Energetics based spike generation of a single neuron: Simulation results and analysis

Frontiers in Neuroenergetics

Volumn , Issue FEB, 2012, Pages

  Venkateswaran, Nagarajan ^a   Sekhar, Sudarshan ^a   Thirupatchur Sanjayasarathy, Thiagarajan ^a   Krishnan, Sharath Navalpakkam ^a   Kabaleeswaran, Dinesh Kannan ^a   Ramanathan, Subbu ^a   Narayanasamy, Narendran ^a   Jagathrakshakan, Sharan Srinivas ^a   Vignesh, S R ^a  

^a WAran Research FoundaTion   (India)

Author keywords

Alzheimer's disease; ATP; Krebs cycle; Mitochondria; Neuroenergetics; Petri nets; Voltage spike; Wavelet transformations

Indexed keywords

ADENYLATE KINASE; CALCIUM; OXIDE;

ALZHEIMER DISEASE; ARTICLE; BRAIN MITOCHONDRION; ELECTRON TRANSPORT; ENDOPLASMIC RETICULUM; ENERGY TRANSFER; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NERVE CELL; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SPECTROSCOPY; SPIKE; SYNAPTIC TRANSMISSION;

EID: 84861905015     PISSN: None     EISSN: 16626427     Source Type: Journal    
DOI: 10.3389/fnene.2012.00002     Document Type: Article

References (54)

