Biology subjects

Takahashi, S.

Publications and source records attributed to Takahashi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Continuous Large Maf Activity Maintains Fast Myofiber Identity and Multicellular Homeostasis in Adult Skeletal Muscle

Fast myofibers are preferentially affected during aging, exhibiting atrophy and shifts toward slower myofiber programs, yet the mechanisms preserving established fast-fiber identity remain unclear. Here, we show that the large Maf transcription factors Mafa, Mafb, and Maf are continuously required to maintain type IIb myofiber identity in adult skeletal muscle. Inducible deletion of large Mafs caused near-complete loss of type IIb fibers, a transition toward type IIx/IIa states, reduced strength, and increased fatigue resistance. RNA-seq and ATAC-seq revealed transcriptional and chromatin accessibility remodeling across the fast myosin locus, characterized by persistent loss of Myh4 expression and increased accessibility around Myh1. Single-nucleus RNA-seq identified transient myonuclei co-expressing multiple myosin isoforms before emergence of a Myh1-dominant state, accompanied by remodeling of non-myonuclear cell populations. These changes shared features with aging- and denervation-associated muscle remodeling. Thus, continuous large Maf activity maintains adult fast myofiber identity and coordinates skeletal muscle tissue homeostasis.

cell biology↗

bioRxiv2026

DiverScan: attention-guided exploratory analysis of animal behaviour across diverse comparative experiments

High-throughput tracking yields rich time-series data of animal behaviour, yet extracting biological insight remains a bottleneck, even for simple control--treatment comparisons. Existing analyses struggle to pinpoint the multiple, nonlinearly intertwined differences hidden in the data and fail to generalise across diverse recording set-ups. Here we present DiverScan, a deep-learning framework for attention-guided exploratory analysis of behavioural time series. DiverScan disentangles condition-dependent behavioural differences by pairing a loss function tailored to data exploration with an attention-branch architecture, and highlights condition-specific behavioural features visually and with explanatory text generated by a large language model. DiverScan is validated on a synthetic benchmark and on datasets from seven laboratories spanning multiple species and both single- and multi-animal behaviour. Beyond recovering known phenotypes, we demonstrate that DiverScan helps researchers generate new hypotheses across these diverse datasets. Available as Jupyter notebooks with a graphical user interface and flexible input formats, DiverScan can integrate into existing behavioural-analysis pipelines.

animal behavior and cognition↗

bioRxiv2026

Resolution-standardized evaluation of ligand atomic coordinates in crystallographic structures using machine learning

Accurate assessment of ligand coordinate-density consistency across different resolutions remains challenging in macromolecular crystallography. We introduce the atomic Box Correlation Coefficient (aBCC), an atom-level metric for evaluating the consistency between ligand atomic coordinates and electron density in a resolution-standardized framework. To predict aBCC values from electron-density maps, we developed QAEmap, a machine-learning model based on three-dimensional convolutional neural networks (3D-CNNs). The model was trained using Fourier-truncated electron-density maps and corresponding ligand coordinates generated from high-resolution structures in the Protein Data Bank. It was evaluated using both Fourier-truncated electron-density maps and experimentally determined PDB structures. was evaluated using both Fourier-truncated electron-density maps and experimentally determined PDB structures.The prediction accuracy gradually decreased with decreasing resolution, but remained reliable up to [~]3.5 [A]. These results demonstrate that aBCC enables resolution-standardized atom-wise evaluation of coordinate-density consistency across different resolutions and provide a foundation for further development and refinement of machine learning-based coordinate validation. SynopsisWe introduce the atomic box correlation coefficient (aBCC), a machine learning-based metric for the resolution-standardized atom-level evaluation of ligand coordinate-density consistency in crystallographic structures. aBCC provides a common framework for assessing and communicating the local coordinate reliability between structural biologists and researchers in structure-based drug discovery.

molecular biology↗

bioRxiv2026

Switching Functional DNA-Binding Modes by Tuning Protein Order-Disorder Equilibria

