1
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Networks behind the morphology and structural design of living systems. Phys Life Rev 2022; 41:1-21. [DOI: 10.1016/j.plrev.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/04/2022] [Indexed: 01/06/2023]
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2
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Herreros P, Ballesteros-Esteban LM, Laguna MF, Leyva I, Sendiña-Nadal I, Holgado M. Neuronal circuits on a chip for biological network monitoring. Biotechnol J 2021; 16:e2000355. [PMID: 33984186 DOI: 10.1002/biot.202000355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/16/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022]
Abstract
Cultured neuronal networks (CNNs) are a robust model to closely investigate neuronal circuits' formation and monitor their structural properties evolution. Typically, neurons are cultured in plastic plates or, more recently, in microfluidic platforms with potentially a wide variety of neuroscience applications. As a biological protocol, cell culture integration with a microfluidic system provides benefits such as accurate control of cell seeding area, culture medium renewal, or lower exposure to contamination. The objective of this report is to present a novel neuronal network on a chip device, including a chamber, fabricated from PDMS, vinyl and glass connected to a microfluidic platform to perfuse the continuous flow of culture medium. Network growth is compared in chips and traditional Petri dishes to validate the microfluidic chip performance. The network assessment is performed by computing relevant topological measures like the number of connected neurons, the clustering coefficient, and the shortest path between any pair of neurons throughout the culture's life. The results demonstrate that neuronal circuits on a chip have a more stable network structure and lifespan than developing in conventional settings, and therefore this setup is an advantageous alternative to current culture methods. This technology could lead to challenging applications such as batch drug testing of in vitro cell culture models. From the engineering perspective, a device's advantage is the chance to develop custom designs more efficiently than other microfluidic systems.
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Affiliation(s)
- Pedro Herreros
- Group of Optics, Photonics and Biophotonics (GOFB), Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain.,Group of Organ and Tissue on-a-chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain
| | - Luis M Ballesteros-Esteban
- Complex Systems Group & GISC, Universidad Rey Juan Carlos, Madrid, Spain.,Group of Biological Networks, Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
| | - María Fe Laguna
- Group of Optics, Photonics and Biophotonics (GOFB), Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain.,Group of Organ and Tissue on-a-chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain.,Departamento de Física Aplicada e Ingeniería de Materiales, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, Madrid, Spain
| | - Inmaculada Leyva
- Complex Systems Group & GISC, Universidad Rey Juan Carlos, Madrid, Spain.,Group of Biological Networks, Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
| | - Irene Sendiña-Nadal
- Complex Systems Group & GISC, Universidad Rey Juan Carlos, Madrid, Spain.,Group of Biological Networks, Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
| | - Miguel Holgado
- Group of Optics, Photonics and Biophotonics (GOFB), Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain.,Group of Organ and Tissue on-a-chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain.,Departamento de Física Aplicada e Ingeniería de Materiales, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, Madrid, Spain
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3
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Lobov SA, Zharinov AI, Makarov VA, Kazantsev VB. Spatial Memory in a Spiking Neural Network with Robot Embodiment. SENSORS 2021; 21:s21082678. [PMID: 33920246 PMCID: PMC8070389 DOI: 10.3390/s21082678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022]
Abstract
Cognitive maps and spatial memory are fundamental paradigms of brain functioning. Here, we present a spiking neural network (SNN) capable of generating an internal representation of the external environment and implementing spatial memory. The SNN initially has a non-specific architecture, which is then shaped by Hebbian-type synaptic plasticity. The network receives stimuli at specific loci, while the memory retrieval operates as a functional SNN response in the form of population bursts. The SNN function is explored through its embodiment in a robot moving in an arena with safe and dangerous zones. We propose a measure of the global network memory using the synaptic vector field approach to validate results and calculate information characteristics, including learning curves. We show that after training, the SNN can effectively control the robot’s cognitive behavior, allowing it to avoid dangerous regions in the arena. However, the learning is not perfect. The robot eventually visits dangerous areas. Such behavior, also observed in animals, enables relearning in time-evolving environments. If a dangerous zone moves into another place, the SNN remaps positive and negative areas, allowing escaping the catastrophic interference phenomenon known for some AI architectures. Thus, the robot adapts to changing world.
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Affiliation(s)
- Sergey A. Lobov
- Neurotechnology Department, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia; (A.I.Z.); (V.A.M.); (V.B.K.)
- Neuroscience and Cognitive Technology Laboratory, Center for Technologies in Robotics and Mechatronics Components, Innopolis University, 1 Universitetskaya Str., 420500 Innopolis, Russia
- Center For Neurotechnology and Machine Learning, Immanuel Kant Baltic Federal University, 14 Nevsky Str., 236016 Kaliningrad, Russia
- Correspondence:
| | - Alexey I. Zharinov
- Neurotechnology Department, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia; (A.I.Z.); (V.A.M.); (V.B.K.)
| | - Valeri A. Makarov
- Neurotechnology Department, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia; (A.I.Z.); (V.A.M.); (V.B.K.)
- Instituto de Matemática Interdisciplinar, Facultad de Ciencias Matemáticas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Victor B. Kazantsev
- Neurotechnology Department, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia; (A.I.Z.); (V.A.M.); (V.B.K.)
- Neuroscience and Cognitive Technology Laboratory, Center for Technologies in Robotics and Mechatronics Components, Innopolis University, 1 Universitetskaya Str., 420500 Innopolis, Russia
- Center For Neurotechnology and Machine Learning, Immanuel Kant Baltic Federal University, 14 Nevsky Str., 236016 Kaliningrad, Russia
- Lab of Neurocybernetics, Russian State Scientific Center for Robotics and Technical Cybernetics, 21 Tikhoretsky Ave., St., 194064 Petersburg, Russia
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Juárez-Vidales JDJ, Pérez-Ortega J, Lorea-Hernández JJ, Méndez-Salcido F, Peña-Ortega F. Configuration and dynamics of dominant inspiratory multineuronal activity patterns during eupnea and gasping generation in vitro. J Neurophysiol 2021; 125:1289-1306. [PMID: 33502956 DOI: 10.1152/jn.00563.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The pre-Bötzinger complex (preBötC), located within the ventral respiratory column, produces inspiratory bursts in varying degrees of synchronization/amplitude. This wide range of population burst patterns reflects the flexibility of the preBötC neurons, which is expressed in variations in the onset/offset times of their activations and their activity during the population bursts, with respiratory neurons exhibiting a large cycle-to-cycle timing jitter both at the population activity onset and at the population activity peak, suggesting that respiratory neurons are stochastically activated before and during the inspiratory bursts. However, it is still unknown whether this stochasticity is maintained while evaluating the coactivity of respiratory neuronal ensembles. Moreover, the preBötC topology also remains unknown. In this study, by simultaneously recording tens of preBötC neurons and using coactivation analysis during the inspiratory periods, we found that the preBötC has a scale-free configuration (mixture of not many highly connected nodes, hubs, with abundant poorly connected elements) exhibiting the rich-club phenomenon (hubs more likely interconnected with each other). PreBötC neurons also produce multineuronal activity patterns (MAPs) that are highly stable and change during the hypoxia-induced reconfiguration. Moreover, preBötC contains a coactivating core network shared by all its MAPs. Finally, we found a distinctive pattern of sequential coactivation of core network neurons at the beginning of the inspiratory periods, indicating that, when evaluated at the multicellular level, the coactivation of respiratory neurons seems not to be stochastic.NEW & NOTEWORTHY By means of multielectrode recordings of preBötC neurons, we evaluated their configuration in normoxia and hypoxia, finding that the preBötC exhibits a scale-free configuration with a rich-club phenomenon. preBötC neurons produce multineuronal activity patterns that are highly stable but change during hypoxia. The preBötC contains a coactivating core network that exhibit a distinctive pattern of coactivation at the beginning of inspirations. These results reveal some network basis of inspiratory rhythm generation and its reconfiguration during hypoxia.
