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Zhai S, Otsuka S, Xu J, Clarke VRJ, Tkatch T, Wokosin D, Xie Z, Tanimura A, Agarwal HK, Ellis-Davies GCR, Contractor A, Surmeier DJ. Ca 2+ -dependent phosphodiesterase 1 regulates the plasticity of striatal spiny projection neuron glutamatergic synapses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590962. [PMID: 38712260 PMCID: PMC11071484 DOI: 10.1101/2024.04.24.590962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Long-term synaptic plasticity at glutamatergic synapses on striatal spiny projection neurons (SPNs) is central to learning goal-directed behaviors and habits. Although considerable attention has been paid to the mechanisms underlying synaptic strengthening and new learning, little scrutiny has been given to those involved in the attenuation of synaptic strength that attends suppression of a previously learned association. Our studies revealed a novel, non-Hebbian, long-term, postsynaptic depression of glutamatergic SPN synapses induced by interneuronal nitric oxide (NO) signaling (NO-LTD) that was preferentially engaged at quiescent synapses. This form of plasticity was gated by local Ca 2+ influx through CaV1.3 Ca 2+ channels and stimulation of phosphodiesterase 1 (PDE1), which degraded cyclic guanosine monophosphate (cGMP) and blunted NO signaling. Consistent with this model, mice harboring a gain-of-function mutation in the gene coding for the pore-forming subunit of CaV1.3 channels had elevated depolarization-induced dendritic Ca 2+ entry and impaired NO-LTD. Extracellular uncaging of glutamate and intracellular uncaging of cGMP suggested that this Ca 2+ -dependent regulation of PDE1 activity allowed for local regulation of dendritic NO signaling. This inference was supported by simulation of SPN dendritic integration, which revealed that dendritic spikes engaged PDE1 in a branch-specific manner. In a mouse model of Parkinson's disease (PD), NO-LTD was absent not because of a postsynaptic deficit in NO signaling machinery, but rather due to impaired interneuronal NO release. Re-balancing intrastriatal neuromodulatory signaling in the PD model restored NO release and NO-LTD. Taken together, these studies provide novel insights into the mechanisms governing NO-LTD in SPN and its role in psychomotor disorders, like PD.
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Day M, Belal M, Surmeier WC, Melendez A, Wokosin D, Tkatch T, Clarke VRJ, Surmeier DJ. GABAergic regulation of striatal spiny projection neurons depends upon their activity state. PLoS Biol 2024; 22:e3002483. [PMID: 38295323 PMCID: PMC10830145 DOI: 10.1371/journal.pbio.3002483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
Synaptic transmission mediated by GABAA receptors (GABAARs) in adult, principal striatal spiny projection neurons (SPNs) can suppress ongoing spiking, but its effect on synaptic integration at subthreshold membrane potentials is less well characterized, particularly those near the resting down-state. To fill this gap, a combination of molecular, optogenetic, optical, and electrophysiological approaches were used to study SPNs in mouse ex vivo brain slices, and computational tools were used to model somatodendritic synaptic integration. In perforated patch recordings, activation of GABAARs, either by uncaging of GABA or by optogenetic stimulation of GABAergic synapses, evoked currents with a reversal potential near -60 mV in both juvenile and adult SPNs. Transcriptomic analysis and pharmacological work suggested that this relatively positive GABAAR reversal potential was not attributable to NKCC1 expression, but rather to HCO3- permeability. Regardless, from down-state potentials, optogenetic activation of dendritic GABAergic synapses depolarized SPNs. This GABAAR-mediated depolarization summed with trailing ionotropic glutamate receptor (iGluR) stimulation, promoting dendritic spikes and increasing somatic depolarization. Simulations revealed that a diffuse dendritic GABAergic input to SPNs effectively enhanced the response to dendritic iGluR signaling and promoted dendritic spikes. Taken together, our results demonstrate that GABAARs can work in concert with iGluRs to excite adult SPNs when they are in the resting down-state, suggesting that their inhibitory role is limited to brief periods near spike threshold. This state-dependence calls for a reformulation for the role of intrastriatal GABAergic circuits.
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Affiliation(s)
- Michelle Day
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Marziyeh Belal
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - William C. Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Alexandria Melendez
- Department of Neurology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Wokosin
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tatiana Tkatch
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
| | - Vernon R. J. Clarke
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
| | - D. James Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
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3
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Frost-Nylén J, Thompson WS, Robertson B, Grillner S. The Basal Ganglia Downstream Control of Action - An Evolutionarily Conserved Strategy. Curr Neuropharmacol 2024; 22:1419-1430. [PMID: 37563813 PMCID: PMC11097981 DOI: 10.2174/1570159x21666230810141746] [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: 12/02/2022] [Revised: 01/30/2023] [Accepted: 02/05/2023] [Indexed: 08/12/2023] Open
Abstract
The motor areas of the cortex and the basal ganglia both contribute to determining which motor actions will be recruited at any moment in time, and their functions are intertwined. Here, we review the basal ganglia mechanisms underlying the selection of behavior of the downstream control of motor centers in the midbrain and brainstem and show that the basic organization of the forebrain motor system is evolutionarily conserved throughout vertebrate phylogeny. The output level of the basal ganglia (e.g. substantia nigra pars reticulata) has GABAergic neurons that are spontaneously active at rest and inhibit a number of specific motor centers, each of which can be relieved from inhibition if the inhibitory output neurons themselves become inhibited. The motor areas of the cortex act partially via the dorsolateral striatum (putamen), which has specific modules for the forelimb, hindlimb, trunk, etc. Each module operates in turn through the two types of striatal projection neurons that control the output modules of the basal ganglia and thereby the downstream motor centers. The mechanisms for lateral inhibition in the striatum are reviewed as well as other striatal mechanisms contributing to action selection. The motor cortex also exerts a direct excitatory action on specific motor centers. An overview is given of the basal ganglia control exerted on the different midbrain/brainstem motor centers, and the efference copy information fed back via the thalamus to the striatum and cortex, which is of importance for the planning of future movements.
