Biology subjects

Komatsu, M.

Publications and source records attributed to Komatsu, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Improved detection and spatiotemporal spectral analysis of neural traveling waves

Traveling waves (TWs) are a fundamental mode of neural dynamics, yet existing detection methods are limited by sensor geometry, spatial-frequency resolution, signal amplitude, and ambiguity between propagating and standing-wave patterns. Here we introduce the Traveling Wave Index (TWINDEX), a framework for three-dimensional spatiotemporal spectral analysis of TWs across temporal frequency, spatial frequency, and propagation direction. TWINDEX generalizes to irregular sensor layouts, and quantifies wave strength as the reduction in circular phase variance produced by a candidate planar wave. This normalization yields robust behavior at both low and high spatial frequencies and suppresses coherent in-phase activity. Directional moments further separate planar from standing waves. We derive analytical links between TWINDEX, parametric planar-wave fit, and distance-phase correlation, and introduce projected distance-phase correlation (ProDPC) for sensitive single-trial planar-wave detection. Applying these methods to large-scale marmoset ECoG and human EEG, we identify alpha/low-beta TWs localized in spatial and temporal frequency, with physiologically plausible propagation speeds. Across trials and epochs, waves occur in oppositely directed propagation modes, demonstrating that alpha/beta activity is associated with both feedforward- and feedback-directed large-scale dynamics.

neuroscience↗

bioRxiv2026

Information Flow and Traveling Waves show distinct cortical trajectories

Traveling waves (TWs) are a hallmark of cortical dynamics, proposed to organize neuronal activity across space and time. Yet their propagation can oppose the causal flow of information, challenging their functional interpretation. We demonstrate this using computational simulations and validate our predictions in electrophysiological recordings. We introduce the Directional Information Flow Field (DIFF), which adapts Granger causality to two-dimensional neural recordings to map directed interactions across cortical networks. In computational models, DIFF recovers the direction and sources of information flow, whereas delays and inhibition can cause TWs to propagate in opposing or orthogonal directions. We validate these findings in human and non-human primate electrophysiological recordings, revealing reversed or orthogonal flow axes, distinct spatial origins, and frequency-dependent differences in feedforward and feedback dynamics. These findings challenge the functional interpretation of TWs and establish DIFF as a complementary framework for revealing directed neural communication underlying cortical dynamics.

neuroscience↗

bioRxiv2026

Macroscale traveling waves link perception, response selection, and vocal production during marmoset vocal interactions

Vocal communication involves a series of cognitive processes, which can be broadly categorized into three components: perceiving communicative signals; deciding whether and how to respond; and generating vocal motor output. These processes must work harmoniously, with integration and bridging between components being crucial for effective communication. Previous research on vocal communication has typically focused on specific brain regions or isolated cognitive functions, often lacking a holistic perspective of macro-scale, whole-cortical dynamics and their role in the complete communication process. Therefore, although the cortical areas associated with each cognitive component have been localized in humans, the macro-scale cortical dynamics underlying the integration of these cognitive processes remain unknown. Building on recent findings linking macro-scale cortical dynamics to behavioral performance, we hypothesized that traveling wave like cross-areal interactions play a role in integrating the three communicative components. To test this hypothesis, we recorded whole-cortical activity using epidural electrocorticography (ECoG) while subject marmosets vocally interacted with partners. We found theta-band activation in several cortical areas, including the parietal and auditory cortices, while listening to partners calls. This activity was further modulated depending on whether the subjects engaged in vocal interactions, potentially representing the transformation of sensory processing into decision-making and vocal motor preparation. Given the widespread nature of this modulation, we next characterized whole-brain activity patterns by employing a novel analytical method, Weakly Orthogonal Conjugate Contrast Analysis (WOCCA). This analysis revealed that cortical activity could be decomposed into two distinct traveling wave like propagation patterns, a rotational and a translational wave, and both waves discriminated communicative conditions consistent with localized activity. The rotational wave further represented vocal motor preparation through trigger-like temporal pattern. In addition, the magnitude of the translational wave immediately before subjects vocal production correlated with the vocal production-induced suppression of high-gamma-band activity, particularly in the prefrontal and auditory cortices. As vocalization-induced suppression is believed to reflect sensory prediction, the translational wave may propagate specific decision-related or acoustic information necessary for subsequent vocal production to local cortical areas. These findings suggest that the brain orchestrates the sequential cognitive processes underlying vocal communication through macro-scale traveling waves.

