Synapses as stochastic concurrent systems

Theoretical Computer Science

Volumn 408, Issue 1, 2008, Pages 66-82

  Bracciali, Andrea ^a   Brunelli, Marcello ^a   Cataldo, Enrico ^a   Degano, Pierpaolo ^a  

^a UNIVERSITY OF PISA   (Italy)

Author keywords

Calyx of Held; Executable models; Process calculi; Short term synaptic plasticity; Stochastic simulations; Systems biology

Indexed keywords

ABS RESINS; BIOMINERALIZATION; ELASTICITY; MATHEMATICAL MODELS; PATHOLOGY; PLASTICITY; PLASTICS; STOCHASTIC CONTROL SYSTEMS; STOCHASTIC PROGRAMMING;

CALYX OF HELD; EXECUTABLE MODELS; PROCESS CALCULI; SHORT-TERM SYNAPTIC PLASTICITY; STOCHASTIC SIMULATIONS; SYSTEMS BIOLOGY;

STOCHASTIC MODELS;

EID: 54449096130     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2008.07.008     Document Type: Article

References (64)

1. Rediscovering Biology - Molecular to Global Perspectives - Neurobiology. http://www.learner.org/channel/courses/biology/support/10_neuro.pdf
2. Becherer U., and Retting J. Vesicle pools docking, priming, and release. Cell Tissue Research 326 (2006) 393-407
3. 2+signal. Nature Neuroscience 8 (2005) 426-434
4. Bracciali A., Brunelli M., Cataldo E., and Degano P. Expressive models for synaptic plasticity. In: Calder M., and Gilmore S. (Eds). Computational Methods in System Biology. CMSB'07. LNBI (2007), Springer, Edinburgh 152-167
5. Bracciali A., Brunelli M., Cataldo E., and Degano P. Stochastic models for the in silico simulation of synaptic processes. BMC Bioinformatics 9 S7 (2008)
6. Calder M., Duguid A., Gilmore S., and Hillston J. Stronger computational modelling of signalling pathways using both continuous and discrete-state methods. In: Priami C. (Ed). Computational Methods in Systems Biology (CMSB06). LNCS vol. 4210 (2006), Springer 63-77
7. Calder M., Gilmore S., and Hillston J. Modelling the influence of rkip on the erk signalling pathway using the stochastic process algebra pepa. Transactions on Computational System Biology VII, LNBI 4230 (2006) 1-23
8. Cardelli L. Brane calculi-interactions of biological membranes. In: Vincent V., and Schachter V. (Eds). Proceedings of Computational Methods in Systems Biology. LNCS vol. 3082 (2004), Springer, Paris 257-280
9. Cardelli L. On process rate semantics. Theoretical Computer Science 391 3 (2008) 190-215
10. Cassman M., Arkin A., Doyle F., Katagiri F., Lauffenburger D., and Stokes C. System Biology - International Research and Development (2007), Springer, The Netherlands
11. Chiarugi D., Curti M., Degano P., and Marangoni R. Vice: A virtual cell. In: Danos V., and Schächter V. (Eds). Computational Methods in Systems Biology. CMSB 2004. LNCS vol. 3082 (2004), Springer 207-220
12. Cooper L.N., Intrator N., Blais B.S., and Shouval H.Z. Theory of Cortical Platicity (2004), World Scientific, New Jersey
13. Dayan P., and Abbot L.F. Theoretical Neuroscience - Computational and Mathematical Modeling of Neural Systems (2001), The MIT Press, Cambridge
14. de~Lange R.P.J., de~Roos A.D.G., and Borst A.G.G. Two modes of vesicle recycling in the rat calyx of Held. Journal of Neuroscience 23 (2003) 10164-10173
15. Destexhe A., Mainen Z.F., and Sejnowski T.J. Synthesis of models for excitable membrane, synaptic transmission and neuromodulation using a common kinetic formulation. Journal of Computational Neuroscience 1 (1994) 195-231
16. Ermentrout B. Simulating, Analyzing, and Animating Dynamical Systems (2002), SIAM, Philadelphia
17. In: Fall C.P., Marland E.S., Wagner J.M., and Tyson J.J. (Eds). Computational Cell Biology (2005), Springer, New York
