Biology subjects

Sato, Y.

Publications and source records attributed to Sato, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Rapid RPA-CRISPR/Cas12a detection of Vibrio coralliilyticus for coral aquaculture disease surveillance

Coral aquaculture is expanding globally to support both the ornamental aquarium trade and reef-restoration initiatives, yet disease outbreaks remain a threat to production, causing potential substantial coral mortality and economic losses. Effective disease management requires early pathogen detection; however, conventional molecular diagnostics are labor-intensive and poorly suited to time-sensitive aquaculture operations. Here, we developed a rapid diagnostic assay for the coral pathogen Vibrio coralliilyticus by implementing recombinase polymerase amplification (RPA) with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas12a-based fluorescent signaling for sensitive and specific detection. The assay was optimized and validated against DNA from seven V. coralliilyticus strains and seven non-target Vibrio species, demonstrating high specificity and a detection limit <10 target copies per reaction within 30 minutes following DNA extraction. Performance of the assay was further evaluated using water from flow-through aquaria containing healthy and diseased Acropora tersa colonies, and results independently validated using droplet digital PCR (ddPCR). Although RPA-CRISPR/Cas12a consistently detected V. coralliilyticus across the tanks holding both healthy and diseased corals, ddPCR indicated substantially higher pathogen abundance in diseased tanks, suggesting that pathogen load rather than the presence alone is a more reliable indicator of disease risk. Incorporating rapid semi-quantification of pathogen abundance in future assay development could therefore improve disease prediction and management. This study demonstrates the potential of CRISPR-based diagnostics as a fast, sensitive, and field deployable tool for routine coral aquaculture biosecurity, enabling earlier intervention and more effective mitigation of disease outbreaks.

molecular biology↗

bioRxiv2026

Causal contribution of motor-parietal network to conscious kinesthetic perception

Bodily awareness, including the conscious experience of limb movement (kinesthesia), is a fundamental form of human consciousness. Tendon vibration-induced kinesthetic illusions provide a tractable model for probing its neural basis. Although previous studies have reported coactivation of the primary motor cortex (M1), the right inferior parietal lobule (IPL), and the right inferior frontal gyrus (IFG) during illusory movement, their causal contributions to conscious kinesthetic experience remain unclear. Here, we combined functional MRI and regional facilitative dual-site transcranial direct current stimulation (tDCS) to establish a causal link between these cortices and illusory foot movement. fMRI revealed that the M1-IPL network supports kinesthetic illusion elicited by bottom-up sensory processing, whereas the IFG plays a role in top-down monitoring of the kinesthetic experience. Critically, concurrent facilitative dual-site tDCS applied to the M1 and IPL significantly enhanced the subjective strength of the illusion, compared with the sham and concurrent tDCS to the M1 and IFG. This effect was replicated without increasing muscle activity in another tDCS study and exceeded those observed with single-site (M1 or IPL) or concurrent higher-order IPL-IFG tDCS. Our findings provide the first compelling causal evidence that conscious kinesthetic perception can be augmented through coordinated interactions between the modality-specific kinesthetic-motor cortex (M1) and the higher-order right inferior parietal cortex (IPL). This coordinated interaction between modality-specific and higher-order cortical regions underlying conscious kinesthetic perception is consistent with the Global Neuronal Workspace hypothesis. Our findings have therefore extended the applicability of this framework from exteroceptive perception to bodily awareness.

