Biology subjects

Fujii, K.

Publications and source records attributed to Fujii, K..

At least 19 recordsLinked to original sources

bioRxiv2026

The emergence of the rice blast fungus (Pyricularia oryzae) coincides with the evolutionary divergence of rice

Rice blast, caused by Pyricularia oryzae, is one of the most destructive diseases threatening global rice production. Reconstructing the evolutionary history of P. oryzae in the context of the well-documented history of rice dispersal provides a powerful framework for predicting the coevolutionary dynamics of crops and their pathogens. However, the absence of fossil evidence has precluded robust estimation of the pathogen's origin and evolutionary timescale. Here, we inferred genome-wide divergence times for P. oryzae using archaeological constraints derived from the emergence and spread of rice cultivation. Our analyses indicate that P. oryzae originated approximately 18,300 years ago, coincident with the divergence of Oryza sativa L. from its ancestral lineage rather than with rice domestication itself. Calibrating the evolutionary history of the pathogen against this host divergence further indicates that P. oryzae reached the Japanese archipelago 2,590 years ago based on nucleotide sequences and 3,030 years ago based on amino acid sequences, closely matching archaeological estimates for the arrival of rice agriculture in Japan. Contrary to the prevailing view that rice blast emerged with rice domestication approximately 10,000 years ago, our results place the origin of P. oryzae before domestication and link its subsequent spread to the expansion of cultivated rice. These findings redefine the evolutionary history of one of the world's most important crop pathogens and establish a temporal framework for understanding crop-pathogen coevolution over millennial timescales.

evolutionary biology↗

bioRxiv2026

Relationship between gonadosomatic index and spawning-capable status based on gonadal histology in the moonfish Mene maculata

The moonfish Mene maculata (Bloch and Schneider, 1801), the sole extant species of the family Menidae, is widely distributed in the Indo-West Pacific. Although its spawning season has previously been inferred from seasonal variation in the gonadosomatic index (GSI), the histological basis for interpreting GSI as an indicator of spawning-capable status remains limited. Here we describe the gonadal structure of male and female M. maculata and evaluate how GSI and standard length relate to spawning-capable status based on germ cell development. The testis was lobular and exhibited an unrestricted spermatogonial distribution, a structure widely observed among neoteleosts, indicating that the phylogenetic distinctiveness of M. maculata was not associated with a distinctive testicular structure. In the spawning-capable female, oocytes at multiple developmental stages, from primary growth to oocyte maturation, co-occurred within the ovary, indicating asynchronous ovarian development. This finding suggests that M. maculata may be a batch spawner rather than a total spawner as previously inferred. The spawning-capable female had a GSI consistent with previously inferred spawning season estimates. By contrast, histologically examined males were spawning capable at GSI values lower than those previously associated with the inferred spawning season, suggesting that male spawning-capable status may persist beyond the period inferred from elevated GSI alone. This study provides the first histological description of reproductive biology in the phylogenetically distinctive M. maculata and establishes a histological basis for interpreting GSI as a reproductive indicator.

ecology↗

bioRxiv2026

A Master-Key DNA System Enabling Programmable Cross-Talks in Biomimetic Networks via An Artificial Chaperone

Biological systems operate through complex molecular networks programmed by genetic information; however, constructing artificial systems with multilayered control remains a significant challenge. Here, we report a simple and integrated master-key system governed by lock DNA and master key DNA, reversibly switching diverse downstream processes ON/OFF and achieving dynamic cross-talks among distinct molecular components. The system utilizes cationic copolymer chaperones as control nodes, based on poly(L-lysine) or poly(allylamine) grafted with hydrophilic side chains, with a peptide nucleic acid (PNA) plug-in that grants sequence-specificity. We demonstrated two proof-of-concept systems: a nucleic acid-based catalytic network responsive to microRNA let-7b and a peptide-mediated transformation of lipid bilayers from two-dimensional sheets to three-dimensional vesicles. Both systems exhibited precise, modular, and programmable control with high robustness, mimicking the governing role of nucleic acids in biological systems. This strategy provides a versatile design framework for constructing biomimetic molecular networks and studying biological systems.

bioengineering↗

bioRxiv2026

Absence of nascent peptides triggers nonfunctional ribosome decay

The nonfunctional rRNA decay (NRD) pathway eliminates defective ribosomes to maintain protein synthesis integrity. Although the Mms1-Rtt101 E3 ligase is known to trigger 25S NRD to clear defective 60S subunits, the specific molecular marks and targets it recognizes remain unknown. Here, we demonstrate that the late-stage maturation factor Reh1 functions as a specific molecular sensor for these defects. While Reh1 is normally displaced from the polypeptide exit tunnel (PET) during successful translation initiation, it is persistently retained on nonfunctional 80S ribosomes incapable of peptide bond formation. This prolonged retention, driven by the absence of a nascent peptide, provides a physical mark that recruits the Mms1 complex via Reh1s N-terminal domain, triggering site-specific ubiquitination of ribosomal protein Rpl19 (uL6). Our findings reveal that the cell repurposes a maturation factor as a sentinel to monitor translation competence, achieving robust detection of diverse ribosomal and maturation defects through a single molecular pathway.