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Affiliation(s)
| | | | - Brita Robertson
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
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4
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Li Y, Zhang B, Liu Z, Wang R. Neural energy computations based on Hodgkin-Huxley models bridge abnormal neuronal activities and energy consumption patterns of major depressive disorder. Comput Biol Med 2023; 166:107500. [PMID: 37797488 DOI: 10.1016/j.compbiomed.2023.107500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Limited by the current experimental techniques and neurodynamical models, the dysregulation mechanisms of decision-making related neural circuits in major depressive disorder (MDD) are still not clear. In this paper, we proposed a neural coding methodology using energy to further investigate it, which has been proven to strongly complement the neurodynamical methodology. We augmented the previous neural energy calculation method, and applied it to our VTA-NAc-mPFC neurodynamical H-H models. We particularly focused on the peak power and energy consumption of abnormal ion channel (ionic) currents under different concentrations of dopamine input, and investigated the abnormal energy consumption patterns for the MDD group. The results revealed that the energy consumption of medium spiny neurons (MSNs) in the NAc region were lower in the MDD group than that of the normal control group despite having the same firing frequencies, peak action potentials, and average membrane potentials in both groups. Dopamine concentration was also positively correlated with the energy consumption of the pyramidal neurons, but the patterns of different interneuron types were distinct. Additionally, the ratio of mPFC's energy consumption to total energy consumption of the whole network in MDD group was lower than that in normal control group, revealing that the mPFC region in MDD group encoded less neural information, which matched the energy consumption patterns of BOLD-fMRI results. It was also in line with the behavioral characteristics that MDD patients demonstrated in the form of reward insensitivity during decision-making tasks. In conclusion, the model in this paper was the first neural network energy computational model for MDD, which showed success in explaining its dynamical mechanisms with an energy consumption perspective. To build on this, we demonstrated that energy consumption levels can be used as a potential indicator for MDD, which also showed a promising pipeline to use an energy methodology for studying other neuropsychiatric disorders.
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Affiliation(s)
- Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China; Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Bing Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Zhiqiang Liu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China; Anesthesia and Brain Function Research Institute, Tongji University School of Medicine, Shanghai, China.
| | - Rubin Wang
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China.
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5
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Zhang Y, He G, Ma L, Liu X, Hjorth JJJ, Kozlov A, He Y, Zhang S, Kotaleski JH, Tian Y, Grillner S, Du K, Huang T. A GPU-based computational framework that bridges neuron simulation and artificial intelligence. Nat Commun 2023; 14:5798. [PMID: 37723170 PMCID: PMC10507119 DOI: 10.1038/s41467-023-41553-7] [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: 06/30/2022] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
Biophysically detailed multi-compartment models are powerful tools to explore computational principles of the brain and also serve as a theoretical framework to generate algorithms for artificial intelligence (AI) systems. However, the expensive computational cost severely limits the applications in both the neuroscience and AI fields. The major bottleneck during simulating detailed compartment models is the ability of a simulator to solve large systems of linear equations. Here, we present a novel Dendritic Hierarchical Scheduling (DHS) method to markedly accelerate such a process. We theoretically prove that the DHS implementation is computationally optimal and accurate. This GPU-based method performs with 2-3 orders of magnitude higher speed than that of the classic serial Hines method in the conventional CPU platform. We build a DeepDendrite framework, which integrates the DHS method and the GPU computing engine of the NEURON simulator and demonstrate applications of DeepDendrite in neuroscience tasks. We investigate how spatial patterns of spine inputs affect neuronal excitability in a detailed human pyramidal neuron model with 25,000 spines. Furthermore, we provide a brief discussion on the potential of DeepDendrite for AI, specifically highlighting its ability to enable the efficient training of biophysically detailed models in typical image classification tasks.
