Synthetic Biology and iGEM: Techniques, Development and Safety Concerns: An Omics Big-data Mining Perspective

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This book focuses on biological engineering techniques, multi-omics big-data integration, and data-mining techniques, as well as cutting-edge researches in principles and applications of several synthetic biology applications. Synthetic biology is a new research area, while it has been rooted from the long-established area including biological engineering, metabolite engineering, and systems biology. This book will discuss the following aspects: (1) introduction to synthetic biology and iGEM, especially focusing on the systematic design, rational engineering, and sustainability of design in the omics ages; (2) synthetic biology–related multi-omics data integration and data mining techniques; (3) the technical issues, development issues, and safety issues of synthetic biology; (4) data resources, web services, and visualizations for synthetic biology; and (5) advancement in concrete research on synthetic biology, with several case studies shown.

Devised as a book on synthetic biology research and education in the omics age, this book has put focuses on systematic design, rational engineering, and sustainability of design for synthetic biology, which will explain in detail and with supportive examples the “What,” “Why,” and “How” of the topic. It is an attempt to bridge the gap between synthetic biology’s research and education side, for best practice of synthetic biology and in-depth insights for the related questions.


Author(s): Kang Ning, Yi Zhan
Publisher: Springer
Year: 2023

Language: English
Pages: 118
City: Singapore

Preface
About the Book
Contents
About the Editors
Chapter 1: Introduction to Synthetic Biology
1.1 The History and Importance of Synthetic Biology
1.1.1 Timeline for the Development of Synthetic Biology (Fig. 1.1)
1.2 Synthetic Biology Techniques
1.2.1 DNA and Gene Synthesis
1.2.2 Sequencing
1.2.3 Microfluidics
1.2.4 Modularity
1.2.5 Modeling
1.2.6 Synthetic Transcription Factors
1.3 Synthetic Biology Applications
1.3.1 Biological Computers
1.3.2 Biosensors
1.3.3 Cell Transformation
1.3.4 Designed Proteins
1.3.5 Designed Nucleic Acid Systems
1.3.6 Space Exploration
1.3.7 Synthetic Life
1.3.8 Drug Delivery Platforms
1.4 The Synthetic Biology Frontiers
1.4.1 Gene Editing
1.4.2 Genome Engineering
1.4.3 De Novo Protein Design
1.4.4 Synthesis of Unnatural Materials
1.4.5 Design of the Gene Circuit
1.4.6 Directed Evolution
1.4.7 Cell Factory/Therapy
1.4.8 Big Data-Assisted Biological Design
1.4.9 Education of Synthetic Biology
1.4.10 Synthetic Biology Community
1.5 The Future Challenges for Synthetic Biology
1.5.1 Automation and Industrialization
1.5.2 Deep Learning for DNA Design
1.5.3 Designing with Whole-Cell Simulations
1.5.4 Biosensing: Detecting Anything, Anywhere
1.5.5 Real-Time Precise Control of Evolution
1.5.6 Cellular Communities and Multicellularity
1.5.7 Custom and Dynamic Synthetic Genomes
1.5.8 Artificial Cells
1.5.9 Materials with DNA-Encoded Properties
1.5.10 Engineered Organisms for Sustainability Goals
1.6 Synthetic Biology Case Studies
References
Chapter 2: iGEM: The Competition on Synthetic Biology
2.1 iGEM´s History and Current Status
2.2 iGEM and Synthetic Biology Research
2.3 iGEM´s Representative Projects
2.3.1 iGEM Project by HUST-China 2021
2.3.2 iGEM Project by HUST-China 2019
2.3.3 iGEM Project by HUST-China 2018