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Affiliation(s)
- Josué de Jesús Juárez-Vidales
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Queretaro, Mexico
| | - Jesús Pérez-Ortega
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Queretaro, Mexico
| | - Jonathan Julio Lorea-Hernández
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Queretaro, Mexico
| | - Felipe Méndez-Salcido
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Queretaro, Mexico
| | - Fernando Peña-Ortega
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Queretaro, Mexico
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5
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Han Y, Zhu H, Zhao Y, Lang Y, Sun H, Han J, Wang L, Wang C, Zhou J. The effect of acute glutamate treatment on the functional connectivity and network topology of cortical cultures. Med Eng Phys 2019; 71:91-97. [PMID: 31311692 DOI: 10.1016/j.medengphy.2019.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 11/24/2022]
Abstract
Microelectrode arrays (MEAs) allow the investigation of the pharmacological and toxicological effects of chemicals on cultured neuronal networks. Understanding the functional connections between neurons and the resulting neuronal networks is important for evaluating drugs that affect synaptic transmission. Therefore, we acutely treated a mature cultured neuronal network on MEAs with accumulating amounts of glutamate and recorded their altered electrophysiology. Subsequently, a cross-covariance analysis was applied to process the spiking activity in the network and to evaluate the connections between neurons. Finally, graph theory was used to assess the functional network properties under acute glutamate treatment. Our data demonstrated that glutamate increased the similarity, connectivity weight, density, and largest-component size of the functional network. In addition, the small-world network topology was altered after glutamate treatment. Our results indicate that the graph theory can advance our understanding of the pharmacological significance of neurotransmitters on neuronal networks.
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Affiliation(s)
- Yao Han
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China; Stem Cell and Tissue Engineering Lab, Institute of Health Service and Transfusion Medicine, Beijing, PR China
| | - Huimin Zhu
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Yuwei Zhao
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Yiran Lang
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Hongji Sun
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Jiuqi Han
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Lubin Wang
- Cognitive and Mental Health Research Center, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Changyong Wang
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China
| | - Jin Zhou
- Department of Neural Engineering and Biological Interdisciplinary Studies, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, PR China.
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6
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Prox J, Smith T, Holl C, Chehade N, Guo L. Integrated biocircuits: engineering functional multicellular circuits and devices. J Neural Eng 2018; 15:023001. [DOI: 10.1088/1741-2552/aaa906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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Huang YT, Chang YL, Chen CC, Lai PY, Chan CK. Positive feedback and synchronized bursts in neuronal cultures. PLoS One 2017; 12:e0187276. [PMID: 29091966 PMCID: PMC5665536 DOI: 10.1371/journal.pone.0187276] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/17/2017] [Indexed: 01/05/2023] Open
Abstract
Synchronized bursts (SBs) with complex structures are common in neuronal cultures. Although the phenomenon of SBs has been discovered for a long time, its origin is still unclear. Here, we investigate the properties of these SBs in cultures grown on a multi-electrode array. We find that structures of these SBs are related to the different developmental stages of the cultures and these structures can be modified by changing the magnesium concentration in the culture medium; indicating that synaptic mechanism is involved in the generation of SBs. A model based on short term synaptic plasticity (STSP), recurrent connections and astrocytic recycling of neurotransmitters has been developed successfully to understand the observed structures of SBs in experiments. A phase diagram obtained from this model shows that networks exhibiting SBs are in a complex oscillatory state due to large enough positive feedback provided by synaptic facilitation and recurrent connections. In this model, while STSP controls the fast oscillations (∼ 100 ms) within a SB, the astrocytic recycling determines the slow time scale (∼10 s) of inter-burst intervals. Our study suggests that glia-neuron interactions can be important in the understanding of the complex dynamics of neuronal networks.
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Affiliation(s)
- Yu-Ting Huang
- Dept. of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan 320, ROC
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Yu-Lin Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Chun-Chung Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Pik-Yin Lai
- Dept. of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan 320, ROC
- * E-mail: (PYL); (CKC)
| | - C. K. Chan
- Dept. of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan 320, ROC
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
- * E-mail: (PYL); (CKC)
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8
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Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks. PLoS Comput Biol 2017; 13:e1005672. [PMID: 28749937 PMCID: PMC5549760 DOI: 10.1371/journal.pcbi.1005672] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 08/08/2017] [Accepted: 07/07/2017] [Indexed: 01/22/2023] Open
Abstract
Developing neuronal systems intrinsically generate coordinated spontaneous activity that propagates by involving a large number of synchronously firing neurons. In vivo, waves of spikes transiently characterize the activity of developing brain circuits and are fundamental for activity-dependent circuit formation. In vitro, coordinated spontaneous spiking activity, or network bursts (NBs), interleaved within periods of asynchronous spikes emerge during the development of 2D and 3D neuronal cultures. Several studies have investigated this type of activity and its dynamics, but how a neuronal system generates these coordinated events remains unclear. Here, we investigate at a cellular level the generation of network bursts in spontaneously active neuronal cultures by exploiting high-resolution multielectrode array recordings and computational network modelling. Our analysis reveals that NBs are generated in specialized regions of the network (functional neuronal communities) that feature neuronal links with high cross-correlation peak values, sub-millisecond lags and that share very similar structural connectivity motifs providing recurrent interactions. We show that the particular properties of these local structures enable locally amplifying spontaneous asynchronous spikes and that this mechanism can lead to the initiation of NBs. Through the analysis of simulated and experimental data, we also show that AMPA currents drive the coordinated activity, while NMDA and GABA currents are only involved in shaping the dynamics of NBs. Overall, our results suggest that the presence of functional neuronal communities with recurrent local connections allows a neuronal system to generate spontaneous coordinated spiking activity events. As suggested by the rules used for implementing our computational model, such functional communities might naturally emerge during network development by following simple constraints on distance-based connectivity. Coordinated spontaneous spiking activity is fundamental for the normal formation of brain circuits during development. However, how ensembles of neurons generate these events remains unclear. To address this question, in the present study, we investigated the network properties that might be required to a neuronal system for the generation of these spontaneous waves of spikes. We performed our study on spontaneously active neuronal cell cultures using high-resolution electrical recordings and a computational network model developed to reproduce our experimental data both quantitatively and qualitatively. Through the analysis of both experimental and simulated data, we found that network bursts are initiated in regions of the network, or “functional communities”, characterized by particular local connectivity properties. We also found that these regions can amplify the background asynchronous spiking activity preceding a network burst and, in this way, can give rise to coordinated spiking events. As a whole, our results suggest the presence of functional communities of neurons in a developing neuronal system that might naturally emerge by following simple constraints on distance-based connectivity. These regions are most likely required for the generation of the spontaneous coordinated activity that can drive activity-dependent circuit formation.
