Comprehensive Biotechnology

Comprehensive Biotechnology

2nd Edition - July 20, 2011

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  • Editor-in-Chief: Murray Moo-Young
  • eBook ISBN: 9780080885049

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The second edition of Comprehensive Biotechnology, Six Volume Set continues the tradition of the first inclusive work on this dynamic field with up-to-date and essential entries on the principles and practice of biotechnology. The integration of the latest relevant science and industry practice with fundamental biotechnology concepts is presented with entries from internationally recognized world leaders in their given fields. With two volumes covering basic fundamentals, and four volumes of applications, from environmental biotechnology and safety to medical biotechnology and healthcare, this work serves the needs of newcomers as well as established experts combining the latest relevant science and industry practice in a manageable format. It is a multi-authored work, written by experts and vetted by a prestigious advisory board and group of volume editors who are biotechnology innovators and educators with international influence.

Key Features

  • All six volumes are published at the same time, not as a series; this is not a conventional encyclopedia but a symbiotic integration of brief articles on established topics and longer chapters on new emerging areas.
  • Hyperlinks provide sources of extensive additional related information; material authored and edited by world-renown experts in all aspects of the broad multidisciplinary field of biotechnology
  • Scope and nature of the work are vetted by a prestigious International Advisory Board including three Nobel laureates
  • Each article carries a glossary and a professional summary of the authors indicating their appropriate credentials
  • An extensive index for the entire publication gives a complete list of the many topics treated in the increasingly expanding field


Researchers, administrators, instructors and students(especially graduates and upper undergraduates) involved in biotechnology-related activities (academia, government, industry, medicine, agriculture, environment concerns, regulatory issues); university departments with programs/courses in the Life Sciences (especially microbiology, molecular biology, biochemistry, biophysics, genetics) and in bio-engineering (especially biochemical engineering, biological engineering, biomedical engineering, environmental engineering, food engineering, pharmaceutical engineering, agricultural engineering); useful for both neophytes and veterans of the field of biotechnology.

Table of Contents

  • Editor-in-Chief

    Volume Editors

    Section Editors

    General Preface

    Nomenclature Guidelines

    Permission Acknowledgments

    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



    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



    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



    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


    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


    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



    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


    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


    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



    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


    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



    1.49.1. Introduction

    1.49.2. Immunoassay Formats

    1.49.3. Applications

    1.49.4. Conclusions

    1.50. Mass Spectrometry



    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


    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

    2.01. Introduction

    2.02. Bioengineering at the Interface between Science and Society


    2.02.1. Introduction

    2.02.2. The Impact of Science and Technology on Society

    2.02.3. Roots and Development of Evolutionary Biology and of Genetics

    2.02.4. Genetic Engineering as a Source of Genetic Variants

    2.02.5. Molecular Mechanisms and Natural Strategies of Spontaneous Genetic Variation

    2.02.6. High Similarity between Natural Biological Evolution and the Contribution of Genetic Engineering to Biological Evolution

