Biology subjects

Yamada, M.

Publications and source records attributed to Yamada, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Auricular vagus nerve stimulation facilitates contextual fear extinction via insular-mPFC pathway without affecting reconsolidation

Cervical vagus nerve stimulation (VNS) suppresses conditioned fear in rodents and may serve as an adjunct to exposure-based therapy for anxiety disorders. Non-invasive auricular VNS reduces conditioned fear also in humans, although the underlying mechanisms remain unclear. Using a contextual fear conditioning paradigm, in which brief re-exposure induces reconsolidation and prolonged re-exposure promotes extinction learning in mice, we examined auricular VNS-induced attenuation of fear. Auricular VNS during prolonged but not during brief re-exposures reduced freezing, indicating selective facilitation of extinction learning. Stimulation during the latter half of prolonged re-exposure, while extinction learning was progressing, reduced fear responses. As a neural circuit mechanism, we focused on projections from the posterior insular cortex (pIC), which receives interoceptive signals, including vagal input, to the medial prefrontal cortex (mPFC), which regulates fear. Auricular VNS increased c-Fos expression in pIC neurons projecting to the mPFC subdivisions: infralimbic and dorsal peduncular cortex (IL/DP). Optogenetic activation of the pIC-IL/DP pathway mimicked the extinction-facilitating effects of auricular VNS, whereas inhibition blocked them. These results demonstrate that auricular VNS promotes extinction learning of contextual fear memory by activating the pIC-IL/DP circuit, providing insight into how vagal afferent stimulation engages insular-prefrontal networks to modulate fear.

neuroscience↗

bioRxiv2026

Conserved RGF1 peptide signaling regulates root meristem development through ROS in Arabidopsis and rice

The root meristem is essential for stem cell maintenance and root development in plants. In Arabidopsis, Root meristem Growth Factor (RGF) peptides and their receptors regulate root meristem size through reactive oxygen species (ROS)-dependent signalling. RGF1-mediated ROS redistribution post-translationally stabilises the root meristem master regulator PLETHORA2 (PLT2). Although genomic studies suggest that RGF-receptor modules are evolutionarily conserved across land plants, their functional characterisation has remained largely limited to Arabidopsis. Here, we show that Oryza sativa RGF1-1 (OsRGF1-1) functions as a rice homologue of Arabidopsis RGF1 (AtRGF1). CRISPR/Cas9-generated Osrgf1-1 mutants exhibited shorter seminal roots, reduced root meristem size, and decreased superoxide (O2*-) accumulation. EdU staining further confirmed that cell proliferation activity was reduced in the Osrgf1-1 mutants. The Osrgf1-1 mutants were sensitive to low concentrations of chemically synthesised mature OsRGF1-1 peptide. This low dose of OsRGF1-1 peptide restored seminal root growth and O2*- accumulation in the Osrgf1-1 mutants but had no detectable effect on the wild type. Functional analyses using Arabidopsis rgfr receptor mutants further demonstrated that OsRGF1-1 is perceived through conserved RGF receptor machinery. Together, our findings provide the first functional evidence that the RGF1-receptor-ROS signalling module is evolutionarily conserved between dicots and monocots in the regulation of root meristem development.

plant biology↗

bioRxiv2026

Glycolipid MPIase is essential for the TAT (Twin-Arginine Translocation) pathway

TAT (Twin-Arginine Translocation) is a preprotein translocation system dedicated to membrane translocation of prefolded proteins in plants and bacteria. The TAT translocon, consisting of the TatABC subunits, drives translocation using proton motive force. However, there have been no reports on the successful reconstitution of the TAT system. In this report, we show that MPIase, a glycolipid that has been known to catalyze membrane protein integration, is essential for the TAT system. Our findings in recombinant Escherichia coli demonstrate that overproducing TatABC increases MPIase levels and that depleting MPIase results in TAT precursor accumulation in the cytosol. Furthermore, co-reconstitution of MPIase with TatABC revealed the translocation activities of TAT substrates in a proton motive force-dependent manner. This is the first successful reconstitution of the TAT system and will be advantageous for understanding its mechanisms.

