{"product_id":"synthetic-biology-isbn-9783527330751","title":"Synthetic Biology","description":"\u003cp\u003e\u003cb\u003eA review of the interdisciplinary field of synthetic biology, from genome design to spatial engineering.\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eWritten by an international panel of experts, \u003ci\u003eSynthetic Biology\u003c\/i\u003e draws from various areas of research in biology and engineering and explores the current applications to provide an authoritative overview of this burgeoning field. The text reviews the synthesis of DNA and genome engineering and offers a discussion of the parts and devices that control protein expression and activity. The authors include information on the devices that support spatial engineering, RNA switches and explore the early applications of synthetic biology in protein synthesis, generation of pathway libraries, and immunotherapy.\u003c\/p\u003e \u003cp\u003eFilled with the most recent research, compelling discussions, and unique perspectives, \u003ci\u003eSynthetic Biology\u003c\/i\u003e offers an important resource for understanding how this new branch of science can improve on applications for industry or biological research.\u003c\/p\u003e \u003cp\u003eAbout the Series Editors xv\u003c\/p\u003e \u003cp\u003e\u003cb\u003ePart I DNA Synthesis and Genome Engineering 1\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Competition and the Future of Reading and Writing DNA 3\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eRobert Carlson\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e1.1 Productivity Improvements in Biological Technologies 3\u003c\/p\u003e \u003cp\u003e1.2 The Origin of Moore’s Law and Its Implications for Biological Technologies 5\u003c\/p\u003e \u003cp\u003e1.3 Lessons from Other Technologies 6\u003c\/p\u003e \u003cp\u003e1.4 Pricing Improvements in Biological Technologies 7\u003c\/p\u003e \u003cp\u003e1.5 Prospects for New Assembly Technologies 8\u003c\/p\u003e \u003cp\u003e1.6 Beyond Programming Genetic Instruction Sets 10\u003c\/p\u003e \u003cp\u003e1.7 Future Prospects 10\u003c\/p\u003e \u003cp\u003eReferences 11\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies:\u003c\/b\u003e \u003cb\u003eModifying Gene Expression in E. coli by Inserting Synthetic DNA Cassettes and Molecular Barcodes 15\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eEmily F. Freed, Gur Pines, Carrie A. Eckert, and Ryan T. Gill\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e2.1 Introduction 15\u003c\/p\u003e \u003cp\u003e2.2 Current Recombineering Techniques 16\u003c\/p\u003e \u003cp\u003e2.2.1 Recombineering Systems 17\u003c\/p\u003e \u003cp\u003e2.2.2 Current Model of Recombination 17\u003c\/p\u003e \u003cp\u003e2.3 Trackable Multiplex Recombineering 19\u003c\/p\u003e \u003cp\u003e2.3.1 TRMR and T2RMR Library Design and Construction 19\u003c\/p\u003e \u003cp\u003e2.3.2 Experimental Procedure 23\u003c\/p\u003e \u003cp\u003e2.3.3 Analysis of Results 24\u003c\/p\u003e \u003cp\u003e2.4 Current Challenges 25\u003c\/p\u003e \u003cp\u003e2.4.1 TRMR and T2RMR are Currently Not Recursive 26\u003c\/p\u003e \u003cp\u003e2.4.2 Need for More Predictable Models 26\u003c\/p\u003e \u003cp\u003e2.5 Complementing Technologies 27\u003c\/p\u003e \u003cp\u003e2.5.1 MAGE 27\u003c\/p\u003e \u003cp\u003e2.5.2 CREATE 27\u003c\/p\u003e \u003cp\u003e2.6 Conclusions 28\u003c\/p\u003e \u003cp\u003eDefinitions 28\u003c\/p\u003e \u003cp\u003eReferences 29\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Site-Directed Genome Modification with Engineered Zinc Finger Proteins 33\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eLauren E. Woodard, Daniel L. Galvan, and Matthew H. Wilson\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e3.1 