    2.02.7. Risk Evaluation of Evolutionary Processes

    2.02.8. Prospects of Bioengineering

    2.02.9. Public Perception of Genetics, Biological Evolution, and Bioengineering

    2.02.10. Call for Sustainability of Cultural Developments

    2.03. Cellular Systems


    2.03.1. Introduction

    2.03.2. Bacteria

    2.03.3. Fungi

    2.03.4. Plant Cells

    2.03.5. Animal Cells

    2.03.6. Human Stem Cells

    2.03.7. Artificial Cells

    2.04. Cell Growth Dynamics


    2.04.1. Introduction

    2.04.2. Models of Cells in Submerged Culture

    2.04.3. Models of Cells in Multiphase Fermentor

    2.05. Reaction Kinetics and Stoichiometry


    2.05.1. Introduction

    2.05.2. Enzyme Kinetics

    2.05.3. Factors Affecting Reaction Kinetics

    2.05.4. Biochemical Reaction Rate Related to Cellular Systems

    2.05.5. Stoichiometry

    2.06. Bioreactor Fluid Dynamics


    2.06.1. Introduction

    2.06.2. Mixing

    2.06.3. Residence Time Measurements of the Gas Flow

    2.06.4. Flow around Single Bubbles

    2.06.5. Flow around Impeller Blades

    2.06.6. Oxygen Mass Transfer

    2.06.7. Flow Patterns in Stirred Tanks

    2.06.8. Flow Patterns in Bubble Columns

    2.06.9. Take-Home Messages

    2.07. Mixing in Bioreactor Vessels


    2.07.1. Introduction

    2.07.2. Characterization of Mixing

    2.07.3. Mixing Models

    2.07.4. Experimental Verification

    2.07.5. The Airlift

    2.07.6. Comparison of the Reactor Types

    2.07.7. Gas-Phase Mixing

    2.07.8. The Meaning of Mixing

    2.07.9. Conclusions

    2.08. Genetic Engineering


    2.08.1. Introduction to Genetic Engineering

    2.08.2. Molecular Cloning and Recombinant DNA Technology

    2.08.3. Molecular Manipulations

    2.08.4. Cellular Manipulations

    2.09. Bio-Feedstocks


    2.09.1. Common Feedstocks

    2.09.2. Lignocellulose

    2.09.3. Use of Perennial Grasses

    2.10. Substrate Hydrolysis


    2.10.1. Introduction

    2.10.2. Substrate for Hydrolysis

    2.10.3. Physical Methods for Hydrolysis

    2.10.4. Chemical Methods for Hydrolysis

    2.10.5. Enzymatic Hydrolysis

    2.10.6. Concluding Remarks

    2.11. Medium Formulation and Development


    2.11.1. Introduction

    2.11.2. Medium Formulation

    2.11.3. Medium Optimization

    2.11.4. Genetic Algorithms

    2.11.5. Platforms for Medium Development

    2.12. Sterilization in Biotechnology


    2.12.1. Introduction

    2.12.2. Sterilization of Gases

    2.12.3. Sterilization of Liquids

    2.12.4. Sterilization of Small Equipment

    2.12.5. Sterilization of Large Equipment

    2.12.6. Validation of Sterilization

    2.12.7. Conclusions

    2.13. Inoculum Preparation



    2.13.1. Introduction

    2.13.2. Criteria for Inoculum Preparation for Fermentation Process

    2.13.3. Inoculum Development Process for Fermentation

    2.13.4. Monitoring Inoculum Development

    2.13.5. Transfer of Inoculum to the Fermentor Vessel or Scale-Up Process

    2.13.6. Inoculum Preparation for Antimicrobial Susceptibility Testing

    2.13.7. Measurement of Bacteria and Inoculum Preparation

    2.13.8. Inoculum Preparation for Viral Cultures

    2.13.9. Inoculum Preparation for Mammalian Cell Culture

    2.13.10. Inoculum for Immunization

    2.13.11. Conclusion

    2.14. Bioreactor Engineering



    2.14.1. Introduction

    2.14.2. Design and Types of Bioreactors

    2.14.3. Effects of Process Parameters on Biological Performances

    2.14.4. Bioreactor Operation Strategy

    2.14.5. Industrial Applications of Bioreactors

    2.14.6. Trends in Bioreactor Engineering

    2.15. Stirred Tank Bioreactors


    2.15.1. Introduction

    2.15.2. Mass and Energy Balances

    2.15.3. Kinetic Models

    2.15.4. Case in Study: Xanthan Gum Production

    2.16. Airlift Bioreactors


    2.16.1. Introduction

    2.16.2. Reactor Configurations

    2.16.3. Power Input

    2.16.4. Gas–Liquid Hydrodynamics

    2.16.5. Mass Transfer

    2.16.6. Heat Transfer

    2.16.7. Mixing

    2.16.8. Applications

    2.16.9. Conclusions

    2.17. Shake-Flask Bioreactors


    2.17.1. Introduction

    2.17.2. Specific Power Input in Shake Flasks

    2.17.3. Out-of-Phase Phenomena in Shake Flasks

    2.17.4. Maximum Energy Dissipation Rate in Shake Flasks

    2.17.5. Gas/Liquid Mass Transfer in Shake Flasks

    2.17.6. Baffled Shake Flasks

    2.17.7. Use of Engineering Parameters for Scale-Up from Shake Flask to Stirred-Tank Reactor

    2.17.8. Fed-Batch and Continuous Cultures in Shake Flasks

    2.17.9. Online Measuring Techniques in Shake Flasks

    2.18. Photobioreactors – Models of Photosynthesis and Related Effects


    2.18.1. Introduction

    2.18.2. The P–I Curve

    2.18.3. Mathematical Representation of Photosynthesis

    2.18.4. Modeling and Interpretation of Irradiance

    2.18.5. The Kinetic Model

    2.18.6. Modeling Photoacclimation

    2.18.7. Photosynthesis in the Bioreactor

    2.18.8. Simulated Illumination–Darkness Cycles

    2.18.9. Experimental Evaluation of Illumination–Darkness Cycles

    2.18.10. Conclusions

    2.19. Disposable Bioreactors


    2.19.1. Introduction

    2.19.2. Types of Single-Use Bioreactors with Disposable Bags

    2.19.3. Conclusions

    2.20. Membrane Bioreactors


    2.20.1. Introduction

    2.20.2. Basic Concepts in Membrane Bioreactors

    2.20.3. Membrane Bioreactors for Production and Separation of Bioactive Molecules

    2.20.4. Membrane Bioreactors for Bioartificial Organs and Engineered-Tissue Culture

    2.20.5. Conclusions

    2.21. Microbioreactors


    2.21.1. Introduction

    2.21.2. Microfluidic Devices

    2.21.3. Microbioreactors for Cell Culturing

    2.21.4. Enzymatic Microreactors

    2.21.5. Future Perspectives of Bioreactor Miniaturization

    2.22. Biofilters


    2.22.1. Introduction

    2.22.2. Types of Biofilters

    2.22.3. Filter Media

    2.22.4. Microorganisms

    2.22.5. Factors Affecting BF Performance

    2.22.6. Design

    2.23. Enzyme Bioreactors


    2.23.1. Introduction

    2.23.2. Forms of Enzymes Used in Enzyme Reactors

    2.23.3. Enzyme Reactors

    2.23.4. Design and Choice of Enzyme Reactors

    2.23.5. Novel Enzyme Reactors

    2.24. Immobilized Cell Bioreactors


    2.24.1. Introduction

    2.24.2. Immobilization of Microbial Cells

    2.24.3. Immobilized Cell Bioreactors: Configuration and Design Characteristics

    2.24.4. Mass Transfer and Biokinetics in Immobilized Cell Bioreactors

    2.24.5. Merits of Immobilized Cell Bioreactors

    2.24.6. Potential Drawbacks

    2.24.7. Concluding Remarks

    2.25. Bioreactors for Solid-State Fermentation


    2.25.1. Introduction

    2.25.2. Classification of SSF Bioreactors and Basic Principles of Operation

    2.25.3. Tray Bioreactors

    2.25.4. Packed-Bed Bioreactors

    2.25.5. Rotating-Drum and Stirred-Drum Bioreactors

    2.25.6. Forcefully Aerated Agitated Bioreactors

    2.25.7. Challenges Related to Changes Provoked by Microbial Growth

    2.25.8. Other Considerations

    2.25.9. Conclusion

    2.26. Bioreactors for Plant Cell Culture


    2.26.1. Introduction

    2.26.2. General Aspects of Plant Cells

    2.26.3. Various Types of Reactors for Plant Cell Culture

    2.26.4. Operation of Plant Cell Reactors

    2.26.5. Industrial Applications and Outlook for the Future

    2.26.6. Summary

    2.27. Bioreactors for Animal Cell Cultures


    2.27.1. Introduction

    2.27.2. Bioreactor Design

    2.27.3. Bioreactors for High Cell Density Cultures

    2.27.4. Automation of Cell Processing toward Clinical Application

    2.27.5. Concluding Remarks

    2.28. Bioreactors for Tissue Engineering



    2.28.1. Introduction

    2.28.2. Engineering Concepts in Tissue Mass Growth

    2.28.3. Reactor Designs for Tissue Engineering

    2.28.4. Noninvasive and Nondestructive Imaging Techniques to Monitor Bioreactor Tissue Cultures

    2.28.5. Conclusions

    2.29. Recombinant Technology


    2.29.1. Introduction

    2.29.2. Mammalian Expression Vectors

    2.29.3. Nonviral Gene Delivery

    2.29.4. Cells

    2.29.5. Host Cell Engineering

    2.29.6. Generation of Recombinant Cell Lines

    2.29.7. Transient Gene Expression

    2.29.8. Regulatory Issues

    2.30. Metabolic Regulation Analysis and Metabolic Engineering


    2.30.1. Introduction

    2.30.2. Metabolic Engineering Practice

    2.30.3. The Effect of Single-Gene Knockouts on the Metabolism

    2.30.4. Global Regulators in Relation to the Cultural Environment

    2.30.5. The Systems Biology Approach

    2.30.6. Conclusion

    2.31. Proteomics, Protein Engineering


    2.31.1. Introduction

    2.31.2. Mass Spectrometry-Based Proteome Profiling Techniques

    2.31.3. Current Advances in Protein Identification: Online and Microfluidic Proteomic Systems

    2.31.4. Current Challenges in Proteomics

    2.32. Heterologous Protein Expression


    2.32.1. Introduction

    2.32.2. Heterologous Protein Expression in Bacterial Cultures

    2.32.3. Heterologous Protein Expression in Yeast Culture

    2.32.4. Heterologous Protein Expression in Insect Cell Culture

    2.32.5. Heterologous Protein Expression in Mammalian Cell culture

    2.32.6. Heterologous Protein Expression in Plant Cell Culture

    2.32.7. Heterologous Protein Expression in Algal Cell Culture

    2.32.8. Heterologous Protein Expression in Moss Culture

    2.32.9. Heterologous Protein Expression in Cell-Free Systems

    2.32.10. Summary and Future Directions

    2.33. Biotransformations


    2.33.1. Introduction

    2.33.2. Enzymes versus Whole Cells

    2.33.3. Extremophiles as a Source of New Enzymes

    2.33.4. Biotransformations as a Source of Chiral Compounds

    2.33.5. Types of Reaction Systems

    2.33.6. Industrial Processes – Overview on Present and Prospective Trends

    2.34. Immobilized Enzymes


    2.34.1. Introduction

    2.34.2. What Are Immobilized Enzymes?

    2.34.3. Classification of Immobilized Enzymes

    2.34.4. Approaches toward Robust Immobilized Enzymes

    2.34.5. Engineering the Immobilized Enzymes

    2.34.6. Prospectives and Future Developments

    2.35. Immobilization Technology


    2.35.1. Introduction

    2.35.2. Strategies for Cell Immobilization

    2.35.3. Products Suitable for Immobilized Cells

    2.35.4. Immobilized-Cell Bioreactors

    2.35.5. Conclusions

    2.36. Immobilized Viable Cell Biocatalysts


    2.36.1. Introduction: Development and Main Application Fields of Immobilized Cell Cultures

    2.36.2. Original Motivation of Viable IC Technology

    2.36.3. Current Data on IC Physiology

    2.36.4. Proteomic Approach and Biofilm Phenotype

    2.36.5. Conclusion

    2.37. Fermentation Processes


    2.37.1. Introduction

    2.37.2. Microbial Growth and Stoichiometry

    2.37.3. Autocatalytic Nature of Microbial Growth

    2.37.4. Cell Yields

    2.37.5. Product Yields

    2.38. Fed-Batch Fermentation – Design Strategies


    2.38.1. Introduction

    2.38.2. Different Types of Fed-Batch Cultivations

    2.38.3. Applications of Fed-Batch Cultivation

    2.38.4. Control Techniques for Fed-Batch Fermentation

    2.38.5. Design of Specific Fed-Batch Cultivation Strategies Using the Mathematical Model of the System

    2.38.6. Model-Based Fed-Batch Cultivation Strategies

    2.38.7. Parameters Used to Control the Fed-Batch Fermentations

    2.38.8. Conclusion

    2.39. Continuous Operation


    2.39.1. Introduction

    2.39.2. Homogeneous System

    2.39.3. Heterogeneous Systems

    2.40. Multistage Continuous High Cell Density Culture


    2.40.1. Introduction

    2.40.2. Historical Background

    2.40.3. High Cell Density Culture

    2.40.4. Multistage Continuous HCDC

    2.40.5. Summary

    2.41. Integrated Production and Separation


    2.41.1. Introduction

    2.41.2. Integration Methodology for Reducing Process Step

    2.41.3. Cross-Sectional Technologies through Integration Methodology

    2.41.4. Separation Techniques for the Integration in Terms of Product Characteristics

    2.41.5. Bioreactor Configuration for the Integration of Production and Separation

    2.41.6. Techniques for ISPR

    2.41.7. Process Integration by Biotechnology

    2.41.8. Perspective for the Process Integration

    2.42. Product Recovery


    2.42.1. Introduction

    2.42.2. Historical Background

    2.42.3. Modular Unit Operations in Downstream Processing

    2.42.4. Integrated Unit Operations in Downstream Processing

    2.42.5. Product Purification

    2.42.6. Product Formulation and Stabilization

    2.42.7. Conclusion

    2.43. Membrane Systems and Technology


    2.43.1. Introduction

    2.43.2. Membrane Materials

    2.43.3. Membrane Configurations

    2.43.4. Characterization of Membranes

    2.43.5. Solute and Particle Deposition

    2.43.6. Membrane Cleaning

    2.43.7. Ultrafiltration and Microfiltration

    2.43.8. Membrane Bioreactors

    2.43.9. Membrane Chromatography

    2.43.10. Membrane Contactors

    2.43.11. Conclusion

    2.44. Cell Disruption


    2.44.1. Introduction

    2.44.2. Characteristics of the Microbial Cell Influencing Resistance to Disruption

    2.44.3. Approaches to Microbial Cell Disruption

    2.44.4. Large-Scale Cell Disruption Technologies

    2.44.5. Laboratory-Scale, and Developing, Cell Disruption Technologies

    2.44.6. Selective Product Release

    2.44.7. Pretreatment to Augment Product Release

    2.44.8. Integration of Biomass Formation and Product Release

    2.44.9. Integration of Product Release and Product Recovery and Purification

    2.44.10. Closing Remarks

    2.45. Autolysis of Yeasts


    2.45.1. Introduction

    2.45.2. Yeast Autolysis Mechanism

    2.45.3. Yeast Autolysis Compounds

    2.45.4. Conclusion

    2.46. Precipitation and Crystallization



    2.46.1. Introduction

    2.46.2. Solid–Liquid Equilibrium: Phase Diagrams

    2.46.3. Modeling of Solid–Liquid Equilibrium

    2.46.4. Crystallization of Proteins

    2.46.5. Developing a Protein Crystallization Process

    2.47. Adsorption and Chromatography


    2.47.1. Introduction

    2.47.2. Molecular Interactions in Adsorption

    2.47.3. Chromatographic Methods

    2.47.4. Theoretical Aspects of Adsorption and Chromatography

    2.47.5. Development of Adsorption and Chromatography

    2.47.6. Conclusions

    2.48. Modeling Chromatographic Separation


    2.48.1. Introduction

    2.48.2. Theoretical Background

    2.48.3. Models for Chromatography

    2.48.4. Case Studies

    2.48.5. Summary

    2.49. Aqueous Two-Phase Systems


    2.49.1. Introduction

    2.49.2. Theoretical Background

    2.49.3. Application of ATPSs for the Recovery of Biological Products

    2.49.4. Conclusions

    2.50. Foam Separations


    2.50.1. Introduction

    2.50.2. Applications of Foam Fractionation

    2.50.3. Mechanism of Foam Fractionation

    2.50.4. Design

    2.50.5. Process Intensification

    2.51. Drying


    2.51.1. Introduction

    2.51.2. Applications

    2.51.3. Traditional Drying Processes

    2.51.4. Other Drying Technologies

    2.51.5. Summary

    2.52. Chiral Separations


    2.52.1. General Introduction

    2.52.2. Crystallization

    2.52.3. Chromatography

    2.52.4. Capillary Electrophoresis

    2.52.5. Liquid–Liquid Extraction

    2.52.6. Membrane-Assisted Separations

    2.52.7. Inclusion Distillation and Precipitation

    2.53. Lab on a Chip – Future Technology for Characterizing Biotechnology Products



    2.53.1. Introduction

    2.53.2. Technology

    2.53.3. Components

    2.53.4. Applications

    2.53.5. Concluding Remarks

    2.54. Protein Refolding/Renaturation


    2.54.1. Introduction

    2.54.2. Inclusion Bodies

    2.54.3. Isolation and Purification of Inclusion Bodies

    2.54.4. Solubilization of Inclusion Bodies

    2.54.5. Mechanism of Protein Aggregation

    2.54.6. Renaturation of Denatured Protein

    2.54.7. Concluding Remarks

    2.55. Biogas Production


    2.55.1. Introduction

    2.55.2. Advantages of the AD Processes

    2.55.3. Microbiology of AD

    2.55.4. Factors Affecting the AD Process

    2.55.5. Types of Anaerobic Reactors

    2.55.6. Effect of Operational and Environmental Variations on AD

    2.55.7. Biogas Utilization

    2.55.8. Biogas Upgrading Methods

    2.55.9. Applications of AD Technology

    2.56. Purification Process Design and the Influence of Product and Technology Platforms


    2.56.1. Introduction

    2.56.2. Impurities

    2.56.3. Purification Unit Operations

    2.56.4. Purification Process Flow-Sheet Organization and Design

    2.56.5. Processing Platforms – Examples and Characteristics

    2.56.6. Conclusions

    2.57. The Proportion of Downstream Costs in Fermentative Production Processes


    2.57.1. Introduction

    2.57.2. Overview of literature data

    2.57.3. Conclusions

    2.58. Biorefinery Engineering



    2.58.1. Introduction

    2.58.2. Feedstock Availability

    2.58.3. Platform of Bioprocess Technologies

    2.58.4. Examples of Current Improvements of Key Biorefinery Processes

    2.58.5. Prospect

    2.59. Instrumentation and Analytical Methods

    2.59.1. Introduction

    2.59.2. Physical Process Parameters

    2.59.3. Cell Mass Measurements

    2.59.4. Analysis of Substrates and Products

    2.59.5. Miscellaneous Techniques

    2.59.6. Conclusions and Remarks

    2.60. Life Cycle Assessment in Biotechnology


    2.60.1. Introduction

    2.60.2. The Methodology of LCA

