Abstract
In the epilepsy field, the creation of large-scale data-driven models that incorporate decades worth of experimental data has led to substantial innovations over current methodologies. Such models and sophisticated visualization software that makes the models truly come to life have brought computational neuroscience closer to reality for all epilepsy researchers. In this chapter, we discuss detailed, data-driven models that have resulted in significant, testable, theoretical advances that have contributed to our knowledge of how large-scale biological neuronal networks interact to promote hyperexcitability and hypersynchrony in epilepsy syndromes. Additionally we elaborate on how computational advances in software infrastructure have greatly increased the accessibility and applicability of computational modeling, especially for biologists who have previously employed only experimental techniques in their research.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Kalani MY, Vaidehi N, Hall SE, et al. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proc Natl Acad Sci U S A 2004;101:3815–20.
Revett K, Ruppin E, Goodall S, Reggia JA. Spreading depression in focal ischemia: a computational study. J Cereb Blood Flow Metab 1998;18:998–1007.
Soltesz I, Staley KJ. Computational Neuroscience in Epilepsy. New York: Elsevier; 2008.
Vierling-Claassen D, Siekmeier P, Stufflebeam S, Kopell NJ. Modeling GABA alterations in schizophrenia: A link between impaired inhibition and altered gamma and beta range auditory entrainment. J Neurophysiol 2008;99(5):2656–71.
Brunel N. Dynamics of networks of randomly connected excitatory and inhibitory spiking neurons. J Physiol, Paris 2000;94:445–63.
Brunel N, Wang XJ. What determines the frequency of fast network oscillations with irregular neural discharges? I. Synaptic dynamics and excitation-inhibition balance. J Neurophysiol 2003;90:415–30.
Dyhrfjeld-Johnsen J, Santhakumar V, Morgan RJ, Huerta R, Tsimring L, Soltesz I. Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. J Neurophysiol 2007;97:1566–87.
Morgan RJ, Soltesz I. Nonrandom connectivity of the epileptic dentate gyrus predicts a major role for neuronal hubs in seizures. Proc Natl Acad Sci U S A 2008;105:6179–84.
Santhakumar V, Aradi I, Soltesz I. Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: A network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol 2005;93:437–53.
Gleeson P, Steuber V, Silver RA. neuroConstruct: A tool for modeling networks of neurons in 3D space. Neuron 2007;54:219–35.
Traub RD, Contreras D, Whittington MA. Combined experimental/simulation studies of cellular and network mechanisms of epileptogenesis in vitro and in vivo. J Clin Neurophysiol 2005;22:330–42.
Traub RD, Wong RK. Cellular mechanism of neuronal synchronization in epilepsy. Science 1982;216:745–7.
Suffczynski P, Lopes da Silva FH, Parra J, et al. Dynamics of epileptic phenomena determined from statistics of ictal transitions. IEEE transactions on bio-medical engineering 2006;53(3):524–32.
Wendling F, Bartolomei F, Bellanger JJ, Chauvel P. Epileptic fast activity can be explained by a model of impaired GABAergic dendritic inhibition. Eur J Neurosci 2002;15:1499–508.
Wendling F, Hernandez A, Bellanger JJ, Chauvel P, Bartolomei F. Interictal to ictal transition in human temporal lobe epilepsy: Insights from a computational model of intracerebral EEG. J Clin Neurophysiol 2005;22:343–56.
Lytton WW. From Computer to Brain: Foundations of Computational Neuroscience New York; 2002.
Amaral DG, Witter MP. The three-dimensional organization of the hippocampal formation: A review of anatomical data. Neuroscience 1989;31:571–91.
Desmond NL, Levy WB. A quantitative anatomical study of the granule cell dendritic fields of the rat dentate gyrus using a novel probabilistic method. J Comp Neurol 1982;212: 131–45.
Lubke J, Frotscher M, Spruston N. Specialized electrophysiological properties of anatomically identified neurons in the hilar region of the rat fascia dentata. J Neurophysiol 1998;79:1518–34.