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9
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Han Y, Li H, Lang Y, Zhao Y, Sun H, Zhang P, Ma X, Han J, Wang Q, Zhou J, Wang C. The Effects of Acute GABA Treatment on the Functional Connectivity and Network Topology of Cortical Cultures. Neurochem Res 2017; 42:1394-1402. [PMID: 28290133 DOI: 10.1007/s11064-017-2190-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/20/2017] [Indexed: 02/05/2023]
Abstract
γ-Aminobutyric acid (GABA) is an inhibitory transmitter, acting on receptor channels to reduce neuronal excitability in matured neural systems. However, electrophysiological responses of whole neuronal ensembles to the exposure to GABA are still unclear. We used micro-electrode arrays (MEAs) to study the effects of the increasing amount of GABA on functional network of cortical neural cultures. Then the recorded data were analyzed by the cross-covariance analysis and graph theory. Results showed that after the GABA treatment, the activity parameters of firing rate, bursting rate, bursting duration and network burst frequency in neural cultures decreased as expected. In addition, the functional connectivity also decreased in similarity, network density, and the size of the largest component. However, small-worldness was not found to be influenced by the acute GABA treatment. Our results support the position that using graph theory to evaluate the functional connectivity of neural cultures may enhance understanding of the pharmacological impact of neurotransmitters on neuronal networks.
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Affiliation(s)
- Yao Han
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Hong Li
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Yiran Lang
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Yuwei Zhao
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Hongji Sun
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Peng Zhang
- Neural Interface& Rehabilitation Technology Research Center, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuan Ma
- Neural Interface& Rehabilitation Technology Research Center, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiuqi Han
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Qiyu Wang
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Jin Zhou
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China.
| | - Changyong Wang
- Department of advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Academy of Military Medical Sciences, Beijing, People's Republic of China.
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10
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Abstract
Networks of protoplasmic tubes of organism Physarum polycehpalum are macro-scale structures which optimally span multiple food sources to avoid repellents yet maximize coverage of attractants. When data are presented by configurations of attractants and behaviour of the slime mould is tuned by a range of repellents, the organism preforms computation. It maps given data configuration into a protoplasmic network. To discover physical means of programming the slime mould computers we explore conductivity of the protoplasmic tubes; proposing that the network connectivity of protoplasmic tubes shows pathway-dependent plasticity. To demonstrate this we encourage the slime mould to span a grid of electrodes and apply AC stimuli to the network. Learning and weighted connections within a grid of electrodes is produced using negative and positive voltage stimulation of the network at desired nodes; low frequency (10 Hz) sinusoidal (0.5 V peak-to-peak) voltage increases connectivity between stimulated electrodes while decreasing connectivity elsewhere, high frequency (1000 Hz) sinusoidal (2.5 V peak-to-peak) voltage stimulation decreases network connectivity between stimulated electrodes. We corroborate in a particle model. This phenomenon may be used for computation in the same way that neural networks process information and has the potential to shed light on the dynamics of learning and information processing in non-neural metazoan somatic cell networks.
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Nieus T, Di Marco S, Maccione A, Amin H, Berdondini L. Investigating cell culture dynamics combining high density recordings with dimensional reduction techniques. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2016; 2015:3759-62. [PMID: 26737111 DOI: 10.1109/embc.2015.7319211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High density multielectrode array recordings with CMOS-MEAs allow to monitor cell culture activity with unprecedent details respect to previous recording techniques. This is clarifying how network activity develops and is motivating the development of novel data analysis tools. Here, in order to advance in the exploitation of the richness of these large-scale array recordings, we introduce a principal component analysis approach that aims at improving on existing methodologies to describe neural activity events within large networks.
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12
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Braun E, Marom S. Universality, complexity and the praxis of biology: Two case studies. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2015; 53:68-72. [PMID: 25903120 DOI: 10.1016/j.shpsc.2015.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
The phenomenon of biology provides a prime example for a naturally occurring complex system. The approach to this complexity reflects the tension between a reductionist, reverse-engineering stance, and more abstract, systemic ones. Both of us are reductionists, but our observations challenge reductionism, at least the naive version of it. Here we describe the challenge, focusing on two universal characteristics of biological complexity: two-way microscopic-macroscopic degeneracy, and lack of time scale separation within and between levels of organization. These two features and their consequences for the praxis of experimental biology, reflect inherent difficulties in separating the dynamics of any given level of organization from the coupled dynamics of all other levels, including the environment within which the system is embedded. Where these difficulties are not deeply acknowledged, the impacts of fallacies that are inherent to naive reductionism are significant. In an era where technology enables experimental high-resolution access to numerous observables, the challenge faced by the mature reductionist-identification of relevant microscopic variables-becomes more demanding than ever. The demonstrations provided here are taken from two very different biological realizations: populations of microorganisms and populations of neurons, thus making the lesson potentially general.
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Affiliation(s)
- Erez Braun
- Technion-Israel Institute of Technology, Israel
| | - Shimon Marom
- Technion-Israel Institute of Technology, Israel.
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13
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Carrillo-Reid L, Lopez-Huerta VG, Garcia-Munoz M, Theiss S, Arbuthnott GW. Cell Assembly Signatures Defined by Short-Term Synaptic Plasticity in Cortical Networks. Int J Neural Syst 2015; 25:1550026. [PMID: 26173906 DOI: 10.1142/s0129065715500264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cell assembly (CA) hypothesis has been used as a conceptual framework to explain how groups of neurons form memories. CAs are defined as neuronal pools with synchronous, recurrent and sequential activity patterns. However, neuronal interactions and synaptic properties that define CAs signatures have been difficult to examine because identities and locations of assembly members are usually unknown. In order to study synaptic properties that define CAs, we used optical and electrophysiological approaches to record activity of identified neurons in mouse cortical cultures. Population analysis and graph theory techniques allowed us to find sequential patterns that represent repetitive transitions between network states. Whole cell pair recordings of neurons participating in repeated sequences demonstrated that synchrony is exhibited by groups of neurons with strong synaptic connectivity (concomitant firing) showing short-term synaptic depression (STD), whereas alternation (sequential firing) is seen in groups of neurons with weaker synaptic connections showing short-term synaptic facilitation (STF). Decreasing synaptic weights of a network promoted the generation of sequential activity patterns, whereas increasing synaptic weights restricted state transitions. Thus in simple cortical networks of real neurons, basic signatures of CAs, the properties that underlie perception and memory in Hebb's original description, are already present.
