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Issue No.02 - March/April (2012 vol.9)
pp: 571-579
I. G. Karafyllidis , Dept. of Electr. & Comput. Eng., Democritus Univ. of Thrace, Xanthi, Greece
Bacteria evolved cell to cell communication processes to gain information about their environment and regulate gene expression. Quorum sensing is such a process in which signaling molecules, called autoinducers, are produced, secreted and detected. In several cases bacteria use more than one autoinducers and integrate the information conveyed by them. It has not yet been explained adequately why bacteria evolved such signal integration circuits and what can learn about their environments using more than one autoinducers since all signaling pathways merge in one. Here quantum information theory, which includes classical information theory as a special case, is used to construct a quantum gate circuit that reproduces recent experimental results. Although the conditions in which biosystems exist do not allow for the appearance of quantum mechanical phenomena, the powerful computation tools of quantum information processing can be carefully used to cope with signal and information processing by these complex systems. A simulation algorithm based on this model has been developed and numerical experiments that analyze the dynamical operation of the quorum sensing circuit were performed for various cases of autoinducer variations, which revealed that these variations contain significant information about the environment in which bacteria exist.
Sensors, Microorganisms, Integrated circuit modeling, Computational modeling, Information processing, Numerical models, Biological system modeling,simulation., Quorum sensing, systems biology, quantum information processing, quantum gates, modeling
I. G. Karafyllidis, "Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 2, pp. 571-579, March/April 2012, doi:10.1109/TCBB.2011.104
[1] B.L. Bassler and R. Losick, “Bacterially Speaking,” Cell, vol. 125, pp. 237-246, 2006.
[2] B.L. Bassler, “How Bacteria Talk to Each Other: Regulation of Gene Expression by Quorum Sensing,” Current Opinion in Microbiology, vol. 2, pp. 582-587, 1999.
[3] S.P. Diggle, S.A. Crusz, and M. Cámara, “Quorum Sensing,” Current Biology, vol. 17, pp. R907-R910, 2007.
[4] S.P. Diggle, A. Gardner, S.A. West, and A.S. Griffin, “Evolutionary Theory of Bacterial Quorum Sensing: When Is a Signal Not a Signal?,” Philosophical Trans. Royal Soc. B, vol. 362, pp. 1241-1249, 2007.
[5] K.H. Nealson, T. Platt, and J.W. Hastings, “Cellular Control of the Synthesis and Activity of the Bacterial Luminescent System,” J. Bacteriology, vol. 104, pp. 313-322, 1970.
[6] K.H. Nealson and J.W. Hastings, “Bacterial Bioluminescence: Its Control and Ecological Significance,” Microbiological Rev., vol. 43, pp. 496-518, 1979.
[7] B.K. Hammer and B.L. Bassler, “Quorum Sensing Controls Biofilm Formation in Vibrio cholerae,” Molecular Microbiology, vol. 50, pp. 101-114, 2003.
[8] M. Hentzer, M.H. Wu, J.B. Andersen, K. Riedel, T.B. Rasmussen, N. Bagge, N. Kumar, M.A. Schembri, Z. Song, P. Kristoffersen, M. Manefield, J.W. Costerton, S. Molin, L. Eberl, P. Steinberg, S. Kjelleberg, N. Høiby, and M. Givskov, “Attenuation of Pseudomonas Aeruginosa Virulence by Quorum Sensing Inhibitors,” The European Molecular Biology Organization J., vol. 22, pp. 3803-3815, 2003.
[9] M. Juhas, L. Eberl, and B. Tümmler, “Quorum Sensing: the Power of Cooperation in the World of Pseudomonas,” Environmental Microbiology, vol. 7, pp. 459-471, 2005.
[10] T.B. Rasmussen, T. Bjarnsholt, M.E. Skindersoe, M. Hentzer, P. Kristoffersen, M. Köte, J. Nielsen, L. Eberl, and M. Givskov M, “Screening for Quorum-Sensing Inhibitors (QSI) by Use of a Novel Genetic System, the QSI Selector,” J. Bacteriology, vol. 187, pp. 1799-1814, 2005.
[11] T.B. Rasmussen, M. Givskov, “Quorum Sensing Inhibitors: A Bargain of Effects,” Microbiology, vol. 152, pp. 895-904, 2006.
[12] P. Mehta, S. Goyal, T. Long, B.L. Bassler, and N.S. Wingreen, “Information Processing and Signal Integration in Bacterial Quorum Sensing,” Molecular Systems Biology, vol. 5, p. 325, 2009.
[13] T. Long, C.K. Tu, Y. Wang, P. Mehta, N.P. Ong, B.L. Bassler, and N.S. Wingreen, “Quantifying the Integration of Quorum-Sensing Signals with Single Cell Resolution,” PloS Biology, vol. 7, pp. 0640-0649, 2009.
[14] F. Tostevin and P.R. ten Wolde, “Mutual Information Between Input and Output Trajectories of Biochemical Networks,” Physical Rev. Letters, vol. 102, pp. 218101-1 - 218101-4, 2009.
