Biotechnology for Biofuel Production and Optimization

Biotechnology for Biofuel Production and Optimization is the compilation of current research findings that cover the entire process of biofuels production from manipulation of genes and pathways to organisms and renewable feedstocks for efficient biofuel production as well as different cultivation techniques and process scale-up considerations. This book captures recent breakthroughs in the interdisciplinary areas of systems and synthetic biology, metabolic engineering, and bioprocess engineering for renewable, cleaner sources of energy.

Chapter 1: Engineering Central Metabolism for Production of Higher Alcohol-based Biofuels

Abstract
Acknowledgments
1.1 Introduction: Longer Chain Bioalcohols as Gasoline Alternatives
1.2 Producing Longer Chain Alcohols Through the Central Metabolism
1.3 Strategies for Improving Higher Alcohol Production
1.4 Successes and Challenges on the Path Towards Commercialization
1.5 Outlook: Overcoming Roadblocks

Chapter 2: Secondary Metabolism for Isoprenoid-based Biofuels

Abstract
Acknowledgments
2.1 Introduction
2.2 Biosynthesis of Isoprenoids
2.3 Engineering of the Isoprenoid Pathways for Biofuels Production
2.4 Engineering of the MVA Pathway for Isoprenoid-based Biofuels
2.5 Concluding Remarks

Chapter 3: Metabolic Engineering for Fatty Acid and Biodiesel Production

Abstract
3.1 Introduction
3.2 Overview of Lipid Metabolism
3.3 Modified Fatty Acid Species
3.4 Conversion of Lipids and Fatty Acids into Biodiesel
3.5 Conversion of Fatty Acids into Additional Oleochemicals
3.6 Host Organism
3.7 Conclusion

Chapter 4: Pathway and Strain Design for Biofuels Production

Abstract
Acknowledgments
4.1 Introduction
4.2 Pathway Design
4.3 Strain Design
4.4 Future Perspectives

Chapter 5: RNA-Based Molecular Sensors for Biosynthetic Pathway Design, Evolution, and Optimization

Abstract
5.1 Introduction to Biofuel Pathways
5.2 RNA-Based Regulatory Elements
5.3 RNA Aptamers for Pathway Intermediates and Products
5.4 Transforming RNA Aptamers into Sensors
5.5 Modeling Biochemical Pathways
5.6 Future Directions for RNA Sensor Design
5.7 Concluding Remarks

Chapter 6: Pathway Assembly and Optimization

Abstract
6.1 Introduction
6.2 Assembly Methods
6.3 Combinatorial Assembly
6.4 Challenges and Future Direction

Chapter 7: Design of Dynamic Pathways

Abstract
Acknowledgments
Summary
7.1 Dynamic Regulation Basics
7.2 Current Progress on Dynamic Pathway Designs
7.3 Tools to Engineer Dynamic Pathways
7.4 Discussion
7.5 Future Trends

Chapter 8: Applications of Constraint-Based Models for Biochemical Production

Abstract
Acknowledgments
8.1 Introduction
8.2 Genome-Scale Metabolic Reconstructions
8.3 Foundations of Constraint-Based Modeling
8.4 Constraint-Based Strain Evaluation Techniques
8.5 Constraint-Based Strain Design Techniques
8.6 Case Studies
8.7 Concluding Remarks

Chapter 9: Biotechnological Strategies for Advanced Biofuel Production: Enhancing Tolerance Phenotypes Through Genome-Scale Modifications

Abstract
Acknowledgments
9.1 Introduction
9.2 Advanced Biofuel Candidates
9.3 Microbial Production Limitations
9.4 The Genome Engineering Toolbox
9.5 Concluding Remarks

Chapter 10: Evolutionary Methods for Improving the Production of Biorenewable Fuels and Chemicals

Abstract
10.1 Introduction
10.2 Mechanisms of Evolution
10.3 Engineered Methods of Evolution
10.4 Evolution for Increased Tolerance
10.5 Evolution for Increased Production
10.6 Enabling Increased Production by Increasing Tolerance
10.7 Reverse Engineering of Evolved Strains
10.8 Modeling of Evolution
10.9 Concluding Statement

Chapter 11: Biomass Utilization

Abstract
Acknowledgments
11.1 Introduction
11.2 Introduction to Biomass
11.3 Pretreatment Technologies for LCB
11.4 Enzymatic Hydrolysis
11.5 Consolidated Bioprocessing (CBP)
11.6 Concluding Remarks

Chapter 12: Ralstonia eutropha H16 as a Platform for the Production of Biofuels, Biodegradable Plastics, and Fine Chemicals from Diverse Carbon Resources

Abstract
Acknowledgments
12.1 Introduction
12.2 Advantages in Substrate and Metabolite Diversity and Flexibility
12.3 Diverse Pathways for Biosynthesis of Value-Added Compounds
12.4 Conclusion and Outlook

Chapter 13: Methane Biocatalysis: Selecting the Right Microbe

Abstract
Acknowledgments
13.1 Introduction
13.2 Methane Biocatalysis: Basic Concepts
13.3 Selecting the Right Microbe: C₁-Oxidation Options
13.4 Selecting the Right Microbe: C₁-Assimilation Options
13.5 Selecting the Right Microbe: Available Cultures
13.6 Looking for a New Microbe: Isolation Strategies
13.7 Concluding Remarks

