Article details

Title: Introduction to the Prion Neural System
Author(s): Luciana Morogan               

Abstract: In history, there were continuous attempts to study, discover, and implement computing ideas or models from the way nature computes. Such an idea is presented at the beginning of this paper by introducing a controversial biological phenomena as the starting idea of our biology inspired computational model, which we called the prion neural system. It is developed as part of an ambitious project to build models of complex systems into a bottom up approach. The construction belongs to the hybrid systems category as we needed to encompass a larger class of systems within the system structure, allowing more flexibility in modeling the dynamic biological phenomena. Using only one of the directions already known was not enough for abstracting a computing model from the structure and the functioning of a living neuron as an evolutionary multi-functional computing system. This is why the design of such a system drove us to a very fruitful interdisciplinary interplay. It combines neural networks, brain calculi or membrane computing under the framework of DNA computing. An introduction to the system construction is presented. It describes the molecular level of the construction. The last section presents a short case study in order to illustrate the system functionality at this level.

Keywords: neural computing, evolutionary computing, natural computing, hybrid intelligent systems, nature inspired computing techniques, evolutionary computing, PrP – prion protein, PrPc – cellular PrP.

References:

[1] T. NATSCHLAEGER – Efficient Computation in Networks of Spiking Neurons: Simulations and Theory, Ph.D. Thesis, Graz University of Technology, Austria, 1999
[2] W. MAASS – Networks of Spiking Neurons: The Third Generation of Neural Network Models, Neural Networks, Vol. 10, No. 9, pp. 1659-1671, 1997
[3] W. MAASS, M. SCHMITT – On the Complexity of Learning for Spiking Neurons with Temporal Coding, Information and Computation, Vol. 153, No. 1, pp. 26-46, Aug. 1999
[4] W. MAASS, T. NATSCHLAEGER – Associative Memory with Networks of Spiking Neurons in Temporal Coding, In L.S. Smith, A. Hamilton (Eds.), “Neuromorphic Systems: Engineering Silicon from Neurobiology”, pp. 21-32, World Scientific, River Edge, NJ, 1998
[5] T. NATSCHLAEGER, W. MAASS – Finding the Key to a Synapse, In T.K. Leen, T.G. Dietterich, V. Tresp (Eds.), “Advances in Neural Information Processing Systems (NIPS 2000)”, Vol. 13, pp. 138-144, The MIT Press, Cambridge, MA, 2001
[6] N. BARBACARI, A. PROFIR, C. ZELINSCHI – Gene Regulatory Network Modelling by Means of Membrane Systems, Pre-proc. of the 6th International Workshop on Membrane Computing, WMC6, pp. 162-178, Vienna, Austria, Jun. 18-21, 2005
[7] G. CIOBANU, Gh. PĂUN, M.J. PÉREZ-JIMÉNEZ – Applications of Membrane Computing, Springer-Verlag, Berlin, Germany, 2006
[8] M. GARCÍA-ARNAU, D. PÉREZ, A. RODRÍGUEZ-PATÓN, P. SOSÍK – Spiking Neural P Systems: Stronger Normal Forms, International Journal of Unconventional Computing, Vol. 5, No. 5, pp. 411-425, 2009
[9] M. IONESCU, D. SBURLAN – Some Applications of Spiking Neural P Systems, Computing and Informatics, Vol. 27, No. 3+, pp. 515-528, 2008
[10] A. LEPORATI, C. ZANDRON, C. FERRETTI, G. MAURI – On the Computational Power of Spiking Neural P Systems, International Journal of Unconventional Computing, Vol. 5, No. 5, pp. 459-473, 2009
[11] Gh. PĂUN – Membrane Computing: An Introduction, Springer-Verlag, Berlin, Germany, 2002
[12] Gh. PĂUN – Computing with Membranes (P Systems): Twenty Six Research Topics, CDMTCS Research Reports, CDMTCS-119, University of Auckland, New Zealand, Feb. 2000
[13] Gh. PĂUN – One More Universality Result for P Systems with Objects on Membranes, International Journal of Computers, Communications & Control, Vol. 1, No. 1, pp. 25-32, 2006
