Biology subjects

Matsumoto, H.

Publications and source records attributed to Matsumoto, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Apical3DTip: Elliptic Cross-section-based Reconstruction for the Embryo Initial Cell of Arabidopsis

BackgroundCell geometry plays a central role in determining division orientation and body axis formation during early embryogenesis in Arabidopsis thaliana. However, quantitative analysis of dynamic three-dimensional (3D) morphology remains challenging because live-imaging studies often rely on two-dimensional (2D) projections, while existing 3D reconstruction approaches, including mesh-based methods, often lose the original orientation information relative to the ovule and require labor-intensive mesh correction. In addition, embryo positional fluctuation caused by floating in liquid medium and continuous growth makes it difficult to analyze temporal morphological changes within a common coordinate system. ResultsWe developed a robust framework for quantitative 3D and four-dimensional (4D; 3D + time) analysis of embryo initial cell (apical cell) morphology. The method first establishes a standardized 3D coordinate system by normalizing cell orientation based on the bottom plane and the optical axis of the observation. Cell morphology is then reconstructed through ellipse-based approximation of serial cross-sections extracted from stacked imaging data, enabling accurate geometric characterization without the need for complex surface mesh reconstruction. To evaluate shape anisotropy, we quantified the apical cell shape in 3D. The framework further supports the characterization of volumetric features of subsequent division, providing a basis for quantifying 3D embryogenesis. ConclusionOur framework provides a simple and noise-reduced approach for quantitative analysis of living cell morphology in 3D. We named the integrated method of combining coordinate normalization with elliptical cross-section-based reconstruction Apical3DTip. This method enables consistent comparison of cell shapes without extensive manual corrections. The method overcomes key limitations of 2D projection-based and mesh-dependent analyses and offers a practical platform for quantifying cell shape and daughter cell shapes in 3D. More broadly, it provides a quantitative foundation for exploring the relationship between cell geometry, morphodynamics, and developmental patterning in living plant embryos.

plant biology↗

bioRxiv2026

Ca2+ oscillations promote microtubule-band turnover and support tip growth in Arabidopsis zygotes

The zygote is the origin of development, and in most angiosperms, it divides asymmetrically to establish the apical-basal axis. In Arabidopsis thaliana, the zygote undergoes tip growth-like polar elongation, using a subapical transverse microtubule band (MT band). Because canonical tip-growing cells rely on longitudinal actin filaments (F-actin), it remains unclear whether and how the zygote employs conserved tip-growth mechanisms. Here, using quantitative live-cell imaging, pharmacological perturbations, and mechanical simulations, we found that oscillatory Ca{superscript 2} waves, a hallmark of tip growth, are coupled to zygote elongation through a bidirectional feedback loop, as in other tip-growing cells. However, Ca{superscript 2} waves were dispensable for overall F-actin alignment but promoted MT band turnover. Our study provides a model showing that the zygote uses a conserved tip-growth module, in which Ca{superscript 2} oscillations and cell elongation reinforce each other, but redirects the target cytoskeleton to the MT band, enabling zygote-specific tip growth for axis formation.

plant biology↗

bioRxiv2026

Distinct Repeat Architecture Landscapes in the Proteomes of Protozoan Parasites

Protozoan parasites cause major infectious diseases and pose persistent challenges to global health, particularly the emergence of drug-resistant strains. Tandem repeats (TRs) and other repetitive architectures are widespread in proteomes, especially in protozoan proteins, where they have been implicated in host-parasite interactions, immune evasion, and antigenicity. However, repeat-containing proteins (RPs) exhibit highly diverse architectures that often extend beyond the simple reiteration of a single motif, making comprehensive and quantitative characterization challenging. In this study, we performed bioinformatics analysis of repeat architectures in protozoan proteins. In addition to the established repeat-detection approaches, we developed a new algorithm, Drepper, which quantifies repeat-architecture complexity. By integrating diverse repeat-related features, we clustered RPs across species and identified distinct groups associated with parasite lineages. Notably, we detected a Plasmodium-specific RP cluster and a Trypanosoma/Leishmania-specific RP cluster; both were characterized by large repeat regions but exhibited contrasting repeat-structure complexity. The Plasmodium-specific RPs showed high complexity, whereas the Trypanosoma/Leishmania-specific RPs displayed significantly low complexity. Functional enrichment analyses indicated that these lineage-associated clusters were enriched in parasite-specific factors. Furthermore, evolutionary analyses suggested that low-complexity repeat architectures may be actively maintained through concerted evolution. Taken together, our results reveal lineage-specific strategies in protozoan repeat architectures and provide a quantitative framework for studying their biological and evolutionary roles.

