1
|
Nag Chowdhury S, Anwar MS, Ghosh D. Cluster formation due to repulsive spanning trees in attractively coupled networks. Phys Rev E 2024; 109:044314. [PMID: 38755838 DOI: 10.1103/physreve.109.044314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/22/2024] [Indexed: 05/18/2024]
Abstract
Ensembles of coupled nonlinear oscillators are a popular paradigm and an ideal benchmark for analyzing complex collective behaviors. The onset of cluster synchronization is found to be at the core of various technological and biological processes. The current literature has investigated cluster synchronization by focusing mostly on the case of attractive coupling among the oscillators. However, the case of two coexisting competing interactions is of practical interest due to their relevance in diverse natural settings, including neuronal networks consisting of excitatory and inhibitory neurons, the coevolving social model with voters of opposite opinions, and ecological plant communities with both facilitation and competition, to name a few. In the present article, we investigate the impact of repulsive spanning trees on cluster formation within a connected network of attractively coupled limit-cycle oscillators. We successfully predict which nodes belong to each cluster and the emergent frustration of the connected networks independent of the particular local dynamics at the network nodes. We also determine local asymptotic stability of the cluster states using an approach based on the formulation of a master stability function. We additionally validate the emergence of solitary states and antisynchronization for some specific choices of spanning trees and networks.
Collapse
Affiliation(s)
- Sayantan Nag Chowdhury
- Department of Environmental Science and Policy, University of California, Davis, Davis, California 95616, USA
- Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Md Sayeed Anwar
- Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Dibakar Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata 700108, India
| |
Collapse
|
2
|
López-León CF, Planet R, Soriano J. Preparation and Mechano-Functional Characterization of PEGylated Fibrin Hydrogels: Impact of Thrombin Concentration. Gels 2024; 10:116. [PMID: 38391447 PMCID: PMC10888336 DOI: 10.3390/gels10020116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Three-dimensional (3D) neuronal cultures grown in hydrogels are promising platforms to design brain-like neuronal networks in vitro. However, the optimal properties of such cultures must be tuned to ensure a hydrogel matrix sufficiently porous to promote healthy development but also sufficiently rigid for structural support. Such an optimization is difficult since it implies the exploration of different hydrogel compositions and, at the same time, a functional analysis to validate neuronal culture viability. To advance in this quest, here we present a combination of a rheological protocol and a network-based functional analysis to investigate PEGylated fibrin hydrogel networks with gradually higher stiffness, achieved by increasing the concentration of thrombin. We observed that moderate thrombin concentrations of 10% and 25% in volume shaped healthy networks, although the functional traits depended on the hydrogel stiffness, which was much higher for the latter concentration. Thrombin concentrations of 65% or higher led to networks that did not survive. Our results illustrate the difficulties and limitations in preparing 3D neuronal networks, and stress the importance of combining a mechano-structural characterization of a biomaterial with a functional one.
Collapse
Affiliation(s)
- Clara F López-León
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelon, E-08028 Barcelona, Spain
| | - Ramon Planet
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelon, E-08028 Barcelona, Spain
| | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelon, E-08028 Barcelona, Spain
| |
Collapse
|
3
|
O'Neill KM, Anderson ED, Mukherjee S, Gandu S, McEwan SA, Omelchenko A, Rodriguez AR, Losert W, Meaney DF, Babadi B, Firestein BL. Time-dependent homeostatic mechanisms underlie brain-derived neurotrophic factor action on neural circuitry. Commun Biol 2023; 6:1278. [PMID: 38110605 PMCID: PMC10728104 DOI: 10.1038/s42003-023-05638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Plasticity and homeostatic mechanisms allow neural networks to maintain proper function while responding to physiological challenges. Despite previous work investigating morphological and synaptic effects of brain-derived neurotrophic factor (BDNF), the most prevalent growth factor in the central nervous system, how exposure to BDNF manifests at the network level remains unknown. Here we report that BDNF treatment affects rodent hippocampal network dynamics during development and recovery from glutamate-induced excitotoxicity in culture. Importantly, these effects are not obvious when traditional activity metrics are used, so we delve more deeply into network organization, functional analyses, and in silico simulations. We demonstrate that BDNF partially restores homeostasis by promoting recovery of weak and medium connections after injury. Imaging and computational analyses suggest these effects are caused by changes to inhibitory neurons and connections. From our in silico simulations, we find that BDNF remodels the network by indirectly strengthening weak excitatory synapses after injury. Ultimately, our findings may explain the difficulties encountered in preclinical and clinical trials with BDNF and also offer information for future trials to consider.
Collapse
Affiliation(s)
- Kate M O'Neill
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
- Biomedical Engineering Graduate Program, Rutgers University, Piscataway, NJ, USA
- Institute for Physical Science & Technology, University of Maryland, College Park, MD, USA
| | - Erin D Anderson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Shoutik Mukherjee
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
| | - Srinivasa Gandu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
- Cell and Developmental Biology Graduate Program, Rutgers University, Piscataway, NJ, USA
| | - Sara A McEwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
- Neuroscience Graduate Program, Rutgers University, Piscataway, NJ, USA
| | - Anton Omelchenko
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
- Neuroscience Graduate Program, Rutgers University, Piscataway, NJ, USA
| | - Ana R Rodriguez
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
- Biomedical Engineering Graduate Program, Rutgers University, Piscataway, NJ, USA
| | - Wolfgang Losert
- Department of Physics, University of Maryland, College Park, MD, USA
- Institute for Physical Science & Technology, University of Maryland, College Park, MD, USA
| | - David F Meaney
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Behtash Babadi
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
| | - Bonnie L Firestein
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.
| |
Collapse
|
4
|
Zanini G, Parodi G, Chiappalone M, Martinoia S. Investigating the reliability of the evoked response in human iPSCs-derived neuronal networks coupled to micro-electrode arrays. APL Bioeng 2023; 7:046121. [PMID: 38130601 PMCID: PMC10735322 DOI: 10.1063/5.0174227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
In vitro models of neuronal networks have emerged as a potent instrument for gaining deeper insights into the intricate mechanisms governing the human brain. Notably, the integration of human-induced pluripotent stem cells (hiPSCs) with micro-electrode arrays offers a means to replicate and dissect both the structural and functional elements of the human brain within a controlled in vitro environment. Given that neuronal communication relies on the emission of electrical (and chemical) stimuli, the employment of electrical stimulation stands as a mean to comprehensively interrogate neuronal assemblies, to better understand their inherent electrophysiological dynamics. However, the establishment of standardized stimulation protocols for cultures derived from hiPSCs is still lacking, thereby hindering the precise delineation of efficacious parameters to elicit responses. To fill this gap, the primary objective of this study resides in delineating effective parameters for the electrical stimulation of hiPSCs-derived neuronal networks, encompassing the determination of voltage amplitude and stimulation frequency able to evoke reliable and stable responses. This study represents a stepping-stone in the exploration of efficacious stimulation parameters, thus broadening the electrophysiological activity profiling of neural networks sourced from human-induced pluripotent stem cells.
Collapse
Affiliation(s)
- Giorgia Zanini
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | - Giulia Parodi
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | | | - Sergio Martinoia
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| |
Collapse
|
5
|
Yamamoto H, Spitzner FP, Takemuro T, Buendía V, Murota H, Morante C, Konno T, Sato S, Hirano-Iwata A, Levina A, Priesemann V, Muñoz MA, Zierenberg J, Soriano J. Modular architecture facilitates noise-driven control of synchrony in neuronal networks. SCIENCE ADVANCES 2023; 9:eade1755. [PMID: 37624893 PMCID: PMC10456864 DOI: 10.1126/sciadv.ade1755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
High-level information processing in the mammalian cortex requires both segregated processing in specialized circuits and integration across multiple circuits. One possible way to implement these seemingly opposing demands is by flexibly switching between states with different levels of synchrony. However, the mechanisms behind the control of complex synchronization patterns in neuronal networks remain elusive. Here, we use precision neuroengineering to manipulate and stimulate networks of cortical neurons in vitro, in combination with an in silico model of spiking neurons and a mesoscopic model of stochastically coupled modules to show that (i) a modular architecture enhances the sensitivity of the network to noise delivered as external asynchronous stimulation and that (ii) the persistent depletion of synaptic resources in stimulated neurons is the underlying mechanism for this effect. Together, our results demonstrate that the inherent dynamical state in structured networks of excitable units is determined by both its modular architecture and the properties of the external inputs.
Collapse
Affiliation(s)
- Hideaki Yamamoto
- Research Institute of Electrical Communication (RIEC), Tohoku University, Sendai, Japan
- Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - F. Paul Spitzner
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Taiki Takemuro
- Research Institute of Electrical Communication (RIEC), Tohoku University, Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Victor Buendía
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- Departamento de Electromagnetismo y Física de la Materia, Universidad de Granada, Granada, Spain
| | - Hakuba Murota
- Research Institute of Electrical Communication (RIEC), Tohoku University, Sendai, Japan
- Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Carla Morante
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Tomohiro Konno
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Shigeo Sato
- Research Institute of Electrical Communication (RIEC), Tohoku University, Sendai, Japan
- Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Ayumi Hirano-Iwata
- Research Institute of Electrical Communication (RIEC), Tohoku University, Sendai, Japan
- Graduate School of Engineering, Tohoku University, Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Japan
| | - Anna Levina
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Miguel A. Muñoz
- Departamento de Electromagnetismo y Física de la Materia, Universidad de Granada, Granada, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
| | | | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| |
Collapse
|
6
|
Razban RM, Pachter JA, Dill KA, Mujica-Parodi LR. Early path dominance as a principle for neurodevelopment. Proc Natl Acad Sci U S A 2023; 120:e2218007120. [PMID: 37053187 PMCID: PMC10120000 DOI: 10.1073/pnas.2218007120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023] Open
Abstract
We perform targeted attack, a systematic computational unlinking of the network, to analyze its effects on global communication across the brain network through its giant cluster. Across diffusion magnetic resonance images from individuals in the UK Biobank, Adolescent Brain Cognitive Development Study and Developing Human Connectome Project, we find that targeted attack procedures on increasing white matter tract lengths and densities are remarkably invariant to aging and disease. Time-reversing the attack computation suggests a mechanism for how brains develop, for which we derive an analytical equation using percolation theory. Based on a close match between theory and experiment, our results demonstrate that tracts are limited to emanate from regions already in the giant cluster and tracts that appear earliest in neurodevelopment are those that become the longest and densest.