Introduction to Zinc Finger DNA-Binding Domains and Cellular Repair Mechanisms 33\u003c\/p\u003e \u003cp\u003e3.1.1 Zinc Finger Proteins 33\u003c\/p\u003e \u003cp\u003e3.1.2 Homologous Recombination 34\u003c\/p\u003e \u003cp\u003e3.1.3 Non-homologous End Joining 35\u003c\/p\u003e \u003cp\u003e3.2 Approaches for Engineering or Acquiring Zinc Finger Proteins 36\u003c\/p\u003e \u003cp\u003e3.2.1 Modular Assembly 37\u003c\/p\u003e \u003cp\u003e3.2.2 OPEN and CoDA Selection Systems 37\u003c\/p\u003e \u003cp\u003e3.2.3 Purchase via Commercial Avenues 38\u003c\/p\u003e \u003cp\u003e3.3 Genome Modification with Zinc Finger Nucleases 38\u003c\/p\u003e \u003cp\u003e3.4 Validating Zinc Finger Nuclease-Induced Genome Alteration and Specificity 40\u003c\/p\u003e \u003cp\u003e3.5 Methods for Delivering Engineered Zinc Finger Nucleases into Cells 41\u003c\/p\u003e \u003cp\u003e3.6 Zinc Finger Fusions to Transposases and Recombinases 41\u003c\/p\u003e \u003cp\u003e3.7 Conclusions 42\u003c\/p\u003e \u003cp\u003eReferences 43\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Rational Efforts to Streamline the Escherichia coli Genome 49\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eGabriella Balikó, Viktor Vernyik, Ildikó Karcagi, Zsuzsanna Györfy, Gábor Draskovits, Tamás Fehér, and\u003c\/i\u003e \u003ci\u003eGyörgy Pósfai\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e4.1 Introduction 49\u003c\/p\u003e \u003cp\u003e4.2 The Concept of a Streamlined Chassis 50\u003c\/p\u003e \u003cp\u003e4.3 The E. coli Genome 51\u003c\/p\u003e \u003cp\u003e4.4 Random versus Targeted Streamlining 54\u003c\/p\u003e \u003cp\u003e4.5 Selecting Deletion Targets 55\u003c\/p\u003e \u003cp\u003e4.5.1 General Considerations 55\u003c\/p\u003e \u003cp\u003e4.5.1.1 Naturally Evolved Minimal Genomes 55\u003c\/p\u003e \u003cp\u003e4.5.1.2 Gene Essentiality Studies 55\u003c\/p\u003e \u003cp\u003e4.5.1.3 Comparative Genomics 56\u003c\/p\u003e \u003cp\u003e4.5.1.4 In silico Models 56\u003c\/p\u003e \u003cp\u003e4.5.1.5 Architectural Studies 56\u003c\/p\u003e \u003cp\u003e4.5.2 Primary Deletion Targets 57\u003c\/p\u003e \u003cp\u003e4.5.2.1 Prophages 57\u003c\/p\u003e \u003cp\u003e4.5.2.2 Insertion Sequences (ISs) 57\u003c\/p\u003e \u003cp\u003e4.5.2.3 Defense Systems 57\u003c\/p\u003e \u003cp\u003e4.5.2.4 Genes of Unknown and Exotic Functions 58\u003c\/p\u003e \u003cp\u003e4.5.2.5 Repeat Sequences 58\u003c\/p\u003e \u003cp\u003e4.5.2.6 Virulence Factors and Surface Structures 58\u003c\/p\u003e \u003cp\u003e4.5.2.7 Genetic Diversity-Generating Factors 59\u003c\/p\u003e \u003cp\u003e4.5.2.8 Redundant and Overlapping Functions 59\u003c\/p\u003e \u003cp\u003e4.6 Targeted Deletion Techniques 59\u003c\/p\u003e \u003cp\u003e4.6.1 General Considerations 59\u003c\/p\u003e \u003cp\u003e4.6.2 Basic Methods and Strategies 60\u003c\/p\u003e \u003cp\u003e4.6.2.1 Circular DNA-Based Method 60\u003c\/p\u003e \u003cp\u003e4.6.2.2 Linear DNA-Based Method 62\u003c\/p\u003e \u003cp\u003e4.6.2.3 Strategy for Piling Deletions 62\u003c\/p\u003e \u003cp\u003e4.6.2.4 New Variations on Deletion Construction 63\u003c\/p\u003e \u003cp\u003e4.7 Genome-Reducing Efforts and the Impact of Streamlining 64\u003c\/p\u003e \u003cp\u003e4.7.1 Comparative Genomics-Based Genome Stabilization and Improvement 64\u003c\/p\u003e \u003cp\u003e4.7.2 Genome Reduction Based on Gene Essentiality 66\u003c\/p\u003e \u003cp\u003e4.7.3 Complex Streamlining Efforts Based on Growth Properties 67\u003c\/p\u003e \u003cp\u003e4.7.4 Additional Genome Reduction Studies 68\u003c\/p\u003e \u003cp\u003e4.8 Selected Research Applications of Streamlined-Genome E. coli 68\u003c\/p\u003e \u003cp\u003e4.8.1 Testing Genome Streamlining Hypotheses 68\u003c\/p\u003e \u003cp\u003e4.8.2 