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Biology subjects

Kawai, T.

Publications and source records attributed to Kawai, T..

At least 19 recordsLinked to original sources

Asymmetric turnover dynamics of Nav1.6 voltage-gated sodium channels at the axon initial segment

Nav1.6 voltage-gated sodium channels are critical for shaping action potentials, and their precise localization at the axon initial segment (AIS) is essential for neuronal excitability. However, the turnover mechanisms that maintain this spatial pattern remain unclear. Here, we present a genetically engineered mouse in which endogenous Nav1.6 carries a Cre-switchable fluorescent tag, enabling us to simultaneously trace the turnover of pre-existing and newly synthesized Nav1.6 without perturbing AIS structure. Using this system, we determine the physiological lifetimes of Nav1.6 at the AIS in vivo and in vitro, and further uncover the spatially asymmetric turnover dynamics, with the proximal and distal AIS organizing a source-to-sink gradient. Based on the quantified parameters, computational modeling clarifies that this asymmetry promotes efficient clearance of older molecules, thereby supporting AIS quality control. Collectively, these findings provide a technical and conceptual foundation for understanding how molecular turnover contributes to AIS homeostasis.

neuroscience↗

Numerical study of spatial and temporal dynamics of integrin clustering during early cell adhesion

Integrins are adhesion proteins that diffuse along the cell membrane, bind to ligands, and cluster with each other in the early stage of cell adhesion. Integrin clustering and its specific spatial distribution play important roles in subsequent biological processes; however, the mechanisms that give rise to their characteristic spatial distribution remain poorly understood. To address this issue, we developed a cell adhesion model that incorporates cell membrane deformation and integrin dynamics. A hybrid continuous/discrete model was applied to represent membrane deformation, whereas Brownian dynamics combined with a transition state model was used to describe integrin dynamics and binding kinetics. Comparison of numerical simulations of cell adhesion to a substrate with experimental observations at the early stage of adhesion successfully reproduced the characteristic spatial distribution of integrin clusters, in which high-density clusters formed at the periphery of the region adhering to the substrate. These results suggest that the cellular-scale distribution of integrin clusters can be reproduced using only minimal elements, such as adhesion-driven membrane deformation and integrin-ligand binding. In addition, we found that the strength of integrin-ligand binding regulates the degree of clustering by changing the size of the part of the membrane that is deformed, thereby mechanically supporting the mechanical involvement of the actin cytoskeleton in integrin clustering. Furthermore, the formation and spatial distribution of integrin clusters were shown to be determined not only by the static mechanical equilibrium of membrane deformation and physical adsorption, but also by membrane spreading/deformation and the dynamic behavior of integrins. This suggests that the size and spatial distribution of integrin clusters may be controllable by modulating the speed of membrane spreading.

biophysics↗

Characterization of Rhizosphere Oxidation Associated with Root Development in Rice Using Planar Oxygen Optodes

Rhizosphere oxidation is a key adaptive mechanism in reductive soil environments, in which oxygen released from roots alters rhizosphere redox conditions and regulates biogeochemical processes. Rice plants possess an internal oxygen transport system, and radial oxygen loss (ROL) from roots is closely associated with root development. However, the spatial patterns of ROL in soil and their relationships with root traits remain poorly characterized. In this study, we developed a multimodal imaging system that integrates planar oxygen optodes with X-ray computed tomography to simultaneously visualize rhizosphere oxidation and root development in rice. Daily time-course tracking of individual crown roots revealed dynamic changes in the spatial distribution and magnitude of rhizosphere oxygen in relation to root elongation and aging. Root thickness was positively correlated with dissolved oxygen levels near root tips. Genotypic comparisons further identified a cultivar with reduced rhizosphere oxidation despite possessing thicker roots among the tested genotypes, thereby indicating the involvement of additional physiological processes. Overall, these findings demonstrate that rhizosphere oxidation is regulated by root growth stage and thickness and dynamically modulated during root development.

