Cover
Related Titles
Title Page
Copyright
List of Contributors
About the Series Editors
1. Chapter 1: Introduction and Overview
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 ¹³C 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
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
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
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
Index
EULA

List of Illustrations

Figure 2.1
Figure 2.2
Figure 2.3
Figure 4.1
Figure 4.2
Figure 4.3
Figure 4.4
Figure 4.5
Figure 4.6
Figure 4.7
Figure 4.8
Figure 4.9
Figure 4.10
Figure 4.11
Figure 4.12
Figure 4.13
Figure 4.14
Figure 4.15
Figure 4.16
Figure 5.1
Figure 5.2
Figure 5.3
Figure 5.4
Figure 5.5
Figure 5.6
Figure 5.7
Figure 5.8
Figure 5.9
Figure 5.10
Figure 5.11
Figure 5.12
Figure 5.13
Figure 5.14
Figure 5.15
Figure 5.16
Figure 5.17
Figure 5.18
Figure 5.19
Figure 6.1
Figure 6.2
Figure 6.3
Figure 6.4
Figure 6.5
Figure 6.6
Figure 6.7
Figure 6.8
Figure 6.9
Figure 7.1
Figure 7.2
Figure 7.3
Figure 7.4
Figure 7.5
Figure 7.6
Figure 7.7
Figure 7.8
Figure 7.9
Figure 7.10
Figure 7.11
Figure 7.12
Figure 7.13
Figure 7.14
Figure 7.15
Figure 7.16
Figure 7.17
Figure 7.18
Figure 8.1
Figure 8.2
Figure 8.3
Figure 8.4
Figure 8.5
Figure 8.6
Figure 8.7
Figure 8.8
Figure 8.9
Figure 8.10
Figure 8.11
Figure 8.12
Figure 8.13
Figure 8.14
Figure 8.15
Figure 8.16
Figure 8.17
Figure 8.18
Figure 8.19
Figure 8.20
Figure 8.21
Figure 8.22
Figure 8.23
Figure 8.24
Figure 8.25
Figure 8.26
Figure 8.27
Figure 8.28
Figure 8.29
Figure 8.30
Figure 8.31
Figure 8.32
Figure 8.33
Figure 8.34
Figure 8.35
Figure 9.1
Figure 9.2
Figure 10.1
Figure 10.2
Figure 10.3
Figure 10.4
Figure 10.5
Figure 10.6
Figure 10.7
Figure 10.8
Figure 10.9
Figure 10.10
Figure 11.1
Figure 11.2
Figure 11.3
Figure 11.4
Figure 12.1
Figure 12.2
Figure 12.3
Figure 12.4
Figure 12.5
Figure 12.6
Figure 13.1
Figure 13.2
Figure 15.1
Figure 15.2
Figure 15.3
Figure 15.4
Figure 15.5
Figure 15.6
Figure 15.7
Figure 15.8
Figure 16.1
Figure 16.2
Figure 16.3
Figure 16.4
Figure 17.1
Figure 17.2
Figure 17.3
Figure 17.4
Figure 17.5
Figure 17.6
Figure 17.7
Figure 17.8
Figure 17.9
Figure 17.10
Figure 17.11
Figure 17.12
Figure 17.13

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Planned Volumes of the “Advanced Biotechnology” Series:

