Dataset Information

Slip-Based Coding of Local Shape and Texture in Mouse S1.

ABSTRACT: Tactile objects have both local geometry (shape) and broader macroscopic texture, but how these different spatial scales are simultaneously encoded during active touch is unknown. In the whisker system, we tested for a shared code based on localized whisker micromotions (stick-slips) and slip-evoked spikes. We trained mice to discriminate smooth from rough surfaces, including ridged gratings and sandpaper. Whisker slips locked to ridges and evoked temporally precise spikes (<10 ms jitter) in somatosensory cortex (S1) that could resolve ridges with ?1 mm accuracy. Slip-sensitive neurons also encoded touch and texture. On rough surfaces, both slip-evoked spikes and an additional non-slip signal elevated mean firing rate, allowing accurate rough-smooth texture decoding from population firing rate. Eighteen percent of neurons were selective among rough surfaces. Thus, slips elicit spatially and temporally precise spiking in S1 that simultaneously encodes local shape (ridges) and is integrated into a macroscopic firing rate code for roughness.

SUBMITTER: Isett BR

PROVIDER: S-EPMC5773356 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

Slip-Based Coding of Local Shape and Texture in Mouse S1.

Isett Brian R BR Feasel Sierra H SH Lane Monet A MA Feldman Daniel E DE

Neuron 20180104 2

Tactile objects have both local geometry (shape) and broader macroscopic texture, but how these different spatial scales are simultaneously encoded during active touch is unknown. In the whisker system, we tested for a shared code based on localized whisker micromotions (stick-slips) and slip-evoked spikes. We trained mice to discriminate smooth from rough surfaces, including ridged gratings and sandpaper. Whisker slips locked to ridges and evoked temporally precise spikes (<10 ms jitter) in som ...[more]

PMID: 29307709

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Project description:BackgroundA structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to another.ResultsThe performance of programs for pairwise local alignment (TLOCAL) and multiple alignment (TCLUSTALW) are readily adapted from existing code for Smith-Waterman pairwise alignment and for multiple sequence alignment using CLUSTALW. The alignment algorithms employed a blocked scoring matrix (TBLOSUM) generated using the frequency of changes in the geometric alphabet of a block of protein structures. TLOCAL was tested on a set of 10 difficult proteins and found to give high quality alignments that compare favorably to those generated by existing pairwise alignment programs. A set of protein comparison involving hinged structures was also analyzed and TLOCAL was seen to compare favorably to other alignment methods. TCLUSTALW was tested on a family of protein kinases and reveal conserved regions similar to those previously identified by a hand alignment.ConclusionThese results show that the encoding of the writhing number as a geometric measure allow high quality structure alignments to be generated using standard algorithms of sequence alignment. This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. Because the geometric measure can employ different window sizes, the method allows the exploration of alignments on different, well-defined length scales.

Dataset Information

Slip-Based Coding of Local Shape and Texture in Mouse S1.

Publications

Slip-Based Coding of Local Shape and Texture in Mouse S1.

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