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Fundamental Bioengineering

Book Description

A thorough introduction to the basics of bioengineering, with a focus on applications in the emerging "white" biotechnology industry.
As such, this latest volume in the "Advanced Biotechnology" series covers the principles for the design and analysis of industrial bioprocesses as well as the design of bioremediation systems, and several biomedical applications. No fewer than seven chapters introduce stoichiometry, kinetics, thermodynamics and the design of ideal and real bioreactors, illustrated by more than 50 practical examples. Further chapters deal with the tools that enable an understanding of the behavior of cell cultures and enzymatically catalyzed reactions, while others discuss the analysis of cultures at the level of the cell, as well as structural frameworks for the successful scale-up of bioreactions. In addition, a short survey of downstream processing options and the control of bioreactions is given.
With contributions from leading experts in industry and academia, this is a comprehensive source of information peer-reviewed by experts in the field.

Table of Contents

  1. Cover
  2. Related Titles
  3. Title Page
  4. Copyright
  5. List of Contributors
  6. About the Series Editors
    1. Chapter 1: Introduction and Overview
  7. Part One: Fundamentals of Bioengineering
    1. Chapter 2: Experimentally Determined Rates of Bio-Reactions
      1. Summary
      2. 2.0 Introduction
      3. 2.1 Mass Balances for a CSTR Operating at Steady State
      4. 2.2 Operation of the Steady-State CSTR
      5. References
    2. Chapter 3: Redox Balances and Consistency Check of Experiments
      1. Summary
      2. 3.1 Black-Box Stoichiometry Obtained in a CSTR Operated at Steady State
      3. 3.2 Calculation of Stoichiometric Coefficients by Means of a Redox Balance
      4. 3.3 Applications of the Redox Balance
      5. 3.4 Composition of the Biomass X
      6. 3.5 Combination of Black-Box Models
      7. 3.6 Application of Carbon and Redox Balances in Bio-Remediation Processes
      8. References
    3. Chapter 4: Primary Metabolic Pathways and Metabolic Flux Analysis
      1. Summary
      2. 4.0 Introduction
      3. 4.1 Glycolysis
      4. 4.2 Fermentative Metabolism: Regenerating the NAD+ Lost in Glycolysis
      5. 4.3 The TCA Cycle: Conversion of Pyruvate to NADH + FADH2, to Precursors or Metabolic Products
      6. 4.4 NADPH and Biomass Precursors Produced in the PP Pathway
      7. 4.5 Oxidative Phosphorylation: Production of ATP from NADH (FADH2) in Aerobic Fermentation
      8. 4.6 Summary of the Biochemistry of Primary Metabolic Pathways
      9. 4.7 Metabolic Flux Analysis Discussed in Terms of Substrate to Product Pathways
      10. 4.8 Metabolic Flux Analysis Discussed in Terms of Individual Pathway Rates in the Network
      11. 4.9 Propagation of Experimental Errors in MFA
      12. 4.10 Conclusions
      13. References
    4. Chapter 5: A Primer to <sup xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops" xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:svg="http://www.w3.org/2000/svg" xmlns:ibooks="http://vocabulary.itunes.apple.com/rdf/ibooks/vocabulary-extensions-1.0">13</sup>C Metabolic Flux AnalysisC Metabolic Flux Analysis
      1. Summary
      2. 5.1 Introduction
      3. 5.2 Input and Output Data of 13C MFA
      4. 5.3 A Brief History of 13C MFA
      5. 5.4 An Illustrative Toy Example
      6. 5.5 The Atom Transition Network
      7. 5.6 Isotopomers and Isotopomer Fractions
      8. 5.7 The Isotopomer Transition Network
      9. 5.8 Isotopomer Labeling Balances
      10. 5.9 Simulating an Isotope Labeling Experiment
      11. 5.10 Isotopic Steady State
      12. 5.11 Flux Identifiability
      13. 5.12 Measurement Models
      14. 5.13 Statistical Considerations
      15. 5.14 Experimental Design
      16. 5.15 Exchange Fluxes
      17. 5.16 Multidimensional Flux Identifiability
      18. 5.17 Multidimensional Flux Estimation
      19. 5.18 The General Parameter Fitting Procedure
      20. 5.19 Multidimensional Statistics
      21. 5.20 Multidimensional Experimental Design
      22. 5.21 The Isotopically Nonstationary Case
      23. 5.22 Some Final Remarks on Network Specification
      24. 5.23 Algorithms and Software Frameworks for 13C MFA
      25. Glossary
      26. References
    5. Chapter 6: Genome-Scale Models
      1. Summary
      2. 6.1 Introduction
      3. 6.2 Reconstruction Process of Genome-Scale Models
      4. 6.3 Genome-Scale Model Prediction
      5. 6.4 Genome-Scale Models of Prokaryotes
      6. 6.5 Genome-Scale Models of Eukaryotes
      7. 6.6 Integration of Polyomic Data into Genome-Scale Models
      8. Acknowledgment
      9. References
    6. Chapter 7: Kinetics of Bio-Reactions
      1. Summary