biochemistry↗

bioRxiv2026

Resting-state heartbeat-evoked potentials are associated with Kalman-derived cardiac prediction errors

The heartbeat-evoked potential (HEP) reflects the cortical processing of cardiac afferent signals. However, it remains unclear whether trial-level interoceptive prediction errors can be quantified directly from spontaneous resting cardiac fluctuations and whether these model-derived errors are associated with HEP amplitude. Here, we applied a Kalman filter, implemented as a sequential Bayesian estimation procedure, to resting-state EEG and ECG recordings from 21 healthy adults to estimate trial-by-trial signed prediction errors in RR-intervals. Positive prediction errors reflected unexpected cardiac deceleration, whereas negative prediction errors reflected unexpected cardiac acceleration. Cluster-based permutation tests showed that unexpected cardiac acceleration was associated with greater fronto-centro-parietal HEP amplitude than unexpected deceleration in an early post-R-peak window, spanning FC1, CP1, Pz, CP2, Cz, C4 and FC2 from 215 to 250 ms. A Bayesian linear mixed-effects model further indicated a credible negative association between signed prediction error and HEP amplitude after controlling for respiratory phase and preceding RR interval. In a secondary connectivity analysis, unexpected acceleration was associated with stronger Cz-to-frontal beta-band phase synchrony during a later post-R-peak window from 250 to 500 ms. Exploratory individual-difference analyses suggested that neuroticism was negatively correlated with late frontal HEP amplitude during unexpected acceleration, but not during unexpected deceleration or when trials were pooled across conditions. These findings demonstrate that spontaneous cardiac fluctuations can be used to derive trial-level computational estimates of interoceptive prediction error and that these estimates are reflected in early HEP amplitude. They further suggest that the cortical processing of unexpected cardiac acceleration may be related to individual differences in affective personality traits.

neuroscience↗

bioRxiv2026

A computational account of how positive performance bias supports cognitive effort

The willingness to exert cognitive effort is essential but is constrained by the subjective cost of effort. Although effortful tasks are often avoided, positive bias about ones own performance may help sustain engagement with cognitive demands. Here, participants completed an effort-based decision-making task and reported trial-by-trial predictions of their own performance, allowing us to quantify performance prediction error (PPE) as the discrepancy between subjective and objective accuracy. The results showed that PPE was predominantly positive and increased with effort level, indicating greater overestimation under higher cognitive demands. Using a computational model, we show that choices were best explained by a learning model in which rewarded trials accompanied by positive PPE decreased subsequent sensitivity to effort. A confidence-based control model did not provide a better account of choices, suggesting that this effect was better captured by positive performance bias than by confidence alone. Our findings provide a computational account of how biased self-evaluation may attenuate the subjective cost of cognitive effort and extend the positive bias literature to the task need for cognitive effort.

neuroscience↗

bioRxiv2026

Dopamine shapes brain metastate dynamics

Dopamines influence on large-scale network dynamics, especially on the default mode network (DMN), remains uncertain, as fMRI studies have produced mixed results. One likely contributor to these discrepancies is reliance on traditional functional connectivity analyses, which typically derive a single metric (e.g., the Pearson correlation coefficient) from the entire time series and thus fail to capture network dynamics. To address this issue, we combined a dopaminergic challenge (mazindol, a dopamine transporter [DAT] reuptake inhibitor), PET, resting-state fMRI, and hidden Markov modeling (HMM) to characterize time-varying alterations in human large-scale functional networks following acute DAT blockade. We found that mazindol-induced increases in endogenous dopamine altered the balance between the brains functional "metastates," two recurrent higher-order network configurations that each encompass multiple HMM-derived brain states. Mazindol increased the time participants spent in an internally oriented cognitive metastate and decreased the time spent in a sensorimotor-perceptual metastate, with the DMN showing the most pronounced lengthening. In exploratory analyses, declines in [{superscript 1}{superscript 1}C]raclopride binding, a PET index of D2 dopamine receptor availability reflecting increased striatal extracellular dopamine levels, tended to show a positive correlation with the prolongation of these cognitive states. These findings indicate that dopamine is closely linked to shifts from sensorimotor and perceptual to cognitive brain metastates, potentially underpinning the prioritization of internally oriented over externally driven psychological processes. Our results highlight the importance of dynamic, time-resolved connectivity approaches for understanding neuromodulatory actions in the human brain and suggest that dopamine helps regulate the dynamic balance between functionally competing large-scale brain networks.

