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Huang C, Zeldenrust F, Celikel T. Cortical Representation of Touch in Silico. Neuroinformatics 2022; 20:1013-1039. [PMID: 35486347 PMCID: PMC9588483 DOI: 10.1007/s12021-022-09576-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2022] [Indexed: 12/31/2022]
Abstract
With its six layers and ~ 12,000 neurons, a cortical column is a complex network whose function is plausibly greater than the sum of its constituents'. Functional characterization of its network components will require going beyond the brute-force modulation of the neural activity of a small group of neurons. Here we introduce an open-source, biologically inspired, computationally efficient network model of the somatosensory cortex's granular and supragranular layers after reconstructing the barrel cortex in soma resolution. Comparisons of the network activity to empirical observations showed that the in silico network replicates the known properties of touch representations and whisker deprivation-induced changes in synaptic strength induced in vivo. Simulations show that the history of the membrane potential acts as a spatial filter that determines the presynaptic population of neurons contributing to a post-synaptic action potential; this spatial filtering might be critical for synaptic integration of top-down and bottom-up information.
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Affiliation(s)
- Chao Huang
- grid.9647.c0000 0004 7669 9786Department of Biology, University of Leipzig, Leipzig, Germany
| | - Fleur Zeldenrust
- grid.5590.90000000122931605Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Tansu Celikel
- grid.5590.90000000122931605Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands ,grid.213917.f0000 0001 2097 4943School of Psychology, Georgia Institute of Technology, Atlanta, GA USA
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da Silva Lantyer A, Calcini N, Bijlsma A, Kole K, Emmelkamp M, Peeters M, Scheenen WJJ, Zeldenrust F, Celikel T. A databank for intracellular electrophysiological mapping of the adult somatosensory cortex. Gigascience 2018; 7:5232232. [PMID: 30521020 PMCID: PMC6302958 DOI: 10.1093/gigascience/giy147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/18/2018] [Indexed: 02/04/2023] Open
Abstract
Background Neurons in the supragranular layers of the somatosensory cortex integrate sensory (bottom-up) and cognitive/perceptual (top-down) information as they orchestrate communication across cortical columns. It has been inferred, based on intracellular recordings from juvenile animals, that supragranular neurons are electrically mature by the fourth postnatal week. However, the dynamics of the neuronal integration in adulthood is largely unknown. Electrophysiological characterization of the active properties of these neurons throughout adulthood will help to address the biophysical and computational principles of the neuronal integration. Findings Here, we provide a database of whole-cell intracellular recordings from 315 neurons located in the supragranular layers (L2/3) of the primary somatosensory cortex in adult mice (9–45 weeks old) from both sexes (females, N = 195; males, N = 120). Data include 361 somatic current-clamp (CC) and 476 voltage-clamp (VC) experiments, recorded using a step-and-hold protocol (CC, N = 257; VC, N = 46), frozen noise injections (CC, N = 104) and triangular voltage sweeps (VC, 10 (N = 132), 50 (N = 146) and 100 ms (N = 152)), from regular spiking (N = 169) and fast-spiking neurons (N = 66). Conclusions The data can be used to systematically study the properties of somatic integration and the principles of action potential generation across sexes and across electrically characterized neuronal classes in adulthood. Understanding the principles of the somatic transformation of postsynaptic potentials into action potentials will shed light onto the computational principles of intracellular information transfer in single neurons and information processing in neuronal networks, helping to recreate neuronal functions in artificial systems.
