Biology subjects

Okumura, M.

Publications and source records attributed to Okumura, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Symmetry breaking and social coordination in children: Using group theory to understand emergent patterns of multi-agent coordination

Predicting patterns of behavioural coordination that emerge in small interacting groups is challenging because goal-directed social action is shaped by complex reciprocal and compensatory dynamics. In this study, we examined whether formal symmetry principles derived from group theory could explain coordination patterns among children performing a triadic jumping task. We investigated how geometric symmetries of the task environment and dispositional (a)symmetries associated with leader-follower tendencies jointly constrain collective behaviour. Forty-seven children were classified into symmetric or asymmetric triads based on teacher evaluations of leadership dispositions. Each triad completed multiple trials of a synchronized jumping game requiring movement between adjacent hoops arranged in triangular or square configurations. Results showed that temporal asymmetries in inter-child movement (first, second, or last to jump) were consistent with group-theoretic predictions. In triangular configurations, observed asymmetries corresponded to the highest-order subgroup defined by task and dispositional symmetries. These findings demonstrate that environmental symmetry exerts a hierarchically dominant constraint on collective coordination, within which actor dispositional (a)symmetries further modulate emerging patterns.

animal behavior and cognition↗

bioRxiv2026

Calibrated ADAMTS13 inhibition prevents cardiovascular shear coagulopathy

Mechanical circulatory support essential for managing severe heart failure frequently triggers bleeding complications, driven by shear stress-induced over-proteolysis of von Willebrand factor (VWF) by ADAMTS13. Inhibiting ADAMTS13 presents a rationale to treat this condition, known as acquired von Willebrand syndrome (AVWS). However, conventional therapeutic strategies remain limited due to the risk of triggering thrombotic thrombocytopenic purpura. Here we show that HA10, a humanized anti-ADAMTS13 antibody, preserves a residual level of ADAMTS13 activity above the thrombosis-associated threshold. Multimodal structural and biophysical analyses--including NMR, SAXS, and SANS--revealed that HA10 bound to the disintegrin-like domain of ADAMTS13, dynamically competing with VWF while leaving 10- 20% residual enzymatic activity. The therapeutic efficacy and safety of HA10 were verified in non-human primate models of AVWS. Our findings establish a novel paradigm of enzymatic calibration rather than complete blockade, offering a mechanistically targeted and safe therapeutic approach for cardiovascular bleeding.

biochemistry↗

bioRxiv2026

Desialylated platelets promote hepatocyte proliferation via the ERK1/2 signaling pathway

Platelets are increasingly recognized as active regulators of tissue repair and liver regeneration beyond their classical roles in hemostasis and thrombosis. Loss of terminal sialic acid from platelet surface glycoproteins, a process known as desialylation, occurs during platelet aging or activation and has been linked to platelet clearance via the asialoglycoprotein receptor (ASGPR) on hepatocytes. However, the mechanisms by which desialylated platelets (D-plts) directly stimulate hepatocyte proliferation remain poorly understood. This study aimed to elucidate the proliferative effects of D-plts on hepatocytes and to identify the underlying signaling mechanisms. D-plts were generated and co-cultured with hepatocyte models exhibiting low or absent levels of asialoglycoprotein receptor 1 (ASGPR1) expression, including HepG2 cells, HuH-7 cells, and human chemically induced liver progenitors. Hepatocyte proliferation was assessed, and the roles of platelet-derived factors and downstream signaling pathways were investigated. Co-culture with D-plts significantly increased hepatocyte proliferation in all three cell models compared with the corresponding controls. Moreover, supernatants derived from stimulated D-plts also significantly enhanced hepatocyte proliferation, suggesting that soluble platelet-derived factors contribute to this effect. Mechanistically, the proliferative effects were mediated predominantly through the ERK1/2 signaling pathway rather than the JAK-STAT pathway in both hepatocytes co-cultured with D-plts and those treated with D-plt-derived supernatants. In conclusion, our findings demonstrate that D-plts directly promote hepatocyte proliferation through an ASGPR-independent pathway, in which ERK1/2 signaling plays a central role. These results highlight a novel mechanism through which platelet desialylation may contribute to liver regeneration. Graphical Abstract(A) Desialylated platelets are readily activated and release increased amounts of EGF, promoting hepatocyte proliferation via the EGF-ERK signaling pathway. (B) Normal platelets show lower reactivity and reduced EGF release than desialylated platelets, resulting in weaker hepatocyte proliferation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/740293v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@d8eb25org.highwire.dtl.DTLVardef@135e644org.highwire.dtl.DTLVardef@1a0a924org.highwire.dtl.DTLVardef@c092e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Chemical Boosting of Foldase Condensates Accelerates Oxidative Protein Folding

