Name: 3d modeling of dendritic spines with synaptic plasticity
Uploaded: 2020-05-18T13:30:00
Description: Watch this Scientific Journal Video about 3D Modeling of Dendritic Spines with Synaptic Plasticity at JoVE.com

This work was supported in part by the Sao Paulo State Science Foundation (FAPESP) grant #2015/50122-0 and IRTG-GRTK 1740/2, by the IBM/FAPESP grant #2016/18825-4, and by the FAPESP grant #2018/06504-4.

NOTE: Please see the Supplementary file 1 for the glossary of terms used in this protocol.
1. Install Blender, CellBlender, and MCell
NOTE: This protocol requires installation of MCell, Blender, and Cell Blender.
<ol>
	<li>Download and install the software on the MCell homepage (https://mcell.org/tutorials_iframe.html). Go to downloads on the top of the page and then follow the step-by-step instructions to download and install the software in the ...

<ol>
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This article presents a method for the construction of 3D meshes for modeling reaction-diffusion synaptic plasticity processes in a dendritic segment with dendritic spines. The developed model contains a dendritic segment with few dendritic spines. The lateral diffusion and reaction of AMPARs with synaptic anchors allow the simulation of the basal dynamics. The critical steps in the protocol are cutting the sphere for the creation of the top of the spine head (Figure 1, ...

Synaptic plasticity has been associated with learning and memory1. Synaptic plasticity, such as long-term potentiation (LTP) and long-term depression (LTD), is associated respectively with the insertion and removal of AMPA receptors (AMPARs) in and out of the synaptic membrane2. The AMPAR synapses are located on top of the small volume structures called dendritic spines3. Each spine contains a protein dense region in the postsynaptic membrane called the postsynaptic density (PSD). Anchor proteins at the PSD trap AMPARs in the synaptic region. There are few copies of AMPARs within a single synapse and the trafficking and reaction of AMPARs with other species in dendritic spines is a stochastic process2,4. There are several compartmental models of synaptic receptor trafficking at dendritic spines5,6,7,8. However, there is a lack of stochastic computational models of the trafficking of AMPARs associated with synaptic plasticity at the 3D structures of the dendrites and their dendritic spines.
Computational modeling is a useful tool to investigate the mechanisms underlying the dynamics of complex systems such as the reaction-diffusion of AMPARs in dendritic spines during the occurrence of synaptic plasticity9,10,11,12. The model can be used to visualize complex scenarios, varying sensitive parameters and making important predictions in scientific conditions involving many variables that are difficult or impossible to control experimental12,13. Defining the level of detail of a computational model is a fundamental step in obtaining accurate information about the modeled phenomenon. An ideal computational model is a delicate balance between complexity and simplicity to capture the essential characteristics of the natural phenomena without being computationally prohibitive. Computational models that are too detailed can be expensive to compute. On the other hand, systems that are poorly detailed can lack the fundamental components that are essential to capture the dynamics of the phenomenon. Although 3D modeling of dendritic spines is computationally more expensive than 2D and 1D, there are conditions, such as in complex systems with many nonlinear variables reacting and diffusing in time and 3D space, for which modeling at a 3D level is essential to obtain insights about the functioning of the system. Further, the complexity can be reduced carefully to preserve the essential characteristics of a lower-dimensional model.
In a stochastic system with few copies of a given species within a small volume, the average dynamics of the system deviates from the average dynamics of a large population. In this case, the stochastic computational modeling of reaction-diffusing particles is required. This work introduces a method for stochastic modeling reaction-diffusion of a few copies of AMPARs in 3D dendritic spines. The purpose of this method is to develop a 3D computational model of a dendritic segment with dendritic spines and their synapses for modeling synaptic plasticity.
The method uses the software&#160;MCell to solve the model numerically, Blender for constructing 3D meshes, and CellBlender to create and visualize the MCell simulations, including the spatiotemporal reaction-diffusion of molecules in 3D meshes14,15,16. Blender is a suite for the creation of meshes and CellBlender is an add-on for the base software Blender. MCell is a Monte Carlo simulator for the reaction-diffusion of single molecules17.
The rationale behind the use of this method consists of modeling synaptic plasticity to achieve a better understanding of this phenomenon in the microphysiological environment of the dendritic spines14. Particularly, this method allows the simulation of homosynaptic potentiation, homosynaptic depression, and heterosynaptic plasticity between dendritic spines14.
The features of this method include modeling the 3D geometric structure of the dendrite and its synapses, the diffusion by random walk, and the chemical reactions of the molecules involved with synaptic plasticity. This method provides the advantage of creating rich environments to test hypotheses and make predictions about the functioning of a complex nonlinear system with a large number of variables. In addition, this method can be applied not only for studying synaptic plasticity but also for studying stochastic reaction-diffusion of molecules in 3D mesh structures in general.
Alternatively, 3D meshes of dendritic structures can be constructed directly in Blender from electron microscope serial reconstructions18. Although meshes based on serial reconstructions provide 3D structures, access to the experimental data is not always available. Thus, the construction of meshes adapted from basic geometric structures, as described in the present protocol, provides flexibility to develop customized dendritic segments with dendritic spines.
Another alternative computational method is the bulk simulation of well-mixed reactions in a regular volume9,10,11,19,20,21,22. The bulk simulations are very efficient in solving the reactions of many species within a single well-mixed volume23, but the bulk approach is extremely slow to solve the reaction-diffusion of molecules within many well-mixed voxels in a high-resolution 3D mesh. On the other hand, the present method using MCell simulations of reaction-diffusion of individual particles works efficiently in high-resolution 3D meshes15.
Before using this method, one should ask whether the phenomenon studied requires a stochastic reaction-diffusion approach in a 3D mesh. If the phenomenon has few copies (less than 1,000) of at least one of the reacting species diffusing in a complex geometric structure with small volume compartments such as dendritic spines, then stochastic modeling of reaction-diffusion in 3D meshes is appropriate for the application.
There are several steps required to construct a 3D computational model of a dendritic segment containing dendritic spines with synaptic plasticity. The main steps are the installation of the proper software for the construction of the model, the construction of a single dendritic spine to be used as a template to create multiple spines, and the creation of a dendritic segment that is connected with multiple dendritic spines. The step for modeling synaptic plasticity consists of inserting anchors at&#160;the PSD region and AMPARs in the dendritic segment and dendritic spines. Then, kinetic reactions between the anchors located at&#160;the PSD and AMPARs are defined to produce complexed anchor-AMPAR species that trap the AMPARs at&#160;the synaptic region. Respectively, the increase and decrease of the affinity between the anchors and the synaptic AMPARs create the process of LTP and LTD.