neuroscience↗

bioRxiv2026

Avian uropygial secretions as a novel bioinsecticide for mosquito vector control

Background: Malaria control relies heavily on interventions targeting mosquito vectors, but the rapid emergence of insecticide resistance threatens the effectiveness of existing approaches. Identifying novel, effective, and environmentally sustainable insecticides is therefore a priority. Birds produce uropygial secretions with well-documented antimicrobial properties, but their potential insecticidal activity against mosquitoes, including malaria vectors, remains unexplored. Methods: We evaluated the insecticidal activity of uropygial secretions from wild house sparrows (Passer domesticus) against the malaria vector Anopheles stephensi and four additional mosquito species of medical importance (Aedes aegypti, Aedes albopictus, Culex pipiens, and Culiseta longiareolata). A total of 2,293 adult mosquitoes were tested using CDC bottle bioassays at three secretion concentrations (0.5, 0.25, and 0.125) and an untreated control. Mosquito mortality was monitored for 120 min. Results: Uropygial secretions caused substantial mosquito knockdown/mortality, with effects increasing with concentration and exposure time. Susceptibility differed significantly among species after 120 min. Notably, An. stephensi was particularly susceptible, reaching knockdown/mortality of 92%, 94%, and 83% at 0.5, 0.25, and 0.125 concentrations, respectively. Conclusions: Our findings provide the first experimental evidence that avian uropygial secretions possess direct insecticidal activity against mosquitoes and identify them as a previously overlooked source of naturally derived insecticidal compounds. The high susceptibility of An. stephensi highlights their potential relevance for developing novel bioinsecticides for malaria vector control.

ecology↗

bioRxiv2026

Epistasis and an oligogenic architecture underlie the strength of a plant-herbivore interaction

1. Interaction strength between consumers and resources is a fundamental driver of eco-evolutionary dynamics, and its genetic architecture is key to predicting the pace of such dynamics. Our understanding of this architecture is limited for three reasons: (i) defense phenotypes do not necessarily translate to interaction strength; (ii) interaction strength is difficult to measure in ways tied to consumer-resource theory; and (iii) association studies typically prioritize detecting large-effect loci rather than characterizing whether interactions are polygenic (many small-effect genes) or oligogenic (few large-effect genes). 2. We address these gaps by examining how genomic variation in the plant Arabidopsis thaliana influences interactions with the aphid herbivore Lipaphis pseudobrassicae in a greenhouse experiment. We grew 390 accessions spanning the species' natural range and measured aphid per-capita population growth as our interaction-strength metric. To test whether a previously identified plant defense gene (AOP2) acts additively or epistatically with other defense loci, we integrated our estimates of aphid population growth with public data on defense chemistry and gene expression. To determine whether the genetic architecture of interaction strength was polygenic or oligogenic, we used a Bayesian sparse linear mixed model that partitions these two components. 3. AOP2 showed epistasis with two other defense genes (MAM1 and GS-OH), indirectly modifying aphid population growth via the production of a specific defense compound (glucosinolate 2-hydroxy-3-butenyl). More broadly, interaction strength showed an oligogenic architecture: top single nucleotide polymorphisms (SNPs) occurred at low minor allele frequencies (< 3%) and grouped into six linkage disequilibrium blocks, including candidate genes outside canonical plant defense pathways. These six blocks explained 47% of the genetic variance in interaction strength, with only 3% additional variance attributable to polygenic effects. 4. Taken together, these results show that plant genomic variation modifies herbivore interaction strength through epistasis among defense genes and rare alleles at few loci. This oligogenic architecture imposes multiple constraints on the potential for rapid evolution, highlighting the need to integrate genomic effects into eco-evolutionary models.

ecology↗

bioRxiv2026

Reduced EEG Complexity and Its Association with Social Communication in Adults with Autism Spectrum Disorder: A Multiscale Entropy Study

Background: Brain functions emerge from temporally organized neural dynamics, and an appropriate level of neural complexity may support flexible information processing. Electroencephalographic (EEG) studies using multiscale entropy (MSE), which quantifies signal complexity across multiple temporal scales, have reported reduced MSE at longer scales in individuals with autism spectrum disorder (ASD). However, most evidence comes from studies of infant and child samples, leaving adult data scarce, and the associations between reduced MSE, clinical symptoms, and social information processing are insufficiently understood. Methods: We recorded and analyzed EEG data from adults with ASD (n = 47) and typically developing (TD) controls (n = 40) during eyes-closed rest and two movie viewing conditions: Inscapes, comprising dynamically changing abstract visual patterns, and Partly Cloudy, an emotionally engaging animated social narrative. Group and condition effects were assessed using cluster-based permutation tests, and associations between MSE and Social Affect (SA) scores from the Autism Diagnostic Observation Schedule, Second Edition (ADOS-2), as well as group differences in event-related MSE changes, were examined using linear mixed-effects models. Results: Across conditions, adults with ASD showed lower MSE at longer scales ({tau} = 16-30), corresponding to effective sampling rates of 12.50-6.67 Hz in the coarse-grained time series, than TD adults. Longer-scale MSE within the ASD-TD difference cluster was negatively associated with ADOS-2 SA scores across diagnostic groups. The difference in event-related MSE change between Social and Non-Social conditions, comparing empathic-pain and mentalizing events in Partly Cloudy with temporally matched non-social windows in Inscapes, was smaller in ASD participants than in TD participants. No significant difference between Social and Non-Social windows was observed among ASD participants, whereas TD participants showed significantly greater MSE change during Social than Non-Social windows. Limitations: This study used a modest sample without an independent replication cohort, and the short event windows limited the precision of the MSE estimation. Conclusions: Reduced longer-scale MSE extends to adults with ASD and is associated with higher ADOS-2 SA scores across diagnostic groups. Event-related findings further suggest attenuated differentiation of longer-scale MSE between socially relevant and matched non-social windows in ASD.

