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Fujii, S.

Publications and source records attributed to Fujii, S..

At least 19 recordsLinked to original sources

Rice blast fungus hijacks a rice RALF peptide to initiate infection

Plant-derived peptides regulate immunity and host-microbe interactions, but whether fungal pathogens exploit endogenous plant peptides for infection-site selection remains largely unknown. Rapid alkalinization factors (RALFs) are a family of plant peptide hormones that contribute to plant development, reproduction, stress responses, and cell-wall organization. Here, we show that OsRALF7, which is an immune-activating peptide in rice (Oryza sativa), is co-opted by the rice blast fungus Magnaporthe oryzae as a host-derived cue for appressorium formation, specialized infection structures required for host penetration. While synthetic OsRALF7 peptide induced defense responses in rice suspension cells, the same peptide induced appressorium formation in M. oryzae. OsRALF7-induced appressorium formation was associated with activation of the cAMP/PKA and Pmk1 MAPK pathways and required a hydrophobic surface. M. oryzae inoculated onto Osralf7 knockout plants formed fewer appressoria, and the positioning of these appressoria relative to the boundaries between two adjacent plant epidermal cells was altered. These findings suggest that OsRALF7 provides positional information for infection initiation for M. oryzae. OsRALF7 localized to the plasma membrane and cell wall in rice, and its appressorium-inducing activity required a conserved YISY motif and cysteine residues. This activity was not conserved in Colletotrichum higginsianum, as RALF23 from Arabidopsis thaliana did not induce appressorium formation but instead showed antifungal activity. Together, these findings uncover a dual function of endogenous plant immune-modulating RALF peptides at the plant-pathogen interface, where they can be exploited by M. oryzae as a host-derived cue for infection initiation while also retaining antifungal activity against other fungal species.

plant biology↗

Stigmatic papilla cells recover nonself pollen acceptance after self-pollen recognition

In Brassicaceae, self-incompatibility is initiated when the pollen ligand SP11/SCR activates the cognate stigma receptor kinase SRK. Although this interaction is usually considered at a single pollen-papilla interface, individual papilla cells encounter mixed pollen loads. Here, using a self-incompatibility-reconstituted Arabidopsis thaliana system, we show that self-pollen recognition transiently delays the hydration and germination of neighboring nonself pollen. The delay was stronger when two self-pollen grains were present but largely disappeared when nonself pollen was applied 2 h after self pollen. Repollination after removal of a self-pollen grain nevertheless revealed persistent inhibition at the original contact site. Live imaging with Lifeact-tdTomato showed that self-pollination transiently broadened F-actin orientations throughout the papilla cell, followed by recovery toward the longitudinal organization of unpollinated cells. Upon self- and non-self-dual pollination, actin-bundle orientation returned toward the papilla long axis prior to the delayed hydration of the non-self-pollen. These observations support the view that the nature of the self-recognition signaling produces a reversible, papilla-wide state that temporarily reduces compatible-pollen acceptance, while local self-rejection persists at the original contact site.

plant biology↗

Evolution of transposons as controlling elements

Transposons were originally described as controlling elements, yet the molecular basis and evolutionary origin of their transcriptional regulatory activities remain elusive. Here, we show that transcriptional regulatory activity is an intrinsic property of transposases (TPases). We demonstrate that the Arabidopsis AtMu1 TPase is sufficient to induce sequence-specific transcriptional activation of cognate copies, revealing a pre-existing cis-regulatory network. We further demonstrate that long-recognized Spm transposon-encoded transcriptional regulator TnpA evolved from an ancestral TPase, linking transcriptional regulators to TPases. Across eukaryotes, we identify multiple domesticated TPase-derived proteins that recurrently lack catalytic residues for transposition, consistent with a one-step regulatory co-option through loss of catalytic activity. Together, our results reveal TPases as autonomous sequence-specific transcriptional regulators and provide a direct evolutionary route from TPases to transcription factors.

genetics↗

Modulating supplementary motor area excitability enhances groove-related pleasure during music listening