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Affiliation(s)
- Yichen Zhang
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
| | - Gan He
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
| | - Lei Ma
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
- Beijing Academy of Artificial Intelligence (BAAI), Beijing, 100084, China
| | - Xiaofei Liu
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
- School of Information Science and Engineering, Yunnan University, Kunming, 650500, China
| | - J J Johannes Hjorth
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, Royal Institute of Technology KTH, Stockholm, SE-10044, Sweden
| | - Alexander Kozlov
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, Royal Institute of Technology KTH, Stockholm, SE-10044, Sweden
- Department of Neuroscience, Karolinska Institute, Stockholm, SE-17165, Sweden
| | - Yutao He
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
| | - Shenjian Zhang
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, Royal Institute of Technology KTH, Stockholm, SE-10044, Sweden
- Department of Neuroscience, Karolinska Institute, Stockholm, SE-17165, Sweden
| | - Yonghong Tian
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
- School of Electrical and Computer Engineering, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institute, Stockholm, SE-17165, Sweden
| | - Kai Du
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
| | - Tiejun Huang
- National Key Laboratory for Multimedia Information Processing, School of Computer Science, Peking University, Beijing, 100871, China
- Beijing Academy of Artificial Intelligence (BAAI), Beijing, 100084, China
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China
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6
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Zhang Y, Du K, Huang T. Heuristic Tree-Partition-Based Parallel Method for Biophysically Detailed Neuron Simulation. Neural Comput 2023; 35:627-644. [PMID: 36746142 DOI: 10.1162/neco_a_01565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/20/2022] [Indexed: 02/08/2023]
Abstract
Biophysically detailed neuron simulation is a powerful tool to explore the mechanisms behind biological experiments and bridge the gap between various scales in neuroscience research. However, the extremely high computational complexity of detailed neuron simulation restricts the modeling and exploration of detailed network models. The bottleneck is solving the system of linear equations. To accelerate detailed simulation, we propose a heuristic tree-partition-based parallel method (HTP) to parallelize the computation of the Hines algorithm, the kernel for solving linear equations, and leverage the strong parallel capability of the graphic processing unit (GPU) to achieve further speedup. We formulate the problem of how to get a fine parallel process as a tree-partition problem. Next, we present a heuristic partition algorithm to obtain an effective partition to efficiently parallelize the equation-solving process in detailed simulation. With further optimization on GPU, our HTP method achieves 2.2 to 8.5 folds speedup compared to the state-of-the-art GPU method and 36 to 660 folds speedup compared to the typical Hines algorithm.
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Affiliation(s)
- Yichen Zhang
- School of Computer Science, Peking University, Beijing 100871, China
| | - Kai Du
- School of Computer Science and Institute for Artificial Intelligence, Peking University, Beijing 100871, China
| | - Tiejun Huang
- School of Computer Science and Institute for Artificial Intelligence, Peking University, Beijing 100871, China
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7
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Day M, Belal M, Surmeier WC, Melendez A, Wokosin D, Tkatch T, Clarke VRJ, Surmeier DJ. State-dependent GABAergic regulation of striatal spiny projection neuron excitability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532627. [PMID: 36993489 PMCID: PMC10055173 DOI: 10.1101/2023.03.14.532627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Synaptic transmission mediated by GABA A receptors (GABA A Rs) in adult, principal striatal spiny projection neurons (SPNs) can suppress ongoing spiking, but its effect on synaptic integration at sub-threshold membrane potentials is less well characterized, particularly those near the resting down-state. To fill this gap, a combination of molecular, optogenetic, optical and electrophysiological approaches were used to study SPNs in mouse ex vivo brain slices, and computational tools were used to model somatodendritic synaptic integration. Activation of GABA A Rs, either by uncaging of GABA or by optogenetic stimulation of GABAergic synapses, evoked currents with a reversal potential near -60 mV in perforated patch recordings from both juvenile and adult SPNs. Molecular profiling of SPNs suggested that this relatively positive reversal potential was not attributable to NKCC1 expression, but rather to a dynamic equilibrium between KCC2 and Cl-/HCO3-cotransporters. Regardless, from down-state potentials, optogenetic activation of dendritic GABAergic synapses depolarized SPNs. This GABAAR-mediated depolarization summed with trailing ionotropic glutamate receptor (iGluR) stimulation, promoting dendritic spikes and increasing somatic depolarization. Simulations revealed that a diffuse dendritic GABAergic input to SPNs effectively enhanced the response to coincident glutamatergic input. Taken together, our results demonstrate that GABA A Rs can work in concert with iGluRs to excite adult SPNs when they are in the resting down-state, suggesting that their inhibitory role is limited to brief periods near spike threshold. This state-dependence calls for a reformulation of the role intrastriatal GABAergic circuits.
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8
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D’Egidio F, Castelli V, Cimini A, d’Angelo M. Cell Rearrangement and Oxidant/Antioxidant Imbalance in Huntington's Disease. Antioxidants (Basel) 2023; 12:571. [PMID: 36978821 PMCID: PMC10045781 DOI: 10.3390/antiox12030571] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Huntington's Disease (HD) is a hereditary neurodegenerative disorder caused by the expansion of a CAG triplet repeat in the HTT gene, resulting in the production of an aberrant huntingtin (Htt) protein. The mutant protein accumulation is responsible for neuronal dysfunction and cell death. This is due to the involvement of oxidative damage, excitotoxicity, inflammation, and mitochondrial impairment. Neurons naturally adapt to bioenergetic alteration and oxidative stress in physiological conditions. However, this dynamic system is compromised when a neurodegenerative disorder occurs, resulting in changes in metabolism, alteration in calcium signaling, and impaired substrates transport. Thus, the aim of this review is to provide an overview of the cell's answer to the stress induced by HD, focusing on the role of oxidative stress and its balance with the antioxidant system.