Physical remodeling of chromatin by non-histone architectural proteins of the High Mobility Group B (HMGB) family is central to eukaryotic transcriptional regulation. Nhp6A, the prototypical single-HMG-box protein from yeast, harbors both ordered and disordered regions enabling it to bind and bend DNA without sequence specificity. Here, we integrate ensemble experiments, single-molecule FRET, statistical mechanical modeling and atomistic simulations to dissect the structural and functional consequences of context-dependent phosphorylation in the ordered domain and its interplay with the intrinsically disordered region in Nhp6A. We find that Nhp6A occupies a narrow thermodynamic window, with a melting temperature close to the growth temperature of its host organism and high unfolding cooperativity, a feature conserved across the HMG-box family. Phosphorylation extents - mimicked by multisite phosphomimetic substitutions at residue positions conserved across fungal taxa - smoothly tuning the conformational equilibria between at least two different substates in the native ensemble, apart from the unfolded state. This intrinsic plasticity enables close packing of Nhp6A on DNA through two degenerate binding modes, accompanied by two distinct DNA bending geometries. DNA rescues a strongly destabilized mutant, T63D, through favorable intermolecular interactions, thus effectively acting as a chaperone driving folding. Our findings thus reveal a conserved sequence-ensemble-dynamics code in Nhp6A wherein not just stability, but also phosphorylation-induced conformational switching, disordered tail dynamics, and DNA binding-bending closely coordinate chromatin accessibility. The combination of marginal stability, large cooperativity and electrostatic frustration emerges as a design principle to encode charge sensitivity into proteins, and may represent a general strategy for multisite post-translational regulation.

biophysics↗

bioRxiv2026

Polyvinylpyrrolidone enhances AAV transduction in vitro and shows preliminary utility for subretinal delivery

Adeno-associated virus (AAV) vectors are widely used for gene delivery, but inefficient transduction can require high vector doses. We tested whether unmodified linear polyvinylpyrrolidone (PVP), a pharmaceutical excipient, can improve AAV formulation without chemical modification of the vector or polymer. PVP10, PVP40, and PVP360 were evaluated in vitro across HEK293, HeLa, MEF, and CHO cells; selected formulations were tested after intravenous delivery, and 3% PVP40 was tested by subretinal delivery. In vitro, 1-3% PVP increased AAV8- and AAV9-mediated GFP expression across multiple cell lines. PVP360 showed broad activity in the initial cross-cell assay, whereas the HEK293 molecular-weight screen identified PVP40 and PVP360 as the most active formulations. The substantial fold increase observed in CHO cells largely reflected the low baseline transduction of the control group. MTT absorbance declined with concentrated PVP360, whereas PVP40 retained transduction-enhancing activity and was selected for local testing. In the HeLa AAV-DJ assay, the response pattern differed between MOI 1,000 and MOI 100; the largest observed increases in GFP-positive area occurred with 1.5% PVP10 and 1.5% PVP360 at MOI 100. Intravenous AAV9 delivery with PVP did not consistently increase ex vivo organ reporter signal. By contrast, subretinal delivery of AAV-PHP.eB with 3% PVP40 produced a 1.79- fold larger mean DsRed-positive area per retinal section, averaged within each eye (Welchs t-test p = 0.063; Bayesian Pr[{Delta} > 0] = 0.952). These findings support further evaluation of PVP40 for local subretinal AAV delivery.

bioengineering↗

bioRxiv2026

Exposure to P. falciparum and common cold viruses shape vaccine responses in early life

Vaccine immunogenicity is consistently lower in low-income countries than in high-income settings, yet the factors driving this disparity remain incompletely understood. Using multiplexed electrochemiluminescence serology, we measured IgG and IgA responses to Expanded Program on Immunization (EPI) vaccines and common childhood viral infections in 89 Ugandan infants. We integrated detailed parasitological surveillance and maternal clinical data to examine how P. falciparum infection history, concurrent parasitemia, maternal gravidity, and early-life viral exposures shaped serological profiles. We found that infants mounted robust responses to most EPI vaccines, but critical gaps in protection persisted for diphtheria, measles and rubella. Children born to primigravid mothers had lower antibody levels at 8 weeks of age, independent of placental malaria and only partially explained by maternal age. Contrary to expectation, cumulative P. falciparum exposure was positively associated with antibody concentrations to diphtheria and varicella, and concurrent parasitemia was positively correlated with responses to multiple antigens. Seroconversion to rhinovirus C was associated with higher IgG and IgA levels to several vaccines. Together, these findings suggest that common microbial exposures during infancy, including respiratory viruses and P. falciparum may positively modulate vaccine responsiveness.