Dynamic biomolecular condensates play crucial roles in intracellular compartmentalization and physiological functions. While engineering tools for compartmentalization have expanded add-on functionalities, directly amplifying the inherent catalytic machinery within biological phase-separated droplets has remained elusive. Herein, we developed a phase-separated oxidative folding reaction chamber based on protein disulfide isomerase A6 (PDIA6) by chemically targeting its active site CxxC motif to enhance enzymatic activity within PDIA6 droplets. A para-substituted N-methylated pyridinylmethanethiol (pMePySH) enhanced the catalytic oxidative folding of bovine pancreatic trypsin inhibitor, proinsulin, and antibody up to 12-fold within in vitro PDIA6 droplets. Furthermore, pMePySH targeted PDIA6 foci within the endoplasmic reticulum, significantly promoting insulin secretion. These findings offer a powerful platform for the spatiotemporal manipulation of protein folding, with profound implications for the scalable manufacturing of therapeutic antibodies and other complex biopharmaceuticals.

bioengineering↗

bioRxiv2026

Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer

Neoadjuvant chemoradiotherapy (CRT) is standard for locally advanced rectal cancer (LARC), yet many patients retain residual disease. To resolve CRT-associated remodeling of the tumor microenvironment, we generated a multimodal spatial atlas from serial sections of paired pretreatment and post-treatment specimens from 24 patients using Xenium single-cell spatial transcriptomics and PhenoCycler multiplex proteomics, profiling 2.8 million cells; matched Visium HD datasets were generated on adjacent serial sections. Resistance was most strongly associated with fibroblast and myeloid programs adjacent to residual tumor. We identify a periostin (POSTN)-expressing CAF subset selectively enriched around residual tumor cells in non-responders, displaying a myofibroblastic phenotype and activating extracellular matrix remodeling, noncanonical WNT signaling, and immunosuppressive pathways. Tumor cells neighboring POSTN+ CAFs show consistent epithelial-mesenchymal transition signatures. Together, this atlas enables interrogation of CRT-induced spatial remodeling and nominates POSTN+ CAFs as key mediators and targets of CRT resistance, with direct relevance to CRT-based combination strategies.

cancer biology↗

bioRxiv2025

Identity and functions of monoaminergic neurons in the predatory nematode Pristionchus pacificus reveal nervous system conservation and divergence

Changes in neurotransmitter usage in homologous neurons may drive evolutionary adaptations in neural circuits across animal phylogeny. The predatory nematode Pristionchus pacificus can be used as a model system to examine nervous system evolution by comparing neurotransmitter expression with that of C. elegans and other nematodes. Here we characterize P. pacificus neurotransmitter expression and function in specific neurons, focusing on its complete set of monoaminergic neurons. We discover patterns of conservation as well as novelties. We examine the roles of monoamines in specific behaviors using neurotransmitter synthesis and vesicular transporter mutants, finding possible differences in the control of host-finding and dispersal behavior.

neuroscience↗

bioRxiv2025

Characterization of heat shock protein expression and its application to temporal gene expression in the nematode Pristionchus pacificus