Mobile Genetic Elements, Mutations, and Evolution 69\u003c\/p\u003e \u003cp\u003e4.8.3 Gene Function and Network Regulation 69\u003c\/p\u003e \u003cp\u003e4.8.4 Codon Reassignment 70\u003c\/p\u003e \u003cp\u003e4.8.5 Genome Architecture 70\u003c\/p\u003e \u003cp\u003e4.9 Concluding Remarks, Challenges, and Future Directions 71\u003c\/p\u003e \u003cp\u003eReferences 73\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology 81\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eAntoine Danchin, Agnieszka Sekowska, and Stanislas Noria\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e5.1 A Prerequisite to Synthetic Biology: An Engineering Definition of What Life Is 81\u003c\/p\u003e \u003cp\u003e5.2 Functional Analysis: Master Function and Helper Functions 83\u003c\/p\u003e \u003cp\u003e5.3 A Life-Specific Master Function: Building Up a Progeny 85\u003c\/p\u003e \u003cp\u003e5.4 Helper Functions 86\u003c\/p\u003e \u003cp\u003e5.4.1 Matter: Building Blocks and Structures (with Emphasis on DNA) 87\u003c\/p\u003e \u003cp\u003e5.4.2 Energy 91\u003c\/p\u003e \u003cp\u003e5.4.3 Managing Space 92\u003c\/p\u003e \u003cp\u003e5.4.4 Time 95\u003c\/p\u003e \u003cp\u003e5.4.5 Information 96\u003c\/p\u003e \u003cp\u003e5.5 Conclusion 97\u003c\/p\u003e \u003cp\u003eAcknowledgments 98\u003c\/p\u003e \u003cp\u003eReferences 98\u003c\/p\u003e \u003cp\u003e\u003cb\u003ePart II Parts and Devices Supporting Control of Protein Expression and Activity 107\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Constitutive and Regulated Promoters in Yeast: How to Design and Make Use of Promoters in S.\u003c\/b\u003e \u003cb\u003ecerevisiae 109\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eDiana S. M. Ottoz and Fabian Rudolf\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e6.1 Introduction 109\u003c\/p\u003e \u003cp\u003e6.2 Yeast Promoters 110\u003c\/p\u003e \u003cp\u003e6.3 Natural Yeast Promoters 113\u003c\/p\u003e \u003cp\u003e6.3.1 Regulated Promoters 113\u003c\/p\u003e \u003cp\u003e6.3.2 Constitutive Promoters 115\u003c\/p\u003e \u003cp\u003e6.4 Synthetic Yeast Promoters 116\u003c\/p\u003e \u003cp\u003e6.4.1 Modified Natural Promoters 116\u003c\/p\u003e \u003cp\u003e6.4.2 Synthetic Hybrid Promoters 117\u003c\/p\u003e \u003cp\u003e6.5 Conclusions 121\u003c\/p\u003e \u003cp\u003eDefinitions 122\u003c\/p\u003e \u003cp\u003eReferences 122\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Splicing and Alternative Splicing Impact on Gene Design 131\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eBeatrix Suess, Katrin Kemmerer, and Julia E. Weigand\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e7.1 The Discovery of “Split Genes” 131\u003c\/p\u003e \u003cp\u003e7.2 Nuclear Pre-mRNA Splicing in Mammals 132\u003c\/p\u003e \u003cp\u003e7.2.1 Introns and Exons: A Definition 132\u003c\/p\u003e \u003cp\u003e7.2.2 The Catalytic Mechanism of Splicing 132\u003c\/p\u003e \u003cp\u003e7.2.3 A Complex Machinery to Remove Nuclear Introns: The Spliceosome 132\u003c\/p\u003e \u003cp\u003e7.2.4 Exon Definition 134\u003c\/p\u003e \u003cp\u003e7.3 Splicing in Yeast 135\u003c\/p\u003e \u003cp\u003e7.3.1 Organization and Distribution of Yeast Introns 135\u003c\/p\u003e \u003cp\u003e7.4 Splicing without the Spliceosome 136\u003c\/p\u003e \u003cp\u003e7.4.1 Group I and Group II Self-Splicing Introns 136\u003c\/p\u003e \u003cp\u003e7.4.2 tRNA Splicing 137\u003c\/p\u003e \u003cp\u003e7.5 Alternative Splicing in Mammals 137\u003c\/p\u003e \u003cp\u003e7.5.1 Different Mechanisms of Alternative Splicing 137\u003c\/p\u003e \u003cp\u003e7.5.2 Auxiliary Regulatory Elements 139\u003c\/p\u003e \u003cp\u003e7.5.3 Mechanisms of Splicing Regulation 140\u003c\/p\u003e \u003cp\u003e7.5.4 Transcription-Coupled Alternative Splicing 