18. Felmy F., Neher E., and Schneggenburger R. Probing the intracellular calcium sensitivity of transmitter release during synaptic facilitation. Neuron 37 (2003) 801-811
19. Frotscher M., Gundelfinger E., Jonas P., Neher E., and Seeburg P. The most important recent advances in synapse research from my point of view-and what remains to be done. Cell Tissue Research 326 (2006) 203-204
20. Gardiner C.W. Handbook of Stochastic Methods - for Physics, Chemistry and the Natural Science (2001), Springer, Berlin
21. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81 (1977) 2340-2361
22. Gillespie D.T., and Petzold L.R. Numerical simulation for biochemical kinetics. In: Szallasi Z., Stelling J., and Perival V. (Eds). System Modeling in Cellular Biology. 1st ed. (2006), The MIT Press, Cambridge 331-354
23. Graham B.P., Wong A.Y.C., and Forsythe I.D. A computational model of synaptic transmission at the calyx of Held. Neurocomputing 38-40 (2001) 37-42
24. Graham B.P., Wong A.Y.C., and Forsythe I.D. A multi-component model of depression at the calyx of Held. Neurocomputing 58-60 (2004) 449-554
25. Habets R.L.P., and Borst J.G.G. Dynamics of the readily releasable pool during post-tetanic potentiation in the rat calyx of Held synapse. Journal of Physiology 581 (2007) 467-478
26. Hillston J. A Compositional Approach to Performance Modelling (1996), Cambridge University Press, Cambridge
27. Hosoi N., Sakaba T., and Neher E. Quantitative analysis of calcium-dependent vesicle recruitment and its functional role at the calyx of Held synapse. Journal of Neuroscience 27 (2007) 14286-14298
28. Van Kampen N.G. Stochastic processes in physics and in chemistry (1992), Elsevier, Amsterdam
29. Kierzek A.M. Stocks: Stochastic kinetic simulations of biochemical system with Gillespie algorithm. Bioinformatics 18 (2002) 470-481
30. Kitano H. Systems biology: A brief overview. Theoretical Computer Science 295 5560 (2002) 1662-1664
31. In: Koch C., and Segev I. (Eds). Methods in Neuronal Modeling (1998), The MIT Press, Cambridge
32. Lecca P., Priami C., Quaglia P., Rossi B., Laudanna C., and Costantin G. A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment. SIMULATION: Transactions of the society for modelling and simulation international 80 4 (2004) 273-288
33. 2+sensor for vesicle fusion. Nature 435 (2005) 497-501
34. 2+ signal for phasic transmitter release at the rat calyx of Held. The Journal of Physiology 547 (2003) 665-689
35. Miculan M., and Bacci G. Modal logics for brane calculus. In: Priami C. (Ed). Computational Methods in Systems Biology. CMSB06. LNCS vol. 4210 (2006), Springer 1-16
36. Milner R. Communicating and Mobile Systems: The π-Calculus (1999), Cambridge University Press
37. Mitra P.P., and Bokil H. Observed brain dynamics (2008), Oxford UP, Oxford
38. Nagasaki M., Onami S., Miyano S., and Kitano H. Bio-calculus: Its concept and molecular interaction. Genome Informatics 10 (1999) 133-143
39. Neher E. A comparison between exocytic control mechanisms in adrenal chromaffin cells and a glutamatergic synapse. Pflugers Arch - European Journal of Physiology 453 (2006) 261-268
40. Neher E. Short-term plasticity turns plastic, Focus on synaptic transmission at the calyx of Held under in vivo-like activity levels. Journal of Neurophysiology 98 (2007) 577-578
41. Phillips A., and Cardelli L. Efficient, correct simulation of biological processes in the stochastic pi-calculus. In: Calder M., and Gilmore S. (Eds). Proceedings of Computational Methods in Systems Biology. LNCS vol. 4695 (2007), Springer, Edinburgh 184-199
