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Comprehensive biotechnology Vol. 1/ principles and practices in industry agriculture medicine and the environment Moo-Young,Murray - Amsterdam: Elsevier, 2011. - 690


1.01. Introduction

1.02. Amino Acid Metabolism

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

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

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

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

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

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

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

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

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

1.12.1. Introduction

1.12.2. Antibiotics

1.12.3. Other Applications of Secondary Metabolites

1.13. Cell Line Isolation and Design

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

1.35.1. Introduction and Scope

1.35.2. Systems Metabolic Engineering

1.35.3. Summary

1.36. Apoptosis

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

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



Dewey Class. No.: 660.6 / MOO/C