immunology↗

bioRxiv2026

Allocation pattern of fruiting bodies in plasmodial slime molds, and threshold size for sporulation of P. polycephalum

The plasmodium of Myxogastria (a group of amoeboid protists) species often crawls around the forest floor to feed while searching for places to form fruiting bodies for reproduction (sporulation). Certain environmental factors that trigger sporulation have been reported; however, other unknown factors are also expected. In this study, we reported field observations of Physarum rigidum and Fuligo septica. Inspired by the field observation, we examined the effects of multiple factors on sporulation in laboratory experiments using Physarum polycephalum. We found that:(1) there was a critical body size below which sporulation did not occur under our experimental conditions and (2) the plasmodium selected its sporulation sites from the available landscape of the experimental arena: dry and low sites for the majority and dry and high sites for the minority. Further analysis revealed that they preferred the edge area at the high site. We discuss the possible ecological importance of the threshold and location preference

animal behavior and cognition↗

bioRxiv2026

Continuous Nuclear Export of p62/SQSTM1 Is Essential for Kidney Homeostasis

The selective autophagy receptor p62/SQSTM1 dynamically shuttles between the nucleus and cytoplasm through distinct nuclear localization and export signals, yet the physiological significance of this trafficking has remained unknown. Here, we generated mice carrying a deletion of the p62 nuclear export signal (dNES) to determine the in vivo role of p62 nuclear export. Homozygous dNES mice developed progressive podocyte injury, glomerulosclerosis, and fatal renal failure by 6-7 weeks of age, whereas heterozygous and dNES/- mice did not develop renal dysfunction. Loss of nuclear export caused constitutive nuclear accumulation of p62, accompanied by the formation of insoluble ubiquitin-positive aggregates and widespread alterations in the renal proteome, including activation of energy metabolism-related pathways and suppression of developmental programs. We previously demonstrated that the lipid peroxidation product 4-hydroxy-2-nonenal (4-HNE) inhibits the nuclear export receptor XPO1, resulting in nuclear retention of p62 in cultured cells. The present findings provide in vivo evidence that continuous nuclear export of p62 is indispensable for maintaining kidney homeostasis and reveal that excessive nuclear accumulation, rather than cytoplasmic depletion, underlies p62-mediated toxicity. Collectively, these findings establish continuous nuclear export of p62 as an essential mechanism for maintaining kidney homeostasis. Significance StatementThe adaptor protein p62/SQSTM1 continuously shuttles between the nucleus and cytoplasm, but the physiological significance of this trafficking has remained unknown. Here, we show that disrupting the nuclear export signal of p62 causes progressive podocyte injury, glomerulosclerosis, and fatal kidney failure through excessive nuclear accumulation and aggregate formation. In contrast, dNES/+ and dNES/- mice remain healthy, demonstrating that excessive nuclear accumulation, rather than cytoplasmic depletion, drives disease. These findings identify continuous nuclear export as a fundamental mechanism that prevents toxic nuclear accumulation of p62 and preserves kidney homeostasis.

cell biology↗

bioRxiv2026

Production of cellobiose from ionic liquid-treated cellulose using the highly thermostable cellobiohydrolase HmCel6A-3SNP at 80°C and analysis of enzymatic accessibility to the substrate

Cellobiose is an important disaccharide used in food, health, and biorefinery applications, but its efficient enzymatic production from crystalline cellulose remains challenging. In this study, crystalline cellulose was dissolved in ionic liquids and regenerated by dilution, and subsequently hydrolyzed at 80{degrees}C using a highly thermostable cellobiohydrolase, HmCel6A-3SNP. The enzyme retained activity in the presence of low concentrations of ionic liquids. Among the pretreatment conditions tested, cellulose treated with 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) showed the highest enzymatic digestibility. After washing to remove residual ionic liquid, the reaction produced reducing sugars at levels 1.5-fold higher than those obtained in the presence of 10% [Bmim]Cl, with cellobiose accounting for approximately 96% of the products. Under the optimized conditions, the hydrolysis yield reached [~]36% after 48 hr. Structural analyses using birefringence imaging, electron microscopy, and Fourier transform infrared spectroscopy indicated that higher-order structural changes in regenerated cellulose strongly influence enzymatic accessibility. These results demonstrate the potential of combining ionic-liquid pretreatment with thermostable enzymes for selective cellobiose production from cellulose.

