Synthetic Biology, Part A: Volume 497

Klappentext Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses many different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. 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. Zusammenfassung Synthetic biology encompasses a variety of different approaches! methodologies and disciplines! and many different definitions exist. This Volume 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. Inhaltsverzeichnis Section I. Measuring and Engineering Central Dogma Processes Sequence-specificity and Energy Landscapes of DNA-binding Molecules Joshua R. Tietjen, Leslie J. Donato, Devesh Bhimisaria and Aseem Z. Ansari Promoter Reliability in Modular Transcriptional Networks Rajat Anand, Navneet Rai and Mukund Thattai The Analysis of ChIP-seq Data Wenxiu Ma and Wing Hung Wong Using DNA Microarrays to Assay Part Function Virgil A. Rhodius and Carol A. Gross Orthogonal gene expression in Escherichia coli Wenlin An and Jason Chin Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation Keith E.J. Tyo, Elke Nevoigt and Gregory Stephanopoulos Section II. Device and System Design, Optimization, and Debugging Design and Connection of Robust Genetic Circuits Ron Weiss Engineering RNAi circuits Yaakov Benenson From SELEX to cell: Dual selections for synthetic riboswitches Joy Sinha, Shana Topp, and Justin P. Gallivan Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells Jeffrey V. Wong, Guang Yao, Joseph R. Nevins and Lingchong You De novo design and construction of an inducible gene expression system in mammalian cells Maria Karlsson, Wilfried Weber and Martin Fussenegger BioBuilding: Using banana-scented bacteria to teach synthetic biology James Dixon and Natalie Kuldell Section III. Device Measurement, Optimization, and Debugging Use of Fluorescence Microscopy to Analyze Genetic Circuit Dynamics Gürol Süel Microfluidics for synthetic biology: From design to execution M. S. Ferry, I. A. Razinkov, J. Hasty Plate-based assays for light-regulated gene expression systems Jeffrey J. Tabor Spatiotemporal control of small GTPases with light using the LOV domain Yi I. Wu, Xiaobo Wang, Li He, Denise Montell and Klaus M. Hahn Light Control of Plasma Membrane Recruitment using the Phy-PIF system Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes Ed Boyden Section IV. Devices for Metabolic Engineering Metabolic Pathway Flux Enhancement by Synthetic Protein Scaffolding John E. Dueber and Weston R. Whitaker A Synthetic Iterative Pathway for ketoacid elongation C. R. Shen, J. C. Liao Section V. Expanding Chasses Synthetic Biology in Streptomyces bacteria Marnix Medema, Rainer Breitling and Eriko Takano Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio Kimberly L. Keller, Judy D. Wall and Swapnil Chhabra Modification of the Genome of Rhodobacter sphaeroides and Construction of Synthetic Operon...

Zusammenfassung
Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume 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.

Inhalt

Section I. Measuring and Engineering Central Dogma Processes

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

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

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

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

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

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

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

7. Design and Connection of Robust Genetic Circuits Ron Weiss

8. Engineering RNAi circuits Yaakov Benenson

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

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

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

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

    Section III. Device Measurement, Optimization, and Debugging

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

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

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

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

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

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

    Section IV. Devices for Metabolic Engineering

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

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

    Section V. Expanding Chasses

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

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

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

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

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

26. Lentiviral Vectors to Study Stochastic Noise in Gene Expression Kate Franz, Abhyudai Singh, and Leor S. Weinberger