Biology subjects

Kawamura, S.

Publications and source records attributed to Kawamura, S..

14 recordsLinked to original sources

bioRxiv2026

Midbody inheritance predicts re-entry into quiescence, but not lineage potential, in mouse hematopoietic stem cells

Hematopoietic stem cells (HSCs) give rise to all blood cell lineages and possess long-term self-renewal potential. HSCs undergo symmetric division for their expansion and asymmetric division to generate one HSCs and one progenitor cells which contribute to production of mature blood cells. The midbody is a structure which is formed in the center of the intercellular bridge during cytokinesis. However, the midbody is either asymmetrically inherited by one daughter cell or symmetrically released after cell division, whether these distinct patterns of midbody inheritance influence HSC fate remain poorly understood. In this study, we designed a fusion protein hmKO2 and MgcRacGAP which is a component of midbody. We then traced the midbody inheritance during cell division and the future cell fates of HSC daughters after division by time-lapse imaging. As a result, we found that the midbody release correlated with the delay of the time to the next division but not to the lineage potential of HSCs, indicating the possibility that midbody remnant plays some roles in cell cycle progression. HighlightHematopoietic stem cells exhibit a low frequency of midbody inheritance. Midbody inheritance does not affect the lineage potential of daughter cells. Midbody loss is associated with delayed entry into the next cell cycle.

cell biology↗

bioRxiv2026

Impact of Cow Parity on the Accuracy of Near-Infrared Spectroscopy for Sustainable Milk Quality Monitoring during Milking

Accurate real-time monitoring of milk quality during milking is essential for sustainable dairy farming, yet factors such as cow parity may affect the performance of near-infrared (NIR) spectroscopic sensing systems. This study investigated how cow parity (the number of calvings) impacts the reliability and accuracy of NIR spectroscopy in assessing key milk quality indicators: fat content, lactose, and somatic cell count (SCC). Experiments were conducted at Hokkaido University with two cows in their second parity. Milk spectra were recorded across 700-1050 nm using the NIR system, while fat and lactose were measured with a MilkoScan device and SCC with a Fossomatic device. Calibration models were developed using first parity, second parity, and combined datasets through partial least squares regression. Model performance was evaluated via coefficients of determination and standard errors of prediction. Results showed comparable accuracy for milk fat and SCC across parities, whereas lactose measurements were more affected. Cross-validation between first and second parity datasets further confirmed parity-dependent variations, particularly for lactose. These findings suggest that cow parity should be considered when implementing NIR-based milk quality monitoring, supporting more precise, resource-efficient, and sustainable dairy management practices.

bioengineering↗

bioRxiv2025

A SABATH family enzyme regulates development via the gibberellin-related pathway in the liverwort Marchantia polymorpha

The SABATH family enzymes are a group of plant-specific methyltransferases that catalyze the methylation of many small molecules, including several plant hormones. While this family emerged anciently before the evolution of land plants from streptophyte algae, little is known about their biological function in plant lineages other than angiosperms. Here, we identified 12 SABATH family genes from the liverwort Marchantia polymorpha and found that MpSABATH2 is essential for its development. Mpsabath2 mutants were severely inhibited in thallus growth and gemma cup formation, while spontaneously forming sexual branches under non-inductive conditions. These phenotypes resembled the developmental responses to far-red light, which was also supported by transcriptome analysis. Further genetic analysis connected this phenomenon with gibberellin (GA)-related metabolism. Blocking GA biosynthesis partially rescued Mpsabath2 phenotypes, which were restored by treatment with the GA precursor, ent-kaurenoic acid. Given that bryophyte and angiosperm SABATH proteins fall into distinct phylogenetic clades, our findings suggest that SABATH family enzymes independently acquired roles in developmental regulation through convergent or parallel evolution in land plants.

plant biology↗

bioRxiv2025

MarpolBase: Genome database for Marchantia polymorpha featuring high quality reference genome sequences

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution--especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases.

genomics↗

bioRxiv2024

Self-Organization of Sinusoidal Vessels in Pluripotent Stem Cell-derived Human Liver Bud Organoids