bioinformatics↗

bioRxiv2026

Capturing self-renewing multipotent neural crest stem cells from human pluripotent stem cells

During embryonic development, neural crest cells (NCCs) represent a multipotent population characterized by an inherently transient nature, rapidly differentiating into various lineages. This instability has presented a fundamental challenge, as it is exceedingly difficult to maintain these cells in a stable, multipotent state in vitro. In this study, we report a robust culture system dependent on Wnt and FGF signaling that enables the long-term (>6 months) expansion of human iPSC-derived neural crest stem cells (NCSCs). These NCSCs retain their self-renewal and differentiation capacity, validated at the single-cell clonal level. ATAC-seq analysis indicated that posterior NCSCs maintain a more permissive chromatin structure at neuronal gene loci. Furthermore, ChIP-seq analysis revealed that the key transcription factor SOX10 binds to the regulatory regions of genes involved in both maintenance and differentiation. This system provides a stable source of human NCSCs, offering a valuable platform for developmental biology, disease modeling, and regenerative medicine.

developmental biology↗

bioRxiv2026

Two-step polar plastid migration via F-actin and microtubules ensures unequal inheritance during asymmetric division of Arabidopsis zygote

The zygote is the origin of development, and in most angiosperms, it divides asymmetrically to establish the apical-basal axis. In Arabidopsis thaliana, various organelles in the zygote undergo polar migration along actin filaments (F-actin), resulting in unequal inheritance, but the behavior of plastids, essential precursors of chloroplasts, has remained unclear. Here, using quantitative live-cell imaging, we reveal that plastids undergo two-step polar migration: they first move apically together with the nucleus along F-actin, and when nuclear migration slows, they switch to microtubule (MT)-dependent migration to move further apically. This results in unequal plastid inheritance by the apical cell. Although these plastids are amyloplasts containing starch granules, starch is dispensable for migration, unlike the gravity response. Instead, a fertilization-activated MAP kinase pathway is required for polar plastid migration. Our results demonstrate that the zygote possesses a spatiotemporal regulatory mechanism that ensures unequal plastid inheritance at the onset of plant ontogeny.

plant biology↗

bioRxiv2025

Promiscuous cytochrome P450s confer metabolic resistance to synthetic auxin herbicides in the weedy grass Echinochloa phyllopogon

Auxinic herbicides are critically important tools for weed control in modern agriculture. Although resistant weed populations have been increasing in recent years, the underlying mechanisms remain largely unknown. In a multiple-herbicide resistant line of the paddy weed Echinochloa phyllopogon, overexpression of catalytically promiscuous CYP81A P450 enzymes has been shown to confer resistance to diverse herbicides. Here, we investigated the role of these P450s in quinclorac resistance in E. phyllopogon. Arabidopsis thaliana plants expressing CYP81A12 and CYP81A21 genes, previously demonstrated to metabolize other herbicides, showed low but detectable levels of quinclorac resistance. A similar activity was also observed for CYP81A24, another promiscuous enzyme present in E. phyllopogon. Moreover, Escherichia coli strains expressing these genes produced putative hydroxylated metabolites of quinclorac. In silico analyses revealed that quinclorac binds stably near the catalytic heme center of CYP81A12, CYP81A21, and CYP81A24, but not CYP81A18, the importance of spatial alignment between the substrate recognition site and the heme center in determining metabolic activity and resistance potential. Consistent with the phenotype of resistant E. phyllopogon, A. thaliana expressing CYP81A12 and CYP81A21 produced significantly less ethylene following quinclorac treatment, linking P450-mediated metabolism to the suppression of quinclorac-induced phytotoxic responses. Finally, we demonstrated that CYP81A enzymes also confer resistance to other auxinic herbicides, florpyrauxifen-benzyl and 2,4-D. These findings provide new insights into the molecular basis of auxinic herbicide resistance and underscore the role of CYP81A P450s in metabolic detoxification and the prevention of herbicide-induced phytotoxic responses.

plant 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↗

bioRxiv2024

Stress-induced organismal death is genetically regulated by the mTOR-Zeste-Phae1 axis

