Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex
- University of Oslo, Norway
- Allen Institute for Brain Science, United States
- Allen Institute, United States
- Norwegian University of Life Sciences, Norway
Abstract
Local field potential (LFP) recordings reflect the dynamics of the current source density (CSD) in brain tissue. The synaptic, cellular and circuit contributions to current sinks and sources are ill-understood. We investigated these in mouse primary visual cortex using public Neuropixels recordings and a detailed circuit model based on simulating the Hodgkin-Huxley dynamics of >50,000 neurons belonging to 17 cell types. The model simultaneously captured spiking and CSD responses and demonstrated a two-way dissociation: Firing rates are altered with minor effects on the CSD pattern by adjusting synaptic weights, and CSD is altered with minor effects on firing rates by adjusting synaptic placement on the dendrites. We describe how thalamocortical inputs and recurrent connections sculpt specific sinks and sources early in the visual response, whereas cortical feedback crucially alters them in later stages. These results establish quantitative links between macroscopic brain measurements (LFP/CSD) and microscopic biophysics-based understanding of neuron dynamics and show that CSD analysis provides powerful constraints for modeling beyond those from considering spikes.
Data availability
The files necessary to run simulations of the different model versions presented in the paper as well as data resulting from simulations of those model versions are publicly available in Dryad: https://doi.org/10.5061/dryad.k3j9kd5b8The experimental data set utilized is publicly available at: https://portal.brain-map.org/explore/circuits/visual-coding-neuropixelsThe code generated for data analysis and producing the figures in this manuscript is publicly available at: https://github.com/atleer/CINPLA_Allen_V1_analysis.git.
-
Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortexDryad Digital Repository, doi:10.5061/dryad.k3j9kd5b8.
-
20191003_AIBS_mouse_ecephys_brain_observatory_1_1DANDI Archive 000021.
Article and author information
Author details
Alexander J Stasik
Funding
Simula School of Research
- Atle E Rimehaug
European Union Horizon 2020 Research and Innovation program (785907)
- Espen Hagen
European Union Horizon 2020 Research and Innovation program (945539)
- Espen Hagen
Research Council of Norway (COBRA - project number 250128)
- Alexander J Stasik
IKTPLUSS-IKT and Digital Innovation (300504)
- Alexander J Stasik
National Institute of Neurological Disorders and Stroke (R01NS122742)
- Yazan N Billeh
- Josh H Siegle
- Kael Dai
- Shawn R Olsen
- Christof Koch
- Anton Arkhipov
National Institute of Biomedical Imaging and Bioengineering (R01EB029813)
- Yazan N Billeh
- Josh H Siegle
- Kael Dai
- Shawn R Olsen
- Christof Koch
- Anton Arkhipov
Allen Institute
- Yazan N Billeh
- Josh H Siegle
- Kael Dai
- Shawn R Olsen
- Christof Koch
- Anton Arkhipov
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Tirin Moore, Howard Hughes Medical Institute, Stanford University, United States
Version history
- Preprint posted: February 25, 2022 (view preprint)
- Received: February 23, 2023
- Accepted: July 10, 2023
- Accepted Manuscript published: July 24, 2023 (version 1)
- Version of Record published: August 1, 2023 (version 2)
- Version of Record updated: August 11, 2023 (version 3)
Copyright
© 2023, Rimehaug et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,488
- views
-
- 219
- downloads
-
- 6
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex
eLife 12:e87169.
https://doi.org/10.7554/eLife.87169
Further reading
-
- Computational and Systems Biology
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here, I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors, and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode Caenorhabditis elegans. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
-
- Computational and Systems Biology
- Ecology
Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed to be an advanced hunting strategy requiring large brains that involve high-level cognition. However, recent findings that collaborative hunting has also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, using computational multi-agent simulations based on deep reinforcement learning, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between states and actions related to distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our computational ecological results emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.
