Biology subjects

Kimata, Y.

Publications and source records attributed to Kimata, Y..

13 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

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

Mitotic CDK4/6 activity sustains spindle checkpoint signalling to prevent mitotic slippage and genomic instability

The precise regulation of cell cycle entry and the maintenance of genome integrity are crucial for preventing tumorigenesis. Cyclin-dependent kinases 4 and 6 (CDK4/6) play pivotal roles in linking mitogenic signals to G1-S phase progression1-3, and their frequent deregulation in various cancers underscores their importance in driving cell proliferation and as therapeutic targets4,5. Despite this, the roles of CDK4/6 beyond the G1/S transition remain underexplored. Here, we uncover a previously unrecognised function of CDK4/6 in mitotic progression through regulation of the spindle assembly checkpoint (SAC)6. Using both cancer and non-transformed human cells, we show that acute CDK4/6 inhibition after G1/S transition leads to premature mitotic exit despite unattached kinetochores, resulting in chromosome missegregation and aneuploidy. Phosphoproteomic analyses and in vitro kinase assays reveal that CDK4 phosphorylates multiple sites on key SAC regulators, including the C-terminal tail of CENP-E, which is critical for BubR1 recruitment to kinetochores and SAC maintenance7,8. CDK4/6 inhibition reduces the phosphorylation of SAC components, attenuating checkpoint signalling and accelerating mitotic slippage. Notably, residual SAC activity persists, suggesting that CDK4/6 strengthens or stabilises SAC signalling rather than being essential for its activation. Thus, CDK4/6 functions extend beyond G1/S control to ensure mitotic fidelity, linking proliferating signals to genome stability and exposing potential vulnerabilities to anti-mitotic therapies in cancer.

cell biology↗

bioRxiv2025

Medium-chain fatty acids mitigate endoplasmic reticulum stress in yeast cells

Upon endoplasmic reticulum (ER) stress, eukaryotic cells commonly trigger cytoprotective transcriptome changes, namely the unfolded protein response (UPR). In yeast Saccharomyces cerevisiae, the UPR is mediated by the transcription factor Hac1, which is induced in response to ER stress. Since Hac1 controls hundreds of genes, the biological phenomena that result from UPR are not yet fully understood. Here, we show that cells carrying a mutation to constitutively express Hac1 abundantly contained C10:0 and C12:0 fatty acids, known as medium-chain fatty acids (MCFs). UPR induction by some ER stress stimuli was attenuated by externally supplied MCFs in cells in which fatty acid elongation was genetically or pharmacologically halted. The cell survival assay also indicated the mitigation of ER stress by the MCFs. Moreover, we demonstrated that MCFs leads to the diffusion of a mutant transmembrane protein aggregated in the ER. We propose that, as a biologically beneficial outcome of UPR, MCFs are produced to change the properties of the ER membrane, such as fluidity, in ER-stressed yeast cells.

molecular biology↗

bioRxiv2025

Title: KymoTip: High-throughput Characterization of Tip-growth Dynamics in Plant Cells

Live imaging data analysis often requires an objective, local, and accurate way of quantification of cell dynamics. In the research field of polarized tip-growth, the cell fluctuations and/or fluctuations in tip position and growth direction hampers automated analyses of huge amounts of imaging sequences. The fluctuated nature in data makes it unclear how cell shape and growth are linked to intracellular events that could be the actual driving force of cell growth. To overcome these difficulties, we developed a powerful and user-friendly tool called KymoTip with an available format. In this software, novel functions such as coordinate normalization, tip-bottom detection, and signal kymograph were implemented. We confirmed that not only plasma membrane-labeled fluorescent images, but also images such as bright-field and cortical microtubule markers --so long as the cell contours can be identified-- are amenable to KymoTip. Furthermore, by combining markers for cell contours with those that visualize intracellular structures, it becomes possible to quantitatively analyze various intracellular events, such as nuclear migration and calcium wave, in conjunction with cellular growth dynamics. Since KymoTip can be handled by non-specialist, it is expected to promote understanding of what happens at the sub- and cellular level with high throughput outcomes. Significance statementFaced with fluctuations in cell coordinates and cell tip positions, position correction of live imaging data and accurate detection of tip position are key challenges in plant developmental biology. We solved them with a powerful and user-friendly tool, KymoTip, that can realize cell position correction, cell tip detection with cell centerline, and quantification of intracellular events.