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Affiliation(s)
| | - Violeta G Lopez-Huerta
- Brain Mechanisms for Behavior Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan
| | - Marianela Garcia-Munoz
- Brain Mechanisms for Behavior Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan
| | | | - Gordon W Arbuthnott
- Brain Mechanisms for Behavior Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan
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14
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Renault R, Sukenik N, Descroix S, Malaquin L, Viovy JL, Peyrin JM, Bottani S, Monceau P, Moses E, Vignes M. Combining microfluidics, optogenetics and calcium imaging to study neuronal communication in vitro. PLoS One 2015; 10:e0120680. [PMID: 25901914 PMCID: PMC4406441 DOI: 10.1371/journal.pone.0120680] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/05/2015] [Indexed: 11/19/2022] Open
Abstract
In this paper we report the combination of microfluidics, optogenetics and calcium imaging as a cheap and convenient platform to study synaptic communication between neuronal populations in vitro. We first show that Calcium Orange indicator is compatible in vitro with a commonly used Channelrhodopsine-2 (ChR2) variant, as standard calcium imaging conditions did not alter significantly the activity of transduced cultures of rodent primary neurons. A fast, robust and scalable process for micro-chip fabrication was developed in parallel to build micro-compartmented cultures. Coupling optical fibers to each micro-compartment allowed for the independent control of ChR2 activation in the different populations without crosstalk. By analyzing the post-stimuli activity across the different populations, we finally show how this platform can be used to evaluate quantitatively the effective connectivity between connected neuronal populations.
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Affiliation(s)
- Renaud Renault
- MSC (Université Paris-Diderot, CNRS-UMR 7057), 5 Rue Thomas Mann, 75013 Paris, France
- Physicochimie Curie (Institut Curie, CNRS-UMR 168, UPMC), Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France
- Department of Complex Systems, Weizmann Institute, Rehovot, Israel
| | - Nirit Sukenik
- Department of Complex Systems, Weizmann Institute, Rehovot, Israel
| | - Stéphanie Descroix
- Physicochimie Curie (Institut Curie, CNRS-UMR 168, UPMC), Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Laurent Malaquin
- Physicochimie Curie (Institut Curie, CNRS-UMR 168, UPMC), Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Jean-Louis Viovy
- Physicochimie Curie (Institut Curie, CNRS-UMR 168, UPMC), Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Jean-Michel Peyrin
- Biological Adaptation and Ageing (CNRS, UMR 8256), F-75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, B2A, Institut de Biologie Paris Seine, F-75005, Paris, France
| | - Samuel Bottani
- MSC (Université Paris-Diderot, CNRS-UMR 7057), 5 Rue Thomas Mann, 75013 Paris, France
| | - Pascal Monceau
- MSC (Université Paris-Diderot, CNRS-UMR 7057), 5 Rue Thomas Mann, 75013 Paris, France
| | - Elisha Moses
- Department of Complex Systems, Weizmann Institute, Rehovot, Israel
| | - Maéva Vignes
- Physicochimie Curie (Institut Curie, CNRS-UMR 168, UPMC), Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France
- Biological Adaptation and Ageing (CNRS, UMR 8256), F-75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, B2A, Institut de Biologie Paris Seine, F-75005, Paris, France
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de Santos-Sierra D, Sendiña-Nadal I, Leyva I, Almendral JA, Ayali A, Anava S, Sánchez-Ávila C, Boccaletti S. Graph-based unsupervised segmentation algorithm for cultured neuronal networks' structure characterization and modeling. Cytometry A 2014; 87:513-23. [DOI: 10.1002/cyto.a.22591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/27/2014] [Accepted: 10/28/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel de Santos-Sierra
- Centre for Biomedical Technology, Universidad Politécnica de Madrid; Madrid Spain
- Group of Biometrics, Biosignals and Security, Universidad Politécnica de Madrid; Madrid Spain
| | - Irene Sendiña-Nadal
- Centre for Biomedical Technology, Universidad Politécnica de Madrid; Madrid Spain
- Complex Systems Group, Universidad Rey Juan Carlos; Madrid Spain
| | - Inmaculada Leyva
- Centre for Biomedical Technology, Universidad Politécnica de Madrid; Madrid Spain
- Complex Systems Group, Universidad Rey Juan Carlos; Madrid Spain
| | - Juan A. Almendral
- Centre for Biomedical Technology, Universidad Politécnica de Madrid; Madrid Spain
- Complex Systems Group, Universidad Rey Juan Carlos; Madrid Spain
| | - Amir Ayali
- Department of Zoology; Tel Aviv University; Tel Aviv Israel
| | - Sarit Anava
- Department of Zoology; Tel Aviv University; Tel Aviv Israel
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School, Tel Aviv University; Tel Aviv Israel
| | - Carmen Sánchez-Ávila
- Group of Biometrics, Biosignals and Security, Universidad Politécnica de Madrid; Madrid Spain
| | - Stefano Boccaletti
- Embassy of Italy in Tel Aviv; Tel Aviv Israel
- CNR-Istituto dei Sistemi Complessi; Florence Italy
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16
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Lavi A, Sheinin A, Shapira R, Zelmanoff D, Ashery U. DOC2B and Munc13-1 differentially regulate neuronal network activity. ACTA ACUST UNITED AC 2013; 24:2309-23. [PMID: 23537531 DOI: 10.1093/cercor/bht081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alterations in the levels of synaptic proteins affect synaptic transmission and synaptic plasticity. However, the precise effects on neuronal network activity are still enigmatic. Here, we utilized microelectrode array (MEA) to elucidate how manipulation of the presynaptic release process affects the activity of neuronal networks. By combining pharmacological tools and genetic manipulation of synaptic proteins, we show that overexpression of DOC2B and Munc13-1, proteins known to promote vesicular maturation and release, elicits opposite effects on the activity of the neuronal network. Although both cause an increase in the overall number of spikes, the distribution of spikes is different. While DOC2B enhances, Munc13-1 reduces the firing rate within bursts of spikes throughout the network; however, Munc13-1 increases the rate of network bursts. DOC2B's effects were mimicked by Strontium that elevates asynchronous release but not by a DOC2B mutant that enhances spontaneous release rate. This suggests for the first time that increased asynchronous release on the single-neuron level promotes bursting activity in the network level. This innovative study demonstrates the complementary role of the network level in explaining the physiological relevance of the cellular activity of presynaptic proteins and the transformation of synaptic release manipulation from the neuron to the network level.