All organisms are exposed to various stressors, which can sometimes lead to organismal death, depending on their intensity. While stress-induced organismal death has been observed in many species, the underlying mechanisms remain unclear. In this study, we investigated the molecular mechanisms of stress-induced organismal death in the fruit fly Drosophila melanogaster. We identified a chymotrypsin-like serine protease Phaedra1 (Phae1) as a death mediator in D. melanogaster larvae. Phae1 expression was upregulated by lethal heat stress (40 {degrees}C) but not non-lethal heat stress (38 {degrees}C or lower). The most prominent induction of Phae1 occurred in the central nervous system (CNS). We found neuro-specific knockdown of Phae1 increased survival and reduced neuronal caspase activity following exposure to lethal heat stress, suggesting that the transcriptional upregulation of Phae1 in the CNS is essential for stress-induced organismal death. We next found via bioinformatic and biochemical analyses that the transcription factor Zeste (Z) bound the Phae1 enhancer region and that z loss-of-function impaired Phae1 induction in the CNS, increasing survival following lethal heat stress. In addition, we found via chemical screening that rapamycin, a chemical inhibitor of mechanistic target of rapamycin (mTOR), suppressed Phae1 expression. Neuro-specific knockdown of mTor reduced the protein levels of both Phae1 and Z, leading to an increase in survival following lethal heat stress. Together, these results indicate that heat stress-induced organismal death in D. melanogaster larvae is regulated by a genetically encoded transcriptional signaling pathway involving the mTOR-Z-Phae1 axis.

physiology↗

bioRxiv2024

Agent-Based Simulation of Cortical Microtubule Band Movement in the Arabidopsis Zygote

Arabidopsis thaliana zygotes form a circumferential cortical microtubule (CMT) band that moves upward along the longitudinal axis of the cylindrical cell; however, how and why this CMT band moves remain unknown. Based on several recently proposed descriptive feedback mechanisms of CMT reorientation, we hypothesized that a directional cue (DC) changes CMT orientation. We constructed an agent-based simulation model with a DC to observe what happens during CMT formation using different parameters. We determined that the output CMT band can become larger than the input DC zone and identified two types of self-organization processes depending on the parameters used. Furthermore, using well-defined parameters that form a static CMT band, we artificially changed the position of the input DC zone, revealing that CMT band movement requires a DC to move at an appropriate speed.

plant biology↗

bioRxiv2024

Temporal changes in surface tension guide the accurate asymmetric division of Arabidopsis zygotes

In most plants, the zygote divides asymmetrically to define the body axis. In Arabidopsis thaliana, the zygote undergoes polar elongation maintaining a transverse band of cortical microtubules (MTs), and divides asymmetrically forming another MT band, preprophase band (PPB). How the MT band is maintained at the actively growing cell tip and whether it contributes to PPB formation remain elusive. By combining live-cell imaging and mechanical simulation, we show that zygote elongation induces a temporal change (large material derivative) in surface tension at the growing tip to maintain the MT band, which in turn supports polar elongation. The MT band then guides PPB to determine the cell division site. Therefore, autonomous mechanical feedback between cell elongation and MT organization ensures the zygote division asymmetry.

plant biology↗

bioRxiv2024

A viscoelastic-plastic deformation model of hemisphere-like tip growth in Arabidopsis zygotes

Plant zygote cells exhibit tip growth, producing a hemisphere-like tip. To understand how this hemisphere-like tip shape is formed, we revisited a viscoelastic-plastic deformation model that enabled us to simultaneously evaluate the shape, stress, and strain of Arabidopsis (Arabidopsis thaliana) zygote cells undergoing tip growth. Altering the spatial distribution of cell wall extensibility revealed that cosine-type distribution and growth in a normal direction to the surface creates a stable hemisphere-like tip shape. Assuming these as constraints for cell elongation, we determined the best-fitting parameters for turgor pressure and wall extensibility to computationally reconstruct an elongating zygote that retained its hemisphere-like shape using only cell contour data, leading to formulation of non-dimensional growth parameters. Our computational results demonstrate the different morphologies in elongating zygotes through effective non-dimensional parameters.

plant biology↗

bioRxiv2024

Deep learning-based cytoskeleton segmentation for accurate high-throughput measurement of cytoskeleton density

Microscopic analyses of cytoskeleton organization are crucial for understanding various cellular activities, including cell proliferation and environmental responses in plants. Traditionally, assessments of cytoskeleton dynamics have been qualitative, relying on microscopy-assisted visual inspection. However, the transition to quantitative digital microscopy has introduced new technical challenges, with segmentation of cytoskeleton structures proving particularly demanding. In this study, we examined the utility of a deep learning-based segmentation method for accurate quantitative evaluation of cytoskeleton organization using confocal microscopic images of the cortical microtubules in tobacco BY-2 cells. The results showed that, although conventional methods sufficed for measurement of cytoskeleton angles and parallelness, the deep learning-based method significantly improved the accuracy of density measurements. To assess the versatility of the method, we extended our analysis to physiologically significant models in the context of changes in cytoskeleton density, namely Arabidopsis thaliana guard cells and zygotes. The deep learning-based method successfully improved the accuracy of cytoskeleton density measurements for quantitative evaluations of physiological changes in both stomatal movement in guard cells and intracellular polarization in elongating zygotes, confirming its utility in these applications. The results demonstrate the effectiveness of deep learning-based segmentation in providing precise and high-throughput measurements of cytoskeleton density, and has the potential to automate and expedite analyses of large-scale image datasets.