plant biology↗

Circadian Regulation of Taste Sensitivity in Human and Rat Active Periods

Most organisms exhibit endogenous 24-h rhythms that align physiology and behavior with the time of day; however, whether taste sensitivity oscillates in a circadian manner remains unclear, limiting our understanding of its role in feeding behavior. Here, we show that sensitivity to sweet and bitter tastes exhibits circadian modulation, peaking during the active period: daytime in humans and the dark phase in nocturnal rats. In humans, the rhythmicity of sweet taste was evident in detection but not recognition thresholds, indicating circadian modulation at the level of primary sensory processing rather than higher-order cognitive processes. In rats, increased sensitivity during the dark phase was accompanied by upregulation of taste-related genes in type II taste cells in tongue. These findings provide evidences that circadian regulation of taste sensitivity is conserved across species and appears to operate predominantly at the peripheral level. This mechanism may have evolved to optimize energy intake while minimizing exposure to dietary toxins, potentially contributing to survival and continuing to influence modern eating behavior through circadian-sensory-nutritional interactions.

physiology↗

Deep Microbial Colonization in 2-Billion-Year-Old Ultramafic Rock from the Bushveld Complex

Archean cratons may provide stable microbial habitats in the deep subsurface, as evidenced by the discovery of billion-year-old crustal fluids1,2. However, the long-term habitability of these cratonic environments is uncertain, as polymetamorphic evolution in most cratons typically destroys microbial habitats through mineral reactions and porosity loss3,4. Preservation of deep microbial habitats is more likely where mantle-derived magma intruded the craton after metamorphic overprinting4. Here we report the discovery of dense microbial colonization at 814 m depth within the 2.05-billion-year-old, unmetamorphosed Bushveld Igneous Complex intrusion, South Africa5. Using advanced contamination-control protocols6,7 and synchrotron-based X-ray spectroscopy, we identified indigenous microbial cells localized at the rims of phlogopite, a hydrous phyllosilicate mineral. Our study reveals that microbial colonization is associated with Fe(III) derived from the structure of phlogopite, where the dehydrogenation likely oxidizes Fe(II) to Fe(III) coupled to H2 generation8. Despite the absence of fracture-driven fluid ingress in the unfractured rock matrix, aqueous alteration evidenced at the rims by potassium removal indicates a self-sustaining habitat driven by an internal redox gradient9. These findings demonstrate that aqueous alteration of ultramafic rocks can sustain isolated microbial life over geological timescales, significantly expanding the potential for long-term habitability on both Earth and Mars4,10.

microbiology↗

PI(4,5)P2-dependence of GABAA receptor channel function revealed by optogenetic manipulation of a binding site

ABSTRACT/SUMMARYIonotropic GABAA receptors (GABAARs) mediate fast inhibitory neurotransmission in mammalian brains. While recent structural studies have identified that phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], a well-established regulator of numerous ion channels, binds to the 1 subunits of GABAARs, the functional relevance of this binding has remained elusive. Here, we combine electrophysiology, molecular dynamics simulations, and a recently developed caged lysine technology to define the role of PI(4,5)P2 in GABAARs. We show that GABAARs are insensitive to acute PI(4,5)P2 depletions by voltage-sensing phosphatase, but sensitivity is conferred by neutralizing the K311 binding site, indicating high-affinity binding. Caging of K311 by use of genetic code expansion recapitulated phenotypes of K311 mutant, conferring sensitivity to PI(4,5)P2 depletion, whereas uncaging restored insensitivity. Furthermore, caging K311 revealed decelerated activation, which then can be accelerated by uncaging. Additionally, PI(4,5)P2-dependence extends to glycine receptors, suggesting PI(4,5)P2 is an important endogenous phospholipid modulator of inhibitory receptor channels.