bioinformatics↗

bioRxiv2025

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

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

plant biology↗

bioRxiv2025

Krüppel Regulates Cell Cycle Exit and Limits Adult Neurogenesis of Mushroom Body Neural Progenitors in Drosophila

In many organisms, including Drosophila and humans, neural progenitors exit the cell cycle and are eliminated by the end of development, thereby restricting adult neurogenesis to specific brain regions. Here, we identify the evolutionarily conserved transcription factor Kruppel (Kr) as a lineage-specific regulator of cell cycle exit and elimination of mushroom body neuroblasts (MBNBs), which generate the learning and memory centre of the Drosophila brain, a structure functionally analogous to the mammalian hippocampus. Neuroblast-specific Kr RNAi and the Irregular facet (KrIf-1) mutation prolong MBNB lifespan, enabling continued neurogenesis in the adult brain. Although Kr is expressed only at low levels in postembryonic MBNBs, its pupal stage-specific depletion or misexpression is sufficient to cause MBNB retention, revealing a previously unrecognised postembryonic function distinct from its established role in embryonic neurogenesis. Mechanistically, persistent MBNBs maintain expression of the early temporal factor IGF2 mRNA-binding protein (Imp) and fail to fully induce the late temporal factors Syncrip (Syp) and Eip93F (E93). Co-depletion of Imp suppresses MBNB retention caused by Kr depletion, demonstrating that Imp is a key downstream effector of Kr. In parallel, Kruppel homolog 1 (Kr-h1), another Kr family transcription factor and a well-established mediator of hormone-responsive transcription, functionally antagonises Kr by suppressing E93 expression: Kr-h1 knockdown partially rescues the Kr depletion phenotype, whereas Kr-h1 overexpression drives tumour-like neuroblast overgrowth. Together, our findings establish Kr as an MBNB-specific coordinator that integrates intrinsic temporal programmes with extrinsic signalling pathways to coordinate neural stem cell termination and neuronal fate transitions, with potential parallels in other organisms.

developmental biology↗

bioRxiv2024

The Conserved Transcription Factor Kruppel Regulates the Survival and Neurogenesis ofMushroom Body Neuroblasts in Drosophila Adult Brains

In various metazoans, including Drosophila and humans, neural progenitors exit the cell cycle and are eliminated by the end of development, limiting adult neurogenesis. We demonstrate that in Drosophila, the conserved transcription factor Kruppel (Kr) controls neurogenic capacity of a specific subset of neuroblasts that forms the mushroom body (MBNBs), analogous to the mammalian hippocampus. The Irregular facet mutation, which alters Kr expression, and neuroblast-specific Kr depletion allow MBNBs, but not other neuroblasts, to persist beyond development and generate neurons in adult brains. Persisting MBNBs express Imp, an RNA-binding protein that promotes neuroblast proliferation and survival. Our results underscore a critical role for Kr in the developmental control of a specific progenitor population, uncovering a novel mechanism controlling adult neurogenesis.

developmental biology↗

bioRxiv2024

Brassinosteroids function as the plant male and female reproductive hormone coordinating gene expression.

