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Sensitivity of signaling pathway dynamics to plasmid transfection and its consequences
1. | Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-101 Gliwice |
2. | Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland |
References:
[1] |
S. T. M. Allard and K. Kopish, Luciferase reporter assays: Powerful, adaptable tools for cell biology research, Cell Notes, 21 (2008), 23-26. |
[2] |
J. Bachmann, A. Raue, M. Schilling, V. Becker, J. Timmer and U. Klingmueller, Predictive mathematical models of cancer signalling pathways, J. Intern. Med., 271 (2012), 155-165.
doi: 10.1111/j.1365-2796.2011.02492.x. |
[3] |
D. Bakstad, A. Adamson, D. G. Spiller and M. R. White, Quantitative measurement of single cell dynamics, Curr. Opin. Biotechnol., 23 (2013), 103-109.
doi: 10.1016/j.copbio.2011.11.007. |
[4] |
S. Basak, M. Behar and A. Hoffmann, Lessons from mathematically modeling the NF-$\kappa$B pathway, Immunol. Rev., 1 (2012), 221-238. |
[5] |
I. Bentwich, A. Avniel, Y. Karov, R. Aharonov, S. Gilad, O. Barad, A. Barzilai, P. Einat, U. Einav, E. Meiri, E. Sharon, Y. Spector and Z. Bentwich, Identification of hundreds of conserved and nonconserved human microRNAs, Nat. Genet., 37 (2005), 766-770.
doi: 10.1038/ng1590. |
[6] |
R. Cheong, A. Bergmann, S. L. Werner, J. Regal and A. Hoffmann, Transient I$\kappa$B kinase activity mediates temporal NF-$\kappa$B dynamics in response to wide range of tumour necrosis factor-$\alpha$ doses, J. Biol. Chem., 281 (2006), 2945-2950. |
[7] |
A. E. Erson-Bensan, Introduction to microRNAs in biological systems, Methods Mol. Biol., 1107 (2014), 1-14.
doi: 10.1007/978-1-62703-748-8_1. |
[8] |
R. C. Friedman, K. K. Farh, C. B. Burge and D. P. Bartel, Most mammalian mRNAs are conserved targets of microRNAs, Genome Res., 19 (2009), 92-105.
doi: 10.1101/gr.082701.108. |
[9] |
A. Grimson, K. K. Farh, W. K. Johnston, P. Garrett-Engele, L. P. Lim and D. Bartel, MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing, Mol. Cell, 27 (2007), 91-105.
doi: 10.1016/j.molcel.2007.06.017. |
[10] |
J. Hayes, P. P. Peruzzi and S. Lawler, MicroRNAs in cancer: Biomarkers, functions and therapy, Trends Mol. Med., 20 (2014), 460-469.
doi: 10.1016/j.molmed.2014.06.005. |
[11] |
P. Iglesias and B. Ingalls (editors), Control Theory and Systems Biology, MIT Press, Cambridge, Mass., 2010. |
[12] |
B. P. Lewis, C. B. Burge and D. P. Bartel, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120 (2005), 15-20. |
[13] |
L. P. Lim, N. C. Lau, E. G. Weinstein, A. Abdelhakim, S. Yekta, M. W. Rhoades, C. B. Burge and D. P. Bartel, The microRNAs of Caenorhabditis elegans, Genes Dev., 17 (2003), 991-1008.
doi: 10.1101/gad.1074403. |
[14] |
T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon and M. Kimmel, Mathematical model of NF$\kappa$B regulatory module, J. Theor. Biol., 228 (2004), 195-215.
doi: 10.1016/j.jtbi.2004.01.001. |
[15] |
J. Smieja, Coupled analytical and numerical approach to uncovering new regulatory mechanisms of intracellular processes, Int. J. Appl. Math. Comp. Sci., 20 (2010), 781-788. |
[16] |
J. Smieja and M. Dolbniak, Experimental data in modeling of intracellular processes, Proc. IASTED Int. Conf. Modelling, Identification and Control (MIC 2015), (2015), 105-109.
doi: 10.2316/P.2015.826-016. |
[17] |
Y. Takei, M. Takigahira, K. Mihara, Y. Tarumi and K. Yanagihara, The metastasis-associated microRNA miR-516a-3p is a novel therapeutic target for inhibiting peritoneal dissemination of human scirrhous gastric cancer, Cancer Res., 71 (2011), 1442-1453.