[14] Gh. PĂUN – Twenty Six Research Topics about Spiking Neural P Systems, Proc. of the 5th Brainstorming Week on Membrane Computing, pp. 263-280, Seville, Spain, Jan. 29 - Feb. 2, 2007
[15] Gh. PĂUN, M.J. PÉREZ-JIMÉNEZ – Membrane Computing: Brief Introduction, Recent Results and Applications, BioSystems, Vol. 85, No. 1, pp. 11-22, Jul. 2006
[16] C.S. CALUDE, Gh. PĂUN – Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing, Taylor & Francis, New York, NY, 2001
[17] M. IONESCU, Gh. PĂUN, T. YOKOMORI – Spiking Neural P Systems, Fundamenta Informaticae, Vol. 71, No. 2-3, pp. 279-308, Aug. 2006
[18] Gh. PĂUN, G. ROZENBERG, A. SALOMAA – DNA Computing: New Computing Paradigms, Springer-Verlag, Berlin, Germany, 1998
[19] Gh. PĂUN, M.J. PÉREZ-JIMÉNEZ – Recent Computability Models Inspired from Biology: DNA and Membrane Computing, Theoria, Vol. 18, No. 1, pp. 71-84, 2003
[20] L.M. MOROGAN – Prion Neural System: Modeling the Binding Affinities between Neurons of a Network, Proc. of the International Conference on Computer Information Systems and Industrial Management Applications, CISIM 2010, pp. 143-147, Krackow, Poland, Oct. 8-10, 2010
[21] D. DORMONT – Biology of Agents Responsible for Transmissible Spongiform Encephalopathies (Prions), Revue Neurologique, Vol. 154, No. 2, pp. 142-151, Mar. 1998
[22] S.B. PRUSINER – Molecular Biology and Genetics of Prion Diseases, Philosophical Transactions: Biological Sciences, Vol. 343, No. 1306, pp. 447-463, Mar. 1994
[23] S.B. PRUSINER, M.R. SCOTT, S.J. DEARMOND, F.E. COHEN – Prion Protein Biology, Cell, Vol. 93, No. 3, pp. 337-348, May 1998
[24] S.J. DEARMOND, S.B. PRUSINER – Etiology and Pathogenesis of Prion Diseases, American Journal of Pathology, Vol. 146, No. 4, pp. 785-811, Apr. 1995
[25] C. WEISSMANN – The Ninth Data Lecture: Molecular Biology of Transmissible Spongiform Encephalopathies, FEBS Letters, Vol. 389, pp. 3-11, Jun. 1996
[26] C. WEISSMANN – Molecular Genetics of Transmissible Spongiform Encephalopathies, The Journal of Biological Chemistry, Vol. 274, No. 1, pp. 3-6, Jan. 1999
[27] M.V. CÂMPEANU – Transmissible Spongiform Encephalopathies, Romanian Medical Life Publishing House, Bucharest, Romania, 2001 (in Romanian)
[28] S. CRONIER, H. LAUDE, J.M. PEYRIN – Prions Can Infect Primary Cultured Neurons and Astrocytes and Promote Neuronal Cell Death, PNAS, Vol. 101, No. 33, pp. 12271-12276, Aug. 2004
[29] C.L. KIM, A. KARINO, N. ISHIGURO, M. SHINAGAWA, M. SATO, M. HORIUCHI – Cell-Surface Retention of PrPC by anti-PrP Antibody Prevents Protease-Resistant PrP Formation, Journal of General Virology, Vol. 85, No. 11, pp. 3473-3482, Nov. 2004
[30] T. JIN, Y. GU, G. ZANUSSO, M. SY, A. KUMAR, M. COHEN, P. GAMBETTI, N. SINGH – The Chaperone Protein BiP Binds to a Mutant Prion Protein and Mediates Its Degradation by the Proteasome, The Journal of Biological Chemistry, Vol. 275, No. 49, pp. 38699-38704, Dec. 2000
[31] Y. CORDEIRO, F. MACHADO, L. JULIANO, M.A. JULIANO, R.R. BRENTANI, D. FOGUEL, J.L. SILVA – DNA Converts Cellular Prion Protein into the Beta-Sheet Conformation and Inhibits Prion Peptide Aggregation, The Journal of Biological Chemistry, Vol. 276, No. 52, pp. 49400-49409, Dec. 2001
[32] B. ALBERTS, A. JOHNSON, J. LEWIS, M. RAFF, K. ROBERTS, P. WALTER – Molecular Biology of the Cell, 4th Edition, Garland Science, New York, NY, 2002
[33] Gh. BENGA – Molecular Biology of Membranes with Medical Applications, “Dacia” Publishing House, Cluj-Napoca, Romania, 1979 (in Romanian)
[34] J. SMYTHIES – The Neuromodulators, International Review of Neurobiology, Vol. 64, Elsevier Academic Press, San Diego, CA, 2005
[35] A.M. ISRAIL – Molecular Biology: Present and Perspectives, Humanitas Publishing House, Bucharest, Romania, 2000 (in Romanian)