neuroscience↗

bioRxiv2026

Radiocesium Uptake in Two Fungal Bed-cultivated Edible Mushroom Species in Forests in Fukushima, Japan

In Japan, mushrooms have long been valued as food resources, but the Fukushima nuclear accident disrupted production and shipment due to radiocesium contamination. Limited knowledge has particularly hindered outdoor fungal bed cultivation. To address this, we conducted cultivation experiments with Lyophyllum decastes and Lepista nuda across 14 broad-leaved deciduous forest sites in Fukushima Prefecture. Air dose rates at 1 m height ranged from 0.04 to 0.89 {micro}Sv/h. Radiocesium concentrations (combined 137Cs and 134Cs, expressed as Bq/kg at 90% water content) in fruit bodies were 0.4-12 (mean 2.3) for Ly. decastes and 0.2-43 (mean 8.1) for Le. nuda. Both species remained below Japans food safety threshold of 100 Bq/kg, indicating that safe cultivation is feasible across broad areas. Uptake patterns differed: concentrations in Ly. decastes correlated with contamination in litter and multiple soil layers, whereas in Le. nuda it correlated only with litter contamination. These findings suggest that clean soil fills for Ly. decastes and clean litter covers for Le. nuda could serve as mitigation strategies tailored to each species. Aggregated transfer factors (2.76 x 10-5 m2/kg for Ly. decastes and 6.60 x 10-5 m2/kg for Le. nuda) were lower than those reported for wild mushrooms. Overall, this study provides new insights into reducing radiocesium assimilation by cultivated mushrooms and supports the revival of outdoor fungal bed cultivation in contaminated landscapes.

ecology↗

bioRxiv2026

Excess Met1-ubiquitination leads to solid aggregate formation

The ubiquitin ligase HOIL-1 has a unique role in controlling quantity of Met1-linked/ linear ubiquitin chains in cells by coordinating action with the ubiquitin ligase HOIP. Both ligases are components of the Linear UBiquitin chain Assembly Complex (LUBAC), the only known ligase complex that is able to generate Met1-linked ubiquitin chains. Although importance of Met1-linked ubiquitin chains in inflammation and immunity is well established, physiological relevance of quantity of these chains remain unknown. Here, we demonstrate that cells expressing catalytically inactive HOIL-1 exhibited significantly higher numbers of -Synuclein, tau, and amyloid beta aggregates. This phenotype is associated with a disruption in late-stage autophagic flux, wherein p62-positive aggregates fail to colocalize with lysosomal markers, leading to impaired clearance. Additionally, a biophysical transition in aggregate properties was observed in vitro, with mutant cells forming more rigid solid-like inclusions, shifting from dynamic and liquid-like condensates. Elevated Met1-linked ubiquitin chains, either through HOIL-1 catalytic inactivation or knockdown of the Met1-linked chain-specific deubiquitinase OTULIN, phenocopied the defects in aggregate clearance. These findings reveal a critical role of HOIL-1 catalytic activity in modulating aggregate clearance through autophagy and maintaining the quantity of Met1-ubiquitin chains, highlighting HOIL-1 as a key factor in proteostasis in neurodegenerative diseases. HighlightsO_LIHOIL-1 catalytic activity prevents neurodegenerative protein aggregate accumulation C_LIO_LIInactive HOIL-1 impairs late-stage autophagic clearance of protein aggregates C_LIO_LILoss of HOIL-1 shifts aggregates to rigid, solid-like states C_LIO_LIExcess Met1-ubiquitin chains drive aggregate solidification C_LI

cell biology↗

bioRxiv2025

Neuropilin 2 functions as a co-inhibitory receptor to regulate antigen-induced inflammation and allograft rejection

