New Frontiers and Applications of Synthetic Biology

New Frontiers and Applications of Synthetic Biology presents a collection of chapters from eminent synthetic biologists across the globe who have established experience and expertise working with synthetic biology. This book offers several important areas of synthetic biology which allow us to read and understand easily. It covers the introduction of synthetic biology and design of promoter, new DNA synthesis and sequencing technology, genome assembly, minimal cells, small synthetic RNA, directed evolution, protein engineering, computational tools, de novo synthesis, phage engineering, a sensor for microorganisms, next-generation diagnostic tools, CRISPR-Cas systems, and more.

This book is a good source for not only researchers in designing synthetic biology, but also for researchers, students, synthetic biologists, metabolic engineers, genome engineers, clinicians, industrialists, stakeholders and policymakers interested in harnessing the potential of synthetic biology in many areas.

Cover image
Title page
Table of Contents
Copyright
Dedication
List of contributors
About the editor
Foreword
Preface
Acknowledgments
Chapter 1. An introduction to advanced technologies in synthetic biology
Abstract
1.1 Introduction
1.2 A brief milestone in synthetic biology
1.3 Advanced technologies in synthetic biology
1.4 Conclusion and future remarks
Acknowledgments
References
Chapter 2. Design and characterization of synthetic promoters
Abstract
2.1 Introduction
2.2 Design and characterization of synthetic promoters in prokaryotes, cyanobacteria, and plants
2.3 Design and characterization of synthetic promoters in higher eukaryotes
2.4 Conclusion
Acknowledgments
References
Chapter 3. Recent development in DNA synthesis technology
Abstract
3.1 Introduction
3.2 Preliminary techniques of DNA synthesis
3.3 Current progress in DNA synthesis technology
3.4 Concluding remarks
References
Chapter 4. Advances, challenges, and opportunities in DNA sequencing technology
Abstract
4.1 Introduction
4.2 Generations of DNA sequencing methods
4.3 Applications of DNA sequencing methods in synthetic biology
4.4 Conclusions and future outlook
References
Chapter 5. Recent developments in genome design and assembly tools
Abstract
5.1 Introduction
5.2 Knowledge as base of genome design: historical evolution
5.3 Genome design, assembly, and editing
5.4 Applications of the genome-editing technology
5.5 Conclusions and future perspectives
5.6 Acknowledgments
References
Chapter 6. Design, building, and challenges in synthetic genomics
Abstract
6.1 Introduction: what is synthetic biology?
6.2 Synthetic genomics
6.3 Synthetic genomes
6.4 Emerging tools for synthetic genome design and assembly
6.5 Putting synthetic in “synthetic genomes”: synthetic genome projects
6.6 Conclusion and future directions
References
Further reading
Chapter 7. Synthetic minimal cells and their applications
Abstract
7.1 Introduction
7.2 Top-down approach for building synthetic minimal cells
7.3 Bottom-up approach for building synthetic cells using existing biochemistry
7.4 Applications
7.5 Conclusion and perspectives
References
Chapter 8. Small RNA-based systems for sensing and therapeutic applications
Abstract
8.1 Introduction
8.2 Methods for engineering RNA sensors based on aptamers and ribozymes
8.3 Ribozymes as biosensors in high-throughput screening arrays
8.4 Designer ribozymes as molecular computing devices
8.5 Ribozyme-based control of gene expression
8.6 External-guided RNA sequences and antisense oligonucleotides
8.7 Future perspective of RNA synthetic biology
8.8 Conclusions
Acknowledgments
References
Chapter 9. High-throughput navigation of the sequence space
Abstract
9.1 Introduction
9.2 What is fitness?
9.3 Tools to generate gene/pathway/genome diversity
9.4 Conclusion
Acknowledgments
References
Chapter 10. Advances in protein engineering and its application in synthetic biology
Abstract
10.1 Introduction
10.2 Protein engineering strategies
10.3 Computer-aided design for protein engineering
10.4 Trends in protein engineering
10.5 Concluding remarks and future perspectives
Acknowledgments
References
Chapter 11. Computational tools for design of synthetic genetic circuits
Abstract
11.1 Introduction
11.2 Components of genetic circuits
11.3 Design principles of synthetic genetic circuits
11.4 Design considerations for circuit architecture
11.5 Use of mathematical modeling to design synthetic genetic circuits
11.6 Examples of mathematical models for construction of synthetic genetic circuits
11.7 Automation of genetic circuit design
11.8 Computational tools for design, modeling, and analysis of synthetic genetic circuits
11.9 Challenges in synthetic genetic circuit design
11.10 Conclusion
References
Chapter 12. Computational tools for synthetic gene optimization
Abstract
12.1 Introduction
12.2 Optimization objectives
12.3 Tools
12.4 Concluding remarks
References
Chapter 13. De novo design and synthesis of biomolecules
Abstract
13.1 Introduction
13.2 De novo design and synthesis of proteins and enzymes
13.3 De novo design of metabolic pathways
References
Chapter 14. A retrobiosynthetic approach for production, conversion, sensing, dynamic regulation and degradation of molecules
Abstract
14.1 Introduction
14.2 Retrobiosynthesis tools
14.3 Pathway engineering
14.4 Biosensor development
14.5 Pathway dynamic regulation
