Biology subjects

Nakagawa, S.

Publications and source records attributed to Nakagawa, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Lineage tracing reveals asynchronous fate restriction in mouse embryos and stem cell-derived embryo models

How a flexible mammalian embryo gives rise to a reproducible body plan remains unclear, partly because cell lineages cannot be followed continuously in vivo. We combined DNA Typewriter lineage recording with tetraploid complementation to reconstruct high-resolution single-cell genealogies across mouse development and built FateVec, an analysis framework that infers fate-bias dynamics and lineage-associated transcriptional programs from reconstructed phylogenies. Loss of developmental potential proved progressive and asynchronous, with multiple lineages acquiring detectable fate bias before morphological diversification at gastrulation. Within the neural crest, most cells remained multipotent over an extended window, while independent founder clades differed markedly in restriction timing. Extending lineage recording to a stem-cell-derived embryo model revealed that cells with shared transcriptional identities can arise from distinct lineage relationships. We further found embryonic-lineage contributions to extraembryonic-like states, exposing an unexplored lineage plasticity. This lineage-resolved view of embryogenesis reveals that cell identity alone predicts neither developmental ancestry nor the timing of fate restriction.

developmental biology↗

bioRxiv2026

A thermoregulatory design principle for transitions into hypometabolism

Mammals entering torpor or hibernation undergo an abrupt transition from normothermia to hypothermia, yet how thermoregulation enables this switch remains poorly understood. Here, we identify dynamical signatures that precede these transitions and a mathematical principle that can generate them. In fasting-induced torpor in mice, body-temperature fluctuations increased before torpor onset, providing an early-warning signal that tracked proximity to the transition better than temperature decline alone. A heat-balance model showed that reducing how strongly the effective heat-loss coefficient depends on body temperature reorganizes thermoregulatory stability, allowing a low-temperature equilibrium to emerge while the normothermic state remains stable. This organization is consistent with a symmetry-broken pitchfork involving a saddle-node. Similar increases in temperature fluctuations preceded hibernation onset in hamsters. These findings link pre-transition temperature dynamics to changes in the underlying thermoregulatory landscape and provide a framework for detecting and understanding transitions from normothermia to hypothermia.

systems biology↗

bioRxiv2026

Disruption of the single-copy GOLDEN2-like gene underlies the classical yellow and yellow-mutable mutations of Japanese morning glory

GOLDEN2-like (GLK) transcription factors are key regulators of chloroplast differentiation and photosynthetic gene expression. The classical yellow mutation in Japanese morning glory (Ipomoea nil) produces yellowish-green leaves, whereas an unstable allele, yellow-mutable, produces green somatic sectors on a yellowish-green background. The gene responsible for these mutations was identified as InGLK, which encodes a GOLDEN2-like transcription factor. The stable yellow mutant carried a 4-bp frameshift insertion in InGLK, whereas two yellow-mutable lines carried the Tpn1-family transposon Tpn12 in intron 5. Excision of Tpn12 in germinal revertants left short footprints and restored the green leaf phenotype. Genome searches identified InGLK as the sole GLK gene in I. nil. Pigment analysis of green somatic reversion sectors and yellowish-green background areas showed that most of the measured photosynthetic pigments were significantly reduced in the yellowish-green background, whereas the chlorophyll a/b ratio was unchanged. Chloroplasts in the yellowish-green tissue retained thylakoid-like membranes and starch granule-like structures but had less distinct grana-like stacks and sparse stromal lamellae-like structures. Wild-type-like chloroplast ultrastructure was restored in germinal revertants. These findings show that loss of function of a single-copy GLK gene broadly reduces photosynthetic pigment accumulation and alters chloroplast internal membrane organization. The yellow mutants of I. nil therefore provide a genetic system for examining non-redundant GLK function.

plant biology↗

bioRxiv2026

InMYB21B Promotes Petal Cell Expansion and Flower Opening in Japanese Morning Glory (Ipomoea nil)