biochemistry↗

bioRxiv2026

Visualization of neuronal morphology of the suprachiasmatic nucleus vasopressin neurons by Cre/FLPe-based genetic two-step sparse labelling - GT-SPARCL

Resolving the morphology of individual neurons in densely packed brain regions remains challenging. Sparse labeling is essential for delineating cellular architecture, yet achieving reproducible low-density labeling e.g. < 1% has been a persistent technical hurdle/problem. We present a genetically encoded two-step strategy, GT-SPARCL (Genetic Two-Step Sparse Cre/FLPe Combination Labeling), which leverages two independent stochastic recombination events to deliver stable, tunable low-density labeling in mice. As a proof of concept, we applied this method to visualizing arginine vasopressin (AVP) neurons in the suprachiasmatic nucleus (SCN), the master circadian pacemaker composed of [~]10,000 neurons per side in mice. Using two-photon imaging of whole-mount SCN blocks, we reconstructed individual AVP neurons and uncovered previously under-resolved morphological heterogeneity. Based on axonal trajectories, we distinguished five structural types, including subclasses with commissural projections to the contralateral SCN and others extending projections beyond the nucleus. The majority ([~]70%) exhibited projections both within and outside the ipsilateral SCN, whereas the second most dominant subset ([~]20%) projected exclusively outside the SCN, representing an output-biased type. In contrast, neurons projecting exclusively within the ipsilateral SCN were exceptionally rare, suggesting that "dedicated" local-circuit AVP neurons do not form a major structural subtype. Collectively, our data indicate that AVP neurons are not structurally uniform but instead comprise diverse projection-defined subtypes, implying subtype-depen-dent contributions to intra-SCN communication, bilateral coupling, and circadian output. Beyond the SCN, our GT-SPARCL method may be applicable for achieving low-density labelling of neurons that can be defined by other specific Cre mouse lines.

neuroscience↗

bioRxiv2026

A Structural Domain in the genomic RNA of SARS-CoV-2 Folds into a Compact Granular Structure without the N protein: A Single-Molecule Fluorescence Spectroscopic Investigation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) packages its single-stranded genomic RNA (gRNA) having about 30,000 nucleotides into virions by forming 35-40 granular ribonucleoprotein (RNP) units. Each RNP unit has a diameter of [~]15 nm. While it is generally assumed that the assembly of these RNPs is driven by the binding of the nucleocapsid (N) protein to the gRNA in the cytoplasm, the precise molecular mechanism remains to be fully elucidated. In this study, we develop an experimental strategy based on single-molecule fluorescence and fluorescence correlation spectroscopies to examine the formation of long-range base pairing within a candidate structural domain corresponding to nt 12230-12686 of the gRNA (gRNA12k). Our results demonstrate that the 5 and 3 regions of gRNA12k autonomously form long-range base pairing in near-physiological buffers containing mono- and divalent cations, independently of the N protein. This domain possesses an extensive secondary structure, is compact, and can unfold and refold reversibly upon heat treatment and cooling. Notably, the addition of the N protein melts the long-range base pairs, and causes the aggregation of multiple molecules of gRNA12k. Based on these observations, we propose a refined mechanism for the genome assembly in SARS-CoV-2: gRNA initially forms autonomous granular structures, which are subsequently reorganized and condensed by the N protein to chaperone the assembly of the entire gRNA. SignificanceSARS-CoV-2 organizes its exceptionally long genomic RNA (gRNA) having about 30,000 nt into 35-40 granular ribonucleoprotein (RNP) units for viral packaging. It has been assumed that the nucleocapsid (N) protein drives the formation of the RNP granules. In this study, we challenge this prevailing view by demonstrating that a specific region of the gRNA sequence inherently encodes the information to fold into a compact, granular architecture independently of any proteins. Unexpectedly, we found that the N protein partially melts the autonomous structures, suggesting that it acts as an RNA chaperone to facilitate flexible genome assembly. Our findings redefine the interplay between viral proteins and gRNA, offering a new perspective on the mechanism of coronavirus replication.