42. Priami C. Stochastic π-calculus. The Computer Journal 36 6 (1995) 578-589
43. Priami C., Regev A., Shapiro E., and Silvermann W. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Theoretical Computer Science 325 1 (2004) 141-167
44. Ramsey S., Orell D., and Bolouri H. Dizzy: Stochastic simulation of large-scale genetic regulatory networks. Journal of Bioinformatics and Computational Biology 3 2 (2005) 415-436
45. Regev A., Panina E., Silverman W., Cardelli L., and Shapiro E. Bioambients: An abstraction for biological compartements. Theoretical Computer Science 325 1 (2004) 141-167
46. Regev A., and Shapiro E. Cellular abstractions: Cells as computation. Nature 419 (2002) 343
47. Sakaba T. Roles of fast-releasing and the slowly-releasing vescicles in synaptic transmission at the calyx of Held. Journal of Neuroscience 26 (2006) 5863-5871
48. Sakaba T., Schneggenburger R., and Neher E. Estimation of quantal parameters at the calyx of Held synapse. Neuroscience Research 44 (2002) 343-356
49. Sakaba T., Stein A., Jahn R., and Neher E. Distinct kinetic changes in neurotransmitter release after snare protein cleavage. Science 309 (2005) 491-494
50. Schneggenburger R., and Forsythe I.D. The calxy of Held. Cell Tissue Research 326 (2006) 311-337
51. Schneggenburger R., and Neher E. Intracellular calcium dependence of transmitter release rates at a fast central synapse. Nature 46 (2000) 889-893
52. Schneggenburger R., and Neher E. Presynaptic calcium and control of vesicle fusion. Current Opinion in Neurobiology 15 (2005) 266-274
53. Schneggenburger R., Sakaba T., and Neher E. Vescicle pools and short-term synaptic depression: Lessons from a large synapse. Trends in Neurosciences 25 (2002) 206-212
54. Smith G.D. Modeling the stochastic gating of ion channels. In: Fall C.P., Marland E.S., Wagner J.M., and Tyson J.J. (Eds). Computational Cell Biology. 2nd ed. (2005), Springer, New York 285-319
55. Smolen P.D., Baxter D.A., and Byrne J.H. Mathematical modeling and analysis of intracellular signaling pathways. In: Byrne J.H., and Roberts J.L. (Eds). From Molecules to Networks - An Introduction to Cellular and Molecular Neuroscience (2004), Elsevier - Academic Press 391-429
56. Sorensen J.B. Formation, stabilization and fusion of the readily releasable pool of secretory vescicles. Pflugers Arch - European Journal of Physiology 448 (2004) 347-362
57. Sudhof T.C. The synaptic vesicle cycle. Annual Review of Neuroscience 27 (2004) 509-547
58. Ullah M., and Wolkenhauer O. Family tree of markov models in systems biology. IET System Biology 1 (2007) 247-254
59. 2+-dependent vescicle pool dynamics and short term synaptic depression. Biophysical Journal 77 (1999) 2418-2429
60. Wilkinson D.J. Stochastic Modelling for System Biology (2006), Chapman and Hall - CRC Press, London
61. Wolfel M., Lou X., and Schneggenburger R. A mechanism intrinsic to the vesicle fusion machinery determines fast and slow transmitter release at a large CNS synapse. Journal of Neuroscience 27 (2007) 3198-3210
62. Wong A.Y.C., Graham B.P., Billups B., and Forsythe I.D. Distinguishing between presynaptic and postsynaptic mechanisms of short-term depression during action potentials trains. Journal of Neuroscience 23 (2003) 4868-4877
63. Zucker R.S., Kullmann D.M., and Schwartz T.L. Release of neurotransmitters. In: Byrne J.H., and Roberts J.L. (Eds). From Molecules to Networks - An Introduction to Cellular and Molecular Neuroscience (2004), Elsevier 197-244
64. Zucker R.S., and Regehr W.G. Short-term synaptic plasticity. Annual Review of Physiology 64 (2002) 355-405