Pleasurable urge to move to music is often referred to as groove. Although previous studies have shown an association between the supplementary motor area (SMA) and the groove experience, its causal role remains unclear. Here, we investigated whether the SMA is causally involved in groove experience during music listening using repetitive transcranial magnetic stimulation. Fifteen healthy participants completed three sessions on separate days: excitatory stimulation (intermittent theta burst stimulation; iTBS) over the SMA, inhibitory stimulation (continuous theta burst stimulation; cTBS) over the SMA, and sham stimulation (iTBS or cTBS) over the vertex. After each stimulation session, participants listened to five high-groove and five low-groove musical excerpts and rated urge-to-move and pleasure on a 0-100 scale. Heart rate was additionally recorded as an exploratory physiological measure during music listening. Linear mixed-effects models (LMM) showed that pleasure ratings, but not urge-to-move ratings, were higher following both iTBS and cTBS compared with sham stimulation. In exploratory LMMs, reduced log-transformed heart rate variability (HRV) significantly predicted higher pleasure ratings. These findings suggest that SMA stimulation modulates the pleasurable component of the groove experience, likely via network-level mechanisms rather than a simple linear relationship between SMA excitability and pleasure. They also raise the possibility that reduced parasympathetic activity, reflected by lower HRV, mediates the stimulation-related increase in musical pleasure. Future studies should investigate the causal roles of other brain regions as well as clarify the directionality between autonomic changes and the groove experience.

neuroscience↗

Evaluating Evo 2 for plant variant effect prediction

The genomic foundation model Evo 2 enables zero-shot variant effect prediction. Here, we evaluate its performance using Arabidopsis thaliana reproductive barrier genes with experimentally confirmed gain- and loss-of-function variants, and show that Evo 2 distinguishes functionally impactful variants. Together with a sign-reversal amplitude metric that recovers a variant missed by standard scoring, these results highlight the potential of Evo 2 for causal variant prioritization in plant GWAS and QTL mapping.

plant biology↗

A pistil peptide toxin-pollen antidote system for reproductive barrier

Summary paragraphPrezygotic reproductive barriers in angiosperms are crucial for female-mediated selection of compatible male gametes. In this study, we identified a biological activity within the stylar tissues of Arabidopsis thaliana pistils that inhibits the elongation of heterospecific pollen tubes. Using genome-wide association studies, we identified a cysteine-rich peptide predominantly expressed in the style as the responsible barrier. This secreted peptide, named Femme fatale (FEM), inhibited pollen tube elongation of heterospecific species and some conspecific strains, both in vivo and in vitro. Importantly, FEMs function was independent of the known reproductive barrier component SPRI1 that functions in the stigmatic papilla cell surface. This means two factors act spatially in sequence to create a multilayered reproductive barrier system against pollen in pistils. We also identified a secreted protein expressed in pollen, Homme capable (HOM), which is encoded by a gene next to FEM. HOM interacts with FEM to counteract its barrier effect and allow pollen tube elongation. The FEM-HOM locus has undergone frequent tandem duplications during Brassicaceae evolution. Dosage differences between the two factors can lead to reproductive incompatibility among lineages. Together, our findings suggest that FEM and HOM form a toxin-antidote system that helps establish reproductive barriers.

plant biology↗

Assessing the Performance of LLMs in Multimodal Information Extraction for Biological Research: A Case Study on LLPS

Advances in experimental techniques have expanded the volume of biological data. This has increased the demand for structured information extraction from papers, with large language models (LLMs) considered promising. However, challenges remain, including limited validation in biology and unclear applicability to multimodal tasks that integrate text with domain-specific figures, such as microscopic images and scatter plots. Here, we developed a multimodal LLM (MLLM)-based workflow to extract the experimental conditions and phase status from the text and figures of experimental papers on liquid-liquid phase separation and validated the effect of various inputs, prompts, and MLLM types. As a result, the Gemini 2.5 Pro-based extraction achieved an F1-score of 0.847 by processing each figure as a processing unit and inputting domain-specific prompts reflecting manual extraction guidance. This study demonstrates the potential and limitations of MLLMs for extracting biological information and provides insights for advancing multimodal approaches in biology.

bioinformatics↗

Musicianship and active musical engagement predict facilitation of auditory-motor plasticity: evidence from auditory-motor paired associative stimulation