Collapse
Affiliation(s)
- Rostam M. Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
| | - Jonathan Asher Pachter
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY11794
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY11794
- Department of Chemistry, Stony Brook University, Stony Brook, NY11794
| | - Lilianne R. Mujica-Parodi
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY11794
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY11794
- Program in Neuroscience, Stony Brook University, Stony Brook, NY11794
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA02129
| |
Collapse
|
7
|
Neuronal Cultures: Exploring Biophysics, Complex Systems, and Medicine in a Dish. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Neuronal cultures are one of the most important experimental models in modern interdisciplinary neuroscience, allowing to investigate in a control environment the emergence of complex behavior from an ensemble of interconnected neurons. Here, I review the research that we have conducted at the neurophysics laboratory at the University of Barcelona over the last 15 years, describing first the neuronal cultures that we prepare and the associated tools to acquire and analyze data, to next delve into the different research projects in which we actively participated to progress in the understanding of open questions, extend neuroscience research on new paradigms, and advance the treatment of neurological disorders. I finish the review by discussing the drawbacks and limitations of neuronal cultures, particularly in the context of brain-like models and biomedicine.
Collapse
|
8
|
Nag Chowdhury S, Rakshit S, Hens C, Ghosh D. Interlayer antisynchronization in degree-biased duplex networks. Phys Rev E 2023; 107:034313. [PMID: 37073037 DOI: 10.1103/physreve.107.034313] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/09/2023] [Indexed: 04/20/2023]
Abstract
With synchronization being one of nature's most ubiquitous collective behaviors, the field of network synchronization has experienced tremendous growth, leading to significant theoretical developments. However, most previous studies consider uniform connection weights and undirected networks with positive coupling. In the present article, we incorporate the asymmetry in a two-layer multiplex network by assigning the ratio of the adjacent nodes' degrees as the weights to the intralayer edges. Despite the presence of degree-biased weighting mechanism and attractive-repulsive coupling strengths, we are able to find the necessary conditions for intralayer synchronization and interlayer antisynchronization and test whether these two macroscopic states can withstand demultiplexing in a network. During the occurrence of these two states, we analytically calculate the oscillator's amplitude. In addition to deriving the local stability conditions for interlayer antisynchronization via the master stability function approach, we also construct a suitable Lyapunov function to determine a sufficient condition for global stability. We provide numerical evidence to show the necessity of negative interlayer coupling strength for the occurrence of antisynchronization, and such repulsive interlayer coupling coefficients cannot destroy intralayer synchronization.
Collapse
Affiliation(s)
- Sayantan Nag Chowdhury
- Department of Environmental Science and Policy, University of California, Davis, California 95616, USA
- Technology Innovation Hub (TIH), IDEAS (Institute of Data Engineering Analytics and Science Foundation), Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | - Sarbendu Rakshit
- Department of Mechanical Engineering, University of California, Riverside, California 92521, USA
| | - Chittaranjan Hens
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
| | - Dibakar Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| |
Collapse
|
9
|
Montalà-Flaquer M, López-León CF, Tornero D, Houben AM, Fardet T, Monceau P, Bottani S, Soriano J. Rich dynamics and functional organization on topographically designed neuronal networks in vitro. iScience 2022; 25:105680. [PMID: 36567712 PMCID: PMC9768383 DOI: 10.1016/j.isci.2022.105680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/05/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Neuronal cultures are a prominent experimental tool to understand complex functional organization in neuronal assemblies. However, neurons grown on flat surfaces exhibit a strongly coherent bursting behavior with limited functionality. To approach the functional richness of naturally formed neuronal circuits, here we studied neuronal networks grown on polydimethylsiloxane (PDMS) topographical patterns shaped as either parallel tracks or square valleys. We followed the evolution of spontaneous activity in these cultures along 20 days in vitro using fluorescence calcium imaging. The networks were characterized by rich spatiotemporal activity patterns that comprised from small regions of the culture to its whole extent. Effective connectivity analysis revealed the emergence of spatially compact functional modules that were associated with both the underpinned topographical features and predominant spatiotemporal activity fronts. Our results show the capacity of spatial constraints to mold activity and functional organization, bringing new opportunities to comprehend the structure-function relationship in living neuronal circuits.
Collapse
Affiliation(s)
- Marc Montalà-Flaquer
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain,Universitat de Barcelona Institute of Complex Systems (UBICS), E-08028 Barcelona, Spain
| | - Clara F. López-León
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain,Universitat de Barcelona Institute of Complex Systems (UBICS), E-08028 Barcelona, Spain
| | - Daniel Tornero
- Laboratory of Neural Stem Cells and Brain Damage, Institute of Neurosciences, University of Barcelona, E-08036 Barcelona, Spain
| | - Akke Mats Houben
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain,Universitat de Barcelona Institute of Complex Systems (UBICS), E-08028 Barcelona, Spain
| | - Tanguy Fardet
- Laboratoire Matière et Systèmes Complexes, Université de Paris, UMR 7057 CNRS, Paris, France,University of Tübingen, Tübingen, Germany,Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Pascal Monceau
- Laboratoire Matière et Systèmes Complexes, Université de Paris, UMR 7057 CNRS, Paris, France
| | - Samuel Bottani
- Laboratoire Matière et Systèmes Complexes, Université de Paris, UMR 7057 CNRS, Paris, France
| | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain,Universitat de Barcelona Institute of Complex Systems (UBICS), E-08028 Barcelona, Spain,Corresponding author
| |
Collapse
|
10
|
Pallares Di Nunzio M, Montani F. Spike Timing-Dependent Plasticity with Enhanced Long-Term Depression Leads to an Increase of Statistical Complexity. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1384. [PMID: 37420407 DOI: 10.3390/e24101384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 07/09/2023]
Abstract
Synaptic plasticity is characterized by remodeling of existing synapses caused by strengthening and/or weakening of connections. This is represented by long-term potentiation (LTP) and long-term depression (LTD). The occurrence of a presynaptic spike (or action potential) followed by a temporally nearby postsynaptic spike induces LTP; conversely, if the postsynaptic spike precedes the presynaptic spike, it induces LTD. This form of synaptic plasticity induction depends on the order and timing of the pre- and postsynaptic action potential, and has been termed spike time-dependent plasticity (STDP). After an epileptic seizure, LTD plays an important role as a depressor of synapses, which may lead to their complete disappearance together with that of their neighboring connections until days after the event. Added to the fact that after an epileptic seizure the network seeks to regulate the excess activity through two key mechanisms: depressed connections and neuronal death (eliminating excitatory neurons from the network), LTD becomes of great interest in our study. To investigate this phenomenon, we develop a biologically plausible model that privileges LTD at the triplet level while maintaining the pairwise structure in the STPD and study how network dynamics are affected as neuronal damage increases. We find that the statistical complexity is significantly higher for the network where LTD presented both types of interactions. While in the case where the STPD is defined with purely pairwise interactions an increase is observed as damage becomes higher for both Shannon Entropy and Fisher information.
Collapse
Affiliation(s)
| | - Fernando Montani
- Instituto de Física de La Plata (IFLP), CONICET-UNLP, La Plata B1900, Buenos Aires, Argentina
| |
Collapse
|
11
|
Warm D, Bassetti D, Schroer J, Luhmann HJ, Sinning A. Spontaneous Activity Predicts Survival of Developing Cortical Neurons. Front Cell Dev Biol 2022; 10:937761. [PMID: 36035995 PMCID: PMC9399774 DOI: 10.3389/fcell.2022.937761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity plays a crucial role in brain development by coordinating the integration of immature neurons into emerging cortical networks. High levels and complex patterns of spontaneous activity are generally associated with low rates of apoptosis in the cortex. However, whether spontaneous activity patterns directly encode for survival of individual cortical neurons during development remains an open question. Here, we longitudinally investigated spontaneous activity and apoptosis in developing cortical cultures, combining extracellular electrophysiology with calcium imaging. These experiments demonstrated that the early occurrence of calcium transients was strongly linked to neuronal survival. Silent neurons exhibited a higher probability of cell death, whereas high frequency spiking and burst behavior were almost exclusively detected in surviving neurons. In local neuronal clusters, activity of neighboring neurons exerted a pro-survival effect, whereas on the functional level, networks with a high modular topology were associated with lower cell death rates. Using machine learning algorithms, cell fate of individual neurons was predictable through the integration of spontaneous activity features. Our results indicate that high frequency spiking activity constrains apoptosis in single neurons through sustained calcium rises and thereby consolidates networks in which a high modular topology is reached during early development.
Collapse
|
12
|
Antonello PC, Varley TF, Beggs J, Porcionatto M, Sporns O, Faber J. Self-organization of in vitro neuronal assemblies drives to complex network topology. eLife 2022; 11:74921. [PMID: 35708741 PMCID: PMC9203058 DOI: 10.7554/elife.74921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/01/2022] [Indexed: 12/17/2022] Open
Abstract
Activity-dependent self-organization plays an important role in the formation of specific and stereotyped connectivity patterns in neural circuits. By combining neuronal cultures, and tools with approaches from network neuroscience and information theory, we can study how complex network topology emerges from local neuronal interactions. We constructed effective connectivity networks using a transfer entropy analysis of spike trains recorded from rat embryo dissociated hippocampal neuron cultures between 6 and 35 days in vitro to investigate how the topology evolves during maturation. The methodology for constructing the networks considered the synapse delay and addressed the influence of firing rate and population bursts as well as spurious effects on the inference of connections. We found that the number of links in the networks grew over the course of development, shifting from a segregated to a more integrated architecture. As part of this progression, three significant aspects of complex network topology emerged. In agreement with previous in silico and in vitro studies, a small-world architecture was detected, largely due to strong clustering among neurons. Additionally, the networks developed in a modular topology, with most modules comprising nearby neurons. Finally, highly active neurons acquired topological characteristics that made them important nodes to the network and integrators of modules. These findings leverage new insights into how neuronal effective network topology relates to neuronal assembly self-organization mechanisms.
