Abstract
This work analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, we introduce and implement a graph-based unsupervised segmentation algorithm that automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by an adjacency matrix in which nodes are identified as neurons or clusters of neurons, and links are the reconstructed connections (neurites) between them. The algorithm is also able to extract all other relevant morphological information characterizing neurons and neurites. More importantly and at variance with other segmentation methods that require fluorescence imaging from immunocytochemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs’ micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.
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References
Achard, S., Bullmore, E.: Efficiency and cost of economical brain functional networks. PLoS Comput. Biol. 3(2), e17 (2007)
Albert, R., Barabási, A.L.: Statistical mechanics of complex networks. Rev. Mod. Phys. 74(1), 47–97 (2002)
Amaral, L.A., Scala, A., Barthelemy, M., Stanley, H.E.: Classes of small-world networks. Proc. Natl. Acad. Sci. USA 97(21), 11,149–11,152 (2000)
Anava, S., Greenbaum, A., Ben Jacob, E., Hanein, Y., Ayali, A.: The regulative role of neurite mechanical tension in network development. Biophys. J. 96(4), 1661–1670 (2009)
Ayali, A.: Editorial: models of invertebrate neurons in culture. J. Mol. Histol. 43(4), 379–81 (2012)
Baker, B.J., Kosmidis, E.K., Vucinic, D., Falk, C.X., Cohen, L.B., Djurisic, M., Zecevic, D.: Imaging brain activity with voltage- and calcium-sensitive dyes. Cell. Mol. Neurobiol. 25(2), 245–282 (2005)
Bakkum, D.J., Chao, Z.C., Gamblen, P., Ben-Ary, G., Shkolnik, A.G., DeMarse, T.B., Potter, S.M.: Embodying cultured networks with a robotic drawing arm. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2007, 2996–2999 (2007)
Barabási, A.L., Albert, R.: Emergence of scaling in random networks. Science 286(5439), 509–512 (1999)
Baruchi, I., Jacob, E.B.: Towards neuro-memory-chip: imprinting multiple memories in cultured neural networks. Phys. Rev. E. 75(5), 050901(R) (2007)
Boccaletti, S., Latora, V., Moreno, Y., Chavez, M., Hwang, D.U.: Complex networks: Structure and dynamics. Phys. Rep. 424, 175–308 (2006)
Boccaletti, S., Bianconi, G., Criado, R., del Genio, C., Gómez-Gardeñes, J., Romance, M., Sendiña-Nadal, I., Wang, Z., Zanin, M.: The structure and dynamics of multilayer networks. Phys. Rep. 544(1), 1–122 (2014)
Bollobás, B.: Random Graphs. Cambridge University Press, Cambridge (2001)
Bologna, L.L., Nieus, T., Tedesco, M., Chiappalone, M., Benfenati, F., Martinoia, S.: Low-frequency stimulation enhances burst activity in cortical cultures during development. Neuroscience 165(3), 692–704 (2010)
Breskin, I., Soriano, J., Moses, E., Tlusty, T.: Percolation in living neural networks. Phys. Rev. Lett. 97, 188,102 (2006)
Buice, M.A., Cowan, J.D.: Statistical mechanics of the neocortex. Prog. Biophys. Mol. Biol. 99, 53–86 (2009)
Chatterjee, N., Sinha, S.: Understanding the mind of a worm: hierarchical network structure underlying nervous system function in C. elegans. Prog. Brain Res. 168, 145–153 (2007) (Elsevier)
Cohen, O., Keselman, A., Moses, E., Martnez, M.R., Soriano, J., Tlusty, T.: Quorum percolation in living neural networks. EPL 89(1), 18008 (2010)
Demarse, T.B., Wagenaar, D.A., Blau, A.W., Potter, S.M.: The neurally controlled animat: Biological brains acting with simulated bodies. Auton. Robot. 11(3), 305–310 (2001)
Downes, J.H., Hammond, M.W., Xydas, D., Spencer, M.C., Becerra, V.M., Warwick, K., Whalley, B.J., Nasuto, S.J.: Emergence of a small-world functional network in cultured neurons. PLoS Comput Biol 8(5), e1002522 (2012)