142\u003c\/p\u003e \u003cp\u003e7.5.5 Alternative Splicing and Nonsense-Mediated Decay 143\u003c\/p\u003e \u003cp\u003e7.5.6 Alternative Splicing and Disease 144\u003c\/p\u003e \u003cp\u003e7.6 Controlled Splicing in S. cerevisiae 145\u003c\/p\u003e \u003cp\u003e7.6.1 Alternative Splicing 145\u003c\/p\u003e \u003cp\u003e7.6.2 Regulated Splicing 146\u003c\/p\u003e \u003cp\u003e7.6.3 Function of Splicing in S. cerevisiae 147\u003c\/p\u003e \u003cp\u003e7.7 Splicing Regulation by Riboswitches 147\u003c\/p\u003e \u003cp\u003e7.7.1 Regulation of Group I Intron Splicing in Bacteria 148\u003c\/p\u003e \u003cp\u003e7.7.2 Regulation of Alternative Splicing by Riboswitches in Eukaryotes 148\u003c\/p\u003e \u003cp\u003e7.8 Splicing and Synthetic Biology 150\u003c\/p\u003e \u003cp\u003e7.8.1 Impact of Introns on Gene Expression 150\u003c\/p\u003e \u003cp\u003e7.8.2 Control of Splicing by Engineered RNA-Based Devices 151\u003c\/p\u003e \u003cp\u003e7.9 Conclusion 153\u003c\/p\u003e \u003cp\u003eAcknowledgments 153\u003c\/p\u003e \u003cp\u003eDefinitions 153\u003c\/p\u003e \u003cp\u003eReferences 153\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Design of Ligand-Controlled Genetic Switches Based on RNA Interference 169\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eShunnichi Kashida and Hirohide Saito\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e8.1 Utility of the RNAi Pathway for Application in Mammalian Cells 169\u003c\/p\u003e \u003cp\u003e8.2 Development of RNAi Switches that Respond to Trigger Molecules 170\u003c\/p\u003e \u003cp\u003e8.2.1 Small Molecule-Triggered RNAi Switches 171\u003c\/p\u003e \u003cp\u003e8.2.2 Oligonucleotide-Triggered RNAi Switches 173\u003c\/p\u003e \u003cp\u003e8.2.3 Protein-Triggered RNAi Switches 174\u003c\/p\u003e \u003cp\u003e8.3 Rational Design of Functional RNAi Switches 174\u003c\/p\u003e \u003cp\u003e8.4 Application of the RNAi Switches 175\u003c\/p\u003e \u003cp\u003e8.5 Future Perspectives 177\u003c\/p\u003e \u003cp\u003eDefinitions 178\u003c\/p\u003e \u003cp\u003eReferences 178\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Small Molecule-Responsive RNA Switches (Bacteria): Important Element of Programming Gene Expression in Response to Environmental Signals in Bacteria 181\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eYohei Yokobayashi\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e9.1 Introduction 181\u003c\/p\u003e \u003cp\u003e9.2 Design Strategies 181\u003c\/p\u003e \u003cp\u003e9.2.1 Aptamers 181\u003c\/p\u003e \u003cp\u003e9.2.2 Screening and Genetic Selection 182\u003c\/p\u003e \u003cp\u003e9.2.3 Rational Design 183\u003c\/p\u003e \u003cp\u003e9.3 Mechanisms 183\u003c\/p\u003e \u003cp\u003e9.3.1 Translational Regulation 183\u003c\/p\u003e \u003cp\u003e9.3.2 Transcriptional Regulation 184\u003c\/p\u003e \u003cp\u003e9.4 Complex Riboswitches 185\u003c\/p\u003e \u003cp\u003e9.5 Conclusions 185\u003c\/p\u003e \u003cp\u003eKeywords with Definitions 185\u003c\/p\u003e \u003cp\u003eReferences 186\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria\u003c\/b\u003e \u003cb\u003e189\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eJason T. Stevens and James M. Carothers\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e10.1 An Introduction to Transcript Control 189\u003c\/p\u003e \u003cp\u003e10.1.1 Why Consider Transcript Control? 