Biology subjects

Morita, S.

Publications and source records attributed to Morita, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Antenna cells of ascidian larvae are gravity-sensing neurons

Ascidians are the closest living relatives of vertebrates, and they share a basic body plan including the dorsal central nervous system. The central nervous system of ascidian tadpole larvae controls their swimming behavior. In particular, for the first few hours after hatching, larvae swim upward. Gravity is sensed by an organ called the otolith, which resides in a brain vesicle. Although this sensory information is thought to be transmitted to two antenna cells abutting the otolith, direct evidence that the antenna cells function as gravity-sensory neurons has been lacking. In the present study, we first identified a regulatory element of the Vglut gene that drives expression in antenna cells and otolith-associated ciliated cells. Using this upstream regulatory element, we specifically overexpressed the apoptosis-inducing gene, Bax, in antenna cells and otolith-associated ciliated cells, and succeeded in their targeted ablation. These Bax-overexpressing larvae lost their preference for upward swimming. Because antenna cells have axons and otolith-associated ciliated cells lack neurites, our observation indicates that antenna cells are the sensory neurons for gravity. In addition, our experimental method for targeted disruption of cells using an enhancer element and Bax provides a valuable tool to examine neural circuit functions at cellular resolution.

zoology↗

bioRxiv2026

A Generalizable Deep Learning Model for Automated 3D Segmentation of Orthopteran Head Anatomy in Micro-CT

Deep learning tools are increasingly used today, particularly in medical segmentation. A gap nonetheless remains in automating segmentation for insects. This work addresses the following question: can a generalist segmentation model, trained on several phylogenetically related orthopteran species, reliably automate head tissue segmentation from micro-CT images? To answer this, we used nnU-Net, a self-configuring 3D deep learning segmentation framework originally developed for medical imaging, whose core function, learning to recognize tissues of interest, applies directly to this context. Six anatomical classes were automated, comparing two training strategies: sequential fine-tuning, which adds species one at a time under the assumption that progressive learning would strengthen predictive power, and from-scratch training, in which the model learns the entire dataset simultaneously. The fine-tuning model (ModelB) reached a Dice coefficient (a measure of overlap between automated segmentation and manual ground truth, ranging from 0 to 1) of 0.7715, compared to 0.7664 for the from-scratch model (ModelC). Although both models produced accurate automated segmentations, no significant difference was found between the two training strategies (paired Wilcoxon test, n = 24, p = 0.243). Despite a dataset limited to 20 individuals and the absence of one method clearly outperforming the other, the models remain usable across the three species studied (Gryllus bimaculatus, Loxoblemmus equestris, L. doenitzi), including in the presence of pronounced sexual dimorphism. It reduces a 20 hour segmentation task to under a minute.

developmental biology↗

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

Static allometry of the horn and pronotal depression in adult Oryctes rhinoceros supports continuous nonlinearity, sexual dimorphism, and size-independent covariation

Exaggerated insect traits often show positive allometry, yet nonlinear scaling can reflect either continuous curvature or discrete morphs. Distinguishing between these alternatives is important because they imply different developmental and evolutionary scenarios. Using cross-sectional data from 1,000 adult Oryctes rhinoceros, we analyzed the static allometry of nine traits with pronotum width as the primary body-size proxy and body length for sensitivity analyses. Cross-validated comparisons among linear, continuous nonlinear, and two-component mixture models showed that continuous nonlinear models improved predictive performance over linear models for horn length and pronotal depression width in both sexes. By contrast, mixture regression did not outperform the best continuous model in either sex, providing no positive support for discrete within-sex dimorphism under the tested model set. After accounting for body size, horn length remained positively associated with pronotal depression width, indicating size-independent covariation. These associations were retained when body length was used instead of pronotum width, supporting robustness to body-size proxy choice. Together, these results support continuous nonlinear adult scaling of the horn and pronotal depression in O. rhinoceros and indicate covariation not attributable solely to body size under the tested model set.

zoology↗

bioRxiv2025

T cell costimulatory and inhibitory signals differentially modulate LAT condensate nucleation propensity after TCR ligation

