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Rosado J, Bui VD, Haas CA, Beck J, Queisser G, Vlachos A. Calcium modeling of spine apparatus-containing human dendritic spines demonstrates an “all-or-nothing” communication switch between the spine head and dendrite. PLoS Comput Biol 2022; 18:e1010069. [PMID: 35468131 PMCID: PMC9071165 DOI: 10.1371/journal.pcbi.1010069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/05/2022] [Accepted: 03/30/2022] [Indexed: 11/19/2022] Open
Abstract
Dendritic spines are highly dynamic neuronal compartments that control the synaptic transmission between neurons. Spines form ultrastructural units, coupling synaptic contact sites to the dendritic shaft and often harbor a spine apparatus organelle, composed of smooth endoplasmic reticulum, which is responsible for calcium sequestration and release into the spine head and neck. The spine apparatus has recently been linked to synaptic plasticity in adult human cortical neurons. While the morphological heterogeneity of spines and their intracellular organization has been extensively demonstrated in animal models, the influence of spine apparatus organelles on critical signaling pathways, such as calcium-mediated dynamics, is less well known in human dendritic spines. In this study we used serial transmission electron microscopy to anatomically reconstruct nine human cortical spines in detail as a basis for modeling and simulation of the calcium dynamics between spine and dendrite. The anatomical study of reconstructed human dendritic spines revealed that the size of the postsynaptic density correlates with spine head volume and that the spine apparatus volume is proportional to the spine volume. Using a newly developed simulation pipeline, we have linked these findings to spine-to-dendrite calcium communication. While the absence of a spine apparatus, or the presence of a purely passive spine apparatus did not enable any of the reconstructed spines to relay a calcium signal to the dendritic shaft, the calcium-induced calcium release from this intracellular organelle allowed for finely tuned “all-or-nothing” spine-to-dendrite calcium coupling; controlled by spine morphology, neck plasticity, and ryanodine receptors. Our results suggest that spine apparatus organelles are strategically positioned in the neck of human dendritic spines and demonstrate their potential relevance to the maintenance and regulation of spine-to-dendrite calcium communication. During the past decade it has become increasingly clear that abnormal synaptic plasticity is a major hallmark of neurological and cognitive disorders. Developing a better understanding of the synaptic plasticity process, which describes the ability of neurons to adapt their contacts in an activity-dependent manner, will lead to improved treatment of many neurological and cognitive disorders. It is known that calcium-dependent events such as synaptic transmission, intracellular calcium release, and calcium wave propagation, are required for many types of synaptic plasticity expression. However, the biological significance of these processes in neurons of the adult human cortex remains unknown. Due to technical limitations and ethical concerns, experimental data addressing this biologically and clinically relevant topic are not available. Therefore, we have implemented a computational model to study the intracellular calcium dynamics in realistic human dendritic spines based on detailed morphological reconstructions. With our model and simulations, we have established the morphological and biological requirements for the propagation of calcium from spines into the dendrites. Our results suggest a critical role for the calcium-storing spine apparatus organelle in regulating calcium homeostasis and propagation in human dendritic spines.
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Affiliation(s)
- James Rosado
- Department of Mathematics, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Viet Duc Bui
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carola A. Haas
- Department of Neurosurgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gillian Queisser
- Department of Mathematics, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GQ); (AV)
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- * E-mail: (GQ); (AV)
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Shirinpour S, Hananeia N, Rosado J, Tran H, Galanis C, Vlachos A, Jedlicka P, Queisser G, Opitz A. Multi-scale modeling toolbox for single neuron and subcellular activity under Transcranial Magnetic Stimulation. Brain Stimul 2021; 14:1470-1482. [PMID: 34562659 PMCID: PMC8608742 DOI: 10.1016/j.brs.2021.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Transcranial Magnetic Stimulation (TMS) is a widely used non-invasive brain stimulation method. However, its mechanism of action and the neural response to TMS are still poorly understood. Multi-scale modeling can complement experimental research to study the subcellular neural effects of TMS. At the macroscopic level, sophisticated numerical models exist to estimate the induced electric fields. However, multi-scale computational modeling approaches to predict TMS cellular and subcellular responses, crucial to understanding TMS plasticity inducing protocols, are not available so far. OBJECTIVE We develop an open-source multi-scale toolbox Neuron Modeling for TMS (NeMo-TMS) to address this problem. METHODS NeMo-TMS generates accurate neuron models from morphological reconstructions, couples them to the external electric fields induced by TMS, and simulates the cellular and subcellular responses of single-pulse and repetitive TMS. RESULTS We provide examples showing some of the capabilities of the toolbox. CONCLUSION NeMo-TMS toolbox allows researchers a previously not available level of detail and precision in realistically modeling the physical and physiological effects of TMS.