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Affiliation(s)
| | | | | | - Michele d’Angelo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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9
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Li Y, Zhang B, Pan X, Wang Y, Xu X, Wang R, Liu Z. Dopamine-Mediated Major Depressive Disorder in the Neural Circuit of Ventral Tegmental Area-Nucleus Accumbens-Medial Prefrontal Cortex: From Biological Evidence to Computational Models. Front Cell Neurosci 2022; 16:923039. [PMID: 35966208 PMCID: PMC9373714 DOI: 10.3389/fncel.2022.923039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
Major depressive disorder (MDD) is a serious psychiatric disorder, with an increasing incidence in recent years. The abnormal dopaminergic pathways of the midbrain cortical and limbic system are the key pathological regions of MDD, particularly the ventral tegmental area- nucleus accumbens- medial prefrontal cortex (VTA-NAc-mPFC) neural circuit. MDD usually occurs with the dysfunction of dopaminergic neurons in VTA, which decreases the dopamine concentration and metabolic rate in NAc/mPFC brain regions. However, it has not been fully explained how abnormal dopamine concentration levels affect this neural circuit dynamically through the modulations of ion channels and synaptic activities. We used Hodgkin-Huxley and dynamical receptor binding model to establish this network, which can quantitatively explain neural activity patterns observed in MDD with different dopamine concentrations by changing the kinetics of some ion channels. The simulation replicated some important pathological patterns of MDD at the level of neurons and circuits with low dopamine concentration, such as the decreased action potential frequency in pyramidal neurons of mPFC with significantly reduced burst firing frequency. The calculation results also revealed that NaP and KS channels of mPFC pyramidal neurons played key roles in the functional regulation of this neural circuit. In addition, we analyzed the synaptic currents and local field potentials to explain the mechanism of MDD from the perspective of dysfunction of excitation-inhibition balance, especially the disinhibition effect in the network. The significance of this article is that we built the first computational model to illuminate the effect of dopamine concentrations for the NAc-mPFC-VTA circuit between MDD and normal groups, which can be used to quantitatively explain the results of existing physiological experiments, predict the results for unperformed experiments and screen possible drug targets.
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Affiliation(s)
- Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Bing Zhang
- Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaochuan Pan
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China
| | - Yihong Wang
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China
| | - Xuying Xu
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China
| | - Rubin Wang
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China
- *Correspondence: Rubin Wang, ;
| | - Zhiqiang Liu
- Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
- Anesthesia and Brain Function Research Institute, Tongji University School of Medicine, Shanghai, China
- Zhiqiang Liu,
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10
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A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Neuroinformatics 2022; 20:241-259. [PMID: 34709562 PMCID: PMC9537196 DOI: 10.1007/s12021-021-09546-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 01/07/2023]
Abstract
Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. Here we focus on the scale of biochemical pathways, which is one of the main objects of study in systems biology. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB® scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model.
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11
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Frost Nylen J, Hjorth JJJ, Grillner S, Hellgren Kotaleski J. Dopaminergic and Cholinergic Modulation of Large Scale Networks in silico Using Snudda. Front Neural Circuits 2021; 15:748989. [PMID: 34744638 PMCID: PMC8568057 DOI: 10.3389/fncir.2021.748989] [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: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Neuromodulation is present throughout the nervous system and serves a critical role for circuit function and dynamics. The computational investigations of neuromodulation in large scale networks require supportive software platforms. Snudda is a software for the creation and simulation of large scale networks of detailed microcircuits consisting of multicompartmental neuron models. We have developed an extension to Snudda to incorporate neuromodulation in large scale simulations. The extended Snudda framework implements neuromodulation at the level of single cells incorporated into large-scale microcircuits. We also developed Neuromodcell, a software for optimizing neuromodulation in detailed multicompartmental neuron models. The software adds parameters within the models modulating the conductances of ion channels and ionotropic receptors. Bath application of neuromodulators is simulated and models which reproduce the experimentally measured effects are selected. In Snudda, we developed an extension to accommodate large scale simulations of neuromodulation. The simulator has two modes of simulation – denoted replay and adaptive. In the replay mode, transient levels of neuromodulators can be defined as a time-varying function which modulates the receptors and ion channels within the network in a cell-type specific manner. In the adaptive mode, spiking neuromodulatory neurons are connected via integrative modulating mechanisms to ion channels and receptors. Both modes of simulating neuromodulation allow for simultaneous modulation by several neuromodulators that can interact dynamically with each other. Here, we used the Neuromodcell software to simulate dopaminergic and muscarinic modulation of neurons from the striatum. We also demonstrate how to simulate different neuromodulatory states with dopamine and acetylcholine using Snudda. All software is freely available on Github, including tutorials on Neuromodcell and Snudda-neuromodulation.
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Affiliation(s)
| | - Jarl Jacob Johannes Hjorth
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, Royal Institute of Technology, Stockholm, Sweden
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, Royal Institute of Technology, Stockholm, Sweden
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Fujimoto H, Notsu E, Yamamoto R, Ono M, Hioki H, Takahashi M, Ito T. Kv4.2-Positive Domains on Dendrites in the Mouse Medial Geniculate Body Receive Ascending Excitatory and Inhibitory Inputs Preferentially From the Inferior Colliculus. Front Neurosci 2021; 15:740378. [PMID: 34658777 PMCID: PMC8511456 DOI: 10.3389/fnins.2021.740378] [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: 07/13/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The medial geniculate body (MGB) is the thalamic center of the auditory lemniscal pathway. The ventral division of MGB (MGV) receives excitatory and inhibitory inputs from the inferior colliculus (IC). MGV is involved in auditory attention by processing descending excitatory and inhibitory inputs from the auditory cortex (AC) and reticular thalamic nucleus (RTN), respectively. However, detailed mechanisms of the integration of different inputs in a single MGV neuron remain unclear. Kv4.2 is one of the isoforms of the Shal-related subfamily of potassium voltage-gated channels that are expressed in MGB. Since potassium channel is important for shaping synaptic current and spike waveforms, subcellular distribution of Kv4.2 is likely important for integration of various inputs. Here, we aimed to examine the detailed distribution of Kv4.2, in MGV neurons to understand its specific role in auditory attention. We found that Kv4.2 mRNA was expressed in most MGV neurons. At the protein level, Kv4.2-immunopositive patches were sparsely distributed in both the dendrites and the soma of neurons. The postsynaptic distribution of Kv4.2 protein was confirmed using electron microscopy (EM). The frequency of contact with Kv4.2-immunopositive puncta was higher in vesicular glutamate transporter 2 (VGluT2)-positive excitatory axon terminals, which are supposed to be extending from the IC, than in VGluT1-immunopositive terminals, which are expected to be originating from the AC. VGluT2-immunopositive terminals were significantly larger than VGluT1-immunopositive terminals. Furthermore, EM showed that the terminals forming asymmetric synapses with Kv4.2-immunopositive MGV dendritic domains were significantly larger than those forming synapses with Kv4.2-negative MGV dendritic domains. In inhibitory axons either from the IC or from the RTN, the frequency of terminals that were in contact with Kv4.2-positive puncta was higher in IC than in RTN. In summary, our study demonstrated that the Kv4.2-immunopositive domains of the MGV dendrites received excitatory and inhibitory ascending auditory inputs preferentially from the IC, and not from the RTN or cortex. Our findings imply that time course of synaptic current and spike waveforms elicited by IC inputs is modified in the Kv4.2 domains.