Background and AimAuditory-motor paired associative stimulation (PAS) probes experience-dependent plasticity in auditory-motor circuits. We tested whether musical experience and musical sophistication modulate PAS-induced facilitation when instrument tones are paired with transcranial magnetic stimulation (TMS) over the left primary motor cortex. MethodSixteen musicians and thirteen non-musicians completed two sessions. Session 1 estimated an individualized inter-stimulus interval (ISI) by testing seven tone-TMS delays (25-300 ms). Session 2 applied PAS at the optimal ISI. Corticospinal excitability was assessed by motor-evoked potentials (MEPs) from right first dorsal interosseus at baseline and post-intervention. Group comparisons and a stepwise multiple regression with Goldsmiths Musical Sophistication Index (Gold-MSI) subscales evaluated predictors of the PAS effect. ResultsA stepwise multiple regression model selected "Group" and "Active Engagement" (Gold-MSI Factor 1) as independent predictors (F (2,26) = 4.59, p = 0.020, adjusted R2 = 0.204), without interaction: musicians exhibited smaller facilitation than non-musicians, and higher Active Engagement predicted greater facilitation across groups. DiscussionThe lack of facilitation in musicians contrasts with somatosensory PAS reports of enhanced plasticity in experts. A modality-specific ceiling effect may contribute, whereby long-term training optimizes auditory-motor transmission, reducing headroom for facilitation. The association with Active Engagement suggests motivational/reward mechanisms--potentially dopaminergic-- gate responsiveness to auditory-motor PAS. ConclusionUnder this protocol, auditory-motor PAS with instrument tones facilitated corticospinal excitability in non-musicians but not in musicians. Individual differences in Active Engagement predicted facilitation, indicating that both group membership and active musical engagement shape susceptibility to auditory-motor associative plasticity.

neuroscience↗

A groove brain-music interface for enhancing individual experience of urge to move

When we listen to music, we often feel a pleasurable urge to move to music, known as groove. While previous studies have identified musical features that contribute to the groove experience, such as syncopation and tempo, they also report individual differences in which kinds of music people experience groove. Therefore, recommending groove-eliciting music requires accounting for individual differences. In this study, we aimed to develop a groove brain-music interface (G-BMI) that generates personalized playlists to maximize each individuals groove experience, using a neurofeedback system based on in-ear EEG. Twenty-four participants listened to three high-groove and three low-groove musical excerpts and rated their "urge to move." Using these ratings and the recorded EEG, we trained two LASSO models to build the G-BMI. Model 1 predicted urge to move from acoustic features extracted with VGGish, a pretrained neural network. Model 2 classified EEG data as recorded during listening to high-groove or low-groove music. Using Model 1, we ranked 7,225 candidate songs by predicted groove and assembled one groove-augmenting and one groove-diminishing playlist. Using Models 1 and 2, we created two additional playlists that updated Model 1 and the ranking in real-time based on in-ear EEG. Participants then listened to all four playlists and rated them on items including "urge to move." The groove-augmenting playlist that incorporated EEG achieved the highest "urge to move" ratings. These findings suggest that a personalized neurofeedback system employing EEG can help maximize individual groove experience.

neuroscience↗

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

Malcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with the aim of understanding the molecular mechanisms underlying key traits in M. littorea, including its survival under harsh conditions, we present a de novo genome assembly consisting of 10 chromosome-scale sequences. We employed a high-fidelity long-read sequencing technology for genome assembly. To anchor the sequences to chromosomes, we developed a single-pollen genotyping method to construct a genetic linkage map based on SNPs derived from transcriptomes of pollen grains, possessing recombinant haploid genomes. We built a genome assembly consisting of 10 chromosome-scale sequences (214 Mb in total) for M. littorea containing 30,861 predicted genes. A comparative genome analysis and gene prediction indicated that the genome of M. littorea is double the size of the Arabidopsis thaliana genome, consistent with a whole-genome duplication followed by gene subfunctionalization and/or neofunctionalization in M. littorea. This study provides a basis for research on M. littorea, an understudied species with ecological and evolutionary significance.