      2. 7.1 Simple Models for Enzymatic Reactions and for Cell Reactions with Unstructured Biomass
      3. 7.2 Variants of Michaelis–Menten and Monod kinetics
      4. 7.3 Summary of Enzyme Kinetics and the Kinetics for Cell Reactions
      5. 7.4 Cell Reactions with Unsteady State Kinetics
      6. 7.5 Cybernetic Modeling of Cellular Kinetics
      7. 7.6 Bioreactions with Diffusion Resistance
      8. 7.7 Sequences of Enzymatic Reactions: Optimal Allocation of Enzyme Levels
      9. References
    7. Chapter 8: Application of Dynamic Models for Optimal Redesign of Cell Factories
      1. Summary
      2. 8.1 Introduction
      3. 8.2 Kinetics of Pathway Reactions: the Need to Measure in a Very Narrow Time Window
      4. 8.3 Tools for In Vivo Diagnosis of Pathway Reactions
      5. 8.4 Examples: The Pentose-Phosphate Shunt and Kinetics of Phosphofructokinase
      6. 8.5 Additional Approaches for Dynamic Modeling Large Metabolic Networks
      7. 8.6 Dynamic Models Used for Redesigning Cell Factories. Examples: Optimal Ethanol Production in Yeast and Optimal Production of Tryptophan in E. Coli
      8. 8.7 Target Identification for Drug Development
      9. References
    8. Chapter 9: Chemical Thermodynamics Applied in Bioengineering
      1. Summary
      2. 9.0 Introduction
      3. 9.1 Chemical Equilibrium and Thermodynamic State Functions
      4. 9.2 Thermodynamic Properties Obtained from Galvanic Cells
      5. 9.3 Conversion of Free Energy Harbored in NADH and FADH2 to ATP in Oxidative Phosphorylation
      6. 9.4 Calculation of Heat of Reaction Q=(−ΔHc) and of (−ΔGc) Based on Redox Balances
      7. References
  8. Part Two: Bioreactors
    1. Chapter 10: Design of Ideal Bioreactors
      1. Summary
      2. 10.0 Introduction
      3. 10.1 The Design Basis for a Once-Through Steady-State CSTR
      4. 10.2 Combination of Several Steady-State CSTRs in Parallel or in Series
      5. 10.3 Recirculation of Biomass in a Single Steady-State CSTR
      6. 10.4 A Steady-State CSTR with Uptake of Substrates from a Gas Phase
      7. 10.5 Fed-Batch Operation of a Stirred Tank Reactor in the Bio-Industry
      8. 10.6 Loop Reactors: a Modern Version of Airlift Reactors
      9. References
    2. Chapter 11: Mixing and Mass Transfer in Industrial Bioreactors
      1. Summary
      2. 11.0 Introduction
      3. 11.1 Definitions of Mixing Processes
      4. 11.2 The Power Input P Delivered by Mechanical Stirring
      5. 11.3 Mixing and Mass Transfer in Industrial Reactors
      6. 11.4 Conclusions
      7. References
  9. Part Three: Downstream Processing
    1. Chapter 12: Product Recovery from the Cultures
      1. Summary
      2. 12.0 Introduction
      3. 12.1 Steps in Downstream Processing and Product Recovery
      4. 12.2 Baker's Yeast
      5. 12.3 Xanthan Gum
      6. 12.4 Penicillin
      7. 12.5 α-A Interferon
      8. 12.6 Insulin
      9. 12.7 Conclusions
      10. References
    2. Chapter 13: Purification of Bio-Products
      1. Summary
      2. 13.1 Methods and Types of Separations in Chromatography
      3. 13.2 Materials Used in Chromatographic Separations
      4. 13.3 Chromatographic Theory
      5. 13.4 Practical Considerations in Column Chromatographic Applications
      6. 13.5 Scale-Up
      7. 13.6 Industrial Applications
      8. 13.7 Some Alternatives to Column Chromatographic Techniques
      9. 13.8 Electrodialysis
      10. 13.9 Electrophoresis
      11. 13.10 Conclusions
      12. References
  10. Part Four: Process Development, Management and Control
    1. Chapter 14: Real-Time Measurement and Monitoring of Bioprocesses
      1. Summary
      2. 14.1 Introduction
      3. 14.2 Variables that should be Known
      4. 14.3 Variables Easily Accessible and Standard
      5. 14.4 Variables Requiring More Monitoring Effort and Not Yet Standard
      6. 14.5 Data Evaluation
      7. References
    2. Chapter 15: Control of Bioprocesses
      1. Summary
      2. 15.1 Introduction
      3. 15.2 Bioprocess Control
      4. 15.3 Principles and Basic Algorithms in Process Control
      5. References
    3. Chapter 16: Scale-Up and Scale-Down
      1. Summary
      2. 16.1 Introduction
      3. 16.2 Description of the Large Scale
      4. 16.3 Scale-Down
      5. 16.4 Investigations at Lab Scale
      6. 16.5 Scale-Up
      7. 16.6 Outlook
      8. References
    4. Chapter 17: Commercial Development of Fermentation Processes
      1. Summary
      2. 17.1 Introduction
      3. 17.2 Basic Principles of Developing New Fermentation Processes
      4. 17.3 Techno-economic Analysis: the Link Between Science, Engineering, and Economy
      5. 17.4 From Fermentation Process Development to the Market
      6. 17.5 The Industrial Angle and Opportunities in the Chemical Industry
      7. 17.6 Evaluation of Business Opportunities
      8. 17.7 Concluding Remarks and Outlook
      9. Acknowledgment
      10. References
  11. Index
  12. EULA