Temporal gene expression systems are widely used to examine gene functions at specific developmental stages. One method applied in temporal gene expression systems in many organisms is the heat-inducible gene expression system, which utilizes a heat shock promoter with evolutionarily conserved heat shock elements. The nematode Pristionchus pacificus is a satellite model system comparable to Caenorhabditis elegans, with unique developmental traits but lacking genetic tools for temporal gene expression. To establish a temporal gene expression system in P. pacificus, we investigated genes that were highly induced by heat shock. RNA-seq analysis revealed thousands of differentially expressed genes after a 2-hour heat shock event. One of the highly induced genes, PPA12242, is an ortholog of C. elegans hsp-16.41, and reporter transgenic animals have indicated that the genomic fragment upstream of this gene can induce gene expression in response to heat shock. PPA12242 can be highly induced in specific larval stages, which seem to be vulnerable to heat stress in some phenotypes. Taken together, we identified a potential heat shock promoter in P. pacificus that is applicable to the temporal gene expression system in this species.

genetics↗

bioRxiv2025

Hippo-activated cells induce non-cell autonomous tumorigenesis in Drosophila

The Hippo pathway is known as a tumor-suppressor pathway, and most related studies have indicated that the inhibition of the Hippo pathway leads to tumorigenesis. However, recent studies have suggested that the activated Hippo pathway can potentially promote tumorigenesis in some contexts. Here, we show that the activated Hippo pathway induces non-cell-autonomous tumorigenesis characterized by tumor markers in the Drosophila wing epithelium. This suggests that the Hippo-activated cells behave similarly to "oncogenic niche cells." We found that the Hippo-activated cells distantly induced tumor-like cells exhibiting aberrant cell proliferation. Moreover, we identified the evolutionarily conserved amino acid transporters, Sat1/2, that redundantly work with the growth factors, Wingless and Spitz, for non-cell autonomous tumorigenesis. Our findings provide novel insights into the Hippo pathway and may be useful in developing cancer treatments targeting the Hippo pathway.

cell biology↗

bioRxiv2025

Covalent anti-HIV compound that induces HIV-1 capsid multimerization and degradation decomposes the viral core

Covalent inhibitors form strong, essentially irreversible interactions with their targets, offering enhanced structural selectivity within the target cavity and prolonged target engagement even at low doses. Here, we report that ACAi-001, an HIV-1 capsid (CA)-targeting compound identified through in silico screening of the hydrophobic cavity in the CA N-terminal domain (CA-NTD), inhibits HIV-1 replication in cell-based assays. ACAi-001 covalently binds CA to induce aberrant CA multimerization and degradation in vitro, a pharmacological property distinct from that of existing CA inhibitors such as lenacapavir. This mechanism was confirmed by Western blotting (WB), size exclusion chromatography (SEC), differential scanning fluorimetry (DSF), and liquid chromatography-mass spectrometry (LC-MS). These results suggest that ACAi-001, with two putative covalent interactions in its chemical structure, binds directly to Ser16 in the N-terminal domain targeting cavity in addition to Cys198 or Cys218 in the C-terminal domain of CA. The treatment of viral particles with ACAi-001 results in the loss of intact, conical HIV-1 cores, as directly visualized by transmission electron microscopy (TEM), establishing the HIV-1 core as the direct target of ACAi-001. These findings demonstrated that ACAi-001 may be a promising next-generation anti-HIV-1 CA inhibitor with unique mechanisms of action, offering new insight into HIV-1 core assembly and disassembly.

microbiology↗

bioRxiv2025

Amyloid fibrils in Alzheimer's disease differently modulate sleep and cortical oscillations in mice depending on the type of amyloid

Alzheimers disease (AD) is characterized by aggregation and deposition of the amyloid-beta (A{beta}) protein in patient brains, with aging playing a crucial role through oxidative stress and neuroinflammation. Sleep disturbances are common in patients with AD, and contribute to their cognitive impairment. However, the association between the aggregation of specific A{beta} species in particular brain regions and its effect on sleep impairment remains unclear. Here, we investigated the effect of A{beta}1-40 (A{beta}40) and A{beta}1-42 (A{beta}42) amyloid fibrils on sleep/wakefulness and cortical oscillations in 3-month old wild-type mice. A{beta}42 aggregated faster and demonstrated distinct structural properties compared with A{beta}40. Bilateral injections into the dentate gyrus of the hippocampus showed that A{beta}42 amyloid fibrils significantly disrupted sleep and cortical activity as well as caused neuronal death, whereas A{beta}40 amyloid fibrils mainly affected cortical oscillations and caused minimal neuronal death. These findings shed light on AD-associated sleep disorders, which are differentially affected by the distinct properties of A{beta}40 and A{beta}42 aggregates.