Flower opening is a complex developmental process involving coordinated changes in cell proliferation and cell expansion. Although several regulators of flower opening have been identified, how transcriptional programs are coordinated with the cellular and metabolic changes underlying petal expansion immediately before flower opening remains incompletely understood. Japanese morning glory (Ipomoea nil) is a suitable model for investigating these processes because its flowers open synchronously at a predictable time. This study aimed to identify transcriptional regulators involved in petal development and flower opening in Japanese morning glory. Temporal analyses of petal growth, sugar metabolism, and gene expression revealed that petal development was driven by both cell proliferation and cell expansion until approximately 48 h before flower opening, whereas cell expansion predominated thereafter. Weighted gene co-expression network analysis identified two genes encoding R2R3-MYB subgroup 19 transcription factors, InMYB21A and InMYB21B, as candidate regulators associated with petal development. CRISPR/Cas9-mediated knockout analysis revealed a prominent role for InMYB21B, whose loss markedly impaired petal cell expansion and prevented flower opening. InMYB21B knockout also impaired stamen and pistil development, resulting in male and female sterility. Starch degradation and glucose accumulation were impaired in InMYB21B knockout petals. Transcriptome analysis revealed delayed transcriptomic progression during petal development and reduced expression of genes associated with starch degradation, sucrose metabolism, cell wall remodeling, and water transport. These findings identify InMYB21B as a key regulator of petal cell expansion and flower opening in Japanese morning glory and show that loss of InMYB21B disrupts both metabolic and transcriptomic progression during late petal development.

plant biology↗

bioRxiv2026

Mouse suppressyn-like 1 is an endogenous retrovirus-derived inhibitor of membrane fusion through direct association with envelope glycoproteins

Cell-cell fusion is essential for placental development and is mediated by endogenous retrovirus (ERV)-derived fusogens known as syncytins. However, how ERV-derived proteins negatively regulate membrane fusion remains largely unknown. Here, we identify a previously uncharacterized murine ERV envelope-derived protein, mouse suppressyn-like 1 (mSUPYNL1), that suppresses syncytin-mediated membrane fusion through a mechanism distinct from that of placental human suppressyn (hSUPYN). Unlike hSUPYN, which acts through receptor interference, mSUPYNL1 inhibits both murine and human syncytin-mediated fusion independently of receptor usage by associating with the surface (SU) subunits of multiple syncytin envelope glycoproteins, revealing a receptor-independent mechanism of fusion suppression. This mechanism extends beyond endogenous fusogens. mSUPYNL1 also associates with the SU glycoprotein (gp46) of Human T-cell Leukemia Virus type 1 (HTLV-1) and suppresses Env-dependent syncytium formation, whereas hSUPYN showed no detectable antiviral activity in this assay. These findings identify mSUPYNL1 as a broad-spectrum inhibitor of envelope glycoprotein-mediated membrane fusion. Analysis of mSUPYNL1 knockout mice revealed that, in contrast to the placenta-restricted expression of hSUPYN, mSUPYNL1 was broadly expressed, with its most prominent localization in decidual stromal and vascular endothelial cells of the pregnant uterus, as well as in hematopoietic tissues such as the spleen and thymus. Together, our findings uncover an evolutionarily distinct class of ERV-derived fusion suppressors that function through envelope glycoprotein recognition instead of receptor interference. Our study expands current models of ERV domestication by demonstrating that retroviral envelope proteins have been independently co-opted not only to promote membrane fusion but also to restrain it, thereby linking placental biology, antiviral defense, and host evolution. HIGHLIGHTSO_LImSUPYNL1 is an endogenous retrovirus-derived membrane fusion inhibitor C_LIO_LImSUPYNL1 binds the SU domains of murine and human syncytins C_LIO_LImSUPYNL1 suppresses HTLV-1 Env-mediated syncytium formation C_LIO_LIDirect envelope recognition enables receptor-independent fusion inhibition C_LI

developmental biology↗

bioRxiv2026

A flexible modelling framework for estimating thermal tolerance and sensitivity

Extreme heat events are becoming more frequent, intense and prolonged, making it urgent to predict how heat intensity and exposure duration combine to threaten organisms. Thermal death time (TDT) and thermal load sensitivity (TLS) models provide this link, but conventional two-stage analyses often discard uncertainty, mishandle censored or overdispersed data and limit inference. Here, we show how the four-parameter log-logistic model can recover TDT/TLS quantities, including thermal tolerance (CTmax), sensitivity (z), critical temperature (Tcrit), heat injury and survival, from one model. Simulations show the joint model reproduces classical estimates when two-stage assumptions hold and is more reliable when they fail. We introduce these workflows as Bayesian and frequentist R packages. Case studies across plant and animal taxa demonstrate this modelling framework can estimate group contrasts and predict survival from realistic field temperature-time series. This framework provides more robust inference and flexible tools for predicting organismal responses to extreme heat events.