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Affiliation(s)
- Hisataka Fujimoto
- Department of Anatomy, Kawasaki Medical School, Kurashiki, Japan.,Department of Ophthalmology, Kawasaki Medical School, Kurashiki, Japan
| | - Eiji Notsu
- Department of Anatomy, Kawasaki Medical School, Kurashiki, Japan
| | - Ryo Yamamoto
- Department of Physiology, Kanazawa Medical University, Uchinada, Japan
| | - Munenori Ono
- Department of Physiology, Kanazawa Medical University, Uchinada, Japan
| | - Hiroyuki Hioki
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Megumu Takahashi
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsufumi Ito
- Research and Education Program for Life Science, University of Fukui, Fukui, Japan.,Department of Anatomy, Kanazawa Medical University, Uchinada, Japan.,Department of Systems Function and Morphology, Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
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13
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Gerster M, Taher H, Škoch A, Hlinka J, Guye M, Bartolomei F, Jirsa V, Zakharova A, Olmi S. Patient-Specific Network Connectivity Combined With a Next Generation Neural Mass Model to Test Clinical Hypothesis of Seizure Propagation. Front Syst Neurosci 2021; 15:675272. [PMID: 34539355 PMCID: PMC8440880 DOI: 10.3389/fnsys.2021.675272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/07/2021] [Indexed: 11/13/2022] Open
Abstract
Dynamics underlying epileptic seizures span multiple scales in space and time, therefore, understanding seizure mechanisms requires identifying the relations between seizure components within and across these scales, together with the analysis of their dynamical repertoire. In this view, mathematical models have been developed, ranging from single neuron to neural population. In this study, we consider a neural mass model able to exactly reproduce the dynamics of heterogeneous spiking neural networks. We combine mathematical modeling with structural information from non invasive brain imaging, thus building large-scale brain network models to explore emergent dynamics and test the clinical hypothesis. We provide a comprehensive study on the effect of external drives on neuronal networks exhibiting multistability, in order to investigate the role played by the neuroanatomical connectivity matrices in shaping the emergent dynamics. In particular, we systematically investigate the conditions under which the network displays a transition from a low activity regime to a high activity state, which we identify with a seizure-like event. This approach allows us to study the biophysical parameters and variables leading to multiple recruitment events at the network level. We further exploit topological network measures in order to explain the differences and the analogies among the subjects and their brain regions, in showing recruitment events at different parameter values. We demonstrate, along with the example of diffusion-weighted magnetic resonance imaging (dMRI) connectomes of 20 healthy subjects and 15 epileptic patients, that individual variations in structural connectivity, when linked with mathematical dynamic models, have the capacity to explain changes in spatiotemporal organization of brain dynamics, as observed in network-based brain disorders. In particular, for epileptic patients, by means of the integration of the clinical hypotheses on the epileptogenic zone (EZ), i.e., the local network where highly synchronous seizures originate, we have identified the sequence of recruitment events and discussed their links with the topological properties of the specific connectomes. The predictions made on the basis of the implemented set of exact mean-field equations turn out to be in line with the clinical pre-surgical evaluation on recruited secondary networks.