neuroscience↗

bioRxiv2025

Lipids Are Involved in Heterochromatin Condensation: A Quantitative Raman and Brillouin Microscopy Study

Chromatin, a fundamental component of eukaryotic genomes, is categorized into euchromatin and heterochromatin, which play distinct roles in gene regulation. Although these two chromatin states are distinguished by their degree of condensation, quantitatively measuring the degree of chromatin condensation, as well as the physical properties of chromatin in living cells, remains challenging. In this study, label-free in situ quantitative imaging was performed using a Raman-Brillouin microscope to visualize the spatial distribution of molecular concentration and viscoelasticity within the nuclear environment of a living cell. A quantitative concentration distribution image of each intracellular biomolecule was obtained by combining Raman imaging with multivariate curve resolution analysis, using a water Raman band as an internal standard. Simultaneous Raman-Brillouin imaging enables the quantitative visualization of viscoelasticity within a cell. Using this approach, we found that, in addition to DNA, heterochromatin is enriched in lipids and that lipids play a critical role in heterochromatin formation, determining its mechanical properties. These findings provide new insights into the mechanism of heterochromatin formation and its chemical and physical properties, leading to a comprehensive understanding of gene regulation and nuclear organization.

biophysics↗

bioRxiv2024

Dysbiosis-associated gut bacterium Ruminococcus gnavus varies at the strain level in ability to utilize key mucin component sialic acid

Ruminococcus gnavus is a prevalent human gut commensal bacterium with known roles in intestinal mucus degradation, including by catabolism of the terminal mucin sugar sialic acid. While R. gnavus is not considered a pathogen, overabundance of this species is correlated with Inflammatory Bowel Disease (IBD), and its sialic acid metabolism may play a role in the dysbiotic state. Interestingly, liberation of mucin-bound sialic acid by R. gnavus yields the distinct product of 2,7-anhydro-N-acetylneuraminic acid (2,7-anhydro-Neu5Ac), in contrast to other known mucin-degrading bacteria, which generate Neu5Ac. This prompted us to look for 2,7-anhydro-Neu5Ac metabolism proteins in the genomes of 77 R. gnavus clinical isolates. We found that 2,7-anhydro-Neu5Ac metabolism is sporadically distributed in this species with respect to phylogeny and strain origin. We measured sialic acid-dependent growth of 12 sequenced isolates, finding that the presence of 2,7-anhydro-Neu5Ac catabolism proteins was predictive of growth on this substrate. Our analysis also uncovered "partial" 2,7-anhydro-Neu5Ac catabolism pathways in two R. gnavus strains, which we determined constitute the canonical Neu5Ac catabolism pathway, previously unreported in this species. These results reveal a notable diversity of sialic acid catabolism across the R. gnavus species, an essential consideration for further investigations into the importance of this metabolism in mucin degradation and in roles of R. gnavus in IBD and other gut dysbioses.

microbiology↗

bioRxiv2024

Predatory aggression evolved through adaptations to noradrenergic circuits

Behaviors are adaptive traits evolving through natural selection. Crucially, the genetic, molecular, and neural modifications that shape behavioral innovations are poorly understood. Here, we identify specialized adaptations linked to the evolution of aggression in the predatory nematode Pristionchus pacificus. Using machine learning, we identified robust behavioral states associated with aggressive episodes. These depend on modifications to the invertebrate noradrenergic pathway, with octopamine promoting predatory bouts, and tyramine antagonistically suppressing predation. Strikingly, aggression coincides with rewiring of key circuits across nematode evolution. We find additional octopaminergic neurons with morphological adaptations, including neurites extending to teeth-like structures, and expanded receptor expression throughout head sensory neurons gating prey detection. Thus, evolutionary adaptations in noradrenergic circuits facilitated the emergence of aggressive behavioral states associated with complex predatory traits.