Co-inhibitory receptors function as central modulators of the immune response to resolve T effector activation and/or to sustain immune homeostasis. Here, using humanized SCID mice, we found that NRP2 is inducible on late effector and exhausted subsets of human CD4+ T cells and that it is co-expressed with established co-inhibitory molecules including PD-1, CTLA4, TIGIT, LAG3 and TIM3. In murine models, we also found that NRP2 is expressed on effector memory CD4+ T cells with an exhausted phenotype and that it functions as a key co-inhibitory molecule. Knockout of NRP2 resulted in hyperactive CD4+ T cell responses, and enhanced inflammation in delayed type hypersensitivity and transplantation models. Following cardiac transplantation, allograft rejection and graft failure was accelerated in global as well as CD4+ T cell-specific knockout recipients, and enhanced alloimmunity was dependent on NRP2 expression on CD4+ T effectors, and not on CD4+Foxp3+ T regulatory cells. Also, knockout T regulatory cells were found to be as efficient as wild type cells in the suppression of effector responses in vitro and in vivo. These collective findings identify NRP2 as a novel coinhibitory receptor and demonstrate that its expression on CD4+ T effector cells is of great functional importance in immunity.

immunology↗

bioRxiv2025

KEAP1 retention in phase-separated p62 bodies drives liver damage in autophagy-deficient conditions

Phase-separated p62 bodies activate NRF2, a key transcription factor for antioxidant response, by sequestering KEAP1, which targets NRF2 for degradation. Although p62 bodies containing KEAP1 are degraded by autophagy, they accumulate in various liver disorders. Their precise disease role remains unclear. We show that excessive KEAP1 retention in p62 bodies and NRF2 activation are major causes of liver damage when autophagy is impaired. In mice with weakened or blocked p62-KEAP1 interactions, KEAP1 retention and NRF2 activation under autophagy-deficient conditions were suppressed. Transcriptome and proteome analyses revealed that NRF2 targets upregulated by autophagy suppression normalized in p62 mutants unable to bind KEAP1. Autophagy deficiency caused organelle accumulation, especially of the ER, regardless of p62 mutation. Liver damage and hepatomegaly from autophagy suppression markedly improved in p62 mutants, particularly those with blocked KEAP1 binding. These findings highlight excessive KEAP1 retention in p62 bodies and defective organelle turnover as key drivers of liver pathology, underscoring the significance of phase separation in vivo.

cell biology↗

bioRxiv2024

Loss of SPNS1, a lysosomal transporter, in the nervous system causes dysmyelination and white matter dysplasia

Protein spinster homolog 1 (SPNS1) is a lysosomal transporter of lysophospholipids and sphingosine, which has recently been identified to be mutated in patients with neurodegeneration. However, its physiological role, especially in the nervous system, remains largely unknown. In this study, we generated, for the first time, nervous system-specific Spns1 knockout mice, Spns1flox/flox;nestin-Cre, and found that the mutant mice develop neurological symptoms, such as epilepsy, and growth retardation, and die by 5 weeks of age. The mutant mice exhibited dysmyelination and oligodendrocyte shedding, while maintaining the neurons. Mutant mouse brains showed accumulation of lysophospholipids, predominantly in regions, such as the olfactory bulb and hippocampus. Furthermore, whereas sphingosine accumulated in the mutant mouse brain, the levels of ceramide and sphingoglycolipids, which are the main myelin components, were decreased. Our findings imply that abnormal sphingosine metabolism causes dysmyelination and white matter dysplasia in brain-specific Spns1-knockout mice, and indicate a possible role of SPNS1 mutation in the pathogenesis of congenital cerebral white matter dysplasia in humans.

cell biology↗

bioRxiv2024

Digital Twin Brain Simulator: Harnessing Primate ECoG Data for Real-Time Consciousness Monitoring and Virtual Intervention