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Affiliation(s)
- Moritz Gerster
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
| | - Halgurd Taher
- Inria Sophia Antipolis Méditerranée Research Centre, MathNeuro Team, Valbonne, France
| | - Antonín Škoch
- National Institute of Mental Health, Klecany, Czechia
- MR Unit, Department of Diagnostic and Interventional Radiology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Jaroslav Hlinka
- National Institute of Mental Health, Klecany, Czechia
- Institute of Computer Science of the Czech Academy of Sciences, Prague, Czechia
| | - Maxime Guye
- Faculté de Médecine de la Timone, Centre de Résonance Magnétique et Biologique et Médicale (CRMBM, UMR CNRS-AMU 7339), Medical School of Marseille, Aix-Marseille Université, Marseille, France
- Assistance Publique -Hôpitaux de Marseille, Hôpital de la Timone, Pôle d'Imagerie, Marseille, France
| | - Fabrice Bartolomei
- Assistance Publique - Hôpitaux de Marseille, Hôpital de la Timone, Service de Neurophysiologie Clinique, Marseille, France
| | - Viktor Jirsa
- Aix Marseille Université, Inserm, Institut de Neurosciences des Systèmes, UMRS 1106, Marseille, France
| | - Anna Zakharova
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
| | - Simona Olmi
- Inria Sophia Antipolis Méditerranée Research Centre, MathNeuro Team, Valbonne, France
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, Sesto Fiorentino, Italy
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14
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Reed JD, Blackwell KT. Prediction of Neural Diameter From Morphology to Enable Accurate Simulation. Front Neuroinform 2021; 15:666695. [PMID: 34149388 PMCID: PMC8209307 DOI: 10.3389/fninf.2021.666695] [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: 02/10/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
Accurate neuron morphologies are paramount for computational model simulations of realistic neural responses. Over the last decade, the online repository NeuroMorpho.Org has collected over 140,000 available neuron morphologies to understand brain function and promote interaction between experimental and computational research. Neuron morphologies describe spatial aspects of neural structure; however, many of the available morphologies do not contain accurate diameters that are essential for computational simulations of electrical activity. To best utilize available neuron morphologies, we present a set of equations that predict dendritic diameter from other morphological features. To derive the equations, we used a set of NeuroMorpho.org archives with realistic neuron diameters, representing hippocampal pyramidal, cerebellar Purkinje, and striatal spiny projection neurons. Each morphology is separated into initial, branching children, and continuing nodes. Our analysis reveals that the diameter of preceding nodes, Parent Diameter, is correlated to diameter of subsequent nodes for all cell types. Branching children and initial nodes each required additional morphological features to predict diameter, such as path length to soma, total dendritic length, and longest path to terminal end. Model simulations reveal that membrane potential response with predicted diameters is similar to the original response for several tested morphologies. We provide our open source software to extend the utility of available NeuroMorpho.org morphologies, and suggest predictive equations may supplement morphologies that lack dendritic diameter and improve model simulations with realistic dendritic diameter.
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Affiliation(s)
- Jonathan D Reed
- Krasnow Institute of Advanced Study, George Mason University, Fairfax, VA, United States.,Department of Biology, George Mason University, Fairfax, VA, United States
| | - Kim T Blackwell
- Krasnow Institute of Advanced Study, George Mason University, Fairfax, VA, United States.,Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, United States
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15
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Grillner S, Robertson B, Kotaleski JH. Basal Ganglia—A Motion Perspective. Compr Physiol 2020; 10:1241-1275. [DOI: 10.1002/cphy.c190045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Lindroos R, Hellgren Kotaleski J. Predicting complex spikes in striatal projection neurons of the direct pathway following neuromodulation by acetylcholine and dopamine. Eur J Neurosci 2020; 53:2117-2134. [DOI: 10.1111/ejn.14891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/15/2020] [Accepted: 06/25/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Robert Lindroos
- Department of Neuroscience Karolinska Institutet Stockholm Sweden
| | - Jeanette Hellgren Kotaleski
- Department of Neuroscience Karolinska Institutet Stockholm Sweden
- Science for Life Laboratory Department of Computational Science and Technology The Royal Institute of Technology Stockholm Sweden
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17
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Hjorth JJJ, Kozlov A, Carannante I, Frost Nylén J, Lindroos R, Johansson Y, Tokarska A, Dorst MC, Suryanarayana SM, Silberberg G, Hellgren Kotaleski J, Grillner S. The microcircuits of striatum in silico. Proc Natl Acad Sci U S A 2020; 117:9554-9565. [PMID: 32321828 PMCID: PMC7197017 DOI: 10.1073/pnas.2000671117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The basal ganglia play an important role in decision making and selection of action primarily based on input from cortex, thalamus, and the dopamine system. Their main input structure, striatum, is central to this process. It consists of two types of projection neurons, together representing 95% of the neurons, and 5% of interneurons, among which are the cholinergic, fast-spiking, and low threshold-spiking subtypes. The membrane properties, soma-dendritic shape, and intrastriatal and extrastriatal synaptic interactions of these neurons are quite well described in the mouse, and therefore they can be simulated in sufficient detail to capture their intrinsic properties, as well as the connectivity. We focus on simulation at the striatal cellular/microcircuit level, in which the molecular/subcellular and systems levels meet. We present a nearly full-scale model of the mouse striatum using available data on synaptic connectivity, cellular morphology, and electrophysiological properties to create a microcircuit mimicking the real network. A striatal volume is populated with reconstructed neuronal morphologies with appropriate cell densities, and then we connect neurons together based on appositions between neurites as possible synapses and constrain them further with available connectivity data. Moreover, we simulate a subset of the striatum involving 10,000 neurons, with input from cortex, thalamus, and the dopamine system, as a proof of principle. Simulation at this biological scale should serve as an invaluable tool to understand the mode of operation of this complex structure. This platform will be updated with new data and expanded to simulate the entire striatum.
