메뉴 건너뛰기




Volumn 109, Issue 1, 2012, Pages 57-71

Computational simulation of a gene regulatory network implementing an extendable synchronous single-input delay flip-flop

Author keywords

Cellular automata; Delay flip flop; Escherichia coli; Finite state machine; Logic gates; Synthetic Biology

Indexed keywords

GREEN FLUORESCENT PROTEIN;

EID: 84861819481     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2012.01.004     Document Type: Article
Times cited : (13)

References (65)
  • 1
    • 0028114541 scopus 로고
    • Molecular computation of solutions to combinatorial problems
    • Adleman L.M. Molecular computation of solutions to combinatorial problems. Science 1994, 266:1021-1024.
    • (1994) Science , vol.266 , pp. 1021-1024
    • Adleman, L.M.1
  • 2
    • 2342613767 scopus 로고    scopus 로고
    • Induction of the SOS response in ultraviolet-irradiated Escherichia coli analyzed by dynamics of LexA, RecA and SulA proteins
    • Aksenov S.V. Induction of the SOS response in ultraviolet-irradiated Escherichia coli analyzed by dynamics of LexA, RecA and SulA proteins. J. Biol. Phys. 1999, 25:263-277.
    • (1999) J. Biol. Phys. , vol.25 , pp. 263-277
    • Aksenov, S.V.1
  • 4
    • 29144482539 scopus 로고    scopus 로고
    • Environmentally controlled invasion of cancer cells by engineered bacteria
    • Anderson J.C., Clarke E.J., Arkin A.P., Voigt C.A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 2006, 355:619-627.
    • (2006) J. Mol. Biol. , vol.355 , pp. 619-627
    • Anderson, J.C.1    Clarke, E.J.2    Arkin, A.P.3    Voigt, C.A.4
  • 5
    • 0032739308 scopus 로고    scopus 로고
    • A second operator is involved in Pseudomonas aeruginosa elastase (lasB) activation
    • Anderson R.M., Zimprich C.A., Rust L. A second operator is involved in Pseudomonas aeruginosa elastase (lasB) activation. J. Bacteriol. 1999, 181:6264-6270.
    • (1999) J. Bacteriol. , vol.181 , pp. 6264-6270
    • Anderson, R.M.1    Zimprich, C.A.2    Rust, L.3
  • 6
    • 84855684934 scopus 로고    scopus 로고
    • Optimality and thermodynamics determine the evolution of transcriptional regulatory networks
    • Avila-Elchiver M., Nagrath D., Yarmush M.L. Optimality and thermodynamics determine the evolution of transcriptional regulatory networks. Mol. Biosyst. 2012, 8:511-530.
    • (2012) Mol. Biosyst. , vol.8 , pp. 511-530
    • Avila-Elchiver, M.1    Nagrath, D.2    Yarmush, M.L.3
  • 8
    • 17844374314 scopus 로고    scopus 로고
    • A synthetic multicellular system for programmed pattern formation
    • Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434:1130-1134.
    • (2005) Nature , vol.434 , pp. 1130-1134
    • Basu, S.1    Gerchman, Y.2    Collins, C.H.3    Arnold, F.H.4    Weiss, R.5
  • 11
    • 0025766223 scopus 로고
    • Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli
    • Baumeister R., Flache P., Melefors O., von G.A., Hillen W. Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli. Nucl. Acids Res. 1991, 19:4595-4600.
    • (1991) Nucl. Acids Res. , vol.19 , pp. 4595-4600
    • Baumeister, R.1    Flache, P.2    Melefors, O.3    von, G.A.4    Hillen, W.5
  • 12
    • 21444457242 scopus 로고    scopus 로고
    • Programmable ligand-controlled riboregulators of eukaryotic gene expression
    • Bayer T.S., Smolke C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005, 23:337-343.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 337-343
    • Bayer, T.S.1    Smolke, C.D.2
  • 13
    • 82255164260 scopus 로고    scopus 로고
    • The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