189\u003c\/p\u003e \u003cp\u003e10.1.2 The RNA Degradation Process in E. coli 190\u003c\/p\u003e \u003cp\u003e10.1.3 The Effects of Translation on Transcript Stability 192\u003c\/p\u003e \u003cp\u003e10.1.4 Structural and Noncoding RNA-Mediated Transcript Control 193\u003c\/p\u003e \u003cp\u003e10.1.5 Polyadenylation and Transcript Stability 195\u003c\/p\u003e \u003cp\u003e10.2 Synthetic Control of Transcript Stability 195\u003c\/p\u003e \u003cp\u003e10.2.1 Transcript Stability Control as a “Tuning Knob” 195\u003c\/p\u003e \u003cp\u003e10.2.2 Secondary Structure at the 5′ and 3′ Ends 196\u003c\/p\u003e \u003cp\u003e10.2.3 Noncoding RNA-Mediated 197\u003c\/p\u003e \u003cp\u003e10.2.4 Model-Driven Transcript Stability Control for Metabolic Pathway Engineering 198\u003c\/p\u003e \u003cp\u003e10.3 Managing Transcript Stability 201\u003c\/p\u003e \u003cp\u003e10.3.1 Transcript Stability as a Confounding Factor 201\u003c\/p\u003e \u003cp\u003e10.3.2 Anticipating Transcript Stability Issues 201\u003c\/p\u003e \u003cp\u003e10.3.3 Uniformity of 5′ and 3′ Ends 202\u003c\/p\u003e \u003cp\u003e10.3.4 RBS Sequestration by Riboregulators and Riboswitches 203\u003c\/p\u003e \u003cp\u003e10.3.5 Experimentally Probing Transcript Stability 204\u003c\/p\u003e \u003cp\u003e10.4 Potential Mechanisms for Transcript Control 205\u003c\/p\u003e \u003cp\u003e10.4.1 Leveraging New Tools 205\u003c\/p\u003e \u003cp\u003e10.4.2 Unused Mechanisms Found in Nature 206\u003c\/p\u003e \u003cp\u003e10.5 Conclusions and Discussion 207\u003c\/p\u003e \u003cp\u003eAcknowledgments 208\u003c\/p\u003e \u003cp\u003eDefinitions 208\u003c\/p\u003e \u003cp\u003eReferences 209\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Small Functional Peptides and Their Application in Superfunctionalizing Proteins 217\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eSonja Billerbeck\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e11.1 Introduction 217\u003c\/p\u003e \u003cp\u003e11.2 Permissive Sites and Their Identification in a Protein 218\u003c\/p\u003e \u003cp\u003e11.3 Functional Peptides 220\u003c\/p\u003e \u003cp\u003e11.3.1 Functional Peptides that Act as Binders 220\u003c\/p\u003e \u003cp\u003e11.3.2 Peptide Motifs that are Recognized by Labeling Enzymes 221\u003c\/p\u003e \u003cp\u003e11.3.3 Peptides as Protease Cleavage Sites 222\u003c\/p\u003e \u003cp\u003e11.3.4 Reactive Peptides 223\u003c\/p\u003e \u003cp\u003e11.3.5 Pharmaceutically Relevant Peptides: Peptide Epitopes, Sugar Epitope Mimics, and Antimicrobial Peptides 223\u003c\/p\u003e \u003cp\u003e11.3.5.1 Peptide Epitopes 224\u003c\/p\u003e \u003cp\u003e11.3.5.2 Peptide Mimotopes 224\u003c\/p\u003e \u003cp\u003e11.3.5.3 Antimicrobial Peptides 225\u003c\/p\u003e \u003cp\u003e11.4 Conclusions 227\u003c\/p\u003e \u003cp\u003eDefinitions 228\u003c\/p\u003e \u003cp\u003eAbbreviations 228\u003c\/p\u003e \u003cp\u003eAcknowledgment 229\u003c\/p\u003e \u003cp\u003eReferences 229\u003c\/p\u003e \u003cp\u003e\u003cb\u003ePart III Parts and Devices Supporting Spatial Engineering 237\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Metabolic Channeling Using DNA as a Scaffold 239\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eMojca Benèina, Jerneja Mori, Rok Gaber, and Roman Jerala\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e12.1 Introduction 239\u003c\/p\u003e \u003cp\u003e12.2 Biosynthetic Applications of DNA Scaffold 242\u003c\/p\u003e \u003cp\u003e12.2.1 l-Threonine 242\u003c\/p\u003e \u003cp\u003e12.2.2 trans-Resveratrol 245\u003c\/p\u003e \u003cp\u003e12.2.3 1,2-Propanediol 246\u003c\/p\u003e \u003cp\u003e12.2.4 Mevalonate 246\u003c\/p\u003e \u003cp\u003e12.3 Design of DNA-Binding Proteins and Target Sites 247\u003c\/p\u003e \u003cp\u003e12.3.1 Zinc Finger Domains 248\u003c\/p\u003e \u003cp\u003e12.3.2 TAL-DNA Binding Domains 249\u003c\/p\u003e \u003cp\u003e12.3.3 Other DNA-Binding Proteins 250\u003c\/p\u003e \u003cp\u003e12.4 DNA Program 250\u003c\/p\u003e \u003cp\u003e12.4.1 Spacers between DNA-Target Sites 250\u003c\/p\u003e \u003cp\u003e12.4.2 Number of DNA Scaffold Repeats 252\u003c\/p\u003e \u003cp\u003e12.4.3 DNA-Target Site Arrangement 