    2.60.3. LCA: Utility and Limitations

    2.60.4. Application of LCA in Food Biotechnology

    2.60.5. Application of LCA in Pharmaceutical Biotechnology

    2.60.6. Application of LCA in Biopolymers

    2.60.7. Application of LCA in Biofuels

    2.60.8. Application of LCA in Biodegradable Waste Management

    2.60.9. Some New Tendencies

    2.61. Metabolic Control



    2.61.1. Introduction

    2.61.2. Regulation of Biological Systems

    2.61.3. Control of Biological Systems

    2.61.4. Network Rigidity

    2.61.5. Biochemical Systems Theory

    2.61.6. Metabolic Control Analysis

    2.61.7. Determination of the Flux Control Coefficients

    2.61.8. In Vivo Applications

    2.61.9. Conclusion

    2.62. Fuzzy Control of Bioprocess


    2.62.1. Direct Inference of Process Variables

    2.62.2. Determination of Process Variables Based on Identification of Culture Phase

    2.62.3. Combination of Fuzzy Inference with Other Methods

    2.62.4. Conclusion

    2.63. Online Control Strategies



    2.63.1. Introduction

    2.63.2. Current Practice of Bioprocess Control

    2.63.3. Advanced Process Control Strategies

    2.63.4. Concluding Remarks

    2.64. Process Optimization


    2.64.1. Introduction

    2.64.2. Review of the Most Relevant Optimization Techniques

    2.64.3. Case Studies

    2.64.4. Conclusions

    2.65. Micro-Biochemical Engineering



    2.65.1. Introduction

    2.65.2. Overview of Micro-Biochemical Engineering

    2.65.3. Examples of Micro-Biochemical Engineering

    2.65.4. Future Challenges in Applying Micro-Biochemical Engineering

    2.65.5. Conclusions

    2.66. Sustainability


    2.66.1. Introduction

    2.66.2. About Sustainability

    2.66.3. Spatial and Temporal Dimensions of Sustainability

    2.66.4. Challenges of Sustainability

    2.66.5. Indicators of Sustainability

    2.66.6. Keys to Sustainable Development in Practice

    2.66.7. Biotechnology and Sustainability

    2.66.8. Renewable Resources and Energy

    2.66.9. Concluding Remarks

    2.67. Nanostructured Biocatalysts


    2.67.1. Introduction

    2.67.2. Nonaqueous Enzymatic Catalysis

    2.67.3. Enzymes in Nanostructures

    2.67.4. Preparation of Enzyme Nanogels

    2.67.5. Molecular Fundamentals of Enzyme Nanogels

    2.67.6. Potential Applications of Enzyme Nanogels as Biocatalysts

    2.67.7. Summary

    2.68. Aseptic Operations


    2.68.1. Introduction

    2.68.2. Design and Procedural Approaches to Minimizing Contamination

    2.68.3. Fermentation/Cell Culture Considerations

    2.68.4. Considerations for Purification and Formulation/Fill

    2.68.5. Validation and Verification

    2.68.6. Sterility Analysis and Culture Purity

    2.68.7. Summary

    2.69. Oxygen Mass Transfer in Bioreactors


    2.69.1. Introduction

    2.69.2. Effect of Various Parameters on Oxygen Mass Transfer

    2.69.3. Conclusions

    2.70. Cavitation in Biotechnology


    2.70.1. Introduction

    2.70.2. Reactor Designs

    2.70.3. Different Applications of Cavitation Concluding Remarks

    2.71. Flow Cytometry


    2.71.1. Introduction

    2.71.2. Description of the FC Technique

    2.71.3. Cell Viability and Functionality

    2.71.4. Applications to Industrial Bioprocesses

    2.71.5. Monitoring and Control of Biotransformations

    2.71.6. Theoretical Applications: Kinetic Modeling

    2.71.7. Devices of Practical Use and Automation of FC Equipments

    2.71.8. Conclusions

    2.72. Cleaning in Place


    2.72.1. Introduction

    2.72.2. Hygiene Agents

    2.72.3. Overview of CIP Systems

    2.72.4. Cleaning Principles

    2.72.5. Other Technological Aspects

    2.73. Ionic Liquids


    2.73.1. Introduction

    2.73.2. Applications of Enzymes in Ionic Liquids

    2.73.3. Environmental Impact of Ionic Liquids

    2.73.4. Conclusions

    2.74. Supercritical Fluids


    2.74.1. Introduction

    2.74.2. Pure Substances as Supercritical Fluids

    2.74.3. Properties of Supercritical Fluids

    2.74.4. Modifiers

    2.74.5. Solubility in a Supercritical Fluid

    2.74.6. Calculations to Predict Whether a Modifier Is Required

    2.74.7. Supercritical Fluid Extraction

    2.74.8. Supercritical Fluid Chromatography

    2.74.9. Supercritical Fluid Particle Engineering

    2.74.10. Supercritical Fluid Tissue Engineering and Regenerative Medicine

    2.74.11. Supercritical Fluids as Alternative Enzymatic Reaction Solvents

    2.74.12. Sterilization Using SF-CO2

    2.74.13. Critical Point Drying of Biological Samples

    2.74.14. Summary

    2.75. Computational Fluid Dynamics



    2.75.1. Introduction

    2.75.2. Fundamentals

    2.75.3. Single-Phase Flow Simulations

    2.75.4. Multiphase Flow Simulations

    2.75.5. CFD in Biochemical Engineering

    2.75.6. Conclusions and Future Perspectives

    3.01. Introduction


    3.02. Industrial Enzymes


    3.02.1. Introduction

    3.02.2. Protease

    3.02.3. Lipase

    3.02.4. Amylase

    3.02.5. Pullulanases

    3.02.6. Pectinases

    3.02.7. Xylanase

    3.02.8. Laccases

    3.02.9. Transglutaminases

    3.02.10. Phytase

    3.02.11. Perspective

    3.03. Multifunctional Enzyme Systems for Plant Cell Wall Degradation



    3.03.1. Introduction

    3.03.2. Diversity of Multifunctional Enzymes

    3.03.3. Inter- and Intra Molecular Synergism

    3.03.4. Intra Molecular Synergism: Clues from Three-Dimensional Structures

    3.03.5. Artificial Chimeras

    3.03.6. Future Perspective

    3.04. Ethanol Production from Sugar-Based Feedstocks


    3.04.1. Introduction

    3.04.2. Feedstocks

    3.04.3. Land Availability Scenarios

    3.04.4. Feedstock Processing for Ethanol

    3.04.5. Conclusions

    3.05. Ethanol from Starch-Based Feedstocks


    3.05.1. Introduction

    3.05.2. Biochemistry of the Ethanol Process

    3.05.3. Yeasts Used in the Process

    3.05.4. Unit Operations Relevant to Ethanol Production

    3.05.5. Environmental Requirements in Fermentation

    3.05.6. Yield Coefficient and Net Rate Expression

    3.05.7. Metabolic Flux Analysis

    3.05.8. Summary

    3.06. Biofuels from Cellulosic Feedstocks


    3.06.1. Introduction

    3.06.2. Cellulosic Biomass

    3.06.3. Conversion of Cellulosic Biomass into Ethanol

    3.06.4. Development of Microorganisms for Fermenting Cellulosic Biomass Hydrolyzates to Ethanol

    3.06.5. Conclusions

    3.07. Biodiesel


    3.07.1. Introduction

    3.07.2. Pyrolysis or Thermal Cracking

    3.07.3. Microemulsions

    3.07.4. Transesterification – Conventional Methods

    3.07.5. Transesterification – Supercritical Fluids

    3.07.6. Transesterification – Enzymatic

    3.07.7. Nonedible Oils as Potential Substrates

    3.07.8. Packed-Bed Reactors Containing Whole-Cell Biocatalysts

    3.07.9. Conclusion and Future Prospects

    3.08. Biofuels and Bioenergy


    3.08.1. Introduction

    3.08.2. History

    3.08.3. Microorganisms

    3.08.4. Metabolic Pathway of Acetone and Butanol Formation

    3.08.5. Genetic Engineering

    3.08.6. Systems Biology

    3.08.7. Fermentation

    3.08.8. Development of Fermentation Technology

    3.09. Microbial Production of 2,3-Butanediol


    3.09.1. Introduction

    3.09.2. Properties and Applications of 2,3-Butanediol

    3.09.3. Microorganisms Producing 2,3-Butanediol

    3.09.4. Metabolic Pathway and Pathway Engineering

    3.09.5. Fermentation of 2,3-Butanediol

    3.09.6. Recovery of 2,3-Butanediol

    3.09.7. Summary and Future Prospects

    3.10. Biogas


    3.10.1. Introduction

    3.10.2. Fundamentals

    3.10.3. AD Process

    3.10.4. Application of Biogas Technology

    3.10.5. Utilization of Biogas

    3.10.6. Perspectives

    3.11. Biohydrogen


    3.11.1. Introduction

    3.11.2. Biophotolysis of Water

    3.11.3. Photofermentation by Photosynthetic Bacteria

    3.11.4. Dark Fermentation

    3.11.5. CO Gas Fermentation

    3.11.6. Closing Remarks

    3.12. Biofuel from Microalgae


    3.12.1. Introduction and Scope

    3.12.2. Major Algal Composition

    3.12.3. Different Types of Biofuels from Microalgae

    3.12.4. Algal Biodiesel Production Pipeline

    3.12.5. Conclusion and Perspectives

    3.13. Citric Acid


    3.13.1. Introduction and Scope

    3.13.2. Properties and Applications of Citric Acid

    3.13.3. Historical Background of Citric Acid Production

    3.13.4. Microorganisms and Biosynthesis of Citric Acid

    3.13.5. Factors Affecting Citric Acid Production by A. niger

    3.13.6. Fermentation Processes for Citric Acid Production

    3.13.7. Product Recovery

    3.13.8. Perspectives for the Future

    3.14. Gluconic and Itaconic Acids


    3.14.1. Introduction and Scope

    3.14.2. d-Gluconic Acid

    3.14.3. Itaconic Acid

    3.14.4. Perspectives for Future

    3.15. Organic Acids



    3.15.1. Introduction

    3.15.2. Succinic Acid Production

    3.15.3. Use of Succinic Acid and Its Derivatives

    3.15.4. Malic Acid Production

    3.15.5. Malic Acid and Its Applications

    3.15.6. Conclusion

    3.16. Fumaric Acid



    3.16.1. Introduction

    3.16.2. Properties and Applications

    3.16.3. Industrial Production Methods

    3.16.4. Fumaric Acid Fermentation Microbiology

    3.16.5. Fermentation Process Development and Optimization

    3.16.6. Conclusion and Future Prospects

    3.17. Industrial Production of Lactic Acid


    3.17.1. Introduction

    3.17.2. General Characteristics of Lactic Acid

    3.17.3. Biological Production of Lactic Acid

    3.17.4. The Cargill Yeast

    3.17.5. Fermentation Carbon Sources

    3.17.6. Purification of Lactic Acid from Fermentation Broth

    3.17.7. An Emergent Commercial Application of Lactic Acid: PLA

    3.18. Acetic and Propionic Acids



    3.18.1. Introduction

    3.18.2. Properties and Applications of Acetic and Propionic Acids

    3.18.3. Microbiology of Acetic Acid Fermentation

    3.18.4. Product Recovery and Purification

    3.18.5. Summary

    3.19. Acrylic Acid



    3.19.1. Introduction

    3.19.2. Process Development

    3.19.3. Proposed Novel Biosynthetic Pathways and Industrial Production Process

    3.19.4. Summary

    3.20. Butyric Acid



    3.20.1. Introduction

    3.20.2. Properties and Uses of Butyric Acid

    3.20.3. Fermentation of Butyric Acid

    3.20.4. Fundamentals and Molecular Manipulation

    3.20.5. Product Recovery

    3.20.6. Summary

    3.21. PHA/PHB


    3.21.1. Introduction

    3.21.2. Production of PHA/PHB by Wild-Type Microorganisms

    3.21.3. PHA Production by Metabolically Engineered Microorganisms

    3.21.4. Applications of PHA/PHB

    3.22. 1,3-Propanediol and Polytrimethyleneterephthalate


    3.22.1. Introduction

    3.22.2. Polytrimethyleneterephthalate

    3.22.3. Properties and Uses of PDO

    3.22.4. Metabolic Pathways and Engineering of PDO Formation

    3.22.5. Fermentation Conditions and Operation Modes

    3.22.6. Recovery and Purification of PDO

    3.22.7. Production Costs and Biorefinery Concept

    3.22.8. Conclusion and Perspectives

    3.23. Antibiotics


    3.23.1. Introduction

    3.23.2. The Miracle of Antibiotics

    3.23.3. The Golden Era of Antibiotic Discovery

    3.23.4. Microbial Genomics and the Failure of Antibiotic Discovery Research

    3.23.5. Medical Need, Antimicrobial Resistance, and the Anti-Infective Marketplace

    3.23.6. The Regulatory Environment for Antibacterials

    3.23.7. Large Pharmaceutical Companies Exit and Biotechnology Enters

    3.23.8. Conclusions

    3.24. Penicillins and Cephalosporins


    3.24.1. Introduction to Penicillins and Cephalosporins

    3.24.2. Structure and Mechanism of Action of Penicillins and Cephalosporins

    3.24.3. Penicillin and Cephalosporin Biosynthesis

    3.24.4. Biotechnological Implications in the Biosynthesis of Penicillins and Cephalosporins

    3.24.5. Future Outlook

    3.25. Tetracyclines and Tetracycline Derivatives


    3.25.1. Introduction and Scope

    3.25.2. Tetracycline Generations and Origins

    3.25.3. First-Generation Tetracyclines

    3.25.4. Antibacterial Uses of the Tetracyclines

    3.25.5. First- and Second-Generation Tetracyclines and Their Semisynthetic Modifications

    3.25.6. Semisynthesis of Third-Generation Tetracyclines: Derivatives of Minocycline, Sancycline, and Doxycycline

    3.25.7. Tetracycline Antibacterial Quantitative Structure-Activity Relationships (QSAR)

    3.25.8. Antibacterial and General Chemical Properties of the Tetracyclines: Uptake and Membrane Activity

    3.25.9. Mechanism of Action and Antibacterial Activity

    3.25.10. Conclusions

    3.26. Microbial Secondary Metabolites


    3.26.1. Introduction

    3.26.2. Source of Bioactive Microbial Secondary Metabolites

    3.26.3. Overview of Bioactivities

    3.26.4. Microbial Product Screening

    3.26.5. Production Processes

    3.26.6. Examples of Successful Secondary Metabolites

    3.26.7. Conclusions

    3.27. Plant Secondary Metabolites



    3.27.1. Plants and Secondary Metabolites

    3.27.2. Heterogeneity of Plant Secondary Metabolites

    3.27.3. Secondary Metabolite Production by Plant Cell Culture

    3.27.4. Signal Transduction Engineering for Enhancing Secondary Metabolite Production

    3.27.5. Modulation of Secondary Metabolic Pathway

    3.27.6. Conclusions and Perspectives

    3.28. Biocatalyzed Production of Fine Chemicals


    3.28.1. Introduction

    3.28.2. Preparation of Fine Chemicals from Renewable Raw Materials

    3.28.3. Whole Cell-Catalyzed Synthesis of Fine Chemicals

    3.28.4. Enzyme-Catalyzed Production of Fine Chemicals

    3.29. Production of Recombinant Proteins by Microbes and Higher Organisms


    3.29.1. Introduction

    3.29.2. Enzyme Production

    3.29.3. Systems for Producing Recombinant Proteins

    3.29.4. Conclusions

    3.30. Vaccines


    3.30.1. Introduction

    3.30.2. Smallpox Vaccine and Other Vaccines of the Nineteenth Century

    3.30.3. The Importance of Vaccines

    3.30.4. Milestones in Vaccine Technology

    3.31. Manufacturing Recombinant Proteins in kg-ton Quantities Using Animal Cells in Bioreactors


    3.31.1. Introduction

    3.31.2. Generation of CHO-Derived Cell Lines

    3.31.3. Improved Recovery of High-Producing Cell Lines

    3.31.4. High-Throughput Bioprocess Development

    3.31.5. Disposable Bioreactors

    3.31.6. Transient Gene Expression

    3.31.7. Conclusions

    3.32. Recent and Emerging Trends and Concerns Related to the Manufacturing and Testing of Monoclonal Antibodies Intended for Clinical Use


    3.32.1. Introduction

    3.32.2. Characterization of mAb Quality Attributes

    3.32.3. QbD/Design Space

    3.32.4. New and Emerging Antibody-Related Products

    3.32.5. Engineering Enhanced mAb Domain Functionality

    3.32.6. Emerging Product Quality Concerns

    3.32.7. Comparability Considerations

    3.32.8. New Analytics

    3.32.9. Platform Technologies

    3.32.10. Emerging Chemistry, Manufacturing and Controls Technology

    3.32.11. Conclusion

    3.33. Therapeutic Enzymes and Biomimetic Substrates


    3.33.1. Introduction

    3.33.2. Nomenclature

    3.33.3. Enzyme Kinetics

    3.33.4. Substrate Considerations

    3.33.5. Complex Heterodisperse Natural Substrates

    3.33.6. Application of Cell-Based Activity Assays to Qualification of Non-Biomimetic Substrates

    3.33.7. Conclusions

    3.34. Cell-Free Production of Pharmaceutical Proteins


    3.34.1. Introduction

    3.34.2. Types of Cell-Free Systems

    3.34.3. Advantages of Cell-Free Protein Production

    3.34.4. Challenges with Cell-Free Protein Production

    3.34.5. Small-Scale Applications

    3.34.6. Novel Pharmaceutical Product Opportunities

    3.34.7. Large-Scale Considerations

    3.34.8. Summary

    3.35. Combination Products Are Not Solely Biological Products, Drugs, or Devices



    3.35.1. Introduction and Definitions

    3.35.2. FDA’s Organization and the Office of Combination Products

    3.35.3. Request for Designation, Primary Mode of Action, and Assignment of Jurisdiction

    3.35.4. How Things Work – Differences in Processes between Centers

    3.35.5. How Things Work – Similarities in Processes between Centers

    3.35.6. The Future

    3.35.7. Conclusions

    3.36. Cellular Therapies


    3.36.1. Introduction

    3.36.2. Sources of Cells and Clinical Applications of Cell Therapy

    3.36.3. Cell-Based Products for Reconstructive or Structural Repair

    3.36.4. Cellular Vaccines

    3.36.5. Adoptive Cell Therapies

    3.36.6. Stem Cell-Derived Therapies

    3.36.7. Cell Isolation and Processing Methods

    3.36.8. Summary

    3.37. Gene Therapies


    3.37.1. Introduction and Scope

    3.37.2. Current Status of Gene Therapy Products in Commerce and Clinical Development

    3.37.3. Challenges Pertinent to the Development of Gene Therapy Products

    3.37.4. Regulatory Issues and Standardization Activities Pertinent to Gene Therapy Products

    3.37.5. Manufacturing of Gene Therapy Products

    3.37.6. Vectors Employed in Gene Therapy Products

    3.37.7. Manufacturing and Purification Strategies

    3.37.8. Product Characterization

    3.37.9. Process Validation

    3.37.10. Product Administration of Gene Therapy Products

    3.37.11. Conclusion

    3.38. Regulatory Aspects of Chemistry Manufacturing and Controls for Investigational New Drug Applications and Biologic License Applications to the United States Food and Drug Administration