Collapse
Affiliation(s)
- Priscila C Antonello
- Department of Biochemistry - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Thomas F Varley
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, United States.,Department of Informatics, Computing, and Engineering, Indiana University, Bloomington, United States
| | - John Beggs
- Department of Physics, Indiana University, Bloomington, United States
| | - Marimélia Porcionatto
- Department of Biochemistry - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, United States
| | - Jean Faber
- Department of Neurology and Neurosurgery - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| |
Collapse
|
13
|
Mechanistic insights into ultrasonic neurostimulation of disconnected neurons using single short pulses. Brain Stimul 2022; 15:769-779. [PMID: 35561960 DOI: 10.1016/j.brs.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/06/2023] Open
Abstract
Ultrasonic neurostimulation is a potentially potent noninvasive therapy, whose mechanism has yet to be elucidated. We designed a system capable of applying ultrasound with minimal reflections to neuronal cultures. Synaptic transmission was pharmacologically controlled, eliminating network effects, enabling examination of single-cell processes. Short single pulses of low-intensity ultrasound were applied, and time-locked responses were examined using calcium imaging. Low-pressure (0.35MPa) ultrasound directly stimulated ∼20% of pharmacologically disconnected neurons, regardless of membrane poration. Stimulation was resistant to the blockade of several purinergic receptor and mechanosensitive ion channel types. Stimulation was blocked, however, by suppression of action potentials. Surprisingly, even extremely short (4μs) pulses were effective, stimulating ∼8% of the neurons. Lower-pressure pulses (0.35MPa) were less effective than higher-pressure ones (0.65MPa). Attrition effects dominated, with no indication of compromised viability. Our results detract from theories implicating cavitation, heating, non-transient membrane pores >1.5nm, pre-synaptic release, or gradual effects. They implicate a post-synaptic mechanism upstream of the action potential, and narrow down the list of possible targets involved.
Collapse
|
14
|
Kim M, Harris RE, DaSilva AF, Lee U. Explosive Synchronization-Based Brain Modulation Reduces Hypersensitivity in the Brain Network: A Computational Model Study. Front Comput Neurosci 2022; 16:815099. [PMID: 35311218 PMCID: PMC8927545 DOI: 10.3389/fncom.2022.815099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/18/2022] [Indexed: 11/29/2022] Open
Abstract
Fibromyalgia (FM) is a chronic pain condition that is characterized by hypersensitivity to multimodal sensory stimuli, widespread pain, and fatigue. We have previously proposed explosive synchronization (ES), a phenomenon wherein a small perturbation to a network can lead to an abrupt state transition, as a potential mechanism of the hypersensitive FM brain. Therefore, we hypothesized that converting a brain network from ES to general synchronization (GS) may reduce the hypersensitivity of FM brain. To find an effective brain network modulation to convert ES into GS, we constructed a large-scale brain network model near criticality (i.e., an optimally balanced state between order and disorders), which reflects brain dynamics in conscious wakefulness, and adjusted two parameters: local structural connectivity and signal randomness of target brain regions. The network sensitivity to global stimuli was compared between the brain networks before and after the modulation. We found that only increasing the local connectivity of hubs (nodes with intense connections) changes ES to GS, reducing the sensitivity, whereas other types of modulation such as decreasing local connectivity, increasing and decreasing signal randomness are not effective. This study would help to develop a network mechanism-based brain modulation method to reduce the hypersensitivity in FM.
Collapse
Affiliation(s)
- MinKyung Kim
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, United States
- Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Richard E. Harris
- Chronic Pain and Fatigue Research Center, Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Alexandre F. DaSilva
- Headache & Orofacial Pain Effort Laboratory, Biologic & Materials Sciences Department, University of Michigan School of Dentistry, Ann Arbor, MI, United States
| | - UnCheol Lee
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, United States
- Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, MI, United States
- *Correspondence: UnCheol Lee,
| |
Collapse
|
15
|
Contreras-Hernández E, Chávez D, Hernández E, Rudomin P. Discrete field potentials produced by coherent activation of spinal dorsal horn neurons. Exp Brain Res 2022; 240:665-686. [PMID: 35001174 DOI: 10.1007/s00221-021-06286-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
In addition to the action potentials generated by the ongoing activation of single dorsal horn neurons in the anesthetized cat, we often recorded small negative field potentials with a fast-rising phase and a slow decay (dIFPs). These potentials could be separated in different classes, each with a specific and rather constant shape and amplitude. They were largest in spinal laminae III-V and gradually faded at deeper locations, without showing the polarity reversal displayed at these depths by the focal potentials produced by stimulation of muscle and cutaneous afferents. We propose that the dIFPs are postsynaptic field potentials generated by strongly coupled sets of dorsal horn neurons displaying a spatial orientation that generates closed field potentials in response to stimulation of high-threshold cutaneous and muscle afferents. These neuronal sets could form part of the spinal inhibitory circuitry that mediates presynaptic inhibition and Ib non-reciprocal postsynaptic inhibition and could be involved in the sensory-motor transformations activated by stimulation of high-threshold cutaneous afferents.
Collapse
Affiliation(s)
- Enrique Contreras-Hernández
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies, National Polytechnic Institute, Ciudad de México, México
| | - Diógenes Chávez
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies, National Polytechnic Institute, Ciudad de México, México
| | - Edson Hernández
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies, National Polytechnic Institute, Ciudad de México, México
| | - Pablo Rudomin
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies, National Polytechnic Institute, Ciudad de México, México. .,El Colegio Nacional, Ciudad de México, México.
| |
Collapse
|
16
|
Rapisardi G, Kryven I, Arenas A. Percolation in networks with local homeostatic plasticity. Nat Commun 2022; 13:122. [PMID: 35013243 PMCID: PMC8748765 DOI: 10.1038/s41467-021-27736-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/30/2021] [Indexed: 12/03/2022] Open
Abstract
Percolation is a process that impairs network connectedness by deactivating links or nodes. This process features a phase transition that resembles paradigmatic critical transitions in epidemic spreading, biological networks, traffic and transportation systems. Some biological systems, such as networks of neural cells, actively respond to percolation-like damage, which enables these structures to maintain their function after degradation and aging. Here we study percolation in networks that actively respond to link damage by adopting a mechanism resembling synaptic scaling in neurons. We explain critical transitions in such active networks and show that these structures are more resilient to damage as they are able to maintain a stronger connectedness and ability to spread information. Moreover, we uncover the role of local rescaling strategies in biological networks and indicate a possibility of designing smart infrastructures with improved robustness to perturbations.
Collapse
Affiliation(s)
- Giacomo Rapisardi
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, E-43007, Tarragona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ivan Kryven
- Mathematical Institute, Utrecht University, Budapestlaan 6, 3508 TA, Utrecht, The Netherlands
- Centre for Complex Systems Studies, 3584 CE, Utrecht, The Netherlands
| | - Alex Arenas
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, E-43007, Tarragona, Spain.
| |
Collapse
|
17
|
Mezzasalma SA, Grassi L, Grassi M. Physical and chemical properties of carbon nanotubes in view of mechanistic neuroscience investigations. Some outlook from condensed matter, materials science and physical chemistry. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 131:112480. [PMID: 34857266 DOI: 10.1016/j.msec.2021.112480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/08/2021] [Accepted: 10/07/2021] [Indexed: 01/17/2023]
Abstract
The open border between non-living and living matter, suggested by increasingly emerging fields of nanoscience interfaced to biological systems, requires a detailed knowledge of nanomaterials properties. An account of the wide spectrum of phenomena, belonging to physical chemistry of interfaces, materials science, solid state physics at the nanoscale and bioelectrochemistry, thus is acquainted for a comprehensive application of carbon nanotubes interphased with neuron cells. This review points out a number of conceptual tools to further address the ongoing advances in coupling neuronal networks with (carbon) nanotube meshworks, and to deepen the basic issues that govern a biological cell or tissue interacting with a nanomaterial. Emphasis is given here to the properties and roles of carbon nanotube systems at relevant spatiotemporal scales of individual molecules, junctions and molecular layers, as well as to the point of view of a condensed matter or materials scientist. Carbon nanotube interactions with blood-brain barrier, drug delivery, biocompatibility and functionalization issues are also regarded.
Collapse
Affiliation(s)
- Stefano A Mezzasalma
- Ruder Bošković Institute, Materials Physics Division, Bijeniška cesta 54, 10000 Zagreb, Croatia; Lund Institute for advanced Neutron and X-ray Science (LINXS), Lund University, IDEON Building, Delta 5, Scheelevägen 19, 223 70 Lund, Sweden.
| | - Lucia Grassi
- Department of Engineering and Architecture, Trieste University, via Valerio 6, I-34127 Trieste, Italy
| | - Mario Grassi
- Department of Engineering and Architecture, Trieste University, via Valerio 6, I-34127 Trieste, Italy.
| |
Collapse
|
18
|
Zendrikov D, Paraskevov A. Emergent population activity in metric-free and metric networks of neurons with stochastic spontaneous spikes and dynamic synapses. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2020.11.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
19
|
Ghirga S, Chiodo L, Marrocchio R, Orlandi JG, Loppini A. Inferring Excitatory and Inhibitory Connections in Neuronal Networks. ENTROPY 2021; 23:e23091185. [PMID: 34573810 PMCID: PMC8465838 DOI: 10.3390/e23091185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
The comprehension of neuronal network functioning, from most basic mechanisms of signal transmission to complex patterns of memory and decision making, is at the basis of the modern research in experimental and computational neurophysiology. While mechanistic knowledge of neurons and synapses structure increased, the study of functional and effective networks is more complex, involving emergent phenomena, nonlinear responses, collective waves, correlation and causal interactions. Refined data analysis may help in inferring functional/effective interactions and connectivity from neuronal activity. The Transfer Entropy (TE) technique is, among other things, well suited to predict structural interactions between neurons, and to infer both effective and structural connectivity in small- and large-scale networks. To efficiently disentangle the excitatory and inhibitory neural activities, in the article we present a revised version of TE, split in two contributions and characterized by a suited delay time. The method is tested on in silico small neuronal networks, built to simulate the calcium activity as measured via calcium imaging in two-dimensional neuronal cultures. The inhibitory connections are well characterized, still preserving a high accuracy for excitatory connections prediction. The method could be applied to study effective and structural interactions in systems of excitable cells, both in physiological and in pathological conditions.