molecular biology↗

bioRxiv2026

The fidelity of mRNA translation as a novel regulatory layer for brain development

Although the fidelity of mRNA translation is essential for maintaining proteome integrity, whether translation error rates vary across cell types and developmental stages in vivo remains largely unexplored. Here, we generate a gain-of-activity dual-luciferase knock-in reporter mouse that enables quantitative monitoring of translation errors in vivo. Using this system, we systematically characterize the spatiotemporal dynamics of translation fidelity across mammalian development. Mature organs exhibit lower error rates than pluripotent embryonic stem cells. Translation fidelity diverges sharply among organs, becoming progressively established during embryonic development, with brain and muscle displaying the highest accuracy. To determine functional significance, we experimentally increased translation errors during cerebral organoid formation and in vitro neuronal differentiation. Elevated error rates reduced neuronal output by impairing neuronal maturation without altering neural progenitor populations. Consistently, differentiated neurons display uniformly elevated fidelity across multiple classes of translation errors, including stop codon readthrough, amino acid misincorporation, and ribosomal frameshifting. These findings demonstrate that translation fidelity is not a fixed intrinsic property of the translation machinery but is developmentally regulated and required for efficient neuronal differentiation. Together, our results identify translation fidelity as a developmentally tuned, tissue-specific dimension of gene expression in vivo.

developmental biology↗

bioRxiv2026

The significance of sukumo (composted indigo leaves) as a microbial source for traditional Japanese indigo dyeing

A critical process in traditional Japanese indigo dyeing is the microbial reduction of indigo within the dye suspension, which consists solely of sukumo (fermented indigo leaves), wood ash lye, and microbial nutrients such as wheat bran. Although sukumo has long been recognized as a potential microbial source, the microbial community dynamics during its production is still largely unexplored, and its contribution to dyeing performance via microbial supply remains poorly characterized. In this study, we investigated the significance of sukumo as a microbial source, in addition to its established role as a pigment source. We conducted a time-series analysis of microbial communities throughout the four-month fermentation process of sukumo, using weekly samples collected from two geographically distinct indigo dyeing studios. Microbial profiling revealed similar successional patterns between the two sites. Notably, in the later stages of fermentation, known indigo-reducing bacteria, such as the genus Oceanobacillus and the family Tissierellaceae, emerged at both locations. Laboratory-scale dyeing experiments using immature sukumo demonstrated that supplementation with a small amount of mature sukumo restored dyeing activity and increased the abundance of Oceanobacillus and Tissierellaceae. Furthermore, the addition of the indigo-reducing isolate Tissierellaceae strain TU-1 to the immature sukumo-based dye suspension led to a marked enhancement in dyeing performance. These findings highlight the critical role of sukumo as a microbial source in traditional indigo dyeing and suggest that prolonged fermentation is essential for nurturing functional indigo-reducing bacteria. This insight provides a foundation for improving dye suspension performance through targeted microbial community management.

microbiology↗

bioRxiv2025

Individual bounded rationality destabilizes cooperative dynamics in human-AI groups

Cooperative dynamics arise from interactions among individuals, including humans and artificial agents, yet it remains unclear how individual-level cognition and motion shape collective dynamics in such human-AI groups. We combined a dynamic cooperative task, in which one attacker was controlled by a human and two by heuristic artificial agents facing a deep reinforcement learning defender, with counterfactual simulations of artificial groups. Across nine task conditions, groups including a human consistently underperformed relative to groups composed solely of artificial agents. Humans exhibited restricted movement options and probabilistic rather than deterministic action choices, which shifted coordination dynamics towards less symmetric, less organized patterns and reduced performance for both individuals and groups. Embedding these boundedly rational movement and decision parameters into artificial agents reproduced human-like behavior and performance declines. These results demonstrate how limitations of a single individual can destabilize cooperative dynamics and provide insights into the design of robust human-AI systems.

animal behavior and cognition↗

bioRxiv2025

Flight trajectory modeling reveals species-specific obstacle avoidance policies in echolocating bats