animal behavior and cognition↗

bioRxiv2024

Ca2+-driven PDIA6 phase separation to ensure proinsulin quality control

The endoplasmic reticulum (ER) plays key roles in protein quality control1,2 and dynamic Ca2+ storage3,4 in eukaryotic cells. However, the protein homeostasis (proteostasis) system that regulates these ER functions is still incompletely characterised. Previous study revealed the importance of oligomerization in the function PDIA1, an ER-resident disulfide isomerase and molecular chaperone, regulates oligomeric states in accordance with client folding5. This result suggests that at least some of the 20 members of other PDI family may undergo regulated self-assembly in order to optimally function. Here, we show that Ca2+ triggers the phase separation of PDIA6 into liquid-like condensates. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the Ca2+-driven condensation of PDIA6 recruits PDIA3 and proinsulin, thus increasing their local concentrations. This process results in the 30-fold enhancement of proinsulin folding and in the inhibition of proinsulin aggregation. Our findings shed light on a condensation-driven Ca2+-mediated proteostasis cascade in the ER by revealing how the efficiency of the protein folding process can be enhanced within quality control granules.

biochemistry↗

bioRxiv2024

Conserved loop of a phase modifier endows protein condensates with fluidity

Dipeptide repeats (DPRs) that are gene products from abnormal hexanucleotide repeat expansion in C9orf72 trigger amyotrophic lateral sclerosis (ALS) through unknown mechanism. This study highlights, importin Karyopherin{beta}2 (Kap{beta}2), which is responsible for nuclear transport and phase modification of RNA-binding proteins (RBPs), as a major DPR target. We demonstrate DPR accumulation in the nucleus via Kap{beta}2-mediated transport, which results in dose-dependent toxicity observed in nematode and yeast models. In vitro interaction studies exploiting chemical probe arrays and biophysical measurements reveal multivalent DPR binding to Kap{beta}2, including at the conserved acidic loop. Refractive index and fluorescence imaging coupled with biochemical assays unveiled that binding of excess DPRs to the acidic loop turns a phase modifier Kap{beta}2 into phase disrupter, resulting more condensed and viscous RBP condensates. Our findings provides molecular insight into C9orf72-ALS related to age and repeat expansion.

biochemistry↗

bioRxiv2024

Glutamate, GABA, and dense-core vesicle secretion regulate predatory feeding in the nematode Pristionchus pacificus

Nematodes are one of the most diverse groups of organisms, found in various environments, and exhibit various feeding behaviours. Pristionchus pacificus displays two types of feeding behaviours: predatory and bacterial feeding. Previously, we showed that the neurotransmitter serotonin plays important roles in regulating predatory feeding in P. pacificus. However, the role of other neurotransmitters in predatory feeding remains unclear. Using the CRISPR/Cas9 system, we generated mutants of the dense-core vesicle (DCV)-based neuropeptide secretion system and genes related to seven neurotransmitters. Predatory assays revealed that the vesicular glutamate transporter Ppa-EAT-4, glutamic acid decarboxylase Ppa-UNC-25 which is involved in GABA synthesis, and the calcium-dependent activator protein for DCV secretion Ppa-UNC-31, play roles in predatory feeding behaviour. We assessed the pharyngeal movement necessary for predation as well as locomotion rate in these mutants. While the Ppa-eat-4 and Ppa-unc-31 mutants decreased predation movement, the Ppa-unc-25 mutant showed a reduction only in bacterial events compared to wild type animals. Additionally, Ppa-unc-25 and Ppa-unc-31 decreased in motor movement, potentially reducing predation efficiency. Together, these results suggest that glutamate, GABA and DCV secretion modulate feeding behaviours in P. pacificus. Our mutant collection of neurotransmitter-related genes will be useful for future analysis of neurobiology and behavioural evolution.

animal behavior and cognition↗

bioRxiv2024

cGMP-dependent pathway and a GPCR kinase are required for photoresponse in the nematode Pristionchus pacificus