    3.38.1. Introduction

    3.38.2. IND Applications

    3.38.3. Biologic License Application

    3.38.4. Comparability Testing

    3.38.5. Communication with the FDA from Pre-IND through Licensure

    3.38.6. Conclusions

    3.39. Raw Materials in the Manufacture of Biotechnology Products


    3.39.1. Introduction: Raw Materials in the Biotechnology Industry

    3.39.2. Regulations on Raw Materials

    3.39.3. Considerations on Raw Materials

    3.39.4. Impact of the Quality of the Raw Material on the Quality of the Final Biotechnology Product

    3.39.5. Control of the Quality of Raw Materials

    3.39.6. Life Cycle of a Raw Material in Biotechnology Products

    3.39.7. Management of Raw Materials in the Context of ICH Guidelines

    3.39.8. Controlling the Risk of Introducing Raw Materials

    3.39.9. Future Directions

    3.40. Characterization of Biotechnological/Biological/Biosimilar Products


    3.40.1. Assessment of Product Characteristics

    3.40.2. Biotechnology Product Characterization, Comparability, Release, and Stability Tool Kits

    3.40.3. Selection of Analytical Methods

    3.40.4. Analytical Method Lifecycle Issues

    3.40.5. Conclusions

    3.41. Protein Glycosylation


    3.41.1. Introduction

    3.41.2. Analysis of Intact Glycoproteins and Glycopeptides

    3.41.3. Analysis of Free Glycans

    3.41.4. Analysis of Monosaccharides

    3.41.5. Glycan Analysis Design for Therapeutic Glycoproteins

    3.42. Immunogenicity Assay Development and Validation


    3.42.1. Introduction

    3.42.2. Development of Binding Antibody Methods

    3.42.3. Validation of Binding Antibody Methods

    3.42.4. Development of NAb Methods

    3.42.5. Validation of NAb Methods

    3.42.6. Practical Considerations and Recommendations

    3.42.7. Concluding Remarks

    3.43. Process Analytical Technology in Bioprocess Development and Manufacturing


    3.43.1. Introduction and Scope

    3.43.2. PAT Tools

    3.43.3. Concluding Remarks

    3.44. Process Validation


    3.44.1. Introduction and Scope

    3.44.2. General Requirements and Considerations

    3.44.3. Process Knowledge

    3.44.4. Validation of the Commercial Process

    3.45. Follow-On Protein Products


    3.45.1. Introduction

    3.45.2. Unique challenges associated with protein products

    3.45.3. Impact of the manufacturing process on product quality

    3.45.4. Impact of product quality on clinical performance

    3.45.5. Conclusions

    3.46. Amino Acid Production


    3.46.1. Introduction

    3.46.2. Microbial Production

    3.46.3. Enzymatic Production

    3.46.4. Future Prospects

    3.47. Lysine



    3.47.1. Introduction

    3.47.2. Biological Properties and Applications of d-Lysine, ε-Poly-l-Lysine, and l-Lysine

    3.47.3. History of Industrial l-Lysine Production

    3.47.4. Different Commercial Production Methods for l-Amino Acids

    3.47.5. Fermentation Is the Dominant Method for Industrial l-Lysine Production

    3.47.6. The l-Lysine Biosynthetic Pathway from Aspartate

    3.47.7. Metabolic Engineering of C. glutamicum for l-Lysine Overproduction

    3.47.8. Alternative Raw Materials and Production Strains for l-Lysine Production

    3.47.9. Conclusions and Perspectives

    3.48. Food-Grade Enzymes



    3.48.1. Introduction

    3.48.2. Sources of Food-Grade Enzymes

    3.48.3. Food-Grade Enzymes Targeted at Processing

    3.48.4. Food-Grade Enzymes Targeted at Preservation

    3.48.5. Production of Food-Grade Enzymes

    3.48.6. Recovery of Food-Grade Enzymes

    3.48.7. Polishing of Food-Grade Enzymes

    3.48.8. Safety Concerns with Food-Grade Enzymes

    3.49. Proteases


    3.49.1. Introduction

    3.49.2. Protease Types

    3.49.3. Principal Industrial Sources/Production Processes

    3.49.4. Principal Applications of Proteases

    3.49.5. Protease Inhibitors

    3.50. Application of Enzymes and Microbes for the Industrial Production of Vitamins and Vitamin-Like Compounds


    3.50.1. Introduction and Scope

    3.50.2. Riboflavin – Vitamin B2

    3.50.3. Niacin – Vitamin B3

    3.50.4. R-Pantothenic Acid and R-Panthenol – Vitamin B5 and Provitamin B5

    3.50.5. Biotin – Vitamin B7

    3.50.6. Cobalamin – Vitamin B12

    3.50.7. l-Ascorbic Acid – Vitamin C

    3.50.8. Phylloquinones and Menaquinones – Vitamin K

    3.50.9. Coenzyme Q10

    3.50.10. Pyrroloquinoline Quinone

    3.50.11. l-Carnitine

    3.50.12. Outlook

    3.51. Fungal Biotechnology in Food and Feed Processing


    3.51.1. Introduction

    3.51.2. Use of Fungi in Dietary Food

    3.51.3. Use of Fruiting Body

    3.51.4. Fungi as and in Processed Food

    3.51.5. Processed Fungal Food as an Alternative to SCPs

    3.51.6. Use of Enzymes in Food and Feed Bioprocessing

    3.51.7. Fungal Enzymes Used in Feed

    3.51.8. Commercial Recombinant Enzymes from Fungi

    3.51.9. Secondary Metabolites from Fungi used in Food and Feed

    3.51.10. Pharmaceutical and Nutraceutical Byproducts from Fungi

    3.51.11. Symbiotic Fungus Termitomyces: A Filamentous Basidiomycota

    3.51.12. Termitomyces clypeatus: An Edible Fungus and Producer of Enzymes

    3.51.13. Bioprocessing of Food by T. clypeatus

    3.51.14. Concluding Remarks and Future Prospects

    3.52. Metabolic Engineering


    3.52.1. Introduction: Evolution of Metabolic Engineering

    3.52.2. Biological Systems

    3.52.3. Desired Products

    3.52.4. Engineering Strategies

    3.52.5. Future Perspectives

    3.53. Synthetic Biology


    3.53.1. Introduction

    3.53.2. Historical Foundation

    3.53.3. Foundational Research and Development

    3.53.4. Enabling Technologies

    3.53.5. Research and Education

    3.53.6. Applications of Synthetic Biology

    3.53.7. Regulatory Debate

    3.53.8. Synbioethics

    3.53.9. Intellectual Property

    3.53.10. Looking Ahead

    3.54. Industrial Biotechnology and Commodity Products


    3.54.1. Introduction

    3.54.2. Upstream Activities

    3.54.3. Downstream Activities

    3.54.4. General Components

    3.54.5. Future Designs and Facility Layouts

    3.55. Bioreactors for Commodity Products


    3.55.1. Introduction

    3.55.2. Classifications of Bioreactors

    3.55.3. Types of Bioreactors

    3.55.4. Bioreactors and Sustainability

    3.56. Integrating Process Scouting Devices (PSDs) With Bench-Scale Devices


    3.56.1. Introduction

    3.56.2. Process Scouting Devices Challenges

    3.56.3. Integrating PSDs with Bench-Scale Devices by Developing a Scale-Up Strategy

    3.56.4. Types of Process Scouting Devices

    3.56.5. Future Developments

    3.56.6. Conclusion

    3.57. Overview of Downstream Processing in the Biomanufacturing Industry


    3.57.1. Introduction and Scope

    3.57.2. Principles of DSP

    3.57.3. Clarification Methods in DSP

    3.57.4. Chromatography for Product Capture and Polishing

    3.57.5. Filtration Methods Used in Product Purification and Formulation

    3.57.6. Crystallization as a Low-Technology Polishing Method

    3.57.7. Current Trends in the Biomanufacturing Industry

    3.58. Nanotechnology


    3.58.1. Introduction

    3.58.2. Types of Nanotechnology

    3.58.3. Bionanotechnology and Nanobiotechnology

    3.58.4. Nanotechnology at the Biological Interface

    3.59. Biosurfactants


    3.59.1. Introduction

    3.59.2. General Aspects

    3.59.3. Applications

    3.59.4. Perspectives and Future Development

    3.59.5. Perspectives for Future Development

    3.60. Bioleaching and Biomining for the Industrial Recovery of Metals


    3.60.1. Introduction

    3.60.2. Microorganisms Involved in Biomining

    3.60.3. Industrial Biomining of Ores

    3.60.4. Environmental Impact of Biomining Activities

    3.60.5. Microbial Metal Solubilization Mechanisms

    3.60.6. Importance of Molecular Biology Studies in Metal Extraction

    3.60.7. Perspectives

    3.61. Biological Control


    3.61.1. Introduction

    3.61.2. Biological Control

    3.61.3. Biopesticides Classification

    3.61.4. Biopesticide Categories

    3.61.5. Biological Control of Aflatoxin Contamination of Crops

    3.61.6. Use of Genetic-Engineering Technology

    3.61.7. Engineering Biological Control Agents

    3.61.8. Integrated Pest Management

    3.61.9. Market

    3.61.10. Conclusion

    4.01. Introduction

    4.02. Plant Biotechnology and GMOs


    4.02.1. Introduction

    4.02.2. The Need for New Agricultural Crops

    4.02.3. The Answer to Twentieth-Century Food Production Problems

    4.02.4. The Adoption of GM Crops

    4.02.5. The Second Generation of GM Crops

    4.02.6. The Future of Agricultural Biotechnology

    4.03. Bioactivity of Herbicides


    4.03.1. Introduction

    4.03.2. Biochemical Pathways and Physiological Processes Involved with Photosynthesis

    4.03.3. Formation of Biological Building Blocks and Their Assembly into Biopolymers

    4.03.4. Other Modes of Action

    4.03.5. Parting Comments

    4.04. Starch Biosynthesis in Higher Plants


    4.04.1. Introduction

    4.04.2. Overview of Starch Structure

    4.04.3. Granule Initiation

    4.04.4. Control of Starch Granule Size

    4.04.5. Starches with Improved Functionalities

    4.04.6. Amylose-Free Starches

    4.04.7. High-Amylose Starches

    4.04.8. Prospects for Altering Amylopectin Structure

    4.04.9. Other Functional Properties

    4.05. Starch Biosynthesis in Higher Plants


    4.05.1. Introduction

    4.05.2. Origins

    4.05.3. The Pathway of Starch Biosynthesis

    4.05.4. The Formation of ADP-glucose by ADP-glucose Pyrophosphorylase

    4.05.5. Glucan Chain Formation by Starch Synthases

    4.05.6. Amylose Biosynthesis

    4.05.7. Amylopectin Biosynthesis

    4.05.8. Starch Synthase I

    4.05.9. Starch Synthase II

    4.05.10. Starch Synthase III

    4.05.11. Starch Synthase IV

    4.05.12. Branching of the Glucan Chain

    4.05.13. The Role of Debranching Enzymes in Amylopectin Synthesis

    4.05.14. Other Enzymes Implicated in the Pathway of Starch Biosynthesis

    4.05.15. Coordination of Enzyme Activities during Starch Granule Synthesis

    4.05.16. Starch Granule Proteins

    4.05.17. Summary and Future Prospects

    4.06. Metabolic Engineering of Higher Plants to Produce Bio-Industrial Oils



    4.06.1. Introduction

    4.06.2. Plant Storage Lipids

    4.06.3. Industrial Uses of Plant Oils

    4.06.4. Seed Oil Biosynthesis

    4.06.5. Oils for Biodiesel Production

    4.06.6. High-Oleic Acid Oils

    4.06.7. Oils Enriched in VLCFAs

    4.06.8. Oils for the Detergent Industry

    4.06.9. Increasing Functionality: FA Modification in Membrane Lipids

    4.06.10. Increasing Seed Oil Content and Producing Oil in Vegetative Tissue

    4.06.11. Platform Crops for Industrial Oil Production

    4.06.12. Potential for Wax-Based Industrial Lipids

    4.06.13. Closing Comments

    4.07. Biodiesel – An Integrated Approach for a Highly Efficient Biofuel


    4.07.1. Overview of the Need and Potential

    4.07.2. Biodiesel Feedstocks

    4.07.3. Genetic Improvement of Feedstock Crop Plants

    4.07.4. Low-Input Production Systems for Feedstock Crops

    4.07.5. Conversion of Oils to Biodiesel

    4.07.6. Pyrolysis – An Alternative

    4.07.7. Fuel Quality and Use in Engines

    4.07.8. Conclusions

    4.08. Matching Crops for Selected Bioproducts


    4.08.1. Introduction

    4.08.2. Biopolymers and Biofiber Composites

    4.08.3. Manufacturing Bioproducts

    4.08.4. Applications of Bioproducts

    4.08.5. Recent Developments and Concluding Remarks

    4.08.6. Acknowledgments

    4.09. Nanotechnologies for Agricultural Bioproducts


    4.09.1. Introduction

    4.09.2. Agricultural Bioproducts

    4.09.3. Nanotechnologies for Agricultural Bioproducts

    4.09.4. Potential Applications and Future Prospects

    4.09.5. Conclusions

    4.10. Transgenic Crops with Producer-Oriented Traits


    4.10.1. Introduction

    4.10.2. Case Study 1 – Herbicide-Tolerant Crops: Roundup Ready Soybean

    4.10.3. Case Study 2 – Insect-Tolerant Crops: Bt Maize

    4.10.4. Case Study 3 – Virus-Tolerant Crops: Papaya

    4.10.5. Case Study 4 – Hybridization Systems: Canola

    4.10.6. The Role of Biotechnology in Future Crop Improvement: The Next Wave

    4.11. Plant Genetic Techniques


    4.11.1. Introduction

    4.11.2. Doubled Haploids

    4.11.3. Molecular Markers

    4.11.4. Quantitative Trait Loci

    4.11.5. Strengths and Weaknesses of LD Mapping

    4.11.6. Marker-Assisted Breeding

    4.11.7. Conclusions and Perspectives on Using DH and Molecular Markers in Plant Breeding

    4.12. Plant Bioinformatics and Microarray Technologies


    4.12.1. Introduction

    4.12.2. Transcriptional Profiling with a Focus on Microarrays

    4.12.3. Identifying Differentially Expressed Genes across Treatments

    4.12.4. Identifying Shared Patterns among Genes and Samples

    4.12.5. Conclusion and Future Directions

    4.13. Increasing Photosynthesis/RuBisCO and CO2-Concentrating Mechanisms



