A review of computational models of neuronal cultures \emph{in vitro}

Konstantin V. Anokhin ; Mikhail S. Burtsev ; Viachesav A. Ilyin ; Ilya I. Kiselev ; Konstantin A. Kukin ; Konstantin V. Lakhman ; Alexander V. Paraskevov ; Roman B. Rybka ; Alexander G. Sboev ; Nikolay V. Tverdokhlebov

Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012) no. 2, pp. 372-397.

Résumé

One of the widely used experimental models in modern neuroscience is neuronal cultures in vitro. Neural networks cultured on multielectrode arrays allow to record large amount of information about the dynamics of neuronal activity, as well as to activate the cells by electrical stimulation. It makes the neuronal cultures a convenient tool for verification of theoretical models of neural networks. The main approaches to computer modeling of the dynamics of activity in the neuron cultures are considered in this review.

Bibliographie

[1] Churchland P. S., Sejnowski T. J., “Perspectives on Cognitive Neuroscience”, Science, 242:4879 (1988), 741–745 | DOI

[2] Deisseroth K., Feng G., Majewska A. K., Miesenböck G., Ting A., Schnitzer M. J., “Next-Generation Optical Technologies for Illuminating Genetically Targeted Brain Circuits”, J. Neurosci., 26:41 (2006), 10380–10386 | DOI

[3] Kravitz A. V., Kreitzer A. C., “Optogenetic manipulation of neural circuitry in vivo”, Current Opinion in Neurobiology, 21:3 (2011), 433–439 | DOI

[4] Soe A. K., Nahavandi S., Khoshmanesh K., “Neuroscience goes on a chip”, Biosensors and Bioelectronics

[5] Hierlemann A., Frey U., Hafizovic S., Heer F., “Growing Cells Atop Microelectronic Chips: Interfacing Electrogenic Cells In Vitro With CMOS-Based Microelectrode Arrays”, Proceedings of the IEEE, 99:2 (2011), 252–284 | DOI

[6] (data obrascheniya 06.07.2012) http://en.wikipedia.org/wiki/Cultured_neuronal_network

[7] Gross G. W., “Simultaneous Single Unit Recording in vitro with a Photoetched Laser Deinsulated Gold Multimicroelectrode Surface”, IEEE Transactions on Biomedical Engineering BME, 26:5 (1979), 273–279 | DOI

[8] Pine J., “Recording action potentials from cultured neurons with extracellular microcircuit electrodes”, Journal of Neuroscience Methods, 2:1 (1980), 19–31 | DOI

[9] Segev R., Shapira Y., Benveniste M., Ben-Jacob E., “Observations and modeling of synchronized bursting in two-dimensional neural networks”, Physical Review E, 64:1 (2001), 011920 | DOI

[10] Segev R., Benveniste M., Shapira Y., Ben-Jacob E., “Formation of electrically active clusterized neural networks”, Physical review letters, 90:16 (2003), 168101 | DOI

[11] Persi E., Horn D., Volman V., Segev R., Ben-Jacob E., “Modeling of Synchronized Bursting Events: The Importance of Inhomogeneity”, Neural Computation, 16:12 (2004), 2577–2595 | DOI | Zbl

[12] Beggs J. M., Plenz D., “Neuronal avalanches in neocortical circuits”, Journal of Neuroscience, 23:35 (2003), 11167

[13] Pasquale V., Massobrio P., Bologna L. L., Chiappalone M., Martinoia S., “Self-organization and neuronal avalanches in networks of dissociated cortical neurons”, Neuroscience, 153:4 (2008), 1354–1369 | DOI

[14] Bakkum D. J., Chao Z. C., Potter S. M., “Spatio-temporal electrical stimuli shape behavior of an embodied cortical network in a goal-directed learning task”, Journal of Neural Engineering, 5 (2008), 310–323 | DOI

[15] Chao Z. C., Bakkum D. J., Potter S. M., “Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior”, PLoS Comput Biol., 4:3 (2008), e1000042 | DOI | MR

[16] Simonov A. Yu., Kazantsev V. B., “Model vozniknoveniya lavinoobraznykh bioelektricheskikh razryadov v neironnykh setyakh mozga”, Pisma v ZhETF, 93:8 (2011), 516–521

