Synthetic Biology Handbook

STANDARDISING BIOLOGY Synthetic Biology: Culture and Bioethical Considerations Introduction Perceptions and Portrayals of Synthetic Biology in Popular Culture and Politics Synthetic Biology in Academic Literature Societal Risks and Responsibilities Posed by Synthetic Biology Governance of Synthetic Biology Conclusions Acknowledgements References Synthetic Biology Standards and Methods of DNA Assembly Introduction Theory and Considerations in Double-Stranded DNA Assembly Assembly Methods in Detail Distributed Construct Assembly Methods Building Combinatorial Complexity during Assembly Emerging Technologies and Conclusions Standardisation of DNA Assembly References Standardised Genetic Output Measurement Introduction Standardisation in Conventional Biology Standardisation in Synthetic Biology Adapting Current Techniques as Synthetic Biology Standards Towards Synthetic Biology Standards for Protein Measurement Conclusions Acknowledgements References ENGINEERING BIOLOGY WITH LEGACY TOOLS Bacterial Cells as Engineered Chassis Introduction Designing and Refactoring Bacterial Genes Bacterial Synthetic Gene Networks Genome-Scale Re-Engineering of Bacterial Cells Engineering Periplasmic Space Re-Imagining the Bacterial Surface and Glycocalyx References Eukaryotae Synthetica: Synthetic Biology in Yeast, Microalgae, and Mammalian Cells Introduction Remodelling Outer Cell Membranes as Engineered Chassis Surfaces Programmable Organelles Eukaryotic Genes and Their Synthetic Counterparts Networks of Synthetic Genes in Mammalian Cells Genome-Scale Engineering in Eukaryotes Synthetic Biotherapeutics References Synthetic Plants Tools and Resources Food Security and Sustainable Agriculture Plant Chassis Engineering to Improve Nutritive Value Synthetic Biology and Green Biopharms Fibre and Fuel Future of Plant Synthetic Biology References CONSTRUCTING NEW BIOLOGIES Theory and Construction of Semi-Synthetic Minimal Cells Introduction Autopoiesis and Minimal Life Semi-Synthetic Approach to the Construction of Minimal Cells Entrapment of Solutes inside Liposomes Biotechnological Perspectives of Synthetic Cells Concluding Remarks Acknowledgements References Design Tools for Synthetic Biology Introduction Mathematical Modelling in Synthetic Biology Part Registries Device Languages Modelling Languages and Tools Network Optimisation Part Engineering DNA Editing Tools CAD Tools and Workflow Systems Summary References New Genetic Codes Introduction Available Orthogonal Pairs and Their Host Systems Using UAAs to Encode Post-Translational Modifications UAAs as Synthetic Biology Tools to Detect Interactions Occurring within Cells Photo-Activatable UAAs Bioorthogonal Chemistry Orthogonal Ribosomes Systemic Optimization of New Genetic Codes References