neuroscience↗

bioRxiv2025

Upregulation of the lncRNA XACT sustains pluripotency, blocks lineage specification, and drives germ cell tumor-like transcriptional programs in human pluripotent stem cells

Long noncoding RNAs (lncRNAs) represent a vast class of regulatory transcripts and are spatiotemporally controlled, yet only a few have been functionally implicated in human development. Here, we identify the X-linked lncRNA XACT, abundantly but transiently expressed during early human embryogenesis, as a critical regulator of pluripotency, lineage specification, and cancer-like states. In human pluripotent stem cells (hPSCs), XACT overexpression--but not depletion--sustains self-renewal without exogenous factors and prevents lineage commitment. Mechanistically, XACT upregulation drives hyper-elevation of the core pluripotency factors OCT4 and NANOG at the protein level by repressing their 3' untranslated regions (UTRs). XACT overexpression confers context-dependent states: in standard hPSC medium it promotes a naive-like program, whereas in the absence of exogenous factors it drives transcriptomic states resembling testicular germ cell tumors, linking misregulation of a developmentally restricted lncRNA to tumorigenic potential. In hPSC-based models of post-implantation development, XACT expression normally declines, whereas its sustained expression disrupts embryonic progression, while depletion has little effect. Finally, transcriptomic analysis of post-implantation human embryos showed that XACT levels correlate positively with pluripotency-associated gene networks. Together, these findings establish XACT as a potent, human-specific modulator of pluripotency and early embryogenesis, and suggest that its aberrant upregulation may underlie both developmental failure and germ cell tumorigenesis.

cell biology↗

bioRxiv2025

Modular platform for therapeutic drug delivery using trifunctional bio-orthogonal macromolecular conjugates

Targeted delivery of macromolecular therapeutics holds great promise for overcoming the limitations of conventional small molecules, enabling modulation of protein-protein interactions and precise genome editing. However, efficient, safe, and cell type-specific delivery remains a major challenge. To address this, we developed a modular platform for synthesizing heterotrifunctional bio-orthogonal macromolecular conjugates (BMCs) by engineering diverse combinations of targeting ligands, cell-penetrating peptides (CPPs), and bioactive cargos. We optimized facile bioconjugation chemistries to generate BMCs with improved yields, structural integrity, and activity. Modular BMCs accommodate diverse components, including antibodies and receptor ligands for targeting, CPPs for intracellular trafficking, and optical probes, therapeutic peptidomimetics, and CRISPR-Cas9 nuclease as cargos to confer specific biological activities. We assayed their utility across multiple applications: BMCs with fluorescently labeled cargo revealed endosomal escape and intracellular accumulation; peptidomimetic MYB transcription factor inhibitor BMCs exhibited potent anti-leukemic activity against acute myeloid leukemia cells; and Cas9 BMCs achieved rapid delivery and cell type-specific gene editing in human cells. The BMC approach enables customizable delivery of functional macromolecules, nominating BMCs as a broadly applicable platform for biomedical applications. One-Sentence SummaryThe establishment of modular platform for synthesizing bio-orthogonal macromolecular conjugates (BMC) enabled fast and targeted delivery of membrane-impermeant macromolecular drugs.

biochemistry↗

bioRxiv2025

RNAi reveals a unique kinesin mediating chloroplast motility in the giant cytoplasm of Bryopsis, a coenocytic green alga