biophysics↗

bioRxiv2026

Cardiac-Detargeted MyoAAV Enables Systemic Nrl-Mediated Fast Myofiber Remodeling and Hypertrophy Across Multiple Skeletal Muscles

Inducing fast myofiber programs offers therapeutic potential for skeletal muscle disorders such as sarcopenia, where fast myofibers are preferentially lost. Engineered muscle-specific AAV (MyoAAV) vectors enable efficient transduction of skeletal muscles after systemic administration; however, cardiac transgene expression limits applications requiring skeletal muscle-selective delivery. We generated modified MyoAAV vectors by incorporating cardiac-specific miR-208a target sequences into the transgene 3'UTR. This design markedly suppressed cardiac expression while preserving skeletal muscle output, with target-site variation enabling tunable trade-offs between cardiac detargeting and skeletal muscle expression levels. We validated this platform using neural retina leucine zipper (Nrl), a large Maf transcription factor regulating type IIb myofiber identity. Systemic delivery of conventional MyoAAV-Nrl caused severe cardiac hypertrophy and uniform lethality within one month. Conversely, incorporating miR-208a target sequences prevented detectable hypertrophy and eliminated mortality during the experimental observation period. This modification significantly reduced cardiac Nrl expression while maintaining skeletal muscle levels, successfully promoting type IIb myofiber formation and hypertrophy across multiple skeletal muscles. These findings demonstrate that miR-208a-mediated cardiac detargeting combined with MyoAAV-Nrl enables safe systemic induction of fast myofiber remodeling and hypertrophy, establishing a platform for gene therapies targeting skeletal muscle disorders associated with fast myofiber loss.

cell biology↗

bioRxiv2026

Fatty acids in the tumor microenvironment reprogram neutrophils to induce immunosuppression via adenosine

As solid tumors progress, the tumor microenvironment (TME) becomes increasingly immunosuppressive, impairing cytotoxic T-cell activity and limiting the efficacy of the immune checkpoint blockade. However, the mechanistic drivers of this immunosuppression remain poorly understood. Here, we identify a tumor-derived lipid-neutrophil-adenosine axis as a critical regulator of immune suppression in advanced colorectal cancer (CRC). We show that fatty acids enriched in tumor interstitial fluid reprogram neutrophils to generate adenosine via PPAR activation, leading to T-cell suppression. Using AB928, a dual A2aR/A2bR adenosine receptor antagonist currently in clinical trials, we restored T-cell proliferation, effector function, and tumor-killing capacity in vitro and in vivo. Importantly, AB928 synergized with anti-PD-1 therapy to enhance survival in an autochthonous model of metastatic CRC. Our findings define a metabolic immune evasion mechanism in the TME and provide a rationale for targeting neutrophil-derived adenosine signaling to improve immunotherapy responses in CRC and other solid tumors.

cancer biology↗

bioRxiv2026

Acute Milk-Protein Intake Enhances Pupil-Linked Executive Function and Esports Performance During Prolonged Play

Prolonged esports play induces cognitive fatigue that is not fully captured by subjective awareness, motivating practical, non-stimulant nutritional strategies supported by objective physiological markers. We here tested whether acute milk protein intake attenuates fatigue-related physiological responses during prolonged esports play and supports subjective state, executive control, and in-game performance. In a randomized, single-blind (assessor-blind), energy-matched controlled crossover study, 15 healthy young adults with esports experience completed two sessions in which they consumed either a milk protein drink or an energy-matched apple juice control before a 3-h virtual soccer task. Physiological measures included pupillometry during gameplay, salivary cortisol, continuous interstitial glucose monitoring, and heart rate. Subjective ratings (VAS) and executive function (flanker task) were assessed across post-ingestion time points, and in-game performance metrics were aggregated within hourly gameplay blocks. Milk protein intake was associated with a coherent pattern of physiological advantages, including larger pupil diameter during gameplay, smoother interstitial glucose dynamics, and lower salivary cortisol, while heart rate showed time-dependent changes without a clear condition effect. These physiological changes co-occurred with higher enjoyment and lower hunger, improved flanker performance, and condition-dependent improvements in in-game performance, most notably higher shot success rate. Additionally, pupil diameter during gameplay was associated with inhibitory-control efficiency on the flanker task. These findings suggest that acute milk protein intake may serve as a practical, non-stimulant nutritional strategy to sustain physiological state and cognitive-behavioral performance during prolonged esports (virtual soccer) play. Highlights- Prolonged esports play models modern digital cognitive activity and cognitive fatigue. - Acute milk protein intake increases pupil diameter during prolonged esports play. - Interstitial glucose dynamics are smoother and salivary cortisol is lower with milk protein. - Enjoyment increases and hunger decreases during 3 h of virtual soccer play. - Executive function and in-game performance improve, most notably shot success rate.