At the forefront of bridging computational brain modeling with personalized medicine, this study introduces a novel, real-time, electrocorticogram (ECoG) simulator based on the digital twin brain concept. Utilizing advanced data assimilation techniques, specifically a Variational Bayesian Recurrent Neural Network model with hierarchical latent units, the simulator dynamically predicts ECoG signals reflecting real-time brain latent states. By assimilating broad ECoG signals from Macaque monkeys across awake and anesthetized conditions, the model successfully updated its latent states in real-time, enhancing the precision of ECoG signal simulations. Behind the successful data assimilation, a self-organization of latent states in the model was observed, reflecting brain states and individuality. This self-organization facilitated simulation of virtual drug administration and uncovered functional networks underlying changes in brain function during anesthesia. These results show that the proposed model is not only capable of simulating brain signals in real-time with high accuracy, but is also useful for revealing underlying information processing dynamics.

neuroscience↗

bioRxiv2023

Diverse Configurations of Erroneous Predictive Coding Across Brain Hierarchies in a Non-Human Primate Model of Autism Spectrum Disorder

In autism spectrum disorder (ASD), atypical sensory experiences are often associated with irregularities in predictive coding, which proposes that the brain creates hierarchical sensory models via a bidirectional process of predictions and prediction errors. However, it remains unclear how these irregularities manifest across different functional hierarchies in the brain. To address this, we used high-density electrocorticography (ECoG) in a non-human primate model of ASD during an auditory task with two layers of temporal control, and applied a quantitative model to quantify the integrity of predictive coding across two distinct hierarchies. Our results demonstrate that ASD is characterized by sensory hypersensitivity and unstable predictions across two brain hierarchies, and reveal the associated spatio-spectro-temporal neural signatures. Importantly, we observe diverse configurations of underestimation or overestimation of sensory regularities within these hierarchies. This work provides a multi-layered biomarker for ASD, contributing to our understanding of its diverse symptoms.

neuroscience↗

bioRxiv2023

Variability in radiocesium activity concentration in growing hardwood shoots in Fukushima, Japan

The radiocesium contamination caused by the Fukushima Daiichi Nuclear Power Plant accident has made it difficult to use coppice woods as bed logs for mushroom cultivation. Evaluating the variability in the radiocesium activity concentration of logs is necessary in order to predict how many coppice woodlands are available for producing mushroom bed logs. To clarify the variability in radiocesium activity concentrations and to estimate the sample size required to estimate these concentrations with sufficient accuracy, we modeled the log-transformed radiocesium activity concentrations in growing shoots of hardwoods. We designed two models: (1) a model with mean concentrations that varied among stands with a standard deviation that was the same among stands, and (2) a model with varying means and standard deviations. We fit the data pertaining to only Quercus serrata to both models and calculated the widely applicable information criterion values. Consequently, we adopted the simpler model (1). Applying the selected model to data for all species, we examined the relationship between the number of measurement individuals and the predictive distribution of the expected concentration. Based on previous recommendations and measurement costs, we proposed that five individuals would be appropriate for estimating radiocesium activity concentration in a stand.

plant biology↗

bioRxiv2023

Epileptic responses in marmosets induced by knockdown of CREB Regulated Transcription Coactivator 1 (CRTC1)

Animal models have contributed greatly to the development of anticonvulsant drugs. However, 20-30% of epilepsy patients still do not achieve adequate seizure control. It is important to understand the biological mechanisms of epilepsy in order to develop treatments and novel anticonvulsant drugs. Here we report CRTC1 knockdown (KD) induced abnormal cFOS expression beyond the injection sites followed by epileptic response by three local injections of short hairpin RNA (shRNA) in marmoset V1. Longitudinal monitoring of cortical-wide neural activity revealed transient changes in high frequency oscillations by cortical electrocorticography throughout the cortex, and a lesion in the temporal lobe was observed by MRI and postmortem histology. shCRTC1 KD marmosets showed severe lesions surrounding the injection site several months after injection. Glial cell activation may occur simultaneously or prior to IEG induction after shCRTC1 injection. Thus, the epileptic process from seizure onset to remission can be studied in this animal model.

