The Computational Neuroscience Unit at OIST in 2020
3D rendering of a hippocampal astrocytic volume and its neighboring synapses
Rendering of a reconstructed hippocampal astrocytic volume (7.07 µm x 6.75 µm x 4.75 µm) from a perfectly isotropic electron microscopy stack (6 nm voxel resolution), together with the twenty-seven fully reconstructed synapses in contact with the astrocyte, zooming in on one synapse. So-called tripartite synapses contain a pre-synaptic neuronal bouton (grey), a post-synaptic neuronal spine (blue), and a perisynaptic astrocytic process (green). The post-synaptic density is visualized in red and the astrocytic endoplasmic reticulum in yellow. The original dataset was kindly provided by Graham Knott. The rendering was performed by Pavel Puchenkov, Scientific Computing and Data Analysis section, Research Support Division, Okinawa Institute of Science and Technology, Japan. Published in: Denizot, A., Veloz Castillo, M.F., Puchenkov, P., Cali, C., De Schutter, E., 2022. The endoplasmic reticulum in perisynaptic astrocytic processes: shape, distribution and effect on calcium activity. (https://doi.org/10.1101/2022.02.28.482292).
Spatially-Extended Simulations Predict the Effect of ER Distribution on Astrocytic Microdomain Ca2+ Activity
Invited talk by Dr. Audrey Denizot at the 8th ACM International Conference on Nanoscale Computing and Communication Virtual Conference, entitled “Spatially-Extended Simulations Predict the Effect of ER Distribution on Astrocytic Microdomain Ca2+ Activity”. This talk was part of the “Astrocytes in modulation of subcellular and cellular molecular neuronal communication” Special Session, chaired by Dr. Jari Hyttinen (https://nanocom.acm.org/nanocom2021/).
Stochastic Reaction-Diffusion and Membrane Potential Combined Simulation in Full Purkinje Dendritic Tree
This video visualizes the result of a spatial stochastic reaction-diffusion and membrane potential combined simulation in a full Purkinje dendritic tree morphology. The model is simulated using parallel STEPS (http://steps.sourceforge.net/) simulator, on the Sango High Performance Cluster at OIST. The left panel shows the time evolution of the calcium concentration in each branch segment of the dendritic tree, and the right panel indicates the correlated membrane potential profile.
The parallel STEPS implementation is described in:
W. Chen and E. De Schutter: Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers. Frontiers in Neuroinformatics 11: 13 (2017).
https://www.frontiersin.org/articles/10.3389/fninf.2017.00013/full
Inositol 1,4,5-Trisphosphate Receptor (IP3R) Model in a Dendritic Spine
This video visualizes the IP3 receptor model in a realistic spine reconstruction, simulated using STEPS (http://steps.sourceforge.net/) simulator. It demonstrates the activation of IP3 receptors on the Endoplasmic Reticulum (ER) membran by cytosolic Ca2+, leading to release of Ca2+ from the ER and the rapid increase of cytosolic Ca2+ concentration, which in turn increases the number of open-state IP3 receptors.
Published in:
W. Chen and E. De Schutter: Python-based geometry preparation and simulation visualization toolkits for STEPS. Frontiers in Neuroinformatics 8: 37 (2014).
https://www.frontiersin.org/articles/10.3389/fninf.2014.00037/full
Anomalous Diffusion in Spiny Dendrite
This video demonstrates the anomalous diffusion effects caused by molecule trapping in dendritic spines, simulated using STEPS (http://steps.sourceforge.net/) simulator. It shows that as the spine density increases, molecules diffuse more slowly along the dendritic shaft as many of them are trapped in the spine heads.
Published in:
W. Chen and E. De Schutter: Python-based geometry preparation and simulation visualization toolkits for STEPS. Frontiers in Neuroinformatics 8: 37 (2014).
https://www.frontiersin.org/articles/10.3389/fninf.2014.00037/full.
Original model:
F. Santamaria, S. Wils, E. De Schutter, G.J. Augustine: Anomalous diffusion in Purkinje cell dendrites caused by spines. Neuron 52: 635-648 (2006).
https://pubmed.ncbi.nlm.nih.gov/17114048/
Synaptically Evoked Dendritic Spikes
Stochasttic gaiting of calcium-activated potassium channels leads to large variation in dendritic calcium bursts in cerebellar Purkinje cells. Watch voltage and calcium influx during two different Purkinje cell dendritic ccalcium bursts.
Originally published in:
H. Anwar, I. Hepburn, H. Nedelescu, W. Chen and E. De Schutter: Stochastic calcium mechanisms cause dendritic calcium spike variability. Journal of Neuroscience 33: 15848-15867.
https://www.jneurosci.org/content/33/40/15848.long
A 3D reconstructed "forest" of neurons
Unraveling the dense neuronal forest of Purkinje cells in the adult cerebellum using combined techniques from genetics, microscopy, and computational anatomy.