ecology↗

bioRxiv2026

A Tripartite Co-culture System Reveals Defensive Mutualism Between a Nanobdellati Symbiont and Its Host

Archaeal symbioses remain among the least understood cellular interactions. Ultra-small Nanobdellati (initially called DPANN) archaea rely on larger hosts for survival, yet their effects on host eco-physiology and their interactions with infecting viruses have not yet been examined experimentally. Here, we established the first stable tripartite co-culture comprising a Nanobdellales symbiont (YN4), its archaeal host (YN4HA), and a virus (MTIV4). We analyzed this system using physiological, genomic, transcriptomic, glycoproteomic, and cryo-electron tomography (cryoET) approaches. CryoET analysis revealed that the Nanobdellales archaeon formed cone-like structures to contact the host, as has been observed in other Nanobdellati-host systems. In this system, the host is infected by the virus. The Nanobdellales archaeon mitigated virus-induced growth inhibition of the host without any detectable fitness cost, indicating a defensive mutualism rather than a strictly parasitic relationship. This protective effect may involve Nanobdellati-driven remodeling of host cell surface glycans, suggesting a previously unrecognized glycan-mediated defense strategy. Overall, our tripartite system provides new insight into complex archaeal interactions in extreme environments that cannot be captured through conventional binary co-culture systems.

microbiology↗

bioRxiv2026

Oxytocin regulates TN-GnRH3 circuit maturation and mate preference through C1q-dependent synaptic mechanisms

Oxytocin is a key regulator of social behavior, yet how it shapes the neural circuits underlying these behaviors remains unclear. Here, we show that oxytocin signaling is required for the proper maturation of terminal nerve gonadotropin-releasing hormone 3 (TN-GnRH3) circuits that regulate female mate preference in medaka. Disruption of oxytocin signaling reduced expression of the complement component C1q, altered microglial properties, and increased TN-GnRH3 innervation in the optic tectum and dorsolateral telencephalon, suggesting impaired synaptic refinement. In addition, TN-GnRH3 neurons in mutants exhibited disrupted clustering and failed to increase firing frequency in response to visual stimulation, indicating functional deficits. Furthermore, c1qb mutants phenocopied the behavioral and neuronal abnormalities observed in oxytocin signaling-deficient mutants. Together, our findings suggest that oxytocin signaling links microglia-associated synaptic refinement to neural circuit maturation, thereby revealing a previously unrecognized role for oxytocin in shaping social behavior.

neuroscience↗

bioRxiv2026

Music exposure reduces anxiety- and depression-like behavior in rodents: a systematic review and multilevel meta-analysis

Anxiety and depressive disorders impose a major global burden, prompting interest in non-pharmacological interventions that may influence affective processes. Music exposure has often been reported to affect anxiety- and depression-like behaviors, but preclinical findings remain heterogeneous and have not been quantitatively synthesized. Prior work has also focused almost entirely on mean behavioral responses, largely overlooking inter-individual variability as a biologically meaningful dimension. We conducted a preregistered systematic review and multilevel meta-analysis of experimental studies testing music exposure in laboratory rodents. Following PRISMA and PRISMA-EcoEvo guidelines, we synthesized 298 effect sizes from 20 studies using multilevel models to account for non-independence among effect sizes. We quantified effects on mean behavior with the log response ratio (lnRR) and effects on variability with the log variability ratio (ln V R). Overall, music exposure was associated with a statistically significant reduction in anxiety- and depression-like behaviors, corresponding to an average decrease of about 18% relative to controls. This mean effect was detected across outcome types and life stages despite substantial heterogeneity. By contrast, music exposure did not produce a statistically significant overall change in inter-individual behavioral variability. Instead, variability responses were context dependent: behavioral assay type and music meta-genre significantly moderated ln V R, with anxiety-like assays tending to show increased variability and depression-like assays tending to show reduced variability under music exposure. These results suggest that music exposure reliably shifts average affect-related behavior without uniformly changing behavioral stability across individuals. Because the evidence comes mainly from short-term exposures in young adult laboratory rodents, generalization beyond similar contexts should remain cautious.

