Literature DB >> 33405228

A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks.

Andras Gyorgy1.   

Abstract

One of the fundamental properties of engineered large-scale complex systems is modularity. In synthetic biology, genetic parts exhibit context-dependent behavior. Here, we describe and quantify a major source of such behavior: retroactivity. In particular, we provide a step-by-step guide for characterizing retroactivity to restore the modular description of genetic modules. Additionally, we also discuss how retroactivity can be leveraged to quantify and maximize robustness to perturbations due to interconnection of genetic modules.

Keywords:  Context-dependence; Gene transcription networks; Loading; Model order reduction; Modularity; Retroactivity; Synthetic biology

Year:  2021        PMID： 33405228     DOI： 10.1007/978-1-0716-1032-9_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  40 in total

1.  Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.

Authors:  Mariette R Atkinson; Michael A Savageau; Jesse T Myers; Alexander J Ninfa
Journal:  Cell       Date:  2003-05-30       Impact factor: 41.582

2.  Long-term monitoring of bacteria undergoing programmed population control in a microchemostat.

Authors:  Frederick K Balagaddé; Lingchong You; Carl L Hansen; Frances H Arnold; Stephen R Quake
Journal:  Science       Date:  2005-07-01       Impact factor: 47.728

Review 3.  Network motifs: theory and experimental approaches.

Authors:  Uri Alon
Journal:  Nat Rev Genet       Date:  2007-06       Impact factor: 53.242

4.  Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli.

Authors:  T Akerlund; K Nordström; R Bernander
Journal:  J Bacteriol       Date:  1995-12       Impact factor: 3.490

5.  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

Review 6.  Overloaded and stressed: whole-cell considerations for bacterial synthetic biology.

Authors:  Olivier Borkowski; Francesca Ceroni; Guy-Bart Stan; Tom Ellis
Journal:  Curr Opin Microbiol       Date:  2016-08-02       Impact factor: 7.934

7.  Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase.

Authors:  Liping Du; Seth Villarreal; Anthony C Forster
Journal:  Biotechnol Bioeng       Date:  2011-12-01       Impact factor: 4.530

Review 8.  Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems.

Authors:  Stefano Cardinale; Adam Paul Arkin
Journal:  Biotechnol J       Date:  2012-05-31       Impact factor: 4.677

9.  A synchronized quorum of genetic clocks.

Authors:  Tal Danino; Octavio Mondragón-Palomino; Lev Tsimring; Jeff Hasty
Journal:  Nature       Date:  2010-01-21       Impact factor: 49.962

10.  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
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  1 in total

1.  Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease.

Authors:  Manoj J Mammen; Chengjian Tu; Matthew C Morris; Spencer Richman; William Mangione; Zackary Falls; Jun Qu; Gordon Broderick; Sanjay Sethi; Ram Samudrala
Journal:  Pharmaceuticals (Basel)       Date:  2022-05-01
  1 in total

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