Patton PE, Mcnaughton B. Connection matrix of the hippocampal-formation .1. the dentate gyrus. Hippocampus 1995;5:245–86.
Staley KJ, Otis TS, Mody I. Membrane properties of dentate gyrus granule cells: Comparison of sharp microelectrode and whole-cell recordings. J Neurophysiol 1992;67:1346–58.
Morgan RJ, Santhakumar V, Soltesz I. Modeling the dentate gyrus. Prog Brain Res 2007;163:639–58.
Ratzliff AH, Santhakumar V, Howard A, Soltesz I. Mossy cells in epilepsy: Rigor mortis or vigor mortis? Trends Neurosci 2002;25:140–4.
Buckmaster PS, Dudek FE. In vivo intracellular analysis of granule cell axon reorganization in epileptic rats. J Neurophysiol 1999;81:712–21.
Sutula TP, Hagen J, Pitkanen A. Do epileptic seizures damage the brain? Curr Opin Neurol 2003;16:189–95.
Buckmaster PS, Zhang GF, Yamawaki R. Axon sprouting in a model of temporal lobe epilepsy creates a predominantly excitatory feedback circuit. J Neurosci 2002;22:6650–8.
Ratzliff AH, Howard AL, Santhakumar V, Osapay I, Soltesz I. Rapid deletion of mossy cells does not result in a hyperexcitable dentate gyrus: Implications for epileptogenesis. J Neurosci 2004;24:2259–69.
Sloviter RS. Hippocampal pathology and pathophysiology in temporal lobe epilepsy. Neurologia (Barcelona, Spain) 1996;11(Suppl 4):29– 32.
Watts DJ, Strogatz SH. Collective dynamics of ‘small-world' networks. Nature 1998;393:440–2.
Watts DJ. Small Worlds Princeton, New Jersey: Princeton UP; 1999.
Santhakumar V, Ratzliff AD, Jeng J, Toth Z, Soltesz I. Long-term hyperexcitability in the hippocampus after experimental head trauma. Ann Neurol 2001;50:708–17.
Rafiq A, Zhang YF, DeLorenzo RJ, Coulter DA. Long-duration self-sustained epileptiform activity in the hippocampal-parahippocampal slice: A model of status epilepticus. J Neurophysiol 1995;74:2028–42.
Netoff TI, Clewley R, Arno S, Keck T, White JA. Epilepsy in small-world networks. J Neurosci 2004;24:8075–83.
Roxin A, Riecke H, Solla SA. Self-sustained activity in a small-world network of excitable neurons. Phys Rev Lett 2004;92:198101.
Buckmaster PS, Dudek FE. Network properties of the dentate gyrus in epileptic rats with hilar neuron loss and granule cell axon reorganization. J Neurophysiol 1997;77:2685–96.
Buckmaster PS, Jongen-Relo AL. Highly specific neuron loss preserves lateral inhibitory circuits in the dentate gyrus of kainate-induced epileptic rats. J Neurosci 1999;19:9519–29.
Cavazos JE, Das I, Sutula TP. Neuronal loss induced in limbic pathways by kindling: evidence for induction of hippocampal sclerosis by repeated brief seizures. J Neurosci 1994;14:3106–21.
Cavazos JE, Sutula TP. Progressive neuronal loss induced by kindling: a possible mechanism for mossy fiber synaptic reorganization and hippocampal sclerosis. Brain Res 1990;527:1–6.
Gorter JA, van Vliet EA, Aronica E, Lopes da Silva FH. Progression of spontaneous seizures after status epilepticus is associated with mossy fibre sprouting and extensive bilateral loss of hilar parvalbumin and somatostatin-immunoreactive neurons. Eur J Neurosci 2001;13:657–69.
Leite JP, Babb TL, Pretorius JK, Kuhlman PA, Yeoman KM, Mathern GW. Neuron loss, mossy fiber sprouting, and interictal spikes after intrahippocampal kainate in developing rats. Epilepsy Res 1996;26:219–31.
