Literature DB >> 19898500

Synthetic biology: understanding biological design from synthetic circuits.

Shankar Mukherji1, Alexander van Oudenaarden.   

Abstract

An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems - from synthetic promoters to the control of cell-cell interactions - has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics.

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Year:  2009        PMID: 19898500      PMCID: PMC3138802          DOI: 10.1038/nrg2697

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  108 in total

1.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

2.  Contributions of low molecule number and chromosomal positioning to stochastic gene expression.

Authors:  Attila Becskei; Benjamin B Kaufmann; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2005-08-07       Impact factor: 38.330

3.  Emerging principles of regulatory evolution.

Authors:  Benjamin Prud'homme; Nicolas Gompel; Sean B Carroll
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-09       Impact factor: 11.205

4.  Signal processing by the HOG MAP kinase pathway.

Authors:  Pascal Hersen; Megan N McClean; L Mahadevan; Sharad Ramanathan
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-14       Impact factor: 11.205

5.  Controlling gene expression in living cells through small molecule-RNA interactions.

Authors:  G Werstuck; M R Green
Journal:  Science       Date:  1998-10-09       Impact factor: 47.728

Review 6.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

7.  Evolvability and hierarchy in rewired bacterial gene networks.

Authors:  Mark Isalan; Caroline Lemerle; Konstantinos Michalodimitrakis; Carsten Horn; Pedro Beltrao; Emanuele Raineri; Mireia Garriga-Canut; Luis Serrano
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

8.  Programming gene expression with combinatorial promoters.

Authors:  Robert Sidney Cox; Michael G Surette; Michael B Elowitz
Journal:  Mol Syst Biol       Date:  2007-11-13       Impact factor: 11.429

9.  A synthetic Escherichia coli predator-prey ecosystem.

Authors:  Frederick K Balagaddé; Hao Song; Jun Ozaki; Cynthia H Collins; Matthew Barnet; Frances H Arnold; Stephen R Quake; Lingchong You
Journal:  Mol Syst Biol       Date:  2008-04-15       Impact factor: 11.429

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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  73 in total

1.  Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling.

Authors:  Ryoji Sekine; Masayuki Yamamura; Shotaro Ayukawa; Kana Ishimatsu; Satoru Akama; Masahiro Takinoue; Masami Hagiya; Daisuke Kiga
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

Review 2.  Computational tools for the synthetic design of biochemical pathways.

Authors:  Marnix H Medema; Renske van Raaphorst; Eriko Takano; Rainer Breitling
Journal:  Nat Rev Microbiol       Date:  2012-01-23       Impact factor: 60.633

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

4.  Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells.

Authors:  Guillermo Rodrigo; Eszter Majer; Satya Prakash; José-Antonio Daròs; Alfonso Jaramillo; Juan F Poyatos
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

Review 5.  Foundations for the design and implementation of synthetic genetic circuits.

Authors:  Adrian L Slusarczyk; Allen Lin; Ron Weiss
Journal:  Nat Rev Genet       Date:  2012-05-18       Impact factor: 53.242

Review 6.  Engineering microbial systems to explore ecological and evolutionary dynamics.

Authors:  Yu Tanouchi; Robert P Smith; Lingchong You
Journal:  Curr Opin Biotechnol       Date:  2012-02-04       Impact factor: 9.740

7.  Engineering of regulated stochastic cell fate determination.

Authors:  Min Wu; Ri-Qi Su; Xiaohui Li; Tom Ellis; Ying-Cheng Lai; Xiao Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-10       Impact factor: 11.205

8.  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

Review 9.  Synthetic nanoelectronic probes for biological cells and tissues.

Authors:  Bozhi Tian; Charles M Lieber
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2013-02-28       Impact factor: 10.745

Review 10.  High-cell-density culture strategies for polyhydroxyalkanoate production: a review.

Authors:  Jaciane Lutz Ienczak; Willibaldo Schmidell; Gláucia Maria Falcão de Aragão
Journal:  J Ind Microbiol Biotechnol       Date:  2013-02-28       Impact factor: 3.346

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