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Affiliation(s)
- Sina Shirinpour
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, USA.
| | - Nicholas Hananeia
- Faculty of Medicine, ICAR3R - Interdisciplinary Centre for 3Rs in Animal Research, Justus-Liebig-University, Giessen, Germany
| | - James Rosado
- Department of Mathematics, Temple University, Philadelphia, USA
| | - Harry Tran
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, USA
| | - Christos Galanis
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany; Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Jedlicka
- Faculty of Medicine, ICAR3R - Interdisciplinary Centre for 3Rs in Animal Research, Justus-Liebig-University, Giessen, Germany
| | | | - Alexander Opitz
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, USA.
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Abstract
The brain is a complex organ operating on multiple scales. From molecular events that inform electrical and biochemical cellular responses, the brain interconnects processes all the way up to the massive network size of billions of brain cells. This strongly coupled, nonlinear, system has been subject to research that has turned increasingly multidisciplinary. The seminal work of Hodgkin and Huxley in the 1950s made use of experimental data to derive a coherent physical model of electrical signaling in neurons, which can be solved using mathematical and computational methods, thus bringing together neuroscience, physics, mathematics, and computer science. Over the last decades numerous projects have been dedicated to modeling and simulation of specific parts of molecular dynamics, neuronal signaling, and neural network behavior. Simulators have been developed around a specific objective and scale, in order to cope with the underlying computational complexity. Often times a dimension reduction approach allows larger scale simulations, this however has the inherent drawback of losing insight into structure-function interplay at the cellular level. This paper gives an overview of the project NeuroBox that has the objective of integrating multiple brain scales and associated physical models into one unified framework. NeuroBox hosts geometry and anatomical reconstruction methods, such that detailed three-dimensional domains can be integrated into numerical simulations of models based on partial differential equations. The project further focusses on deriving numerical methods for handling complex computational domains, and to couple multiple spatial dimensions. The latter allows the user to specify in which parts of the biological problem high-dimensional representations are necessary and where low-dimensional approximations are acceptable. NeuroBox offers workflow user interfaces that are automatically generated with VRL-Studio and can be controlled by non-experts. The project further uses uG4 as the numerical backend, and therefore accesses highly advanced discretization methods as well as hierarchical and scalable numerical solvers for very large neurobiological problems.
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Grein S, Qi G, Queisser G. Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis. Front Comput Neurosci 2020; 14:42. [PMID: 32676020 PMCID: PMC7333680 DOI: 10.3389/fncom.2020.00042] [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: 10/30/2019] [Accepted: 04/17/2020] [Indexed: 12/02/2022] Open
Abstract
Neuron classification is an important component in analyzing network structure and quantifying the effect of neuron topology on signal processing. Current quantification and classification approaches rely on morphology projection onto lower-dimensional spaces. In this paper a 3D visualization and quantification tool is presented. The Density Visualization Pipeline (DVP) computes, visualizes and quantifies the density distribution, i.e., the "mass" of interneurons. We use the DVP to characterize and classify a set of GABAergic interneurons. Classification of GABAergic interneurons is of crucial importance to understand on the one hand their various functions and on the other hand their ubiquitous appearance in the neocortex. 3D density map visualization and projection to the one-dimensional x, y, z subspaces show a clear distinction between the studied cells, based on these metrics. The DVP can be coupled to computational studies of the behavior of neurons and networks, in which network topology information is derived from DVP information. The DVP reads common neuromorphological file formats, e.g., Neurolucida XML files, NeuroMorpho.org SWC files and plain ASCII files. Full 3D visualization and projections of the density to 1D and 2D manifolds are supported by the DVP. All routines are embedded within the visual programming IDE VRL-Studio for Java which allows the definition and rapid modification of analysis workflows.