The induction of tissue-specific vessels in in vitro living tissue systems remains challenging. Here, we directly differentiated human pluripotent stem cells into CD32b+ putative liver sinusoidal progenitors (iLSEP) by dictating developmental pathways. By devising an inverted multilayered air-liquid interface (IMALI) culture, hepatic endoderm, septum mesenchyme, arterial and sinusoidal quadruple progenitors self-organized to generate and sustain hepatocyte-like cells neighbored by divergent endothelial subsets composed of CD32blowCD31high, LYVE1+STAB1+CD32bhighCD31lowTHBD-vWF-, and LYVE1-THBD+vWF+ cells. Wnt2 mediated sinusoidal-to-hepatic intercellular crosstalk potentiates hepatocyte differentiation and branched endothelial network formation. Intravital imaging revealed iLSEP developed fully patent human vessels with functional sinusoid-like features. Organoid-derived hepatocyte- and sinusoid-derived coagulation factors enabled correction of in vitro clotting time with Factor V, VIII, IX, and XI deficient patients plasma and rescued the severe bleeding phenotype in hemophilia A mice upon transplantation. Advanced organoid vascularization technology allows for interrogating key insights governing organ-specific vessel development, paving the way for coagulation disorder therapeutics.

developmental biology↗

bioRxiv2023

Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity

Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unknown mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48 induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 showed a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice developed autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.

cell biology↗

bioRxiv2023

Influence of colour vision on attention to, and impression of, complex aesthetic images

Humans exhibit colour vision variations due to genetic polymorphisms, with trichromacy being the most common, while some people are classified as dichromats. Whether genetic differences in colour vision affect the way of viewing complex images remains unknown. Here, we investigated how people with different colour vision focused their gaze on aesthetic paintings by eye-tracking while freely viewing digital rendering of paintings and assessed individual impressions through a decomposition analysis of adjective ratings for the images. Gaze concentrated areas among trichromats were more highly correlated than those among dichromats. However, compared to the brief dichromatic experience with the simulated images, there was little effect of innate colour vision differences. These results indicate that chromatic information is instructive as a cue for guiding attention, whereas the impression of each person is unaffected by colour-vision genetics and would be normalised to their own sensory experience through ones own colour space.

neuroscience↗

bioRxiv2023

Harnessing deep learning to analyze cryptic morphological variability of Marchantia polymorpha

Characterizing phenotypes is a fundamental aspect of biological sciences, although it can be challenging due to various factors. For instance, the liverwort (Marchantia polymorpha), a model system for plant biology, exhibits morphological variability, making it difficult to identify and quantify distinct phenotypic features using objective measures. To address this issue, we utilized a deep learning-based image classifier that can handle plant images directly without manual extraction of phenotypic features, and analyzed bright-field images of M. polymorpha. This dioicous plant species exhibits morphological differences between male and female wild accessions at an early stage of gemmaling growth, although it remains elusive whether the differences are attributable to sexual dimorphism or autosomal genetic variation. To dissect the genomic factors, we established a male and female set of recombinant inbred lines (RILs) from a set of male and female wild accessions. We then trained deep-learning models to classify the sexes of the RILs and the wild accessions. Our results showed that the trained classifiers accurately classified male and female gemmalings of wild accessions in the first week of growth, confirming the intuition of plant researchers in a reproducible and objective manner. In contrast, the RILs were less distinguishable, indicating that the differences between the parental wild accessions arose from autosomal variations instead of sexual dimorphism. Furthermore, we validated our trained models by an "explainable AI" technique that highlights image regions relevant to the classification. Our findings demonstrate that the classifier-based approach provides a powerful tool for analyzing plant species that lack standardized phenotyping metrics.

plant biology↗

bioRxiv2022

MarpolBase Expression: A Web-based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha is equipped with a wide range of molecular and genetic tools and resources that have led to its wide use to explore the evo-devo aspects of land plants. Although its diverse transcriptome data are rapidly accumulating, there is no extensive yet user-friendly tool to exploit such a compilation of data and to summarize results with the latest annotations. Here, we have developed a web-based suite of tools, MarpolBase Expression (MBEX, https://marchantia.info/mbex/), where users can visualize gene expression profiles, identify differentially expressed genes, perform co-expression and functional enrichment analyses, and summarize their comprehensive output in various portable formats. Using oil body biogenesis as an example, we demonstrated that the results generated by MBEX were consistent with the published experimental evidence and also revealed a novel transcriptional network in this process. MBEX should facilitate the exploration and discovery of the genetic and functional networks behind various biological processes in M. polymorpha, and promote our understanding of the evolution of land plants.

