Synthetic Biology: Methods and Protocols

Part I: Gene Circuits and Biochemical Pathways

1. Re-Factoring Glycolytic Genes for Targeted Engineering of Catabolism in Gram-Negative Bacteria

            Alberto Sánchez-Pascuala, Pablo I. Nikel, and Víctor de Lorenzo

2. Negative Regulation Gene Circuits for Efflux Pump Control

            Daniel A. Charlebois, Junchen Diao, Dmitry Nevozhay, and Gábor Balázsi

3. Methods for Generating Microbial Co-Cultures that Grow in the Absence of Fixed Carbon or Nitrogen

            Matthew J. Smith and Matthew B. Francis

4. Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits

            Ryan Marshall and Vincent Noireaux

5. Transformation of an Exotic Yeast Species into a Platform Organism: A Case Study for Engineering Glycolipid Production in the Yeast Starmerella bombicola

6. Sortase A-Assisted Metabolic Enzyme Ligation in Escherichia coli for Enhancing Metabolic Flux

            Takuya Matsumoto, Tsutomu Tanaka, and Akihiko Kondo

Part II: Genome Editing and Modification

7. Construction of CRISPR Libraries for Functional Screening

            Carsten-P. Carstens, Katherine A. Felts, and Sarah E. Johns

8. Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering

            Jongoh Shin, Namil Lee, Suhyung Cho, and Byung-Kwan Cho

9. Dynamic Management of Codon Compression for Saturation Mutagenesis

            Gur Pines and Ryan T. Gill

10. Designed Transcriptional Regulation in Mammalian Cells Based on TALE- and CRISPR/dCas9

            Tina Lebar and Roman Jerala

11. Combinatorial Evolution of DNA with RECODE

            Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, and Jian Chen

12. Genome Editing in Penicillium chrysogenum Using Cas9 Ribonucleoprotein Particles

13. Targeted Gene Knockout Using Nuclease-Assisted Vector Integration: Hemi- and Homozygous Deletion of JAG1

            Michael Gapinske, Nathan Tague, Jackson Winter, Gregory H. Underhill, Pablo Perez-Pinera

14. Programming Biomaterial Interactions Using Engineered Living Cells

            Keith C. Heyde and Warren C. Ruder

15. Rapid Control of Genome Editing in Human Cells by Chemical-Inducible CRISPR-Cas Systems

            Kaiwen Ivy Liu, Muhammad Nadzim Bin Ramli, Norfala-Aliah Binte Sutrisnoh, and Meng How Tan

16. Production of a Human Cell Line with a Plant Chromosome

            Naoki Wada, Yasuhiro Kazuki, Kanako Kazuki, Toshiaki Inoue, Kiichi Fukui, and Mitsuo Oshimura

17. Bacterial Genome Editing with CRISPR-Cas9: Taking Clostridium beijerinckii as an Example

18. CRISPR-Cas9-Mediated Genome Editing and Transcriptional Control in Yarrowia lipolytica

            Cory Schwartz and Ian Wheeldon

19. Construction and Integration of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells

            Tingting Wang and Zhen Xie

Part III: Genome Language and Computing

20. Bio-Algorithmic Workflows for Standardized Synthetic Biology Constructs

            Angel Goñi-Moreno and Victor de Lorenzo

21. Engineering Genomes with Genotype Specification Language

            Erin H. Wilson, Chris Macklin, and Darren Platt

22. Automated Visualization of Genetic Designs Using DNAplotlib

            Vittorio Bartoli, Daniel O.R. Dixon, and Thomas E. Gorochowski

23. DNA-Based Analog Computing

            Daniel Fu, Shalin Shah, Tianqi Song, and John Reif

Part IV: Molecular Assembly

24. DNA Assembly with the DATEL Method

            Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, and Jian Chen

25. EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology

            Hung-En Lai, Simon Moore, Karen Polizzi, and Paul Freemont

26. Designing and Assembling Plasmids for Construction of Escherichia coli Biosensor for Vibrio cholerae Detection

            Maciej B. Holowko and Chueh Loo Poh

27. A Rapid Combinatorial Approach to Assembling Synthetic Prokaryotic and Eukaryotic Protein Expression Vectors

            Rebecca Mullinax, Sarah Johns, Denise Rhodes, Vivian Zhang, Nancy McKinney, Katie Felts, Carsten Carstens, and Peter Sheffield

28. Standardized Cloning and Curing of Plasmids

29. STAR: A Simple TAL Effector Assembly Reaction Using Isothermal Assembly

            Sabine Gogolok, Ute Köber, and Steven M. Pollard