Preface IX Volume 1 1 Synthetic Biology: Implications and Uses 1 Sanjay Vashee, Mikkel A. Algire, Michael G. Montague, and Michele S. Garfynkel Part I Biological Basis 33 2 The Emergence of the First Cells 35 Antoine Danchin 3 Regulation of Gene Expression 61 Anil Kumar, Sarika Garg and Neha Garg 4 Interactome 121 Teresa M. Przytycka and Dong-Yeon Cho 5 Microbiomes 153 Ramana Madupu, Yu-Hui Rogers, Doug Rusch, Jason Miller, Konstantinos Krampis, and Karen E. Nelson Part II Modeling 179 6 Dynamics of Biomolecular Networks 181 Emanuele Cozzo, Joaquin Sanz, and Yamir Moreno 7 E-Cell: Computer Simulation of the Cell 211 Pawan K. Dhar, Kouichi Takahashi, Yoichi Nakayama, and Masaru Tomita 8 SynBioSS Designer Modeling Suite 229 Konstantinos Biliouris, Emma Weeding, and Yiannis N. Kaznessis Part III Modular Parts and Circuits 247 9 Synthetic Gene Circuits 249 Barbara Jusiak, Ramiz Daniel, Fahim Farzadfard, Lior Nissim, Oliver Purcell, Jacob Rubens and Timothy K. Lu 10 DNA Origami Nanorobots 305 Ido Bachelet 11 RNAi Synthetic Logic Circuits for Sensing, Information Processing, and Actuation 333 Zhen Xie, Liliana Wroblewska, and Ron Weiss 12 Synthetic Hybrid Biosensors 357 Apoorv Shanker, Kangwon Lee, and Jinsang Kim 13 Synthetic Biology in Metabolic Engineering: From Complex Biochemical Pathways to Compartmentalized Metabolic Processes a Vitamin Connection 393 Evelyne Deery, Stefanie Frank, Andrew Lawrence, Simon Moore, Susanne Schroeder, and Martin J. Warren Volume 2 Part IV Synthetic Genomes 441 14 The Minimal Gene-Set Machinery 443 Rosario Gil 15 Production of Mitochondrial Genome and Chromosomal DNA Segments Highly Engineered for Use in Mouse Genetics by a Bacillus subtilis-Based BGM Vector System 479 Mitsuhiro Itaya 16 Synthetic Genetic Polymers Functioning to Store and Propagate Information by Genetic Alphabet Expansion 505 Ichiro Hirao Part V Diseases and Therapeutics 521 17 Synthetic Biology Approaches for Regenerative Medicine 523 Elise Cachat, Kim C. Martin, and Jamie A. Davies 18 The Synthetic Biology Approach to Stem Cells and Regenerative Medicine 541 Boon Chin Heng, and Martin Fussenegger 19 Synthetic Biology Approaches to Cell Therapy 559 Sung-Ho Paek and Warren C. Ruder 20 Synthetic Biology Approaches for Vaccine Development 589 Sam H. Shen, Bruce Futcher, Chen Yang, and Eckard Wimmer Part VI Chemicals Production 617 21 Metabolic Engineering for the Production of Diols 619 Katarzyna Leja, Dorota Samul, Piotr Kubiak, Agnieszka Drozdzynska, Alicja Kosmider, Wojciech Juzwa, Mariusz Lesiecki, and Katarzyna Czaczyk 22 Synthetic Biology in Biofuels Production 665 Rahul Singh, Anu Jose Mattam, Pavan Jutur, and Syed Shams Yazdani 23 Synthetic Biology of Antibiotic Production 699 Eriko Takano and Rainer Breitling Index 723