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Affiliation(s)
- Ayal Lavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anton Sheinin
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronit Shapira
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Daniel Zelmanoff
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Uri Ashery
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Biffi E, Piraino F, Pedrocchi A, Fiore GB, Ferrigno G, Redaelli A, Menegon A, Rasponi M. A microfluidic platform for controlled biochemical stimulation of twin neuronal networks. BIOMICROFLUIDICS 2012; 6:24106-2410610. [PMID: 22655017 PMCID: PMC3360721 DOI: 10.1063/1.3699975] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/16/2012] [Indexed: 05/04/2023]
Abstract
Spatially and temporally resolved delivery of soluble factors is a key feature for pharmacological applications. In this framework, microfluidics coupled to multisite electrophysiology offers great advantages in neuropharmacology and toxicology. In this work, a microfluidic device for biochemical stimulation of neuronal networks was developed. A micro-chamber for cell culturing, previously developed and tested for long term neuronal growth by our group, was provided with a thin wall, which partially divided the cell culture region in two sub-compartments. The device was reversibly coupled to a flat micro electrode array and used to culture primary neurons in the same microenvironment. We demonstrated that the two fluidically connected compartments were able to originate two parallel neuronal networks with similar electrophysiological activity but functionally independent. Furthermore, the device allowed to connect the outlet port to a syringe pump and to transform the static culture chamber in a perfused one. At 14 days invitro, sub-networks were independently stimulated with a test molecule, tetrodotoxin, a neurotoxin known to block action potentials, by means of continuous delivery. Electrical activity recordings proved the ability of the device configuration to selectively stimulate each neuronal network individually. The proposed microfluidic approach represents an innovative methodology to perform biological, pharmacological, and electrophysiological experiments on neuronal networks. Indeed, it allows for controlled delivery of substances to cells, and it overcomes the limitations due to standard drug stimulation techniques. Finally, the twin network configuration reduces biological variability, which has important outcomes on pharmacological and drug screening.
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Choi JH, Kim JH, Heo R, Lee KJ. Modulating the precision of recurrent bursts in cultured neural networks. PHYSICAL REVIEW LETTERS 2012; 108:138103. [PMID: 22540729 DOI: 10.1103/physrevlett.108.138103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Indexed: 05/31/2023]
Abstract
Synchronized bursts are a very common feature in biological neural networks, and they play an important role in various brain functions and neurological diseases. This Letter investigates "recurrent synchronized bursts" induced by a single pulse stimulation in cultured networks of rat cortical neurons. We look at how the precision in their arrival times can be modified by a noble time-delayed stimulation protocol, which we term as "Δt training." The emergence of recurrent bursts and the change of the precision in their arrival times can be explained by the stochastic resonance of a damped, subthreshold, neural oscillation.
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Affiliation(s)
- Joon Ho Choi
- Center for Cell Dynamics and Department of Physics, Korea University, Seoul 136-701, Korea
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19
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Tanada N, Sakurai T, Mitsuno H, Bakkum DJ, Kanzaki R, Takahashi H. Dissociated neuronal culture expressing ionotropic odorant receptors as a hybrid odorant biosensor—proof-of-concept study. Analyst 2012; 137:3452-8. [DOI: 10.1039/c2an35058k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Maffezzoli A, Wanke E. Explorative Data Analysis of In-Vitro Neuronal Network Behavior Based on an Unsupervised Learning Approach. Mach Learn 2012. [DOI: 10.4018/978-1-60960-818-7.ch812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the present chapter authors want to expose new insights in the field of Computational Neuroscience at regard to the study of neuronal networks grown in vitro. Such kind of analyses can exploit the availability of a huge amount of data thanks to the use of Multi Electrode Arrays (MEA), a multi-channel technology which allows capturing the activity of several different neuronal cells for long time recordings. Given the possibility of simultaneous targeting of various sites, neuroscientists are so applying such recent technology for various researches. The chapter begins by giving a brief presentation of MEA technology and of the data produced in output, punctuating some of the pros and cons of MEA recordings. Then we present an overview of the analytical techniques applied in order to extrapolate the hidden information from available data. Then we shall explain the approach we developed and applied on MEAs prepared in our cell culture laboratory, consisting of statistical methods capturing the main features of the spiking, in particular bursting, activity of various neuron, and performing data dimensionality reduction and clustering, in order to classify neurons according to their spiking properties having showed correlated features. Finally the chapter wants to furnish to neuroscientists an overview about the quantitative analysis of in-vitro spiking activity data recorded via MEA technology and to give an example of explorative analysis applied on MEA data. Such study is based on methods from Statistics and Machine Learning or Computer Science but at the same time strictly related to neurophysiological interpretations of the putative pharmacological manipulation of synaptic connections and mode of firing, with the final aim to extract new information and knowledge about neuronal networks behavior and organization.
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Affiliation(s)
| | - E. Wanke
- Università degli Studi di Milano-Bicocca, Italy
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21
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Self-organizing circuit assembly through spatiotemporally coordinated neuronal migration within geometric constraints. PLoS One 2011; 6:e28156. [PMID: 22132234 PMCID: PMC3222678 DOI: 10.1371/journal.pone.0028156] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 11/02/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Neurons are dynamically coupled with each other through neurite-mediated adhesion during development. Understanding the collective behavior of neurons in circuits is important for understanding neural development. While a number of genetic and activity-dependent factors regulating neuronal migration have been discovered on single cell level, systematic study of collective neuronal migration has been lacking. Various biological systems are shown to be self-organized, and it is not known if neural circuit assembly is self-organized. Besides, many of the molecular factors take effect through spatial patterns, and coupled biological systems exhibit emergent property in response to geometric constraints. How geometric constraints of the patterns regulate neuronal migration and circuit assembly of neurons within the patterns remains unexplored. METHODOLOGY/PRINCIPAL FINDINGS We established a two-dimensional model for studying collective neuronal migration of a circuit, with hippocampal neurons from embryonic rats on Matrigel-coated self-assembled monolayers (SAMs). When the neural circuit is subject to geometric constraints of a critical scale, we found that the collective behavior of neuronal migration is spatiotemporally coordinated. Neuronal somata that are evenly distributed upon adhesion tend to aggregate at the geometric center of the circuit, forming mono-clusters. Clustering formation is geometry-dependent, within a critical scale from 200 µm to approximately 500 µm. Finally, somata clustering is neuron-type specific, and glutamatergic and GABAergic neurons tend to aggregate homo-philically. CONCLUSIONS/SIGNIFICANCE We demonstrate self-organization of neural circuits in response to geometric constraints through spatiotemporally coordinated neuronal migration, possibly via mechanical coupling. We found that such collective neuronal migration leads to somata clustering, and mono-cluster appears when the geometric constraints fall within a critical scale. The discovery of geometry-dependent collective neuronal migration and the formation of somata clustering in vitro shed light on neural development in vivo.