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Affiliation(s)
- Stephan Grein
- Department of Mathematics, Temple University, Philadelphia, PA, United States
| | - Guanxiao Qi
- Institute of Neuroscience and Medicine (INM-10), Research Centre Jülich, Jülich, Germany
| | - Gillian Queisser
- Department of Mathematics, Temple University, Philadelphia, PA, United States
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Breit M, Kessler M, Stepniewski M, Vlachos A, Queisser G. Spine-to-Dendrite Calcium Modeling Discloses Relevance for Precise Positioning of Ryanodine Receptor-Containing Spine Endoplasmic Reticulum. Sci Rep 2018; 8:15624. [PMID: 30353066 PMCID: PMC6199256 DOI: 10.1038/s41598-018-33343-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/18/2018] [Indexed: 12/15/2022] Open
Abstract
The endoplasmic reticulum (ER) forms a complex endomembrane network that reaches into the cellular compartments of a neuron, including dendritic spines. Recent work discloses that the spine ER is a dynamic structure that enters and leaves spines. While evidence exists that ER Ca2+ release is involved in synaptic plasticity, the role of spine ER morphology remains unknown. Combining a new 3D spine generator with 3D Ca2+ modeling, we addressed the relevance of ER positioning on spine-to-dendrite Ca2+ signaling. Our simulations, which account for Ca2+ exchange on the plasma membrane and ER, show that spine ER needs to be present in distinct morphological conformations in order to overcome a barrier between the spine and dendritic shaft. We demonstrate that RyR-carrying spine ER promotes spine-to-dendrite Ca2+ signals in a position-dependent manner. Our simulations indicate that RyR-carrying ER can initiate time-delayed Ca2+ reverberation, depending on the precise position of the spine ER. Upon spine growth, structural reorganization of the ER restores spine-to-dendrite Ca2+ communication, while maintaining aspects of Ca2+ homeostasis in the spine head. Our work emphasizes the relevance of precise positioning of RyR-containing spine ER in regulating the strength and timing of spine Ca2+ signaling, which could play an important role in tuning spine-to-dendrite Ca2+ communication and homeostasis.
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Affiliation(s)
- Markus Breit
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Marcus Kessler
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Martin Stepniewski
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany. .,Bernstein Center Freiburg, University of Freiburg, Freiburg, 79104, Germany.
| | - Gillian Queisser
- Department of Mathematics, Temple University, Philadelphia, USA.
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Breit M, Queisser G. What Is Required for Neuronal Calcium Waves? A Numerical Parameter Study. JOURNAL OF MATHEMATICAL NEUROSCIENCE 2018; 8:9. [PMID: 30006849 PMCID: PMC6045568 DOI: 10.1186/s13408-018-0064-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/15/2018] [Indexed: 06/03/2023]
Abstract
Neuronal calcium signals propagating by simple diffusion and reaction with mobile and stationary buffers are limited to cellular microdomains. The distance intracellular calcium signals can travel may be significantly increased by means of calcium-induced calcium release from internal calcium stores, notably the endoplasmic reticulum. The organelle, which can be thought of as a cell-within-a-cell, is able to sequester large amounts of cytosolic calcium ions via SERCA pumps and selectively release them into the cytosol through ryanodine receptor channels leading to the formation of calcium waves. In this study, we set out to investigate the basic properties of such dendritic calcium waves and how they depend on the three parameters dendrite radius, ER radius and ryanodine receptor density in the endoplasmic membrane. We demonstrate that there are stable and abortive regimes for calcium waves, depending on the above morphological and physiological parameters. In stable regimes, calcium waves can travel across long dendritic distances, similar to electrical action potentials. We further observe that abortive regimes exist, which could be relevant for spike-timing dependent plasticity, as travel distances and wave velocities vary with changing intracellular architecture. For some of these regimes, analytic functions could be derived that fit the simulation data. In parameter spaces, that are non-trivially influenced by the three-dimensional calcium concentration profile, we were not able to derive such a functional description, demonstrating the mathematical requirement to model and simulate biochemical signaling in three-dimensional space.
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Affiliation(s)
- Markus Breit
- G-CSC, Goethe University Frankfurt, Frankfurt am Main, Germany
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Mörschel K, Breit M, Queisser G. Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph. Neuroinformatics 2018; 15:247-269. [PMID: 28447297 DOI: 10.1007/s12021-017-9329-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.
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Affiliation(s)
- Konstantin Mörschel
- Goethe Center for Scientific Computing, Goethe University Frankfurt, Kettenhofweg 139, 60325, Frankfurt am Main, Germany
| | - Markus Breit
- Goethe Center for Scientific Computing, Goethe University Frankfurt, Kettenhofweg 139, 60325, Frankfurt am Main, Germany
| | - Gillian Queisser
- Department of Mathematics, Temple University, 1805 N Broad Street, Philadelphia, PA, 19122-6094, USA.
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