253\u003c\/p\u003e \u003cp\u003e12.5 Applications of DNA-Guided Programming 254\u003c\/p\u003e \u003cp\u003eDefinitions 255\u003c\/p\u003e \u003cp\u003eReferences 256\u003c\/p\u003e \u003cp\u003e\u003cb\u003e13 Synthetic RNA Scaffolds for Spatial Engineering in Cells 261\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eGairik Sachdeva, Cameron Myhrvold, Peng Yin, and Pamela A. Silver\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e13.1 Introduction 261\u003c\/p\u003e \u003cp\u003e13.2 Structural Roles of Natural RNA 261\u003c\/p\u003e \u003cp\u003e13.2.1 RNA as a Natural Catalyst 262\u003c\/p\u003e \u003cp\u003e13.2.2 RNA Scaffolds in Nature 263\u003c\/p\u003e \u003cp\u003e13.3 Design Principles for RNA Are Well Understood 263\u003c\/p\u003e \u003cp\u003e13.3.1 RNA Secondary Structure is Predictable 264\u003c\/p\u003e \u003cp\u003e13.3.2 RNA can Self-Assemble into Structures 265\u003c\/p\u003e \u003cp\u003e13.3.3 Dynamic RNAs can be Rationally Designed 265\u003c\/p\u003e \u003cp\u003e13.3.4 RNA can be Selected in vitro to Enhance Its Function 266\u003c\/p\u003e \u003cp\u003e13.4 Applications of Designed RNA Scaffolds 266\u003c\/p\u003e \u003cp\u003e13.4.1 Tools for RNA Research 266\u003c\/p\u003e \u003cp\u003e13.4.2 Localizing Metabolic Enzymes on RNA 267\u003c\/p\u003e \u003cp\u003e13.4.3 Packaging Therapeutics on RNA Scaffolds 269\u003c\/p\u003e \u003cp\u003e13.4.4 Recombinant RNA Technology 269\u003c\/p\u003e \u003cp\u003e13.5 Conclusion 270\u003c\/p\u003e \u003cp\u003e13.5.1 New Applications 270\u003c\/p\u003e \u003cp\u003e13.5.2 Technological Advances 270\u003c\/p\u003e \u003cp\u003eDefinitions 271\u003c\/p\u003e \u003cp\u003eReferences 271\u003c\/p\u003e \u003cp\u003e\u003cb\u003e14 Sequestered: Design and Construction of Synthetic Organelles 279\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eThawatchai Chaijarasphong and David F. Savage\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e14.1 Introduction 279\u003c\/p\u003e \u003cp\u003e14.2 On Organelles 281\u003c\/p\u003e \u003cp\u003e14.3 Protein-Based Organelles 283\u003c\/p\u003e \u003cp\u003e14.3.1 Bacterial Microcompartments 283\u003c\/p\u003e \u003cp\u003e14.3.1.1 Targeting 285\u003c\/p\u003e \u003cp\u003e14.3.1.2 Permeability 287\u003c\/p\u003e \u003cp\u003e14.3.1.3 Chemical Environment 288\u003c\/p\u003e \u003cp\u003e14.3.1.4 Biogenesis 289\u003c\/p\u003e \u003cp\u003e14.3.2 Alternative Protein Organelles: A Minimal System 290\u003c\/p\u003e \u003cp\u003e14.4 Lipid-Based Organelles 292\u003c\/p\u003e \u003cp\u003e14.4.1 Repurposing Existing Organelles 293\u003c\/p\u003e \u003cp\u003e14.4.1.1 The Mitochondrion 293\u003c\/p\u003e \u003cp\u003e14.4.1.2 The Vacuole 294\u003c\/p\u003e \u003cp\u003e14.5 De novo Organelle Construction and Future Directions 295\u003c\/p\u003e \u003cp\u003eAcknowledgments 297\u003c\/p\u003e \u003cp\u003eReferences 297\u003c\/p\u003e \u003cp\u003e\u003cb\u003ePart IV Early Applications of Synthetic Biology: Pathways, Therapies, and Cell-Free Synthesis 307\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003e15 Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems 309\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eJennifer A. Schoborg and Michael C. Jewett\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e15.1 Introduction 309\u003c\/p\u003e \u003cp\u003e15.2 Background\/Current Status 311\u003c\/p\u003e \u003cp\u003e15.2.1 Platforms 311\u003c\/p\u003e \u003cp\u003e15.2.1.1 Prokaryotic Platforms 311\u003c\/p\u003e \u003cp\u003e15.2.1.2 Eukaryotic Platforms 312\u003c\/p\u003e \u003cp\u003e15.2.2 Trends 314\u003c\/p\u003e \u003cp\u003e15.3 Products 316\u003c\/p\u003e \u003cp\u003e15.3.1 Noncanonical Amino Acids 316\u003c\/p\u003e \u003cp\u003e15.3.2 Glycosylation 316\u003c\/p\u003e \u003cp\u003e15.3.3 Antibodies 318\u003c\/p\u003e \u003cp\u003e15.3.4 Membrane Proteins 318\u003c\/p\u003e \u003cp\u003e15.4 High-Throughput Applications 320\u003c\/p\u003e \u003cp\u003e15.4.1 Protein Production and Screening 320\u003c\/p\u003e \u003cp\u003e15.4.2 Genetic Circuit Optimization 321\u003c\/p\u003e \u003cp\u003e15.5 Future of the Field 321\u003c\/p\u003e \u003cp\u003eDefinitions 322\u003c\/p\u003e \u003cp\u003eAcknowledgments 322\u003c\/p\u003e \u003cp\u003eReferences 323\u003c\/p\u003e \u003cp\u003e\u003cb\u003e16 Applying Advanced DNA Assembly Methods to Generate Pathway Libraries 331\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eDawn T. Eriksen, Ran Chao, and Huimin Zhao\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e16.1 Introduction 331\u003c\/p\u003e \u003cp\u003e16.2 Advanced DNA Assembly Methods 333\u003c\/p\u003e \u003cp\u003e16.3 Generation of Pathway Libraries 334\u003c\/p\u003e \u003cp\u003e16.3.1 In vitro Assembly Methods 335\u003c\/p\u003e \u003cp\u003e16.3.2 In vivo Assembly Methods 339\u003c\/p\u003e \u003cp\u003e16.3.2.1 In vivo Chromosomal Integration 339\u003c\/p\u003e \u003cp\u003e16.3.2.2 In vivo Plasmid Assembly and One-Step Optimization Libraries 340\u003c\/p\u003e \u003cp\u003e16.3.2.3 In vivo Plasmid Assembly and Iterative Multi-step Optimization Libraries 341\u003c\/p\u003e \u003cp\u003e16.4 Conclusions and Prospects 343\u003c\/p\u003e \u003cp\u003eDefinitions 343\u003c\/p\u003e \u003cp\u003eReferences 344\u003c\/p\u003e \u003cp\u003e\u003cb\u003e17 Synthetic Biology in Immunotherapy and Stem Cell Therapy Engineering 349\u003cbr\u003e\u003c\/b\u003e\u003ci\u003ePatrick Ho and Yvonne Y. Chen\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e17.1 The Need for a New Therapeutic Paradigm 349\u003c\/p\u003e \u003cp\u003e17.2 Rationale for Cellular Therapies 350\u003c\/p\u003e \u003cp\u003e17.3 Synthetic Biology Approaches to Cellular Immunotherapy Engineering 351\u003c\/p\u003e \u003cp\u003e17.3.1 CAR Engineering for Adoptive T-Cell Therapy 352\u003c\/p\u003e \u003cp\u003e17.3.2 Genetic Engineering to Enhance T-Cell Therapeutic Function 357\u003c\/p\u003e \u003cp\u003e17.3.3 Generating Safer T-Cell Therapeutics with Synthetic Biology 359\u003c\/p\u003e \u003cp\u003e17.4 Challenges and Future Outlook 362\u003c\/p\u003e \u003cp\u003eAcknowledgment 364\u003c\/p\u003e \u003cp\u003eDefinitions 364\u003c\/p\u003e \u003cp\u003eReferences 365\u003c\/p\u003e \u003cp\u003e\u003cb\u003ePart V Societal Ramifications of Synthetic Biology 373\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003e18 Synthetic Biology: From Genetic Engineering 2.0 to Responsible Research and Innovation 375\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eLei Pei and Markus Schmidt\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e18.1 Introduction 375\u003c\/p\u003e \u003cp\u003e18.2 Public Perception of the Nascent Field of Synthetic Biology 376\u003c\/p\u003e \u003cp\u003e18.2.1 Perception of Synthetic Biology in the United States 377\u003c\/p\u003e \u003cp\u003e18.2.2 Perception of Synthetic Biology in Europe 379\u003c\/p\u003e \u003cp\u003e18.2.2.1 European Union 379\u003c\/p\u003e \u003cp\u003e18.2.2.2 Austria 379\u003c\/p\u003e \u003cp\u003e18.2.2.3 Germany 381\u003c\/p\u003e \u003cp\u003e18.2.2.4 Netherlands 382\u003c\/p\u003e \u003cp\u003e18.2.2.5 United Kingdom 383\u003c\/p\u003e \u003cp\u003e18.2.3 Opinions from Concerned Civil Society Groups 384\u003c\/p\u003e \u003cp\u003e18.3 Frames and Comparators 384\u003c\/p\u003e \u003cp\u003e18.3.1 Genetic Engineering: Technology as Conflict 386\u003c\/p\u003e \u003cp\u003e18.3.2 Nanotechnology: Technology as Progress 387\u003c\/p\u003e \u003cp\u003e18.3.3 Information Technology: Technology as Gadget 387\u003c\/p\u003e \u003cp\u003e18.3.4 SB: Which Debate to Come? 388\u003c\/p\u003e \u003cp\u003e18.4 Toward Responsible Research and Innovation (RRI) in Synthetic Biology 389\u003c\/p\u003e \u003cp\u003e18.4.1 Engagement of All Societal Actors – Researchers, Industry, Policy Makers, and Civil Society – and Their Joint Participation in the Research and Innovation 390\u003c\/p\u003e \u003cp\u003e18.4.2 Gender Equality 391\u003c\/p\u003e \u003cp\u003e18.4.3 Science Education 392\u003c\/p\u003e \u003cp\u003e18.4.4 Open Access 392\u003c\/p\u003e \u003cp\u003e18.4.5 Ethics 394\u003c\/p\u003e \u003cp\u003e18.4.6 Governance 395\u003c\/p\u003e \u003cp\u003e18.5 Conclusion 396\u003c\/p\u003e \u003cp\u003eAcknowledgments 397\u003c\/p\u003e \u003cp\u003eReferences 397\u003c\/p\u003e \u003cp\u003eIndex 403\u003c\/p\u003e \u003cp\u003e\u003cb\u003eSang Yup Lee\u003c\/b\u003e is Distinguished Professor at the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST).\u003c\/p\u003e \u003cp\u003e\u003cb\u003eJens Nielsen\u003c\/b\u003e is Professor and Director to Chalmers University of Technology, Sweden. He has received numerous Danish and international awards including the Nature Mentor Award.\u003c\/p\u003e \u003cp\u003e\u003cb\u003eProfessor Gregory Stephanopoulos\u003c\/b\u003e is the W. H. Dow Professor of Chemical Engineering at the Massachusetts Institute of Technology and Director of the MIT Metabolic Engineering Laboratory. \u003c\/p\u003e \u003cp\u003e\u003cb\u003eA review of the interdisciplinary field of synthetic biology, from genome design to spatial engineering\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eWritten by an international panel of experts, \u003ci\u003eSynthetic Biology\u003c\/i\u003e draws from various areas of research in biology and engineering and explores the current applications to provide an authoritative overview of this burgeoning field. The text reviews the synthesis of DNA and genome engineering and offers a discussion of the parts and devices that control protein expression and activity. The authors include information on the devices that support spatial engineering, RNA switches and explore the early applications of synthetic biology in protein synthesis, generation of pathway libraries, and immunotherapy.\u003c\/p\u003e \u003cp\u003eFilled with the most recent research, compelling discussions, and unique perspectives, \u003ci\u003eSynthetic Biology\u003c\/i\u003e offers an important resource for understanding how this new branch of science can improve on applications for industry or biological research.\u003c\/p\u003e \u003cp\u003e \u003cb\u003e \u003c\/b\u003e\u003c\/p\u003e \u003cb\u003eAdvanced Biotechnology\u003c\/b\u003e\u003cbr\u003e Biotechnology is a broad, interdisciplinary field of science, combining biological sciences and relevant engineering disciplines, that is becoming increasingly important as it benefits the environment and society. Recent years have seen substantial advances in all areas of biotechnology, resulting in the emergence of brand new fields. To reflect this progress, Sang Yup Lee (KAIST, South Korea), Jens Nielsen (Chalmers University, Sweden), and Gregory Stephanopoulos (MIT, USA) have joined forces as the editors of a new Wiley-VCH book series. Advanced Biotechnology will cover all pertinent aspects of the field and each volume will be prepared by eminent scientists who are experts on the topic in question.","brand":"Wiley-Blackwell","offers":[{"title":"Default Title","offer_id":47990123495653,"sku":"NP9783527330751","price":184.95,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9783527330751.jpg?v=1761786603","url":"https:\/\/k12savings.com\/products\/synthetic-biology-isbn-9783527330751","provider":"K12savings","version":"1.0","type":"link"}