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Shein-Idelson M, Ben-Jacob E, Hanein Y. Engineered neuronal circuits: a new platform for studying the role of modular topology. FRONTIERS IN NEUROENGINEERING 2011; 4:10. [PMID: 21991254 PMCID: PMC3180629 DOI: 10.3389/fneng.2011.00010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 08/23/2011] [Indexed: 12/05/2022]
Abstract
Neuron–glia cultures serve as a valuable model system for exploring the bio-molecular activity of single cells. Since neurons in culture can be conveniently recorded with great fidelity from many sites simultaneously, it has long been suggested that uniform cultured neurons may also be used to investigate network-level mechanisms pertinent to information processing, activity propagation, memory, and learning. But how much of the functionality of neural circuits can be retained in vitro remains an open question. Recent studies utilizing patterned networks suggest that they provide a most useful platform to address fundamental questions in neuroscience. Here we review recent efforts in the realm of patterned networks’ activity investigations. We give a brief overview of the patterning methods and experimental approaches commonly employed in the field, and summarize the main results reported in the literature. The general picture that emerges from these reports indicates that patterned networks with uniform connectivity do not exhibit unique activity patterns. Rather, their activity is very similar to that of unpatterned uniform networks. However, by breaking the connectivity homogeneity, using a modular architecture, it is possible to introduce pronounced topology-related gating and delay effects. These findings suggest that patterned cultured networks may serve as a new platform for studying the role of modularity in neuronal circuits.
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23
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Eytan D. Representation and learning in neuronal networks: a conceptual nervous system approach. Rambam Maimonides Med J 2011; 2:e0054. [PMID: 23908812 PMCID: PMC3678800 DOI: 10.5041/rmmj.10054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The work presented in this review describes the use of large cortical networks developing ex vivo, in a culture dish, to study principles underlying synchronization, adaptation, learning, and representation in neuronal assemblies. The motivation to study neuronal networks ex vivo is outlined together with a short description of recent results in this field. Following a short description of the experimental system, a set of basic results will be presented that concern self-organization of activity, dynamical and functional properties of neurons and networks in response to external stimulation. This short review ends with an outline of future questions and research directions.
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24
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From foundational issues in artificial intelligence to intelligent memristive nano-devices. INT J MACH LEARN CYB 2011. [DOI: 10.1007/s13042-011-0016-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Biffi E, Menegon A, Regalia G, Maida S, Ferrigno G, Pedrocchi A. A new cross-correlation algorithm for the analysis of "in vitro" neuronal network activity aimed at pharmacological studies. J Neurosci Methods 2011; 199:321-7. [PMID: 21605596 DOI: 10.1016/j.jneumeth.2011.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/08/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022]
Abstract
Modern drug discovery for Central Nervous System pathologies has recently focused its attention to in vitro neuronal networks as models for the study of neuronal activities. Micro Electrode Arrays (MEAs), a widely recognized tool for pharmacological investigations, enable the simultaneous study of the spiking activity of discrete regions of a neuronal culture, providing an insight into the dynamics of networks. Taking advantage of MEAs features and making the most of the cross-correlation analysis to assess internal parameters of a neuronal system, we provide an efficient method for the evaluation of comprehensive neuronal network activity. We developed an intra network burst correlation algorithm, we evaluated its sensitivity and we explored its potential use in pharmacological studies. Our results demonstrate the high sensitivity of this algorithm and the efficacy of this methodology in pharmacological dose-response studies, with the advantage of analyzing the effect of drugs on the comprehensive correlative properties of integrated neuronal networks.
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Affiliation(s)
- E Biffi
- Politecnico di Milano, Bioengineering Department, Neuroengineering and Medical Robotics Laboratory, p.zza Leonardo da Vinci 32, 20133 Milano, Italy.
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26
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Shein Idelson M, Ben-Jacob E, Hanein Y. Innate synchronous oscillations in freely-organized small neuronal circuits. PLoS One 2010; 5:e14443. [PMID: 21203438 PMCID: PMC3010988 DOI: 10.1371/journal.pone.0014443] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/30/2010] [Indexed: 12/03/2022] Open
Abstract
Background Information processing in neuronal networks relies on the network's ability to generate temporal patterns of action potentials. Although the nature of neuronal network activity has been intensively investigated in the past several decades at the individual neuron level, the underlying principles of the collective network activity, such as the synchronization and coordination between neurons, are largely unknown. Here we focus on isolated neuronal clusters in culture and address the following simple, yet fundamental questions: What is the minimal number of cells needed to exhibit collective dynamics? What are the internal temporal characteristics of such dynamics and how do the temporal features of network activity alternate upon crossover from minimal networks to large networks? Methodology/Principal Findings We used network engineering techniques to induce self-organization of cultured networks into neuronal clusters of different sizes. We found that small clusters made of as few as 40 cells already exhibit spontaneous collective events characterized by innate synchronous network oscillations in the range of 25 to 100 Hz. The oscillation frequency of each network appeared to be independent of cluster size. The duration and rate of the network events scale with cluster size but converge to that of large uniform networks. Finally, the investigation of two coupled clusters revealed clear activity propagation with master/slave asymmetry. Conclusions/Significance The nature of the activity patterns observed in small networks, namely the consistent emergence of similar activity across networks of different size and morphology, suggests that neuronal clusters self-regulate their activity to sustain network bursts with internal oscillatory features. We therefore suggest that clusters of as few as tens of cells can serve as a minimal but sufficient functional network, capable of sustaining oscillatory activity. Interestingly, the frequencies of these oscillations are similar those observed in vivo.
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Affiliation(s)
| | - Eshel Ben-Jacob
- School of Physics, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (EB-J); (YH)
| | - Yael Hanein
- School of Electrical Engineering, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (EB-J); (YH)
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27
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Feldt S, Wang JX, Shtrahman E, Dzakpasu R, Olariu E, Zochowski M. Functional clustering in hippocampal cultures: relating network structure and dynamics. Phys Biol 2010; 7:046004. [PMID: 20978314 DOI: 10.1088/1478-3975/7/4/046004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures.
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Affiliation(s)
- S Feldt
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA.
