Literature DB >> 23676681

Synthetic analog computation in living cells.

Ramiz Daniel1, Jacob R Rubens, Rahul Sarpeshkar, Timothy K Lu.   

Abstract

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

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Year:  2013        PMID: 23676681     DOI: 10.1038/nature12148

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  27 in total

1.  Reprogramming control of an allosteric signaling switch through modular recombination.

Authors:  John E Dueber; Brian J Yeh; Kayam Chak; Wendell A Lim
Journal:  Science       Date:  2003-09-26       Impact factor: 47.728

2.  Programmable single-cell mammalian biocomputers.

Authors:  Simon Ausländer; David Ausländer; Marius Müller; Markus Wieland; Martin Fussenegger
Journal:  Nature       Date:  2012-07-05       Impact factor: 49.962

3.  Signaling motifs and Weber's law.

Authors:  James E Ferrell
Journal:  Mol Cell       Date:  2009-12-11       Impact factor: 17.970

4.  A synthetic genetic edge detection program.

Authors:  Jeffrey J Tabor; Howard M Salis; Zachary Booth Simpson; Aaron A Chevalier; Anselm Levskaya; Edward M Marcotte; Christopher A Voigt; Andrew D Ellington
Journal:  Cell       Date:  2009-06-26       Impact factor: 41.582

5.  Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs.

Authors:  Luca Giorgetti; Trevor Siggers; Guido Tiana; Greta Caprara; Samuele Notarbartolo; Teresa Corona; Manolis Pasparakis; Paolo Milani; Martha L Bulyk; Gioacchino Natoli
Journal:  Mol Cell       Date:  2010-02-12       Impact factor: 17.970

6.  Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli.

Authors:  Daniel Madar; Erez Dekel; Anat Bren; Uri Alon
Journal:  BMC Syst Biol       Date:  2011-07-12

7.  A synthetic biology framework for programming eukaryotic transcription functions.

Authors:  Ahmad S Khalil; Timothy K Lu; Caleb J Bashor; Cherie L Ramirez; Nora C Pyenson; J Keith Joung; James J Collins
Journal:  Cell       Date:  2012-08-03       Impact factor: 41.582

8.  Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones.

Authors:  Jadwiga Wild; Zdenka Hradecna; Waclaw Szybalski
Journal:  Genome Res       Date:  2002-09       Impact factor: 9.043

9.  Cis-interactions between Notch and Delta generate mutually exclusive signalling states.

Authors:  David Sprinzak; Amit Lakhanpal; Lauren Lebon; Leah A Santat; Michelle E Fontes; Graham A Anderson; Jordi Garcia-Ojalvo; Michael B Elowitz
Journal:  Nature       Date:  2010-04-25       Impact factor: 49.962

10.  A fast, robust and tunable synthetic gene oscillator.

Authors:  Jesse Stricker; Scott Cookson; Matthew R Bennett; William H Mather; Lev S Tsimring; Jeff Hasty
Journal:  Nature       Date:  2008-10-29       Impact factor: 49.962

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  122 in total

1.  Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations.

Authors:  Fahim Farzadfard; Timothy K Lu
Journal:  Science       Date:  2014-11-14       Impact factor: 47.728

2.  Inner Workings: DNA for data storage and computing.

Authors:  Megan Scudellari
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-29       Impact factor: 11.205

3.  Epigenetic memory emerging from integrated transcription bursts.

Authors:  Volker Kurz; Edward M Nelson; Nicolas Perry; Winston Timp; Gregory Timp
Journal:  Biophys J       Date:  2013-09-17       Impact factor: 4.033

4.  Synthetic biology: Synthetic gene networks that smell.

Authors:  Fahim Farzadfard; Timothy K Lu
Journal:  Nat Chem Biol       Date:  2017-02-15       Impact factor: 15.040

Review 5.  The log-dynamic brain: how skewed distributions affect network operations.

Authors:  György Buzsáki; Kenji Mizuseki
Journal:  Nat Rev Neurosci       Date:  2014-02-26       Impact factor: 34.870

6.  Lightening the load in synthetic biology.

Authors:  Eric Klavins
Journal:  Nat Biotechnol       Date:  2014-12       Impact factor: 54.908

7.  Quantifying cellular capacity identifies gene expression designs with reduced burden.

Authors:  Francesca Ceroni; Rhys Algar; Guy-Bart Stan; Tom Ellis
Journal:  Nat Methods       Date:  2015-04-06       Impact factor: 28.547

8.  Robust, tunable genetic memory from protein sequestration combined with positive feedback.

Authors:  Tatenda Shopera; William R Henson; Andrew Ng; Young Je Lee; Kenneth Ng; Tae Seok Moon
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

9.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

10.  Synthetic metabolic computation in a bioluminescence-sensing system.

Authors:  Natalia Barger; Phyana Litovco; Ximing Li; Mouna Habib; Ramez Daniel
Journal:  Nucleic Acids Res       Date:  2019-11-04       Impact factor: 16.971

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