biophysics↗

Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis

Psoriasis is a chronic inflammatory skin disorder driven by amplified communication between immune cells and keratinocytes. Here, we show that imiquimod (IMQ) triggers organelle stress responses that directly contribute to this pathogenic circuit. In dendritic cells (DCs), IMQ promotes formation of ER-mitochondria contact sites (MAMs), inducing ER stress and activation of the unfolded protein response (UPR). These pathways act independently of, yet converge with, TLR7/MyD88 signaling to enhance IL-23 expression. IMQ also increases cytosolic Ca{superscript 2}+, facilitating NLRP3 inflammasome activation and release of mitochondrial DNA (mtDNA). In parallel, keratinocytes exposed to IMQ activate UPR-dependent genes, including Defb14 (mBD14), a psoriasis-associated antimicrobial peptide. Extracellular mtDNA and mBD14 then cooperatively stimulate plasmacytoid DCs through TLR9, establishing a feed-forward inflammatory loop. We further identify Gelsolin as a direct IMQ-binding protein that mitigates IMQ-induced ER stress; its loss amplifies ER stress, UPR activation, and oxidative stress, and its expression is reduced in human psoriatic lesions. Thus, MAM-UPR signaling links intracellular organelle stress to the intercellular networks that drive psoriatic inflammation, with Gelsolin acting as a critical intrinsic safeguard.

immunology↗

AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images

High-speed atomic force microscopy (HS-AFM) enables direct visualization of protein dynamics under near-physiological conditions, yet its intrinsic limitation to surface topography prevents atomic-level structural characterization. We present AFM-Fold, a generative AI-based framework that reconstructs three-dimensional protein conformations directly from AFM images. AFM-Fold combines a rotation-equivariant convolutional neural network, which extracts low-dimensional collective variables (CVs) from AFM images, with a guided diffusion process that generates conformations consistent with the inferred CVs. Using pseudo-AFM images of adenylate kinase, AFM-Fold accurately reproduced not only the open and closed conformations, but also intermediate states. Application to 159 experimental HS-AFM frames of the flagellar protein FlhAC further demonstrated that AFM-Fold outperforms rigid-body fitting and captures time-correlated domain motions that reflect underlying conformational dynamics. AFM-Fold enables rapid, physically plausible structure estimation from individual AFM images, typically within one minute per frame, without relying on molecular dynamics simulations. This unified and computationally efficient pipeline opens a route to high-throughput structural analysis of HS-AFM movies.

biophysics↗

Vertical rooting caused by enhanced functional allele of qSOR1 improves rice yield under drought stress

Drought considerably affects crop productivity, and its severity is being intensified by climate change. Therefore, enhancing drought resistance is a crucial priority in crop breeding for ensuring sustainable agriculture. The root system architecture (RSA) influences the efficiency of water acquisition from land; therefore, a deep RSA is advantageous for avoiding drought stress. Here, we demonstrated that deeper RSA promoted by the qSOR1-v mutant allele (an enhanced functional allele of the quantitative trait locus for SOIL SURFACE ROOTING 1) significantly improves rice yield under drought when compared to the deep RSA achieved through the functional qSOR1 allele that originated from natural variation. The qSOR1-v mutant exhibited stronger root gravitropism than the wild type. This was characterized by a more pronounced polarization of auxin on the lower side during root curvature, leading to a robust vertical rooting phenotype that was consistently expressed across different soil-water environments. Additionally, the qSOR1-v mutation site was well conserved among angiosperm orthologs, and the corresponding mutation in LZY3 of Arabidopsis (qSOR1 ortholog) resulted in a steeper root growth angle. The rice introgression line, which was substituted from the functional qSOR1 allele to qSOR1-v through marker-assisted selection, showed vertical rooting, resulting in increased grain yield in an upland field under drought stress. No yield penalty was observed for this line under well-watered upland conditions than the original variety. These findings highlight the potential of qSOR1-v and corresponding mutations in angiosperm orthologs to promote vertical rooting across plant species, which can help sustain crop yields in drought-prone areas. Significance StatementGenetic modification of the root system architecture in crops represents a viable strategy for the development of climate-resilient crops. This study identified the qSOR1-v allele that consistently demonstrates a vertical rooting phenotype in rice across diverse growth conditions, from dry to wet. The preservation of the qSOR1 and LZY3 orthologs in angiosperms provides opportunities for the development of genotypes characterized by vertical rooting. The introgression of the qSOR1-v allele enhanced drought resistance under upland conditions. These findings underscore the potential of these genetic modifications to improve crop resilience in an era characterized by water scarcity.

plant biology↗

Fast-spiking neurons in monkey orbitofrontal cortex underlie economic value computation

