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Refinement and standardization of synthetic biological parts and devices

Abstract

The ability to quickly and reliably engineer many-component systems from libraries of standard interchangeable parts is one hallmark of modern technologies. Whether the apparent complexity of living systems will permit biological engineers to develop similar capabilities is a pressing research question. We propose to adapt existing frameworks for describing engineered devices to biological objects in order to (i) direct the refinement and use of biological 'parts' and 'devices', (ii) support research on enabling reliable composition of standard biological parts and (iii) facilitate the development of abstraction hierarchies that simplify biological engineering. We use the resulting framework to describe one engineered biological device, a genetically encoded cell-cell communication receiver named BBa_F2620. The description of the receiver is summarized via a 'datasheet' similar to those widely used in engineering. The process of refinement and characterization leading to the BBa_F2620 datasheet may serve as a starting template for producing many standardized genetically encoded objects.

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Figure 1
Figure 2
Figure 3: A prototypical 'datasheet' that summarizes current knowledge of the behavior of the receiver BBa_F2620.

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Acknowledgements

We thank T. Knight; R. Rettberg; members of the Endy, Knight and Sauer labs and staff of the Registry of Standard Biological Parts for discussions, advice and materials throughout the work. We thank R. Brent, U. RajBhandary, C. Smolke, B. Studier and anonymous reviewers for comments on earlier versions of this manuscript. This research was supported by grants to D.E. from the US National Science Foundation, Defense Advanced Research Projects Agency and National Institutes of Health. B.C. was supported by a National University of Ireland training fellowship. Additional support was provided by the Massachusetts Institute of Technology.

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Authors

Contributions

B.C. and D.E. initiated the work. B.C., D.E. and A.L. designed the experiments. B.C. and A.L. performed the experiments. B.C., A.L. and D.E. analyzed the data and wrote the paper.

Corresponding author

Correspondence to Drew Endy.

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Figures 1–5, Tables 1–3 (PDF 1560 kb)

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Canton, B., Labno, A. & Endy, D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26, 787–793 (2008). https://doi.org/10.1038/nbt1413

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