<table>
	<tbody>
		<tr>
			<td>Blender</td>
			<td>Blender Foundation</td>
			<td></td>
			<td>https://www.blender.org/</td>
		</tr>
		<tr>
			<td>CellBlender</td>
			<td>University of Pittsburgh</td>
			<td></td>
			<td>https://mcell.org/</td>
		</tr>
		<tr>
			<td>Mcell</td>
			<td>University of Pittsburgh</td>
			<td></td>
			<td>https://mcell.org/</td>
		</tr>
	</tbody>
</table>

3d modeling of dendritic spines with synaptic plasticity

Computational modeling of diffusion and reaction of chemical species in a three-dimensional (3D) geometry is a fundamental method to understand the mechanisms of synaptic plasticity in dendritic spines. In this protocol, the detailed 3D structure of the dendrites and dendritic spines is modeled with meshes on the software Blender with CellBlender. The synaptic and extrasynaptic regions are defined on the mesh. Next, the synaptic receptor and synaptic anchor molecules are defined with their diffusion constants. Finally, the chemical reactions between synaptic receptors and synaptic anchors are included and the computational model is solved numerically with the software MCell. This method describes the spatiotemporal path of every single molecule in a 3D geometrical structure. Thus, it is very useful to study the trafficking of synaptic receptors in and out of the dendritic spines during the occurrence of synaptic plasticity. A limitation of this method is that the high number of molecules slows the speed of the simulations. Modeling of dendritic spines with this method allows the study of homosynaptic potentiation and depression within single spines and heterosynaptic plasticity between neighbor dendritic spines.

These results provide the steps for the construction of a 3D mesh that simulates a dendritic spine with a spine head and spine neck (Figure 1 to Figure 4). In addition, multiple dendritic spines can be inserted in a single dendritic segment (Figure 5) to study heterosynaptic plasticity of AMPARs14. The PSD on the top of the spine head (Figure 6) is the place where synaptic anchor...

Watch this Scientific Journal Video about 3D Modeling of Dendritic Spines with Synaptic Plasticity at JoVE.com

3D Modeling of Dendritic Spines with Synaptic Plasticity

The protocol develops a three-dimensional (3D) model of a dendritic segment with dendritic spines for modeling synaptic plasticity. The constructed mesh can be used for computational modeling of AMPA receptor trafficking in the long-term synaptic plasticity using the software program Blender with CellBlender and MCell.

Computational modeling of diffusion and reaction of chemical species in a three-dimensional (3D) geometry is a fundamental method to understand the ...

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