Brassinosteroids (BRs) are steroid hormones identified in plants. Besides promoting cell elongation and division, BRs facilitate the development of both male and female reproductive tissues. In animals, reproductive steroid hormones play an essential role in reproductive tissue development by regulating gene expression. Here, we focused on the function of BRs during fertilization. We measured the content of biologically active BRs, brassinolide (BL) and castasterone (CS), in the reproductive tissues of Arabidopsis thaliana. Both BL and CS accumulated abundantly in pollen grains and in larger amounts in pistils than in leaves. To evaluate BL function during fertilization, we used an in vitro guidance assay with exogenously applied BL. Although pollen tubes need to be elongated through the pistils for efficient capacitation, BL treatment promoted pollen tube capacitation and improved attraction to ovules in vitro. Transcriptome analysis demonstrated that BL treatment induced the expression of half of the genes expressed in pollen tubes that elongated through the pistils. These results indicated that BL supplied from pistils is a key factor for pollen tube capacitation. However, using the bri1 mutant for the guidance assay resulted in reduced pollen tube capacitation, suggesting that BRI1-signaling in pistils is also important. Furthermore, BRs act on ovules. Exogenous BL application to ovules maintained guidance capacity by promoting the expression of small secreted proteins involved in pollen tube attraction and gamete fusion. Overall, BRs play a significant role as male and female reproductive hormones throughout the plant fertilization process.

plant biology↗

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↗

bioRxiv2022

Chemical screen of Arabidopsis zygote and proteomics in tobacco BY-2 cells identify general plant cell division inhibitors

Cell division is essential for growth and development and involves events such as spindle assembly, chromosome separation, and cell plate formation. In plants, the tools used to control these events at the desired time are still poor because the genetic approach is ineffective owing to a high redundancy and lethality, as well as harmful side effects. Accordingly, we screened cell division-affecting compounds, with a focus on Arabidopsis thaliana zygotes, which individually develop in maternal ovules; the cell division was reliably traceable without time-lapse observations. We then identified the target events of the identified compounds using tobacco BY-2 cells for live-cell imaging and proteomics. As a result, we isolated two compounds, PD-180970 and PP2. PD-180970 disrupts microtubule (MT) organization and, thus, nuclear separation, presumably by inhibiting MT-associated proteins (MAP70). PP2 affected class II Kinesin-12 localization at the phragmoplast emerging site and impaired cytokinesis. Moreover, neither chemical caused irreversible damage to viability but they were effective in multiple plant species such as cucumber (Cucumis sativus) and moss (Physcomitrium patens). We propose that the combination of chemical screening based on Arabidopsis zygotes and target event specification focusing on tobacco BY-2 cells can be used to effectively identify novel tools and transiently control specific cell division events that are conserved in diverse plant species.

plant biology↗

bioRxiv2017

Proteolytic control of centrosome activity by APC/C-Polo maintains oocyte fate in Drosophila

A universal feature of metazoan reproduction is the elimination of the maternal centrosomes prior to the end of oogenesis. In animals that have a syncytial cyst stage of oocyte development, including Drosophila and mouse, the germline centrosomes undergo a migration to all reside within the oocyte. However, the functional significance of centrosome transport within the female germline and the mechanism orchestrating this event are still a mystery. The Anaphase Promoting Complex/Cyclosome (APC/C) is a multi-subunit ubiquitin ligase (E3) that temporally regulates progression of the cell cycle as well as the centrosome cycle. By altering the negative regulation of the cooperating ubiquitin conjugating enzyme (E2), Vihar/Ube2c, we show that temporal control of APC/C activity ensures centrosome stability and migration during early Drosophila oogenesis. When there is perduring APC/C activity, Polo kinase is precociously targeted for destruction, which results in centriole instability and decreased centrosome transport to the oocyte. We show that decreased centrosome transport correlates with a decreased accumulation of pericentriolar material (PCM) proteins on the oocyte nucleus, which results in a weakening of the structural integrity of the egg chamber and loss of oocyte fate - the overall consequence being a reduction in female fertility. Considering the conserved roles of the APC/C and Polo kinase throughout the animal kingdom and the fact that many animals have a syncytial stage of egg development, our results provide insight into the general necessity of gametic centrosome transport for female fertility.

developmental biology↗