Collapse
Affiliation(s)
- Silvia Ghirga
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia (IIT), Viale Regina Elena 291, 00161 Roma, Italy;
| | - Letizia Chiodo
- Engineering Department, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00154 Roma, Italy;
| | - Riccardo Marrocchio
- Institute of Sound and Vibration Research, Highfield Campus, University of Southampton, Southampton SO17 1BJ, UK;
| | | | - Alessandro Loppini
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia (IIT), Viale Regina Elena 291, 00161 Roma, Italy;
- Engineering Department, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00154 Roma, Italy;
- Correspondence:
| |
Collapse
|
20
|
O'Neil SD, Rácz B, Brown WE, Gao Y, Soderblom EJ, Yasuda R, Soderling SH. Action potential-coupled Rho GTPase signaling drives presynaptic plasticity. eLife 2021; 10:63756. [PMID: 34269176 PMCID: PMC8285108 DOI: 10.7554/elife.63756] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/06/2021] [Indexed: 12/30/2022] Open
Abstract
In contrast to their postsynaptic counterparts, the contributions of activity-dependent cytoskeletal signaling to presynaptic plasticity remain controversial and poorly understood. To identify and evaluate these signaling pathways, we conducted a proteomic analysis of the presynaptic cytomatrix using in vivo biotin identification (iBioID). The resultant proteome was heavily enriched for actin cytoskeleton regulators, including Rac1, a Rho GTPase that activates the Arp2/3 complex to nucleate branched actin filaments. Strikingly, we find Rac1 and Arp2/3 are closely associated with synaptic vesicle membranes in adult mice. Using three independent approaches to alter presynaptic Rac1 activity (genetic knockout, spatially restricted inhibition, and temporal optogenetic manipulation), we discover that this pathway negatively regulates synaptic vesicle replenishment at both excitatory and inhibitory synapses, bidirectionally sculpting short-term synaptic depression. Finally, we use two-photon fluorescence lifetime imaging to show that presynaptic Rac1 activation is coupled to action potentials by voltage-gated calcium influx. Thus, this study uncovers a previously unrecognized mechanism of actin-regulated short-term presynaptic plasticity that is conserved across excitatory and inhibitory terminals. It also provides a new proteomic framework for better understanding presynaptic physiology, along with a blueprint of experimental strategies to isolate the presynaptic effects of ubiquitously expressed proteins.
Collapse
Affiliation(s)
| | - Bence Rácz
- Department of Anatomy and Histology, University of Veterinary Medicine, Budapest, Hungary
| | - Walter Evan Brown
- Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Yudong Gao
- Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Erik J Soderblom
- Department of Cell Biology, Duke University Medical Center, Durham, United States.,Proteomics and Metabolomics Shared Resource and Center for Genomic and Computational Biology, Duke University Medical Center, Durham, United States
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, United States
| | - Scott H Soderling
- Department of Neurobiology, Duke University Medical Center, Durham, United States.,Department of Cell Biology, Duke University Medical Center, Durham, United States
| |
Collapse
|
21
|
Parkinson's disease patient-specific neuronal networks carrying the LRRK2 G2019S mutation unveil early functional alterations that predate neurodegeneration. NPJ PARKINSONS DISEASE 2021; 7:55. [PMID: 34215735 PMCID: PMC8253775 DOI: 10.1038/s41531-021-00198-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 06/02/2021] [Indexed: 11/08/2022]
Abstract
A deeper understanding of early disease mechanisms occurring in Parkinson’s disease (PD) is needed to reveal restorative targets. Here we report that human induced pluripotent stem cell (iPSC)-derived dopaminergic neurons (DAn) obtained from healthy individuals or patients harboring LRRK2 PD-causing mutation can create highly complex networks with evident signs of functional maturation over time. Compared to control neuronal networks, LRRK2 PD patients’ networks displayed an elevated bursting behavior, in the absence of neurodegeneration. By combining functional calcium imaging, biophysical modeling, and DAn-lineage tracing, we found a decrease in DAn neurite density that triggered overall functional alterations in PD neuronal networks. Our data implicate early dysfunction as a prime focus that may contribute to the initiation of downstream degenerative pathways preceding DAn loss in PD, highlighting a potential window of opportunity for pre-symptomatic assessment of chronic degenerative diseases.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Neuronal circuits overcome imbalance in excitation and inhibition by adjusting connection numbers. Proc Natl Acad Sci U S A 2021; 118:2018459118. [PMID: 33723048 DOI: 10.1073/pnas.2018459118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The interplay between excitation and inhibition is crucial for neuronal circuitry in the brain. Inhibitory cell fractions in the neocortex and hippocampus are typically maintained at 15 to 30%, which is assumed to be important for stable dynamics. We have studied systematically the role of precisely controlled excitatory/inhibitory (E/I) cellular ratios on network activity using mice hippocampal cultures. Surprisingly, networks with varying E/I ratios maintain stable bursting dynamics. Interburst intervals remain constant for most ratios, except in the extremes of 0 to 10% and 90 to 100% inhibitory cells. Single-cell recordings and modeling suggest that networks adapt to chronic alterations of E/I compositions by balancing E/I connectivity. Gradual blockade of inhibition substantiates the agreement between the model and experiment and defines its limits. Combining measurements of population and single-cell activity with theoretical modeling, we provide a clearer picture of how E/I balance is preserved and where it fails in living neuronal networks.
Collapse
|
24
|
Altered Fast Synaptic Transmission in a Mouse Model of DNM1-Associated Developmental Epileptic Encephalopathy. eNeuro 2021; 8:ENEURO.0269-20.2020. [PMID: 33372033 PMCID: PMC7986544 DOI: 10.1523/eneuro.0269-20.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/05/2022] Open
Abstract
Developmental epileptic encephalopathies (DEEs) are severe seizure disorders that occur in infants and young children, characterized by developmental delay, cognitive decline, and early mortality. Recent efforts have identified a wide variety of genetic variants that cause DEEs. Among these, variants in the DNM1 gene have emerged as definitive causes of DEEs, including infantile spasms and Lennox–Gastaut syndrome. A mouse model of Dnm1-associated DEE, known as “Fitful” (Dnm1Ftfl), recapitulates key features of the disease, including spontaneous seizures, early lethality, and neuronal degeneration. Previous work showed that DNM1 is a key regulator of synaptic vesicle (SV) endocytosis and synaptic transmission and suggested that inhibitory neurotransmission may be more reliant on DNM1 function than excitatory transmission. The Dnm1Ftfl variant is thought to encode a dominant negative DNM1 protein; however, the effects of the Dnm1Ftfl variant on synaptic transmission are largely unknown. To understand these synaptic effects, we recorded from pairs of cultured mouse cortical neurons and characterized all four major connection types [excitation of excitation (E-E), inhibition of inhibition (I-I), E-I, I-E]. Miniature and spontaneous EPSCs and IPSCs were larger, but less frequent, at all Dnm1Ftfl synaptic types, and Dnm1Ftfl neurons had reduced expression of excitatory and inhibitory SV markers. Baseline evoked transmission, however, was reduced only at inhibitory synapses onto excitatory neurons, because of a smaller pool of releasable SVs. In addition to these synaptic alterations, Dnm1Ftfl neurons degenerated later in development, although their activity levels were reduced, suggesting that Dnm1Ftfl may impair synaptic transmission and neuronal health through distinct mechanisms.
Collapse
|
25
|
Chowdhury SN, Rakshit S, Buldú JM, Ghosh D, Hens C. Antiphase synchronization in multiplex networks with attractive and repulsive interactions. Phys Rev E 2021; 103:032310. [PMID: 33862752 DOI: 10.1103/physreve.103.032310] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
A series of recent publications, within the framework of network science, have focused on the coexistence of mixed attractive and repulsive (excitatory and inhibitory) interactions among the units within the same system, motivated by the analogies with spin glasses as well as to neural networks, or ecological systems. However, most of these investigations have been restricted to single layer networks, requiring further analysis of the complex dynamics and particular equilibrium states that emerge in multilayer configurations. This article investigates the synchronization properties of dynamical systems connected through multiplex architectures in the presence of attractive intralayer and repulsive interlayer connections. This setting enables the emergence of antisynchronization, i.e., intralayer synchronization coexisting with antiphase dynamics between coupled systems of different layers. We demonstrate the existence of a transition from interlayer antisynchronization to antiphase synchrony in any connected bipartite multiplex architecture when the repulsive coupling is introduced through any spanning tree of a single layer. We identify, analytically, the required graph topologies for interlayer antisynchronization and its interplay with intralayer and antiphase synchronization. Next, we analytically derive the invariance of intralayer synchronization manifold and calculate the attractor size of each oscillator exhibiting interlayer antisynchronization together with intralayer synchronization. The necessary conditions for the existence of interlayer antisynchronization along with intralayer synchronization are given and numerically validated by considering Stuart-Landau oscillators. Finally, we also analytically derive the local stability condition of the interlayer antisynchronization state using the master stability function approach.
Collapse
Affiliation(s)
- Sayantan Nag Chowdhury
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata-700108, India
| | - Sarbendu Rakshit
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata-700108, India
| | - Javier M Buldú
- Laboratory of Biological Networks, Center for Biomedical Technology-UPM, Madrid 28223, Spain
- Complex Systems Group and GISC, Universidad Rey Juan Carlos, Móstoles 28933, Spain
- Unmanned Systems Research Institute, Northwestern Polytechnical University, Xi'an 710072, China
| | - Dibakar Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata-700108, India
| | - Chittaranjan Hens
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata-700108, India
| |
Collapse
|
26
|
Estévez-Priego E, Teller S, Granell C, Arenas A, Soriano J. Functional strengthening through synaptic scaling upon connectivity disruption in neuronal cultures. Netw Neurosci 2020; 4:1160-1180. [PMID: 33409434 PMCID: PMC7781611 DOI: 10.1162/netn_a_00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/15/2020] [Indexed: 11/16/2022] Open
Abstract
An elusive phenomenon in network neuroscience is the extent of neuronal activity remodeling upon damage. Here, we investigate the action of gradual synaptic blockade on the effective connectivity in cortical networks in vitro. We use two neuronal cultures configurations-one formed by about 130 neuronal aggregates and another one formed by about 600 individual neurons-and monitor their spontaneous activity upon progressive weakening of excitatory connectivity. We report that the effective connectivity in all cultures exhibits a first phase of transient strengthening followed by a second phase of steady deterioration. We quantify these phases by measuring GEFF, the global efficiency in processing network information. We term hyperefficiency the sudden strengthening of GEFF upon network deterioration, which increases by 20-50% depending on culture type. Relying on numerical simulations we reveal the role of synaptic scaling, an activity-dependent mechanism for synaptic plasticity, in counteracting the perturbative action, neatly reproducing the observed hyperefficiency. Our results demonstrate the importance of synaptic scaling as resilience mechanism.