neuroscience↗

bioRxiv2023

Mechanistic insights into the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control

Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Herein, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and subsequently CDK5RAP3, the last of which is an adaptor for ufmylating ribosomal subunit RPL26. When CDK5RAP3 was absent from the E3 complex, UFBP1 ufmylation occurred, a process thought to drive ER-phagy. Further, upon treatment with anisomycin, an inducer of disome formation, the UFM1 E3 complex associated with ufmylated RPL26 on the 60S ribosomal subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results clarify the molecular mechanism of the UFM1 system and provide new insights into the role of ufmylation.

biochemistry↗

bioRxiv2023

Distributed representations of prediction error signals across the cortical hierarchy are synergistic

An important question concerning inter-areal communication in the cortex is whether these interactions are synergistic, i.e. brain signals can either share common information (redundancy) or they can encode complementary information that is only available when both signals are considered together (synergy). Here, we dissociated cortical interactions sharing common information from those encoding complementary information during prediction error processing. To this end, we computed co-information, an information-theoretical measure that distinguishes redundant from synergistic information among brain signals. We analyzed auditory and frontal electrocorticography (ECoG) signals in five common awake marmosets performing two distinct auditory oddball tasks and investigated to what extent event-related potentials (ERP) and broadband (BB) dynamics encoded redundant and synergistic information during auditory prediction error processing. In both tasks, we observed multiple patterns of synergy across the entire cortical hierarchy with distinct dynamics. The information conveyed by ERPs and BB signals was highly synergistic even at lower stages of the hierarchy in the auditory cortex, as well as between auditory and frontal regions. Using a brain-constrained neural network, we simulated the spatio-temporal patterns of synergy and redundancy observed in the experimental results and further demonstrated that the emergence of synergy between auditory and frontal regions requires the presence of strong, long-distance, feedback and feedforward connections. These results indicate that the distributed representations of prediction error signals across the cortical hierarchy can be highly synergistic.

neuroscience↗

bioRxiv2022

Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response

NRF2 is a transcription factor responsible for antioxidant stress responses that is usually regulated in a redox-dependent manner. p62 bodies formed by liquid-liquid phase separation contain Ser349-phosphorylated p62, which participates in the redox-independent activation of NRF2. However, the regulatory mechanism and physiological significance of phosphorylation remain unclear. Herein, we identify ULK1 as a kinase responsible for phosphorylation of p62. ULK1 co-localizes with p62 bodies, and directly interacts with p62. This phosphorylation allows KEAP1 to be retained within p62 bodies, activating NRF2. p62S351E/+ mice are phosphomimetic knock-in mice in which Ser351 corresponding to human Ser349 is replaced by Glu. These mice, but not phosphodefective p62S351A/S351A mice, exhibit NRF2 hyperactivation and growth retardation, the latter caused by malnutrition and dehydration due to obstruction of the esophagus and forestomach secondary to hyperkeratosis. p62S351E/+ mice are a phenocopy of systemic Keap1-knockout mice. Our results expand our understanding of the physiological importance of the redox-independent NRF2 activation pathway and provide new insight into the role of phase separation in this process.

cell biology↗

bioRxiv2021

Constructing the hierarchy of predictive auditory sequences in the marmoset brain