doi: 10.1158/0008-5472.CAN-10-2530. |
[18] |
D. A. Turner, P. Paszek, D. J. Woodcock, C. A. Horton, Y. Wang, D. G. Spiller, D. A. Rand, M. R. H. White and C. V. Harper, Physiological levels of TNF $\alpha$ stimulation induce stochastic dynamics of NF-$\kappa$B responses in single living cells, J. Cell Sci., 324 (2010), 2834-2843. |
[19] |
J. J. Tyson, R. Albert, A. Goldbeter, P. Ruoff and J. Sible, Biological switches and clocks, J. R. Soc. Interface, 5 (2008), S1-S8.
doi: 10.1098/rsif.2008.0179.focus. |
[20] |
A. V. Orang, R. Safaralizadeh and M. Kazemzadeh-Bavili, Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int. J. Genomics, 2014 (2014), 970607. |
[21] |
X. Wang, Y. Li, X. Xu and Y. H. Wang, Toward a system-level understanding of microRNA pathway via mathematical modeling, Biosystems, 100 (2010), 31-38.
doi: 10.1016/j.biosystems.2009.12.005. |
[22] |
R. A. Williams, J. Timmis and E. E. Qwarnstrom, Computational models of the NF-$\kappa$B signalling pathway, Computation, 2 (2014), 131-158. |
[23] |
X. Xue, W. Xia and H. Wenzhong, A modeled dynamic regulatory network of NF-kB and IL-6 mediated by miRNA, BioSystems, 114 (2013), 214-218. |
[24] |
F. Yan, H. Liu and Z. Liu, Dynamic analysis of the combinatorial regulation involving transcription factors and microRNAs in cell fate decisions, Bioch et Biophysica Acta, 1844 (2014), 248-257.
doi: 10.1016/j.bbapap.2013.06.022. |
[25] |
W. Zhou, Y. Li, X. Wang, L. Wu and Y. Wang, MiR-206-mediated dynamic mech-anism of the mammalian circadian clock, BMC Syst. Biol., 5 (2011), 141. |
show all references
References:
[1] |
S. T. M. Allard and K. Kopish, Luciferase reporter assays: Powerful, adaptable tools for cell biology research, Cell Notes, 21 (2008), 23-26. |
[2] |
J. Bachmann, A. Raue, M. Schilling, V. Becker, J. Timmer and U. Klingmueller, Predictive mathematical models of cancer signalling pathways, J. Intern. Med., 271 (2012), 155-165.
doi: 10.1111/j.1365-2796.2011.02492.x. |
[3] |
D. Bakstad, A. Adamson, D. G. Spiller and M. R. White, Quantitative measurement of single cell dynamics, Curr. Opin. Biotechnol., 23 (2013), 103-109.
doi: 10.1016/j.copbio.2011.11.007. |
[4] |
S. Basak, M. Behar and A. Hoffmann, Lessons from mathematically modeling the NF-$\kappa$B pathway, Immunol. Rev., 1 (2012), 221-238. |
[5] |
I. Bentwich, A. Avniel, Y. Karov, R. Aharonov, S. Gilad, O. Barad, A. Barzilai, P. Einat, U. Einav, E. Meiri, E. Sharon, Y. Spector and Z. Bentwich, Identification of hundreds of conserved and nonconserved human microRNAs, Nat. Genet., 37 (2005), 766-770.
doi: 10.1038/ng1590. |
[6] |
R. Cheong, A. Bergmann, S. L. Werner, J. Regal and A. Hoffmann, Transient I$\kappa$B kinase activity mediates temporal NF-$\kappa$B dynamics in response to wide range of tumour necrosis factor-$\alpha$ doses, J. Biol. Chem., 281 (2006), 2945-2950. |
[7] |
A. E. Erson-Bensan, Introduction to microRNAs in biological systems, Methods Mol. Biol., 1107 (2014), 1-14.
doi: 10.1007/978-1-62703-748-8_1. |
[8] |
R. C. Friedman, K. K. Farh, C. B. Burge and D. P. Bartel, Most mammalian mRNAs are conserved targets of microRNAs, Genome Res., 19 (2009), 92-105.
