Free Access
Issue |
Math. Model. Nat. Phenom.
Volume 4, Number 3, 2009
Cancer modelling (Part 2)
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Page(s) | 97 - 116 | |
DOI | https://doi.org/10.1051/mmnp/20094304 | |
Published online | 05 June 2009 |
- B. Alberts, A. Johnson, J. Lewis, K. Roberts, P. Walter. Molecular Biology of the Cell, Fourth Edition. Garland Science, Taylor and Francis Group Ltd, Oxford, 2002. [Google Scholar]
- E. Appella, C.W. Anderson. Post-transcriptional modifications and activation of p53 by genotoxic stresses. Eur. J. Biochem., 268 (2001), 2764–2772. [CrossRef] [PubMed] [Google Scholar]
- D. Bennett. Applications of Delay Differential Equations in Physiology and Epidemiology. PhD Thesis, University of Surrey, 2005. [Google Scholar]
- S. Bernard, B. Cajavec, L. Pujo-Menjouet, M.C. Mackey, H. Herzel. Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations. Phil. Trans. R. Soc. A, 364 (2006), 1155–1170. [CrossRef] [Google Scholar]
- A. Ciliberto, B. Novak, J.J. Tyson. Steady states and oscillations in the p53/mdm2 network. Cell Cycle, 4 (2005), 488–493. [CrossRef] [PubMed] [Google Scholar]
- M.L. Dequeant, E. Glynn, K. Gaudenz, M. Wahl, J. Chen, A. Mushegian, O. Pourquie. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science, 314 (2006), 1595–1598. [CrossRef] [PubMed] [Google Scholar]
- B. Ermentrout. Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students. Society for Industrial and Applied Mathematics, Philadelphia, 2002. [Google Scholar]
- C.P. Fall, E.S. Marland, J.M. Wagner, J.J. Tyson. Interdisciplinary Applied Mathematics, Mathematical Biology: Computational Cell Biology. Springer-Verlag, New York, 2002. [Google Scholar]
- R.S. Foo, Y.J. Nam, M.J. Ostreicher, M.D. Metzl, R.S. Whelan, C.F. Peng, A.W. Ashton, W. Fu, K. Mani, S.F. Chin, E. Provenzano, I. Ellis, N. Figg, S. Pinder, M.R. Bennett, C. Caldas, R.N. Kitsis. Regulation of p53 tetramerization and nuclear export by ARC. Proc. Natl. Acad. Sci. USA, 104 (2007), 20826–20831. [CrossRef] [Google Scholar]
- S.J. Gallagher, R.F. Kefford, H. Rizos. The ARF tumour suppressor. Intl. J. Biochem. Cell Biol., 38 (2006), 1637–1641. [CrossRef] [Google Scholar]
- Y. Haupt, R. Maya, A. Kazaz, M. Oren. Mdm2 promotes the rapid degradation of p53. Nature, 387 (1997), 296–299. [CrossRef] [PubMed] [Google Scholar]
- H. Hirata, S. Yoshiura, T. Ohtsuka, Y. Bessho, T. Harada, K. Yoshikawa, R. Kageyama R. Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science, 298 (2002), 840–843. [CrossRef] [PubMed] [Google Scholar]
- T.R. Hupp, A. Sparks, D.P. Lane. Small peptides activate the latent sequence-specific DNA binding function of p53. Cell, 83 (1995), 237–245. [CrossRef] [PubMed] [Google Scholar]
- B.N. Kholodenko. Cell signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol., 7 (2006), 165–176. [CrossRef] [PubMed] [Google Scholar]
- S. Krishna, M.H. Jensen, K. Sneppen. Minimal model of spiky oscillations in NF-κB. Proc. Natl. Acad. Sci. USA, 103 (2006), 10840–10845. [CrossRef] [Google Scholar]
- A. Kusumi, S. Yasushi, Y. Mutsuya. Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J., 65 (1993), 2021–2040. [CrossRef] [PubMed] [Google Scholar]