neuroscience↗

bioRxiv2026

Ropinirole hydrochloride mitigates oxidative stress and neuroinflammation via the PI3K-mTOR pathway in TDP-43 hiPSC-derived microglial-like cells

BackgroundAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron loss accompanied by neuroinflammation, oxidative stress, and impaired proteostasis, with pathological aggregation of TDP-43 as its defining hallmark. Microglia are recognized as central contributors to ALS pathogenesis, yet the mechanisms underlying their intrinsic dysfunction in the context of TDP-43 remain insufficiently characterized. MethodsWe characterized microglia-like cells (iMGLs) differentiated from isogenic TDP-43 M337V human induced pluripotent stem cell lines. We performed integrated functional assays, transcriptomic profiling and drug repurposing analysis to systematically compare mutant and control iMGLs. To assess therapeutic potential, we evaluated the effects of ROPI, a dopamine D2 receptor agonist previously advanced to clinical trials for ALS, on disease-relevant phenotypes in TDP-43 iMGLs. ResultsTDP-43M337V/M337V iMGLs presented ALS-associated abnormalities, including cytoplasmic TDP-43 accumulation with impaired phagocytosis and elevated oxidative stress, impaired autophagy and mitophagy, altered cytokine profiles, and reduced ferritin levels. Building on our previous identification of ropinirole hydrochloride as neuroprotective for ALS motor neurons, we now show that it confers therapeutic benefits in mitigating microglial pathology. ROPI treatment significantly reduced oxidative stress and caspase-3/7 activity and partially restored cytokine homeostasis in TDP-43M337V/M337V iMGLs, independent of autophagy/mitophagy modulation. Transcriptomic profiling revealed that ropinirole modulated disease-associated gene expression signatures involving protein folding, extracellular matrix organization, and oxidative stress responses. Furthermore, connectivity map-based analysis prioritized PI3K-Akt-mTOR inhibitors as candidates for reversing TDP-43 iMGL signatures, and ropinirole was found to modulate mTOR signaling. These converging lines of evidence support a mechanistic role for ropinirole in restoring microglial homeostasis via PI3K-mTOR pathway regulation. Taken together, our findings position ropinirole as a promising candidate dual action therapeutic candidate capable of targeting both neuronal and microglial dysfunction in ALS, suggesting broader applicability of ropinirole in modulating neuroinflammatory cascades across other neurodegenerative conditions. ConclusionRopinirole broadens ALS therapy from motor neurons to microglia, underscoring its promise for integrated and clinically meaningful treatment strategies.

neuroscience↗

bioRxiv2026

TSUMUGI: a platform for phenotype-driven gene network identification from comprehensive knockout mouse phenotyping data