animal behavior and cognition↗

bioRxiv2026

Identification of a pharmacokinetic interaction between teicoplanin and sulfo-butyl ether-β-cyclodextrin, an excipient in the intravenous posaconazole formulation

Patients undergoing hematopoietic stem cell transplantation (HSCT) often receive multiple antibiotics and antifungals concurrently, making it crucial to understand their potential pharmacokinetic interactions of these agents. We report here an interaction between the glycopeptide antibiotic teicoplanin (TEIC) and sulfo-butyl ether-{beta}-cyclodextrin (SBECD), a solubilizing excipient in the intravenous formulation of posaconazole (PSCZ). We performed a single-center retrospective analysis of patients who underwent HSCT and received oral and intravenous PSCZ during TEIC therapy. The associations between PSCZ administration and TEIC concentration-to-dose (C/D) ratios were evaluated using linear mixed-effects models. We also examined the effects of intravenous PSCZ and SBECD on TEIC pharmacokinetics in rats by assessing the area under the concentration-time curve (AUC) and urinary excretion of total TEIC and its components. In addition, molecular docking and in vitro protein-binding assays were conducted to investigate the interaction between TEIC and SBECD. In patients who underwent HSCT, TEIC C/D ratio was significantly lower following intravenous PSCZ administration than without administration. In contrast, the effect of oral PSCZ administration relative to non-administration was not statistically significant. In rats, intravenous PSCZ and SBECD decreased the AUC of TEIC and increased urinary excretion, particularly in the A2 group. Docking simulations indicated that the hydrophobic side chain of TEIC A2-2 fit within the SBECD cavity, and in vitro assays confirmed SBECD concentration-dependent increases in TEIC unbound fractions. The co-administration of intravenous PSCZ containing SBECD may reduce TEIC protein binding, thereby enhancing renal excretion.

pharmacology and toxicology↗

bioRxiv2025

Fast phylogenetic generalised linear mixed-effects modelling using the glmmTMB R package

Phylogenetic generalised linear mixed models (PGLMMs) help ecologists to distinguish ecological drivers from other processes shaping evolutionary patterns, yet existing implementations are often limited in distributional scope or computational speed. We compare five R packages for fitting PGLMMs and highlight the new covariance structure propto in the general-purpose GLMM package glmmTMB. Simulations show that glmmTMB fits PGLMMs faster overall than brms, MCMCglmm, INLA, and phyr, while producing similar model estimates. We present the first practical application of glmmTMB for fitting phylogenetic random effects using likelihood-based models that accommodate repeated measures, demonstrated through case studies of evolutionary trait data. By improving both speed and flexibility, glmmTMB broadens access to PGLMM and supports deeper insights into trait evolution and diversification.

evolutionary biology↗

bioRxiv2025

Revisiting the in vivo Functions of Coilin in Mice

Cajal bodies (CBs), first identified in the early 20th century, are classic nuclear structures organized primarily by the protein coilin. Although CBs have long been implicated in snRNA modification and maturation, their precise roles in mice remain unclear. Here, we revisit the functions of CBs by using genome editing to generate mice that lack nearly the entire coilin protein, retaining only the first seven amino acids. Mass-spectrometry analyses showed reduced 2'-O-methylation of U2 snRNA in coilin mutant liver; however, these reductions had minimal impact on overall gene expression and pre-mRNA splicing patterns. Additionally, detailed analysis recapitulated previously reported testicular size reductions and newly revealed decreased proportions of high-quality sperm. We also identified novel coilin-containing condensates distinct from genuine CBs in the nuclear pocket of elongating spermatids. Our findings implicate that coilin orchestrates membraneless organelles in various compartments, playing multifunctional roles beyond classical CB formation.

molecular biology↗

bioRxiv2025

Discovery of a Selective Inhibitor of ZIP14 with Therapeutic Potential for Cancer-associated Cachexia