[17] Segev R., Baruchi I., Hulata E., Ben-Jacob E., “Hidden neuronal correlations in cultured networks”, Physical Review-Series A, 92:11 (2004), 118102–118300

[18] Tsodyks M., Uziel A., Markram H., “Synchrony generation in recurrent networks with frequency-dependent synapses”, J. Neurosci., 20:1 (2000), 825–835

[19] Wagenaar D. A., Pine J., Potter S. M., “An extremely rich repertoire of bursting patterns during the development of cortical cultures”, BMC neuroscience, 7:1 (2006), 11 | DOI

[20] Robinson H. P., Kawahara M., Jimbo Y., Torimitsu K., Kuroda Y., Kawana A., “Periodic Synchronized Bursting and Intracellular Calcium Transients Elicited by Low Magnesium in Cultured Cortical Neurons”, J. Neurophysiol., 70:4 (1993), 1606–1616

[21] Meister M., Wong R. O., Baylor D. A., Shatz C. J., “Synchronous Bursts of Action Potentials in Ganglion Cells of the Developing Mammalian Retina”, Science, 252:5008 (1991), 939–943 | DOI

[22] Engel A. K., Konig P., Kreiter A. K., Schillen T. B., Singer W., “Temporal coding in the visual cortex: new vistas on integration in the nervous system”, Trends in Neurosciences, 15:6 (1992), 218–226 | DOI

[23] Shahaf G., Marom S., “Learning in Networks of Cortical Neurons”, J. Neurosci., 21:22 (2001), 8782–8788

[24] Marom S., Eytan D., “Learning in ex-vivo developing networks of cortical neurons”, Development, Dynamics and Pathiology of Neuronal Networks: from Molecules to Functional Circuits, 147, Elsevier, 2005, 189–199 | DOI

[25] DeMarse T. B., Wagenaar D. A., Blau A. W., Potter S. M., “The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies”, Auton Robots, 11:3 (2001), 305–310 | DOI | Zbl

[26] DeMarse T. B., Dockendorf K. P., “Adaptive flight control with living neuronal networks on microelectrode arrays”, Proc. of 2005 IEEE International Joint Conference on Neural Networks, IJCNN2005 (Montreal, Canada), v. 3, 2005, 1548–1551 | DOI

[27] Novellino A., D'Angelo P., Cozzi L., Chiappalone M., Sanguineti V., Martinoia S., “Connecting Neurons to a Mobile Robot: An In Vitro Bidirectional Neural Interface”, Computational Intelligence and Neuroscience, 2007 (2007), 1–13 | DOI

[28] le Feber J., Stegenga J., Rutten W. L. C., “The Effect of Slow Electrical Stimuli to Achieve Learning in Cultured Networks of Rat Cortical Neurons”, PLoS ONE, 5:1 (2010), e8871 | DOI

[29] Warwick K., Xydas D., Nasuto S. J., Becerra V. M., Hammond M. W., Downes J. H., Marshall S., Whalley B. J., “Controlling a mobile robot with a biological brain”, Defence Science Journal, 60:1 (2010), 5–14

[30] Mulas M., Massobrio P., Martinoia S., Chiappalone M., “A simulated neuro-robotic environment for bi-directional closed-loop experiments”, Paladyn. Journal of behavioral robotics, 1 (2011), 179–186 | DOI

[31] Izhikevich E. M., Which model to use for cortical spiking neurons?, Neural Networks, IEEE Transactions on, 15:5 (2004), 1063–1070 | DOI

[32] Tsodyks Misha, Uziel A., Markram H. T., “Synchrony Generation in Recurrent Networks with Frequency-Dependent Synapses”, J. Neurosci., 20:1 (2000), RC50–RC50

[33] Koch C., Biophysics of computation: information processing in single neurons, Oxford University Press, USA, 2005 | Zbl

[34] Gerstner W., Kistler W. M., Spiking neuron models: Single neurons, populations, plasticity, Cambridge Univ Pr., 2002 | MR | Zbl