Linker for activation of T cells (LAT) is a membrane-surface scaffold protein that assembles key signaling molecules upon T cell receptor (TCR) activation. Recent observations have revealed LAT assembly occurs in discretized condensates traceable to single molecular TCR activation events. Moreover, the condensation process occurs abruptly, but after a distinct delay, indicative of a type of phase transition. Here we examine the effects of costimulatory (CD80, CD86) and inhibitory (PD-L1) ligands on the nucleation propensity of LAT condensation. We utilize single molecule mobility tracking to resolve the moment a pMHC molecule binds to TCR combined with intracellular imaging to measure the time delay between pMHC:TCR binding and nucleation of the corresponding LAT condensate. These delay time distributions reflect the propensity function for stochastic nucleation of the LAT condensate and provide a measure of the effective signal strength from a single, activated TCR. The results reveal that CD28 stimulation by CD80 or CD86 causes a distinct reduction in the mean delay time to LAT condensation while PD-L1 is mildly antagonistic to the process. Collectively, these observations strengthen evidence that probability and timing of the LAT nucleation process itself is tightly associated with signal propagation downstream from individual TCR activation events.

biophysics↗

bioRxiv2025

Sex-specific doublesex regulation targeting the color-patterning gene h underlies the evolution of wing sexual dimorphism in the harlequin ladybug Harmonia axyridis

Organisms on Earth show various forms of sexual dimorphism, including ornaments, weapon traits, and pheromone glands, which has been acquired through sexual selection during evolution. Although the genetic basis of sexual trait has been investigated in diverse species, its evolutionary origin, evolutionary mode, and evolvability remain poorly understood. To address these issues, we investigated the strain-specific sexual dimorphism in elytral color patterns of the harlequin ladybug, Harmonia axyridis, a species with over 200 color morphs. The most basal Red-nSpots type color morph exhibits sexual dimorphism, whereas other derived color morphs have lost it. To investigate how this loss of sexual dimorphism is associated with the emergence of novel color morphs, we investigated the genetic basis of sexual dimorphism by focusing on the master sex differentiation gene, doublesex (dsx). We show that dsx regulates color pattern dimorphism by negatively modulating black spot size in males. This modulation is primarily mediated by the transcriptional regulation of the color patterning gene, h (Drosophila pannier ortholog). Intraspecific comparative ATAC-seq analysis of the pupal wings revealed that, at the h locus, not the absolute number of Dsx-binding motifs but the proportion of open chromatin regions containing Dsx-binding motifs relative to those lacking such motifs was reduced in strains that had lost sexual dimorphism and acquired novel color patterns, implying that sexual dimorphism evolves based on the balance between novel CREs and Dsx-binding motif density. The present study provides a fundamental molecular framework for understanding how a secondary sexual trait evolves within H. axyridis.

evolutionary biology↗

bioRxiv2025

Somatic gene repression ensures physical segregation of germline and soma in Drosophila embryos

In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryos body during early embryogenesis. This physical segregation of germline from the soma has been long believed to be crucial for germline development, but the mechanisms controlling this segregation and its developmental significance remain unclear. Here, in Drosophila, we show that somatic gene silencing in the germline is essential for maintaining this segregation. We showed that primordial germ cells (pole cells) lacking the Nanos- and Polar granule component (Pgc)-dependent dual repression mechanism caused misexpression of widespread somatic genes. They formed abnormal cellular protrusions, invaded adjacent somatic epithelium, and intermingled with somatic cells. These mislocalized pole cells ultimately underwent cell death, whereas properly segregated cells survived. Notably, the knockdown of miranda (mira), one of the somatic genes expressed ectopically in the pole cells lacking this repression mechanism, rescued these phenotypes. Our findings provide the first evidence that somatic gene silencing in germline is essential for preserving the physical segregation between germline and soma, highlighting its role in ensuring germline viability during early development.