ZIP14/SLC39A14, a membrane-bound metal transporter, is essential for systemic metal homeostasis and has been implicated in inflammatory and metabolic disorders, including cancer-associated cachexia. Despite its biological and therapeutic significance, no selective inhibitors have been identified. Here, we identify 1-phenyl-8-(2-phenylethyl)-1,3,8-triazaspiro[4.5]decan-4-one (PPTD) as the first selective small-molecule inhibitor of ZIP14. PPTD efficiently blocks ZIP14-mediated uptake of zinc, iron, manganese, and cadmium, while sparing the closely related transporter ZIP8/SLC39A8. Mechanistically, PPTD binds specifically to a pocket formed at the dimer interface of ZIP14, as revealed by AlphaFold3 structural prediction, ligand-interaction profiling, structure-activity analyses, and site-directed mutagenesis, providing direct evidence for a targeted inhibition mechanism. ZIP14-driven metal influx promotes reactive oxygen species and lipid peroxidation, leading to cytotoxicity, which PPTD effectively reverses. In vivo, PPTD ameliorates major features of cancer cachexia in mice, including weight loss, reduced survival, muscle wasting, impaired locomotor activity, and disease progression. PPTD thus provides both a chemical probe to dissect ZIP14 function and a potential therapeutic candidate for cancer cachexia, establishing a foundation for the development of therapies targeting ZIP14-mediated metal dysregulation.

biochemistry↗

bioRxiv2025

LOBSTERS: a modular vector series with a diverse set of Cas nucleases and plasmid selection markers for multiplex genome editing in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a central model organism in genetics and synthetic biology, yet efficient multiplex genome editing remains difficult because many toolkits are restricted by limited plasmid selection markers and reduced efficiency when targeting multiple loci. In our previous work, we introduced a CRISPR-based system incorporating three nucleases with distinct PAM specificities but it was available only with the URA3 marker. Here we present LOBSTERS, an expanded modular vector series that retains the PAM-diverse nucleases (SpCas9, SaCas9, and enAsCas12a) while extending marker options to seven. This design enables the simultaneous use of multiple plasmids in one transformation, supporting scalable and flexible genome editing. Proof-of-concept experiments demonstrated efficient ADE2 and ADE3 deletions with colorimetric readouts, coordinated tagging of essential proteins (Cdc3 and Cse4) without compromising function, and recapitulation of three quantitative trait variants (RME1, TAO3, and MKT1) underlying sporulation efficiency. Together these results establish LOBSTERS as a robust and versatile platform for multiplex genome editing in S. cerevisiae. By enabling coordinated modification of essential proteins, genetic interactions, and quantitative trait variants, LOBSTERS provides a broadly applicable resource for functional cell biology and synthetic biology in yeast. Significance StatementO_LILOBSTERS integrates three PAM-diverse nucleases with seven plasmid selection markers, overcoming the single-marker limitation of previous yeast genome editing toolkits. C_LIO_LIThe system enables efficient simultaneous editing at multiple loci, demonstrated by functional tagging of essential proteins and recapitulation of quantitative trait variants. C_LIO_LIBy broadening the editable space and lowering barriers to complex genotype construction, LOBSTERS provides a widely applicable resource for yeast cell biology and synthetic biology. C_LI

molecular biology↗

bioRxiv2025

A lipid-driven, microbe-independent mechanism of acne via Lrig1+ follicular progenitor cells

Long-chain saturated fatty acids (lcSFAs) are abundant in the skin, but their pathogenic roles in acne remain unclear. In human sebum profiling, C16:0, the most abundant lcSFA, was the only fatty acid significantly elevated in acne and correlated with inflammatory comedone counts. We then established a mouse model that faithfully recapitulates human acne phenotypes, in which topical C16:0 penetrated the epidermis and induced sebocyte hyperplasia, comedogenesis, and follicular inflammation. Mechanistically, C16:0 activated keratinization and inflammatory pathways and drove sebocyte-lineage differentiation from Lrig1+progenitor cells, which function as cutaneous lipid sensors. These effects persisted in germ-free mice and were unaffected by fatty acid transporter modulation, while MyD88 signaling was partially required for inflammatory cell recruitment. Together, our findings identified C16:0 as a human acne-associated lipid that recapitulates disease hallmarks through a microbe-independent, lipid-driven pathway, highlighting Lrig1+cells as central hubs in remodeling of the pilosebaceous unit.