    4.13.1. Introduction

    4.13.2. Improvement of RuBisCO’s Enzymatic Properties

    4.13.3. Engineering Regulation of RuBisCO Activation

    4.13.4. Increasing CO2 Concentration in the Vicinity of RuBisCO

    4.13.5. Conclusions

    4.14. Photosynthesis and Productivity of Vascular Plants in Controlled and Field Environments


    4.14.1. Introduction

    4.14.2. Leaf Source Strength

    4.14.3. Whole-Plant Traits Relating to Source and Sink Strength

    4.14.4. Optimizing Photosynthesis and Productivity in Controlled and Field Environments

    4.14.5. Conclusions

    4.15. Roles of Dark Respiration in Plant Growth and Productivity


    4.15.1. Introduction

    4.15.2. Genetic Modification of Glycolytic Enzymes

    4.15.3. Genetic Modification of OPPP Enzymes

    4.15.4. Genetic Modification of TCA Cycle Enzymes

    4.15.5. Genetic Modification of Aerobic Respiratory Pathway Enzymes

    4.15.6. Genetic Modification of Anaerobic Respiratory Enzymes

    4.15.7. Conclusion

    4.16. Improving Plant Nitrogen-Use Efficiency


    4.16.1. Introduction

    4.16.2. What Is NUE?

    4.16.3. Agronomic Approaches for Improving NUE

    4.16.4. Transgenic Efforts to Improve NUE

    4.16.5. Quantitative Trait Loci Mapping to Find New Targets for Manipulation

    4.16.6. Improving NUE: A Systems Biology Approach

    4.16.7. Global Status of NUE

    4.17. Circadian Clocks/Photoperiodism and Crop Quality


    4.17.1. Introduction and Scope

    4.17.2. Introduction to Biological Rhythms and the Plant Circadian Clock

    4.17.3. The Genetic and Molecular Nature of the Plant Circadian Clock in the Model Plant Species A. thaliana

    4.17.4. Plant Processes Regulated by the Circadian Clock

    4.17.5. Adaptive Significance of Plant Circadian Rhythms

    4.17.6. Photoperiodism and the Plant Circadian Clock

    4.17.7. Manipulation of Photoperiod-Sensitive Reproductive and Vegetative Organ Initiation in Crop Plants

    4.17.8. Abiotic and Biotic Stress Tolerance and the Plant Circadian Clock

    4.17.9. Photosynthetic Carbon Metabolism

    4.17.10. Nitrogen Acquisition and Assimilation

    4.17.11. Conclusions

    4.18. Breadfruit


    4.18.1. Introduction: Breadfruit (Artocarpus altilis)

    4.18.2. Traditional Propagation of Breadfruit

    4.18.3. Advantages of Micropropagation of Breadfruit

    4.18.4. Micropropagation and Bioreactor Production of Breadfruit

    4.18.5. Conclusions

    4.19. Wines


    4.19.1. Introduction

    4.19.2. Grape Cultivars

    4.19.3. Grape-Growing Regions of the World

    4.19.4. Grape and Wine Genomics

    4.19.5. Genetically Modified Yeasts for Wine Production

    4.19.6. GMO Grapevines and Fermentation Organisms in Grape and Wine Production

    4.20. Sulfur Metabolism in Plants and Related Biotechnologies


    4.20.1. Introduction

    4.20.2. Sulfur Metabolism

    4.20.3. Sulfur-Containing Secondary Metabolite in Plants/Microbes and Their Importance/Role

    4.20.4. Biotechnology Based on Sulfur Metabolism

    4.20.5. Conclusion and Future Challenges

    4.21. Emerging Roles for Plant Terpenoids


    4.21.1. Introduction to Plant Terpenoids and Scope

    4.21.2. Carotenoids and Apocarotenoid Products

    4.21.3. Isoprene Emission

    4.21.4. Menthol

    4.21.5. Taxol

    4.21.6. Iridoid Glycosides

    4.21.7. Conclusions

    4.22. Antibody Production in planta


    4.22.1. Introduction

    4.22.2. Antibody Expression in planta

    4.22.3. Purification of Plant-Derived Antibodies

    4.22.4. Applications of Plant-Derived Antibodies

    4.22.5. Conclusion

    4.23. Microalgae as Bioreactors for Production of Pharmaceutical Proteins



    4.23.1. Introduction

    4.23.2. C. reinhardtii as Protein Expression Platforms

    4.23.3. Pharmaceutically Relevant Proteins Produced in Transplastomic C. reinhardtii

    4.23.4. Chlamydomonas Chloroplast Expression Systems and Strategies to Increase Recombinant Protein Expression

    4.23.5. Conclusions

    4.24. Algal Chemostats


    4.24.1. Introduction

    4.24.2. Chemostat Design

    4.24.3. Limiting Nutrients

    4.24.4. Multiple-Organism Studies

    4.24.5. Product Technology Using Chemostats

    4.24.6. Toxin Studies Using Chemostats

    4.24.7. Chemostats in Algal Symbiont Studies

    4.24.8. Ecostats

    4.25. Improvement of Ginseng by In Vitro Culture



    4.25.1. Introduction

    4.25.2. Plant Growth Characteristics

    4.25.3. Micropropagation

    4.25.4. In Vitro Growth Requirements of Panax Species

    4.25.5. Summary and Conclusions

    4.26. Can Plants Really Improve Indoor Air Quality?


    4.26.1. Introduction

    4.26.2. Phytoremediation in the Indoor Environment

    4.26.3. Gas Exchange between the PPM and Its Surroundings

    4.26.4. Effluent Quality

    4.26.5. Conclusions

    4.27. Regulating the Ripening Process


    4.27.1. Introduction

    4.27.2. Model Systems for Fruit Development

    4.27.3. Ethylene Synthesis and Fruit Ripening

    4.27.4. Ethylene Perception and Fruit Ripening

    4.27.5. Cell-Wall Metabolism and Fruit Ripening

    4.27.6. The Role of Light in Fruit Ripening

    4.27.7. Insights into Developmental Control from Ripening Mutants

    4.27.8. Future Directions

    4.28. Pre- and Postharvest Treatments Affecting Nutritional Quality


    4.28.1. Introduction

    4.28.2. Inhibition of Ethylene Biosynthesis

    4.28.3. Inhibition of Ethylene Action

    4.28.4. Phospholipase D Inhibition Technologies

    4.28.5. Effects of Pre- and Postharvest Treatments on Firmness

    4.28.6. Effects of Pre- and Postharvest Treatments on Color and Phenolics

    4.28.7. Effects of Pre- and Postharvest Treatments on Antioxidant Levels

    4.28.8. Effects of Pre- and Postharvest Treatments on Aroma

    4.29. Embryo Genomics State of the Art


    4.29.1. Introduction

    4.29.2. Decoding the Genome of Livestock

    4.29.3. The Rise of Omics

    4.29.4. The Single Gene Phenotypes

    4.29.5. Applications in Animal Biotechnology

    4.29.6. The Necessary Link between Reproductive Biology and the Exploitation of the Genetic Information

    4.29.7. The Emerging Role of Epigenetics

    4.29.8. The DNA-Based Tools for the Study of Gene Expression

    4.29.9. Microarray versus Deep Sequencing

    4.29.10. Conclusion

    4.30. Aquaculture Genomics


    4.30.1. Introduction

    4.30.2. Required Resources for the Whole Genome Sequence Assembly

    4.30.3. Required Resources for the Whole Genome Sequence Annotation

    4.30.4. Whole Genome Sequencing

    4.30.5. Aquaculture Genomics and Performance Traits

    4.31. Epigenetics and Animal Health


    4.31.1. Introduction and Scope

    4.31.2. Epigenetic Mechanisms Regulating Gene Activity

    4.31.3. Epigenetic Regulation of the NEI

    4.31.4. Environmental Quos That Contribute to the Epigenetic Programming of Genes Associated with Disease

    4.31.5. Molecular Approaches to Studying Epigenetics

    4.31.6. Conclusion

    4.32. Quest for Novel Muscle Pathway Biomarkers by Proteomics in Beef Production


    4.32.1. Introduction and Scope

    4.32.2. New Insights in to Muscle Biology

    4.32.3. Identification of Markers of Beef Tenderness

    4.32.4. Conclusion

    4.33. From Stem Cell to Gamete


    4.33.1. Introduction

    4.33.2. Oogenesis In Vivo

    4.33.3. In Vitro Germ Cell Development from Stem Cells

    4.33.4. Potential Applications of In Vitro-Generated Female Gametes

    4.34. Stem Cells and Animal Therapies


    4.34.1. Introduction

    4.34.2. Stem Cell Therapies in Domestic Species

    4.34.3. Summary and Perspectives

    4.34.4. Conclusion

    4.35. Flow Cytometric Sorting of Mammalian Sperm for Predetermination of Sex


    4.35.1. Introduction

    4.35.2. Sex Preselection

    4.35.3. Flow Cytometric Sorting of Sperm

    4.35.4. Delivery of Sexed Sperm

    4.35.5. Sorting of Frozen–Thawed Sperm

    4.35.6. Concluding Remarks

    4.36. Animal Cloning


    4.36.1. Introduction

    4.36.2. Technical Aspects of Animal Cloning by NT

    4.36.3. Cloning Applications

    4.36.4. Problems of SCNT Cloning

    4.36.5. Nuclear Reprogramming in SCNT Embryos

    4.36.6. Gene Expression in SCNT Cloned Embryos

    4.36.7. Effects of Cell Cycle Coordination on SCNT Cloning

    4.36.8. Effect of Cell Differentiation on SCNT Cloning

    4.36.9. Alternatives to Facilitate Nuclear Reprogramming in SCNT Embryos

    4.36.10. Concluding Remarks

    4.37. Transgenesis


    4.37.1. Introduction

    4.37.2. SCNT: Current Methodology for Transgenic Animal Production

    4.37.3. Emerging Transgenic Technologies

    4.37.4. Applications of Transgenic Domestic Animals

    4.37.5. Health and Welfare of Transgenic Farm Animals

    4.37.6. Safety Aspects and Outlook

    4.38. Arrest or Survive


    4.38.1. Introduction

    4.38.2. Survival of the Early Embryo

    4.38.3. Factors Involved in Embryo Loss

    4.38.4. Why Does an Embryo Arrest?

    4.38.5. Metabolomic Signatures: Markers for Embryo Health

    4.39. Heat Stress and Climate Change


    4.39.1. Introduction – the Impact of Heat Stress on Animal Production

    4.39.2. Homeothermy

    4.39.3. Use of Biotechnology to Enhance Genetic Thermotolerance

    4.39.4. Uses of Biotechnology to Facilitate Physiological Manipulation to Counteract Effects of Heat Stress

    4.39.5. Final Perspective

    4.40. Analytical Methods – Functional Foods and Dietary Supplements


    4.40.1. Introduction

    4.40.2. Bioactive Compounds Used in Functional Foods and Dietary Supplements

    4.40.3. Phenolic Compounds

    4.40.4. Omega-3 Fatty Acids and Conjugated Linoleic Acid (CLA)

    4.40.5. Carotenoids

    4.40.6. Phytosterols

    4.40.7. Coenzyme Q10

    4.40.8. Vitamins

    4.40.9. Glucosamine

    4.40.10. Chondroitin Sulfate

    4.40.11. Dietary Fiber

    4.40.12. Selected Botanicals

    4.40.13. Conclusions

    4.41. Plant Derived Bioactives


    4.41.1. Introduction

    4.41.2. Indigestible Carbohydrates

    4.41.3. Essential Fatty Acids

    4.41.4. Proteins and Peptides

    4.41.5. Polyphenolic Compounds

    4.41.6. Carotenoids

    4.41.7. Conclusions

    4.42. Functional Properties of Dietary Fiber


    4.42.1. Introduction

    4.42.2. Sources and Chemistry of Dietary Fiber

    4.42.3. Physiological Properties of Dietary Fiber

    4.42.4. Functional Properties of Dietary Fiber

    4.42.5. Applications of Dietary Fibers in Food Products

    4.42.6. Conclusions

    4.43. Resistant Starches in Foods


    4.43.1. Introduction

    4.43.2. Definition and Classification of RS

    4.43.3. Strategies for the Enhancement of RS

    4.43.4. Determination of RS

    4.43.5. Future Directions

    4.44. Plant Sterols


    4.44.1. Introduction

    4.44.2. Occurrence and Structure

    4.44.3. Metabolism of Plant Sterols

    4.44.4. Physiological Aspects of Plant Sterols in Human Health

    4.44.5. Plant Sterols and Coronary Heart Disease Risk

    4.44.6. Factors Affecting Efficacy of Plant Sterols

    4.44.7. Combination Therapies of Plant Sterols

    4.44.8. Safety of Plant Sterols

    4.44.9. Conclusion

    4.45. Soy Protein Functionality


    4.45.1. Introduction

    4.45.2. Soy Storage Proteins: Glycinin and β-Conglycinin

    4.45.3. Adsorption of Soy Proteins at Interfaces: Emulsifying Properties

    4.45.4. Gelling Properties of Soy Protein

    4.45.5. Conclusions

    4.46. Egg Components for Heart Health


    4.46.1. Introduction

    4.46.2. Composition of Egg

    4.46.3. Pathogenesis of Cardiovascular Diseases

    4.46.4. Cholesterol Content and Level of Cardiovascular Risk

    4.46.5. PUFA-Enriched Egg Improves Heart Health

    4.46.6. Antihypertensive Bioactive Peptides from Eggs

    4.46.7. Egg Antioxidants Improve Cardiovascular Health

    4.46.8. Other Beneficial Effects Improve CVD Risk

    4.46.9. Conclusion and Notes

    4.47. Enzyme Technology – Dairy Industry Applications


    4.47.1. Introduction

    4.47.2. Industrially Important Enzymes Indigenous to Milk

    4.47.3. Exogenous Enzymes Employed in the Manufacture of Dairy Products [15]

    4.48. Gut Microbiology – A Relatively Unexplored Domain


    4.48.1. Introduction

    4.48.2. Diversity of the Gut Microbiota

    4.48.3. Immunomodulatory Effects of Gut Microbes

    4.48.4. Complementation of the Gut Microbiota

    4.48.5. Use of Animal Models to Study the Microbiota–Host Interaction

    4.49. Probiotics


    4.49.1. Introduction

    4.49.2. Microorganisms

    4.49.3. Probiogenomics

    4.49.4. Selection of Probiotic Strains

    4.49.5. Technology

    4.49.6. Probiotic Food Products

    4.49.7. The Probiotic Concept

    4.49.8. Safety Considerations

    4.49.9. Conclusions

    4.50. Novel Lipid Substitutes


    4.50.1. Introduction

    4.50.2. Traditional Fat Crystal Networks

    4.50.3. Novel Lipid Substitutes

    4.50.4. Modifying the Crystal Structure of Novel Lipid Substitutes

    4.50.5. Summary and Future Directions

    4.51. Microwave Dehydration of Food and Food Ingredients