developmental biology↗

bioRxiv2025

Kinetic Proofreading through Parallel Reactions on a Single T Cell Receptor

T cells can recognize a few molecules of cognate antigen amongst vastly outnumbering non-cognate ligands. The T cell receptor (TCR) differentiates antigens based on antigen-TCR binding dwell time through a kinetic proofreading process. Historically, this has been modeled as the ligated receptor undergoing a series of reactions before producing a signal. In such a sequential mechanism, the number of steps is a key determinant of discrimination fidelity. Here, we consider two features of the molecular mechanism of TCR activation that diverge from a sequential process and suggest that an alternative kinetic proofreading mechanism may be at play. First, activation processes of multiple ITAM domains of the TCR represent parallel reaction sequences taking place on a single TCR molecule. Second, the states of the parallel proofreading reactions are integrated to produce a binary output from each TCR in the form of a discrete LAT condensation event, which may or may not occur. We examine a revised kinetic proofreading scheme based on parallel reactions followed by an integration step (multi-thread scheme) and compare its performance with the sequential scheme in a stochastic setting. A distinct difference in a multi-thread scheme is that multiplicity of the parallel reaction threads provides an additional means to increase discrimination fidelity. This relieves the need for fine-tuned kinetics among chemically distinct reaction steps, which is a major hurdle for physical implementation of a sequential mechanism. Lastly, we reinterpret previously reported experimental observations and find that various proofreading behaviors are well described as proofreading through parallel reaction threads. Significance StatementThe kinetic proofreading mechanism by which T cells discriminate antigen has attracted interest from both physical and immunological perspectives. The proofreading process has generally been modeled as a multi-step sequence of reactions, and many experimental observations have been interpreted based on this presumed mechanism. However, these models do not capture key molecular features of the TCR signaling mechanism, including ITAM multiplicity and LAT condensation. Here, we find distinct consequences of these molecular features by examining kinetic models and reinterpreting published experimental data. ITAM multiplicity offers multiple parallel reaction threads, re-integrated by the LAT condensation step, which readily improves discrimination fidelity up to the observed levels. Multi-thread reactions are suggested to play a central role in amplifying TCR kinetic proofreading performance.

biophysics↗

bioRxiv2025

The rice ethylene receptor OsERS1 negatively regulates the shoot growth and salt tolerance in rice seedlings

Ethylene is a gaseous plant hormone that regulates various aspects of growth and development. It promotes shoot growth in etiolated rice seedlings, which is crucial for seedling establishment and has significant agricultural implications. Of the five ethylene receptors in rice, OsERS1 is the most abundantly expressed in seedlings. Therefore, we investigated the localization and role of OsERS1 in shoot growth. When expressed in rice protoplasts, OsERS1 was localized in the endoplasmic reticulum. Knockout mutants of OsERS1 exhibited enhanced shoot growth in etiolated seedlings under normal and ethylene-treated conditions. Additionally, the induction of ethylene-responsive genes was increased in the mutants, indicating an elevated ethylene response due to OsERS1 knockout. The mutants also showed increased salt tolerance. In conclusion, our findings suggest that OsERS1 negatively regulates shoot growth and salt tolerance in etiolated rice seedlings.

plant biology↗

bioRxiv2024

Implication of S-1 biomarkers on aging and prognosis in elderly patients with lung cancer treated by adjuvant S-1 chemotherapy: Accompanying results of the Setouchi Lung Cancer Group Study 1201

BACKGROUNDSThe management of elderly patients presents several challenges due to age-related declines; however recent recommendations advocate for age not being the sole determinant for adjuvant treatment decisions in patients with non-small cell lung cancer (NSCLC). Aging may alter expression levels of 5-fluorouracil (5-FU) biomarkers. METHODSExpression changes with aging were explored using The Cancer Genome Atlas (TCGA) database. 5-FU-related biomarker expressions, including thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD), orotate phosphoribosyltransferase, epidermal growth factor receptor (EGFR), and excision repair cross-complementation group-1 (ERCC1), were assessed by the quantitative reverse-transcription PCR assays in 89 NSCLCs elderly patients ([≥] 75 years old) receiving adjuvant S-1, an oral fluoropyrimidine agent, therapy in a SLCG1201 trial. RESULTS: TCGA database analysis (n=955) indicated decreased TS expression with aging, particularly in those 75 or older. In the SCLG1201 trial, univariate analysis revealed that high EGFR and low TS expressions correlated with favorable recurrence-free survival (RFS)(p=0.0264) and overall survival (OS)(p=0.0365), respectively. Multivariable analysis confirmed pathological stage as an independent prognostic factor for both RFS and OS (p=0.0052 and 0.0352, respectively). EGFR mutant tumors (n=27) showed significantly higher DPD (p=0.0066) and EGFR (p<0.0001) expressions, and lower TS(p=0.0125) and ERCC1(p=0.0015) expressions. CONCLUSIONDespite pathological stage being an independent prognostic factor, high EGFR and low TS expressions may predict better clinical outcomes in elderly NSCLC patients using adjuvant S-1. The age-related decrease in TS expression supports the potential benefit of 5-FU-based therapy in them compared to younger patients. Further research is warranted to validate these clinical implications.

