Biology subjects

Tanabe, T.

Publications and source records attributed to Tanabe, T..

4 recordsLinked to original sources

bioRxiv2022

Whole-Brain Three-Dimensional Imaging of RNAs at Single-Cell Resolution

Whole-brain three-dimensional (3D) imaging is desirable to obtain a comprehensive and unbiased view of architecture and neural circuitry. However, current spatial analytic methods for brain RNAs are limited to thin sections or small samples. Here, we combined multiple new techniques to develop TRIC-DISCO, a new pipeline that allows imaging of RNA spatial distributions in whole adult mouse brains. First, we developed Tris-mediated retention of in situ hybridization signal during clearing (TRIC), which produces highly transparent tissue while maintaining the RNA signal intensities. We then combined TRIC with DISCO clearing (TRIC-DISCO) by controlling temperature during the in situ hybridization chain reaction (isHCR) to ensure uniform whole-brain staining. This pipeline eliminates the requirements for both strict RNase-free environments and workflow-compatible RNase inhibitors. Our TRIC-DISCO pipeline enables simple and robust, single-cell, whole-brain, 3D imaging of transcriptional signatures, cell-identity markers, and noncoding RNAs across the entire brain.

neuroscience↗

bioRxiv2020

Activity-dependent genetic recombination in disgust-associated bitter taste-responsive neurons of the central nucleus of amygdala in male mice

A bitter substance induces specific orofacial and somatic behavioral reactions such as gapes in mice as well as monkeys and humans. These reactions have been proposed to represent affective disgust, and therefore, understanding the neuronal basis of the reactions would pave the way to understand affective disgust. It is crucial to identify and access the specific neuronal ensembles that are activated by bitter substances, such as quinine, the intake of which induces disgust reactions. However, the method to access the quinine-activated neurons has not been fully established yet. Here, we show evidence that a targeted recombination in active populations (TRAP) method, induces genetic recombination in the quinine-activated neurons in the central nucleus of the amygdala (CeA). CeA is one of the well-known emotional centers of the brain. We found that the intraoral quinine infusion, that resulted in disgust reactions, increased both cFos-positive cells and Arc-positive cells in the CeA. By using Arc-CreER;Ai3 TRAP mice, we induced genetic recombination in the quinine-activated neurons and labelled them with fluorescent protein. We confirmed that the quinine-TRAPed fluorescently-labelled cells preferentially coexpressed Arc after quinine infusion. Our results suggest that the TRAP method can be used to access specific functional neurons in the CeA.

neuroscience↗

bioRxiv2018

CHANCE: a method that enables a researcher to fully know the content of consciousness of a subject in scientific experiments

The content of consciousness (cC) constitutes an essential part of human life and is at the very heart of the hard problem of consciousness. The cC of a person (e.g., study participant) has been examined indirectly by evaluating the persons behavioral reports, bodily signs, or neural signals. However, the measures do not reflect the full spectrum of the persons cC. In this paper, we define a method, called "CHANging Consciousness Epistemically" (CHANCE), to consciously experience a cC that would be identical to that experienced by another person, and thus directly know the entire spectrum of the others cC. In addition, the ontologically subjective knowledge about a persons cC may be considered epistemically objective and scientific data. The CHANCE method comprises two empirical steps: (1) identifying the minimally sufficient, content-specific neural correlates of consciousness (mscNCC) and (2) reproducing a specific mscNCC in different brains.

neuroscience↗

bioRxiv2017

Gauss-power mixing distributions comprehensively describe stochastic variations in RNA-seq data

MotivationGene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution although the physiological basis of this assumption remain unclear.\n\nResultsIn this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent distribution profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, the distribution profiles could be described by a Gauss-power mixing distribution derived from a simple model of a stochastic transcriptional network containing a feedback loop. The distribution profiles of gene expression levels were roughly classified as Gaussian, power law-like containing a long tail, and mixed. The fitting function predicted that gene expression levels with long-tailed distributions would be strongly influenced by feedback regulation. Thus, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian distribution and those of genes encoding nucleic acid-binding proteins and transcription factors exhibiting long-tailed distributions.\n\nAvailabilityFastq files of RNA-seq experiments were deposited into the DNA Data Bank of Japan Sequence Read Archive as accession no. DRA005887. Quantified expression data are available in supplementary information.\n\nContactawa@hiroshima-u.ac.jp\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