Inhibitory interneurons are fundamental constituents of cortical circuits that process information to shape economic behaviors. However, the role of inhibitory interneurons in this process in the core cortical reward region, the orbitofrontal cortex (OFC), remains elusive. Here, we show that presumed parvalbumin-containing GABAergic interneurons (fast-spiking neurons, FSNs) differ from regular-spiking pyramidal neurons (RSNs) in computing economic value. While monkeys perceived a visual lottery for probability and magnitude of rewards, identified FSNs constituted 12% of OFC neurons and showed high-frequency firing rates and wide dynamic ranges, which are both key intrinsic cellular characteristics regulating cortical computation. We found that FSNs showed stronger neural modulation compared to RSNs in signaling probability and magnitude information. Unambiguously, both neural populations signaled the expected values, but FSNs processed the reward information more strongly under the influence of dynamic range. Thus, stronger FSN signals may appear with wider dynamic range for expected value computation.

neuroscience↗

The Knock-In Atlas: A web resource for targeted protein trap by CRISPR/Cas9 in human and mouse cell lines

Various cell engineering techniques have been developed by leveraging the CRISPR-Cas9 technology, but large-scale resources for targeted gene knock-in are still limited. Here we introduce the Knock-in Atlas, a web resource for gene tagging by fluorescent proteins by inserting artificial exons in target gene introns. To produce knock-in cells efficiently and reproducibly, we carefully chose and catalogued guide RNAs (gRNAs) for targeting genes in the human and mouse genomes by taking the gRNA efficacy scores and protein structures around the insertion sites into account. As of August 2025, we have characterized knock-in cell lines for 350 proteins, with a focus on RNA binding proteins, by flow cytometry and confocal microscopy. The transfection and flow cytometry protocols were optimized for several cell lines including HEK293T, eHAP1, HeLa, THP-1, Neuro2a, mouse embryonic fibroblast (MEF) and mouse embryonic stem cell (mESC). A website has been launched to organize the results of initial characterization including flow cytometry data after transfection, confocal microscopy, and western blot results for the genes for which knock-in HEK293T cell lines were already made. The site also provides a database to organize the information of pre-designed gRNAs for the human and mouse genomes. .

molecular biology↗

Zinc is a Key Regulator of the Sperm-Specific K+ Channel (Slo3) Function

The voltage- and pH-gated Slo3 potassium channel is exclusively expressed in mammalian spermatozoa. Its sensitivity to both voltage and alkalization plays a crucial role in sperm fertility, which is tightly coupled to the capacitation process. Here we show that sperm-enriched divalent cation Zn2+ undergoes dynamic alteration in spermatozoa during capacitation. We also found that intracellular Zn2+ regulates alkalinization-induced hyperpolarization in mouse spermatozoa which is mediated by Slo3 channel. Further examination of zinc regulation in mouse Slo3 (mSlo3) revealed that, in Xenopus oocyte expression system, intracellular zinc directly inhibits mouse Slo3 currents in dose-dependent manner at micromolar concentrations, with exceptionally slow dissociation. By combining MD simulations and electrophysiology, we also identified amino acid residues contributing to the Zn2+ slow dissociation from Slo3 channels. Our studies uncover the importance of intracellular zinc dynamics and its regulatory role in ion channels during sperm capacitation.

physiology↗

Mechanosensing by Piezo1 regulates osteoclast differentiation via PP2A-Akt axis in periodontitis

