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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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Daria VR, Castañares ML, Bachor HA. Spatio-temporal parameters for optical probing of neuronal activity. Biophys Rev 2021; 13:13-33. [PMID: 33747244 PMCID: PMC7930150 DOI: 10.1007/s12551-021-00780-2] [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: 12/13/2020] [Accepted: 01/01/2021] [Indexed: 12/28/2022] Open
Abstract
The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.
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Affiliation(s)
- Vincent R. Daria
- Research School of Physics, The Australian National University, Canberra, Australia
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | | | - Hans-A. Bachor
- Research School of Physics, The Australian National University, Canberra, Australia
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Bono J, Wilmes KA, Clopath C. Modelling plasticity in dendrites: from single cells to networks. Curr Opin Neurobiol 2017; 46:136-141. [PMID: 28888857 DOI: 10.1016/j.conb.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/23/2017] [Indexed: 02/06/2023]
Abstract
One of the key questions in neuroscience is how our brain self-organises to efficiently process information. To answer this question, we need to understand the underlying mechanisms of plasticity and their role in shaping synaptic connectivity. Theoretical neuroscience typically investigates plasticity on the level of neural networks. Neural network models often consist of point neurons, completely neglecting neuronal morphology for reasons of simplicity. However, during the past decades it became increasingly clear that inputs are locally processed in the dendrites before they reach the cell body. Dendritic properties enable local interactions between synapses and location-dependent modulations of inputs, rendering the position of synapses on dendrites highly important. These insights changed our view of neurons, such that we now think of them as small networks of nearly independent subunits instead of a simple point. Here, we propose that understanding how the brain processes information strongly requires that we consider the following properties: which plasticity mechanisms are present in the dendrites and how do they enable the self-organisation of synapses across the dendritic tree for efficient information processing? Ultimately, dendritic plasticity mechanisms can be studied in networks of neurons with dendrites, possibly uncovering unknown mechanisms that shape the connectivity in our brains.
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Affiliation(s)
- Jacopo Bono
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Katharina A Wilmes
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Claudia Clopath
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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Poznanski RR, Cacha LA, Al-Wesabi YMS, Ali J, Bahadoran M, Yupapin PP, Yunus J. Solitonic conduction of electrotonic signals in neuronal branchlets with polarized microstructure. Sci Rep 2017; 7:2746. [PMID: 28566682 PMCID: PMC5451471 DOI: 10.1038/s41598-017-01849-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 04/07/2017] [Indexed: 11/25/2022] Open
Abstract
A model of solitonic conduction in neuronal branchlets with microstructure is presented. The application of cable theory to neurons with microstructure results in a nonlinear cable equation that is solved using a direct method to obtain analytical approximations of traveling wave solutions. It is shown that a linear superposition of two oppositely directed traveling waves demonstrate solitonic interaction: colliding waves can penetrate through each other, and continue fully intact as the exact pulses that entered the collision. These findings indicate that microstructure when polarized can sustain solitary waves that propagate at a constant velocity without attenuation or distortion in the absence of synaptic transmission. Solitonic conduction in a neuronal branchlet arising from polarizability of its microstructure is a novel signaling mode of electrotonic signals in thin processes (<0.5 μm diameter).
