Journal Article

Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region

Migliore, Rosanna, Lu, Huanxiang, Petitjean, Fabien, Mercer, Audrey, Kanari, Lida, Schürmann, Felix, Romani, Armando, Kurban, Kerem, Vanherpe, Liesbeth, Planas, Judit, Abdellah, Marwan, Freund, Tamás F., Sood, Vishal, Van Geit, Werner, Lange, Sigrun, Sáray, Sára, Kaufmann, Anna-Kristin, King, James Gonzalo, Boci, Elvis, Budd, Julian, Gevaert, Michael, Lupascu, Carmen Alina, Giacalone, Elisabetta, Favreau, Cyrille, Herttuainen, Joni, Thomson, Alex M., Román Guerrero, Nadir, Kumbhar, Pramod, Ivaska, Genrich, Ecker, András, Rai, Pranav, Shi, Ying, Delemontex, Thomas, Hernando, Juan B., Ramaswamy, Srikanth, Arnaudon, Alexis, Sy, Mohameth François, Markram, Henry, Colangelo, Cristina, Antonietti, Alberto, Káli, Szabolcs, Bella, Davide, Courcol, Jean-Denis, Riquelme, Juan Luis, Migliore, Michele, Falck, Joanne, Muller, Eilif, Reimann, Michael W.

2024

Overview

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to integrate information obtained from diverse experimental approaches. To address this challenge, we present a community-based, full-scale in silico model of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to potentially address a range of scientific questions. In this article, we describe the methods used to set up simulations to reproduce in vitro and in vivo experiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce experimental findings. Finally, we make data, code, and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This community-based model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Acetylcholine - metabolism / Agreements / Animals / Biological models / Biology and Life Sciences / Brain / Brain research / CA1 Region, Hippocampal - physiology / Cognitive ability / Computer Simulation / Computer-generated environments / Datasets / Experimental data / Funding / Grants / Hippocampus / Hippocampus (Brain) / Information processing / Medicine and Health Sciences / Methods / Methods and Resources / Models, Neurological / Navigation behavior / Neurosciences / Physiological aspects / Rats / Rats as laboratory animals / Realism / Reconstruction / Scale models / Simulation / Simulation methods / Spatial memory / Structure-function relationships / Synapses - physiology / Theta Rhythm - physiology