cell biology↗

bioRxiv2024

Investigating EMT-mediated resistance to EGFR tyrosine kinase inhibitors in NSCLC using innovative organoid models

BackgroundEpithelial-mesenchymal transition (EMT) has emerged as a key mechanism underlying resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in EGFR-mutant non-small cell lung cancer (NSCLC). However, the intricacies of EMT-mediated resistance, driven by tumor microenvironment (TME) interactions, remain enigmatic. This study aimed to probe EMT-induced resistance in NSCLC using innovative in vitro organoid models. MethodsWe generated organoids by co-culturing EGFR-mutant NSCLC cells (HCC827, H1975), mesenchymal stem cells and endothelial cells. Drug susceptibility was compared between organoids and spheroids (cancer cells only) using EGFR TKIs - Gefitinib, Afatinib, Osimertinib. EMT marker (E-cadherin, ZEB1) expression was analyzed via immunofluorescence and western blotting. The effects of Bevacizumab and miR200c on overcoming resistance were also investigated. ResultsThe study identified a significant link between EMT and EGFR-TKI resistance. Notable findings included the decrease of E-cadherin and an increase in ZEB1, both of which influenced EMT and resistance to treatment. Bevacizumab showed promise in improving drug resistance and mitigating EMT, suggesting an involvement of the VEGF cascade. Transfection with miR200c was associated with improved EMT and drug resistance, further highlighting the role of EMT in TKI resistance. ConclusionsThis study offered vital insights into EMT-driven EGFR TKI resistance, highlighting the utility of organoid models in evaluating resistance modulated by TME interactions. Our findings reveal promising directions for overcoming EMT-mediated resistance involving Bevacizumab and miR200c, warranting further in vivo validation.

cancer biology↗

bioRxiv2023

Low blood concentration of alcohol enhances activity related to stopping failure in the right inferior frontal cortex

This study investigated the effects of low doses of alcohol, which are acceptable for driving a car, on inhibitory control and neural processing using the stop-signal task (SST) in 17 healthy right-handed social drinkers. The study employed simultaneous functional magnetic resonance imaging and electromyography (EMG) recordings to assess behavioural and neural responses under conditions of low-dose alcohol (breath-alcohol concentration of 0.15 mg/L) and placebo. The results demonstrated that even a small amount of alcohol consumption prolonged Go reaction times in the SST and modified stopping behaviour, as evidenced by a decrease in the frequency and magnitude of partial response EMG that did not result in button pressing during successful inhibitory control. Furthermore, alcohol intake enhanced neural activity during failed inhibitory responses in the right inferior frontal cortex, suggesting its potential role in behavioural adaptation following stop-signal failure. These findings suggest that even low levels of alcohol consumption within legal driving limits can greatly impact both the cognitive performance and brain activity involved in inhibiting responses. This research provides important evidence on the neurobehavioural effects of low-dose alcohol consumption, with implications for understanding the biological basis of impaired motor control and decision-making and potentially informing legal guidelines on alcohol consumption.

neuroscience↗

bioRxiv2023

Comprehensive and quantitative analysis of intracellular structure polarization at the apical-basal axis in elongating Arabidopsis zygotes

A comprehensive and quantitative evaluation of multiple intracellular structures or proteins is a promising approach to provide a deeper understanding of and new insights into cellular polarity. In this study, we developed an image analysis pipeline to obtain intensity profiles of fluorescent probes along the apical-basal axis in elongating Arabidopsis thaliana zygotes based on two-photon live-cell imaging data. This technique showed the intracellular distribution of actin filaments, mitochondria, microtubules, and vacuolar membranes along the apical-basal axis in elongating zygotes from the onset of cell elongation to just before asymmetric cell division. Hierarchical cluster analysis of the quantitative data on intracellular distribution revealed that the zygote may be compartmentalized into two parts, with a boundary located 43.6% from the cell tip, immediately after fertilization. To explore the biological significance of this compartmentalization, we examined the positions of the asymmetric cell divisions from the dataset used in this distribution analysis. We found that the cell division plane was reproducibly inserted 20.5% from the cell tip. This position corresponded well with the midpoint of the compartmentalized apical region, suggesting a potential relationship between the zygote compartmentalization, which begins with cell elongation, and the position of the asymmetric cell division.