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Edited by John Villadsen

Fundamental Bioengineering

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ISSN: 2365-3035

Print ISBN: 978-3-527-33674-6

ePDF ISBN: 978-3-527-69746-5

ePub ISBN: 978-3-527-69745-8

Mobi ISBN: 978-3-527-69747-2

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List of Contributors

Basti Bergdahl

Danmarks Tekniske Universitet

Novo Nordisk Foundation Center for Biosustainability

Kogle Allé 6

2970 Hørsholm

Denmark

Jochen Förster

Danmarks Tekniske Universitet

Novo Nordisk Foundation Center for Biosustainability

Kogle Allé 6

2970 Hørsholm

Denmark

Thomas Grotkjær

Novozymes A/S

Biomass Conversion Business Development

Novo Allé

2880 Bagsvaerd

Copenhagen

Denmark

Markus Herrgård

Danmarks Tekniske Universitet

Novo Nordisk Foundation Center for Biosustainability

Kogle Allé 6

2970 Hørsholm

Denmark

Jakob Kjøbsted Huusom

Technical University of Denmark

Department of Chemical and Biochemical Engineering

Anker Engelunds Vej 1

Bygning 101A

2800 Kgs Lyngby

Denmark

Daniel Machado

Universidade do Minho

Centro de Engenharia Biológica

4710-057 Braga

Portugal

Sunil Nath

Indian Institute of Technology, Delhi

Department of Biochemical Engineering and Biotechnology

Hauz Khas

New Delhi 110016

India

Sebastian Niedenführ

Forschungszentrum Jülich GmbH

Institute of Bio- and Geosciences

IBG-1: Biotechnology

52425 Jülich

Germany

Katharina Nöh

Forschungszentrum Jülich GmbH

Institute of Bio- and Geosciences

IBG-1: Biotechnology

52425 Jülich

Germany

Henk Noorman

DSM Biotechnology Center

A. Fleminglaan 1

2613 CA Delft

The Netherlands

Matthias Reuss

University of Stuttgart

Stuttgart Research Center Systems Biology

Nobelstr. 15

70569 Stuttgart

Germany

Nikolaus Sonnenschein

Danmarks Tekniske Universitet

Novo Nordisk Foundation Center for Biosustainability

Kogle Allé 6

2970 Hørsholm

Denmark

Bernhard Sonnleitner

Zurich University of Applied Sciences (ZHAW)

Institute for Chemistry and Biological Chemistry (ICBC)

Biochemical Engineering

Einsiedlerstrasse 29

8820 Waedenswil

Switzerland

John Villadsen

Technical University of Denmark (DTU)

Department of Chemical and Biochemical Engineering

Building 229

2800 Kgs Lyngby

Denmark

Wolfgang Wiechert

Forschungszentrum Jülich GmbH

Institute of Bio- and Geosciences

IBG-1: Biotechnology

52425 Jülich

Germany

About the Series Editors

Sang Yup Lee is Distinguished Professor at the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology. At present, Prof. Lee is the Director of the Center for Systems and Synthetic Biotechnology, Director of the BioProcess Engineering Research Center, and Director of the Bioinformatics Research Center. He has published more than 500 journal papers, 64 books, and book chapters, and has more than 580 patents (either registered or applied) to his credit. He has received numerous awards, including the National Order of Merit, the Merck Metabolic Engineering Award, the ACS Marvin Johnson Award, Charles Thom Award, Amgen Biochemical Engineering Award, Elmer Gaden Award, POSCO TJ Park Prize, and HoAm Prize. He is Fellow of American Association for the Advancement of Science, the American Academy of Microbiology, American Institute of Chemical Engineers, Society for Industrial Microbiology and Biotechnology, American Institute of Medical and Biological Engineering, the World Academy of Science, the Korean Academy of Science and Technology, and the National Academy of Engineering of Korea. He is also Foreign Member of National Academy of Engineering, USA. In addition, he is honorary professor of the University of Queensland (Australia), honorary professor of the Chinese Academy of Sciences, honorary professor of Wuhan University (China), honorary professor of Hubei University of Technology (China), honorary professor of Beijing University of Chemical Technology (China), and advisory professor of the Shanghai Jiaotong University (China). Apart from his academic associations, Prof. Lee is the editor-in-chief of the Biotechnology Journal and is also contributing to numerous other journals as associate editor and board member. Prof. Lee is serving as a member of Presidential Advisory Committee on Science and Technology (South Korea).

Jens Nielsen is Professor and Director to Chalmers University of Technology (Sweden) since 2008. He obtained an MSc degree in chemical engineering and a PhD degree (1989) in biochemical engineering from the Technical University of Denmark (DTU) and after that established his independent research group and was appointed full professor there in 1998. He was Fulbright visiting professor at MIT in 1995–1996. At DTU, he founded and directed the Center for Microbial Biotechnology. Prof. Nielsen has published more than 350 research papers and coauthored more than 40 books, and he is inventor of more than 50 patents. He has founded several companies that have raised more than 20 million in venture capital. He has received numerous Danish and international awards and is member of the Academy of Technical Sciences (Denmark), the National Academy of Engineering (USA), the Royal Danish Academy of Science and Letters, the American Institute for Medical and Biological Engineering and the Royal Swedish Academy of Engineering Sciences.