    • Blakes J., Twycross J., Romero-Campero F.J., Krasnogor N. The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. Bioinformatics 2011, 27:3323-3324.
    • (2011) Bioinformatics , vol.27 , pp. 3323-3324
    • Blakes, J.1    Twycross, J.2    Romero-Campero, F.J.3    Krasnogor, N.4
  • 14
    • 67650671869 scopus 로고    scopus 로고
    • Harnessing nature's toolbox: regulatory elements for synthetic biology
    • Boyle P.M., Silver P.A. Harnessing nature's toolbox: regulatory elements for synthetic biology. J. R. Soc. Interface 2009, 6(Suppl. 4):S535-S546.
    • (2009) J. R. Soc. Interface , vol.6 , Issue.SUPPL. 4
    • Boyle, P.M.1    Silver, P.A.2
  • 15
    • 33748028819 scopus 로고    scopus 로고
    • Autogenous and nonautogenous control of response in a genetic network
    • Camas F.M., Blazquez J., Poyatos J.F. Autogenous and nonautogenous control of response in a genetic network. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:12718-12723.
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 12718-12723
    • Camas, F.M.1    Blazquez, J.2    Poyatos, J.F.3
  • 16
    • 34250754425 scopus 로고    scopus 로고
    • Adaptive explicit-implicit tau-leaping method with automatic tau selection
    • Cao Y., Gillespie D.T., Petzold L.R. Adaptive explicit-implicit tau-leaping method with automatic tau selection. J. Chem. Phys. 2007, 126:224101.
    • (2007) J. Chem. Phys. , vol.126 , pp. 224101
    • Cao, Y.1    Gillespie, D.T.2    Petzold, L.R.3
  • 18
    • 36249017917 scopus 로고    scopus 로고
    • Programming gene expression with combinatorial promoters
    • Cox R.S.I., Surette M.G., Elowitz M.B. Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 2007, 3:145.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 145
    • Cox, R.S.I.1    Surette, M.G.2    Elowitz, M.B.3
  • 19
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 2002, 9:67-103.
    • (2002) J. Comput. Biol. , vol.9 , pp. 67-103
    • de Jong, H.1
  • 20
    • 77951576054 scopus 로고    scopus 로고
    • Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria
    • de Jong H., Ranquet C., Ropers D., Pinel C., Geiselmann J. Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst. Biol. 2010, 4:55.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 55
    • de Jong, H.1    Ranquet, C.2    Ropers, D.3    Pinel, C.4    Geiselmann, J.5
  • 22
    • 0141757323 scopus 로고    scopus 로고
    • Reprogramming control of an allosteric signaling switch through modular recombination
    • Dueber J.E., Yeh B.J., Chak K., Lim W.A. Reprogramming control of an allosteric signaling switch through modular recombination. Science 2003, 301:1904-1908.
    • (2003) Science , vol.301 , pp. 1904-1908
    • Dueber, J.E.1    Yeh, B.J.2    Chak, K.3    Lim, W.A.4
  • 23
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 25
    • 0035675837 scopus 로고    scopus 로고
    • Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing
    • Fuqua C., Parsek M.R., Greenberg E.P. Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu. Rev. Genet. 2001, 35:439-468.
    • (2001) Annu. Rev. Genet. , vol.35 , pp. 439-468
    • Fuqua, C.1    Parsek, M.R.2    Greenberg, E.P.3
  • 26
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 27
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81:2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 28
    • 32044445314 scopus 로고    scopus 로고
    • Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants
    • Goryachev A.B., Toh D.J., Lee T. Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems 2006, 83:178-187.
    • (2006) Biosystems , vol.83 , pp. 178-187
    • Goryachev, A.B.1    Toh, D.J.2    Lee, T.3