plant biology↗

bioRxiv2021

Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

The light-harvesting-reaction center (LH1-RC) core complex of purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides is characterized by the presence of both a dimeric form and a monomeric form. Following structure determination of the monomeric LH1-RC including its previously unrecognized component designated protein-U (Nat. Commun. 12, 6300, 2021), here we present cryo-EM structures of the dimeric LH1-RC from native Rba. sphaeroides IL106 at 2.75 [A] resolution and from an LH1-RC monomer lacking protein-U ({Delta}U) at 2.64 [A] resolution. The native dimeric core complex reveals many asymmetric features in the arrangement of its two monomeric components including the structural integrity of protein-U, the overall LH1 organization, and the rigidities of the proteins and pigments that form the complex. PufX polypeptides play a critical role in connecting two monomers, with one PufX interacting at its N-terminus with another PufX and an LH1 {beta}-polypeptide in another monomer, in good agreement with biochemical analyses. One of the proteins-U was only partially identified in the dimeric structure, signaling significantly different degrees of disorder in the two monomers. The {Delta}U LH1-RC monomer revealed a half-moon-shaped structure containing 11 - and 10 {beta}-polypeptides (compared with 14 of each in the wild type), indicating a critical role for protein-U in controlling the number of {beta}-subunits required for correct assembly and stabilization of the LH1-RC dimer. The structural features are discussed in relation to the unusual topology of intracytoplasmic photosynthetic membranes and an assembly model proposed for the native Rba. sphaeroides dimeric LH1-RC complex in membranes of wild-type cells.

biochemistry↗

bioRxiv2021

Open-source personal pipetting robots with live-cell incubation and microscopy compatibility

Liquid handling robots have the potential to automate many procedures in life sciences. However, they are not in widespread use in academic settings, where funding, space and maintenance specialists are usually limiting. In addition, current robots require lengthy programming by specialists and are incompatible with most academic laboratories with constantly changing small-scale projects. Here, we present the Pipetting Helper Imaging Lid (PHIL), an inexpensive, small, open-source personal liquid handling robot. It is designed for inexperienced users, with self-production from cheap commercial and 3D-printable components and custom control software. PHIL successfully automated pipetting for e.g. tissue immunostainings and stimulations of live stem and progenitor cells during time-lapse microscopy. PHIL is cheap enough for any laboratory member to have their own personal pipetting robot(s), and enables users without programming skills to easily automate a large range of experiments.

bioengineering↗

bioRxiv2021

A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

We present a cryo-EM structure of the monomeric light-harvesting-reaction center (LH1-RC) core complex from photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides at 2.9 [A] resolution. The LH1 complex forms a C-shaped structure composed of 14 {beta}-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its pores. Our findings offer a new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.

biochemistry↗

bioRxiv2020

Remodeling mechanisms determine size distributions in developing retinal vasculature

The development of retinal blood vessels has extensively been used as a model to study vascular pattern formation. To date, various quantitative measurements, such as size distribution have been performed, but the relationship between pattern formation mechanisms and these measurements remains unclear. In the present study, we first quantitatively measured the island size distribution in the retinal vascular network and found that it tended to exhibit an exponential distribution. We were able to recapitulate this distribution pattern in a theoretical model by implementing the stochastic disappearance of vessel segments around arteries could reproduce the observed exponential distribution of islands. Second, we observed that the diameter distribution of the retinal artery segment obeyed a power law;. We theoretically showed that an equal bifurcation branch pattern and Murrays law could reproduce this pattern. This study demonstrates the utility of examining size distribution for understanding the mechanisms of vascular pattern formation.

developmental biology↗

bioRxiv2020

Changes in subcellular structures and states of Pumilio1 regulate the translation of target Mad2 and Cyclin B1 mRNAs

Temporal and spatial control of mRNA translation has emerged as a major mechanism for promoting diverse biological processes. However, the molecular nature of temporal control of translation remains unclear. In oocytes, many mRNAs are deposited as a translationally repressed form and are translated at appropriate timings to promote the progression of meiosis and development. Here, we show that changes in structures and states of the RNA-binding protein Pumilio1 regulate the translation of target mRNAs and progression of oocyte maturation. Pumilio1 was shown to bind to Mad2 and Cyclin B1 mRNAs, assemble highly clustered solid-like aggregates, and surround Mad2 and Cyclin B1 RNA granules in mouse oocytes. These Pumilio1 aggregates were dissolved by phosphorylation prior to the translational activation of target mRNAs. Stabilization of Pumilio1 aggregates prevented the translational activation of target mRNAs and oocyte maturation. Together, our results provide an aggregation-dissolution model for the temporal and spatial control of translation.

cell biology↗