    4.51.1. Introduction

    4.51.2. Background Information on Microwave Energy and Microwave Dehydration

    4.51.3. Microwave-Applicator Designs

    4.51.4. Microwave Dehydration

    4.51.5. Microwave-Assisted Fluidized-Bed Drying

    4.51.6. Microwave-Assisted Freeze-Drying

    4.51.7. Food Culture and Probiotics

    4.51.8. Conclusions

    4.52. Active and Intelligent Packaging Materials


    4.52.1. Introduction

    4.52.2. Antimicrobial AFP

    4.52.3. Vapor and Gas Scavengers

    4.52.4. Intelligent Packaging

    4.52.5. Conclusion: Acceptance and Safety issues of AFP and IFP

    4.53. Antimicrobials from Plants – Food Preservation and Shelf-Life Extension


    4.53.1. Introduction

    4.53.2. Major Groups of Antimicrobial Compounds from Plants

    4.53.3. Antimicrobial Activities

    4.53.4. Mechanisms

    4.53.5. Applications

    4.53.6. Conclusion

    4.54. Biosensors for Foodborne Pathogen Detection


    4.54.1. Introduction

    4.54.2. Target Microbes

    4.54.3. Conventional Microbiological Detection and Enumeration

    4.54.4. Diagnostics for Pathogen Detection

    4.54.5. Microbial Capture and Concentration

    4.54.6. Transduction Strategies

    4.54.7. Conclusions and Future Directions

    4.55. Microemulsions as Nanoscale Delivery Systems


    4.55.1. Literature Review

    4.55.2. Controlled Release of Food-Based Ingredients

    4.55.3. Conclusion

    4.56. Origins and Compositional Analysis of Novel Foods


    4.56.1. Introduction

    4.56.2. Unique Animal Bio-Processed Foods

    4.56.3. Conclusions

    4.57. Nutrigenomics


    4.57.1. Introduction

    4.57.2. Alcohol

    4.57.3. Caffeine

    4.57.4. Dietary Fat

    4.57.5. Fruits and Vegetables

    4.57.6. Micronutrients

    4.57.7. Conclusions

    4.58. Plant and Endophyte Relationships


    4.58.1. Introduction: Plant Nutrient Management and Agricultural Productivity

    4.58.2. Endophyte Nutrient Uptake

    4.58.3. Enhancing Root Growth

    4.58.4. Nitrogen Fixation

    4.58.5. Other Endophytic Mechanisms Affecting Plant Nutrient Status

    4.58.6. Application of Endophytes to Agriculture

    4.58.7. Conclusions

    4.59. Disease Resistance/Pathology/Fusarium


    4.59.1. Introduction

    4.59.2. Fusarium Life Cycles

    4.59.3. Economic Impacts of Fusarium Infections and Their Toxins

    4.59.4. Plant–Pathogen Interactions and Plant Resistance Mechanisms

    4.59.5. Biotechnological Approaches to Resistance in Plants

    4.59.6. F. graminearum

    4.59.7. F. culmorum

    4.59.8. F. verticillioides

    4.59.9. F. oxysporum

    4.60. Plant Biochemistry


    4.60.1. Introduction

    4.60.2. Leguminous Antifungal Proteins

    4.60.3. Nonleguminous Antifungal Proteins

    4.60.4. Conclusion and Future Perspectives

    4.61. Biological Control and Biotechnological Amelioration in Managed Ecosystems


    4.61.1. Introduction

    4.61.2. Biocontrol of Weeds

    4.61.3. Biocontrol of Plant Pathogens

    4.61.4. Biocontrol of Plant Pathogens and Insect Pests by Pollinator Vectors

    4.61.5. Biocontrol of Insect, Mite, and Nematode Pests

    4.61.6. Biocontrol of Vertebrate Pests

    4.61.7. Biocontrol in Veterinary and Medical Applications

    4.61.8. Production, Deployment, and Establishment of Biocontrol Agents

    4.61.9. Genetic Engineering and Biological Control

    4.61.10. Ecological Considerations

    4.62. Genetic Basis of Disease Resistance in the Honey Bee (Apis mellifera L.)


    4.62.1. Introduction

    4.62.2. Colony Collapse Disorder and Parasites

    4.62.3. Genetic Basis of Disease Resistance

    4.62.4. Conclusion

    4.63. Food Safety, Genetically Engineered Foods and Perception


    4.63.1. Introduction

    4.63.2. Use New Media

    4.64. Socio-Environmental Factors Influencing Food Behavior


    4.64.1. Introduction

    4.64.2. The Economic Environment

    4.64.3. Social Determinants of Healthy Eating

    4.64.4. Influences of the Physical Environment on Healthy Eating

    4.64.5. The Interaction of Determinants – The Obesogenic Environment

    4.64.6. Policy

    4.64.7. Conclusion

    4.65. Policy and Novel Foods from Animal Sources


    4.65.1. Introduction

    4.65.2. Background

    4.65.3. Food Derived from Animal Clones and Their Progeny: A Case Study

    4.65.4. Specific Legislations Governing Food Products Derived from Biotechnology-Derived Animals

    4.65.5. Conclusion

    5.01. Introduction

    5.02. Functional Biomaterials


    5.02.1. Introduction

    5.02.2. Current Use of Materials in Medicine

    5.02.3. Functionality in Biomaterials

    5.02.4. Conclusions

    5.03. Biomaterials/Cryogels


    5.03.1. Introduction

    5.03.2. Production of Cryogels in Semi-Frozen Systems

    5.03.3. Cryogel Characterization

    5.03.4. Cryogel Properties

    5.03.5. Composite Cryogel Materials: Inherent Features and Applications

    5.03.6. Cryogels in Biomedicine and Biotechnology

    5.04. Biomaterials


    5.04.1. Introduction

    5.04.2. Principle of Electrospinning

    5.04.3. Electrospun Biomaterials: A Wide Range of Possibilities

    5.04.4. Applications of Electrospun Biomaterials

    5.04.5. Biocompatibility of Electrospun Biomaterials

    5.04.6. Electrospun Biomaterials for 3D Tissue Regeneration

    5.04.7. Current Challenges with Electrospun Biomaterials

    5.04.8. Conclusion

    5.05. Mesoscale Engineering of Collagen as a Functional Biomaterial



    5.05.1. Introduction

    5.05.2. Two Application Streams for Engineered Tissues

    5.05.3. Which Cell Support Materials to Use: Indirect and Direct TE?

    5.05.4. Interstitial Cell Seeding: Cell-Matrix Embedding from the Start

    5.05.5. Structure of Collagen – A Raw Material for Weavers?

    5.05.6. Collagen Materials: Engineering the Basics

    5.05.7. Building Blocks

    5.05.8. Antigenicity

    5.05.9. Collagen Purity (and Antigenicity)

    5.05.10. Bottom-Up Collagen Engineering, Where Is the Bottom – Amino Acids or Tropocollagen?

    5.05.11. Conclusion

    5.06. Biomaterials


    5.06.1. Introduction

    5.06.2. Temperature-Responsive Intelligent Surfaces for Chromatographic Separation

    5.06.3. Temperature-Responsive Intelligent Surfaces for Cell Culture

    5.07. Surface Modification to Improve Biocompatibility


    5.07.1. Introduction

    5.07.2. Surface Events, Interactions, and Material Characteristics

    5.07.3. Surface Modification

    5.07.4. Future

    5.07.5. Conclusions

    5.08. Cryopreservation



    5.08.1. Introduction

    5.08.2. Cryopreservation Methodology

    5.08.3. Natural Tissue Cryopreservation

    5.08.4. Engineered Tissue Cryopreservation

    5.08.5. Future Challenges

    5.09. The Artificial Organ



    5.09.1. Introduction

    5.09.2. Materials of Encapsulation

    5.09.3. Properties of the Microcapsules

    5.09.4. Applications of Encapsulated Cells

    5.09.5. Conclusions and Future Considerations

    5.10. Isolation of Mesenchymal Stem Cells from Bone Marrow Aspirate


    5.10.1. The Cellular Composition of Bone Marrow

    5.10.2. Why Isolate MSC Populations?

    5.10.3. Separation Techniques

    5.10.4. Conclusions

    5.11. Nanoimprint Lithography and Its Application in Tissue Engineering and Biosensing


    5.11.1. Introduction

    5.11.2. Biosensing Applications of NIL

    5.11.3. Application of NIL in Tissue Engineering

    5.11.4. Appendix: Additional References

    5.12. Microfluidic Technology and Its Biological Applications


    5.12.1. Introduction

    5.12.2. Microfluidic Technology

    5.12.3. Basic Components in Microfluidic Systems

    5.12.4. Biological Applications

    5.12.5. Concluding Remarks

    5.13. Multifunctional Biosensor Development and Manufacture


    5.13.1. Introduction

    5.13.2. Biomolecule Immobilization

    5.13.3. Transduction Technologies

    5.13.4. Potentiometric Transduction

    5.13.5. Optical Transduction

    5.13.6. Nanowire Arrays

    5.13.7. Micromechanical

    5.13.8. Recent Developments

    5.13.9. Conclusions

    5.14. Treating Intracranial Aneurysms – A Review of Existing and Emerging Methods


    5.14.1. Introduction

    5.14.2. Existing Options for Treating Intracranial Aneurysms

    5.14.3. Cerebral Stents for Direct Treatment of Intracranial Aneurysms

    5.14.4. Conclusions

    5.15. RNA Interference (RNAi) Technology


    5.15.1. Introduction

    5.15.2. The Discovery of the Phenomena

    5.15.3. The Mechanism of RNAi

    5.15.4. The Discovery of miRNA Pathway and Functions of miRNA

    5.15.5. The Generation of siRNA

    5.15.6. The Assessment of siRNA Specificity and Off-Target Effects

    5.15.7. The Progress of siRNA Drug Development

    5.15.8. Conclusion Remarks

    5.16. Rheology and Its Applications in Biotechnology


    5.16.1. Introduction

    5.16.2. Shear Rheometry

    5.16.3. Material Rheology

    5.16.4. Other Rheological Considerations

    5.16.5. Applications

    5.16.6. Conclusion

    5.17. Biological Fluid Mechanics



    5.17.1. Introduction

    5.17.2. Vascular Diseases

    5.17.3. Computational Biofluid Techniques

    5.17.4. Evolving to Multiscale, Multiphysics Models

    5.17.5. Epilogue

    5.18. Mechanobiology of Bone


    5.18.1. Introduction

    5.18.2. Fundamental Cell Mechanics

    5.18.3. A Case Study of Mechanobiology: Bone

    5.18.4. Bone Anatomy

    5.18.5. The Osteocyte

    5.18.6. Basic Mechanics of Solid Materials

    5.18.7. A Top-Down Approach to Bone Mechanosensation: What Happens to a Bone When You Take a Step?

    5.18.8. The Effect of Fluid Flow on the Osteocyte

    5.18.9. Nonmechanical Fluid Flow Effects on the Osteocyte

    5.18.10. Intracellular Signaling Downstream of Mechanical Deformation

    5.18.11. Osteocyte Mechanotransduction Guides Bone Remodeling

    5.18.12. How BMUs Remodel Bone

    5.18.13. Outcome of Bone Remodeling

    5.18.14. Biomedical Applications

    5.18.15. Summary

    5.19. Biofluids | Microcirculation


    5.19.1. Introduction

    5.19.2. Interaction between Blood Cells and the Capillary Wall

    5.19.3. Transcapillary Exchange of Fluid and Solute

    5.19.4. Transport of HA across the Synovial Lining of Joint Cavities

    5.19.5. Summary and Future Perspective

    5.20. Emerging Trends in Tissue Engineering



    5.20.1. Introduction

    5.20.2. Tissue-Engineering Strategies

    5.20.3. Microscale Technologies

    5.20.4. Bioreactors

    5.20.5. Translation into Clinical Applications

    5.20.6. Cell Sourcing

    5.20.7. Future Directions

    5.20.8. Conclusion

    5.21. Cartilage Tissue Engineering Using Embryonic Stem Cells


    5.21.1. Introduction and Scope

    5.21.2. OA Pathophysiology

    5.21.3. Current Therapeutic Strategies for Cartilage Defects

    5.21.4. Cartilage Biology and Chondrogenesis

    5.21.5. Stem Cells

    5.21.6. Cartilage Tissue Engineering Using ESCs

    5.21.7. Conclusions

    5.22. Tissue Engineering



    5.22.1. Introduction and Overview

    5.22.2. Clinical Need

    5.22.3. Skeletal Stem Cells – Identification, Expansion, and Differentiation

    5.22.4. Growth Factors

    5.22.5. Matrices for Bone Regeneration

    5.22.6. Interactive Role of Vasculature in Skeletal Regeneration

    5.22.7. In vivo Models of Skeletal Regeneration

    5.22.8. Clinical Translation

    5.22.9. Summary

    5.23. Tendon Tissue Engineering


    5.23.1. Introduction

    5.23.2. Rotator Cuff Anatomy

    5.23.3. Etiology of Tears

    5.23.4. Reduced Tendon Healing

    5.23.5. Tissue-Engineering Approach

    5.23.6. What Are Stem Cells?

    5.23.7. Stem Cell Identification

    5.23.8. Potential Uses in Other Fields

    5.23.9. Application to Tendon

    5.23.10. Rotator Cuff Tendon Application

    5.23.11. Which Procedure for Which Patients?

    5.23.12. Determining Ideal Conditions

    5.23.13. Potential Problems

    5.23.14. Conclusions

    5.23.15. Biological Agents

    5.23.16. Scaffolds

    5.23.17. Conclusions and the Future

    5.24. Complexity in Modeling of Cartilage Tissue Engineering


    5.24.1. Introduction

    5.24.2. Nutrients and Wastes

    5.24.3. Cell Proliferation/Death

    5.24.4. Matrix Deposition

    5.24.5. Permeability/Diffusivity

    5.24.6. Mechanical Property

    5.24.7. Different Culture Systems

    5.24.8. In Vivo Tissue Engineering

    5.24.9. Discussion

    5.25. Tissue Engineering of Fibrocartilaginous Tissues



    5.25.1. Introduction

    5.25.2. Anatomy, Structure, and Function

    5.25.3. Composition of the Extracellular Matrix and Its Organization

    5.25.4. Pathologies and Current Treatments of the Fibrocartilages

    5.25.5. Tissue Engineering

    5.25.6. Conclusion

    5.26. Tissue Engineering of Normal and Abnormal Bone Marrow


    5.26.1. Introduction

    5.26.2. BM Structure

    5.26.3. Modeling Artificial Niches

    5.26.4. Perturbations in the BM Microenvironment

    5.26.5. Conclusion

    5.27. Evaluation of Silk as a Scaffold for Musculoskeletal Regeneration – the Path from the Laboratory to Clinical Trials