Echolocating bats routinely navigate complex wild environments with remarkable agility, yet it remains unclear whether their flight trajectories reflect reproducible internal control strategies or are merely the result of improvised reactive behavior. To address this question, we recorded flight paths and pulse emissions of Rhinolophus nippon and Miniopterus fuliginosus as they navigated seven obstacle-rich arenas in complete darkness. Using a machine learning model--a variational recurrent neural network (VRNN)--we show that bat flight is governed by a consistent internal policy. Trained on only part of each trajectory, our model accurately predicted future flight paths across arenas and individuals, preserving key features such as turning direction, obstacle-avoidance arcs, and velocity profiles. The models ability to faithfully reproduce species-specific strategies despite differences in sonar and flight morphology supports the existence of structured internal control in bat navigation. Our approach reveals that bat flight, while appearing improvisational, is in fact guided by internal policies that can be directly inferred from trajectory data, without relying on hand-crafted assumptions. Furthermore, the data-driven model developed here enables a priori testing of flight-path reorganization by virtually imposing environmental changes and analysing the resulting predicted trajectories, providing a powerful tool for biomimetic robotic design and for forecasting ecological responses to landscape transformation.

ecology↗

bioRxiv2025

A key spectral tuning site of UV-sensitive vertebrate non-visual opsin Opn5

Opsins are photoreceptive proteins responsible for visual and non-visual photoreceptions in animals. In general, vertebrates have multiple visual and non-visual opsins whose spectral sensitivities range from the UV to the red region. Among these opsins, Opn5 has been widely identified in vertebrates from fishes to primates and functions as a non-visual opsin in various tissues including the retina and brain. Vertebrate Opn5 has been characterized as a UV-sensitive bistable opsin. Thus, Opn5 provides one of the molecular mechanisms determining the short wavelength limit that vertebrates can detect. In this study, we searched for the amino acid residue responsible for the UV light sensitivity of Opn5. Our mutational analysis revealed that Opn5 acquired visible light sensitivity by the substitution of Lys91 with an amino acid other than arginine or tyrosine residue. In addition, the mutations at Lys91 altered the preferential binding of the retinal isomers in Opn5. Therefore, the conservation of Lys91 among vertebrate Opn5 proteins would be necessary to enable Opn5 to work as the shortest wavelength sensor in various tissues.

biochemistry↗

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

Identifying simultaneous inhibition of riboflavin metabolism and MEK as a novel therapeutic strategy for pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge with a survival rate of approximately 10%, largely due to the lack of diagnostic and therapeutic options. To identify novel therapeutic targets for PDAC, we previously developed a Drosophila melanogaster model, the 4-hit fly, which mimics the alterations in KRAS, TP53, CDKN2A, and SMAD4 genes observed in PDAC. Through whole-body genetic screening using the 4-hit model, we identified riboflavin (RF) metabolism as a novel potential therapeutic target for PDAC. Additionally, transcript levels of four out of five genes that are involved in RF metabolism were elevated in human PDAC compared to non-tumor tissues. Roseoflavin (RoF), an antimetabolite of RF, resulted in a variety range of metabolic changes, decreased mitochondrial respiratory chain activity, and suppressed proliferation in cultured PDAC cells. Furthermore, the combination of RoF with the MEK inhibitor drug trametinib significantly suppressed the growth of human PDAC xenografts compared to either treatment alone. These findings underscore that dual targeting of RF metabolism and MEK represents a novel therapeutic strategy for PDAC.

cancer biology↗

bioRxiv2024

Analysis of coordinated group behavior based on role-sharing: Practical application from an experimental task to a 3-on-3 basketball game as a pilot study

A group often shares a common goal and accomplishes a task that is difficult to complete alone by distributing roles. In such coordination, the nonverbal behavior among three or more members complicates the explanation of the mechanism due to complex and dynamic interactions. In cognitive science, a crucial role is indicated: to intervene moderately with others and adjust the whole balance without interrupting their main smooth interactions, using an experimental task. The findings suggest that resilient helping actions in the third role support to coordination. These actions are similar to off-ball movements in team sports, which involve an on-ball player and have recently been the focus of sports science because their characteristics are not represented in common statistical data, such as a shooting success rate. Hence, a new perspective for discussing coordination has emerged, as existing theories, such as synchronization--where movements between players are spontaneously matched and organized--cannot explain the mentioned role. However, there is a lack of investigation and discussion regarding whether these findings are applicable to real-world activities. Therefore, this study applied the experimental findings to the field of sports. We developed a 3-on-3 basketball game in which the offensive role of intervention decision and adjustment is key for winning and introduced it to the practice of a female university team as a pilot study. Participants repeatedly engaged in the mini-game, and the playing was compared before and after receiving tips of this role. Consequently, in the bins of the relatively large distance between the participant required to the relevant role and each defensive player, the frequencies after receiving these tips were significantly higher. Furthermore, the winning rate on the offensive team improved temporarily; however, the effects were not maintained. These suggest that spacing skill, which maintains reasonable distances from the other players, creates favorable situations for coordination. This study may bridge the gap between controlled experiments and real-world applications and make an educational contribution; it may recommend practice design for the acquisition of spacing skill related to the crucial role.