neuroscience↗

bioRxiv2026

Extended genomic regions flanking ultraconserved elements allow efficient species identification and intraspecific diversity assessment in coral

Genetically informed conservation is critically important to ensure that interventions benefit the population of interest. In corals, preserving genetic diversity and accurate species identification are crucial for the sexual propagation. While various methods exist for species identification and measuring intraspecific variation, obtaining and analysing molecular data that enables rapid yet informed decisions on broodstock choice and progeny quality assurance remains challenging. Here we present a novel approach towards resource effective intraspecific genetic profiling by targeting extended genomic regions around ultra-conserved elements (UCEs). By sorting loci by parsimony informativeness and using a locus window size as small as 5000 bp upstream and downstream of the UCE, we identified a subset of 500 UCE-associated loci that can accurately resolve phylogenetic relationships among species and assess intraspecific variation with accuracy comparable to a whole-genome dataset, while. This method was validated using existing population genomic data from six species of staghorn coral (Acropora hyacinthus, Acropora tersa, Acropora pectinata, Acropora sp. "VI-3", Acropora kenti and Acropora cf. spathulata). The phylogeny produced by the UCE subset is congruent with the phylogeny based on complete data. With the moderate number and length of target genomic region sizes providing a balance between resolution and sequencing effort, this study provides a proof-of-concept approach towards developing fast, scalable, and cost-effective workflows using a real-time long-read sequencers such as Oxford Nanopore Technologies. The methodology has the broad potential to be applied to support genetic assessment across taxa where taxonomic uncertainty is common, improving confidence in experimental frameworks and conservation decisions.

genomics↗

bioRxiv2026

Minocycline engages microglia in the midbrain periaqueductal grey to attenuate hypoxia-triggered panic-like behaviour in rats

Panic disorder (PD) is a chronic and highly disabling psychiatric disorder characterised by recurrent and unexpected panic attacks, with underlying neurobiological mechanisms poorly understood. Emerging evidence suggests that inflammatory processes may contribute to the triggering of panic attacks, with a subset of PD patients exhibiting alterations in circulating cytokine levels, while animal studies indicate that an immunoresponsive microglial phenotype may contribute to the disorders pathophysiology. Minocycline, a tetracycline-class antibiotic that crosses the blood-brain barrier, exerts anti-inflammatory effects and has demonstrated therapeutic potential in attenuating panic attacks, supporting its potential as an alternative strategy for reducing PD-related symptoms by modulating microglial activity. In this study, we investigated whether exposure of male Sprague-Dawley rats to a panicogenic stimulus, hypoxia (7% O2), is followed by microglial morphological remodelling in the midbrain periaqueductal grey (PAG), a well-known panic-associated structure, at baseline and after minocycline treatment. The effects of hypoxia on the expression of panic-like jumping behaviour were measured during the respiratory challenge, whereas microglial morphology was assessed at 1, 6, or 24h following the aversive stimulus. In a second experiment, the effects of minocycline (30 mg/kg, i.p., administered once daily for 5 days) on the immediate behavioural responses to hypoxia were compared with those produced by an acute administration of alprazolam (2 mg/kg, i.p.), a benzodiazepine widely used in the clinical management of PD. Minocycline effects on microglial morphology in the PAG were also assessed. Our findings show that hypoxia elicited robust jumping behaviour, without affecting overall locomotion. This panicogenic effect was accompanied by marked and time-dependent microglial morphological changes in the dorsomedial (dmPAG) and ventrolateral (vlPAG) columns of the PAG, consistent with a shift towards an immunoresponsive phenotype. Notably, minocycline, similarly to alprazolam, reduced the number of jumps, indicating a panicolytic effect, while also preventing hypoxia-induced microglial remodelling in the dmPAG. Altogether, these findings suggest a role for microglia in regulating hypoxia-induced panic- like behaviour, indicating that microglial inhibition, as achieved here with minocycline, represents a promising therapeutic strategy for preventing panic attacks.