Collapse
Affiliation(s)
- Estefanía Estévez-Priego
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Sara Teller
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Clara Granell
- GOTHAM Lab – Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
| | - Alex Arenas
- Departament d’Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, Tarragona, Spain
| | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| |
Collapse
|
27
|
Zheng Q, Shen J, Xu Y. Turing instability in the reaction-diffusion network. Phys Rev E 2020; 102:062215. [PMID: 33466067 DOI: 10.1103/physreve.102.062215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
It is an established fact that a positive wave number plays an essential role in Turing instability. However, the impact of a negative wave number on Turing instability remains unclear. Here, we investigate the effect of the weights and nodes on Turing instability in the FitzHugh-Nagumo model, and theoretical results reveal genesis of Turing instability due to a negative wave number through the stability analysis and mean-field method. We obtain the Turing instability region in the continuous media system and provide the relationship between degree and eigenvalue of the network matrix by the Gershgorin circle theorem. Furthermore, the Turing instability condition about nodes and the weights is provided in the network-organized system. Additionally, we found chaotic behavior because of interactions between I Turing instability and II Turing instability. Besides, we apply this above analysis to explaining the mechanism of the signal conduction of the inhibitory neuron. We find a moderate coupling strength and corresponding number of links are necessary to the signal conduction.
Collapse
Affiliation(s)
- Qianqian Zheng
- School of Science, Xuchang University, Xuchang 461000, China
- Department of Applied Mathematics, Northwestern Polytechnical University, Xian 710072, China
| | - Jianwei Shen
- School of Mathematics and Statistics, North China University of Water Resources and Electric Power, Zhengzhou 450046, China
| | - Yong Xu
- Department of Applied Mathematics, Northwestern Polytechnical University, Xian 710072, China
| |
Collapse
|
28
|
Ludl AA, Soriano J. Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits. Front Comput Neurosci 2020; 14:77. [PMID: 32982710 PMCID: PMC7488194 DOI: 10.3389/fncom.2020.00077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
Scaffolds and patterned substrates are among the most successful strategies to dictate the connectivity between neurons in culture. Here, we used numerical simulations to investigate the capacity of physical obstacles placed on a flat substrate to shape structural connectivity, and in turn collective dynamics and effective connectivity, in biologically-realistic neuronal networks. We considered μ-sized obstacles placed in mm-sized networks. Three main obstacle shapes were explored, namely crosses, circles and triangles of isosceles profile. They occupied either a small area fraction of the substrate or populated it entirely in a periodic manner. From the point of view of structure, all obstacles promoted short length-scale connections, shifted the in- and out-degree distributions toward lower values, and increased the modularity of the networks. The capacity of obstacles to shape distinct structural traits depended on their density and the ratio between axonal length and substrate diameter. For high densities, different features were triggered depending on obstacle shape, with crosses trapping axons in their vicinity and triangles funneling axons along the reverse direction of their tip. From the point of view of dynamics, obstacles reduced the capacity of networks to spontaneously activate, with triangles in turn strongly dictating the direction of activity propagation. Effective connectivity networks, inferred using transfer entropy, exhibited distinct modular traits, indicating that the presence of obstacles facilitated the formation of local effective microcircuits. Our study illustrates the potential of physical constraints to shape structural blueprints and remodel collective activity, and may guide investigations aimed at mimicking organizational traits of biological neuronal circuits.
Collapse
Affiliation(s)
- Adriaan-Alexander Ludl
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.,Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain.,Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain.,Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| |
Collapse
|
29
|
Maltby CJ, Schofield JPR, Houghton SD, O’Kelly I, Vargas-Caballero M, Deinhardt K, Coldwell MJ. A 5' UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation. Nucleic Acids Res 2020; 48:9822-9839. [PMID: 32870280 PMCID: PMC7515701 DOI: 10.1093/nar/gkaa699] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/18/2022] Open
Abstract
RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodelling attributed to normal cellular function. In this study, we characterise the G4 formation of a (GGN)13 repeat found within the 5' UTR of the potassium 2-pore domain leak channel Task3 mRNA. Biophysical analyses show that this (GGN)13 repeat forms a parallel G4 in vitro exhibiting the stereotypical potassium specificity of G4s, remaining thermostable under physiological ionic conditions. Through mouse brain tissue G4-RNA immunoprecipitation, we further confirm that Task3 mRNA forms a G4 structure in vivo. The G4 is inhibitory to translation of Task3 in vitro and is overcome through activity of a G4-specific helicase DHX36, increasing K+ leak currents and membrane hyperpolarisation in HEK293 cells. Further, we observe that this G4 is fundamental to ensuring delivery of Task3 mRNA to distal primary cortical neurites. It has been shown that aberrant Task3 expression correlates with neuronal dysfunction, we therefore posit that this G4 is important in regulated local expression of Task3 leak channels that maintain K+ leak within neurons.
Collapse
Affiliation(s)
- Connor J Maltby
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - James P R Schofield
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Steven D Houghton
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Ita O’Kelly
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | | | - Katrin Deinhardt
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Mark J Coldwell
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| |
Collapse
|
30
|
Gabrieli D, Schumm SN, Vigilante NF, Parvesse B, Meaney DF. Neurodegeneration exposes firing rate dependent effects on oscillation dynamics in computational neural networks. PLoS One 2020; 15:e0234749. [PMID: 32966291 PMCID: PMC7510994 DOI: 10.1371/journal.pone.0234749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/01/2020] [Indexed: 12/26/2022] Open
Abstract
Traumatic brain injury (TBI) can lead to neurodegeneration in the injured circuitry, either through primary structural damage to the neuron or secondary effects that disrupt key cellular processes. Moreover, traumatic injuries can preferentially impact subpopulations of neurons, but the functional network effects of these targeted degeneration profiles remain unclear. Although isolating the consequences of complex injury dynamics and long-term recovery of the circuit can be difficult to control experimentally, computational networks can be a powerful tool to analyze the consequences of injury. Here, we use the Izhikevich spiking neuron model to create networks representative of cortical tissue. After an initial settling period with spike-timing-dependent plasticity (STDP), networks developed rhythmic oscillations similar to those seen in vivo. As neurons were sequentially removed from the network, population activity rate and oscillation dynamics were significantly reduced. In a successive period of network restructuring with STDP, network activity levels returned to baseline for some injury levels and oscillation dynamics significantly improved. We next explored the role that specific neurons have in the creation and termination of oscillation dynamics. We determined that oscillations initiate from activation of low firing rate neurons with limited structural inputs. To terminate oscillations, high activity excitatory neurons with strong input connectivity activate downstream inhibitory circuitry. Finally, we confirm the excitatory neuron population role through targeted neurodegeneration. These results suggest targeted neurodegeneration can play a key role in the oscillation dynamics after injury.
Collapse
Affiliation(s)
- David Gabrieli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Samantha N. Schumm
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nicholas F. Vigilante
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brandon Parvesse
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David F. Meaney
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
31
|
Serratto GM, Pizzi E, Murru L, Mazzoleni S, Pelucchi S, Marcello E, Mazzanti M, Passafaro M, Bassani S. The Epilepsy-Related Protein PCDH19 Regulates Tonic Inhibition, GABA AR Kinetics, and the Intrinsic Excitability of Hippocampal Neurons. Mol Neurobiol 2020; 57:5336-5351. [PMID: 32880860 PMCID: PMC7541378 DOI: 10.1007/s12035-020-02099-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022]
Abstract
PCDH19 encodes for protocadherin-19 (PCDH19), a cell-adhesion molecule of the cadherin superfamily preferentially expressed in the brain. PCDH19 mutations cause a neurodevelopmental syndrome named epileptic encephalopathy, early infantile, 9 (EIEE9) characterized by seizures associated with cognitive and behavioral deficits. We recently reported that PCDH19 binds the alpha subunits of GABAA receptors (GABAARs), modulating their surface availability and miniature inhibitory postsynaptic currents (mIPSCs). Here, we investigated whether PCDH19 regulatory function on GABAARs extends to the extrasynaptic receptor pool that mediates tonic current. In fact, the latter shapes neuronal excitability and network properties at the base of information processing. By combining patch-clamp recordings in whole-cell and cell-attached configurations, we provided a functional characterization of primary hippocampal neurons from embryonic rats of either sex expressing a specific PCDH19 short hairpin (sh)RNA. We first demonstrated that PCDH19 downregulation reduces GABAAR-mediated tonic current, evaluated by current shift and baseline noise analysis. Next, by single-channel recordings, we showed that PCDH19 regulates GABAARs kinetics without altering their conductance. In particular, GABAARs of shRNA-expressing neurons preferentially exhibit brief openings at the expense of long ones, thus displaying a flickering behavior. Finally, we showed that PCDH19 downregulation reduces the rheobase and increases the frequency of action potential firing, thus indicating neuronal hyperexcitability. These findings establish PCDH19 as a critical determinant of GABAAR-mediated tonic transmission and GABAARs gating, and provide the first mechanistic insights into PCDH19-related hyperexcitability and comorbidities.
Collapse
Affiliation(s)
| | - Erika Pizzi
- Department of Bioscience, University of Milan, 20133, Milan, Italy
| | - Luca Murru
- Institute of Neuroscience, CNR, 20129, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milan, Italy
| | - Sara Mazzoleni
- Institute of Neuroscience, CNR, 20129, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, 20129, Milan, Italy
| | - Silvia Pelucchi
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133, Milan, Italy
| | - Elena Marcello
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133, Milan, Italy
| | - Michele Mazzanti
- Department of Bioscience, University of Milan, 20133, Milan, Italy
| | - Maria Passafaro
- Institute of Neuroscience, CNR, 20129, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milan, Italy
| | - Silvia Bassani
- Institute of Neuroscience, CNR, 20129, Milan, Italy. .,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milan, Italy.
| |
Collapse
|
32
|
Kumar R, Huang YT, Chen CC, Tzeng SF, Chan CK. Astrocytic Regulation of Synchronous Bursting in Cortical Cultures: From Local to Global. Cereb Cortex Commun 2020; 1:tgaa053. [PMID: 34296118 PMCID: PMC8153059 DOI: 10.1093/texcom/tgaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/14/2020] [Accepted: 08/12/2020] [Indexed: 11/12/2022] Open
Abstract
Synchronous bursting (SB) is ubiquitous in neuronal networks and independent of network structure. Although it is known to be driven by glutamatergic neurotransmissions, its underlying mechanism remains unclear. Recent studies show that local glutamate recycle by astrocytes affects nearby neuronal activities, which indicate that the local dynamics might also be the origin of SBs in networks. We investigated the effects of local glutamate dynamics on SBs in both cultures developed on multielectrode array (MEA) systems and a tripartite synapse simulation. Local glutamate uptake by astrocytes was altered by pharmacological targeting of GLT-1 glutamate transporters, whereas neuronal firing activities and synaptic glutamate level was simultaneously monitored with MEA and astrocyte-specific glutamate sensors (intensity-based glutamate-sensing fluorescent reporter), respectively. Global SB properties were significantly altered on targeting GLT-1. Detailed simulation of a network with astrocytic glutamate uptake and recycle mechanisms, conforming with the experimental observations, shows that astrocytes function as a slow negative feedback to neuronal activities in the network. SB in the network can be realized as an alternation between positive and negative feedback in the neurons and astrocytes, respectively. An understanding of glutamate trafficking dynamics is of general application to explain how astrocyte malfunction can result in pathological seizure-like phenomena in neuronal systems.
