Literature DB >> 26686885

Build to understand: synthetic approaches to biology.

Le-Zhi Wang1, Fuqing Wu, Kevin Flores, Ying-Cheng Lai, Xiao Wang.   

Abstract

In this review we discuss how synthetic biology facilitates the task of investigating genetic circuits that are observed in naturally occurring biological systems. Specifically, we give examples where experimentation with synthetic gene circuits has been used to understand four fundamental mechanisms intrinsic to development and disease: multistability, stochastic gene expression, oscillations, and cell-cell communication. Within each area, we also discuss how mathematical modeling has been employed as an essential tool to guide the design of novel gene circuits and as a theoretical basis for exploring circuit topologies exhibiting robust behaviors in the presence of noise.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 26686885      PMCID: PMC4837018          DOI: 10.1039/c5ib00252d

Source DB:  PubMed          Journal:  Integr Biol (Camb)        ISSN: 1757-9694            Impact factor:   2.192


  142 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.  Delay-induced stochastic oscillations in gene regulation.

Authors:  Dmitri Bratsun; Dmitri Volfson; Lev S Tsimring; Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

3.  A pathway and genetic factors contributing to elevated gene expression noise in stationary phase.

Authors:  Nicholas J Guido; Philina Lee; Xiao Wang; Timothy C Elston; J J Collins
Journal:  Biophys J       Date:  2007-09-21       Impact factor: 4.033

4.  Quasi-potential landscape in complex multi-stable systems.

Authors:  Joseph Xu Zhou; M D S Aliyu; Erik Aurell; Sui Huang
Journal:  J R Soc Interface       Date:  2012-08-29       Impact factor: 4.118

5.  A plausible model for the digital response of p53 to DNA damage.

Authors:  Lan Ma; John Wagner; John Jeremy Rice; Wenwei Hu; Arnold J Levine; Gustavo A Stolovitzky
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-26       Impact factor: 11.205

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

Review 7.  Systems biology of stem cell fate and cellular reprogramming.

Authors:  Ben D Macarthur; Avi Ma'ayan; Ihor R Lemischka
Journal:  Nat Rev Mol Cell Biol       Date:  2009-09-09       Impact factor: 94.444

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

View more
  5 in total

1.  Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.

Authors:  Taylor Firman; Gábor Balázsi; Kingshuk Ghosh
Journal:  Biophys J       Date:  2017-11-07       Impact factor: 4.033

2.  A single layer artificial neural network type architecture with molecular engineered bacteria for reversible and irreversible computing.

Authors:  Kathakali Sarkar; Deepro Bonnerjee; Rajkamal Srivastava; Sangram Bagh
Journal:  Chem Sci       Date:  2021-11-09       Impact factor: 9.825

3.  Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution.

Authors:  Yolanda Schaerli; Alba Jiménez; José M Duarte; Ljiljana Mihajlovic; Julien Renggli; Mark Isalan; James Sharpe; Andreas Wagner
Journal:  Mol Syst Biol       Date:  2018-09-10       Impact factor: 11.429

4.  Absolute quantification of translational regulation and burden using combined sequencing approaches.

Authors:  Thomas E Gorochowski; Irina Chelysheva; Mette Eriksen; Priyanka Nair; Steen Pedersen; Zoya Ignatova
Journal:  Mol Syst Biol       Date:  2019-05-03       Impact factor: 11.429

5.  Critical Comparison of MaxCal and Other Stochastic Modeling Approaches in Analysis of Gene Networks.

Authors:  Taylor Firman; Jonathan Huihui; Austin R Clark; Kingshuk Ghosh
Journal:  Entropy (Basel)       Date:  2021-03-17       Impact factor: 2.524

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.