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28
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Shteingart H, Raichman N, Baruchi I, Ben-Jacob E. Wrestling model of the repertoire of activity propagation modes in quadruple neural networks. Front Comput Neurosci 2010; 4. [PMID: 20890451 PMCID: PMC2947946 DOI: 10.3389/fncom.2010.00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 07/14/2010] [Indexed: 11/18/2022] Open
Abstract
The spontaneous activity of engineered quadruple cultured neural networks (of four-coupled sub-networks) exhibits a repertoire of different types of mutual synchronization events. Each event corresponds to a specific activity propagation mode (APM) defined by the order of activity propagation between the sub-networks. We statistically characterized the frequency of spontaneous appearance of the different types of APMs. The relative frequencies of the APMs were then examined for their power-law properties. We found that the frequencies of appearance of the leading (most frequent) APMs have close to constant algebraic ratio reminiscent of Zipf's scaling of words. We show that the observations are consistent with a simplified “wrestling” model. This model represents an extension of the “boxing arena” model which was previously proposed to describe the ratio between the two activity modes in two coupled sub-networks. The additional new element in the “wrestling” model presented here is that the firing within each network is modeled by a time interval generator with similar intra-network Lévy distribution. We modeled the different burst-initiation zones’ interaction by competition between the stochastic generators with Gaussian inter-network variability. Estimation of the model parameters revealed similarity across different cultures while the inter-burst-interval of the cultures was similar across different APMs as numerical simulation of the model predicts.
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Affiliation(s)
- Hanan Shteingart
- Interdisciplinary Center for Neural Computation, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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29
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Phase-dependent effects of stimuli locked to oscillatory activity in cultured cortical networks. Biophys J 2010; 98:2452-8. [PMID: 20513388 DOI: 10.1016/j.bpj.2010.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 02/05/2010] [Accepted: 02/16/2010] [Indexed: 11/20/2022] Open
Abstract
The archetypal activity pattern in cultures of dissociated neurons is spontaneous network-wide bursting. Bursts may interfere with controlled activation of synaptic plasticity, but can be suppressed by the application of stimuli at a sufficient rate. We sinusoidally modulated (4 Hz) the pulse rate of random background stimulation (RBS) and found that cultures were more active, burst less frequently, and expressed oscillatory activity. Next, we studied the effect of phase-locked tetani (four pulses, 200 s(-1)) on network activity. Tetani were applied to one electrode at the peak or trough of mRBS stimulation. We found that when tetani were applied at the peak of modulated RBS (mRBS), a significant potentiation of poststimulus histograms (PSTHs) occurred. Conversely, tetani applied at the trough resulted in a small but insignificant depression of PSTHs. In addition to PSTHs, electrode-specific firing rate profiles within spontaneous bursts before and after mRBS were analyzed. Here, significant changes in firing rate profiles were found only for stimulation at the peak of mRBS. Our study shows that rhythmic activity in culture is possible, and that the network responds differentially to strong stimuli depending on the phase at which they are delivered. This suggests that plasticity mechanisms may be differentially accessible in an oscillatory state.
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30
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Gandolfo M, Maccione A, Tedesco M, Martinoia S, Berdondini L. Tracking burst patterns in hippocampal cultures with high-density CMOS-MEAs. J Neural Eng 2010; 7:056001. [PMID: 20720282 DOI: 10.1088/1741-2560/7/5/056001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work, we investigate the spontaneous bursting behaviour expressed by in vitro hippocampal networks by using a high-resolution CMOS-based microelectrode array (MEA), featuring 4096 electrodes, inter-electrode spacing of 21 µm and temporal resolution of 130 µs. In particular, we report an original development of an adapted analysis method enabling us to investigate spatial and temporal patterns of activity and the interplay between successive network bursts (NBs). We first defined and detected NBs, and then, we analysed the spatial and temporal behaviour of these events with an algorithm based on the centre of activity trajectory. We further refined the analysis by using a technique derived from statistical mechanics, capable of distinguishing the two main phases of NBs, i.e. (i) a propagating and (ii) a reverberating phase, and by classifying the trajectory patterns. Finally, this methodology was applied to signal representations based on spike detection, i.e. the instantaneous firing rate, and directly based on voltage-coded raw data, i.e. activity movies. Results highlight the potentialities of this approach to investigate fundamental issues on spontaneous neuronal dynamics and suggest the hypothesis that neurons operate in a sort of 'team' to the perpetuation of the transmission of the same information.
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Affiliation(s)
- M Gandolfo
- Neuroengineering and Bio-nano Technology Group, Department of Biophysical and Electronic Engineering, University of Genova, Vai Opera Pia 11a, 16145 Genova, Italy.
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GAFAROV F, KHUSNUTDINOV N, GALIMYANOV F. MORPHOLESS NEURONS COMPROMISE THE DEVELOPMENT OF CORTICAL CONNECTIVITY. J Integr Neurosci 2009; 8:35-48. [DOI: 10.1142/s0219635209002058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 02/05/2009] [Indexed: 01/16/2023] Open
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Baruchi I, Volman V, Raichman N, Shein M, Ben-Jacob E. The emergence and properties of mutual synchronization in in vitro coupled cortical networks. Eur J Neurosci 2009; 28:1825-35. [PMID: 18973597 DOI: 10.1111/j.1460-9568.2008.06487.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the emergence of mutual synchronization and activity propagation in coupled neural networks from rat cortical cells grown on a micro-electrode array for parallel activity recording of dozens of neurons. The activity of each sub-network by itself is marked by the formation of synchronized bursting events (SBE) - short time windows of rapid neuronal firing. The joint activity of two coupled networks is characterized by the formation of mutual synchronization, i.e. the formation of SBE whose activity starts at one sub-network and then propagates to the other. The sub-networks switch roles in initiating the mutual SBE. However, spontaneous propagation (initiation) asymmetry emerges - one of the sub-networks takes on the role of initiating substantially more mutual SBE than the other, despite the fact that the two are engineered to be similar in size and cell density. Analysis of the interneuron correlations in the SBE also reveals the emergence of activity (function) asymmetry - one sub-network develops a more organized structure of correlations. We also show activity propagation and mutual synchronization in four coupled networks. Using computer simulations, we propose that the function asymmetry reflects asymmetry between the internal connectivity of the two networks, whereas the propagation asymmetry reflects asymmetry in the connectivity between the sub-networks. These results agree with the experimental findings that the initiation and function asymmetry can be separately regulated, which implies that information transfer (activity propagation) and information processing (function) can be regulated separately in coupled neural networks.
