Literature DB >> 19478183

Synthetic gene networks that count.

Ari E Friedland1, Timothy K Lu, Xiao Wang, David Shi, George Church, James J Collins.   

Abstract

Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.

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Year:  2009        PMID: 19478183      PMCID: PMC2690711          DOI: 10.1126/science.1172005

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  28 in total

1.  Construction of a genetic toggle switch in Escherichia coli.

Authors:  T S Gardner; C R Cantor; J J Collins
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

3.  Directed evolution of the site specificity of Cre recombinase.

Authors:  Stephen W Santoro; Peter G Schultz
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-19       Impact factor: 11.205

4.  Directed evolution of a genetic circuit.

Authors:  Yohei Yokobayashi; Ron Weiss; Frances H Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-25       Impact factor: 11.205

Review 5.  Phage integrases: biology and applications.

Authors:  Amy C Groth; Michele P Calos
Journal:  J Mol Biol       Date:  2004-01-16       Impact factor: 5.469

6.  Programmable cells: interfacing natural and engineered gene networks.

Authors:  Hideki Kobayashi; Mads Kaern; Michihiro Araki; Kristy Chung; Timothy S Gardner; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-24       Impact factor: 11.205

7.  Engineered riboregulators enable post-transcriptional control of gene expression.

Authors:  Farren J Isaacs; Daniel J Dwyer; Chunming Ding; Dmitri D Pervouchine; Charles R Cantor; James J Collins
Journal:  Nat Biotechnol       Date:  2004-06-20       Impact factor: 54.908

8.  New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.

Authors:  J B Andersen; C Sternberg; L K Poulsen; S P Bjorn; M Givskov; S Molin
Journal:  Appl Environ Microbiol       Date:  1998-06       Impact factor: 4.792

9.  A protein-counting mechanism for telomere length regulation in yeast.

Authors:  S Marcand; E Gilson; D Shore
Journal:  Science       Date:  1997-02-14       Impact factor: 47.728

10.  An engineered epigenetic transgene switch in mammalian cells.

Authors:  Beat P Kramer; Alessandro Usseglio Viretta; Marie Daoud-El-Baba; Dominique Aubel; Wilfried Weber; Martin Fussenegger
Journal:  Nat Biotechnol       Date:  2004-06-06       Impact factor: 54.908

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  195 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.  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.  Tracking, tuning, and terminating microbial physiology using synthetic riboregulators.

Authors:  Jarred M Callura; Daniel J Dwyer; Farren J Isaacs; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-16       Impact factor: 11.205

Review 4.  Where microbiology meets microengineering: design and applications of reporter bacteria.

Authors:  Jan Roelof van der Meer; Shimshon Belkin
Journal:  Nat Rev Microbiol       Date:  2010-07       Impact factor: 60.633

Review 5.  Synthetic RNA switches as a tool for temporal and spatial control over gene expression.

Authors:  Andrew L Chang; Joshua J Wolf; Christina D Smolke
Journal:  Curr Opin Biotechnol       Date:  2012-02-03       Impact factor: 9.740

Review 6.  Recent advances and opportunities in synthetic logic gates engineering in living cells.

Authors:  Vijai Singh
Journal:  Syst Synth Biol       Date:  2014-08-28

7.  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

Review 8.  Synthetic biology devices for in vitro and in vivo diagnostics.

Authors:  Shimyn Slomovic; Keith Pardee; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-24       Impact factor: 11.205

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.  The incoherent feedforward loop can provide fold-change detection in gene regulation.

Authors:  Lea Goentoro; Oren Shoval; Marc W Kirschner; Uri Alon
Journal:  Mol Cell       Date:  2009-12-11       Impact factor: 17.970

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