neuroscience↗

bioRxiv2026

The 329HHK331 motif is essential for Alzheimer's disease tau filament fold

Cryo-electron microscopy (cryo-EM) has revealed disease-specific tau filament folds, yet the local sequence elements that determine them remain poorly understood. Here we focused on the 329HHK331 motif near an inter-protofilament interface in Alzheimers disease (AD)-type tau filaments, and analyzed recombinant dGAE filaments of wild-type (WT) and mutants in this motif. All mutants formed amyloid-like filaments in vitro, but their morphologies differed. In cultured cells, WT filaments efficiently seeded WT tau aggregation. Filaments with three-residue changes (deletion or Ala substitution) showed almost no seeding activity, whereas two-residue deletions retained partial activity. Cryo-EM showed that WT dGAE filaments form a quadruple helical filament of two protofilament dimers. Each dimer comprises two C-shaped protofilaments, centered on a 333GGG335-mediated inter-protofilament interaction and supported by flanking 329HHK331-336QVE338 contacts. Three-residue alterations abolished interactions with the QVE motif at the protofilament interface, thereby displacing 333GGG335 and forming non-C-shaped protofilament structures that are intrinsically poor templates for tau seeding. By contrast, two-residue deletions maintained the C-shaped protofilament structure because the remaining residue formed alternative inter-protofilament interactions. These findings suggest that the 329HHK331 region is a key determinant of the AD-like C-shaped protofilament fold and link this motif to tau seeding, providing insight into disease-specific tau filament formation.

neuroscience↗

bioRxiv2026

A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi

Fungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition, extracellular signaling, nutrient exchange, immune modulation, and control of microbial competitors. In filamentous pathogens such traits are frequently associated with compartmentalized genomes, including rapidly evolving secreted proteins known as effectors and expanded receptor families, but it remains unclear whether similar genomic principles shape mutualistic fungal symbioses. Here, we generated a chromosome-scale super-pangenome for the lichen-forming genus Peltigera, comprising 41 mycobiont assemblies representing eleven species, together with genomes of associated Nostoc and, in tripartite species, Coccomyxa photobionts. The mycobiont genomes revealed extensive variation in genome size, transposable element content, biosynthetic gene clusters, and lineage-specific gene content, with pronounced expansions in tripartite species. Across Peltigera, secreted protein encoding genes were preferentially located in TE-rich regions. We further identified Starship-like transposon elements, expanded antimicrobial protein repertoires, and a large, previously underestimated repertoire of fungal GPCRs dominated by Pth11-like receptors. Layer-specific transcriptomics of a P. rufescens thallus showed differential expression of several interaction-associated gene families, e.g. lectins, antimicrobial proteins and Pth11-like GPCRs. These data indicate that pathogenic and mutualistic fungi might exhibit shared genomic principles, including genome compartmentalization, mobile-element-associated diversification, and the expansion of molecular repertoires involved in recognition, extracellular control and signaling.

genomics↗

bioRxiv2026

Osteopontin Upregulation Defines a Pre-Rupture State in Thoracic Aortic Aneurysms in Mice and Humans