- G. Lahav, N. Rosenfield, A. Sigal, N. Geva-Zatorsky, A.J. Levine, M.B. Elowitz, U. Alon. Dynamics of the p53-mdm2 feedback loop in individual cells. Nat. Gen., 36 (2004), 147–150. [CrossRef] [PubMed] [Google Scholar]
- R. Lev Bar-Or, R. Maya, L.A. Segel, U. Alon, A.J. Levine, M. Oren. Generation of oscillations by the p53-mdm2 feedback loop: a theoretical and experimental study. Proc. Natl. Acad. Sci. USA, 97 (2000), 11250–11255. [CrossRef] [Google Scholar]
- J. Lewis. Autoinhibition with transcriptional delay: a simple mechanism for the Zebrafish somitogenesis oscillator. Curr. Biol., 13 (2003), 1398–1408. [CrossRef] [PubMed] [Google Scholar]
- H. Lodish, A. Berk, P. Matsudaira, C.A. Kaiser, M. Krieger, M.P. Scott, S.L. Zipursky, J. Darnell. Molecular Cell Biology. W.F. Freeman and Company, New York, 2003. [Google Scholar]
- J. Luo, M. Li, Y. Tang, M. Laszkowska, R.G. Roeder, W. Gu. Acetylation of p53 augments its site-specific DNA binding both in vitro and in vivo. Proc. Natl. Acad. Sci. USA, 101 (2004), 2259–2264. [CrossRef] [Google Scholar]
- L. Ma, J. Wagner, J.J. Rice, W. Hu, A.J. Levine, G.A. Stolovitzky. A plausible model for the digital response of p53 to DNA damage. Proc. Natl. Acad. Sci. USA, 102 (2005), 14266–14271. [CrossRef] [Google Scholar]
- S.M. Mendrysa, M.E. Perry. The p53 tumor suppressor protein does not regulate expression of is own inhibitor, MDM2, except under conditions of stress. Mol. Cell Biol., 20 (2000), 2023–2030. [CrossRef] [PubMed] [Google Scholar]
- J. Meyers, J. Craig, D.J. Odde. Potential for control of signaling pathways via cell size and shape. Curr. Biol., 16 (2006), 1685–1693. [CrossRef] [PubMed] [Google Scholar]
- G.I. Mihalas, Z. Simon, G. Balea, E. Popa. Possible oscillatory behaviour in p53-mdm2 interaction computer simulation. J. Biol. Syst., 8 (2000), 21–29. [Google Scholar]
- N.A.M. Monk. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr. Biol., 13 (2003), 1409–1413. [CrossRef] [PubMed] [Google Scholar]
- C.W. Mullineaux, A. Nenniger, N. Ray, C. Robinson. Diffusion of green fluorescent protein in three cell environments in Escherichia coli. J. Bacteriol., 188 (2006), 3442-3448. [CrossRef] [PubMed] [Google Scholar]
- D.E. Nelson, A.E. Ihekwaba, M. Elliott, J.R. Johnson, C.A. Gibney, B.E. Foreman, G. Nelson, V. See, C.A. Horton, D.G. Spiler, S.W. Edwards, H.P. McDowell, J.F. Unitt, E. Sullivan, R. Grimley, N. Benson, D. Broomhead, D.B. Kell, M.R. White. Oscillations in NF-κB signaling control de dynamics of gene expression. Science, 306 (2004), 704–708. [CrossRef] [PubMed] [Google Scholar]
- S.R. Neves, P. Tsokas, A. Sarkar, E.A. Grace, P. Rangamani, S.M. Taubenfeld, C.M. Alberini, J.C. Schaff, R.D. Blitzer, I.I. Moraru, R. Iyengar. Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell, 133 (2008), 666–680. [CrossRef] [PubMed] [Google Scholar]
- L. Nie, M. Sasaki, C.G. Maki C.G. Regulation of p53 nuclear export through sequential changes in conformation and ubiquitination. J. Biol. Chem., 282 (2007), 14616–14625. [CrossRef] [PubMed] [Google Scholar]
- B.A. Ogunnaike. Elucidating the digital control mechanism for DNA damage repair with the p53-mdm2 system: single cell data analysis and ensemble modelling. J. R. Soc. Interface, 3 (2006), 175–184. [CrossRef] [PubMed] [Google Scholar]