RNA interference (RNAi) is a powerful tool for protein knockdown and is widely used in model animals and plants. Here, we applied this technique to Bryopsis, the green feather alga that develops a >10 cm coenocytic body in the wild and in laboratory culture. We mixed in vitro-transcribed double-stranded RNA (dsRNA) with extruded cytoplasm in the presence of polyethylene glycol or injected it directly into the cytoplasm, followed by thallus regeneration. After several days, we observed a reduction in the target gene transcript as well as expected phenotypes, indicating the effectiveness of RNAi. We prepared dsRNAs for the sole myosin and all 34 kinesin genes of the model Bryopsis strain, and performed RNAi and time-lapse microscopy to trace chloroplast movement. In addition to KCBP-type kinesins known to drive retrograde chloroplast transport in land plants, RNAi of a Bryopsidales-specific kinesin-14 (Kin14VIc) almost completely suppressed chloroplast motility. Cytoplasmic microtubules remained broadly aligned parallel to the main axis of the thallus following Kin14VIc RNAi. Purified Kin14VIc motor protein showed microtubule-gliding activity and, when artificially tetramerised, processive motility in vitro ([~]250 nm/s), similar to plant KCBP. Thus, this study introduces a powerful gene loss-of-function tool in a coenocytic organism and identifies a uniquely evolved kinesin as a critical driver of chloroplast motility in the giant cytoplasm.

cell biology↗

bioRxiv2024

Advancing Remote and Low-Resource Healthcare Delivery with Microbiopsy Skin Sample mRNA Housekeeping Gene Stability Analysis Across Various Temperatures

In the clinical dermatology setting, conventional skin sampling methods such as punch, shave, or excision biopsy are invasive, requiring local anesthesia and after-procedure care. These methods also necessitate immediate processing and cold storage to preserve high-quality nucleic acid, limiting their use in remote and low-resource regions. The microbiopsy, a minimally invasive device designed for sub-millimetre skin sampling, offers an alternative that may overcome these limitations by providing genetic profiles from the viable epidermis. We examined skin patient samples (5 microbiopsies, 3 individuals) stored across five conditions temperature conditions expected to be encountered during commercial shipping. RNA was extracted for TaqMan assay Real-Time PCR on the Fluidgim Dynamic Array targeting three housekeeping genes (ACTB, GAPDH, and RPLP0). Housekeeping genes were successfully detected at comparable levels in samples across non-control conditions, contrasting with positive control samples which showed a trend toward lower gene expression detection. In conclusion, we have established that microbiopsy samples stored in the RNA preservation agent can withstand uncontrolled temperatures likely to be encountered during commercial shipping. This could have a significant impact on enabling access to molecular diagnostic testing in an era of increasing personalized medicine and to address the long-standing need to improve remote healthcare delivery.

genomics↗

bioRxiv2024

A Rab-Kinesin12-Fused kinase module couples vesicle delivery and phragmoplast remodelling during cytokinesis in Arabidopsis

Cytokinesis is a key process in the development of multicellular organisms, through both formative and proliferative divisions. In land plants, successful cytokinesis requires precise targeting of Golgi-derived vesicles to the future division plane by the phragmoplast, a cytoskeletal structure that undergoes continuous remodelling. Endomembrane trafficking and phragmoplast remodelling are tightly coupled, indicating the existence of active crosstalk. However, although many molecular regulators of membrane trafficking and cytoskeletal organisation are known, it remains poorly understood how these processes are co-ordinated. Here, we describe a regulatory module consisting of the membrane-associated GTPase RAB-A2a, cytoskeleton-associated Class II Kinesin-12s, and the Fused kinase orthologue TIO. We provide evidence that the interaction between these molecules at the midzone is essential for cytokinesis in Arabidopsis through simultaneously targeting vesicles to the midzone and coupling phragmoplast remodelling to vesicle delivery.

plant biology↗

bioRxiv2024

Analysis of coordinated group behavior based on role-sharing: Practical application from an experimental task to a 3-on-3 basketball game as a pilot study