[35] Burkitt A. N., “A review of the integrate-and-fire neuron model. I: Homogeneous synaptic input”, Biological cybernetics, 95:1 (2006), 1–19 | DOI | MR | Zbl

[36] Burkitt A. N., “A review of the integrate-and-fire neuron model. II: Inhomogeneous synaptic input and network properties”, Biological cybernetics, 95:2 (2006), 97–112 | DOI | MR | Zbl

[37] Hodgkin A. L., Huxley A. F., “A quantitative description of membrane current and its application to conduction and excitation in nerve”, The Journal of physiology, 117:4 (1952), 500–544

[38] Hodgkin A. L., Huxley A. F., Katz B., “Measurement of current-voltage relations in the membrane of the giant axon of Loligo”, The Journal of physiology, 116:4 (1952), 424–448

[39] Izhikevich E. M., “Simple model of spiking neurons”, Neural Networks, IEEE Transactions on, 14:6 (2003), 1569–1572 | DOI | MR

[40] Fitzhugh R., “Impulses and physiological states in theoretical models of nerve membrane”, Biophysical journal, 1:6 (1961), 445–466 | DOI

[41] Nagumo J., Arimoto S., Yoshizawa S., “An active pulse transmission line simulating nerve axon”, Proceedings of the IRE, 50:10 (1962), 2061–2070 | DOI

[42] Izhikevich E. M., Edelman G. M., “Large-scale model of mammalian thalamocortical systems”, Proceedings of the national academy of sciences, 105:9 (2008), 3593 | DOI

[43] Dayan P., Abbott L. F., Abbott L., Theoretical neuroscience: Computational and mathematical modeling of neural systems, 2001 | MR

[44] Tsodyks M. V., Markram H., “The neural code between neocortical pyramidal neurons depends on neurotransmitter release probability”, Proceedings of the National Academy of Sciences, 94:2 (1997), 719 | DOI

[45] Bi G., Poo M., “Synaptic modification by correlated activity: Hebb's postulate revisited”, Annual review of neuroscience, 24:1 (2001), 139–166 | DOI

[46] Sjöström P. J., Rancz E. A., Roth A., Hausser M., “Dendritic excitability and synaptic plasticity”, Physiological reviews, 88:2 (2008), 769–840 | DOI

[47] Song S., Miller K. D., Abbott L. F., “Competitive Hebbian learning through spike-timing-dependent synaptic plasticity”, Nature neuroscience, 3 (2000), 919–926 | DOI

[48] Gritsun T. A., Le Feber J., Stegenga J., Rutten W. L., “Network bursts in cortical cultures are best simulated using pacemaker neurons and adaptive synapses”, Biological cybernetics, 102:4 (2010), 293–310 | DOI | MR

[49] Massobrio P., Martinoia S., “Modelling small-patterned neuronal networks coupled to microelectrode arrays”, Journal of Neural Engineering, 5 (2008), 350 | DOI

[50] Richards C. D., Shiroyama T., Kitai S. T., “Electrophysiological and immunocytochemical characterization of GABA and dopamine neurons in the substantia nigra of the rat”, Neuroscience, 80:2 (1997), 545–557 | DOI

[51] Latham P. E., Richmond B. J., Nelson P. G., Nirenberg S., “Intrinsic dynamics in neuronal networks. I: Theory”, Journal of Neurophysiology, 83:2 (2000), 808–827

[52] Latham P. E., Richmond B. J., Nirenberg S., Nelson P. G., “Intrinsic dynamics in neuronal networks. II: Experiment”, Journal of neurophysiology, 83:2 (2000), 828–835

[53] Carnevale N. T., Hines M. L., The NEURON book, Cambridge Univ Pr., 2006

[54] Reeke G. N. et al. (eds.), Modeling in the Neurosciences: From Biological Systems to Neuromimetic Robotics, 2nd ed., CRC Press, 2005, 736 pp.

[55] Chao Z. C., Bakkum D. J., Wagenaar D. A., Potter S. M., “Effects of random external background stimulation on network synaptic stability after tetanization”, Neuroinformatics, 3:3 (2005), 263–280 | DOI