- J. Owen. Topological proteomics: a new approach to drug discovery. Drug Discovery Today, 6 (2001), 1081–1082. [CrossRef] [PubMed] [Google Scholar]
- I.G. Pearce, M.A.J. Chaplain, P.G. Schoeld, A.R.A. Anderson, S.F. Hubbard. Modelling the spatio-temporal dynamics of multi-species host-parasitoid interactions: heterogeneous patterns and ecological implications. J. Theor. Biol., 241 (2006), 876–886. [PubMed] [Google Scholar]
- S. Pigolotti, S. Krishna, M.H. Jensen. Oscillation patterns in negative feedback loops. Proc. Natl. Acad. Sci. USA, 104 (2007), 6533–6537. [Google Scholar]
- W. Schubert. Cytomics in characterizing toponomes: towards the biological code of the cell. Cytometry, 69A (2006), 209–211. [CrossRef] [Google Scholar]
- J.A. Sherratt, M.A. Lewis, A.C. Fowler. Ecological chaos in the wake of invasion. Proc. Natl. Acad. Sci. USA, 92 (1995), 2524–2528. [CrossRef] [Google Scholar]
- J.A. Sherratt, B.T. Eagen, M.A. Lewis. Oscillations and chaos behind predatorprey invasion: mathematical artifact or ecological reality? Philos. Trans. R. Soc. London B, 52 (1997), 79–92. [Google Scholar]
- J.A. Sherratt. Periodic travelling waves in cyclic predatorprey systems, Ecol. Lett., 352 (2001), 21–38. [Google Scholar]
- Shieh S.Y., Ikeda M., Taya Y., Prives C. DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2. Cell, 91 (1997), 325–334. [CrossRef] [PubMed] [Google Scholar]
- Srividya, J., Gopinathan, M.S., Schnells, S. The effects of time delays in a phosphorylation-dephosphorylation pathway, Biophys. Chem., 125 (2007), 286–297. [CrossRef] [PubMed] [Google Scholar]
- Y. Tang, W. Zhao, Y. Chen, Y. Zhao, W. Gu. Acetylation is indispensable for p53 activation. Cell, 133 (2008), 612–626. [CrossRef] [PubMed] [Google Scholar]
- G. Tiana, M.H. Jensen, K. Sneppen. Time delay as a key to apoptosis induction in the p53 network, Eur. Phys. J. B, 29 (2002), 135–140. [CrossRef] [EDP Sciences] [Google Scholar]
- G. Tiana, S. Krishna, S. Pigolotti, M.H. Jensen, K. Sneppen. Oscillations and temporal signalling in cells. Phys. Biol., 4 (2007), R1–R17. [CrossRef] [PubMed] [Google Scholar]
- K.H. Vousden, D.P. Lane. p53 in health and disease. Nat. Mol. Cell Biol., 8 (2007), 275–283. [CrossRef] [Google Scholar]
- J. Wagner, L. Ma, J.J. Rice, W. Hu, A.J. Levine, G.A. Stolovitzky. p53-mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback. I.E.E. Proc. Syst. Biol., 152 (2005), 109–118. [CrossRef] [Google Scholar]
- C. Wawra, M. Kuhl, H.A. Kestler. Extended analyses of the Wnt/β-catenin pathway: robustness and oscillatory behaviour. FEBS Lett., 581 (2007), 4043–4048. [CrossRef] [PubMed] [Google Scholar]
- O. Wolkenhauer, M. Ullah, P. Wellstead, K.H. Cho. The dynamic systems approach to control and regulation of intracellular networks. FEBS Lett., 579 (2005), 1846–1853. [CrossRef] [PubMed] [Google Scholar]
- A. Zauberman, D. Flusberg, Y. Haupt, Y. Barak, M. Oren. A functional p53-response intronic promoter is contained within the human mdm2 gene. Nucleic Acids Res., 23 (1995), 2584–2592. [CrossRef] [PubMed] [Google Scholar]
- W.B.J. Zimmerman. Multiphysics Modeling With Finite Element Methods, Series on Stability, Vibration and Control of Systems, Series A - Vol.18. World Scientific Publishing Company, London, 2006. [Google Scholar]
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