animal behavior and cognition↗

bioRxiv2024

Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated

Quinoa, an annual allotetraploid plant native to the Andean highlands of South America, is emerging as an important seed crop for global food and nutrition security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats (Gypsy and Copia), representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 64,945 and 65,303 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.

plant biology↗

bioRxiv2023

RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.

molecular biology↗

bioRxiv2023

Enucleation of the C. elegans embryo revealed the mechanism of dynein-dependent spacing between microtubule asters

The centrosome is a major microtubule-organizing center in animal cells. The intracellular positioning of the centrosomes is important for proper cellular function. One of the features of centrosome positioning is the spacing between centrosomes. The spacing activity is mediated by microtubules extending from the centrosomes; however, the underlying mechanisms are not fully understood. To characterize the spacing activity in the Caenorhabditis elegans embryo, a genetic setup was developed to produce enucleated embryos. The centrosome duplicated multiple times in the enucleated embryo, which enabled us to characterize the chromosome-independent spacing activity between sister and non-sister centrosome pairs. We knocked down genes in the enucleated embryo and found that the timely spacing was dependent on cytoplasmic dynein. Based on these results, we propose a stoichiometric model of cortical and cytoplasmic pulling forces for the spacing between centrosomes. We also found a dynein-independent but non-muscle myosin II-dependent movement of the centrosomes in a later cell cycle phase. The dynein-dependent spacing mechanisms for positioning the centrosomes revealed in this study is likely functioning in the cell with nucleus and chromosomes, including the processes of centrosome separation and spindle elongation.

cell biology↗

bioRxiv2023

Activation of prefrontal parvalbumin interneurons ameliorates treatment-resistant working memory deficit even under continuous antipsychotic treatment in a mouse model of schizophrenia

BACKGROUNDOne of the critical unmet medical needs in schizophrenia is a remedy for cognitive deficits. However, the neural circuit mechanisms of them remain unresolved. In addition, despite the patients with schizophrenia cannot stop taking antipsychotics due to a high rate of discontinuation-induced relapse, previous studies using animal models of schizophrenia have not considered these clinical situations. METHODSHere, we employ multi-dimensional approaches, including histological analysis in the prelimbic cortex, LC-MS/MS-based in vivo dopamine D2 receptor occupancy analysis for antipsychotic drugs, in vivo calcium imaging and behavioral analyses of mice using chemogenetic manipulation, to investigate neural mechanisms and potential therapeutic interventions for working memory deficit in a mouse model with chronic phencyclidine (PCP) administration that resembles the schizophrenia symptomatology. RESULTSChronic PCP administration led to abnormalities in excitatory and inhibitory synapses, including dendritic spines of pyramidal neurons, vesicular glutamate transporter 1 (VGLUT1) positive terminals, and parvalbumin (PV) positive GABAergic interneurons, in layer 2-3 of the prelimbic cortex. Continuous olanzapine, which achieved a sustained therapeutic window of dopamine D2 receptor occupancy (60-80%) in the striatum, did not affect these synaptic abnormalities and working memory deficit in the PCP-treated mice. We found that the selective prelimbic PV activation, using hM3D(Gq)-DREADD system confirmed by in vivo calcium imaging, restored working memory deficit, even under continuous olanzapine treatment. CONCLUSIONSOur study raises a possibility that intervention in prefrontal PV neurons leads to an add-on therapy to antipsychotics targeting amelioration of treatment-resistant cognitive deficits in schizophrenia.

neuroscience↗

bioRxiv2022

Collaborative hunting in artificial agents with deep reinforcement learning

Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed as an advanced hunting strategy requiring large brains that involve high level cognition. However, recent findings that collaborative hunting have also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes using computational multi-agent simulation based on deep reinforcement learning. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between observations and actions via distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our results of computational ecology emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.

animal behavior and cognition↗

bioRxiv2021

Phosphate starvation response precedes drought response in field-grown plants

Drought severely damages crop production, even under conditions so mild that the leaves show no signs of wilting. However, it is unclear how field-grown plants respond to mild drought. Here, we show through 6 years of field trials that ridges are a useful experimental tool to mimic mild drought stress in the field. Mild drought reduces inorganic phosphate levels in the leaves to activate the phosphate starvation response in soybean plants in the field. Using Arabidopsis thaliana and its mutant plants grown in pots under controlled environments, we demonstrate that phosphate starvation response (PSR) occurs before abscisic acid response under progressive mild drought and that PSR plays a crucial role in plant growth under mild drought. Our observations in the field and laboratory using model crop and experimental plants provide insight into the molecular response to mild drought in field-grown plants and the relationship between nutrition and drought stress response.

plant biology↗