pharmacology and toxicology↗

bioRxiv2024

Discrete protein condensation events govern calcium signal dynamics in T cells

Calcium level variations, which occur downstream of T cell receptor (TCR) signaling, are an essential aspect of T cell antigen recognition. Although coordinated ion channel activities are known to drive calcium oscillations in other cell types, observations of nonperiodic and heterogeneous calcium patterns in T cells are inconsistent with this mechanism. Here, we track the complete ensemble of individual molecular peptide-major histocompatibility complex (pMHC) binding events to TCR, while simultaneously imaging LAT condensation events and calcium level. Individual LAT condensates induce a rapid and additive calcium response, which quickly attenuates upon condensate dissolution. No evidence of cooperativity between LAT condensates or oscillatory calcium response was detected. These results reveal stochastic LAT protein condensation events as a primary driver of calcium signal dynamics in T cells. One-Sentence SummaryCa2+ fluctuations in T cells reflect stochastic protein condensation events triggered by single molecular antigen-TCR binding.

biophysics↗

bioRxiv2023

Combined blockade of CXCR4 and PD-1 enhances intratumoral dendritic cell activation and immune responses against HCC

Immune checkpoint inhibitors (ICIs) have transformed systemic therapy for unresectable hepatocellular carcinoma (HCC). Nevertheless, their efficacy is limited to a small percentage of patients, leaving an opportunity for enhancement through synergistic combination therapies. We tested here the combined blockade of programmed death receptor 1 (PD-1) and CXCR4, a receptor for CXCL12 and a key mediator of immunosuppression in the tumor microenvironment in orthotopic grafted and autochthonous models of HCC. We evaluated tumor growth and survival outcomes and examined the underlying mechanisms using immunofluorescence, flow cytometry, RNA-sequencing, and transgenic mice experiments. Combined anti-CXCR4/PD-1 therapy had a robust impact on tumor growth and significantly prolonged survival in all murine preclinical models. The combination treatment successfully reprogrammed antigen-presenting cells, revealing the role of conventional type 1 dendritic cells (cDC1s) in the tumor microenvironment. Moreover, DC reprogramming enhanced anti-cancer immunity by facilitating CD8 T-cell accumulation and activation in the HCC tissue. The effectiveness of the anti-CXCR4 antibody/ICI combination treatment was compromised entirely in Batf3-KO mice deficient in cDC1 cells. Thus, combined ICI therapy with an anti-CXCR4 antibody has the potential to augment the anti-cancer effects and improve survival outcomes in HCC via reprogramming intra-tumoral cDC1 cells.

cancer biology↗

bioRxiv2023

Preventing NK cell activation in the damaged liver induced by cabozantinib/PD-1 blockade increases survival in hepatocellular carcinoma models

Combining multikinase inhibitors with immune checkpoint blockade improves tumor control in hepatocellular carcinoma (HCC), but survival benefits remain inconsistent. To define this discordance, we integrated COSMIC-312 with orthotopic and autochthonous murine HCC models with or without liver fibrosis. In patients treated with cabozantinib plus atezolizumab, baseline liver function stratified overall survival but not progression-free survival, indicating uncoupling of tumor control from survival. In contrast, sorafenib outcomes tracked with both endpoints, supporting a treatment-specific effect rather than a purely prognostic effect of liver status. In murine HCC models, cabozantinib plus PD-1 blockade induced comparable tumor regression regardless of liver condition, but improved survival only in mice with preserved liver function, whereas fibrotic hosts developed hepatotoxicity. Immune profiling revealed compartment-specific remodeling, with enhanced cytotoxic T-cell programs in tumors but expansion of NK-lineage innate lymphocytes with ILC1-like features in fibrotic liver. Depletion of NK1.1-positive cells reduced liver injury and restored survival without compromising antitumor efficacy, whereas CD4-positive or CD8-positive T-cell depletion did not protect from hepatotoxicity. Transcriptomic, single-cell, adoptive-transfer, and human in vitro studies supported a model in which the fibrotic liver niche promotes NK-to-ILC1-like reprogramming, hepatocyte stress signaling, and TNF/TRAIL-associated epithelial injury. Consistently, cabozantinib and nivolumab showed liver-predominant remodeling of CD56-positive innate lymphocyte-enriched populations in human HCC samples, and ex vivo TGF-beta induced ILC1-like phenotypic changes in human NK cells. These findings identify liver fibrosis as a host determinant that can limit the survival benefit of multikinase inhibitor immunotherapy by promoting innate immune-mediated hepatotoxicity despite preserved tumor control in HCC. One Sentence SummaryLiver fibrosis limits the survival benefit of multikinase inhibitor immunotherapy in hepatocellular carcinoma by promoting innate immune-mediated hepatotoxicity despite preserved tumor control.

cancer biology↗

bioRxiv2023

Selective elimination of CD169+ macrophages in lymph nodes invaded by breast cancers