1. Arnaudeau, S., Kelley, W. L., Walsh, J. V. Jr., and Demaurex, N. (2001). Mitochondria recycle Ca(2+) to the endoplasmic reticulum and prevent the depletion of neighboring endoplasmic reticulum regions. J. Biol. Chem. 276, 29430-29439.
2. Attwell, D., and Gibb, A. (2005). Neu-roenergetics and the kinetic design of excitatory synapses. Nat. Rev. Neurosci. 6, 841-849.
3. Attwell, D., and Laughlin, S. B. (2001). An energy budget for signaling in the grey matter of the brain. J. Cereb. Blood Flow Metab. 21, 1133-1145.
4. Babinec, P., and Babincov, M. (2002). Spatial distribution of ion channel activity in biological membranes: the role of noise. Bioelectrochemistry 56,167-170.
5. Baker, H. L., Errington, R. J., Davies, S. C, and Campbel, A. K. (2002). A mathematical model predicts that calreticulin interacts with the endoplasmic reticulum Ca2H-ATPase. Biophys. J. 82, 582-590.
6. Beard, D. A., and Qian, H. (2008). Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge: Cambridge University Press.
7. Buchholtz, R, Golowasch, J., Epstein, I. R., and Marder, E. (1992). Mathematical model of an identified stom-atogastric ganglion neuron. J. Neu-rophysiol 67, 332-340.
8. Cloutier, M., Bolger, F. B., Lowry, J. P., and Wellstead, P. (2009). An integrative dynamic model of brainenergy metabolism using in vivo neurochemical measurements. J. Comput. Neurosci. 27, 391-414.
9. Duchen, M. R. (2000). Mitochondria and calcium: from cell signalling to cell death. J. Physiol. (Lond.) 529, 57-68.
10. Echtay, K. S., Murphy, M. P., Smith, R. A. J., Talbot, D. A., and Brand, M. D. (2002). Superoxide activates mitochondrial uncoupling protein 2 from the matrix side. J. Biol. Chem. 277,47129-47135.
11. Fienberg, S. E. (1974). Stochastic models for single neuron firing trains: a survey. Biometrics 30, 399-427.
12. Fitzhugh, R. (1955). Mathematical models of threshold phenomena in the nerve membrane. Bull. Math. Biophys. 17,257-278.
13. Green, D. R., and Green, D. R. (2005). Apoptotic pathways: ten minutes to dead. Cell 121,671-674.
14. Hardy, J., and Selkoe, D. J. (2002). The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 297, 2209.
15. Harrison, L. M., David, O., and Frit-son, K. J. (2005). Stochastic models of neuronal dynamics. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360, 1075-1091.
16. Hayashi, Y., Shi, S. H., Esteban, J. A., Pic-cini, A., Poncer, J. C, and Malinow, R. (2000). Driving AMPA receptors into synapses by LTP and CaMKII: requirement for GluRl and PDZ domain interaction. Science 287, 2262-2267.
17. Hirai, K., Aliev, G., Nunomura, A., Fujioka, H., Russell, R. L., Atwood, C. S., Johnson, A. B., Kress, Y., Vin-ters, H. V., Tabaton, M., Shimo-hama, S., Cash, A. D., Siedlak, S. L., Harris, P. L., Jones, P. K., Petersen, R. B., Perry, G., and Smith, M. A. (2001). Mitochondrial abnormalities in Alzheimer's disease. J. Neurosci. 21, 3017-3023.
18. Hodgkin, A. L., and Huxley, A. F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. (Lond.) 117, 500-544.
19. Jager, S., Handschin, C, St-Pierre, J., and Spiegelman, B. M. (2007). AMP-activated protein kinase (AMPK) action in skeletal muscle via direct phosphory-lation of PGC-la. PNAS 104, 12017-12022.
20. Jouaville, L. S., Pinton, P., Bastianutto, C, Rutter, G. A., and Rizzuto, R. (1999). Regulation of mitochondrial ATP synthesis by calcium: evidence for a long-term metabolic priming. Proc. Natl. Acad. Sci. U.S.A. 96, 13807-13812.
21. Kandel, E. R., Schwartz, J., and Jessell, T. (1991). Principles of Neurosdence, 4th Edn. New York: McGraw-Hill.
22. Keizer, K. (2002). Computational Cell Biology. New York: Springer Publications.
23. Linden, D. J. (2001). The expression of cerebellar LTD in culture is not associated with changes in AMPA-receptor kinetics, agonist affinity, or unitary conductance. Proc. Natl. Acad. Sci. U.S.A. 98, 14066-14071.
24. Mattson, M. P., Gleichmann, M., and Cheng, A. (2008). Mitochondria in neuroplasticity and neurological disorders. J. Neurosci. 60, 748-766.
25. Mogilevskaya, E., Demin, O., and Goryanin, I. (2006). Kinetic model of mitochondrial Krebs cycle: unraveling the mechanism of salicylate hepatotoxic effects. J. Biol. Phys. 32, 245-271.
26. Mohan, A. (2008). The MMINi-DASS Simulator and its Application to Visual Pathway Connectivity Prediction. [A thesis submitted to WAran Research FoundaTion]. Available at: http://www.warftindia.org/Ashutosh.pdf
27. Mohan, A., Nagarajan, V., Sekhar, S., Sharath, N. K., Thiagarajan, T. S., Ramanathan, S., and Kannan, D. (2010a). "Energetics based simulation of large-scale 3D neuronal network: energetics-based models," in Frontiers Neuroscience Conference Abstract: Neuroinformatics 2010, Kobe, doi: 10.3389/conf.fnins.2010.13.00092