A group often shares a common goal and accomplishes a task that is difficult to complete alone by distributing roles. In such coordination, the nonverbal behavior among three or more members complicates the explanation of the mechanism due to complex and dynamic interactions. In cognitive science, a crucial role is indicated: to intervene moderately with others and adjust the whole balance without interrupting their main smooth interactions, using an experimental task. The findings suggest that resilient helping actions in the third role support to coordination. These actions are similar to off-ball movements in team sports, which involve an on-ball player and have recently been the focus of sports science because their characteristics are not represented in common statistical data, such as a shooting success rate. Hence, a new perspective for discussing coordination has emerged, as existing theories, such as synchronization--where movements between players are spontaneously matched and organized--cannot explain the mentioned role. However, there is a lack of investigation and discussion regarding whether these findings are applicable to real-world activities. Therefore, this study applied the experimental findings to the field of sports. We developed a 3-on-3 basketball game in which the offensive role of intervention decision and adjustment is key for winning and introduced it to the practice of a female university team as a pilot study. Participants repeatedly engaged in the mini-game, and the playing was compared before and after receiving tips of this role. Consequently, in the bins of the relatively large distance between the participant required to the relevant role and each defensive player, the frequencies after receiving these tips were significantly higher. Furthermore, the winning rate on the offensive team improved temporarily; however, the effects were not maintained. These suggest that spacing skill, which maintains reasonable distances from the other players, creates favorable situations for coordination. This study may bridge the gap between controlled experiments and real-world applications and make an educational contribution; it may recommend practice design for the acquisition of spacing skill related to the crucial role.

animal behavior and cognition↗

bioRxiv2024

Superiority illusion in older adults: volume and functional connectivity of the precuneus

AimPositive thinking, which has been known to extend the lifespan, tends to increase with age. One specific form of positive thinking, the superiority illusion (SI), involves the belief that one is better than others. Despite its potential benefits in aging, the neural basis of the SI in elderly populations remains underexplored. MethodsThis study combined a behavioral task, voxel-based morphometry (VBM), and resting-state functional connectivity (rsFC) analyses to investigate the neural substrates of the SI in a cohort of 100 participants, including young (N = 33), middle-aged (N = 33), and older adults (N = 34). ResultsOur findings indicated that higher SI scores in older adults were correlated with greater gray matter volume in the right precuneus and stronger rsFC between the right precuneus and the left lateral occipital cortex. However, these correlations were not evident in younger and middle-aged groups. ConclusionsOur findings underscore the importance of the right precuneus and its connectivity in the manifestation of the SI, particularly in older adults, highlighting its potential role in adaptive aging processes.

neuroscience↗

bioRxiv2024

Class II Kinesin-12 facilitates cell plate formation by transporting cell plate materials in the phragmoplast

Cell plate formation in plants is a complex process orchestrated by the targeted delivery of Golgi-derived and endosomal vesicles containing cell plate components to the phragmoplast midzone. It has long been hypothesised that vesicles are directionally transported along phragmoplast microtubules by motor proteins. However, the mechanisms governing the accumulation and immobilisation of vesicles at the phragmoplast midzone remain elusive, and the motor protein responsible has yet to be identified. Here, we show that the plant-specific class II Kinesin-12 (Kinesin12-II) functions as a motor protein that drives vesicle transport towards the phragmoplast midzone in the moss Physcomitrium patens. In kinesin12-II mutants, the directional movement of cell plate materials towards the midzone and their retention were abolished, resulting in delayed cell plate formation and phragmoplast disassembly. A macroscopic phenotype arising from Kinesin12-II disruption was the impediment to gametophore development. We showed that this defect was attributable to the production of aneuploid cells in the early gametophore, where chromosome missegregation occurred because of the incomplete disassembly of phragmoplast microtubules in the preceding cell cycle. These findings suggest that plant Kinesin-12 has evolved to acquire a unique and critical function that facilitates cell plate formation in the presence of phragmoplasts.

plant biology↗

bioRxiv2024

A neuroimaging dataset during sequential color qualia similarity judgments with and without reports