Light sensing is a critical function in most organisms and is mediated by photoreceptor proteins and phototransduction. Although most nematodes lack eyes, some species exhibit phototaxis. In the nematode Caenorhabditis elegans, the unique photoreceptor protein Cel-LITE-1, its downstream G proteins, and cyclic GMP (cGMP)-dependent pathways are required for phototransduction. However, the mechanism of light-sensing in other nematodes remains unknown. To address this question, we used the nematode Pristionchus pacificus, which was established as a satellite model organism for comparison with C. elegans. Similar to C. elegans, illumination with short-wavelength light induces avoidance behavior in P. pacificus. Opsin, cryptochrome/photolyase, and lite-1 were not detected in the P. pacificus genome using orthology and domain prediction-based analyses. To identify the genes related to phototransduction in P. pacificus, we conducted forward genetic screening for light-avoidance behavior and isolated four light-unresponsive mutants. Whole-genome sequencing and genetic mapping revealed that the cGMP-dependent pathway and Ppa-grk-2, which encodes a G protein-coupled receptor kinase (GRK) are required for light avoidance. Although the cGMP-dependent pathway is conserved in C. elegans phototransduction, GRK is not necessary for light avoidance in C. elegans. This suggests similarities and differences in light-sensing mechanisms between the two species. Using a reverse genetics approach, we showed that GABA and glutamate were involved in light avoidance. Through reporter analysis and suppression of synapse transmission, we identified candidate photosensory neurons. These findings advance our understanding of the diversity of phototransduction in nematodes even in the absence of eyes. Author summaryNematodes are a highly diverse group of animals found in a wide variety of habitats and sensory systems. In particular, light-induced behavior has been found to differ among species. The photoreceptor and its downstream pathways in Caenorhabditis elegans have been identified, revealing unique and distinct characteristics compared to those in other animals. However, the mechanisms of photoreception in other nematodes remain largely unknown. This study focused on the analysis of the photoreception mechanisms in Pristionchus pacificus, a species for which many genetic and molecular tools are available. Similar to C. elegans, P. pacificus also exhibits light avoidance behavior towards short-wavelength light; however, known animal photoreceptor genes could not be identified in the P. pacificus genome using bioinformatic approaches. Using forward and reverse genetic approaches, we found that certain genes and neurons are required for light avoidance, some of which are conserved in C. elegans photoreception. These results suggest that the light-sensing mechanisms of C. elegans and P. pacificus are similar, yet there are differences between the two species. These findings highlight the various light-sensing mechanisms in nematodes.

genetics↗

bioRxiv2024

Antifungal potency of terbinafine as a therapeutic agent against Exophiala dermatitidis in vitro

SynopsisO_ST_ABSBackgroundC_ST_ABSExophiala dermatitidis (E. dermatitidis), which causes skin infections or respiratory diseases, is occasionally fatal in immunocompromised patients. ObjectivesHere, we report the unique antifungal potency of terbinafine (TRB), which targets squalene epoxidase, against E. dermatitidis (SQLEED) using various in vitro approaches. MethodsBased on the human SQLE crystal structure, we created a structure model of SQLEED using SWISS-MODEL and determined the best-fitting model of TRB to the SQLEED. The versatile antifungal activities, including fungicidal activity, biofilm inhibition, biofilm eradication activity, and the combination effect of TRB, posaconazole (PSC), and amphotericin B (AmB) with great antifungal potency against E. dermatitidis were evaluated using crystal violet and cell viability assay. ResultsClinically isolated E. dermatitidis increased most vigorously at 30{degrees}C but decreased at 40{degrees}C. E. dermatitidis hyphae elongated and attached to a cell scaffold, forming a membrane-like biofilm that was distinct from the cell-free biofilm. In the binding model, TRB formed an H-bond with Y102 and was surrounded by key amino acid residues of SQLEED corresponding to TRB-resistant mutations in Trichophyton rubrum, showing an appropriate interaction. Among TRB, PSC, and AmB with potent antifungal activities, TRB and PSC showed more potent antibiofilm activities than AmB. In addition, TRB and PSC exhibited residual potency without incubation against E. dermatitidis, decreasing the growth at lower concentrations than AmB. In contrast, AmB exhibited strong time-dependent killing and eradication activities. The combination of TRB and PSC was more effective than that of TRB and AmB or PSC and AmB in vitro. ConclusionsAlthough the tissue migration of TRB must be considered, these data suggest that TRB and PSC may be useful agents and a potent combination in severely immunocompromised patients with refractory and systemic E. dermatitidis infection.

microbiology↗