BackgroundThoracic aortic aneurysm (TAA) is a life-threatening condition with an unpredictable lisk of rupture. Current clinical parameters have limited ability to accurately predict imminent rupture. Osteopontin (OPN) has been implicated in aortic aneurysm pathology, however, it role as a marker of imminent rupture remains. unclear. We investigated the dynamics of OPN expression dynamics in a mouse model with predictable rupture timing and validated our findings in human TAA. MethodsOne-month-old fibrillin-1 hypomorphic (Fbn1mgR/mgR) mice were used as a TAA model; with wild-type (WT) mice served as controls. Angiotensin II (AngII) was administered to Fbn1mgR/mgR to induce acute aortic rupture. Single-section transcriptome analysis and immunofluorescence staining were performed on ascending aortic tissue at 24 and 72 hours after AngII infusion, with pre-treatment Fbn1mgR/mgR and WT mice serving as controls. To determine conservation in human disease, we reanalyzed publicly available single-cell RNA sequencing data from ascending thoracic aortic aneurysm (ATAA) patients. ResultsAngII infusion induced progressive mortality beginning at 24 hours, with approximately 60% survival at 72 hours and nearly no survival by 8 days in Fbn1mgR/mgR mice. At this pre-rupture time point, OPN showed prominent upregulation at both mRNA and protein levels in ascending aortic tissues compared to controls. Immunofluorescence staining revealed increased OPN expression in the aortic wall, particularly in regions exhibiting structural deterioration. Reanalysis of human ATAA single-cell data showed elevated OPN expression compared to controls, with enrichment in immune cell populations, especially macrophages. Within the macrophage compartment, subcluster analysis identified a stress-responsive subpopulation (MC1) that was markedly expanded and almost exclusively composed of ATAA-derived cells, representing the primary source of OPN upregulation. ConclusionsOPN upregulation represents a conserved molecular signature of the pre-rupture state in TAA across mice and humans. Our mode, which enables predictable rupture timing, allowed the capture of acute pre-rupture molecular changes, suggesting OPN as a potential biomarker for predicting imminent aortic rupture.

molecular biology↗

bioRxiv2026

DNA Double-decker Ring Scaffolded Nanodisc for Self-assembly of Membrane Protein into Lipid Bilayer

Membrane models of scaffolded discoidal lipid bilayers called nanodiscs have proven to be a valuable tool for the study of membrane proteins in a native environment. DNA-scaffolded membrane model has emerged as an alternative tool for membrane protein studies. Taking advantage of the designability of DNA nanostructure, we created a double-decker double-stranded DNA ring (DDring) to self-assemble DNA-based nanodiscs (DNA-ND). The DDring is 17 nm wide and 4 nm high, and equipped with 28 alkyl chains on the inside that can interact with each hydrophobic leaflet of the lipid bilayer. We further demonstrate the functionality of DNA-ND membrane model with the assembly of membrane proteins. DDrings are suited to neutral or cationic charged phospholipids and detergents. This study provides more insights into the potential use of DNA- assisted nanodiscs for membrane protein characterization.

bioengineering↗

bioRxiv2026

Figra: A WebAssembly-based Excel Add-in for publication-quality scientific visualization with ggplot2

Data visualization is a critical step in scientific communication. Most researchers rely on subscription-based software for this purpose, which requires ongoing licensing costs. Free alternatives such as R and Python offer publication-quality output but demand programming expertise that many researchers do not possess. Artificial intelligence tools can assist with figure generation but remain frustrating when users wish to fine-tune specific visual parameters to their preference. Meanwhile, Microsoft Excel, the most widely used tool for scientific data storage and management, offers limited visualization capabilities, forcing researchers to transfer their data to external software as an extra step before creating figures. Here we present Figra, a free Excel Office Add-in that eliminates this extra step by enabling publication-quality ggplot2-based figure generation directly within Excel, with simple and direct control over every visual option. Figra leverages WebAssembly technology (webR) to execute R code entirely within the browser, requiring no R installation, no subscription, and no server connection. The add-in supports over 20 chart types spanning distribution plots, grouped comparisons, time-series, scatter plots, and specialized curve-fitting analyses. For applicable chart types, Figra performs automated or manual statistical analysis supporting both paired and unpaired designs across two or more groups. Additionally, Figra exports simplified, executable R code that reproduces the displayed figure, serving as an educational tool for researchers wishing to learn ggplot2. Figra is open-source and freely available at https://h20gg702.github.io/figra-pages/index.html while the source code is provided at https://github.com/h20gg702/Figra.

bioinformatics↗

bioRxiv2026

Modeling interregional propagation of α-synuclein in human striatal-midbrain assembloids