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Affiliation(s)
- J J Johannes Hjorth
- Science for Life Laboratory, School of Electrical Engeneering and Computer Science, Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Alexander Kozlov
- Science for Life Laboratory, School of Electrical Engeneering and Computer Science, Royal Institute of Technology, SE-10044 Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Ilaria Carannante
- Science for Life Laboratory, School of Electrical Engeneering and Computer Science, Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | | | - Robert Lindroos
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Yvonne Johansson
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Anna Tokarska
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Matthijs C Dorst
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | | | - Gilad Silberberg
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engeneering and Computer Science, Royal Institute of Technology, SE-10044 Stockholm, Sweden;
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institutet, SE-17165 Stockholm
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18
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Lahiri AK, Bevan MD. Dopaminergic Transmission Rapidly and Persistently Enhances Excitability of D1 Receptor-Expressing Striatal Projection Neurons. Neuron 2020; 106:277-290.e6. [PMID: 32075716 PMCID: PMC7182485 DOI: 10.1016/j.neuron.2020.01.028] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/26/2019] [Accepted: 01/22/2020] [Indexed: 12/13/2022]
Abstract
Substantia nigra dopamine neurons have been implicated in the initiation and invigoration of movement, presumably through their modulation of striatal projection neuron (SPN) activity. However, the impact of native dopaminergic transmission on SPN excitability has not been directly demonstrated. Using perforated patch-clamp recording, we found that optogenetic stimulation of nigrostriatal dopamine axons rapidly and persistently elevated the excitability of D1 receptor-expressing SPNs (D1-SPNs). The evoked firing of D1-SPNs increased within hundreds of milliseconds of stimulation and remained elevated for ≥ 10 min. Consistent with the negative modulation of depolarization- and Ca2+-activated K+ currents, dopaminergic transmission accelerated subthreshold depolarization in response to current injection, reduced the latency to fire, and transiently diminished action potential afterhyperpolarization. Persistent modulation was protein kinase A dependent and associated with a reduction in action potential threshold. Together, these data demonstrate that dopaminergic transmission potently increases D1-SPN excitability with a time course that could support subsecond and sustained behavioral control.
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Affiliation(s)
- Asha K Lahiri
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mark D Bevan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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19
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Amsalem O, Eyal G, Rogozinski N, Gevaert M, Kumbhar P, Schürmann F, Segev I. An efficient analytical reduction of detailed nonlinear neuron models. Nat Commun 2020; 11:288. [PMID: 31941884 PMCID: PMC6962154 DOI: 10.1038/s41467-019-13932-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022] Open
Abstract
Detailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these models are computationally expensive, considerably curtailing their utility. Neuron_Reduce is a new analytical approach to reduce the morphological complexity and computational time of nonlinear neuron models. Synapses and active membrane channels are mapped to the reduced model preserving their transfer impedance to the soma; synapses with identical transfer impedance are merged into one NEURON process still retaining their individual activation times. Neuron_Reduce accelerates the simulations by 40-250 folds for a variety of cell types and realistic number (10,000-100,000) of synapses while closely replicating voltage dynamics and specific dendritic computations. The reduced neuron-models will enable realistic simulations of neural networks at unprecedented scale, including networks emerging from micro-connectomics efforts and biologically-inspired "deep networks". Neuron_Reduce is publicly available and is straightforward to implement.
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Affiliation(s)
- Oren Amsalem
- Department of Neurobiology, Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Guy Eyal
- Department of Neurobiology, Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Noa Rogozinski
- Department of Neurobiology, Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Michael Gevaert
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, 1202, Geneva, Switzerland
| | - Pramod Kumbhar
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, 1202, Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, 1202, Geneva, Switzerland
| | - Idan Segev
- Department of Neurobiology, Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
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20
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Kumbhar P, Hines M, Fouriaux J, Ovcharenko A, King J, Delalondre F, Schürmann F. CoreNEURON : An Optimized Compute Engine for the NEURON Simulator. Front Neuroinform 2019; 13:63. [PMID: 31616273 PMCID: PMC6763692 DOI: 10.3389/fninf.2019.00063] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/04/2019] [Indexed: 12/01/2022] Open
Abstract
The NEURON simulator has been developed over the past three decades and is widely used by neuroscientists to model the electrical activity of neuronal networks. Large network simulation projects using NEURON have supercomputer allocations that individually measure in the millions of core hours. Supercomputer centers are transitioning to next generation architectures and the work accomplished per core hour for these simulations could be improved by an order of magnitude if NEURON was able to better utilize those new hardware capabilities. In order to adapt NEURON to evolving computer architectures, the compute engine of the NEURON simulator has been extracted and has been optimized as a library called CoreNEURON. This paper presents the design, implementation, and optimizations of CoreNEURON. We describe how CoreNEURON can be used as a library with NEURON and then compare performance of different network models on multiple architectures including IBM BlueGene/Q, Intel Skylake, Intel MIC and NVIDIA GPU. We show how CoreNEURON can simulate existing NEURON network models with 4-7x less memory usage and 2-7x less execution time while maintaining binary result compatibility with NEURON.