Eckmann, J.P., Feinerman, O., Gruendlinger, L., Moses, E., Soriano, J., Tlusty, T.: The physics of living neural networks. Phys. Rep. 449(13), 54–76 (2007) (Nonequilibrium physics: From complex fluids to biological systems III. Living systems)
Feldt, S., Bonifazi, P., Cossart, R.: Dissecting functional connectivity of neuronal microcircuits: experimental and theoretical insights. Trends Neurosci. 34(5), 225–236 (2011)
Fuchs, E., Ayali, A., Robinson, A., Hulata, E., Ben-Jacob, E.: Coemergence of regularity and complexity during neural network development. Dev Neurobiol 67(13), 1802–1814 (2007)
Fuchs, E., Ayali, A., Ben-Jacob, E., Boccaletti, S.: The formation of synchronization cliques during the development of modular neural networks. Phys. Biol. 6(3), 036018 (2009)
Grienberger, C., Konnerth, A.: Imaging calcium in neurons. Neuron 73(5), 862–885 (2012)
Harrison, R.G., Greenman, M.J., Mall, F.P., Jackson, C.M.: Observations of the living developing nerve fiber. Anat. Rec. 1(5), 116–128 (1907)
Honey, C.J., Kötter, R., Breakspear, M., Sporns, O.: Network structure of cerebral cortex shapes functional connectivity on multiple time scales. Proc. Natl. Acad. Sci. USA 104(24), 10,240–10,245 (2007)
Honey, C.J., Sporns, O., Cammoun, L., Gigandet, X., Thiran, J.P., Meuli, R., Hagmann, P.: Predicting human resting-state functional connectivity from structural connectivity. Proc. Natl. Acad. Sci. USA 106(6), 2035–2040 (2009)
Jacobi, S., Soriano, J., Moses, E.: BDNF and NT-3 increase velocity of activity front propagation in unidimensional hippocampal cultures. J. Neurophysiol. 104(6), 2932–2939 (2010)
Latora, V., Marchiori, M.: Economic small-world behavior in weighted networks. EPJ B 32(2), 249–263 (2003)
Li, D., Li, G., Kosmidis, K., Stanley, H.E., Bunde, A., Havlin, S.: Percolation of spatially constraint networks. EPL 93(6), 68004 (2011)
Maeda, E., Robinson, H.P., Kawana, A.: The mechanisms of generation and propagation of synchronized bursting in developing networks of cortical neurons. J. Neurosci. 15(10), 6834–6845 (1995)
Marom, S., Shahaf, G.: Development, learning and memory in large random networks of cortical neurons: lessons beyond anatomy. Q. Rev. Biophys. 35(1), 63–87 (2002)
Meijering, E.: Neuron tracing in perspective. Cytometry A 77(7), 693–704 (2010)
Melli, G., Höke, A.: Dorsal root ganglia sensory neuronal cultures: a tool for drug discovery for peripheral neuropathies. Expert. Opin. Drug Discov. 4(10), 1035–1045 (2009)
Morin, F.O., Takamura, Y., Tamiya, E.: Investigating neuronal activity with planar microelectrode arrays: achievements and new perspectives. J. Biosci. Bioeng. 100(2), 131–143 (2005)
Newman, M.E.J.: Assortative mixing in networks. Phys. Rev. Lett. 89(20), 208701 (2002)
Orlandi, J.G., Soriano, J., Alvarez-Lacalle, E., Teller, S., Casademunt, J.: Noise focusing and the emergence of coherent activity in neuronal cultures. Nat. Phys. 9, 582–590 (2013)
Rad, A.A., Sendiña-Nadal, I., Papo, D., Zanin, M., Buldú, J.M., del Pozo, F., Boccaletti, S.: Topological measure locating the effective crossover between segregation and integration in a modular network. Phys. Rev. Lett. 108, 228,701 (2012)
de Santos, D., Lorente, V., de la Paz, F., Cuadra, J.M., Alvarez-Sánchez, J.R., Fernández, E., Ferrández, J.M.: A client-server architecture for remotely controlling a robot using a closed-loop system with a biological neuroprocessor. Robot. Auton. Syst. 58(12), 1223–1230 (2010)
de Santos-Sierra, D., Arriaga-Gómez, M.F., Bailador, G., Avila, C.S.: Low computational cost multilayer graph-based segmentation algorithms for hand recognition on mobile phones. In: 2014 International Carnahan Conference on Security Technology (ICCST), pp. 1–5
