Fundamental bioengineering

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...

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Detalles Bibliográficos
Otros Autores:	Villadsen, John, editor (editor)
Formato:	Libro electrónico
Idioma:	Inglés
Publicado:	Weinheim, Germany : Wiley-VCH 2016.
Edición:	1st ed
Colección:	Advanced biotechnology.
Materias:	Bioengineering.
Ver en Biblioteca Universitat Ramon Llull:	https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009849087206719

Tabla de Contenidos:

Fundamental Bioengineering
Contents
List of Contributors
About the Series Editors
1: Introduction and Overview
Part One: Fundamentals of Bioengineering
2: Experimentally Determined Rates of Bio-Reactions
Summary
2.0 Introduction
2.1 Mass Balances for a CSTR Operating at Steady State
2.2 Operation of the Steady-State CSTR
References
3: Redox Balances and Consistency Check of Experiments
Summary
3.1 Black-Box Stoichiometry Obtained in a CSTR Operated at Steady State
3.2 Calculation of Stoichiometric Coefficients by Means of a Redox Balance
3.3 Applications of the Redox Balance
3.4 Composition of the Biomass X
3.5 Combination of Black-Box Models
3.6 Application of Carbon and Redox Balances in Bio-Remediation Processes
References
4. Primary Metabolic Pathways and Metabolic Flux Analysis
Summary
4.0 Introduction
4.1 Glycolysis
4.2 Fermentative Metabolism: Regenerating the NAD+ Lost in Glycolysis
4.3 The TCA Cycle: Conversion of Pyruvate to NADH + FADH2, to Precursors or Metabolic Products
4.4 NADPH and Biomass Precursors Produced in the PP Pathway
4.5 Oxidative Phosphorylation: Production of ATP from NADH (FADH2) in Aerobic Fermentation
4.6 Summary of the Biochemistry of Primary Metabolic Pathways
4.7 Metabolic Flux Analysis Discussed in Terms of Substrate to Product Pathways
4.8 Metabolic Flux Analysis Discussed in Terms of Individual Pathway Rates in the Network
4.9 Propagation of Experimental Errors in MFA
4.10 Conclusions
References
5. A Primer to 13C Metabolic Flux Analysis
Summary
5.1 Introduction
5.2 Input and Output Data of 13C MFA
5.3 A Brief History of 13C MFA
5.4 An Illustrative Toy Example
5.5 The Atom Transition Network
5.6 Isotopomers and Isotopomer Fractions
5.7 The Isotopomer Transition Network.
5.8 Isotopomer Labeling Balances
5.9 Simulating an Isotope Labeling Experiment
5.10 Isotopic Steady State
5.11 Flux Identifiability
5.12 Measurement Models
5.13 Statistical Considerations
5.14 Experimental Design
5.15 Exchange Fluxes
5.16 Multidimensional Flux Identifiability
5.17 Multidimensional Flux Estimation
5.18 The General Parameter Fitting Procedure
5.19 Multidimensional Statistics
5.20 Multidimensional Experimental Design
5.21 The Isotopically Nonstationary Case
5.22 Some Final Remarks on Network Specification
5.23 Algorithms and Software Frameworks for 13C MFA
Glossary
References
6. Genome-Scale Models
Summary
6.1 Introduction
6.2 Reconstruction Process of Genome-Scale Models
6.3 Genome-Scale Model Prediction
6.3.1 Mathematical Description of Biochemical Reaction Systems
6.3.2 Constraint-Based Modeling
6.3.3 Pathway Analysis
6.3.4 Flux Balance Analysis
6.3.5 Engineering Applications of Constraint-Based Modeling
6.4 Genome-Scale Models of Prokaryotes
6.4.1 Escherichia coli
6.4.2 Other Prokaryotes
6.4.3 Prokaryotic Communities
6.5 Genome-Scale Models of Eukaryotes
6.5.1 Saccharomyces cerevisiae
6.5.2 Other Unicellular Eukaryotes
6.5.3 Other Multicellular Eukaryotes
6.6 Integration of Polyomic Data into Genome-Scale Models
6.6.1 Integration of Transcriptomics and Proteomics Data
6.6.2 Metabolomics Data
6.6.3 Integration of Multiple Omics
Acknowledgment
References
7. Kinetics of Bio-Reactions
Summary
7.1 Simple Models for Enzymatic Reactions and for Cell Reactions with Unstructured Biomass
7.2 Variants of Michaelis-Menten and Monod kinetics
7.3 Summary of Enzyme Kinetics and the Kinetics for Cell Reactions
7.4 Cell Reactions with Unsteady State Kinetics
7.5 Cybernetic Modeling of Cellular Kinetics.
7.6 Bioreactions with Diffusion Resistance
7.7 Sequences of Enzymatic Reactions: Optimal Allocation of Enzyme Levels
References
8. Application of Dynamic Models for Optimal Redesign of Cell Factories
Summary
8.1 Introduction
8.2 Kinetics of Pathway Reactions: the Need to Measure in a Very Narrow Time Window
8.2.1 Sampling
8.2.2 Quenching and Extraction
8.2.3 Analysis
8.2.4 Examples for Quantitative Measurements of Metabolites in Stimulus-Response Experiments
8.3 Tools for In Vivo Diagnosis of Pathway Reactions
8.3.1 Modular Decomposition of the Network: the Bottom-Up Approach
