메뉴 건너뛰기




Volumn 95, Issue 7, 2008, Pages 3137-3145

Stochastic modeling of gene positive autoregulation networks involving signal molecules

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ESCHERICHIA COLI PROTEIN; SDIA PROTEIN, E COLI; TRANSACTIVATOR PROTEIN;

EID: 55949126736     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.127175     Document Type: Article
Times cited : (2)

References (25)
  • 1
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • Raser, J., and E. O'Shea. 2005. Noise in gene expression: origins, consequences, and control. Science. 309:2010-2013.
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.1    O'Shea, E.2
  • 2
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao, C., D. Wolf, and A. Arkin. 2002. Control, exploitation and tolerance of intracellular noise. Nature. 420:231-237.
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.1    Wolf, D.2    Arkin, A.3
  • 3
    • 0033083733 scopus 로고    scopus 로고
    • It's a noisy business! Genetic regulation at the nanomolar scale
    • McAdams, H., and A. Arkin. 1999. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15:65-69.
    • (1999) Trends Genet , vol.15 , pp. 65-69
    • McAdams, H.1    Arkin, A.2
  • 4
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • McAdams, H., and A. Arkin. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA. 94:814-819.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 814-819
    • McAdams, H.1    Arkin, A.2
  • 5
    • 22144458274 scopus 로고    scopus 로고
    • Markov chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli
    • Zhou, B., D. Beckwith, L. Jarboe, and J. Liao. 2005. Markov chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli. Biophys. J. 88:2541-2553.
    • (2005) Biophys. J , vol.88 , pp. 2541-2553
    • Zhou, B.1    Beckwith, D.2    Jarboe, L.3    Liao, J.4
  • 6
    • 33846113021 scopus 로고    scopus 로고
    • A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways
    • DOI:10.1038/msb4100107
    • Li, J., L. Wang, Y. Hashimoto, C.-Y. Tsao, T. Wood, J. Valdes, E. Zafiriou, and W. Bentley. 2006. A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways. Mol. Sys. Biol. DOI:10.1038/msb4100107.
    • (2006) Mol. Sys. Biol
    • Li, J.1    Wang, L.2    Hashimoto, Y.3    Tsao, C.-Y.4    Wood, T.5    Valdes, J.6    Zafiriou, E.7    Bentley, W.8
  • 7
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • Arkin, A., J. Ross, and H. McAdams. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics. 149:1633-1648.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.3
  • 8
    • 0038271880 scopus 로고    scopus 로고
    • Prediction and measurement of an autoregulatory genetic module
    • Isaacs, F., J. Hasty, C. Cantor, and J. Collins. 2003. Prediction and measurement of an autoregulatory genetic module. Proc. Natl. Acad. Sci. USA. 100:7714-7719.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7714-7719
    • Isaacs, F.1    Hasty, J.2    Cantor, C.3    Collins, J.4
  • 9
    • 17144456808 scopus 로고    scopus 로고
    • Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
    • Becskei, A., B. Seraphin, and L. Serrano. 2001. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20:2528-2535.
    • (2001) EMBO J , vol.20 , pp. 2528-2535
    • Becskei, A.1    Seraphin, B.2    Serrano, L.3
  • 10
    • 0036532226 scopus 로고    scopus 로고
    • Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability
    • Ferrell, J. 2002. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Chem. Biol. 6:140-148.
    • (2002) Curr. Opin. Chem. Biol , vol.6 , pp. 140-148
    • Ferrell, J.1
  • 11
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
    • Kepler, T., and T. Elston. 2001. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81:3116-3136.
    • (2001) Biophys. J , vol.81 , pp. 3116-3136
    • Kepler, T.1    Elston, T.2
  • 12
    • 0026017101 scopus 로고
    • The Vibrio fischeri LUXR protein is capable of bidirectional stimulation of transcription and both positive and negative regulation of the luxr gene
    • Shadel, G., and T. Baldwin. 1991. The Vibrio fischeri LUXR protein is capable of bidirectional stimulation of transcription and both positive and negative regulation of the luxr gene. J. Bacteriol. 173:568-574.
    • (1991) J. Bacteriol , vol.173 , pp. 568-574
    • Shadel, G.1    Baldwin, T.2
  • 13
    • 0034875301 scopus 로고    scopus 로고
    • DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli
    • DeLisa, M., C.-F. Wu, L. Wang, J. Valdes, and W. Bentley. 2001. DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J. Bacteriol. 183:5239-5247.
    • (2001) J. Bacteriol , vol.183 , pp. 5239-5247
    • DeLisa, M.1    Wu, C.-F.2    Wang, L.3    Valdes, J.4    Bentley, W.5
  • 14
    • 0027957161 scopus 로고
    • Quorum sensing in bacteria: The Luxr-Luxi family of cell density-responsive transcriptional regulators
    • Fuqua, W., S. Wintans, and E. Greenberg. 1994. Quorum sensing in bacteria: the Luxr-Luxi family of cell density-responsive transcriptional regulators. J. Bacteriol. 176:269-275.
    • (1994) J. Bacteriol , vol.176 , pp. 269-275
    • Fuqua, W.1    Wintans, S.2    Greenberg, E.3
  • 15
    • 3142764130 scopus 로고    scopus 로고
    • Cell-to-cell signaling in Escherichia coli and Salmonella enterica
    • Ahmer, B. 2004. Cell-to-cell signaling in Escherichia coli and Salmonella enterica. Mol. Microbiol. 82:933-945.
    • (2004) Mol. Microbiol , vol.82 , pp. 933-945
    • Ahmer, B.1
  • 16
    • 0033622527 scopus 로고    scopus 로고
    • SdiA, an Escherichia coli homologue of quorum-sensing regulators, controls the expression of virulence factors in enterohemorrhagic Escherichia coli o157:h7
    • Kanamaru, K., I. Tatsuno, T. Tobe, and C. Sasakawa. 2000. SdiA, an Escherichia coli homologue of quorum-sensing regulators, controls the expression of virulence factors in enterohemorrhagic Escherichia coli o157:h7. Mol. Microbiol. 38:805-816.
    • (2000) Mol. Microbiol , vol.38 , pp. 805-816
    • Kanamaru, K.1    Tatsuno, I.2    Tobe, T.3    Sasakawa, C.4
  • 17
    • 0035053171 scopus 로고    scopus 로고
    • Mapping stress-induced changes in autoinducer AI-2 production in chemostat-cultivated Escherichia coli k-12
    • DeLisa, M., J. Valdes, and W. Bentley. 2001. Mapping stress-induced changes in autoinducer AI-2 production in chemostat-cultivated Escherichia coli k-12. J. Bacteriol. 183:2918-2928.
    • (2001) J. Bacteriol , vol.183 , pp. 2918-2928
    • DeLisa, M.1    Valdes, J.2    Bentley, W.3
  • 20
    • 85031359921 scopus 로고    scopus 로고
    • 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella, 2, 2nd Ed. F. Neidhart, R. Curtiss, J. Ingraham, E. Lin, K. Low, B. Magasanik, W. Reznikoff, M. Riley, M. Schaechter, and H. Umbarger, editors. ASM Press, Washington, DC.
    • 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella, Vol. 2, 2nd Ed. F. Neidhart, R. Curtiss, J. Ingraham, E. Lin, K. Low, B. Magasanik, W. Reznikoff, M. Riley, M. Schaechter, and H. Umbarger, editors. ASM Press, Washington, DC.
  • 21
    • 0018175833 scopus 로고
    • Functional mRNA half lives in Escherichia coli
    • Pedersen, S., and S. Reeh. 1978. Functional mRNA half lives in Escherichia coli. Mol. Gen. Genet. 166:329-336.
    • (1978) Mol. Gen. Genet , vol.166 , pp. 329-336
    • Pedersen, S.1    Reeh, S.2
  • 22
    • 0029861143 scopus 로고    scopus 로고
    • The N-end rule: Functions, mysteries, uses
    • Varshavsky, A. 1996. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA. 93:12142-12149.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12142-12149
    • Varshavsky, A.1
  • 23
    • 0026417345 scopus 로고
    • Molecular design of expression systems: Comparison of different repressor control configurations using molecular mechanism models
    • Chen, W., J. Bailey, and S. Lee. 1991. Molecular design of expression systems: comparison of different repressor control configurations using molecular mechanism models. Biotechnol. Bioeng. 38:679-687.
    • (1991) Biotechnol. Bioeng , vol.38 , pp. 679-687
    • Chen, W.1    Bailey, J.2    Lee, S.3
  • 24
    • 0032499741 scopus 로고    scopus 로고
    • Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
    • Goss, P., and J. Peccoud. 1998. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. USA. 95:6750-6755.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6750-6755
    • Goss, P.1    Peccoud, J.2
  • 25
    • 85031355549 scopus 로고    scopus 로고
    • 1.5.0. PERFORM Performability Engineering Research Group, University of Illinois at Urbana-Champaign, Illinois
    • Sanders, W. 2004. Mobius User Manual, Ver. 1.5.0. PERFORM Performability Engineering Research Group, University of Illinois at Urbana-Champaign, Illinois.
    • (2004) Mobius User Manual, Ver
    • Sanders, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.