28. Mohan, A., Nagarajan, V., Ramanathan, S., Sekhar, S., Thiagarajan, T. S., Kannan, D., and Sharath, N. K. (2010b). "Energetics-based simulation of 3D neuronal network: neurogenesis-inspired structure generation," in Frontiers Neuroscience Conference Abstract: Neuroinformatics 2010, Kobe, doi: 10.3389/conf.fnins.2010.13.00097
29. Oja, E. (1982). A simplified neuron model as a principal component analyzer.J. Math. Biol. 15,267-273.
30. Parekh, A. B. (2003). Mitochondr-ial regulation of intracellular Ca2+ signaling: more than just simple Ca2+ buffers. News Physiol. Sci. 18, 252-256.
31. Rail, W. (1957). Membrane time constant of motoneurons. Science 126, 454.
32. Rail, W. (1959). Branching dendritic trees and motoneuron membrane resistivity. Exp. Neurol 1,491-527.
33. Rail, W. (1960). Membrane potential transients and membrane time constant of motoneurons. Exp. Neurol. 2,503-532.
34. Ramanathan, S. (2011). 3D Neuronal Structure: Towards Generation, Simulation and Optimization for Brain Specific Region. [A thesis submitted to WAran Research Foundation]. Available at: www.warftindia.org/Subbu.pdf
35. Remy, S., and Spruston, N. (2007). Dendritic spikes induce single-burst long-term potentiation. Proc. Natl. Acad. Sci. U.S.A. 104,17192-17197.
36. Reutimann, J. A. (1999). Model of synaptic short-term plasticity and its adaptation.
37. Rousset, S., Alves-Guerra, M. C, Mozo, J., Miroux, B., Cassard-Doulcier, A. M., Bouillaud, R, and Ricquier, D. (2004). The biology of uncoupling proteins. Diabetes 53(Suppl. 1), S130-S135.
38. Schulman, R. G., and Rothman, D. L. (2004). Brain Energetics and Neuronal Activity. Chichester: Wiley.
39. Schuss, Z., Nadler, B., and Eisenberg, R. S. (2001). Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model. Phys. Rev. EStat. Nonlin. Soft Matter Phys. 64,036116.
40. Sherwood, C. C, Stimpson, C. D., Raghanti, M. N., Wildman, D. E. Uddin, M., Grossman, L. I., Goodman, M., Redmond, J. C, Bonar, C. J., Erwin, J. M., and Hof, P. R. (2006). Evolution of increased glia-neuron ratios in the human frontal cortex. Proc. Natl. Acad. Sci. U.S.A. 103, 13606-13611.
41. Shulman, R. G., and Rothman, D. L. (eds) (2005). Brain Energetics, and Neuronal Activity. Chichester: John Wiley and Sons Limited, 315.
42. Sklar, B. (2001). Digital Communications: Fundamentals and Applications. New Jersey: Prentice Hall.
43. Steinberg, J. P., Huganir, R. L., and Linden, D. J. (2004). N-ethylmaleimide-sensitive factor is required for the synaptic incorporation and removal of AMPA receptors during cerebellar long-term depression. Proc. Natl. Acad. Sci. U.S.A. 101, 18212-18216.
44. Siidhof, T. C. (2004). The synaptic vesicle cycle. Annu. Rev. Neurosci. 27, 509-547.
45. Tsodyks, M., Uziel, A., and Markram, H. (2000). Synchrony generation in recurrent networks with frequency-dependent synapses. J. Neurosci. 20, RC50.
46. Turrens, J. F. (1997). Superoxide production by the mitochondrial respiratory chain. Biosci. Rep. 17,3-8.
47. Van Pelt, J., Van Ooyen, A., and Uylings, H. B. M. (2001). "Modeling dendritic geometry and the development of nerve connections," in Computational Neuroscience: Realistic Modeling for Experimentalists, ed. E. De Schutter (Boca Raton: CRC Press), 179-208.
48. Venkateswaran, N., Elangovan, V. K., Ganesan, K., Sagar, T. R. S., Aananthakrishanan, S., Ramalingam, S., Gopalakrishnan, S., Manivannan, M., Srinivasan, D., Krishnamurthy, V., Chandrasekar, K., Venkatesan, V., Subramaniam, B., Sangkar, V., Vasudevan, A., Ganapa-thy, S., Murali, S., and Thyagarajan, M. (2008). "On the concept of simultaneous execution of multiple applications on hierarchically based cluster and the silicon operating system," in IEEE International Symposium on Parallel and Distributed Processing, 2008, Miami, FL.
49. Venkateswaran, N., Kabaleeswaran, D. K., Vignesh, S. R., Ramanathan, S., Jagathrakshakan, S. S., Narayanasamy, N., Sekhar, S., Krishnan, N. S., and Thiagarajan, T. S. (2011). "Single neuron development - a neurogenesis inspired structure generation model," in Frontiers Neuroinformatics Conference Abstract, Boston. doi: 10.3389/conf.fninf.2011.08.00162
50. Volman, V, Ben-Jacob, E., and Levine, H. (2007). The astrocyte as a gatekeeper of synaptic information transfer. Neural. Comput. 19, 303-326.
51. Weber, J. T., De Zeeuw, C. I., Linden, D. J., and Hansel, C. (2003). Long-term depression of climbing fiber-evoked calcium transients in Purk-inje cell dendrites. Proc. Natl. Acad. Sci. U.S.A. 100, 2878-2883.
52. Yu, T. P., McKinney, S., Lester, H. A., and Davidson, N. (2001). y-Aminobutyric acid type A receptors modulate cAMP-mediated long-term potentiation and long-term depression at mono-synaptic CA3-CA1 synapses. Proc. Natl. Acad. Sci. U.S.A. 98, 5264-5269.
53. Zeviani, M., and Di Donato, S. (2004). Mitochondrial disorders. Brain 127, 2153-2172.
54. Zong, H., Ren, J. M., Young, L. H., Pypaert, M., Mu, J., Birnbaum, M. J., and Shulman, G. I. (2002). AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation. Proc. Natl. Acad. Sci. U.S.A. 99, 15983-15987.