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Affiliation(s)
- Itay Baruchi
- School of Physics & Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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Shein M, Volman V, Raichman N, Hanein Y, Ben-Jacob E. Management of synchronized network activity by highly active neurons. Phys Biol 2008; 5:036008. [DOI: 10.1088/1478-3975/5/3/036008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Bakkum DJ, Chao ZC, Potter SM. Long-term activity-dependent plasticity of action potential propagation delay and amplitude in cortical networks. PLoS One 2008; 3:e2088. [PMID: 18461127 PMCID: PMC2324202 DOI: 10.1371/journal.pone.0002088] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2007] [Accepted: 04/06/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The precise temporal control of neuronal action potentials is essential for regulating many brain functions. From the viewpoint of a neuron, the specific timings of afferent input from the action potentials of its synaptic partners determines whether or not and when that neuron will fire its own action potential. Tuning such input would provide a powerful mechanism to adjust neuron function and in turn, that of the brain. However, axonal plasticity of action potential timing is counter to conventional notions of stable propagation and to the dominant theories of activity-dependent plasticity focusing on synaptic efficacies. METHODOLOGY/PRINCIPAL FINDINGS Here we show the occurrence of activity-dependent plasticity of action potential propagation delays (up to 4 ms or 40% after minutes and 13 ms or 74% after hours) and amplitudes (up to 87%). We used a multi-electrode array to induce, detect, and track changes in propagation in multiple neurons while they adapted to different patterned stimuli in controlled neocortical networks in vitro. The changes did not occur when the same stimulation was repeated while blocking ionotropic gabaergic and glutamatergic receptors. Even though induction of changes in action potential timing and amplitude depended on synaptic transmission, the expression of these changes persisted in the presence of the synaptic receptor blockers. CONCLUSIONS/SIGNIFICANCE We conclude that, along with changes in synaptic efficacy, propagation plasticity provides a cellular mechanism to tune neuronal network function in vitro and potentially learning and memory in the brain.
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Affiliation(s)
- Douglas J. Bakkum
- Laboratory for Neuroengineering, Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zenas C. Chao
- Laboratory for Neuroengineering, Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Steve M. Potter
- Laboratory for Neuroengineering, Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Raichman N, Ben-Jacob E. Identifying repeating motifs in the activation of synchronized bursts in cultured neuronal networks. J Neurosci Methods 2008; 170:96-110. [PMID: 18281097 DOI: 10.1016/j.jneumeth.2007.12.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 12/23/2007] [Accepted: 12/30/2007] [Indexed: 11/15/2022]
Affiliation(s)
- Nadav Raichman
- School of Physics and Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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36
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Ben-Jacob E, Hanein Y. Carbon nanotube micro-electrodes for neuronal interfacing. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b805878b] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Fuchs E, Ayali A, Robinson A, Hulata E, Ben-Jacob E. Coemergence of regularity and complexity during neural network development. Dev Neurobiol 2007; 67:1802-14. [PMID: 17701997 DOI: 10.1002/dneu.20557] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the growing recognition that rhythmic and oscillatory patterns are widespread in the brain and play important roles in all aspects of the function of our nervous system, there has been a resurgence of interest in neuronal synchronized bursting activity. Here, we were interested in understanding the development of synchronized bursts as information-bearing neuronal activity patterns. For that, we have monitored the morphological organization and spontaneous activity of neuronal networks cultured on multielectrode-arrays during their self-executed evolvement from a mixture of dissociated cells into an active network. Complex collective network electrical activity evolved from sporadic firing patterns of the single neurons. On the system (network) level, the activity was marked by bursting events with interneuronal synchronization and nonarbitrary temporal ordering. We quantified these individual-to-collective activity transitions using newly-developed system level quantitative measures of time series regularity and complexity. We found that individual neuronal activity before synchronization was characterized by high regularity and low complexity. During neuronal wiring, there was a transient period of reorganization marked by low regularity, which then leads to coemergence of elevated regularity and functional (nonstochastic) complexity. We further investigated the morphology-activity interplay by modeling artificial neuronal networks with different topological organizations and connectivity schemes. The simulations support our experimental results by showing increased levels of complexity of neuronal activity patterns when neurons are wired up and organized in clusters (similar to mature real networks), as well as network-level activity regulation once collective activity forms.
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Affiliation(s)
- E Fuchs
- Department of Zoology, Tel-Aviv University, Tel-Aviv 69978, Israel
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Madhavan R, Chao ZC, Potter SM. Plasticity of recurring spatiotemporal activity patterns in cortical networks. Phys Biol 2007; 4:181-93. [PMID: 17928657 DOI: 10.1088/1478-3975/4/3/005] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
How do neurons encode and store information for long periods of time? Recurring patterns of activity have been reported in various cortical structures and were suggested to play a role in information processing and memory. To study the potential role of bursts of action potentials in memory mechanisms, we investigated patterns of spontaneous multi-single-unit activity in dissociated rat cortical cultures in vitro. Spontaneous spikes were recorded from networks of approximately 50 000 neurons and glia cultured on a grid of 60 extracellular substrate- embedded electrodes (multi-electrode arrays). These networks expressed spontaneous culture- wide bursting from approximately one week in vitro. During bursts, a large portion of the active electrodes showed elevated levels of firing. Spatiotemporal activity patterns within spontaneous bursts were clustered using a correlation-based clustering algorithm, and the occurrences of these burst clusters were tracked over several hours. This analysis revealed spatiotemporally diverse bursts occurring in well-defined patterns, which remained stable for several hours. Activity evoked by strong local tetanic stimulation resulted in significant changes in the occurrences of spontaneous bursts belonging to different clusters, indicating that the dynamical flow of information in the neuronal network had been altered. The diversity of spatiotemporal structure and long-term stability of spontaneous bursts together with their plastic nature strongly suggests that such network patterns could be used as codes for information transfer and the expression of memories stored in cortical networks.
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Affiliation(s)
- Radhika Madhavan
- Laboratory for Neuroengineering, Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
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Li Y, Zhou W, Li X, Zeng S, Luo Q. Dynamics of learning in cultured neuronal networks with antagonists of glutamate receptors. Biophys J 2007; 93:4151-8. [PMID: 17766359 PMCID: PMC2098743 DOI: 10.1529/biophysj.107.111153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cognitive dysfunction may result from abnormality of ionotropic glutamate receptors. Although various forms of synaptic plasticity in learning that rely on altering of glutamate receptors have been considered, the evidence is insufficient from an informatics view. Dynamics could reflect neuroinformatics encoding, including temporal pattern encoding, spatial pattern encoding, and energy distribution. Discovering informatics encoding is fundamental and crucial to understanding the working principle of the neural system. In this article, we analyzed the dynamic characteristics of response activities during learning training in cultured hippocampal networks under normal and abnormal conditions of ionotropic glutamate receptors, respectively. The rate, which is one of the temporal configurations, was decreased markedly by inhibition of alpha-amino-3-hydroxy-5-methylisoxazole-4-proprionic acid (AMPA) receptors. Moreover, the energy distribution in different characteristic frequencies was changed markedly by inhibition of AMPA receptors. Spatial configurations, including regularization, correlation, and synchrony, were changed significantly by inhibition of N-methyl-d-aspartate receptors. These results suggest that temporal pattern encoding and energy distribution of response activities in cultured hippocampal neuronal networks during learning training are modulated by AMPA receptors, whereas spatial pattern encoding of response activities is modulated by N-methyl-d-aspartate receptors.
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Affiliation(s)
- Yanling Li
- The Key Laboratory of Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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