doi: 10.1101/gr.082701.108. |
[9] |
A. Grimson, K. K. Farh, W. K. Johnston, P. Garrett-Engele, L. P. Lim and D. Bartel, MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing, Mol. Cell, 27 (2007), 91-105.
doi: 10.1016/j.molcel.2007.06.017. |
[10] |
J. Hayes, P. P. Peruzzi and S. Lawler, MicroRNAs in cancer: Biomarkers, functions and therapy, Trends Mol. Med., 20 (2014), 460-469.
doi: 10.1016/j.molmed.2014.06.005. |
[11] |
P. Iglesias and B. Ingalls (editors), Control Theory and Systems Biology, MIT Press, Cambridge, Mass., 2010. |
[12] |
B. P. Lewis, C. B. Burge and D. P. Bartel, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120 (2005), 15-20. |
[13] |
L. P. Lim, N. C. Lau, E. G. Weinstein, A. Abdelhakim, S. Yekta, M. W. Rhoades, C. B. Burge and D. P. Bartel, The microRNAs of Caenorhabditis elegans, Genes Dev., 17 (2003), 991-1008.
doi: 10.1101/gad.1074403. |
[14] |
T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon and M. Kimmel, Mathematical model of NF$\kappa$B regulatory module, J. Theor. Biol., 228 (2004), 195-215.
doi: 10.1016/j.jtbi.2004.01.001. |
[15] |
J. Smieja, Coupled analytical and numerical approach to uncovering new regulatory mechanisms of intracellular processes, Int. J. Appl. Math. Comp. Sci., 20 (2010), 781-788. |
[16] |
J. Smieja and M. Dolbniak, Experimental data in modeling of intracellular processes, Proc. IASTED Int. Conf. Modelling, Identification and Control (MIC 2015), (2015), 105-109.
doi: 10.2316/P.2015.826-016. |
[17] |
Y. Takei, M. Takigahira, K. Mihara, Y. Tarumi and K. Yanagihara, The metastasis-associated microRNA miR-516a-3p is a novel therapeutic target for inhibiting peritoneal dissemination of human scirrhous gastric cancer, Cancer Res., 71 (2011), 1442-1453.
doi: 10.1158/0008-5472.CAN-10-2530. |
[18] |
D. A. Turner, P. Paszek, D. J. Woodcock, C. A. Horton, Y. Wang, D. G. Spiller, D. A. Rand, M. R. H. White and C. V. Harper, Physiological levels of TNF $\alpha$ stimulation induce stochastic dynamics of NF-$\kappa$B responses in single living cells, J. Cell Sci., 324 (2010), 2834-2843. |
[19] |
J. J. Tyson, R. Albert, A. Goldbeter, P. Ruoff and J. Sible, Biological switches and clocks, J. R. Soc. Interface, 5 (2008), S1-S8.
doi: 10.1098/rsif.2008.0179.focus. |
[20] |
A. V. Orang, R. Safaralizadeh and M. Kazemzadeh-Bavili, Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int. J. Genomics, 2014 (2014), 970607. |
[21] |
X. Wang, Y. Li, X. Xu and Y. H. Wang, Toward a system-level understanding of microRNA pathway via mathematical modeling, Biosystems, 100 (2010), 31-38.
doi: 10.1016/j.biosystems.2009.12.005. |
[22] |
R. A. Williams, J. Timmis and E. E. Qwarnstrom, Computational models of the NF-$\kappa$B signalling pathway, Computation, 2 (2014), 131-158. |
[23] |
X. Xue, W. Xia and H. Wenzhong, A modeled dynamic regulatory network of NF-kB and IL-6 mediated by miRNA, BioSystems, 114 (2013), 214-218. |
[24] |
F. Yan, H. Liu and Z. Liu, Dynamic analysis of the combinatorial regulation involving transcription factors and microRNAs in cell fate decisions, Bioch et Biophysica Acta, 1844 (2014), 248-257.
doi: 10.1016/j.bbapap.2013.06.022. |
[25] |
W. Zhou, Y. Li, X. Wang, L. Wu and Y. Wang, MiR-206-mediated dynamic mech-anism of the mammalian circadian clock, BMC Syst. Biol., 5 (2011), 141. |
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