[15] C.E. Shannon, “A Mathematical Theory of Communication,” Bell Systems Technical J., vol. 27, pp. 379-423, 1948.
[16] M.A. Nielsen and I.L. Chuang, Quantum Computation and Quantum Information. Cambridge Univ. Press, 2000.
[17] S. Somma, G. Ortiz, J.E. Gubernatis, E. Knill, and R. Laflamme, “Simulating Physical Phenomena by Quantum Networks,” Physical Rev. A, vol. 65, pp. 042323-1 - 042323-17, 2002.
[18] W.H. Miller, “Quantum Dynamics of Complex Molecular Systems,” Proc. Nat'l Academy of Science USA, vol. 102, pp. 6660-6664, 2005.
[19] S. Peil, “Imitating Quantum Mechanics: Qubit Based Model for Simulation,” Physical Rev. A, vol 79, pp. 042320-1 - 042320-8, 2009.
[20] D.A. Meyer, “Physical Quantum Algorithms,” Computer Physics Comm., vol. 146, pp. 295-301, 2002.
[21] R.D. Somma, S. Boixo, H. Barmum, and E. Knill, “Quantum Simulations of Classical Annealing Processes,” Physical Rev. Letters, vol. 101, pp. 130504-1 - 130504-4, 2008.
[22] I.G. Karafyllidis, “Definition and Evolution of Quantum Cellular Automata with Two Qubits Per Cell,” Physical Rev. A, vol. 70, pp. 044301-1 - 044301-4, 2004.
[23] I.G. Karafyllidis, “Quantum Computer Simulator Based on the Circuit Model of Quantum Computation,” IEEE Trans. Circuits and Systems I, vol. 52, no. 8, pp. 1590-1596, Aug. 2005.
[24] C.M. Waters and B.L. Bassler, “The Vibrio harveyi Quorum Sensing System Uses Shared Regulatory Components to Discriminate between Multiple Autoinducers,” Genes and Development, vol. 20, pp. 2754-2767, 2009.
[25] K.B. Xavier and B.L. Bassler, “LuxS Quorum Sensing: More than Just a Numbers Game,” Current Opinion in Microbiology, vol. 6, pp. 191-197, 2003.
[26] J.M. Henke and B.L. Bassler, “Three Parallel Quorum-Sensing Systems Regulate Gene Expression in Vibrio harveyi,” J. Bacteriology, vol. 186, pp. 6902-6914, 2004.
[27] J.C. Anderson, C.A. Voigt, and A.P. Arkin, “Environmental Signal Integration by a Modular and Gate,” Molecular Systems Biology, vol. 3, article 133, 2007.
[28] S.K. Banik, A.T. Fenley, and R.V. Kulkarni, “A Model for Signal Transduction during Quorum Sensing in Vibrio harveyi,” Physical Biology, vol. 6, p. 046008, 2009.
[29] J.M. Rabaey, A. Chandrakasan, and B. Nicolic, Digital Integrated Circuits. Prentice Hall, 2003.
[30] R.P. Feynman, A. Hey, T. Hey, and R.W. Allen, Feynman Lectures on Computation. Westview Press, 2000.
[31] E. Baake, M. Baake, and H. Wagner, “Quantum Mechanical versus Classical Probability in Biological Evolution,” Physical Rev. E, vol. 57, pp. 1191-1192, 1998.
[32] D. Saakian and C.K. Hu, “Eigen Model as a Quantum Spin Chain: Exact Dynamics,” Physical Rev. E, vol. 69, pp. 021913-1 - 021913-5, 2004.
[33] B.R. Frieden and R.A. Gatenby, “Conditions for Correspondence between Hartree Scattering and Biological Growth,” Physical Rev. E, vol. 78, pp. 041902-1 - 041902-8, 2008.
[34] B.E. Baaquie, Quantum Finance. Cambridge Univ. Press, 2004.
[35] G.S. Engel, T.R. Calhoun, E.L. Read, T.K. Ahn, T. Mancal, Y.C. Cheng, R.E. Blankenship, and G.R. Fleming, “Evidence for Wavelike Energy Transfer through Quantum Coherence in Photosynthetic Systems,” Nature, vol. 446, pp. 782-786, 2007.
[36] M.B. Plenio and S.F. Huelga, “Dephasing-Assisted Transport: Quantum Networks and Biomolecules,” New J. Physics, vol. 10, pp. 1-14, 2008.
[37] R. Somma, G. Ortiz, J.E. Gubernatis, E. Knill, and R. Laflamme, “Simulating Physical Phenomena by Quantum Networks,” Physical Rev. A, vol. 65, pp. 042323-1 - 042323-17, 2002.
[38] I. Buluta and F. Nori, “Quantum Simulators,” Science, vol. 326, pp. 108-111, 2009.
[39] M.A. Nielsen and I.L. Chuang, Quantum Computation and Quantum Information. Cambridge Univ. Press, 2004.
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