Synthetic Biology, Part A book cover

Synthetic Biology, Part A

Methods for Part/Device Characterization and Chassis Engineering

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.

Audience

Researchers and students in cell, molecular and developmental biology

Included in series
Methods in Enzymology

Hardbound, 714 Pages

Published: May 2011

Imprint: Academic Press

ISBN: 978-0-12-385075-1

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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