Synthetic Biology, Part A: Methods for Part/Device Characterization and Chassis Engineering

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Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation.

  • Encompasses a variety of different approaches, methodologies and disciplines
  • Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation
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Product Details

  • ISBN-13: 9780123850751
  • Publisher: Elsevier Science
  • Publication date: 6/6/2011
  • Pages: 714
  • Product dimensions: 6.10 (w) x 9.10 (h) x 1.70 (d)

Table of Contents

Section I. Measuring and Engineering Central Dogma Processes

  1. Sequence-specificity and Energy Landscapes of DNA-binding Molecules
  2. Joshua R. Tietjen, Leslie J. Donato, Devesh Bhimisaria and Aseem Z. Ansari

  3. Promoter Reliability in Modular Transcriptional Networks
  4. Rajat Anand, Navneet Rai and Mukund Thattai

  5. The Analysis of ChIP-seq Data
  6. Wenxiu Ma and Wing Hung Wong

  7. Using DNA Microarrays to Assay Part Function
  8. Virgil A. Rhodius and Carol A. Gross

  9. Orthogonal gene expression in Escherichia coli
  10. Wenlin An and Jason Chin

  11. Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation
  12. Keith E.J. Tyo, Elke Nevoigt and Gregory Stephanopoulos

    Section II. Device and System Design, Optimization, and Debugging

  13. Design and Connection of Robust Genetic Circuits
  14. Ron Weiss

  15. Engineering RNAi circuits
  16. Yaakov Benenson

  17. From SELEX to cell: Dual selections for synthetic riboswitches
  18. Joy Sinha, Shana Topp, and Justin P. Gallivan

  19. Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells
  20. Jeffrey V. Wong, Guang Yao, Joseph R. Nevins and Lingchong You

  21. De novo design and construction of an inducible gene expression system in mammalian cells
  22. Maria Karlsson, Wilfried Weber and Martin Fussenegger

  23. BioBuilding: Using banana-scented bacteria to teach synthetic biology
  24. James Dixon and Natalie Kuldell

    Section III. Device Measurement, Optimization, and Debugging

  25. Use of Fluorescence Microscopy to Analyze Genetic Circuit Dynamics
  26. Gürol Süel

  27. Microfluidics for synthetic biology: From design to execution
  28. M. S. Ferry, I. A. Razinkov, J. Hasty

  29. Plate-based assays for light-regulated gene expression systems
  30. Jeffrey J. Tabor

  31. Spatiotemporal control of small GTPases with light using the LOV domain
  32. Yi I. Wu, Xiaobo Wang, Li He, Denise Montell and Klaus M. Hahn

  33. Light Control of Plasma Membrane Recruitment using the Phy-PIF system
  34. Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner

  35. Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes
  36. Ed Boyden

    Section IV. Devices for Metabolic Engineering

  37. Metabolic Pathway Flux Enhancement by Synthetic Protein Scaffolding
  38. John E. Dueber and Weston R. Whitaker

  39. A Synthetic Iterative Pathway for ketoacid elongation
  40. C. R. Shen, J. C. Liao

    Section V. Expanding Chasses

  41. Synthetic Biology in Streptomyces bacteria
  42. Marnix Medema, Rainer Breitling and Eriko Takano

  43. Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio
  44. Kimberly L. Keller, Judy D. Wall and Swapnil Chhabra

  45. Modification of the Genome of Rhodobacter sphaeroides and Construction of Synthetic Operons
  46. Paul R. Jaschke, Rafael G. Saer, Stephan Noll and J. Thomas Beatty

  47. Synthetic Biology in Cyanobacteria: Engineering and Analyzing Novel Functions
  48. Thorsten Heidorn, Daniel Camsund, Hsin-Ho Huang, Pia Lindberg, Paulo Oliveira, Karin Stensjö, and Peter Lindblad

  49. Developing a Synthetic Signal Transduction System in Plants
  50. Kevin J. Morey, Mauricio S. Antunes, Kirk D. Albrecht, Tessa A. Bowen, Jared F. Troupe, Keira L. Havens and June I. Medford

  51. Lentiviral Vectors to Study Stochastic Noise in Gene Expression

Kate Franz, Abhyudai Singh, and Leor S. Weinberger

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