Are Quasi-Steady-State Approximated Models Suitable for Quantifying Intrinsic Noise Accurately?

PloS One
Dola Sengupta, Sandip Kar

Abstract

Large gene regulatory networks (GRN) are often modeled with quasi-steady-state approximation (QSSA) to reduce the huge computational time required for intrinsic noise quantification using Gillespie stochastic simulation algorithm (SSA). However, the question still remains whether the stochastic QSSA model measures the intrinsic noise as accurately as the SSA performed for a detailed mechanistic model or not? To address this issue, we have constructed mechanistic and QSSA models for few frequently observed GRNs exhibiting switching behavior and performed stochastic simulations with them. Our results strongly suggest that the performance of a stochastic QSSA model in comparison to SSA performed for a mechanistic model critically relies on the absolute values of the mRNA and protein half-lives involved in the corresponding GRN. The extent of accuracy level achieved by the stochastic QSSA model calculations will depend on the level of bursting frequency generated due to the absolute value of the half-life of either mRNA or protein or for both the species. For the GRNs considered, the stochastic QSSA quantifies the intrinsic noise at the protein level with greater accuracy and for larger combinations of half-life values of mRNA and ...Continue Reading

References

Dec 9, 1998·Cell·F C HolstegeR A Young
Apr 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yulei WangPatrick O Brown
Sep 19, 2002·Proceedings of the National Academy of Sciences of the United States of America·Peter S SwainEric D Siggia
Apr 11, 2003·Nature·William J BlakeJ J Collins
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Farren J IsaacsJ J Collins
Jan 11, 2005·The Journal of Chemical Physics·Yang CaoLinda R Petzold
May 11, 2005·Nature Reviews. Genetics·Mads KaernJames J Collins
Aug 11, 2005·Physical Review Letters·A J McKane, T J Newman
Oct 22, 2005·The Journal of Chemical Physics·Yang CaoLinda R Petzold
Mar 17, 2006·Nature Reviews. Microbiology·Wiep Klaas SmitsJan-Willem Veening
Aug 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Archana BelleErin K O'Shea
Mar 24, 2007·Science·Gürol M SüelMichael B Elowitz
Apr 5, 2007·Physical Biology·Rajesh Karmakar, Indrani Bose
Jan 19, 2008·Science·Juan M Pedraza, Johan Paulsson
Mar 28, 2008·Nature Cell Biology·Guang YaoLingchong You
Oct 31, 2008·Nature Reviews. Molecular Cell Biology·Béla Novák, John J Tyson
Nov 8, 2008·Proceedings of the National Academy of Sciences of the United States of America·Vahid Shahrezaei, Peter S Swain
Nov 18, 2008·Nature Structural & Molecular Biology·Daniel ZenklusenRobert H Singer
Dec 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Baltazar D AgudaClay B Marsh
Feb 28, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sandip KarJohn J Tyson
Oct 17, 2009·Current Opinion in Chemical Biology·Mario NiepelPeter K Sorger
Oct 21, 2009·PLoS Biology·Stefano Di TaliaFrederick R Cross
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Claude Gérard, Albert Goldbeter
Sep 9, 2010·PLoS Computational Biology·Amrita X Sarkar, Eric A Sobie
Mar 17, 2011·BMC Systems Biology·Thanneer M Perumal, Rudiyanto Gunawan
Apr 29, 2011·Molecular Systems Biology·Guang YaoLingchong You
May 20, 2011·Nature·Björn SchwanhäusserMatthias Selbach
Feb 8, 2014·Journal of Theoretical Biology·Laura CantiniLuigi Barletti
Oct 1, 2014·Proceedings of the National Academy of Sciences of the United States of America·K Wesley OvertonClifford L Wang

❮ Previous
Next ❯

Software Mentioned

XPP
MATLAB
QSSA
SSA
AUT
AUTO

Related Concepts

Related Feeds

Cell Fate Conversion By mRNA

mRNA-based technology is being studied as a potential technology that could be used to reprogram cell fate. This technique provides the potential to generate safe reprogrammed cells that can be used for clinical applications. Here is the latest research on cell fate conversion by mRNA.