Collapse
Affiliation(s)
- Ravi Kumar
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei 115, Taiwan, R.O.C
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan, R.O.C
| | - Yu-Ting Huang
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan, R.O.C
| | - Chun-Chung Chen
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan, R.O.C
| | - Shun-Fen Tzeng
- Department of Life Sciences, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C
| | - Chi-Keung Chan
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan, R.O.C
| |
Collapse
|
33
|
Fernández-García S, Orlandi JG, García-Díaz Barriga GA, Rodríguez MJ, Masana M, Soriano J, Alberch J. Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington's disease. BMC Biol 2020; 18:58. [PMID: 32466798 PMCID: PMC7254676 DOI: 10.1186/s12915-020-00794-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/12/2020] [Indexed: 12/31/2022] Open
Abstract
Background Network alterations underlying neurodegenerative diseases often precede symptoms and functional deficits. Thus, their early identification is central for improved prognosis. In Huntington’s disease (HD), the cortico-striatal networks, involved in motor function processing, are the most compromised neural substrate. However, whether the network alterations are intrinsic of the striatum or the cortex is not fully understood. Results In order to identify early HD neural deficits, we characterized neuronal ensemble calcium activity and network topology of HD striatal and cortical cultures. We used large-scale calcium imaging combined with activity-based network inference analysis. We extracted collective activity events and inferred the topology of the neuronal network in cortical and striatal primary cultures from wild-type and R6/1 mouse model of HD. Striatal, but not cortical, HD networks displayed lower activity and a lessened ability to integrate information. GABAA receptor blockade in healthy and HD striatal cultures generated similar coordinated ensemble activity and network topology, highlighting that the excitatory component of striatal system is spared in HD. Conversely, NMDA receptor activation increased individual neuronal activity while coordinated activity became highly variable and undefined. Interestingly, by boosting NMDA activity, we rectified striatal HD network alterations. Conclusions Overall, our integrative approach highlights striatal defective network integration capacity as a major contributor of basal ganglia dysfunction in HD and suggests that increased excitatory drive may serve as a potential intervention. In addition, our work provides a valuable tool to evaluate in vitro network recovery after treatment intervention in basal ganglia disorders.
Collapse
Affiliation(s)
- S Fernández-García
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
| | - J G Orlandi
- Complexity Science Group, Department of Physics and Astronomy, Faculty of Science, University of Calgary, Calgary, AB, T2N 1N4, Canada.,Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028, Barcelona, Spain
| | - G A García-Díaz Barriga
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
| | - M J Rodríguez
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
| | - M Masana
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
| | - J Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028, Barcelona, Spain.,Universitat de Barcelona Institute of Complex Systems (UBICS), 08028, Barcelona, Spain
| | - J Alberch
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain. .,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain. .,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, 08036, Barcelona, Spain.
| |
Collapse
|
34
|
Sumi T, Yamamoto H, Hirano-Iwata A. Suppression of hypersynchronous network activity in cultured cortical neurons using an ultrasoft silicone scaffold. SOFT MATTER 2020; 16:3195-3202. [PMID: 32096811 DOI: 10.1039/c9sm02432h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The spontaneous activity pattern of cortical neurons in dissociated culture is characterized by burst firing that is highly synchronized among a wide population of cells. The degree of synchrony, however, is excessively higher than that in cortical tissues. Here, we employed polydimethylsiloxane (PDMS) elastomers to establish a novel system for culturing neurons on a scaffold with an elastic modulus resembling brain tissue, and investigated the effect of the scaffold's elasticity on network activity patterns in cultured rat cortical neurons. Using whole-cell patch clamp to assess the scaffold effect on the development of synaptic connections, we found that the amplitude of excitatory postsynaptic current, as well as the frequency of spontaneous transmissions, was reduced in neuronal networks grown on an ultrasoft PDMS with an elastic modulus of 0.5 kPa. Furthermore, the ultrasoft scaffold was found to suppress neural correlations in the spontaneous activity of the cultured neuronal network. The dose of GsMTx-4, an antagonist of stretch-activated cation channels (SACs), required to reduce the generation of the events below 1.0 event per min on PDMS substrates was lower than that for neurons on a glass substrate. This suggests that the difference in the baseline level of SAC activation is a molecular mechanism underlying the alteration in neuronal network activity depending on scaffold stiffness. Our results demonstrate the potential application of PDMS with biomimetic elasticity as cell-culture scaffold for bridging the in vivo-in vitro gap in neuronal systems.
Collapse
Affiliation(s)
- Takuma Sumi
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Hideaki Yamamoto
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan. and WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Ayumi Hirano-Iwata
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan. and WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
35
|
Schumm SN, Gabrieli D, Meaney DF. Neuronal Degeneration Impairs Rhythms Between Connected Microcircuits. Front Comput Neurosci 2020; 14:18. [PMID: 32194390 PMCID: PMC7063469 DOI: 10.3389/fncom.2020.00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
Synchronization of neural activity across brain regions is critical to processes that include perception, learning, and memory. After traumatic brain injury (TBI), neuronal degeneration is one possible effect and can alter communication between neural circuits. Consequently, synchronization between neurons may change and can contribute to both lasting changes in functional brain networks and cognitive impairment in patients. However, fundamental principles relating exactly how TBI at the cellular scale affects synchronization of mesoscale circuits are not well understood. In this work, we use computational networks of Izhikevich integrate-and-fire neurons to study synchronized, oscillatory activity between clusters of neurons, which also adapt according to spike-timing-dependent plasticity (STDP). We study how the connections within and between these neuronal clusters change as unidirectional connections form between the two neuronal populations. In turn, we examine how neuronal deletion, intended to mimic the temporary or permanent loss of neurons in the mesoscale circuit, affects these dynamics. We determine synchronization of two neuronal circuits requires very modest connectivity between these populations; approximately 10% of neurons projecting from one circuit to another circuit will result in high synchronization. In addition, we find that synchronization level inversely affects the strength of connection between neuronal microcircuits - moderately synchronized microcircuits develop stronger intercluster connections than do highly synchronized circuits. Finally, we find that highly synchronized circuits are largely protected against the effects of neuronal deletion but may display changes in frequency properties across circuits with targeted neuronal loss. Together, our results suggest that strongly and weakly connected regions differ in their inherent resilience to damage and may serve different roles in a larger network.
Collapse
Affiliation(s)
- Samantha N. Schumm
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - David Gabrieli
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - David F. Meaney
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, United States
- Penn Center for Brain Injury and Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
36
|
Jensen's force and the statistical mechanics of cortical asynchronous states. Sci Rep 2019; 9:15183. [PMID: 31645611 PMCID: PMC6811577 DOI: 10.1038/s41598-019-51520-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/28/2019] [Indexed: 12/02/2022] Open
Abstract
Cortical networks are shaped by the combined action of excitatory and inhibitory interactions. Among other important functions, inhibition solves the problem of the all-or-none type of response that comes about in purely excitatory networks, allowing the network to operate in regimes of moderate or low activity, between quiescent and saturated regimes. Here, we elucidate a noise-induced effect that we call “Jensen’s force” –stemming from the combined effect of excitation/inhibition balance and network sparsity– which is responsible for generating a phase of self-sustained low activity in excitation-inhibition networks. The uncovered phase reproduces the main empirically-observed features of cortical networks in the so-called asynchronous state, characterized by low, un-correlated and highly-irregular activity. The parsimonious model analyzed here allows us to resolve a number of long-standing issues, such as proving that activity can be self-sustained even in the complete absence of external stimuli or driving. The simplicity of our approach allows for a deep understanding of asynchronous states and of the phase transitions to other standard phases it exhibits, opening the door to reconcile, asynchronous-state and critical-state hypotheses, putting them within a unified framework. We argue that Jensen’s forces are measurable experimentally and might be relevant in contexts beyond neuroscience.
Collapse
|
37
|
Okujeni S, Egert U. Self-organization of modular network architecture by activity-dependent neuronal migration and outgrowth. eLife 2019; 8:47996. [PMID: 31526478 PMCID: PMC6783273 DOI: 10.7554/elife.47996] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022] Open
Abstract
The spatial distribution of neurons and activity-dependent neurite outgrowth shape long-range interaction, recurrent local connectivity and the modularity in neuronal networks. We investigated how this mesoscale architecture develops by interaction of neurite outgrowth, cell migration and activity in cultured networks of rat cortical neurons and show that simple rules can explain variations of network modularity. In contrast to theoretical studies on activity-dependent outgrowth but consistent with predictions for modular networks, spontaneous activity and the rate of synchronized bursts increased with clustering, whereas peak firing rates in bursts increased in highly interconnected homogeneous networks. As Ca2+ influx increased exponentially with increasing network recruitment during bursts, its modulation was highly correlated to peak firing rates. During network maturation, long-term estimates of Ca2+ influx showed convergence, even for highly different mesoscale architectures, neurite extent, connectivity, modularity and average activity levels, indicating homeostatic regulation towards a common set-point of Ca2+ influx.