2.3.4 iGEM Project by XMU-China 2020
2.4 iGEM Needs a Great Leap Forward
2.5 iGEM: Bright Futures Toward Better Synthetic Biology
References
Chapter 3: Synthetic Biology-Related Multiomics Data Integration and Data Mining Techniques
3.1 Introduction to Multiomics
3.2 Timeline of Omics Development
3.3 Databases and Tools for Omics Studies
3.4 Multiomics Applications
3.5 Future Perspectives
References
Chapter 4: Synthetic Biology: Technical Issues
4.1 Introduction and Background
4.2 DNA Synthesis and Assembly
4.2.1 DNA Synthesis
4.2.2 Biobricks and Standardization
4.2.3 Homologous Recombination
Different Models of Homologous Recombination
Application of Homologous Recombination: Gene Knockout
4.2.4 Golden Gate and Gibson Assembly
Golden Gate
Gibson Assembly
4.2.5 Transformation-Associated Recombination (TAR)
4.3 Gene-Editing Technology
4.3.1 Cre-loxP and Conditional Editing
4.3.2 ZFN and TALEN
4.3.3 CRISPR/Cas
4.3.4 MAGE/CAGE
CAGE
Integrated Application of MAGE and CAGE in Evolutionary
4.4 Directed Evolution and Artificial Design
4.4.1 Directed Evolution: PACE and RAGE
4.4.2 Artificial Design Tools
4.5 Chassis
4.5.1 From Microorganisms to Cells
4.5.2 Animals and Plants
4.5.3 Cell-Free System
References
Chapter 5: Synthetic Biology: Development Issues
5.1 Challenges Faced by Synthetic Biology
5.1.1 Predictability
Data Collection
Tools and Technology of Biological Design
5.1.2 Competitiveness of Supply Chains
5.1.3 Accessibility
5.2 The Lack of a Standard Platform to Evaluate the Effectiveness of the Synthetic System
5.2.1 Systems Modeling, Standards, and Metrology
5.3 iGEM´s Issues
5.3.1 iGEM: Is It for Elites or Commons?
References
Chapter 6: Synthetic Biology: Safety Issues
6.1 Biosafety Issues
6.1.1 The ``Creation´´ of Life
6.1.2 Biosafety
6.1.3 Biosecurity
6.2 Design Principles for Safety Control
6.2.1 Potential Risks of Synthetic Biology
6.2.2 Biosafety Concerns
6.2.3 Ethical Concerns
6.3 Code of Action for Safety Control
6.3.1 Code of Conduct for Scientists
6.3.2 Nationwide Governance
6.3.3 Efforts by International Societies
References
Chapter 7: Synthetic Biology: Data Resources, Web Services, and Visualizations
7.1 iGEM Registry
7.1.1 iGEM Registry Overview
7.1.2 Catalog
7.1.3 Repository
7.1.4 Assembly
7.2 Literature Resources
7.2.1 PubMed Database (an Important Source of Literature Download)
7.2.2 NCBI Bookshelf
7.2.3 BLAST
7.2.4 Blast-Type Selection
7.2.5 Result Analysis
7.3 Tools
7.3.1 ENTREZ Search System
EMBL-EBI Database
7.3.2 Service
Data Retrieval
Protein Function Analysis
Sequence Similarity Analysis
Multiple Sequence Alignment
Double Sequence Alignment
7.3.3 Phylogenetic Analysis
7.3.4 Sequence Format Conversion
7.3.5 Sequence Statistics
7.3.6 Sequence of Translation
7.4 Databases
7.4.1 GenBank
GenBank Overview
7.4.2 DDBJ
DDBJ Overview
Database
Data Retrieval
Data Analysis
7.4.3 UniProt
UniProt Overview
Database
UniParc
UniProtKB
UniRef
Proteomes
7.4.4 OpenWetWare
OpenWetWare Overview
Reference Materials
References
Chapter 8: Synthetic Biology: Case Studies
8.1 iGEM Project by HUST-China 2021
8.2 iGEM Project by HUST-China 2019
8.3 iGEM Project by HUST-China 2018
8.4 iGEM Project by HUST-China 2017
8.5 iGEM Project by XMU-China 2020
8.6 iGEM Project by TUDelft 2017
8.7 iGEM Project by TJUSLS China 2016
8.8 iGEM Project by SCAU-China 2016
8.9 iGEM Project by SJTU-Software 2019
References
Chapter 9: Concluding Remarks
References
Appendix
Databases for Synthetic Biology
Software for Synthetic Biology