8.4 Examples: The Pentose-Phosphate Shunt and Kinetics of Phosphofructokinase
8.4.1 Kinetics of the Irreversible Reactions of the Pentose-Phosphate Shunt
8.4.2 Kinetics of the Phophofructokinase I (PFK1)
8.5 Additional Approaches for Dynamic Modeling Large Metabolic Networks
8.5.1 Generalized Mass Action
8.5.2 S-Systems Approach
8.5.3 Convenience Kinetics
8.5.4 Log-Lin and Lin-Log Approaches
8.6 Dynamic Models Used for Redesigning Cell Factories. Examples: Optimal Ethanol Production in Yeast and Optimal Production of Tryptophan in E. Coli
8.6.1 Dynamic Model
8.6.2 Metabolic Control (Sensitivity) Analysis
8.6.3 Synthesis Amplification of Hexose Transporters
8.6.4 Objective Function
8.6.5 Optimal Solutions
8.6.6 Flux Optimization of Tryptophan Production with E. Coli [67]
8.7 Target Identification for Drug Development
References
9. Chemical Thermodynamics Applied in Bioengineering
Summary
9.0 Introduction
9.1 Chemical Equilibrium and Thermodynamic State Functions
9.2 Thermodynamic Properties Obtained from Galvanic Cells
9.3 Conversion of Free Energy Harbored in NADH and FADH2 to ATP in Oxidative Phosphorylation.
9.4 Calculation of Heat of Reaction Q=(- ΔHc) and of (- ΔGc) Based on Redox Balances
References
Part Two: Bioreactors
10. Design of Ideal Bioreactors
Summary
10.0 Introduction
10.1 The Design Basis for a Once-Through Steady-State CSTR
10.2 Combination of Several Steady-State CSTRs in Parallel or in Series
10.3 Recirculation of Biomass in a Single Steady-State CSTR
10.4 A Steady-State CSTR with Uptake of Substrates from a Gas Phase
10.5 Fed-Batch Operation of a Stirred Tank Reactor in the Bio-Industry
10.6 Loop Reactors: a Modern Version of Airlift Reactors
References
11. Mixing and Mass Transfer in Industrial Bioreactors
Summary
11.0 Introduction
11.1 Definitions of Mixing Processes
11.2 The Power Input P Delivered by Mechanical Stirring
11.3 Mixing and Mass Transfer in Industrial Reactors
11.4 Conclusions
References
Part Three: Downstream Processing
12. Product Recovery from the Cultures
Summary
12.0 Introduction
12.1 Steps in Downstream Processing and Product Recovery
12.2 Baker's Yeast
12.3 Xanthan Gum
12.4 Penicillin
12.5 α-A Interferon
12.6 Insulin
12.7 Conclusions
References
13. Purification of Bio-Products
Summary
13.1 Methods and Types of Separations in Chromatography
13.2 Materials Used in Chromatographic Separations
13.3 Chromatographic Theory
13.4 Practical Considerations in Column Chromatographic Applications
13.5 Scale-Up
13.6 Industrial Applications
13.7 Some Alternatives to Column Chromatographic Techniques
13.8 Electrodialysis
13.9 Electrophoresis
13.10 Conclusions
References
Part Four: Process Development, Management and Control
14. Real-Time Measurement and Monitoring of Bioprocesses
Summary
14.1 Introduction
14.2 Variables that should be Known.
14.3 Variables Easily Accessible and Standard
14.4 Variables Requiring More Monitoring Effort and Not Yet Standard
14.4.1 Biomass
14.4.2 Products and Substrates
14.5 Data Evaluation
References
15. Control of Bioprocesses
Summary
15.1 Introduction
15.2 Bioprocess Control
15.2.1 Design Variables in Bioreactor Control
15.2.2 Challenges with Respect to Control of a Bioreactor
15.3 Principles and Basic Algorithms in Process Control
15.3.1 Open Loop Control
15.3.2 Feed-forward and Feedback Control
15.3.3 Single-Loop PID Control
15.3.4 Diagnostic Control Strategies
15.3.5 Plant-Wide Control Design
References
16. Scale-Up and Scale-Down
Summary
16.1 Introduction
16.2 Description of the Large Scale
16.2.1 Mixing
16.2.2 Mass Transfer
16.2.3 CO2 Removal
16.2.4 Cooling
16.2.5 Gas-Liquid Separation
16.3 Scale-Down
16.3.1 One-Compartment Systems
16.3.2 Two-Compartment Systems
16.4 Investigations at Lab Scale
16.4.1 Gluconic Acid
16.4.2 Lipase
16.4.3 Baker's Yeast
16.4.4 Penicillin
16.5 Scale-Up
16.6 Outlook
References
17. Commercial Development of Fermentation Processes
Summary
17.1 Introduction
17.2 Basic Principles of Developing New Fermentation Processes
17.3 Techno-economic Analysis: the Link Between Science, Engineering, and Economy
17.3.1 Value Drivers and Production Costs of Fermentation Processes
17.3.2 Assessment of New Fermentation Technologies
17.3.3 Assessment of Competing Petrochemical Technologies
17.4 From Fermentation Process Development to the Market
17.4.1 The Value Chain of the Chemical Industry
17.4.2 Innovation and Substitution Patterns in the Chemical Industry
17.5 The Industrial Angle and Opportunities in the Chemical Industry
17.6 Evaluation of Business Opportunities.
17.7 Concluding Remarks and Outlook.

Fundamental bioengineering

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