14.6 Degradation routes
14.7 Machine learning in retrobiosynthesis
14.8 Integration of retrobiosynthesis tools into automated workflows
14.9 Conclusions and future perspectives
Acknowledgments
References
Chapter 15. Advances in engineering of bacteriophages for therapeutic applications
Abstract
15.1 Phage therapy
15.2 Engineering techniques
15.3 Isolation, purification, and characterization
15.4 Therapeutic applications
15.5 Conclusion
References
Chapter 16. Design of synthetic biology for the detection of microorganisms
Abstract
16.1 Introduction
16.2 Nucleic acids–based detection
16.3 Other biosignature-based microbe detection
16.4 Conclusions
Acknowledgments
References
Chapter 17. Design of synthetic biological devices for detection and targeting human diseases
Abstract
17.1 Introduction
17.2 Synthetic biology and metabolic disease sensing/treatment
17.3 Synthetic biology and cancer targeting
17.4 Synthetic biology approach for sensing of infectious agents
17.5 Synthetic biology approaches for toxicity sensing using engineered cells
17.6 Conclusion and future perspectives
References
Chapter 18. Engineering cell-based therapies
Abstract
18.1 Introduction
18.2 Synthetic biology tools for gene expression control in mammalian cells
18.3 Engineering mammalian cells for diverse applications
18.4 Synthetic biology approaches to boost immune cell therapy in cancer
18.5 Engineering immune cells to suppress autoimmunity
18.6 Other players in T-cell-based therapies efficacy
18.7 Conclusion
Competing interests
References
Chapter 19. Development of next-generation diagnostic tools using synthetic biology
Abstract
19.1 Introduction to synthetic biology and diagnostics
19.2 Platforms for biosensors
19.3 Genetic circuits
19.4 RNA regulators
19.5 CRISPR–Cas
19.6 Direct detection biosensors
19.7 Activity-based molecular sensors
19.8 Conclusions and future perspectives
References
Chapter 20. Advances and application of CRISPR-Cas systems
Abstract
20.1 Introduction to CRISPR-Cas systems
20.2 Applications of CRISPR-Cas systems in bacteria
20.3 Application of CRISPR-Cas systems in plants
20.4 Applications of CRISPR-Cas systems in human cells
20.5 Concluding remarks and future perspectives
Acknowledgments
References
Chapter 21. Synthetic biology for smart drug biosynthesis and delivery
Abstract
21.1 Introduction
21.2 Synthetic biology for therapeutic production
21.3 Choosing the host organism
21.4 Natural hosts
21.5 Multiple hosts
21.6 Choosing enzymatic steps pathway
21.7 Optimizing the pathway yield
21.8 Pathway gene expression analysis
21.9 Protein engineering and operated evolution
21.10 Genome engineering
21.11 The relevance of targeted therapy through synthetic biology
21.12 Synthetic biology techniques for the biopharmaceutical industry
21.13 Gene synthesis error prevention technologies
21.14 Synthetic proteins
21.15 Synthetic biology and microencapsulation
21.16 Effect of synthetic biology on the discovery and development of drugs
21.17 Synthetic biology versus metabolic engineering
21.18 Synthetic biology versus drug discovery
21.19 Application of the synthetic biology approach to personalized medicine
21.20 Synthetic biology and custom approach to pathogenic microbes
21.21 Synthetic biology and customized cancer approach
21.22 Synthetic biology and cell therapy
21.23 Synthetic biology and vaccine
21.24 Synthetic biology and personalized cancer treatment
21.25 Regulatory problems linked to synthetic biology
21.26 Funding for synthetic biology study
21.27 Future prospects for synthetic biology
21.28 Conclusion
References
Chapter 22. Design and applications of self-assembled soft living materials using synthetic biology
Abstract
22.1 Introduction
22.2 Design
22.3 Applications
22.4 Future perspectives
References
Chapter 23. Synthetic gene circuits for higher-order information processing
Abstract
23.1 Introduction
23.2 Synthetic higher-order information processing gene circuits for complex computation
23.3 Understanding biological phenomena through the bottom-up synthetic biology approach
23.4 Application-based synthetic gene circuits
23.5 Challenges and outlook
References
Chapter 24. Cell-free synthetic biology as an emerging biotechnology
Abstract
24.1 Introduction
24.2 Cell-free protein synthesis platforms
24.3 Functional protein production
24.4 Genetic circuits
24.5 Metabolic engineering
24.6 Conclusions and perspective
Acknowledgments
Competing financial interests
References
Chapter 25. Recent development and applications of xeno nucleic acids
Abstract
25.1 Introduction
25.2 Structural diversity and applications of XNAs
25.3 Expansion of genetic code alphabet
25.4 Conclusion and future remarks
Acknowledgments
References
Chapter 26. Developments in the use of microfluidics in synthetic biology
Abstract
26.1 Introduction
26.2 Microfluidic technology
26.3 Applications of microfluidics in synthetic biology
26.4 Conclusion
References
Chapter 27. Implications of synthetic biology research and development: a structured ethical analysis
Abstract
27.1 Introduction
27.2 Respect
27.3 Well-being
27.4 Autonomy
27.5 Fairness
27.6 Matrix integration
27.7 Conclusions
References
Index

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

New Frontiers and Applications of Synthetic Biology

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Vijai Singh

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