics – The Combination of Analytical Biochemistry, Biology, and Informatics

Glossary

Acknowledgments

1.33.1. Introduction

1.33.2. Technologies Used to Measure Metabolites

1.33.3. Metabolomics Approaches

1.33.4. Bioinformatics: What Can It Do

1.33.5. What Does the Informatician Need to Analyze the High-Density Data?

1.33.6. Data Preprocessing: From Raw to Sense

1.33.7. Requirements and Problems of Statistical and Multivariant Analysis of Metabolomics Data

1.33.8. Conclusions

1.34. Theory and Applications of Proteomics

Glossary

1.34.1. Introduction

1.34.2. Proteomics Technologies

1.34.3. Separation Technologies

1.34.4. Quantitative Proteomics

1.34.5. Data Processing

1.34.6. Applications in Biotechnology

1.35. Systems Metabolic Engineering for the Production of Non-innate Chemical Compounds

Glossary

1.35.1. Introduction and Scope

1.35.2. Systems Metabolic Engineering

1.35.3. Summary

1.36. Apoptosis

Glossary

1.36.1. Introduction

1.36.2. Apoptosis Regulators and Executioners

1.36.3. Apoptotic Pathways

1.36.4. Apoptosis and Autophagy

1.36.5. Inhibition of Apoptosis

1.36.6. Apoptosis affects Metabolic Pathways

1.36.7. Conclusion

1.37. Design Principles of Self-assembling Peptides and Their Potential Applications

Glossary

1.37.1. Introduction

1.37.2. Design Principles of Self-Assembling Peptides

1.37.3. Applications of Self-Assembling Peptides

1.38. Rational Design of Strategies Based on Metabolic Control Analysis

Glossary

Acknowledgments

1.38.1. Introduction

1.38.2. Fundamentals of Metabolic Control Analysis

1.38.3. Modulation of Clinically and Biotechnologically Relevant Metabolism

1.38.4. Concluding Remarks

1.39. Unfolded Protein Response

Glossary

Acknowledgments

1.39.1. Introduction

1.39.2. Molecular Mechanism of the UPR

1.39.3. Stress Responses in Other Organelles

1.39.4. Concluding Remarks

1.40. Cell Migration

Glossary

Acknowledgments

1.40.1. Introduction

1.40.2. Biological Mechanisms for Cell Migration

1.40.3. Cell Migration in Selected Physiological Systems

1.40.4. Approaches for Measuring Cell Migration

1.40.5. Summary and Outlook

1.41. Biofilms

Glossary

1.41.1. Introduction

1.41.2. Model Systems for Growing and Analyzing Biofilms

1.41.3. Heterogeneity in Biofilms

1.41.4. Stages of Biofilm Development

1.41.5. Regulation of Biofilm Development

1.41.6. Biofilm Infections

1.41.7. Pathogenicity and Antibiotic Resistance of Biofilms

1.41.8. Antibiotics Act as Signals that Stimulate Biofilm Formation

1.41.9. Concluding Remarks

1.42. Flow Cytometry

Glossary

1.42.1. Introduction

1.42.2. Principles and Instrumentation

1.42.3. Data Representation

1.42.4. Common Applications

1.43. Biological Imaging by Superresolution Light Microscopy

Glossary

Acknowledgments

1.43.1. Introduction

1.43.2. The Case for Superresolution Microscopy Techniques

1.43.3. Near-Field Scanning Optical Microscopy

1.43.4. Stimulated Emission Depletion

1.43.5. Superresolution Structured Illumination Microscopy

1.43.6. Photoactivation Localization Microscopy, Fluorescence Photoactivation Localization Microscopy, and Stochastic Optical Reconstruction Microscopy

1.43.7. Conclusions

1.44. Cell Isolation from Tissue

Glossary

1.44.1. Introduction

1.44.2. Tissue/Organ Procurement

1.44.3. Tissue/Organ Preservation

1.44.4. Tissue/Organ Rinsing

1.44.5. Tissue/Organ Fragmentation

1.44.6. Cell Dissociation

1.44.7. Purification

1.44.8. Cell Yield, Viability, and Purity Assessment

1.44.9. Conclusions

1.45. Nanobiotechnology

1.45.1. Introduction

1.45.2. Nanoparticles

1.45.3. Role of Nanobiotechnology in Molecular Diagnostics

1.45.4. Pharmaceutical Applications of Nanobiotechnology

1.45.5. Role of Nanobiotechnology in Biological Therapies

1.45.6. Clinical Nanomedicine

1.45.7. Nanooncology

1.45.8. Nanoneurology

1.45.9. Nanocardiology

1.45.10. Nanosurgery

1.45.11. Nanorobotics

1.45.12. Role of Nanobiotechnology for the Development of Personalized Medicine

1.45.13. Safety Issues of Nanoparticles

1.45.14. Future Prospects of Nanobiotechnology

1.46. Effects of Shear Stress on Cells

Glossary

1.46.1. Introduction

1.46.2. Shear Stress

1.46.3. Mechanisms of Mechanosignaling

1.46.4. Role of Shear Stress on ECs

1.46.5. Shear Stress Plays a Role in Stem Cell Fate

1.47. Viruses and Virus-Like Particles in Biotechnology

Glossary

Acknowledgments

1.47.1. Introduction

1.47.2. Types of Viruses

1.47.3. Types of VLPs

1.47.4. Production Platforms: A Focus on Animal Cell Technology

1.47.5. Applications: Prevention and Treatment

1.47.6. Bioengineering Challenges

1.47.7. Concluding Remarks and Future Trends

1.48. Mathematical Models in Biotechnology

Glossary

1.48.1. Introduction

1.48.2. Metabolic Network Models and Flux Balance Analysis

1.48.3. Reverse Engineering of Gene Regulatory Networks

1.48.4. Continuous Ordinary Differential Equation-Based Dynamic Models

1.48.5. Single-Cell Models and Stochastic Simulations

1.48.6. Qualitative Models: Fuzzy Logic and Petri Nets

1.48.7. Conclusion

1.49. Immunoassays in Biotechnology

Glosssary

Acknowledgments

1.49.1. Introduction

1.49.2. Immunoassay Formats

1.49.3. Applications

1.49.4. Conclusions

1.50. Mass Spectrometry

Glossary

Acknowledgments

1.50.1. Introduction

1.50.2. Recent Ionization Techniques

1.50.3. Commonly Used Mass (m/z) Analyzers

1.50.4. Online and Offline Coupling of MS with Liquid Chromatography and Electrophoresis

1.50.5. Quantitative Analysis (i-tag, i-traq, etc.)

1.50.6. Concluding Remarks

1.51. Bioprocessing Techniques

Glossary

1.51.1. Introduction

1.51.2. Production Strain Development

1.51.3. Fermentation Process

1.51.4. Product Recovery and Purification

1.51.5. Process Validation

1.51.6. Process Documentation

1.51.7. Conclusion