de Santos-Sierra, D., Sendiña-Nadal, I., Leyva, I., Almendral, J.A., Anava, S., Ayali, A., Papo, D., Boccaletti, S.: Emergence of small-world anatomical networks in self-organizing clustered neuronal cultures. PLoS ONE 9(1), e85828 (2014)
de Santos-Sierra, D., Sendiña-Nadal, I., Leyva, I., Almendral, J.A., Ayali, A., Anava, S., Sánchez-Ávila, C., Boccaletti, S.: Graph-based unsupervised segmentation algorithm for cultured neuronal networks’ structure characterization and modeling. Cytometry A 87A, 513–523 (2015)
de Sierra-Santos, D.: Self-organizing cultured neural networks: image analysis techniques for longitudinal tracking and modeling of the underlying network structure. PhD thesis, Technical University of Madrid (2015)
Schmeltzer, C., Soriano, J., Sokolov, I.M., Rüdiger, S.: Percolation of spatially constrained Erdős–Rényi networks with degree correlations. Phys. Rev. E 89, 012116 (2014)
Segev, R., Benveniste, M., Shapira, Y., Ben-Jacob, E.: Formation of electrically active clusterized neural networks. Phys. Rev. Lett. 90(16), 168101 (2003)
Sendiña-Nadal, I., Soriano, J.: Cultivos neuronales: sistemas modelo para comprender la dinámica y la conectividad en redes. In: Maestú, F., del Pozo, F., Pereda, E. (eds.) Conectividad funcional y anatómica en el cerebro humano: Análisis de señales y aplicaciones en ciencias de la salud, pp. 103–113. Elsevier, Amsterdam (2015)
Shefi, O., Ben-Jacob, E., Ayali, A.: Growth morphology of two-dimensional insect neural networks. Neurocomputing 44–46, 635–643 (2002)
Shefi, O., Golding, I., Segev, R., Ben-Jacob, E., Ayali, A.: Morphological characterization of in vitro neuronal networks. Phys. Rev. E 66, 021905 (2002)
Sombati, S., Delorenzo, R.J.: Recurrent spontaneous seizure activity in hippocampal neuronal networks in culture. J. Neurophysiol. 73(4), 1706–1711 (1995)
Soriano, J., Rodríguez Martínez, M., Tlusty, T., Moses, E.: Development of input connections in neural cultures. Proc. Natl. Acad. Sci. USA 105(37), 13758–13763 (2008)
Sun, J.J., Kilb, W., Luhmann, H.J.: Self-organization of repetitive spike patterns in developing neuronal networks in vitro. Eur. J. Neurosci. 32(8), 1289–1299 (2010)
Teller, S., Granell, C., De Domenico, M., Soriano, J., Gómez, S., Arenas, A.: Emergence of assortative mixing between clusters of cultured neurons. PLoS Comput. Biol. 10(9), e1003796 (2014)
van Pelt, J., Vajda, I., Wolters, P.S., Corner, M.A., Ramakers, G.J.A.: Dynamics and plasticity in developing neuronal networks in vitro. Prog. Brain Res. 147, 173–188 (2005)
Watts, D., Strogatz, S.: Collective dynamics of “small-world” networks. Nature 393, 440–442 (1998)
Watts, D.J.: Small worlds: the dynamics of networks between order and randomness. Princeton University Press, Princeton, NJ (1999)
White, J.G., Southgate, E., Thomson, J.N., Brenner, S.: The structure of the nervous system of the nematode caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314(1165), 1–340 (1986)
Wilson, S.W.: Knowledge growth in an artificial animal. In: Proceedings of the 1st International Conference on Genetic Algorithms, L. Erlbaum Associates Inc., Hillsdale, NJ, USA, pp. 16–23 (1985)
Woiterski, L., Claudepierre, T., Luxenhofer, R., Jordan, R., Kaes, J.: Stages of neuronal network formation. New. J. Phys. 15(025029), 1–15 (2013)
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de Santos-Sierra, D., Leyva, I., Almendral, J.A., Boccaletti, S., Sendiña-Nadal, I. (2019). Self-organized Cultured Neuronal Networks: Longitudinal Analysis and Modeling of the Underlying Network Structure. In: Carballido-Landeira, J., Escribano, B. (eds) Biological Systems: Nonlinear Dynamics Approach. SEMA SIMAI Springer Series, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-030-16585-7_4
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