Chapter 14: Photosynthetic Platform Strain Selection: Strain Selection Considerations and Large-Scale Production Limitations

Abstract
14.1 Introduction
14.2 Platform Strain Selection
14.3 Limitations/Large-Scale Production Considerations
14.4 Current Industrial Production
14.5 Conclusion

Chapter 15: Interpreting and Designing Microbial Communities for Bioprocess Applications, from Components to Interactions to Emergent Properties

Abstract
Acknowledgments
15.1 Introduction
15.2 Definitions
15.3 Ecological Theories for Interpreting and Designing Communities
15.4 Case Studies of Communities with Interpretation
15.5 Conclusions

Chapter 16: Cell-Free Biotechnologies

Abstract
16.1 Cell Free Biotechnology for Value Added Products
16.2 Cell Free Biotechnology for Fuel Production
16.3 Cell Free Biotechnology for Energy Conversion
16.4 Enzyme Stability
16.5 Enzyme Immobilization
16.6 Conclusions

Chapter 17: Microbial Electrochemical Cells and Biorefinery Energy Efficiency

Abstract
Acknowledgments
17.1 Introduction
17.2 Principles of BES Technology
17.3 Conversion of Substrates Present in Biorefinery Process Water Using BES Systems
17.4 Optimization of energy conversion in biorefinery
17.5 High-efficiency Biorefinery Process Schemes Implementing BES
17.6 Comparison with Alternate Technologies for Hydrogen Production
17.7 Advantages of Hydrogen in Comparison to Methane as a Coproduct
17.8 Status of the MEC Technology
17.9 Scale-up Issues and Future Directions

Chapter 18: Photobiohybrid Solar Conversion with Metalloenzymes and Photosynthetic Reaction Centers

Abstract
Acknowledgments
18.1 Introduction
18.2 Biological Catalysts for Production of Reduced Products and Fuels
18.3 Biological Antenna: Photoelectrochemical Biofuels Production Systems Based on Photosystem I
18.4 Perspectives

Chapter 19: Scale-Up—Bioreactor Design and Culture Optimization

Abstract
19.1 Introduction
19.2 General Scale-Up Process
19.3 Microalgal Photobioreactors
19.4 Design Performance of Microalgal Photobioreactors
19.5 Microalgal Culture Optimization
19.6 Concluding Remarks

Chapter 20: Scale-Up Considerations for Biofuels

Abstract
20.1 Introduction
20.2 Aeration in Large-Scale Cultures
20.3 Other Operating Concerns for Large-Scale Cultures
20.4 Process and Culture Optimization Strategies
20.5 Concluding Remarks

CE

Carrie A Eckert

Carrie A. Eckert, PhD., is a Senior Research Scientist with a joint appointment at the National Renewable Energy Laboratory (NREL) and the University of Colorado, Boulder, Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO. Eckert received a B.S. in Biology from the University of South Dakota (1999) and a Ph.D. in Molecular Biology at the University of Colorado, Anschutz Campus under the supervision of Dr. Paul Megee where she studied chromosome segregation in Saccharomyces cerevisiae (2006). After a short Howard Hughes Medical Institute (HHMI) postdoctoral fellowship with Dr. James Maller studying cell cycle regulation in Xenopus laevis egg extracts (Pharmacology, University of Colorado, Anschutz campus), she began postdoctoral studies at the National Renewable Energy Laboratory in 2008 and became a staff scientist in 2011. Her work at NREL has involved the study of hydrogenases and metabolic engineering in diverse microbes including Synechocystis sp. PCC6803, Ralstonia eutropha H16, and Rubrivivax gelatinosus CBS. More recent work includes the metabolic engineering of bioethylene production in E. coli as a part of a collaborative project with the Gill lab, as well as a collaborative project with Kiverdi working on metabolic engineering of microbes for terpenoid production using Syngas as a feedstock.

Affiliations and expertise

National Renewable Energy Laboratory (NREL); University of Colorado, Boulder; the Renewable and Sustainable Energy Institute (RASEI), Golden, CO, USA

CT

Cong T Trinh

Cong T. Trinh, PhD., is a Professor of Chemical and Biomolecular Engineering at the University of Tennessee Knoxville (UTK). Trinh received his B.S. in Chemical Engineering (with summa cum laude, honors thesis) at the University of Houston and earned his Ph.D. in Chemical Engineering at the University of Minnesota, Twin Cities. To continue his interests in biofuels research, he has worked at the Energy Biosciences Institute, University of California, Berkeley as a postdoctoral scholar. At UTK, his research interests focus on understanding and engineering cellular metabolism with the ultimate goal to design, construct, and characterize cells with optimized metabolic functionalities. These engineered cells are utilized as efficient and robust whole-cell biocatalysts exhibiting only desirable properties specifically tailored for biotechnological applications related to energy, health, and environment.

Affiliations and expertise

Dept of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, TN, USA; BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA

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