    5.27.1. Introduction

    5.27.2. Common Types of Silk Scaffolds

    5.27.3. A Review of Studies of Silk Scaffolds for Musculoskeletal Tissue Engineering

    5.27.4. An Evaluation of Silk as a Scaffold for Musculoskeletal Repair – in the Context of Medical Device Regulations

    5.27.5. Summary

    5.28. Tissue-Engineering Technology for Tissue Repair and Regeneration



    5.28.1. Introduction

    5.28.2. Basic Principles of Tissue engineering

    5.28.3. Tissue Generation with Tissue-Engineering Technology

    5.28.4. Application of Engineered Tissue for Tissue Repair

    5.28.5. Clinical Application of Engineered Tissue Repair

    5.28.6. Development of Engineered Tissue Products

    5.28.7. Summary

    5.29. Induced Pluripotent Stem Cells and Their Application to Personalized Therapy


    5.29.1. Introduction

    5.29.2. hiPSCs Are Similar to, but Not Identical to, hESCs

    5.29.3. Generating hiPSCs

    5.29.4. Genetic Manipulation of hiPSCs

    5.29.5. Generating Differentiated Cell Populations

    5.29.6. Transplantation of hiPSC-Derived Cells

    5.29.7. Patient Safety

    5.29.8. Conclusion

    5.30. Expansion of Hematopoietic Stem/Progenitor Cells


    5.30.1. Introduction

    5.30.2. Sources of HSPCs

    5.30.3. Requirement of Expansion Folds and Quality of HSPCs

    5.30.4. Expansion of HSPCs under Common Static Culture Condition

    5.30.5. Expansion of HSPCs under Dynamic Bioreactor Culture Conditions

    5.30.6. Mimicking the In Vivo Microenvironment to Expand HSPCs

    5.30.7. Brief Introduction of Clinical Application Tests with Expanded HSPCs

    5.30.8. Summary

    5.31. Umbilical Cord Blood Stem Cell Banking


    5.31.1. Introduction and Scope

    5.31.2. Cord Blood Bank Models

    5.31.3. Advantages and Disadvantages of Unrelated Cord Blood Hematopoietic Stem Cell Transplants

    5.31.4. The Provision of Altruistic Unrelated Cord Blood Banked Units from Public Cord Blood Banks

    5.31.5. The Regulation of Cord Blood Banks

    5.31.6. Improving the Quality of Cord Blood Units for Human Use

    5.32. Stem Cell Therapy to Treat Heart Failure



    5.32.1. Introduction – Cell-Based Therapy for Cardiac Disease

    5.32.2. Major Unmet and Compelling Clinical Need Drives Stem Cell Research and Trials in Heart Failure

    5.32.3. Current Therapies in Heart Failure

    5.32.4. Mechanisms of Cardiac Regeneration

    5.32.5. Which Stem Cells Type Can Be Suitable for Cardiac Cell Therapy?

    5.32.6. Cell Delivery

    5.32.7. Clinical Trials with Bone Marrow-Derived Stem Cells

    5.32.8. Conclusions and Future Challenges

    5.33. Expansion of hMSCs and Their Application


    5.33.1. Introduction

    5.33.2. Isolation of hMSCs

    5.33.3. Expansion of hMSCs

    5.33.4. Quality Control

    5.33.5. Application of hMSCs

    5.33.6. Summary

    5.34. Cell Therapy for Parkinson’s Disease


    5.34.1. Introduction

    5.34.2. ESCs or NSCs: Pros and Cons

    5.34.3. Concluding Remarks

    5.35. Stem Cell Therapy Facility Design


    5.35.1. Introduction

    5.35.2. Stem Cell Transplantation Area

    5.35.3. Stem Cells and Regenerative Medicine Technology Research Center Design

    5.35.4. Conclusion

    5.36. Stem Cell Research and Molecular Markers in Medicine


    5.36.1. Introduction

    5.36.2. Definition and Characteristics of MSCs

    5.36.3. Sources of Other MSCs

    5.36.4. Application of Human MSCs in Regenerative Medicine

    5.36.5. Aging and Replicative Senescence Affect the Use of MSCs in Regenerative Therapy

    5.36.6. Osteogenesis and Angiogenesis: Applications in Regenerative Therapy

    5.37. Stem Cell Therapy – MRI for In Vivo Monitoring of Cell and Tissue Function



    5.37.1. Introduction

    5.37.2. MRI for Tracking Stem Cell Fate

    5.37.3. Applications of Stem Cell Tracking

    5.37.4. MRI for Measuring Tissue Function after Stem Cell Therapy

    5.37.5. Conclusions

    5.38. Cryopreservation of Stem Cells



    5.38.1. Introduction

    5.38.2. Stem Cells

    5.38.3. Cryopreservation

    5.38.4. Cryopreservation of Stem Cells

    5.38.5. Concluding Remarks

    5.39. Biopharmaceutical Development


    5.39.1. Introduction

    5.39.2. Development of Vaccines

    5.39.3. The Biopharmaceutical Development Pipeline

    5.39.4. Regulatory Requirements

    5.39.5. Selection of Biotherapeutic Protein Expression Systems

    5.39.6. Development of Mammalian Cell Lines

    5.39.7. Development of Mammalian Expression Vectors

    5.39.8. Cell Culturing and Product Generation

    5.39.9. Downstream Processing of Biopharmaceuticals

    5.39.10. Viral Inactivation of Biologics

    5.39.11. Process Analytical Technology

    5.39.12. Formulation and Drug Delivery Systems

    5.39.13. Biosimilars

    5.39.14. Conclusions

    5.40. Bioseparations


    5.40.1. Introduction

    5.40.2. Tangential Flow MF

    5.40.3. Depth Filtration

    5.40.4. Sterile Filtration

    5.40.5. Virus Filtration

    5.40.6. Membrane Chromatography

    5.40.7. Ultrafiltration

    5.40.8. High-Performance Tangential Flow Filtration

    5.41. Pharmaceutical Proteins – Structure, Stability, and Formulation


    5.41.1. Introduction

    5.41.2. The Structure of Proteins

    5.41.3. The Stability of Proteins

    5.41.4. Formulation and Stabilization of Proteins in the Liquid State

    5.41.5. Solid-State Protein Formulations

    5.41.6. Conclusions

    5.42. In Vitro Cancer Model for Drug Testing


    5.42.1. Introduction

    5.42.2. In Vitro Cancer Model

    5.42.3. 2D versus 3D Cancer Model

    5.42.4. 3D Models

    5.42.5. Summary

    5.43. In Vitro Micro-Tissue and -Organ Models for Toxicity Testing


    5.43.1. Introduction

    5.43.2. Development of In Vitro Tissue Models

    5.43.3. Progress in Toxicity Testing Using In Vitro Micro-Tissue Models

    5.43.4. Commercial Development of In Vitro Micro-Tissue Models for Toxicity Testing

    5.43.5. Summary

    5.44. Development of In Vitro Neural Models for Drug Discovery and Toxicity Screening



    5.44.1. Introduction

    5.44.2. Cell Sources

    5.44.3. Cell Culture Methods

    5.44.4. In Vitro Cell-Based Assay

    5.44.5. Discussion

    5.45. In Vitro Chronic Neurotoxicity Assays


    5.45.1. Introduction

    5.45.2. NT2.D1 Cells: Background

    5.45.3. NT2.D1 and Toxicity Evaluation

    5.45.4. NT2.D1s and Developmental Neurotoxicity

    5.45.5. 3-D Culture: Available Models and Applications

    5.45.6. Models of the BBB

    5.45.7. The Future – In Vitro Chronic Models of Neurotoxicity

    5.46. The Delivery of Drugs – Peptides and Proteins


    5.46.1. Introduction

    5.46.2. The Delivery of Peptides and Proteins

    5.46.3. Routes of Peptide and Protein Administration

    5.46.4. Conclusions

    5.47. Enzyme-Sensitive Biomaterials for Drug Delivery



    5.47.1. Introduction

    5.47.2. Enzyme-Sensitive Polymer–Drug Conjugate

    5.47.3. Enzyme-Sensitive Hydrogel

    5.47.4. Enzyme-Sensitive Particulate Carriers

    5.47.5. Conclusions

    5.48. Drug Delivery Using Microneedles


    5.48.1. Introduction

    5.48.2. The Skin Structure

    5.48.3. Variation of Skin Thickness

    5.48.4. Types of Microneedles

    5.48.5. Methods of Drug Delivery Using Microneedles

    5.48.6. Microneedle Fabrication

    5.48.7. Materials of Fabrication

    5.48.8. Method of Coating Solid Microneedles

    5.48.9. Uses and Applications in Drug Delivery

    5.48.10. Advantages and Limitations of Microneedles

    5.48.11. Mathematical Models of Transdermal Delivery by Microneedles

    5.48.12. Conclusion

    5.49. Carbon Nanotube for Drug Delivery and Controlled Release


    5.49.1. Introduction

    5.49.2. CNT Processing and Measurement

    5.49.3. Drug Delivery

    5.49.4. Toxicology

    5.50. Drug Delivery Across the Blood–Brain Barrier


    5.50.1. Introduction

    5.50.2. Transport Across the BBB

    5.50.3. CNS Delivery Strategies

    5.50.4. Conclusions

    5.51. Organ Transplant


    5.51.1. Overview

    5.51.2. Introduction to Transplantation

    5.51.3. Focus on Antibody-Mediated Allograft Rejection

    5.51.4. Small Animal Models in Studying AMR

    5.51.5. Experimental Progress in Prevention of AMR Using Free Bone Grafting

    5.51.6. Strategy to Prevent AMR in Presensitized Recipients through Terminal Complement Blockade

    5.51.7. Summary and Conclusions

    5.52. Artificial Organs


    5.52.1. Introduction

    5.52.2. Kidney Anatomy and Physiology

    5.52.3. Principles of Modern Dialysis

    5.52.4. Improved Dialysis Therapies

    5.52.5. Emerging Technologies in Tissue Engineering and Regenerative Medicine

    5.52.6. Conclusions and Future Prospects

    5.53. Artificial Organs | Pancreas



    5.53.1. Introduction

    5.53.2. Artificial Pancreas

    5.53.3. Cell- and Tissue-Based Therapies for IDD

    5.53.4. Concluding Remarks

    5.54. Hemoglobin-Based Blood Substitutes – Preparation Technologies and Challenges


    5.54.1. Introduction

    5.54.2. Brief History of Blood Substitute Research

    5.54.3. Preparation Technologies for Blood Substitutes

    5.54.4. The Application Prospect of Blood Substitutes

    5.54.5. Problems with Current Blood Substitutes

    5.54.6. Future Prospect

    5.55. Blood Detoxication


    5.55.1. Introduction

    5.55.2. Membrane Techniques

    5.55.3. Adsorption Techniques

    5.55.4. Combined Use of Both Membrane and Adsorption Techniques

    5.55.5. Perspectives

    5.56. Novel and Current Techniques to Produce Endotoxin-Free Dialysate in Dialysis Centers


    5.56.1. Introduction

    5.56.2. Ceramic Membranes

    5.56.3. Ceramic Membranes for Endotoxin Removal

    5.56.4. Conclusions and Future Perspectives

    6.01. Introduction

    6.02. Biodegradation


    6.02.1. Introduction and Scope

    6.02.2. Traditional and Cultural Techniques

    6.02.3. Omics and Related Techniques

    6.02.4. Summary Example

    6.03. Systems Biology Approaches to Bioremediation



    6.03.1. Introduction

    6.03.2. Back to the Environment

    6.03.3. What Is in a Genome

    6.03.4. The Catabolic Gene Landscape: Methods and Abstractions

    6.03.5. Categories of Environmental Metabolites

    6.03.6. Pan-Enzymes

    6.03.7. The Global Biodegradation Network

    6.03.8. The Environmental Fate of Chemical Pollutants

    6.03.9. Chemical Logic versus Microbiological Sense

    6.03.10. Translating Biodegradation Knowledge into Predictive Power

    6.03.11. Metabolic Engineering of Biodegradation: From Systems to Synthetic Biology

    6.03.12. Conclusion

    6.04. Molecular Approaches for the Analysis of Natural Attenuation and Bioremediation


    6.04.1. Introduction

    6.04.2. Detection of Degradative Genes

    6.04.3. Community Fingerprinting

    6.04.4. Metagenomics

    6.04.5. Conclusions

    6.05. New Developments and Applications of Microarrays for Microbial Community Analysis in Natural and Impacted Ecosystems



    6.05.1. Introduction

    6.05.2. Microarrays for Microbial Analysis

    6.05.3. Future Perspectives

    6.06. Metagenomics for Bioremediation


    6.06.1. Introduction: Molecular Tools Used to Study Environmental Communities

    6.06.2. Potential of Metagenomics for Bioremediation

    6.06.3. Application of Metagenomics to Contaminated Environments

    6.06.4. Conclusions – Advancing the Field

    6.07. In Situ Bioremediation


    6.07.1. Introduction

    6.07.2. Unsaturated Zone Treatment Methods

    6.07.3. Saturated Zone Treatment Methods

    6.07.4. Use of Inocula

    6.07.5. Monitoring Methods

    6.07.6. Conclusions and Future Prospects

    6.08. Bioaugmentation as a Strategy for the Treatment of Persistent Pollutants


    6.08.1. Introduction

    6.08.2. Site-Specific Bioaugmentation Strategies

    6.08.3. Pros and Cons of Bioaugmentation

    6.08.4. Future Directions

    6.08.5. Conclusions

    6.09. Bioavailability and Bioaccessibility as Key Factors in Bioremediation


    6.09.1. Introduction: Bioavailability, Bioaccessibility, and Chemical Activity

    6.09.2. Bioavailability Processes

    6.09.3. Biological Adaptations Improving Bioavailability

    6.09.4. Measuring and Predicting Bioavailability and Bioaccessibility

    6.09.5. Influencing Bioavailability

    6.09.6. Bioavailability and Environmental Regulation

    6.10. Biodegradability of Recalcitrant Aromatic Compounds


    6.10.1. Introduction and Scope

    6.10.2. The Nature of Aromatic Compounds and Their Sources

    6.10.3. Overview of Microbial Biodegradation Principles and Their Application to Aromatic Hydrocarbons

    6.10.4. Interactions between Habitat Characteristics, Microbes, and Aromatic Compounds Determine Their Biodegradability

    6.10.5. Summary

    6.11. Proteomic Applications to Elucidate Bacterial Aromatic Hydrocarbon Metabolic Pathways



    6.11.1. Introduction

    6.11.2. Traditional Approaches to the Study of Aromatic Hydrocarbon Metabolic Pathways

    6.11.3. Proteomic Applications to the Study of Bacterial Degradation of Aromatic Hydrocarbons

    6.11.4. Monocyclic and Low-Molecular-Weight Aromatic Hydrocarbons

    6.11.5. Proteomic Analysis of Samples from HMW PAH Degradation

    6.11.6. Conclusions

    6.12. Rieske-Type Dioxygenases



    6.12.1. Introduction

    6.12.2. Degradation of Toluene, Benzene, and Ethylbenzene

    6.12.3. Degradation of Isopropylbenzene (Cumene)

    6.12.4. Degradation of Other Alkylbenzenes with Side Chains of Three or More Carbon Atoms

    6.12.5. Degradation of Xylenes

    6.12.6. Degradation of Styrene

    6.12.7. Degradation of Biphenyl

    6.12.8. Degradation of Naphthalene

    6.12.9. Degradation of PAHs

    6.12.10. Concluding Remarks

    6.13. Dehalogenation of Polychlorinated Dibenzo-p-Dioxins and Dibenzofurans, Polychlorinated Biphenyls, and Brominated Flame Retardants, and Potential as a Bioremediation Strategy