Parkinsons disease is characterized by the progressive degeneration of dopaminergic (DA) neurons in the substantia nigra that project to the striatum. Postmortem studies have found that -synuclein pathology spreads across brain regions in a prion-like manner. Human three-dimensional neural tissues provide experimentally tractable platforms for clarifying the molecular pathology of synucleinopathy that overcome the limitations of postmortem brain studies. In this study, we established a human striatal-midbrain assembloid model enabling spatially and temporally controlled -synuclein induction after formation of the nigrostriatal pathway within hStrMAs. Human induced pluripotent stem cells (hiPSCs) were differentiated into striatal spheroids and midbrain spheroids, which were fused to reconstruct the nigrostriatal pathway in vitro. Histological, electrophysiological, and single-cell RNA sequencing analyses confirmed the generation of region-specific neuronal populations, including striatal GABAergic neurons and midbrain DA neurons, and demonstrated that distinct forebrain and ventral midbrain identities were preserved within assembloids. To model synucleinopathy, we generated a doxycycline-inducible -synuclein hiPSC line, permitting selective induction of -synuclein expression in the striatal region after assembloid formation. Spatially restricted -synuclein induction resulted in the progressive accumulation of phosphorylated and fibrillar -synuclein in midbrain DA neurons, indicating interregional propagation through established neural circuits. Transcriptomic analysis of the midbrain region revealed significant downregulation of DA identity and synaptic function genes, suggesting functional impairment of DA neurons following -synuclein propagation. These findings demonstrate that the human neural circuit architecture contributes to the interregional propagation of -synuclein pathology. Our controllable human assembloid platform provides a powerful experimental framework for dissecting the mechanisms of pathological protein spread and developing therapeutic strategies targeting molecular pathology in neurodegenerative diseases. Significance statementOne pathological feature of Parkinsons disease is the progressive spread of -synuclein pathology across brain regions. However, the molecular mechanisms underlying this process remain poorly understood. In this study, we established a human striatal-midbrain assembloid model in which -synuclein expression can be spatially restricted and temporally induced after the nigrostriatal pathway is formed, thus enabling the experimental dissection of interregional -synuclein propagation across brain regions. We demonstrated that -synuclein pathology initiated in the striatal region propagated to midbrain dopaminergic neurons, leading to disease-relevant molecular and transcriptional alterations. These findings provide direct evidence that human neural circuits contribute to the spread of synucleinopathy and offer a controllable human model for studying disease progression and therapeutic strategies.

neuroscience↗

bioRxiv2026

Bacteria rewire fungal antimicrobial gene expression in microbial arms races

Microbial communities are shaped by antagonistic interactions, yet how competitors evade antimicrobial strategies in a community context remains unclear. Fungi deploy antimicrobial proteins (AMPs) to suppress bacterial niche competitors, but how bacteria counteract these defences is unknown. Here we show that soil microbiota suppress fungal AMP expression, revealing a previously unrecognized mode of intermicrobial interference. In the soil-borne pathogen Verticillium dahliae, AMP genes are highly conserved yet broadly repressed in the presence of natural microbial communities. This repression extends across diverse fungi, suggesting a widespread phenomenon. Correlation analyses of AMP expression and community compositions linked the bacterial genera Leptothrix and Devosia to repression of the V. dahliae AMPs VdL1 and VdD1, respectively. Both AMPs antagonize these bacterial taxa, and microbiota-mediated repression of VdL1 reduces its contribution to fungal soil colonization. Together, our findings reveal that bacteria can evade fungal antagonism by suppressing AMP deployment, highlighting community-level control of microbial competition.

microbiology↗

bioRxiv2026

Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia

Understanding crop population history requires genetic material that predates modern breeding. Here, we analyzed historical seeds of rice landraces assembled in Southeast Asia from 1957 to 1958. Target capture resequencing of coding regions yielded high-quality genomic data from 66 historical accessions (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the previously described major regional structure was recovered. Within the historical collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to the traditional growth seasons (fifth- and tenth-month rice). Notably, the fifth-month rice accessions were assigned to the recently reported Vietnam-I5 cluster. Admixture graph, f-statistics, and qpAdm analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage; however, this relationship was not fully explained by sampled indica, japonica, or aus proxies. Together, these results show that major components of the present-day indica regional structure were already present before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice. HighlightGenomic analyses of historical indica rice seeds reveal that a distinctive northern Vietnamese lineage and a genetic continuum across southern Vietnam, Cambodia, and Thailand predated modern cultivar replacement.