Our brains constantly generate predictions of sensory input that are compared with actual inputs, propagate the prediction-errors through a hierarchy of brain regions, and subsequently update the internal predictions of the world. However, the essential feature of predictive coding, the notion of hierarchical depth and its neural mechanisms, remains largely unexplored. Here, we investigated the hierarchical depth of predictive auditory processing by combining functional magnetic resonance imaging (fMRI) and high-density whole-brain electrocorticography (ECoG) in marmoset monkeys during an auditory local-global paradigm in which the temporal regularities of the stimuli were designed at two hierarchical levels. The prediction-errors and prediction updates were examined as neural responses to auditory mismatches and omissions. Using fMRI, we identified a hierarchical gradient along the auditory pathway: midbrain and sensory regions represented local, short-time-scale predictive processing followed by associative auditory regions, whereas anterior temporal and prefrontal areas represented global, long-time-scale sequence processing. The complementary ECoG recordings confirmed the activations at cortical surface areas and further differentiated the signals of prediction-error and update, which were transmitted via putatively bottom-up {gamma} and top-down {beta} oscillations, respectively. Furthermore, omission responses caused by absence of input, reflecting solely the two levels of prediction signals that are unique to the hierarchical predictive coding framework, demonstrated the hierarchical predictions in the auditory, temporal, and prefrontal areas. Thus, our findings support the hierarchical predictive coding framework, and outline how neural circuits and spatiotemporal dynamics are used to represent and arrange a hierarchical structure of auditory sequences in the marmoset brain.

neuroscience↗

bioRxiv2021

Droplets of amyotrophic lateral sclerosis-associated p62/SQSTM1 mutants show slower inner fluidity

A series of amyotrophic lateral sclerosis (ALS)-related proteins such as FUS, TDP-43 and hnRNPA1 has an ability to be liquid-liquid phase separation, and their disease-related mutations cause the transition of their responsible liquid droplets to aggregates. Missense mutations in SQSTM1/p62, which have been identified throughout the gene, are associated with ALS, frontotemporal degeneration (FTD) and Pagets disease of bone. SQSTM1/p62 protein forms liquid-droplets through the interaction with ubiquitinated proteins, and the droplet serves as a platform of autophagosome formation and anti-oxidative stress response via the LC3-interacting region (LIR) and Keap1-interacting region (KIR), respectively. However, it remains unclear whether ALS/FTD-related p62 mutations in LIR and KIR form aberrant liquid droplets, cause defective autophagy and stress response or both. To evaluate the effects of ALS/FTD-related p62 mutations in LIR and KIR on a major oxidative stress system, the Keap1-Nrf2 pathway and the autophagic turnover, we developed systems that enable to monitor them with high sensitivity. These systems revealed that some mutants but not all have their less abilities on the Nrf2-activation and show the delayed turnover. By contrast, while the sufficient ability to form liquid droplets, all droplets consisting of p62 mutants showed slower inner fluidity. These results indicate that like other ALS-related mutant proteins, a primary defect in ALS/FTD with p62 missense mutations is a qualitative change of p62-liquid droplets.

cell biology↗

bioRxiv2019

Broadband Signal Rather than Frequency-Specific Rhythms Underlies Prediction Error in the Primate Auditory Cortex

Detection of statistical irregularities, measured as a prediction error response, is fundamental to the perceptual monitoring of the environment. We studied whether prediction error response is associated with neural oscillations or asynchronous broadband activity. Electrocorticography (ECoG) was carried out in three male monkeys, who passively listened to the auditory roving oddball stimuli. Local field potentials (LFP) recorded over the auditory cortex underwent spectral principal component analysis, which decoupled broadband and rhythmic components of the LFP signal. We found that the broadband component captured the prediction error response, whereas none of the rhythmic components were associated with statistical irregularities of sounds. The broadband component displayed more stochastic, asymmetrical multifractal properties than the rhythmic components, which revealed more self-similar dynamics. We thus conclude that the prediction error response is captured by neuronal populations generating asynchronous broadband activity, defined by irregular dynamical states which, unlike oscillatory rhythms, appear to enable the neural representation of auditory prediction error response. Significance StatementThis study aimed to examine the contribution of oscillatory and asynchronous components of auditory local field potentials in the generation of prediction error responses to sensory irregularities, as this has not been directly addressed in the previous studies. Here, we show that mismatch negativity - an auditory prediction error response - is driven by the asynchronous broadband component of potentials recorded in the auditory cortex. This finding highlights the importance of non-oscillatory neural processes in the predictive monitoring of the environment. At a more general level, the study demonstrates that stochastic neural processes, which are often disregarded as neural noise, do have a functional role in the processing of sensory information.

neuroscience↗