Mathern GW, Bertram EH, Babb TL, et al. In contrast to kindled seizures, the frequency of spontaneous epilepsy in the limbic status model correlates with greater aberrant fascia dentata excitatory and inhibitory axon sprouting, and increased staining for N-methyl-D-aspartate, AMPA and GABA(A) receptors. Neuroscience 1997;77:1003–19.
van Vliet EA, Aronica E, Tolner EA, Lopes da Silva FH, Gorter JA. Progression of temporal lobe epilepsy in the rat is associated with immunocytochemical changes in inhibitory interneurons in specific regions of the hippocampal formation. Exp Neurol 2004;187:367–79.
Zappone CA, Sloviter RS. Translamellar disinhibition in the rat hippocampal dentate gyrus after seizure-induced degeneration of vulnerable hilar neurons. J Neurosci 2004;24:853–64.
Gabriel S, Njunting M, Pomper JK, et al. Stimulus and potassium-induced epileptiform activity in the human dentate gyrus from patients with and without hippocampal sclerosis. J Neurosci 2004;24:10416–30.
Blumcke I, Suter B, Behle K, et al. Loss of hilar mossy cells in Ammon's horn sclerosis. Epilepsia 2000;41(Suppl 6):S174–80.
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: Simple building blocks of complex networks. Science 2002;298:824–7.
Reigl M, Alon U, Chklovskii DB. Search for computational modules in the C. elegans brain. BMC Biol 2004;2:25.
Sporns O, Kotter R. Motifs in brain networks. PLoS Biol 2004;2:e369.
Prill RJ, Iglesias PA, Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005;3:e343.
Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999;286:509–12.
Song S, Sjostrom PJ, Reigl M, Nelson S, Chklovskii DB. Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol 2005;3:e68.
Yoshimura Y, Callaway EM. Fine-scale specificity of cortical networks depends on inhibitory cell type and connectivity. Nat Neurosci 2005;8:1552–9.
Yoshimura Y, Dantzker JL, Callaway EM. Excitatory cortical neurons form fine-scale functional networks. Nature 2005;433:868–73.
Walter C, Murphy BL, Pun RY, Spieles-Engemann AL, Danzer SC. Pilocarpine-induced seizures cause selective time-dependent changes to adult-generated hippocampal dentate granule cells. J Neurosci 2007;27:7541–52.
Crook S, Gleeson P, Howell F, Svitak J, Silver RA. MorphML: Level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics 2007;5:96–104.
Goddard NH, Hucka M, Howell F, Cornelis H, Shankar K, Beeman D. Towards NeuroML: Model description methods for collaborative modelling in neuroscience. Philos Trans R Soc Lond B Biol Sci 2001;356:1209–28.
Sik A, Penttonen M, Buzsaki G. Interneurons in the hippocampal dentate gyrus: An in vivo intracellular study. Eur J Neurosci 1997;9:573–88.
Li XG, Somogyi P, Tepper JM, Buzsaki G. Axonal and dendritic arborization of an intracellularly labeled chandelier cell in the Ca1 region of rat hippocampus. Exp Brain Res 1992;90:519–25.
Buckmaster PS, Yamawaki R, Zhang GF. Axon arbors and synaptic connections of a vulnerable population of interneurons in the dentate gyrus in vivo. J Comp Neurol 2002;445:360–73.
Buckmaster PS, Wenzel HJ, Kunkel DD, Schwartzkroin PA. Axon arbors and synaptic connections of hippocampal mossy cells in the rat in vivo. J Compar Neurol 1996;366:270–92.
Acknowledgments
Funding to IS was provided by NIH grant NS35915 and funding to RM by the UCI MSTP.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Morgan, R.J., Soltesz, I. (2009). Complexity Untangled: Large-Scale Realistic Computational Models in Epilepsy. In: Baraban, S. (eds) Animal Models of Epilepsy. Neuromethods, vol 40. Humana Press. https://doi.org/10.1007/978-1-60327-263-6_10
Download citation
DOI: https://doi.org/10.1007/978-1-60327-263-6_10
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-262-9
Online ISBN: 978-1-60327-263-6
eBook Packages: Springer Protocols