SummaryDeciphering complex organismal phenotypes requires elucidation of coordinated functions among multiple genes, yet this remains a fundamental challenge in functional genetics. The International Mouse Phenotyping Consortium (IMPC) has recently established a comprehensive phenotypic atlas based on systematic single-gene knockout mouse lines, providing an unprecedented resource for gene-phenotype associations in mammals. However, extracting phenotype-associated multiple gene relationships remains challenging. Here, we present TSUMUGI, a platform that identifies a phenotype-driven gene network by leveraging gene-phenotype associations from the IMPC. TSUMUGI enables users to initiate analyses from a user-specified phenotype or gene list and interactively explore a gene network. In addition, TSUMUGI highlights human disease-associated genes, supports flexible network filtering, and allows seamless export of a gene network for downstream analyses. By linking shared phenotypic signatures to putative functional gene modules, TSUMUGI provides a framework for systematic interpretation and hypothesis generation of complex organismal phenotypes. Availability and implementationThe web application is available online at https://larc-tsukuba.github.io/tsumugi/. The command-line tools are distributed via PyPI (https://pypi.org/project/TSUMUGI) and Bioconda (https://bioconda.github.io/recipes/tsumugi/README.html). Source code and documentation are hosted at GitHub (https://github.com/akikuno/TSUMUGI-dev) and archived on Zenodo (https://doi.org/10.5281/zenodo.18464478) under the MIT license.

bioinformatics↗

bioRxiv2026

Chromid-like secondary replicons as key sites of biosynthetic gene clusters in Ktedonobacteria

Soils harbour immense biosynthetic gene cluster (BGC) diversity that can mediate microbial interactions, yet this potential is still mapped unevenly across the tree of life. Ktedonobacteria--a class of actinomycete-like bacteria within phylum Chloroflexota--are widespread in terrestrial environments and repeatedly dominate pioneer communities in extremely oligotrophic volcanic bare-ground soils; however, their secondary metabolism and genome architecture remain poorly characterised. Here, we integrate targeted cultivation using volcanic soils from Mount Zao with genome-resolved metagenomics and public genomes to analyse 183 ktedonobacterial genomes. Using antiSMASH and BiG-SLiCE, we identified 1,546 BGCs comprising 1,162 non-redundant gene-cluster families (GCFs). In our dataset, nearly one quarter of genomes encode [≥]10 distinct GCFs, and several family-level clades show mean GCF counts comparable to those in genus Streptomyces. Most ktedonobacterial BGCs are highly divergent from reference collections and exhibit unusually low intra-genomic redundancy, suggesting broad, underexplored chemotypes. Long-read assemblies from ten strains reveal recurrent 1.6-3.5 Mb chromid-like secondary replicons with chromosome-like composition but distinct maintenance signatures. These replicons are consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the current knowledge of the phylogenetic landscape of soil biosynthetic diversity and highlight chromid-like secondary replicons as major genomic reservoirs for specialised metabolism in Ktedonobacteria.

microbiology↗

bioRxiv2026

Joint Pupillometry and Heart Rate Monitoring Identify Zone-Like High Performance in Esports

Modern digital activities, such as esports, combine intense cognitive demands with limited whole-body movement, weakening calibration between subjective awareness and functional states. Cognitive deterioration during prolonged esports precedes subjective fatigue, suggesting subjective flow likewise fails to reveal efficient cognitive-sensorimotor performance states. Although efficient cognitive-sensorimotor performance may involve central-autonomic coordination reflected in intrapersonal pupil-heart synchrony, the functional role of this coordination remains largely unknown. We hypothesized that, during esports play, central-autonomic coordination contributes to an efficient cognitive-sensorimotor performance state that subjective flow fails to capture. Fourteen young men completed sessions involving watching a fighting game, playing against a computer-controlled opponent, and competing against another person. We assessed pupil diameter, heart rate, subjective flow, subjective workload, and objective in-game performance. Esports competition increased subjective flow without improving objective in-game performance and reduced combat efficiency, demonstrating a subjectively optimal experience need not signal high in-game performance efficiency. Data-driven clustering identified a low-reactivity state combining superior objective in-game performance with lower subjective workload. This state showed selectively sustained pupil-heart synchrony. Reduced workload partly accounted for the association between pupil-heart synchrony and objective in-game performance. Our findings suggest that individuals fail to recognize periods of high in-game performance efficiency, as cognitive deterioration escapes awareness during prolonged esports. This efficiency is associated with pupil-heart synchrony, supporting the hypothesis that central-autonomic coordination contributes to an efficient cognitive-sensorimotor performance state. Pupil-heart synchrony may therefore serve as a mechanism-based biomarker for detecting efficient states beyond awareness, optimizing objective task performance and the timing of recovery in demanding digital environments.

neuroscience↗