cell biology↗

bioRxiv2023

Classification of patients with COVID-19 by blood RNA endotype: A prospective cohort study

BackgroundAlthough the development of vaccines has considerably reduced the severity of COVID-19, its incidence is still high. Hence, a targeted approach based on RNA endotypes of a population should be developed to help design biomarker-based therapies for COVID-19. ObjectivesWe evaluated the major RNAs transcribed in blood cells during COVID-19 using PCR to further elucidate its pathogenesis and determine predictive phenotypes in COVID-19 patients. Study designIn a discovery cohort of 40 patients with COVID-19, 26,354 RNAs were measured on day 1 and day 7. Five RNAs associated with disease severity and prognosis were derived. In a validation cohort of 153 patients with COVID-19 treated in the intensive care unit, we focused on prolactin (PRL), and toll-like receptor 3 (TLR3) among RNAs, which have a strong association with prognosis, and evaluated the accuracy for predicting survival of PRL-to-TL3 ratios (PRL/TLR3) with the areas under the ROC curves (AUC). The validation cohort was divided into two groups based on the cut-off value in the ROC curve with the maximum AUC. The two groups were defined by high PRL/TLR3 (n=47) and low PRL/TLR3 groups (n=106) and the clinical outcomes were compared. ResultsIn the validation cohort, the AUC for PRL/TLR3 was 0.79, showing superior prognostic ability compared to severity scores such as APACHE II and SOFA. The high PRL/TLR3 group had a significantly higher 28-day mortality than the low PRL/TLR3 group (17.0% vs 0.9%, P<0.01). ConclusionsA new RNA endotype classified using high PRL/TLR3 was associated with mortality in COVID-19 patients.

genetics↗

bioRxiv2022

A novel micro-ECoG recording method for recording multisensory neural activity from the parietal to temporal cortexes in mice

Characterization of inter-regional interactions in brain is essential for understanding the mechanism relevant to normal brain function and neurological disease. The recently developed flexible micro ()-electrocorticography (ECoG) device is one prominent method used to examine large-scale cortical activity across multiple regions. The sheet-shaped ECoG electrodes arrays can be placed on a relatively wide area of cortical surface beneath the skull by inserting the device into the space between skull and brain. Although rats and mice are useful tools for neuroscience, current ECoG recording methods in these animals are limited to the parietal region of cerebral cortex. Recording cortical activity from the temporal region of cortex in mice has proven difficult because of surgical barriers created by the skull and surrounding temporalis muscle anatomy. Here, we developed a sheet-shaped 64-channel ECoG device that allows access to the mouse temporal cortex, and we determined the factor determining the appropriate bending stiffness for the ECoG electrode array. We also established a surgical technique to implant the electrode arrays into the epidural space over a wide area of cerebral cortex covering from the barrel field to olfactory (piriform) cortex, which is the deepest region of the cerebral cortex. Using histology and computed tomography (CT) images, we confirmed that the tip of the ECoG device reached to the most ventral part of cerebral cortex without causing noticeable damage to the brain surface. Moreover, the device simultaneously recorded somatosensory and odor stimulus-evoked neural activity from dorsal and ventral parts of cerebral cortex in awake and anesthetized mice. These data indicate that our ECoG device and surgical techniques enable the recording of large-scale cortical activity from the parietal to temporal cortex in mice, including somatosensory and olfactory cortices. This system will provide more opportunities for the investigation of physiological functions from wider areas of the mouse cerebral cortex than those currently available with existing ECoG techniques.

neuroscience↗

bioRxiv2022

Subjective Audibility Modulates the Susceptibility to Sound-Induced Flash Illusion

When a brief flash is presented along with two brief sounds, the single flash is often perceived as two flashes. This phenomenon is called a sound-induced flash illusion, in which the auditory sense, with its relatively higher reliability in providing temporal information, modifies the visual perception. Decline of audibility due to hearing impairment is known to make subjects less susceptible to the flash illusion. However, the effect of decline of audibility on susceptibility to the illusion has not been directly investigated in subjects with normal hearing. The present study investigates the relationship between audibility and susceptibility to the illusion by varying the sound pressure level of the stimulus. In the task for reporting the number of auditory stimuli, the lowering of the sound pressure level caused the rate of perceiving two sounds to decrease on account of forward masking. The occurrence of the illusory flash was reduced as the intensity of the second auditory stimuli decreased, and was significantly correlated with the rate of perceiving the two auditory stimuli. These results suggest that the susceptibility to sound-induced flash illusion depends on the subjective audibility of each sound.

animal behavior and cognition↗