cell biology↗

bioRxiv2025

A simple and versatile plasma membrane staining method for visualizing living cell morphology in reproductive tissues across diverse plant species

Plant reproduction involves dynamic spatiotemporal changes that occur deep within maternal tissues. In ovules of Arabidopsis thaliana (A. thaliana), one of the two synergid cells degenerates at fertilization, while the fertilized egg cell (zygote) undergoes directional elongation followed by asymmetric division to initiate embryonic patterning. However, morphological analysis of these events has been hampered by the limitations of conventional cell wall staining, which fails to label cells lacking complete walls, and by the requirement for transgenic fluorescent reporters to visualize cell outlines. Here, we report that the membrane-specific fluorescent dye FM4-64 readily permeates ovules, allowing clear visualization of reproductive cell morphology both before and after fertilization. This staining method supports high-resolution time-lapse imaging and quantitative analysis of early embryogenesis in living tissues. Importantly, it is applicable not only to the angiosperm A. thaliana but also to the liverwort Marchantia polymorpha (M. polymorpha) and the fern Ceratopteris richardii (C. richardii), enabling the visualization of live reproductive cell structures within maternal tissues and revealing fertilization-associated morphological changes. This simple and robust method thus provides a valuable tool for spatiotemporal and quantitative analyses of reproductive processes across a broad range of plant species, without the need to generate transgenic lines.

plant biology↗

bioRxiv2025

Integrated Multi-omic Profiling Reveals Early Regulatory Events in Dexamethasone Muscle Atrophy

Skeletal muscle atrophy and weakness are major contributors to morbidity, prolonged recovery, and long-term disability across a wide range of diseases. Atrophy is caused by breakdown of sarcomeric proteins resulting in loss of muscle mass and strength. Molecular mechanism underlying the onset of muscle atrophy and its progression have been analysed in patients, mice, and cell culture but the complementarity of these model systems remains to be explored. Here, we applied deep-coverage transcriptomic and proteomic profiling to characterize dynamic changes during dexamethasone-induced atrophy in the widely used murine skeletal muscle cell line C2C12. Comparison with published datasets confirmed that muscle differentiation is well recapitulated in C2C12 myotubes. Under dexamethasone treatment, this model was particularly suited to capture early atrophy events. We identified alterations in mitochondrial gene expression and differential alternative splicing events during early-stage myotube atrophy. This dataset complements existing in vivo data and provides novel insights into the regulatory processes during skeletal muscle wasting.

molecular biology↗

bioRxiv2025

Underappreciated role of environmental enrichment in alleviating depression and anxiety: Quantitative evidence synthesis of rodent models

Environmental enrichment has long been recognized as a non-pharmacological intervention to mitigate mental health issues, yet its efficacy, and heterogeneity of treatment effects across experimental contexts remain underexplored. Heterogeneity of treatment effects, which reflects variability in individual responses to interventions, is a critical factor in determining the generalizability and personalization needs of treatments. Here, we conducted a registered meta-analysis of 62 studies and 1,112 comparisons in rodent models to evaluate the impact of environmental enrichment on depressive and anxiety-like behaviours. We found that environmental enrichment reduced these behaviours of animal models by 16% on average and decreased inter-individual variability by 12%, indicating not only effectiveness but also low heterogeneity of treatment effects, which suggests consistent effects across individuals. Environmental enrichment further nullified the adverse effects of stressors, demonstrating a significant antagonistic interaction. These effects were robust across multiple sensitivity analyses, including model-based predictions, post-stratification, multi-model inference, publication bias correction, and critical appraisal of study quality. Moderator analyses highlighted the importance of exposure timing and the inclusion of social enrichment components. Taken together, our pre-clinical evidence on rodent models supports environmental enrichment as a low-cost, scalable, and biologically grounded intervention with translational relevance for developing equitable and accessible treatments for depression and anxiety. Given the importance of innovation and personalization in mental health care, the low heterogeneity of treatment effects of environmental enrichment positions it as a promising avenue for non-pharmacological therapeutic strategies that can be broadly applied without extensive tailoring.

animal behavior and cognition↗