plant biology↗

bioRxiv2026

The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP

The multifunctional AAA+ ATPase p97/VCP is a pivotal regulator of cellular proteostasis, extracting polyubiquitinated substrates from protein complexes or organelle membranes for proteasomal degradation. Mutations in p97 are linked to a broad spectrum of neurodegenerative disorders, including multisystem proteinopathy and amyotrophic lateral sclerosis. Here, we provide insights into the basis of dysfunction in p97D395G, implicated in vacuolar tauopathy, using an integrated structural approach. The mutation destabilizes the interaction network in the transient ADP.Pi state previously identified in p97WT and alters the dynamics of the linker between the tandem ATPase domains, resulting in decreased ATPase activity. We further demonstrate that the D395G mutation sensitizes p97 to oxidative stress by enhancing C522 oxidation, thereby perturbing nucleotide binding in D2, and define the functional basis of this oxidative inactivation of p97. These findings reveal redox control as a key regulatory layer of the p97 ATPase cycle and provide a mechanistic framework for how oxidative stress contributes to p97-associated neurodegeneration.

molecular biology↗

bioRxiv2026

Dissecting oligogenic and polygenic indirect genetic effects through the lens of neighbor genotypic identity

Individual phenotypes often depend on the genotypes of other individuals within a group. These phenomena are termed indirect genetic effects (IGEs) and have been distinguished from direct genetic effects (DGEs) using quantitative genetic models. Recent studies have utilized high-resolution polymorphism data to enable genomic prediction (GP) and genome-wide association study (GWAS) of IGEs, but unified methods remain limited. Here we integrate polygenic and oligogenic IGEs using a multi-kernel mixed model incorporating two random effects with a single covariance parameter. Underlying this implementation, the Ising model of ferromagnetics enabled us to simplify locus-wise and background IGEs for GWAS and GP, respectively. Our simulations demonstrated that, while the previous and present models exhibited similar performance, the present model can infer a trade-off between DGEs and IGEs. By applying this method to three species of woody plants, we found evidence for intergenotypic competition in aspen and apple trees, but limited evidence in climbing grapevines. Based on GWAS, we also detected significant variants associated with the competitive IGEs on the apple trunk growth. Our study offers a flexible implementation for GWAS/GP of IGEs, thereby providing an effective tool to dissect the genetic architecture of group performance.

genetics↗

bioRxiv2026

Calcium Dynamics During Pollen Tube Reception in Arabidopsis Ovules

In flowering plants, pollen tubes communicate with ovular cells to achieve precise one-to-one pollen tube reception. The final step of this communication between the pollen tube and synergid cells has been extensively investigated and visualized by calcium imaging. Synergid cells exhibit characteristic cytoplasmic calcium concentration oscillations, which are thought to play a critical role in pollen tube reception. However, their significance and relationship with calcium dynamics in the entire ovule remain unclear. Here, we show, using the calcium sensor GCaMP6s, that proteins involved in asparagine-linked glycosylation (N-linked glycosylation) are required for normal calcium oscillations in synergid cells but are not essential for pollen tube reception. Using a semi-in vivo assay in Arabidopsis thaliana, we found that the amplitude of these oscillations prior to rapid pollen tube growth across the filiform apparatus was reduced in mutants lacking the oligosaccharyltransferase (OST) 3/6 subunit or alpha1,2-glucosyltransferase (ALG) 10, both of which are involved in N-linked glycosylation. Notably, these mutants did not exhibit reduced fertility attributable to defects in the female gametophyte but instead showed a polytubey phenotype due to a sporophytic defect. These findings suggest that N-linked glycans mediate communication between synergid cells and the pollen tube and indicate that the typical pattern of calcium oscillations in synergid cells is not essential for triggering pollen tube rupture. Furthermore, we show that sporophytic tissues of the ovule exhibit calcium waves that propagate toward the funiculus in correlation with pollen tube contact and rupture, implying that ovular tissues can potentially transmit these signals distantly beyond the ovule. Together, these findings reveal previously unrecognized intercellular calcium signaling and its significance in pollen tube reception by the ovule.

plant biology↗