genomics↗

Pleasure in groove is associated with neuromelanin levels in the substantia nigra of younger healthy individuals: A neuromelanin-sensitive MRI study

The pleasurable urge to move in response to music is called groove. Prior research has suggested a potential link between groove and dopamine function. However, no studies to date have directly investigated the relationship between the two. Here, we aimed to assess individual dopamine function in the substantia nigra of healthy individuals using neuromelanin-sensitive magnetic resonance imaging (NM-MRI), a non-invasive method associated with dopamine function, and to investigate the relationship between the individual dopamine proxy index and sensitivity to the groove experience. In this study, 15 younger (< 48 years) and 16 older ([greater double equals]48 years) healthy individuals participated. Participants listened to ten musical excerpts and rated the groove experience based on "pleasure" and "wanting to move." To assess whether the groove experience is related to NM levels, type of musical excerpts, and sex, we analyzed with linear mixed-effects regression models. The results showed that higher NM levels (p = 0.032) and male sex (p = 0.034) were associated with higher pleasure ratings in the younger group. For the "urge to move" ratings, type of musical excerpts was associated with ratings in both groups (ps < 0.001), where high-groove music (Janata et al., 2012) receiving higher ratings. Taken together, these results suggest that the "pleasure" aspect of the groove experience in younger individuals was related to dopamine levels in the substantia nigra, but may not be associated with the "urge to move." Thus, pleasure and the urge to move are likely to involve distinct dopaminergic pathways and mechanisms, warranting further investigation.

neuroscience↗

Membranous interacting partners of phage-type plastid RNA polymerase have limited impact on plastid gene expression during chloroplast development

In vascular plants, genes in the plastid genome are transcribed by two types of RNA polymerases, namely bacterial-type nuclear-encoded and phage-type plastid-encoded plastid RNA polymerases (NEP and PEP, respectively). Eudicots, including Arabidopsis, carry two isoforms of NEP, RPOTp and RPOTmp. NEPs transcribe multiple plastid-encoded genes including subunits of PEP and translocon, thus are indispensable for the maintenance of plastids. However, regulatory mechanisms of NEPs are largely unknown. RPOTmp transcribes the 16S rRNA gene from a specific promoter in the seeds during vernalization, and its mutation in Arabidopsis retards the chloroplast development. As interacting partners of RPOTmp, two NEP-INTERACTING PROTEINs (NIP1 and NIP2) have been identified and suggested to suppress RPOTmp activity by tethering RPOTmp to the thylakoid membrane during chloroplast development in the presence of light, but their precise roles in transcriptional regulation remain to be addressed. From these previous reports, we hypothesize that functions of RPOTmp would depend on the light conditions and expression of NIPs. To gain insight into how RPOTmp is controlled, we performed functional analysis of RPOTmp and NIPs using Arabidopsis mutants during germination in the dark and de-etiolation processes under light. We found that RPOTmp-dependent transcription of 16S rRNA is active in imbibed seeds and remains basal level throughout the post-germination processes, regardless of light conditions. We also demonstrated a limited impact of NIPs on RPOTmp function during these processes. Our phylogenetic analysis indicates that NIPs have distinct evolutionary profiles compared to RPOTmp, and Arabidopsis is unlikely to have additional NIP-like proteins in plastids. Based on these findings, we propose a modified model of RPOTmp regulation during chloroplast development: RPOTmp activity remains stable throughout the process of the chloroplast differentiation and is unaffected by light and NIPs.

plant biology↗

Disturbed proteostasis is the key event that triggers cellular senescence through the regulation of chromatin organization and genome stability