Mechanical stimulus to the multicellular bone unit (MBU) plays a key role in normal bone remodeling, whereas disuse osteoporosis, for example, represents loss of bone owing to lack of mechanical stresses. The analogy can be applied to a variety of pathogenic bone lytic complications, including periodontitis, in which local mechanical stress appears to be diminished. The activation of mechanosensitive Piezo1 Ca2+ channel expressed by osteoblasts and osteocytes in the MBU elicits the osteogenic signals in those cells. However, since osteoclast (OC)-specific Piezo1-gene knockout mice showed no skeletal phenotype, it has been assumed that Piezo1 might not play any role in OC-mediated bone remodeling. Here, however, we showed that mechanical stimulation of Piezo1 expressed on preosteoclasts (pre-OCs) downmodulates OC formation and, hence, bone resorptive activity in periodontitis, accompanied by significantly reduced expression of NFATc1, a master transcription factor for RANKL-induced OC-genesis. We know that the Ca2+/calcineurin/NFAT axis upregulates NFATc1 activation in pre-OCs. Interestingly, Piezo1-elicited Ca2+ influx did not affect NFATc1 expression. Instead, PP2A-mediated dephosphorylation of Akt downregulated NFATc1 in Piezo1-activated pre-OCs. However, systemic administration with Yoda1, a Piezo1 chemical agonist, or local injection of PP2A agonist, significantly downregulated the bone resorption induced in a mouse model of periodontitis, together with reduced numbers of TRAP+/phospho-Akt+ pre-OCs in local bone. These results suggest that mechanosensing by Piezo1 expressed on pre-OCs can downmodulate the RANKL-induced OC-genesis via the PP2A/Akt-dephosphorylation pathway, but that such Piezo1-mediated downregulation of bone resorption is attenuated in periodontitis. Significance StatementThe mechanosensitive Ca2+ channel Piezo1 plays important regulatory roles in a variety of cellular activities. RANKL-mediated OC-genesis requires permissive co-stimulatory signal from ITAM receptors, such as OSCAR and TREM2, to trigger the calcineurin/calmodulin signaling axis via Ca2+ oscillation, thereby upregulating NFATc1 expression. Activation of Piezo1 remarkably suppressed RANKL-induced NFATc1 activation which, in turn, reduced OC-genesis. Such mechanical activation of Piezo1 expressed on pre-OCs induced intracellular Ca2+ influx. Nonetheless, PP2A-mediated dephosphorylation of Akt, not the calcineurin/calmodulin pathway, suppressed NFATc1 in RANKL-elicited OC-genesis and resultant bone resorption, both in vitro and in vivo. These results indicate that mechanostress applied to pre-OCs can downregulate pathogenic OC-genesis and that Piezo1, as the mediator, is a novel molecular target for the development of anti-osteolytic therapies.

cell biology↗

Inhibition of SARS-CoV-2 infection by Porphyromonas gingivalis and the oral microbiome

The COVID-19 pandemic persists despite the availability of vaccines, and it is therefore crucial to develop new therapeutic and preventive approaches. In this study, we investigated the potential role of the oral microbiome in SARS-CoV-2 infection. Using an in vitro SARS-CoV-2 pseudovirus infection assay, we found a potent inhibitory effect exerted by Porphyromonas gingivalis on SARS-CoV-2 infection mediated by known P. gingivalis compounds such as phosphoglycerol dihydroceramide (PGDHC) and gingipains as well as by unknown bacterial factors. We found that the gingipain-mediated inhibition of infection is likely due to cytotoxicity, while PGDHC inhibited virus infection by an unknown mechanism. Unidentified factors present in P. gingivalis supernatant inhibited SARS-CoV-2 likely via the fusion step of the virus life cycle. We addressed the role of other oral bacteria and found certain periodontal pathogens capable of inhibiting SARS-CoV-2 pseudovirus infection by inducing cytotoxicity on target cells. In the human oral cavity, we observed the modulatory activity of oral microbial communities varied among individuals in that some saliva-based cultures were capable of inhibiting while others were enhancing infection. These findings contribute to our understanding of the complex relationship between the oral microbiome and viral infections, offering potential avenues for innovative therapeutic strategies in combating COVID-19.

microbiology↗

Generating an organ-deficient animal model using a multi-targeted CRISPR-Cas9 system

Gene-knockout animal models with organ-deficient phenotypes used for blastocyst complementation are generally not viable. Animals need to be maintained as heterozygous mutants, and homozygous mutant embryos yield only one-fourth of all embryos. In this study, we generated organ-deficient embryos using the CRISPR-Cas9-sgRNAms system that induces cell death with a single-guide RNA (sgRNAms) targeting multiple sites in the genome. The Cas9-sgRNAms system interrupted cell proliferation and induced cell ablation in vitro. The mouse model had Cas9 driven by the Foxn1 promoter with a ubiquitous expression cassette of sgRNAms at the Rosa26 locus (Foxn1Cas9; Rosa26_ms). It showed an athymic phenotype similar to that of nude mice but was not hairless. Eventually, a rat cell-derived thymus in an interspecific chimera was generated by blastocyst complementation of Foxn1Cas9; Rosa26_ms mouse embryos with rat embryonic stem cells. Theoretically, half of the total embryos have the Cas9-sgRNAms system because Rosa26_ms could be maintained as homozygous.