Recent neuroscientific research has advanced our understanding of consciousness, yet the connection between specific qualitative aspects of consciousness, known as "qualia," and particular brain regions or networks remains elusive. Traditional methods that rely on verbal descriptions from participants pose challenges in neuroimaging studies. To address this, our group has introduced a novel "qualia structure" paradigm that leverages exhaustive, structural, and relational comparisons among qualia instead of verbal reports. In this study, we present the first fMRI dataset that captures relational similarity judgments among two out of nine color qualia per trial from 35 participants. This dataset also includes a "no-report" condition in half of the trials to assess the impact of overt reporting. Additionally, each participants color discriminability was evaluated with a hue test conducted outside the scanner. Our data offer valuable insights into the brain functions associated with color qualia and contribute to a deeper understanding of the neural foundations of consciousness.

neuroscience↗

bioRxiv2024

Glutathione supersulphide regulates T-cell receptor signalling

Immunometabolism regulates functions and fates of immune cells including T cells. Supersulphides, which are universal metabolites containing catenated sulphur atoms, have various physiological functions based on their unique redox properties. Here we found that activation of T-cell receptor (TCR) signalling was accompanied by supersulphide decrease, which suggests a regulatory contribution of sulphur metabolism to immune function. Consistently, inhibiting supersulphide synthesis facilitated TCR activation and exacerbated allergen-induced type 2 inflammation in mice. Supplementation with glutathione trisulphide (GSSSG), a major endogenous supersulphide, suppressed TCR signalling in naive CD4+ T cells and their differentiation and effectively alleviated the inflammation. Docking simulation revealed interaction of GSSSG with CD3{varepsilon} chain in the TCR/CD3 complex, which was supported by mass spectrometry detection of persulphidated glutathionylation at a functionally important CXXC motif of CD3{varepsilon} chain. This study identified a new post-translational modification with supersulfides and demonstrated a critical contribution of sulphur metabolism to TCR signalling regulation.

biochemistry↗

bioRxiv2024

Importin α4 deficiency induces psychiatric disorder-related behavioral deficits and neuroinflammation in mice.

Importin 4, which is encoded by the Kpna4 gene, is a well characterized nuclear-cytoplasmic transport factor known to mediate transport of transcription factors including NF-{kappa}B. Here, we report that Kpna4 knock-out (KO) mice exhibit psychiatric disorder-related behavioral abnormalities such as anxiety-related behaviors, deceased social interaction and sensorimotor gating deficits. Contrary to a previous study predicting attenuated NF-{kappa}B activity as a result of Kpna4 deficiency, we observed a significant increase in expression levels of NF-{kappa}B genes and pro-inflammatory cytokines such as TNF, Il1{beta} or Il-6 in the Prefrontal Cortex or Basolateral Amygdala of the KO mice. Moreover, examination of inflammatory responses in primary cells revealed that Kpna4 deficient cells have an increased inflammatory response, which was rescued by addition of not only full-length, but also a nuclear transport deficient truncation mutant of importin 4, suggesting contribution of its non-transport functions. Furthermore, RNAseq of sorted adult Microglia and Astrocytes and subsequent transcription factor analysis suggested increases in Polycomb repressor complex 2 (PRC2) activity in Kpna4 KO cells. Taken together, importin 4 deficiency induces psychiatric disorder-related behavioral deficits in mice, along with an increased inflammatory response and possible alteration of PRC2 activity in glial cells.

neuroscience↗

bioRxiv2023

A transposase-derived gene required for human brain development

DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in human cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement, and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements. In the brain cortex, loss of Pgbd5 leads to aberrant differentiation and gene expression of distinct neuronal populations, including specific types of glutamatergic neurons, which explains the features of PGBD5 deficiency in humans. Thus, PGBD5 might be a transposase-derived enzyme required for brain development in mammals. One-Sentence SummaryPiggyBac Transposable Element Derived 5 (PGBD5) is required for brain development in humans and mice through genetic and epigenetic mechanisms.

neuroscience↗