Mammalian cells undergo irreversible proliferation arrest when exposed to stresses, a phenomenon termed cellular senescence. Various types of stress induce cellular senescence; nonetheless, senescent cells show similar phenotypes overall. Thus, cells undergo cellular senescence through the similar mechanisms, regardless of the type of stress encountered. Here we aimed to reveal the mechanisms underlying cellular senescence. We have previously shown that lamin b receptor (LBR), which is a protein that regulates heterochromatin organization, was downregulated in senescent cells, and downregulation of LBR induced cellular senescence. Additionally, we have shown that downregulation of protein synthesis effectively suppressed cellular senescence. Thereby, chromatin organization and protein synthesis are implicated in the regulation of cellular senescence. We examined the roles of them in cellular senescence and found that protein synthesis was upregulated during the induction of cellular senescence, and upregulated protein synthesis caused disturbed proteostasis that led to the decreased function of LBR. Furthermore, we showed that decreased LBR function induced cellular senescence through altered chromatin organization and increased genome instability. Importantly, these findings revealed a link between protein synthesis and chromatin organization and accounted for the phenotypes of senescent cells which show disturbed proteostasis, altered chromatin organization, and increased genome instability. Our findings provided the general model for the mechanisms of cellular senescence.

cell biology↗

Enhanced Subjective Performance Achievement in Wind Instrument Playing through Positive Memory Recall: Effects of Sympathetic Activation and Emotional Valence

Controlling physiological and psychological states before a performance is essential for professional musicians to realize their full potential. However, the characteristics of the optimal pre-performance state remain unclear. While an increase in sympathetic nervous system activity is typically observed before performance, when associated with anxiety, it can degrade the performance quality. This study examined whether recalling positive autobiographical performance memories enhances subjective performance achievement, accompanied by increased emotional arousal, valence, and autonomic nervous system activity. Thirty-six professional wind instrument players participated in the study. Prior to performing musical pieces, participants engaged in one of three conditions: (1) recalling positive autobiographical memories, (2) recalling negative autobiographical memories, or (3) imagining routine pre-performance activities (no-memory condition). During the memory recall phase, heart rate was measured. After each performance, participants rated their subjective arousal, valence, and performance achievement. We calculated the heart rate variability indices, specifically SD1 (reflecting parasympathetic nervous system activity) and SD2/SD1 (reflecting sympathetic nervous system activity). The results showed that performance achievement, arousal, and valence were significantly higher in the positive than in the negative condition. Our path analysis further revealed that an increase in SD2/SD1 did not directly predict performance achievement; instead, it was associated with an increase in emotional valence, which in turn led to improved performance. These findings suggest that recalling positive performance memories activates sympathetic nervous system activity and fosters positive emotions, thereby enhancing the performance achievement of professional musicians.

neuroscience↗

Mora-ERP-based RNN-Transformer for decoding single-trial EEGs during silent Japanese speeches

We developed a method for decoding single-trial electroencephalography (EEG) during silent Japanese speeches. In order to cope with problems that there would be always noises in single-trial EEGs, a recurrent neural network (RNN) was used which could reproduce signals under noises. Each of silent-mora-related potentials and the single-trial EEG minus the event-related potential (ERP) were assigned to the signal and the noise, respectively, with reference to the averaging principle. Next, in our Transformer, dot product between the RNN output and the single-trial EEG after positional encoding then Softmax with Loss yielded probabilities of moras, each of which consists of silent Japanese words, phrases or part of sentences. The present decoding was completed by tracing the maximal probability at each block representing time. Average mora error rates (MERs) on pretrained and validated performances for the patient was as low as 1.5 % and 0 %, respectively. The performance for the testing would be refined by many single-trial EEGs during silent Japanese speeches obtained by EEG Web interfaces. This method might be applied to other "mora" languages.

neuroscience↗

A chill brain-music interface for enhancing music chills with personalized playlists