bioengineering↗

Distinct roles of the orbitofrontal cortex, ventral striatum, and dopamine neurons in counterfactual thinking of decision outcomes

Individuals often assess past decisions by comparing what was gained with what would have been gained had they acted differently. Thoughts of past alternatives that counter what actually happened are called "counterfactuals". Recent theories emphasize the role of the prefrontal cortex in processing counterfactual outcomes in decision-making, although how subcortical regions contribute to this process remains to be elucidated. Here we report a clear distinction among the roles of the orbitofrontal cortex, ventral striatum and midbrain dopamine neurons in processing counterfactual outcomes in monkeys. Our findings suggest that actually-gained and counterfactual outcome signals are both processed in the cortico-subcortical network constituted by these regions but in distinct manners, and integrated only in the orbitofrontal cortex in a way to compare these outcomes. This study extends the prefrontal theory of counterfactual thinking and provides key insights regarding how the prefrontal cortex cooperates with subcortical regions to make decisions using counterfactual information. TeaserCortical and subcortical systems both contribute to counterfactual thinking of decision outcomes but in distinct manners.

neuroscience↗

DNA methylation signature in NSD2 loss-of-function variants appeared similar to that in Wolf-Hirschhorn syndrome

PurposeWolf-Hirschhorn syndrome (WHS), a contiguous gene syndrome caused by the hemizygous deletion of the distal short arm of chromosome 4 where NSD2 is, reportedly exhibits specific DNA methylation signatures in peripheral blood cells. However, responsible genomic loci for signatures are unreported. The objective of the study is to define the loci of WHS-related DNA methylation signatures and to explore the role of NSD2 for the signatures. MethodsWe conducted genome-wide methylation analysis of individuals with WHS or NSD2 variants using array. We studied genome-edited knock in mice or induced pluripotent stem cells to explore the function of NSD2 variants which are observed in congenital anomaly cases. ResultsThree undiagnosed cases with NSD2 variants showed WHS-related DNA methylation signatures. These variants were validated to be NSD2 loss-of-function in induced pluripotent stem cells or genome-edited knock-in mice. p.Pro905Leu variant decreased Nsd2 protein levels, and changed Histone H3-Lysine 36 demethylation levels in similar way in the same genomic regions as Nsd2 knock out mice regulated. Nsd2 knock out mice exhibited common DNA methylation changes. ConclusionThese results revealed that WHS-related DNA methylation signatures are dependent on NSD2 dysfunction and are useful in diagnosing NSD2 variants of unknown significance.

genetics↗

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Multiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) is an next-generation sequencing library construction method developed for the analysis of DNA in ecology. Although MIG-seq can generate libraries from low-quality DNA, few polymorphisms can be obtained in species with small genomes. In this study, we developed degenerate oligonucleotide primer MIG-seq (dpMIG-seq) as an effective polymorphism discovery method that allows for variation in the number of polymorphisms while retaining the advantages of MIG-seq, including independence from DNA quality. In dpMIG-seq, a proportion of the simple sequence repeats in the primer sequence of the first PCR in MIG-seq was changed to degenerate oligonucleotides to enable annealing to a wider range of sequences. In tests of several crop species other than wheat, the number of loci that could be sequenced using dpMIG-seq with a data volume of 0.3 gigabases (Gb) was increased compared with that sequenced using MIG-seq. In wheat, the number of polymorphisms obtained via dpMIG-seq was higher than that obtained via MIG-seq when a data volume of about [≥]2 Gb was obtained. In dpMIG-seq, different loci could be sequenced by changing the positions of the degenerate oligonucleotides. By applying dpMIG-seq, we constructed a linkage map consisting of 5,142 markers for the rice inter-subspecies F2 population, and we detected quantitative trait loci for heading date in the regions where known heading-related genes were located. Overall, our results show that dpMIG-seq is a useful tool for the genetic analysis of crop species.

genetics↗