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Affiliation(s)
- Angelica da Silva Lantyer
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Niccolò Calcini
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Ate Bijlsma
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Koen Kole
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Melanie Emmelkamp
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Manon Peeters
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Wim J J Scheenen
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Fleur Zeldenrust
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
| | - Tansu Celikel
- Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Heyedaalseweg 135, 6525 HJ, Nijmegen - the Netherlands
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Kole K, Komuro Y, Provaznik J, Pistolic J, Benes V, Tiesinga P, Celikel T. Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation. Gigascience 2018; 6:1-6. [PMID: 29020745 PMCID: PMC5965344 DOI: 10.1093/gigascience/gix081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/16/2017] [Indexed: 12/03/2022] Open
Abstract
Experience-dependent plasticity (EDP) is essential for anatomical and functional
maturation of sensory circuits during development. Although the principal synaptic and
circuit mechanisms of EDP are increasingly well studied experimentally and
computationally, its molecular mechanisms remain largely elusive. EDP can be readily
studied in the rodent barrel cortex, where each “barrel column” preferentially represents
deflections of its own principal whisker. Depriving select whiskers while sparing their
neighbours introduces competition between barrel columns, ultimately leading to weakening
of intracortical, translaminar (i.e., cortical layer (L)4-to-L2/3) feed-forward excitatory
projections in the deprived columns. The same synapses are potentiated in the neighbouring
spared columns. These experience-dependent alterations of synaptic strength are thought to
underlie somatosensory map plasticity. We used RNA sequencing in this model system to
uncover cortical-column and -layer specific changes on the transcriptome level that are
induced by altered sensory experience. Column- and layer-specific barrel cortical tissues
were collected from juvenile mice with all whiskers intact and mice that received 11–12
days of long whisker (C-row) deprivation before high-quality RNA was purified and
sequenced. The current dataset entails an average of 50 million paired-end reads per
sample, 75 base pairs in length. On average, 90.15% of reads could be uniquely mapped to
the mm10 reference mouse genome. The current data reveal the transcriptional changes in
gene expression in the barrel cortex upon altered sensory experience in juvenile mice and
will help to molecularly map the mechanisms of cortical plasticity.
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Affiliation(s)
- Koen Kole
- Department of Neurophysiology, Heyendaalseweg 135, 6525 HJ Nijmegen, the Netherlands.,Department of Neuroinformatics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ Nijmegen, the Netherlands
| | - Yutaro Komuro
- Department of Neurophysiology, Heyendaalseweg 135, 6525 HJ Nijmegen, the Netherlands
| | - Jan Provaznik
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | - Jelena Pistolic
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | - Paul Tiesinga
- Department of Neuroinformatics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ Nijmegen, the Netherlands
| | - Tansu Celikel
- Department of Neurophysiology, Heyendaalseweg 135, 6525 HJ Nijmegen, the Netherlands
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Kole K, Lindeboom RGH, Baltissen MPA, Jansen PWTC, Vermeulen M, Tiesinga P, Celikel T. Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience 2017; 6:1-10. [PMID: 29020746 PMCID: PMC5632293 DOI: 10.1093/gigascience/gix082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/16/2017] [Indexed: 02/04/2023] Open
Abstract
Experience-dependent plasticity (EDP) powerfully shapes neural circuits by inducing long-lasting molecular changes in the brain. Molecular mechanisms of EDP have been traditionally studied by identifying single or small subsets of targets along the biochemical pathways that link synaptic receptors to nuclear processes. Recent technological advances in large-scale analysis of gene transcription and translation now allow systematic observation of thousands of molecules simultaneously. Here we employed label-free quantitative mass spectrometry to address experience-dependent changes in the proteome after sensory deprivation of the primary somatosensory cortex. Cortical column- and layer-specific tissue samples were collected from control animals, with all whiskers intact, and animals whose C-row whiskers were bilaterally plucked for 11–14 days. Thirty-three samples from cortical layers (L) 2/3 and L4 spanning across control, deprived, and first- and second-order spared columns yielded at least 10 000 peptides mapping to ∼5000 protein groups. Of these, 4676 were identified with high confidence, and >3000 were found in all samples. This comprehensive database provides a snapshot of the proteome after whisker deprivation, a protocol that has been widely used to unravel the synaptic, cellular, and network mechanisms of EDP. Complementing the recently made available transcriptome for identical experimental conditions (see the accompanying article by Kole et al.), the database can be used to (i) mine novel targets whose translation is modulated by sensory organ use, (ii) cross-validate experimental protocols from the same developmental time point, and (iii) statistically map the molecular pathways of cortical plasticity at a columnar and laminar resolution.
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Affiliation(s)
- Koen Kole
- Department of Neurophysiology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ, Nijmegen, the Netherlands.,Department of Neuroinformatics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ, Nijmegen, the Netherlands
| | - Rik G H Lindeboom
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Paul Tiesinga
- Department of Neuroinformatics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ, Nijmegen, the Netherlands
| | - Tansu Celikel
- Department of Neurophysiology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Heyendaalseweg 135, 6525 HJ, Nijmegen, the Netherlands
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