Music chills are pleasurable experiences while listening to music, often accompanied by physical responses, such as goosebumps1,2. Enjoying music that induces chills is central to music appreciation, and engages the reward system in the brain3-5. However, the specific songs that trigger chills vary with individual preferences6, and the neural substrates associated with musical rewards differ among individuals7-9, making it challenging to establish a standard method for enhancing music chills. In this study, we developed the Chill Brain-Music Interface (C-BMI), a closed-loop neurofeedback system that uses in-ear electroencephalogram (EEG) for song selection. The C-BMI generates personalized playlists aimed at evoking chills by integrating individual song preferences and neural activity related to music reward processing. Twenty-four participants listened to both self-selected and other-selected songs, reporting higher pleasure levels and experiencing more chills in their self-selected songs. We constructed two LASSO regression models to support the C-BMI. Model 1 predicted pleasure based on the acoustic features of the self-selected songs. Model 2 classified the EEG responses when participants listened to self-selected versus other-selected songs. Model 1 was applied to over 7,000 candidate songs, predicting pleasure scores. We used these predicted scores and acoustic similarity to the self-selected songs to rank songs that were likely to induce pleasure. Using this ranking, four tailored playlists were generated. Two playlists were designed to augment pleasure by selecting top-ranked songs, one of which incorporated real-time pleasure estimates from Model 2 to continuously update Model 1 and refine song rankings. Additionally, two playlists aimed to diminish pleasure, with one updated using Model 2. We found that the pleasure-augmenting playlist with EEG-based updates elicited more chills and higher pleasure levels than pleasure-diminishing playlists. Our results indicate that C-BMI using in-ear EEG data can enhance music-induced chills.

neuroscience↗

A Nostalgia Brain-Music Interface for Enhancing Nostalgia, Well-Being, and Memory Vividness in Young and Elderly Individuals

Music-evoked nostalgia has the potential to assist in recalling autobiographical memories and enhancing well-being. However, nostalgic music preferences vary from person to person, presenting challenges for applying nostalgia-based music interventions in clinical settings, such as a non-pharmacological approach. To address these individual differences, we developed the Nostalgia Brain-Music Interface (N-BMI), a neurofeedback system that recommends nostalgic songs tailored to each individual. This system is based on prediction models of nostalgic feelings, developed by integrating subjective nostalgia ratings, acoustic features and in-ear electroencephalographic (EEG) data during song listening. To test the effects of N-BMI on nostalgic feelings, well-being, and memory recall, seventeen elderly and seventeen young participants took part in the study. The N-BMI was personalized for each individual, and songs were recommended under two conditions: the "nostalgia condition", where songs were selected to enhance nostalgic feelings, and the "control condition", to reduce nostalgic feelings. We found nostalgic feelings, well-being, and memory vividness were significantly higher after listening to the recommended songs in the nostalgia condition compared to the control condition in both groups. This indicates that the N-BMI enhanced nostalgic feelings, well-being, and memory recall across both groups. The N-BMI paves the way for innovative therapeutic interventions, including non-pharmacological approaches.

neuroscience↗

Lower-Limb Muscle Synergies in Musician's Dystonia: A Case Study of a Drummer

Musicians dystonia (MD) is a movement disorder characterized by involuntary muscle contractions specifically triggered by playing an instrument. This condition often leads to a loss of fine motor control, threatening the careers of affected musicians. While MD is commonly associated with the hands, it can also affect the lower limbs, particularly in drummers. Understanding the muscle coordination involved in MD is crucial for comprehending its neurological mechanisms, yet the muscle coordination of lower-limb dystonia has not been thoroughly explored. This study aimed to investigate the differences in lower-limb muscle synergies in a drummer with MD, utilizing Non-negative Matrix Factorization (NMF) to analyze coordinated muscle activity patterns during drumming tasks. A 36-year-old male professional drummer with lower-limb MD was instructed to play a drum set in time with a metronome set at 80 beats per minute. The task involved striking the bass drum pedal in time with the downbeat. Electromyographic (EMG) data were collected from ten muscles in the right lower limb. The data were analyzed using NMF to extract muscle synergies and compare the number of synergies, spatial modules, and temporal modules between the data with and without dystonia symptoms. The number of muscle synergies did not differ significantly between the data with and without symptoms. Notably, changes were observed in both the spatial and temporal modules of muscle synergies. Spatial modules revealed the appearance of dystonia-specific muscle synergy, which is considered related to compensatory movement. Temporal modules showed significant earlier overactivation in timing, which is considered the direct manifestation of dystonia symptoms. These findings indicate that lower-limb dystonia in drummers affects the spatial and temporal profiles of muscle synergies. This study underscores the importance of considering both spatial and temporal modules of muscle synergy in understanding and treating lower-limb dystonia in drummers. Further research is needed to validate these findings and apply muscle synergy analysis for the clinical assessment of lower-limb dystonia in drummers.

neuroscience↗