  • 29
    • 33646565046 scopus 로고    scopus 로고
    • A tightly regulated inducible expression system utilizing the fim inversion recombination switch
    • Ham T.S., Lee S.K., Keasling J.D., Arkin A.P. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol. Bioeng. 2006, 94:1-4.
    • (2006) Biotechnol. Bioeng. , vol.94 , pp. 1-4
    • Ham, T.S.1    Lee, S.K.2    Keasling, J.D.3    Arkin, A.P.4
  • 30
    • 50949122967 scopus 로고    scopus 로고
    • Design and construction of a double inversion recombination switch for heritable sequential genetic memory
    • Ham T.S., Lee S.K., Keasling J.D., Arkin A.P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS One 2008, 3:e2815.
    • (2008) PLoS One , vol.3
    • Ham, T.S.1    Lee, S.K.2    Keasling, J.D.3    Arkin, A.P.4
  • 31
    • 74049088689 scopus 로고    scopus 로고
    • Eukaryotic systems broaden the scope of synthetic biology
    • Haynes K.A., Silver P.A. Eukaryotic systems broaden the scope of synthetic biology. J. Cell Biol. 2009, 187:589-596.
    • (2009) J. Cell Biol. , vol.187 , pp. 589-596
    • Haynes, K.A.1    Silver, P.A.2
  • 32
    • 0032483501 scopus 로고    scopus 로고
    • Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites
    • Head C.G., Tardy A., Kenney L.J. Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites. J. Mol. Biol. 1998, 281:857-870.
    • (1998) J. Mol. Biol. , vol.281 , pp. 857-870
    • Head, C.G.1    Tardy, A.2    Kenney, L.J.3
  • 35
    • 84861792149 scopus 로고    scopus 로고
    • A gene regulatory network design of a synchronous single-input delay flip-flop
    • The MIT Press
    • Hoteit I., Kharma N., Varin L. A gene regulatory network design of a synchronous single-input delay flip-flop. ECAL 2011 2011, 342-347. The MIT Press. 11th ed.
    • (2011) ECAL 2011 , pp. 342-347
    • Hoteit, I.1    Kharma, N.2    Varin, L.3
  • 36
    • 0036372791 scopus 로고    scopus 로고
    • The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology
    • Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J., Kitano H. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Pac. Symp. Biocomput. 2002, 450-461.
    • (2002) Pac. Symp. Biocomput. , pp. 450-461
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.5    Kitano, H.6
  • 40
    • 34250273116 scopus 로고
    • Generalized Runge-Kutta methods of order four with stepsize control for stiff ordinary differential equations
    • Kaps P., Rentrop P. Generalized Runge-Kutta methods of order four with stepsize control for stiff ordinary differential equations. Numer. Math. 1979, 33:55-68.
    • (1979) Numer. Math. , vol.33 , pp. 55-68
    • Kaps, P.1    Rentrop, P.2
  • 43
    • 4344703213 scopus 로고    scopus 로고
    • BioLogic gates enable logical transcription control in mammalian cells
    • Kramer B.P., Fischer C., Fussenegger M. BioLogic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 2004, 87:478-484.
    • (2004) Biotechnol. Bioeng. , vol.87 , pp. 478-484
    • Kramer, B.P.1    Fischer, C.2    Fussenegger, M.3
  • 47
    • 10744220974 scopus 로고    scopus 로고
    • Mechanism of Pseudomonas aeruginosa RhlR transcriptional regulation of the rhlAB promoter
    • Medina G., Juarez K., Valderrama B., Soberon-Chavez G. Mechanism of Pseudomonas aeruginosa RhlR transcriptional regulation of the rhlAB promoter. J. Bacteriol. 2003, 185:5976-5983.
    • (2003) J. Bacteriol. , vol.185 , pp. 5976-5983
    • Medina, G.1    Juarez, K.2    Valderrama, B.3    Soberon-Chavez, G.4
  • 50
    • 0025122786 scopus 로고
    • Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity
    • Reinitz J., Vaisnys J.R. Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity. J. Theor. Biol. 1990, 145:295-318.
    • (1990) J. Theor. Biol. , vol.145 , pp. 295-318
    • Reinitz, J.1    Vaisnys, J.R.2
  • 52
    • 0021688529 scopus 로고
    • Kinetic analysis of mutations affecting the cII activation site at the PRE promoter of bacteriophage lambda
    • Shih M.C., Gussin G.N. Kinetic analysis of mutations affecting the cII activation site at the PRE promoter of bacteriophage lambda. Proc. Natl. Acad. Sci. U.S.A. 1984, 81:6432-6436.
    • (1984) Proc. Natl. Acad. Sci. U.S.A. , vol.81 , pp. 6432-6436
    • Shih, M.C.1    Gussin, G.N.2
  • 53
    • 84861808575 scopus 로고    scopus 로고
    • Quorum sensing: coordinating group behavior through intercellular signals
    • Springer, US, C.A. Nickerson, M.J. Schurr (Eds.)
    • Shrout J.D., Parsek M.R. Quorum sensing: coordinating group behavior through intercellular signals. Molecular Paradigms of Infectious Disease 2006, 404-437. Springer, US. C.A. Nickerson, M.J. Schurr (Eds.).
    • (2006) Molecular Paradigms of Infectious Disease , pp. 404-437
    • Shrout, J.D.1    Parsek, M.R.2
  • 54
    • 33845527888 scopus 로고    scopus 로고
    • Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors
    • Steindler L., Venturi V. Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors. FEMS Microbiol. Lett. 2007, 266:1-9.
    • (2007) FEMS Microbiol. Lett. , vol.266 , pp. 1-9
    • Steindler, L.1    Venturi, V.2
  • 55
    • 40649083597 scopus 로고    scopus 로고
    • Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression
    • Stekel D.J., Jenkins D.J. Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst. Biol. 2008, 2:6.
    • (2008) BMC Syst. Biol. , vol.2 , pp. 6
    • Stekel, D.J.1    Jenkins, D.J.2
  • 57
    • 0345060796 scopus 로고    scopus 로고
    • Chemical communication among bacteria
    • Taga M.E., Bassler B.L. Chemical communication among bacteria. Proc. Natl. Acad. Sci. U.S.A. 2003, 100(Suppl. 2):14549-14554.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , Issue.SUPPL. 2 , pp. 14549-14554
    • Taga, M.E.1    Bassler, B.L.2
  • 58
    • 33644841410 scopus 로고    scopus 로고
    • A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes
    • Tecon R., Wells M., van der Meer J.R. A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes. Environ. Microbiol. 2006, 8:697-708.
    • (2006) Environ. Microbiol. , vol.8 , pp. 697-708
    • Tecon, R.1    Wells, M.2    van der Meer, J.R.3
  • 60
    • 77953343521 scopus 로고    scopus 로고
    • Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study
    • Twycross J., Band L.R., Bennett M.J., King J.R., Krasnogor N. Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. BMC Syst. Biol. 2010, 4:34.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 34
    • Twycross, J.1    Band, L.R.2    Bennett, M.J.3    King, J.R.4    Krasnogor, N.5
  • 61
    • 0035965273 scopus 로고    scopus 로고
    • Neural model of the genetic network
    • Vohradsky J. Neural model of the genetic network. J. Biol. Chem. 2001, 276:36168-36173.
    • (2001) J. Biol. Chem. , vol.276 , pp. 36168-36173
    • Vohradsky, J.1
  • 65
    • 0034608954 scopus 로고    scopus 로고
    • Phosphatase activity of histidine kinase EnvZ without kinase catalytic domain
    • Zhu Y., Qin L., Yoshida T., Inouye M. Phosphatase activity of histidine kinase EnvZ without kinase catalytic domain. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:7808-7813.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 7808-7813
    • Zhu, Y.1    Qin, L.2    Yoshida, T.3    Inouye, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.