    6.13.1. Introduction

    6.13.2. Sediment Contamination: Legacy Pollutants and Emerging Challenges

    6.13.3. Biodehalogenation and Dehalorespiration of Organohalides

    6.13.4. Sediment Bioremediation: Engineering Challenges

    6.14. Microbial Degradation of Polychlorinated Biphenyls



    6.14.1. Introduction

    6.14.2. Chemistry and Environmental Fate of PCBs

    6.14.3. Biodegradation of PCBs by Higher Organisms

    6.14.4. Bacterial Transformation of PCBs

    6.14.5. Engineered Systems for Bacterial Degradation of PCBs

    6.14.6. Genetically Modified Bacteria for PCB Biodegradation

    6.14.7. Conclusions

    6.15. Biodegradation and Bioremediation of TNT and Other Nitro Explosives


    6.15.1. Introduction

    6.15.2. Nitroaromatic Explosives

    6.15.3. Nitramine Explosives

    6.15.4. Nitroester and Nitroalkane Explosives

    6.15.5. Bioremediation of Environments Contaminated by Nitro Explosives

    6.15.6. Conclusion and Perspectives

    6.16. Oxidative Fungal Enzymes for Bioremediation



    6.16.1. Introduction

    6.16.2. Fungi

    6.16.3. Oxidative Fungal Enzymes

    6.16.4. Optimizing Bioremediation

    6.16.5. Practical Approach

    6.16.6. Concluding Remarks

    6.17. Biotechnological Strategies Applied to the Decontamination of Soils Polluted with Heavy Metals


    6.17.1. Soil Contamination

    6.17.2. Heavy Metal Contamination

    6.17.3. Soil Microorganisms – Structure and Analysis Tools

    6.17.4. Microorganisms and the Contamination by Heavy Metals

    6.17.5. Biological Methods of Remediation – Bioremediation

    6.17.6. Phytoremediation

    6.17.7. Metallophyte Plants

    6.17.8. Interaction between Microorganisms and Plants

    6.17.9. Rhizoremediation

    6.17.10. Conclusion and Final Remarks

    6.18. Phytofiltration of Heavy Metals


    6.18.1. Introduction

    6.18.2. Selection of the Plant Species Offering the Best Performance

    6.18.3. Selection of the Most Appropriate Phytofiltration System

    6.18.4. Factors Affecting Metal Uptake by Plants

    6.18.5. Treatment and Disposal of Biomass Containing Metals

    6.18.6. Concluding Remarks

    6.19. Phycoremediation


    6.19.1. Introduction

    6.19.2. Nutrient Removal Utilizing Microalgae Strains with Special Attributes

    6.19.3. Removal of Heavy Metals

    6.19.4. Biodegradation of Toxic and Persistent Organic Pollutants

    6.19.5. Use of Immobilized Microalgae and Cyanobacteria for Nutrient and Heavy Metal Removal

    6.19.6. Concluding Remarks

    6.20. Transgenic Plants and Associated Bacteria for Phytoremediation of Organic Pollutants



    6.20.1. Introduction

    6.20.2. Phytoremediation: Cleaning Up Pollution with Plants and Associated Bacteria

    6.20.3. Transgenic Plants and Bacteria for Phytoremediation

    6.20.4. Conclusions

    6.21. Potential for Enhanced Phytoremediation of Landfills Using Biosolids – A Review


    6.21.1. Introduction

    6.21.2. Environmental Issues of Landfill

    6.21.3. Postclosure Treatment

    6.21.4. Phytoremediation of Landfills

    6.21.5. Use of Biosolids in Landfill Phytoremediation

    6.21.6. Conclusion

    6.22. Methanotrophs



    6.22.1. Introduction

    6.22.2. A Brief Overview of Methanotrophs

    6.22.3. Cultivation of Methanotrophs

    6.22.4. Potential Applications of Methanotrophs in Environmental Bioengineering

    6.22.5. Engineering Challenges in the Use of Methanotrophs in Environmental Biotechnology

    6.22.6. Conclusions and Future Prospects

    6.23. Petroleum Spill Control with Biological Means


    6.23.1. Introduction

    6.23.2. Fate (Weathering) of Oil Spills

    6.23.3. Biostimulation

    6.23.4. Bioaugmentation

    6.23.5. Bioaugmentation or Biostimulation?

    6.24. Biological Wastewater Treatment Systems


    6.24.1. Introduction

    6.24.2. Life and Nutrient Transformation Processes

    6.24.3. Microbial Carbon and Phosphorus Processes

    6.24.4. Nitrogen Transformation Processes

    6.24.5. Reaction Kinetics in Biological Treatment Systems

    6.24.6. Biological Wastewater Treatment Systems

    6.24.7. WWTPs – The Activated Sludge Process

    6.25. Ecological Models



    6.25.1. Introduction

    6.25.2. Wastewater Treatment Model Terminology

    6.25.3. Wastewater Treatment Model Compartments

    6.25.4. Plant-Wide Models

    6.25.5. Guidelines for Application of WWTP Models

    6.25.6. A General Framework for Application of WWTP Models

    6.25.7. Major Limitations of Activated Sludge Models

    6.26. Activated Sludge Model-Based Modeling of Membrane Bioreactor Processes



    6.26.1. Introduction

    6.26.2. Application of Unmodified ASMs to MBR Processes

    6.26.3. Application of Modified ASMs to MBR Processes

    6.26.4. Outlook and Future Perspectives

    6.26.5. Conclusions

    6.27. Biological Nitrogen Removal from Domestic Wastewater


    6.27.1. Introduction

    6.27.2. N-Removal Processes Based on Heterotrophic Denitrification

    6.27.3. Advanced N-Removal Processes by Autotrophic Denitrification

    6.27.4. Emerging Technologies and New Challenges in Urban WWTP

    6.27.5. Conclusions

    6.28. Biotechnological Methods for Nutrient Removal from Wastewater with Emphasis on the Denitrifying Phosphorus Removal Process


    6.28.1. Introduction

    6.28.2. Biological–Chemical Phosphorus Removal

    6.28.3. Historical Background

    6.28.4. Biochemical and Microbiological Aspects

    6.28.5. Denitrifying Phosphorus Removal

    6.28.6. Future Perspectives

    6.28.7. Summary

    6.29. Constructed Wetlands for Water Treatment


    6.29.1. Introduction

    6.29.2. Constructed Wetland Design

    6.29.3. Constructed Wetland Bioprocesses

    6.29.4. Limitations of Wetland Bioprocesses

    6.29.5. Models for Constructed Wetland Performance Determination

    6.29.6. Conclusions

    6.30. Attached Growth Biological Systems in the Treatment of Potable Water and Wastewater


    6.30.1. Introduction

    6.30.2. Water Treatment

    6.30.3. Wastewater Treatment

    6.30.4. Summary

    6.31. Kinetics and Modeling of Anaerobic Treatment and Biotransformation Processes


    6.31.1. Introduction

    6.31.2. Principles of Anaerobic Treatment

    6.31.3. Kinetics and Modeling

    6.31.4. Anaerobic Biotransformation Processes

    6.32. Anaerobic Treatment of Organic Sulfate-Rich Wastewaters


    6.32.1. Introduction

    6.32.2. Anaerobic Treatment of Organic Sulfate-Rich Wastewaters

    6.32.3. Two-Phase Anaerobic Treatment

    6.32.4. Effect of Low pH on Anaerobic Microbial Conversions

    6.32.5. Toxicity

    6.32.6. Concluding Remarks

    6.33. Biotechnological Aspects of the Use of Methane as Electron Donor for Sulfate Reduction


    6.33.1. Sulfate-Containing Wastewaters and Biological Sulfate Reduction

    6.33.2. Electron Donors for Biological Sulfate Reduction of Wastewaters from Power Plants and Metallurgical Industries

    6.33.3. Methane as Electron Donor for Sulfate Reduction

    6.33.4. Concluding Remarks

    6.34. Sulfate Reduction for Inorganic Waste and Process Water Treatment



    6.34.1. Introduction

    6.34.2. Waste and Process Streams with Sulfate

    6.34.3. Electron Donor and Carbon Source for Sulfate Reduction

    6.34.4. Effect of Process Conditions on Sulfate Reduction

    6.34.5. Bioreactor Types Used for Sulfate Reduction

    6.34.6. Sulfate-Reducing Applications and Metal Recovery

    6.34.7. Future Prospects for Sulfate Reduction

    6.35. Anaerobic Biotreatment of Municipal Sewage Sludge


    6.35.1. Introduction

    6.35.2. Sludge Production and Characterization

    6.35.3. Theory of Anaerobic Digestion

    6.35.4. Process Configurations

    6.35.5. Process Benefits

    6.35.6. Biosolids Disposal and Reuse

    6.36. Anaerobic Digestion of the Organic Fraction of Municipal Solid Waste for Methane Production


    6.36.1. Background

    6.36.2. Waste Characteristics and Collection Strategies

    6.36.3. The Importance for AD Design of Having Appropriate Values for B0 and G0

    6.36.4. The Attainment of Representative Values for B0

    6.36.5. Sorting/Preparation Technologies

    6.36.6. AD Technologies and Performances

    6.36.7. Carbon Footprint and Global Warming Potential of AD of Biowaste

    6.36.8. A Case Study: AD as a Service Technology for the Territory

    6.36.9. Conclusions

    6.37. Occurrence, Toxicity, and Biodegradation of Selected Emerging Priority Pollutants in Municipal Sewage Sludge


    6.37.1. Introduction

    6.37.2. Phthalic Acid Esters (Phthalates), PAEs

    6.37.3. Polycyclic Aromatic Hydrocarbons (PAHs)

    6.37.4. Surface-Active Agents (Surfactants)

    6.37.5. Conclusions

    6.38. Biodegradation of Micropollutants and Prospects for Water and Wastewater Biotreatment



    6.38.1. Introduction

    6.38.2. Persistence and Effects of Micropollutants in the Environment

    6.38.3. Properties of Micropollutants

    6.38.4. Micropollutants in Activated Sludge Systems

    6.38.5. Prospects for Water and Wastewater Biotreatment

    6.38.6. Conclusions

    6.39. Microbial Sensors for Monitoring and Control of Aerobic, Anoxic, and Anaerobic Bioreactors in Wastewater Treatment


    6.39.1. Introduction

    6.39.2. Biosensors for Control of Aerobic Processes

    6.39.3. Biosensors for Control of Anaerobic Digestion

    6.39.4. Denitrification Control Biosensors

    6.39.5. Other Types of Biosensors

    6.39.6. Conclusions

    6.40. Efficiency and Sustainability of Urban Wastewater Treatment with Maximum Separation of the Solid and Liquid Fraction


    6.40.1. Introduction

    6.40.2. Actual Situation in Wastewater Treatment Plants

    6.40.3. Sustainability in Wastewater Treatment

    6.40.4. Overall Technology Ranking

    6.40.5. Conclusions

    6.41. Biotreatment of Drinking Water


    6.41.1. Introduction: Bacteria and Biofiltration – A Serendipitous Partnership

    6.41.2. Biofilms and Oligotrophic Growth

    6.41.3. Different Types of Biofilters

    6.41.4. Parameters and Methodology for Biofiltration Monitoring

    6.41.5. Conclusions, Questions, and Future Perspectives

    6.42. Agriculture and Agro-Industrial Wastes, Byproducts, and Wastewaters


    6.42.1. Introduction

    6.42.2. Guidelines for the Valorization of Agriculture and Agro-Industrial Wastes and Wastewaters

    6.42.3. Biomass Resources

    6.42.4. Wastewaters

    6.42.5. Byproducts of the Olive-Oil Extraction Industry: An Emblematic Case

    6.42.6. Conclusions

    6.43. Production of Fine Chemicals by (Bio)Transformation of Agro-Food Byproducts and Wastes



    6.43.1. Introduction

    6.43.2. Extraction and Extraction Techniques

    6.43.3. Modification of Carbohydrates

    6.43.4. Modification of Lipids (Oils and Fats) and Glycerol

    6.43.5. Modification of Proteins

    6.43.6. Modification of Phenol Derivatives

    6.43.7. Production of d-Glucurono-γ-Lactone from Corn Wastes – A Case Study

    6.43.8. Conclusions

    6.45. Application of White-Rot Fungi in Transformation, Detoxification, or Revalorization of Agriculture Wastes



    6.45.1. Introduction

    6.45.2. Fungal Transformation of Hazardous Organic Compounds in the Bioremediation of Polluted Soils and Industrial Wastewaters

    6.45.3. Application of White-Rot Fungi and Laccases in the Pulp and Paper Industry

    6.45.4. Revalorization of byproducts from Agriculture

    6.45.5. The Role of White-Rot Fungi and Their Enzymes on Second-Generation Bioethanol

    6.45.6. Concluding Remarks

    6.46. A Microbial Perspective on Ethanolic Lignocellulose Fermentation


    6.46.1. Introduction

    6.46.2. Fermenting Microorganisms

    6.46.3. Conclusions and Perspectives

    6.47. Techno-Economic Aspects of Ethanol Production from Lignocellulosic Agricultural Crops and Residues


    6.47.1. Introduction

    6.47.2. Which Process Steps Can Be Considered Most Important?

    6.47.3. Process Modeling

    6.47.4. Conclusions

    6.48. Biohydrogen Production from Agricultural Agrofood-Based Resources


    6.48.1. Introduction

    6.48.2. Light-Driven Biohydrogen Production

    6.48.3. Dark Fermentation

    6.48.4. Strategies to Increase Biohydrogen Yields

    6.48.5. Conclusions

    6.49. Microbial Fuel Cells and Bioelectrochemical Systems

    6.49.1. Introduction: BES in the Context of Industrial and Environmental Biotechnology

    6.49.2. Fundamentals of Microbial Extracellular Electron-Transfer Processes

    6.49.3. Microbial BES Generating Electricity: MFCs

    6.49.4. Microbial BES for the Production of Chemicals: Microbial Electrolysis Cells

    6.49.5. Microbial BES for Analytical Application: Microbial Biosensors

    6.49.6. Microbial BES for Remediation of Contaminated Sites

    6.50. Vanillin Production from Agro-Industrial Wastes


    6.50.1. Introduction

    6.50.2. Bioconversion of Ferulic Acid into Vanillin

    6.50.3. Corn-Based Processes

    6.50.4. Rice-Based Processes

    6.50.5. Wheat-Based Processes

    6.50.6. Non-Cereal-Based Processes

    6.50.7. Conclusions

    6.51. Mixed Culture Processes for Polyhydroxyalkanoate Production from Agro-Industrial Surplus/Wastes as Feedstocks


    6.51.1. What Are Polyhydroxyalkanoates?

    6.51.2. How Are PHAs Synthesized by Microbial Cells?

    6.51.3. Governing the Selective Pressure for PHA-Storing Organisms in FF Processes

    6.51.4. How Can Mixed Culture Processes Convert Organic Byproducts into PHAs?

    6.51.5. Concluding Remarks and Future Perspectives

    6.52. Biosorption for Industrial Applications


    6.52.1. Introduction

    6.52.2. Biosorption Material Preparation

    6.52.3. Biosorbent Material Processing and Formulation

    6.52.4. Biosorption Process Principles

    6.52.5. Biosorption Process Example

    6.52.6. Conclusion

    6.53. BT Technology for the Control of Methane Emissions from Permafrost and Natural Gas Hydrates


    6.53.1. Introduction

    6.53.2. Oxic and Anoxic Methane Oxidation

    6.53.3. Methane-Oxidizing Consortia and Biofilms

    6.53.4. Membrane-Attached Bioreactors

    6.53.5. Technical-Scale Methanotrophic Membrane Biofilm Reactors

    6.53.6. Concluding Remarks

    6.54. Molecular Aspects of Microbial Dissimilatory Reduction of Radionuclides


    6.54.1. Introduction

    6.54.2. Phylogenetic Diversity of Dissimilatory Radionuclide-Reducing Microorganisms

    6.54.3. Enzymatic Aspects of Microbial Dissimilatory Reduction of Radionuclides

    6.54.4. Genomic Aspects of Microbial Dissimilatory Reduction of Radionuclides

    6.54.5. In situ Bioremediation Potential of Dissimilatory Radionuclide-Reducing Microorganisms

    6.54.6. Conclusions

    6.55. Today’s Wastes, Tomorrow’s Materials for Environmental Protection



    6.55.1. Introduction

    6.55.2. Case Histories Illustrating Bioconversion of Wastes into New Materials

Product details

  • No. of pages: 5320
  • Language: English
  • Copyright: © Pergamon 2011
  • Published: July 20, 2011
  • Imprint: Pergamon
  • eBook ISBN: 9780080885049

About the Editor in Chief

Murray Moo-Young

Murray Moo-Young
Murray Moo-Young is a distinguished professor emeritus at the University of Waterloo, Canada. Before academia, he worked in England for the British Ministry of Industry. A Jamaican-Chinese Canadian, Murray received his degrees from the University of London (BSc Chemistry, PhD Biochemical Engineering) and University of Toronto (MASc Chemical Engineering) followed by a postdoctoral fellowship at the University of Edinburgh. He has been a visiting professor at top universities worldwide including MIT, UC Berkeley, University of Oxford, Federal Polytechnic Institute Lausanne, University of Karlsruhe, Dalian University of Science and Technology and Osaka University. To date, his research has produced 13 books, nine patents and over 355 papers. He is an international consultant to industry and government and the executive editor of the journal Biotechnology Advances (Impact Factor 8.250). Dr. Moo-Young's honors include the top awards of the Canadian Society for Chemical Engineering and the American Chemical Society, Biochemical Technology Division. As an elected fellow of the American Institute for Medical and Biological Engineering (FAIMBE) and the Royal Society of Canada (FRSC), "the highest accolade for an academic in Canada", Dr. Moo-Young has come to be known as a leader in the field of biotechnology.

Affiliations and Expertise

University of Waterloo, Canada

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