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Affiliation(s)
- Pramod Kumbhar
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Michael Hines
- Department of Neuroscience, Yale University, New Haven, CT, United States
| | - Jeremy Fouriaux
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Aleksandr Ovcharenko
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - James King
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Fabien Delalondre
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
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21
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A computational model for gonadotropin releasing cells in the teleost fish medaka. PLoS Comput Biol 2019; 15:e1006662. [PMID: 31437161 PMCID: PMC6726249 DOI: 10.1371/journal.pcbi.1006662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 09/04/2019] [Accepted: 08/01/2019] [Indexed: 01/16/2023] Open
Abstract
Pituitary endocrine cells fire action potentials (APs) to regulate their cytosolic Ca2+ concentration and hormone secretion rate. Depending on animal species, cell type, and biological conditions, pituitary APs are generated either by TTX-sensitive Na+ currents (INa), high-voltage activated Ca2+ currents (ICa), or by a combination of the two. Previous computational models of pituitary cells have mainly been based on data from rats, where INa is largely inactivated at the resting potential, and spontaneous APs are predominantly mediated by ICa. Unlike in rats, spontaneous INa-mediated APs are consistently seen in pituitary cells of several other animal species, including several species of fish. In the current work we develop a computational model of gonadotropin releasing cells in the teleost fish medaka (Oryzias latipes). The model stands out from previous modeling efforts by being (1) the first model of a pituitary cell in teleosts, (2) the first pituitary cell model that fires sponateous APs that are predominantly mediated by INa, and (3) the first pituitary cell model where the kinetics of the depolarizing currents, INa and ICa, are directly fitted to voltage-clamp data. We explore the firing properties of the model, and compare it to the properties of previous models that fire ICa-based APs. We put a particular focus on how the big conductance K+ current (IBK) modulates the AP shape. Interestingly, we find that IBK can prolong AP duration in models that fire ICa-based APs, while it consistently shortens the duration of the predominantly INa-mediated APs in the medaka gonadotroph model. Although the model is constrained to experimental data from gonadotroph cells in medaka, it may likely provide insights also into other pituitary cell types that fire INa-mediated APs. Excitable cells elicit electrical pulses called action potentials (APs), which are generated and shaped by a combination of ion channels in the cell membrane. Since one type of ion channels is permeable to Ca2+ ions, there is typically an influx of Ca2+ during an AP. Pituitary cells therefore use AP firing to regulate their cytosolic Ca2+ concentration, which in turn controls their hormone secretion rate. The amount of Ca2+ that enters during an AP depends strongly on how long it lasts, and it is therefore important to understand the mechanisms that control this. Pituitary APs are generally mediated by a combination of Ca2+ channels and Na+ channels, and the relative contributions of from the two vary between cell types, animal species and biological conditions. Previous computer models have predominantly been adapted to data from pituitary cells which tend to fire Ca2+-based APs. Here we develop a new model, adapted to data from pituitary cells in the fish medaka, which APs that are predominantly Na+-based, and compare its dynamical properties to the previous models that fire Ca2+-based APs.
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22
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Essa MM, Moghadas M, Ba-Omar T, Walid Qoronfleh M, Guillemin GJ, Manivasagam T, Justin-Thenmozhi A, Ray B, Bhat A, Chidambaram SB, Fernandes AJ, Song BJ, Akbar M. Protective Effects of Antioxidants in Huntington’s Disease: an Extensive Review. Neurotox Res 2019; 35:739-774. [DOI: 10.1007/s12640-018-9989-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023]
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23
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Morita K, Kawaguchi Y. A Dual Role Hypothesis of the Cortico-Basal-Ganglia Pathways: Opponency and Temporal Difference Through Dopamine and Adenosine. Front Neural Circuits 2019; 12:111. [PMID: 30687019 PMCID: PMC6338031 DOI: 10.3389/fncir.2018.00111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/29/2018] [Indexed: 01/07/2023] Open
Abstract
The hypothesis that the basal-ganglia direct and indirect pathways represent goodness (or benefit) and badness (or cost) of options, respectively, explains a wide range of phenomena. However, this hypothesis, named the Opponent Actor Learning (OpAL), still has limitations. Structurally, the OpAL model does not incorporate differentiation of the two types of cortical inputs to the basal-ganglia pathways received from intratelencephalic (IT) and pyramidal-tract (PT) neurons. Functionally, the OpAL model does not describe the temporal-difference (TD)-type reward-prediction-error (RPE), nor explains how RPE is calculated in the circuitry connecting to the DA neurons. In fact, there is a different hypothesis on the basal-ganglia pathways and DA, named the Cortico-Striatal-Temporal-Difference (CS-TD) model. The CS-TD model differentiates the IT and PT inputs, describes the TD-type RPE, and explains how TD-RPE is calculated. However, a critical difficulty in this model lies in its assumption that DA induces the same direction of plasticity in both direct and indirect pathways, which apparently contradicts the experimentally observed opposite effects of DA on these pathways. Here, we propose a new hypothesis that integrates the OpAL and CS-TD models. Specifically, we propose that the IT-basal-ganglia pathways represent goodness/badness of current options while the PT-indirect pathway represents the overall value of the previously chosen option, and both of these have influence on the DA neurons, through the basal-ganglia output, so that a variant of TD-RPE is calculated. A key assumption is that opposite directions of plasticity are induced upon phasic activation of DA neurons in the IT-indirect pathway and PT-indirect pathway because of different profiles of IT and PT inputs. Specifically, at PT→indirect-pathway-medium-spiny-neuron (iMSN) synapses, sustained glutamatergic inputs generate rich adenosine, which allosterically prevents DA-D2 receptor signaling and instead favors adenosine-A2A receptor signaling. Then, phasic DA-induced phasic adenosine, which reflects TD-RPE, causes long-term synaptic potentiation. In contrast, at IT→iMSN synapses where adenosine is scarce, phasic DA causes long-term synaptic depression via D2 receptor signaling. This new Opponency and Temporal-Difference (OTD) model provides unique predictions, part of which is potentially in line with recently reported activity patterns of neurons in the globus pallidus externus on the indirect pathway.
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Affiliation(s)
- Kenji Morita
- Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study, Tokyo, Japan
| | - Yasuo Kawaguchi
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, Graduate University for Advanced Studies, Okazaki, Japan
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