Breast cancer cells suppress the host immune system to efficiently invade the lymph nodes; however, the underlying mechanism remains incompletely understood. Here, we report that metastasized breast cancer cells selectively eliminate CD169+ lymph node sinus macrophages, an initiator of anti-cancer immunity, from the lymph nodes. The comparison between paired lymph nodes with and without metastasis from the same patients demonstrated that the number of CD169+ macrophages was reduced in metastatic lymph nodes, whereas the numbers of other major immune cell types were unaltered. We also detected the infiltration of CD169+ macrophages into metastasized cancer tissues depending on sections, suggesting that CD169+ macrophages were gradually eliminated after anti-cancer reactions. Furthermore, CD169+ macrophage elimination was prevalent in major breast cancer subtypes and correlated with breast cancer staging. Collectively, we propose that metastasized breast cancer cells dispel CD169+ macrophages from lymph nodes in a phased manner, disabling a critical step of anti-cancer immunity.

cancer biology↗

bioRxiv2023

A stress sensor IRE1α is required for bacterial exotoxin-induced inflammasome activation in tissue-resident macrophages

Cholera toxin (CT), a bacterial exotoxin composed of one A subunit (CTA) and five B subunits (CTB), functions as an immune adjuvant. CTB can induce production of interleukin-1{beta} (IL-1{beta}), a proinflammatory cytokine, in synergy with a lipopolysaccharide (LPS), from resident peritoneal macrophages (RPMs) through the pyrin and NLRP3 inflammasomes. However, how CTB or CT activates these inflammasomes in the macrophages has been unclear. Here, we clarified the roles of IRE1, an endoplasmic reticulum (ER) stress sensor, in CT-induced IL-1{beta} production from RPMs. In RPMs, CTB is incorporated into ER and induced ER stress responses, depending on GM1, a cell membrane ganglioside. IRE1-deficient RPMs showed a significant impairment of CT- or CTB-induced IL-1{beta} production, indicating that IRE1 was required for CT- or CTB-induced IL-1{beta} production from RPMs. This study first demonstrates the critical roles of IRE1 in activation of both NLRP3 and pyrin inflammasomes in tissue-resident macrophages. One sentence summaryIRE1 is required for NLRP3 and pyrin-mediated IL-1{beta} production

immunology↗

bioRxiv2023

Forecasting fish recruitment using machine learning methods: A case study of arabesque greenling

Fish recruitment prediction is a central topic in fisheries science. We use a machine learning method for predicting the recruitment of Arabesque greenling in Hokkaido, Japan. Biological, fisheries-related, and environmental factors were included in the predictive models as feature variables. A gradient boosting model (GBM) showed better predictive performance compared with a linear regression model (LRM) and a random forest model (RFM) in terms of relative bias and relative root mean square error for recruitment prediction in the last 5 years. The most influential feature for GBM was spawning stock biomass in the last year, followed by the fishing rate for older fish. The sea surface temperature (SST) was a very weak predictor in the GBM but was the most influential feature in the LRM. The difference among models suggests the importance of nonlinearity and variable interactions. Machine learning methods will greatly contribute to fish recruitment forecast and thereby sustainable fisheries management.

ecology↗

bioRxiv2023

Epigenetic mechanisms to propagate histone acetylation by p300/CBP

Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryo-electron microscopy structures in which a p300/CBP multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone NT acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization.

biochemistry↗

bioRxiv2023

Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus

Rhinoceros beetle (Trypoxylus dichotomus) males have pitchfork-shaped head horns, which they use to pry rival males from the trunks of trees. In the largest males these horns can be three times the length of horns in the two closest sister species. Because this weapon functions as a lever, longer horns should lift with less force than shorter horns (the paradox of the weakening combatant) unless other elements of the weapon system (e.g., input lever length, muscle mass) evolve to compensate. We used next-generation sequencing approaches to consolidate 23 sample locations into 8 genetically distinguishable populations, reconstructing their historical relationships and providing a comprehensive picture of the evolution of this horn lever system. We show that head horns likely increased in length independently in the Northern and Southern lineages. In both instances this resulted in weaker lifting forces, but this mechanical disadvantage was later ameliorated, to some extent and in some locations, by subsequent reductions to horn length, changes in muscle size, or by an increase in input lever length (head height). Our results reveal an exciting geographic mosaic of differences in weapon size, weapon force, and in the extent and nature of mechanical compensation. Reconstructing the evolution of this weapon system offers critical insights towards meaningfully linking mating system dynamics, selection patterns, and diversity in sexually selected traits.

evolutionary biology↗