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Affiliation(s)
- R R Poznanski
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
| | - L A Cacha
- Laser Centre, IBNU SINA ISIR, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Y M S Al-Wesabi
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - J Ali
- Laser Centre, IBNU SINA ISIR, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - M Bahadoran
- Department of Physics, Shiraz University of Technology, Shiraz, 313-71555, Iran
| | - P P Yupapin
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, District 7, Vietnam
- Faculty of Electrical & Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, District 7, Vietnam
| | - J Yunus
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
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Antic SD, Empson RM, Knöpfel T. Voltage imaging to understand connections and functions of neuronal circuits. J Neurophysiol 2016; 116:135-52. [PMID: 27075539 DOI: 10.1152/jn.00226.2016] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/11/2016] [Indexed: 12/30/2022] Open
Abstract
Understanding of the cellular mechanisms underlying brain functions such as cognition and emotions requires monitoring of membrane voltage at the cellular, circuit, and system levels. Seminal voltage-sensitive dye and calcium-sensitive dye imaging studies have demonstrated parallel detection of electrical activity across populations of interconnected neurons in a variety of preparations. A game-changing advance made in recent years has been the conceptualization and development of optogenetic tools, including genetically encoded indicators of voltage (GEVIs) or calcium (GECIs) and genetically encoded light-gated ion channels (actuators, e.g., channelrhodopsin2). Compared with low-molecular-weight calcium and voltage indicators (dyes), the optogenetic imaging approaches are 1) cell type specific, 2) less invasive, 3) able to relate activity and anatomy, and 4) facilitate long-term recordings of individual cells' activities over weeks, thereby allowing direct monitoring of the emergence of learned behaviors and underlying circuit mechanisms. We highlight the potential of novel approaches based on GEVIs and compare those to calcium imaging approaches. We also discuss how novel approaches based on GEVIs (and GECIs) coupled with genetically encoded actuators will promote progress in our knowledge of brain circuits and systems.
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Affiliation(s)
- Srdjan D Antic
- Stem Cell Institute, Institute for Systems Genomics, UConn Health, Farmington, Connecticut
| | - Ruth M Empson
- Department of Physiology, Brain Research New Zealand, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; and
| | - Thomas Knöpfel
- Division of Brain Sciences, Department of Medicine and Centre for Neurotechnology, Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
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Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW. Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 2016; 316:344-66. [PMID: 26746357 PMCID: PMC4724569 DOI: 10.1016/j.neuroscience.2015.12.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/08/2023]
Abstract
Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium (Ca(2+)) regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. The network contained 776 compartmental neurons arranged in the cortical layers, connected using synapses containing AMPA/NMDA/GABAA/GABAB receptors. Metabotropic glutamate receptors (mGluR) produced inositol triphosphate (IP3) which caused the release of Ca(2+) from endoplasmic reticulum (ER) stores, with reuptake by sarco/ER Ca(2+)-ATP-ase pumps (SERCA), and influence on HCN channels. Stimulus-induced depolarization led to Ca(2+) influx via NMDA and voltage-gated Ca(2+) channels (VGCCs). After a delay, mGluR activation led to ER Ca(2+) release via IP3 receptors. These factors increased HCN channel conductance and produced firing lasting for ∼1min. The model displayed inter-scale synergies among synaptic weights, excitation/inhibition balance, firing rates, membrane depolarization, Ca(2+) levels, regulation of HCN channels, and induction of persistent activity. The interaction between inhibition and Ca(2+) at the HCN channel nexus determined a limited range of inhibition strengths for which intracellular Ca(2+) could prepare population-specific persistent activity. Interactions between metabotropic and ionotropic inputs to the neuron demonstrated how multiple pathways could contribute in a complementary manner to persistent activity. Such redundancy and complementarity via multiple pathways is a critical feature of biological systems. Mediation of activation at different time scales, and through different pathways, would be expected to protect against disruption, in this case providing stability for persistent activity.
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Affiliation(s)
- S A Neymotin
- Department of Physiology & Pharmacology, SUNY Downstate, 450 Clarkson Avenue, Brooklyn, NY 11203, USA; Department of Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - R A McDougal
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - A S Bulanova
- Department of Physiology & Pharmacology, SUNY Downstate, 450 Clarkson Avenue, Brooklyn, NY 11203, USA; Department of Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - M Zeki
- Department of Mathematics, Zirve University, 27260 Gaziantep, Turkey.
| | - P Lakatos
- Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA.
| | - D Terman
- Department of Mathematics, The Ohio State University, 231 W 18th Avenue, Columbus, OH 43210, USA.
| | - M L Hines
- Department of Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - W W Lytton
- Department of Physiology & Pharmacology, SUNY Downstate, 450 Clarkson Avenue, Brooklyn, NY 11203, USA; Department of Neurology, SUNY Downstate, 450 Clarkson Avenue, Brooklyn, NY 11203, USA; Department Neurology, Kings County Hospital Center, 451 Clarkson Avenue, Brooklyn, NY 11203, USA.
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