Biology subjects

Noda, Y.

Publications and source records attributed to Noda, Y..

4 recordsLinked to original sources

bioRxiv2025

Validation of EEG data assimilation-based prefrontal excitation-inhibition balance estimation using TMS-EEG

The excitation and inhibition (E/I) balance of neural circuits is a crucial index reflecting neurophysiological homeostasis. Although several cutting-edge methods have been established to assess E/I balance in an intact brain, they have inherent limitations, such as difficulties in tracking changes in E/I balance over time. To tackle this issue, we have proposed neural-mass-model-based tracking of the brain states using a data assimilation (DA) scheme in our previous work. However, although we verified that sleep-dependent changes in E/I balance can be estimated from electroencephalography data, the neurophysiological validity of the method was not evaluated. Therefore, in the current study, we directly compared estimated E/I states based on the DA methods with the concurrent transcranial magnetic stimulation and electroencephalography (TMS-EEG) based methods. The results showed that the E/I changes estimated by the DA-based method correlated significantly with E/I in the dorsolateral prefrontal cortex, as indexed by TMS-evoked EEG. These findings indicate that our proposed method can estimate neurophysiologically valid changes in E/I balance.

neuroscience↗

bioRxiv2024

Diurnal regulation of SOS Pathway and Sodium Excretion Underlying Salinity Tolerance of Vigna marina

Vigna marina (Barm.) Merr. is adapted to tropical marine beaches and has an outstanding tolerance to salt stress. Given there are growing demands for cultivating crops in saline soil or with saline water, it is important to understand how halophytic species are adapted to the saline environments. Here we revealed by positron emitting tracer imaging system (PETIS) that V. marina actively excretes sodium from the root during the light period but not in the dark period. The following whole genome sequencing accompanied with forward genetic study identified a QTL region harboring SOS1, encoding plasma membrane Na+/H+ antiporter, which was associated with not only salt tolerance but also ability of sodium excretion. We also found the QTL region contained a large structural rearrangement that suppressed recombination across [~]20 Mbp, fixing multiple gene loci potentially involved in salt tolerance. RNA-seq and promoter analyses revealed SOS1 in V. marina was highly expressed even without salt stress and its promoter shared common cis-regulatory motifs with those exhibiting similar expression profile. Interestingly, the cis-regulatory motifs seemed installed by a transposable element (TE) insertion. Though not identified by genetic analysis, the transcriptome data also revealed SOS2 transcription was under diurnal regulation, explaining the pattern of sodium excretion together with up-regulated expression of SOS1. Furthermore, we demonstrated that, under a condition of mild salt stress, the plants with the diurnally regulated SOS pathway outperformed those with the constitutively activated one.

plant biology↗

bioRxiv2023

NMDAR Phosphoproteome Controls Synaptic Growth and Learning

In the mammalian brain, NMDA receptors (NMDARs) activation triggers a calcium-dependent signal transduction cascade resulting in postsynaptic remodeling and behavioral learning. However, the phosphoprotein signal flow through this transduction network is poorly understood. Here, we show that NMDAR-dependent phosphorylation drives the assembly of protein signaling complexes that regulate synaptic morphology and behavior. We performed large-scale phosphoproteomic analyses of protein kinase target proteins in successive layers of the signaling network in mouse striatal/accumbal slices. NMDARs activation resulted in the phosphorylation of 194 proteins, including Rho GTPase regulators. CaMKII-mediated phosphorylation of ARHGEF2 increased its RhoGEF activity, thereby activating the RhoA-Rho-kinase pathway. Subsequent phosphoproteomics of Rho-kinase revealed 221 protein targets, including SHANK3. Experimental validation revealed a pathway from NMDAR-dependent calcium influx through CaMKII, ARHGEF2, Rho-kinase, and SHANK3 to coordinate assembly of an actin-tethered postsynaptic complex of SHANK3/NMDAR/PSD95/DLGAP3 for spine growth and aversive learning. These findings show that NMDARs initiate metabolic phosphorylation for learning.

neuroscience↗

bioRxiv2023

Relationship Between Domain and Function of the Yeast RNase T2, Rny1p, Which Mediates rRNA Degradation upon Starvation

RNase T2 is ubiquitous across diverse organisms, playing essential roles despite its simple enzymatic activity. In Saccharomyces cerevisiae, RNase T2, known as Rny1p, localizes in vacuoles and mediates rRNA degradation during autophagy of ribosomes. In this study, we elucidated novel aspects of ribosome degradation mechanisms and the function of Rny1p. First, we discovered that most ribosomes are degraded by selective autophagy, where Rsa1p is the specific receptor of ribosomes to be degraded. Complex structure prediction suggested that Rsa1p also interacts with Atg8p. Furthermore, we observed that the accumulation of rRNA in vacuoles, due to the lack of Rny1p, leads to a decrease in bulk autophagic activity. This decrease in autophagic activity may explain the inability of Rny1p-deficient strains to adapt to starvation conditions. Second, our structural prediction and biochemical analyses indicate that a C-terminal extension, characteristic in fungal RNase T2 including Rny1p, is not necessary for rRNA degradation but for anchoring to the cell wall. Together with molecular phylogenetic analysis, a species-specific role of RNase T2 conferred by the C-terminal extension is suggested.

molecular biology↗