Collapse
Affiliation(s)
- Samora Okujeni
- Laboratory for Biomicrotechnology, Department of Microsystems Engineering-IMTEK, University of Freiburg, Freiburg, Germany.,Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Ulrich Egert
- Laboratory for Biomicrotechnology, Department of Microsystems Engineering-IMTEK, University of Freiburg, Freiburg, Germany.,Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
| |
Collapse
|
38
|
Teppola H, Aćimović J, Linne ML. Unique Features of Network Bursts Emerge From the Complex Interplay of Excitatory and Inhibitory Receptors in Rat Neocortical Networks. Front Cell Neurosci 2019; 13:377. [PMID: 31555093 PMCID: PMC6742722 DOI: 10.3389/fncel.2019.00377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022] Open
Abstract
Spontaneous network activity plays a fundamental role in the formation of functional networks during early development. The landmark of this activity is the recurrent emergence of intensive time-limited network bursts (NBs) rapidly spreading across the entire dissociated culture in vitro. The main excitatory mediators of NBs are glutamatergic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) and N-Methyl-D-aspartic-acid receptors (NMDARs) that express fast and slow ion channel kinetics, respectively. The fast inhibition of the activity is mediated through gamma-aminobutyric acid type A receptors (GABAARs). Although the AMPAR, NMDAR and GABAAR kinetics have been biophysically characterized in detail at the monosynaptic level in a variety of brain areas, the unique features of NBs emerging from the kinetics and the complex interplay of these receptors are not well understood. The goal of this study is to analyze the contribution of fast GABAARs on AMPAR- and NMDAR- mediated spontaneous NB activity in dissociated neonatal rat cortical cultures at 3 weeks in vitro. The networks were probed by both acute and gradual application of each excitatory receptor antagonist and combinations of acute excitatory and inhibitory receptor antagonists. At the same time, the extracellular network-wide activity was recorded with microelectrode arrays (MEAs). We analyzed the characteristic NB measures extracted from NB rate profiles and the distributions of interspike intervals, interburst intervals, and electrode recruitment time as well as the similarity of spatio-temporal patterns of network activity under different receptor antagonists. We show that NBs were rapidly initiated and recruited as well as diversely propagated by AMPARs and temporally and spatially maintained by NMDARs. GABAARs reduced the spiking frequency in AMPAR-mediated networks and dampened the termination of NBs in NMDAR-mediated networks as well as slowed down the recruitment of activity in all networks. Finally, we show characteristic super bursts composed of slow NBs with highly repetitive spatio-temporal patterns in gradually AMPAR blocked networks. To the best of our knowledge, this study is the first to unravel in detail how the three main mediators of synaptic transmission uniquely shape the NB characteristics, such as the initiation, maintenance, recruitment and termination of NBs in cortical cell cultures in vitro.
Collapse
Affiliation(s)
- Heidi Teppola
- Computational Neuroscience Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jugoslava Aćimović
- Computational Neuroscience Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marja-Leena Linne
- Computational Neuroscience Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| |
Collapse
|
39
|
Chandran P, Gopal R, Chandrasekar VK, Athavan N. Chimera states in coupled logistic maps with additional weak nonlocal topology. CHAOS (WOODBURY, N.Y.) 2019; 29:053125. [PMID: 31154761 DOI: 10.1063/1.5084301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate the occurrence of coexisting domains of partially coherent and incoherent patterns or simply known as chimera states in a network of globally coupled logistic maps upon addition of weak nonlocal topology. We find that the chimera states survive even after we disconnect nonlocal connections of some of the nodes in the network. Also, we show that the chimera states exist when we introduce symmetric gaps in the nonlocal coupling between predetermined nodes. We ascertain our results, for the existence of chimera states, by carrying out the recurrence quantification analysis and by computing the strength of incoherence. We extend our analysis for the case of small-world networks of coupled logistic maps and found the emergence of chimeralike states under the influence of weak nonlocal topology.
Collapse
Affiliation(s)
- P Chandran
- Department of Physics, H.H. The Rajah's College, Pudukkottai 622 001, Tamil Nadu, India
| | - R Gopal
- Centre for Nonlinear Science & Engineering, School of Electrical & Electronics Engineering, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - V K Chandrasekar
- Centre for Nonlinear Science & Engineering, School of Electrical & Electronics Engineering, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - N Athavan
- Department of Physics, H.H. The Rajah's College, Pudukkottai 622 001, Tamil Nadu, India
| |
Collapse
|
40
|
Abstract
The firing rate of neuronal spiking in vitro and in vivo significantly varies over extended timescales, characterized by long-memory processes and complex statistics, and appears in spontaneous as well as evoked activity upon repeated stimulus presentation. These variations in response features and their statistics, in face of repeated instances of a given physical input, are ubiquitous in all levels of brain-behavior organization. They are expressed in single neuron and network response variability but even appear in variations of subjective percepts or psychophysical choices and have been described as stemming from history-dependent, stochastic, or rate-determined processes.But what are the sources underlying these temporally rich variations in firing rate? Are they determined by interactions of the nervous system as a whole, or do isolated, single neurons or neuronal networks already express these fluctuations independent of higher levels? These questions motivated the application of a method that allows for controlled and specific long-term activation of a single neuron or neuronal network, isolated from higher levels of cortical organization.This chapter highlights the research done in cultured cortical networks to study (1) the inherent non-stationarity of neuronal network activity, (2) single neuron response fluctuations and underlying processes, and (3) the interface layer between network and single cell, the non-stationary efficacy of the ensemble of synapses impinging onto the observed neuron.
Collapse
|
41
|
Ma C, Chen HS, Lai YC, Zhang HF. Statistical inference approach to structural reconstruction of complex networks from binary time series. Phys Rev E 2018; 97:022301. [PMID: 29548109 DOI: 10.1103/physreve.97.022301] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Indexed: 12/20/2022]
Abstract
Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains challenging. We articulate a statistical inference based approach to this problem. In particular, exploiting the expectation-maximization (EM) algorithm, we develop a method to ascertain the neighbors of any node in the network based solely on binary data, thereby recovering the full topology of the network. A key ingredient of our method is the maximum-likelihood estimation of the probabilities associated with actual or nonexistent links, and we show that the EM algorithm can distinguish the two kinds of probability values without any ambiguity, insofar as the length of the available binary time series is reasonably long. Our method does not require any a priori knowledge of the detailed dynamical processes, is parameter-free, and is capable of accurate reconstruction even in the presence of noise. We demonstrate the method using combinations of distinct types of binary dynamical processes and network topologies, and provide a physical understanding of the underlying reconstruction mechanism. Our statistical inference based reconstruction method contributes an additional piece to the rapidly expanding "toolbox" of data based reverse engineering of complex networked systems.
Collapse
Affiliation(s)
- Chuang Ma
- School of Mathematical Science, Anhui University, Hefei 230601, China
| | - Han-Shuang Chen
- School of Physics and Material Science, Anhui University, Hefei 230601, China
| | - Ying-Cheng Lai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Hai-Feng Zhang
- School of Mathematical Science, Anhui University, Hefei 230601, China.,Center of Information Support and Assurance Technology, Anhui University, Hefei 230601, China.,Department of Communication Engineering, North University of China, Taiyuan, Shan'xi 030051, China
| |
Collapse
|
42
|
Matsumura R, Yamamoto H, Hayakawa T, Katsurabayashi S, Niwano M, Hirano-Iwata A. Dependence and Homeostasis of Membrane Impedance on Cell Morphology in Cultured Hippocampal Neurons. Sci Rep 2018; 8:9905. [PMID: 29967389 PMCID: PMC6028398 DOI: 10.1038/s41598-018-28232-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/20/2018] [Indexed: 11/09/2022] Open
Abstract
The electrical impedance of cell membranes is important for excitable cells, such as neurons, because it strongly influences the amount of membrane potential change upon a flow of ionic current across the membrane. Here, we report on an investigation of how neuronal morphology affects membrane impedance of cultured hippocampal neurons. Microfabricated substrates with patterned scaffolding molecules were used to restrict the neurite growth of hippocampal neurons, and the impedance was measured via whole-cell patch-clamp recording under the inhibition of voltage-dependent ion channels. Membrane impedance was found to depend inversely on the dendrite length and soma area, as would be expected from the fact that its electrical property is equivalent to a parallel RC circuit. Moreover, we found that in biological neurons, the membrane impedance is homeostatically regulated to impede changes in the membrane area. The findings provide direct evidence on cell-autonomous regulation of neuronal impedance and pave the way towards elucidating the mechanism responsible for the resilience of biological neuronal networks.
Collapse
Affiliation(s)
- Ryosuke Matsumura
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hideaki Yamamoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.
- WPI-AIMR, Tohoku University, Sendai, Japan.
| | - Takeshi Hayakawa
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Shutaro Katsurabayashi
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Michio Niwano
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Kansei Fukushi Research Institute, Tohoku Fukushi University, 6-149-1 Kunimigaoka, Aoba-ku, Sendai, 989-3201, Japan
| | - Ayumi Hirano-Iwata
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| |
Collapse
|
43
|
Priesemann V, Shriki O. Can a time varying external drive give rise to apparent criticality in neural systems? PLoS Comput Biol 2018; 14:e1006081. [PMID: 29813052 PMCID: PMC6002119 DOI: 10.1371/journal.pcbi.1006081] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 06/14/2018] [Accepted: 03/08/2018] [Indexed: 02/01/2023] Open
Abstract
The finding of power law scaling in neural recordings lends support to the hypothesis of critical brain dynamics. However, power laws are not unique to critical systems and can arise from alternative mechanisms. Here, we investigate whether a common time-varying external drive to a set of Poisson units can give rise to neuronal avalanches and exhibit apparent criticality. To this end, we analytically derive the avalanche size and duration distributions, as well as additional measures, first for homogeneous Poisson activity, and then for slowly varying inhomogeneous Poisson activity. We show that homogeneous Poisson activity cannot give rise to power law distributions. Inhomogeneous activity can also not generate perfect power laws, but it can exhibit approximate power laws with cutoffs that are comparable to those typically observed in experiments. The mechanism of generating apparent criticality by time-varying external fields, forces or input may generalize to many other systems like dynamics of swarms, diseases or extinction cascades. Here, we illustrate the analytically derived effects for spike recordings in vivo and discuss approaches to distinguish true from apparent criticality. Ultimately, this requires causal interventions, which allow separating internal system properties from externally imposed ones.
