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

Romani Armando

Antonietti Alberto

Bella Davide

Budd Julian Martin Leslie

Giacalone Elisabetta

Kurban Kerem

Sáray Sára

Abdellah Marwan

Arnaudon Alexis

Boci Elvis

Colangelo Cristina

Courcol Jean-Denis

Delemontex Thomas

Ecker András

Falck Joanne

Favreau Cyrille

Gevaert Michael

Hernando Juan B.

Herttuainen Joni

Ivaska Genrich

Kanari Lida

Kaufmann Anna-Kristin

King James Gonzalo

Kumbhar Pramod

Lange Sigrun

Lu Huanxiang

Lupascu Carmen Alina

Migliore Rosanna

Petitjean Fabien

Planas Judit

Freund Tamás

Káli Szabolcs

2024

01.06. Biológiai tudományok

01.06.03. Biokémia és molekuláris biológia

01.06.07. Genetika és örökléstan

03.01.04. Immunológia

03.01.05. Idegtudományok (benne pszichofiziológia)

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.

angol

angol

Folyóiratcikk

PeerReviewed

text

https://publikacio.ppke.hu/id/eprint/3613/1/journal.pbio.3002861.pdf

Romani Armando; Antonietti Alberto; Bella Davide; Budd Julian Martin Leslie; Giacalone Elisabetta; Kurban Kerem; Sáray Sára; Abdellah Marwan; Arnaudon Alexis; Boci Elvis; Colangelo Cristina; Courcol Jean-Denis; Delemontex Thomas; Ecker András; Falck Joanne; Favreau Cyrille; Gevaert Michael; Hernando Juan B.; Herttuainen Joni; Ivaska Genrich; Kanari Lida; Kaufmann Anna-Kristin; King James Gonzalo; Kumbhar Pramod; Lange Sigrun; Lu Huanxiang; Lupascu Carmen Alina; Migliore Rosanna; Petitjean Fabien; Planas Judit; Freund Tamás; Káli Szabolcs: Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region. PLOS BIOLOGY, 22 (11). ISSN 1544-9173 (2024)

MTMT:35598681 10.1371/journal.pbio.3002861

https://publikacio.ppke.hu/id/eprint/3613/

https://doi.org/10.1371/journal.pbio.3002861

MTMT:35598681 10.1371/journal.pbio.3002861