Gregory Stephanopoulos is the W.H. Dow Professor of Chemical Engineering at the Massachusetts Institute of Technology (MIT, USA) and Director of the MIT Metabolic Engineering Laboratory. He is also Instructor of Bioengineering at Harvard Medical School (since 1997). He received his BS degree from the National Technical University of Athens and his PhD from the University of Minnesota (USA). He has coauthored about 400 research papers and 50 patents, along with the first textbook on metabolic engineering. He has been recognized by numerous awards from the American Institute of Chemical Engineers (AIChE) (Wilhelm, Walker and Founders awards), American Chemical Society (ACS), Society of Industrial Microbiology (SIM), BIO (Washington Carver Award), the John Fritz Medal of the American Association of Engineering Societies, and others. In 2003, he was elected member of the National Academy of Engineering (USA) and in 2014 President of AIChE.

1
Introduction and Overview

John Villadsen

Bioengineering is a relatively new addition to a long list of terms starting with “bio.” It is broadly defined as “the application of engineering principles to biological systems.” Bioengineering can include elements of chemical, electrical and mechanical engineering, computer science, materials, chemistry and biology. The systems that are analyzed range from cell cultures and enzymes applied in the bio-industry and in bioremediation to prosthetics, construction of models for organs such as liver, drug-delivery systems and numerous other subjects in biomedical engineering, all requiring an understanding of transport phenomena (mass, heat, and momentum transfer) and kinetics, combined in often large mathematical models. Besides a working knowledge of these core chemical engineering disciplines, a successful study of a problem in bioengineering requires an insight into the core disciplines of biology and biochemistry, specifically in human physiology when the goal is, for example, to construct a new cancer drug delivery system.

In this volume, coauthored by nine scientists, mostly working in academic institutions or in the bio-industry, the focus is on application of bioengineering in the emerging “white biotechnology” industry. The design of bioremediation systems closely follows the principles of analysis and design of industrial bioprocesses. This text will also prove valuable for environmental engineers. The biomedical applications of the text are, however, also quite obvious. Thus, the important but complex application of mesenchymal stem cells to treat osteoporosis is based on an optimal growth strategy of the cell culture on a scaffold at the right liquid flow with the right oxygen and nutrient availability. Here, kinetics and transport phenomena are coupled to basic biology and biochemistry, and design of the system is based on a complex model for the interaction between scaffold, cells, and nutrients.

In Chapters 5, 6, and 8, the reader will find self-contained accounts of the tools that together make it possible to understand the behavior of cell cultures and enzymatically catalyzed reactions: The interaction of metabolic network reactions in steady state and during transients, analyzed by mathematical models and solved by state-of-the-art computer software.

In Chapter 16, a structural framework for successful scale-up of bioreactions from laboratory scale to large industrial scale is presented. In Chapter 17, the sequence of management decisions that may lead to new business ventures in the bio-industry is discussed.

The analyses of cultures on the level of the cell are authored by three leading European scientists. Each author gives - as far as possible - a complete account of his subject, illustrated with examples and with sufficient detail to give readers, both in industry and in graduate classes at universities, a fair chance to understand and utilize the very powerful analytical tools presented in the three chapters.

The two Chapters 16 and 17 on large-scale bioreactors and on the business opportunities in the bio-industry are written by leading experts from two major bio-industrial companies, DSM in the Netherlands and Novozymes in Denmark. These chapters could serve as guidelines for prospective business ventures in the industry.

Although the focus of this book is on the bioreactor, Chapters 12 and 13 cover further processing of the effluent from the bioreactor. The author, a distinguished Indian bioscientist, gives a short introduction to the subject of downstream processing. Also, a survey of measuring, monitoring, and control of bioreactions is included. In Chapter 14, a leading expert on chemical analysis to capture key fermentation variables and on using the experimental data in analysis of fermentation broths gives an easy-to-read but largely complete survey of the subject. In Chapter 15, a young expert in control of chemical processes, discusses control problems in bioreactors, specifically addressing the challenges of bio-system control.

Finally, the content of the book is tied together by seven chapters (2, 3, 4, 7, 9, 10, and 11) written by the editor of this work. These chapters introduce a common nomenclature for the whole book, with introductory material on stoichiometry, kinetics, thermodynamics, and design of ideal and real bioreactors. It is hoped that the introductory chapters, illustrated with many simple examples, will make it easier to read the advanced chapters, especially since there are frequent cross references between introductory and advanced chapters.

Part One
Fundamentals of Bioengineering