Collapse
Affiliation(s)
- Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Bernstein Center for Computational Neuroscience Göttingen, Göttingen, Germany
| | - Oren Shriki
- Department of Cognitive and Brain Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| |
Collapse
|
44
|
An S, Zhao YF, Lü XY, Wang ZG. Quantitative evaluation of extrinsic factors influencing electrical excitability in neuronal networks: Voltage Threshold Measurement Method (VTMM). Neural Regen Res 2018; 13:1026-1035. [PMID: 29926830 PMCID: PMC6022462 DOI: 10.4103/1673-5374.233446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The electrical excitability of neural networks is influenced by different environmental factors. Effective and simple methods are required to objectively and quantitatively evaluate the influence of such factors, including variations in temperature and pharmaceutical dosage. The aim of this paper was to introduce ‘the voltage threshold measurement method’, which is a new method using microelectrode arrays that can quantitatively evaluate the influence of different factors on the electrical excitability of neural networks. We sought to verify the feasibility and efficacy of the method by studying the effects of acetylcholine, ethanol, and temperature on hippocampal neuronal networks and hippocampal brain slices. First, we determined the voltage of the stimulation pulse signal that elicited action potentials in the two types of neural networks under normal conditions. Second, we obtained the voltage thresholds for the two types of neural networks under different concentrations of acetylcholine, ethanol, and different temperatures. Finally, we obtained the relationship between voltage threshold and the three influential factors. Our results indicated that the normal voltage thresholds of the hippocampal neuronal network and hippocampal slice preparation were 56 and 31 mV, respectively. The voltage thresholds of the two types of neural networks were inversely proportional to acetylcholine concentration, and had an exponential dependency on ethanol concentration. The curves of the voltage threshold and the temperature of the medium for the two types of neural networks were U-shaped. The hippocampal neuronal network and hippocampal slice preparations lost their excitability when the temperature of the medium decreased below 34 and 33°C or increased above 42 and 43°C, respectively. These results demonstrate that the voltage threshold measurement method is effective and simple for examining the performance/excitability of neuronal networks.
Collapse
Affiliation(s)
- Shuai An
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu Province, China
| | - Yong-Fang Zhao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu Province, China
| | - Xiao-Ying Lü
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Zhi-Gong Wang
- Institute of RF- & OE-ICs, Southeast University, Nanjing; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| |
Collapse
|
45
|
Rubinson M, Levit-Binnun N, Peled A, Naim-Feil J, Freche D, Moses E. Hierarchy measurement for modeling network dynamics under directed attacks. Phys Rev E 2017; 96:052307. [PMID: 29347771 DOI: 10.1103/physreve.96.052307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Indexed: 11/07/2022]
Abstract
A fundamental issue in the dynamics of complex systems is the resilience of the network in response to targeted attacks. This paper explores the local dynamics of the network attack process by investigating the order of removal of the nodes that have maximal degree, and shows that this dynamic network response can be predicted from the graph's initial connectivity. We demonstrate numerically that the maximal degree M(τ) of the network at time step τ decays exponentially with τ via a topology-dependent exponent. Moreover, the order in which sites are removed can be approximated by considering the network's "hierarchy" function h, which measures for each node V_{i} how many of its initial nearest neighbors have lower degree versus those that have a higher one. Finally, we show that the exponents we identified for the attack dynamics are related to the exponential behavior of spreading activation dynamics. The results suggest that the function h, which has both local and global properties, is a novel nodal measurement for network dynamics and structure.
Collapse
Affiliation(s)
- M Rubinson
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - N Levit-Binnun
- Sagol Center for Brain and Mind, Baruch Ivcher School of Psychology, Interdisciplinary Center (IDC), Herzliya, Israel
| | - A Peled
- Institute for Psychiatric Studies, Sha'ar Menashe Mental Health Center, Sha'ar Menashe, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - J Naim-Feil
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel.,Sagol Center for Brain and Mind, Baruch Ivcher School of Psychology, Interdisciplinary Center (IDC), Herzliya, Israel
| | - D Freche
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel.,Sagol Center for Brain and Mind, Baruch Ivcher School of Psychology, Interdisciplinary Center (IDC), Herzliya, Israel
| | - E Moses
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
46
|
Nguyen TD, O’Connor KD, Sheth K, Bolle N. Mapping functional connectivity of bursting neuronal networks. APPLIED NETWORK SCIENCE 2017; 2:15. [PMID: 30443570 PMCID: PMC6214252 DOI: 10.1007/s41109-017-0037-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/30/2017] [Indexed: 06/09/2023]
Abstract
Using single-cell laser scanning photostimulation (LSPS) combined with broad-field calcium imaging, we measured the functional connectivity of neuronal cultures before and after the developmental appearance of network bursting. From these data, network properties were determined for these relatively large neuronal networks. Based on these properties, we found that although 'small-world' network behavior existed throughout this time period, only average node degree and global efficiency correlate with the development of network bursting while clustering and local efficiency remained relatively constant.
Collapse
Affiliation(s)
- Tuan D. Nguyen
- The College of New Jersey, Department of Physics, Ewing, 08628 NJ USA
| | - Kelly D. O’Connor
- The College of New Jersey, Department of Physics, Ewing, 08628 NJ USA
| | - Krishna Sheth
- The College of New Jersey, Department of Physics, Ewing, 08628 NJ USA
| | - Nick Bolle
- The College of New Jersey, Department of Physics, Ewing, 08628 NJ USA
| |
Collapse
|
47
|
Orlandi JG, Casademunt J. Noise focusing in neuronal tissues: Symmetry breaking and localization in excitable networks with quenched disorder. Phys Rev E 2017; 95:052304. [PMID: 28618531 DOI: 10.1103/physreve.95.052304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/07/2022]
Abstract
We introduce a coarse-grained stochastic model for the spontaneous activity of neuronal cultures to explain the phenomenon of noise focusing, which entails localization of the noise activity in excitable networks with metric correlations. The system is modeled as a continuum excitable medium with a state-dependent spatial coupling that accounts for the dynamics of synaptic connections. The most salient feature is the emergence at the mesoscale of a vector field V(r), which acts as an advective carrier of the noise. This entails an explicit symmetry breaking of isotropy and homogeneity that stems from the amplification of the quenched fluctuations of the network by the activity avalanches, concomitant with the excitable dynamics. We discuss the microscopic interpretation of V(r) and propose an explicit construction of it. The coarse-grained model shows excellent agreement with simulations at the network level. The generic nature of the observed phenomena is discussed.
Collapse
Affiliation(s)
- Javier G Orlandi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.,Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, Canada T2N 1N4
| | - Jaume Casademunt
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.,Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, E-08028 Barcelona, Spain
| |
Collapse
|
48
|
Hernández-Navarro L, Orlandi JG, Cerruti B, Vives E, Soriano J. Dominance of Metric Correlations in Two-Dimensional Neuronal Cultures Described through a Random Field Ising Model. PHYSICAL REVIEW LETTERS 2017; 118:208101. [PMID: 28581813 DOI: 10.1103/physrevlett.118.208101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 06/07/2023]
Abstract
We introduce a novel random field Ising model, grounded on experimental observations, to assess the importance of metric correlations in cortical circuits in vitro. Metric correlations arise from both the finite axonal length and the heterogeneity in the spatial arrangement of neurons. The experiments consider the response of neuronal cultures to an external electric stimulation for a gradually weaker connectivity strength between neurons, and in cultures with different spatial configurations. The model can be analytically solved in the metric-free, mean-field scenario. The presence of metric correlations precipitates a strong deviation from the mean field. Null models of the same networks that preserve the distribution of connections recover the mean field. Our results show that metric-inherited correlations in spatial networks dominate the connectivity blueprint, mask the actual distribution of connections, and may emerge as the asset that shapes network dynamics.
Collapse
Affiliation(s)
- Lluís Hernández-Navarro
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Catalonia, Spain
| | - Javier G Orlandi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
- Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, Canada T2N 1N4
| | - Benedetta Cerruti
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Eduard Vives
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Catalonia, Spain
| | - Jordi Soriano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Catalonia, Spain
| |
Collapse
|
49
|
Stern S, Rotem A, Burnishev Y, Weinreb E, Moses E. External Excitation of Neurons Using Electric and Magnetic Fields in One- and Two-dimensional Cultures. J Vis Exp 2017. [PMID: 28518110 DOI: 10.3791/54357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A neuron will fire an action potential when its membrane potential exceeds a certain threshold. In typical activity of the brain, this occurs as a result of chemical inputs to its synapses. However, neurons can also be excited by an imposed electric field. In particular, recent clinical applications activate neurons by creating an electric field externally. It is therefore of interest to investigate how the neuron responds to the external field and what causes the action potential. Fortunately, precise and controlled application of an external electric field is possible for embryonic neuronal cells that are excised, dissociated and grown in cultures. This allows the investigation of these questions in a highly reproducible system. In this paper some of the techniques used for controlled application of external electric field on neuronal cultures are reviewed. The networks can be either one dimensional, i.e. patterned in linear forms or allowed to grow on the whole plane of the substrate, and thus two dimensional. Furthermore, the excitation can be created by the direct application of electric field via electrodes immersed in the fluid (bath electrodes) or by inducing the electric field using the remote creation of magnetic pulses.
Collapse
Affiliation(s)
- Shani Stern
- Laboratory of Genetics, The Salk Institute for Biological Studies
| | - Assaf Rotem
- Department of Physics and SEAS, Harvard University
| | - Yuri Burnishev
- Department of Physics of Complex Systems, Weizmann Institute of Science
| | - Eyal Weinreb
- Department of Physics of Complex Systems, Weizmann Institute of Science
| | - Elisha Moses
- Department of Physics of Complex Systems, Weizmann Institute of Science;
| |
Collapse
|
50
|
Paraskevov AV, Zendrikov DK. A spatially resolved network spike in model neuronal cultures reveals nucleation centers, circular traveling waves and drifting spiral waves. Phys Biol 2017; 14:026003. [PMID: 28333685 DOI: 10.1088/1478-3975/aa5fc3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We show that in model neuronal cultures, where the probability of interneuronal connection formation decreases exponentially with increasing distance between the neurons, there exists a small number of spatial nucleation centers of a network spike, from where the synchronous spiking activity starts propagating in the network typically in the form of circular traveling waves. The number of nucleation centers and their spatial locations are unique and unchanged for a given realization of neuronal network but are different for different networks. In contrast, if the probability of interneuronal connection formation is independent of the distance between neurons, then the nucleation centers do not arise and the synchronization of spiking activity during a network spike occurs spatially uniform throughout the network. Therefore one can conclude that spatial proximity of connections between neurons is important for the formation of nucleation centers. It is also shown that fluctuations of the spatial density of neurons at their random homogeneous distribution typical for the experiments in vitro do not determine the locations of the nucleation centers. The simulation results are qualitatively consistent with the experimental observations.
Collapse
Affiliation(s)
- A V Paraskevov
- National Research Centre "Kurchatov Institute", 123182 Moscow, Russia. Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
| | | |
Collapse
|