Biology subjects

Kubo, T.

Publications and source records attributed to Kubo, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan

Understanding the evolutionary origins of globally noxious weeds provides insights into the genetic background of weediness. Among species of Echinochloa, the hexaploid E. crus-galli was previously thought to have arisen through hybridization and allopolyploidization between tetraploid E. oryzicola and an undiscovered diploid species, although they exhibit marked differences in both ecological and morphological characteristics. Recently, in Japan, unknown tetraploid Echinochloa plants were discovered that exhibit distinct ecological and morphological characteristics from those of E. oryzicola, with some traits showing greater similarity to those of E. crus-galli. In this study, we investigated the relationships between well-known Echinochloa species and these unknown tetraploid plants, hereafter referred to as ''ninja''. Subgenome-based read mapping analysis and phylogenetic analysis revealed that ninja possesses a distinct genomic composition, while showing close relationships to E. oryzicola in both its chloroplast and nuclear genomes. Furthermore, the identification of a very small number of ninja x E. oryzicola hybrids among field-collected individuals suggests that these two species rarely hybridize in the wild. Although ninja and E. oryzicola showed similar genomic compositions, ninja has a broader habitat range, partially overlapping with that of E. oryzicola and extending into areas occupied by E. crus-galli. Our findings indicate the possibility that hexaploid E. crus-galli may have originated from a tetraploid Echinochloa species other than E. oryzicola.

plant biology↗

bioRxiv2026

Transcriptomic and physiological analyses reveal a salinity-induced growth suppression and defense activation in spring barley

Salinity is a major abiotic stress that severely limits plant growth and productivity, causing substantial yield losses. Despite barleys relative tolerance to salinity, the underlying physiological and molecular mechanisms remain incompletely understood. In this study, we employed an integrative approach combining agronomic, physiological, biochemical, and transcriptomic analyses to investigate salinity responses in the spring barley cultivar Giza 134 under both field and lysimeter-based conditions. Salinity stress significantly reduced growth and yield-related traits, with more pronounced effects observed under lysimeter-imposed salinity, reflecting higher stress intensity. These reductions were associated with impaired water status, altered leaf structural traits, and declines in photosynthetic pigment content. In contrast, proline accumulation increased, indicating activation of osmotic adjustment mechanisms. Salinity also disrupted ionic homeostasis, as evidenced by elevated Na+ levels, reduced K+ content, and an increased Na+/K+ ratio. Enhanced lipid peroxidation and elevated catalase and peroxidase activities suggested increased oxidative stress and activation of antioxidant defenses. Transcriptome profiling identified 4,298 differentially expressed genes, including 1,764 upregulated and 2,534 downregulated genes. Functional enrichment analyses revealed upregulation of pathways related to stress adaptation, redox regulation, and metabolic reprogramming, while genes associated with photosynthesis, ribosome biogenesis, and protein synthesis were strongly suppressed. Several novel stress-responsive genes involved in signaling, osmoprotection, antioxidant defense, and central metabolism were highly induced, supported by coordinated enrichment of cis-regulatory motifs in their promoter regions. Together, these findings provide a comprehensive physiological and molecular framework for salinity tolerance in Giza 134 and highlight candidate genes and pathways for breeding salt-resilient cultivars suited to saline-prone environments.

plant biology↗

bioRxiv2026

Cross-domain encoding models reveal shared and domain-specific neural representations across language and mathematics

Whether language and mathematics rely on shared or distinct neural representations remains an unresolved question in cognitive neuroscience. Here we combine latent features from a large language model (LLM) with vertex-wise encoding models to examine cross-domain generalization between language and mathematics. Thirty-two participants performed sentence comprehension and calculation tasks during fMRI, and encoding models were trained using features embedded in a common latent space. Cross-domain prediction identified cortical regions associated with partially shared representations, most prominently the left 55b, while control analyses suggested that these effects could not be fully explained by low-level visual processing or simple task-general factors. Task-specificity contrasts revealed stronger language-related prediction in the left anterior superior temporal and angular gyri and math-related prediction in the left precentral and intraparietal sulci. Model-weight analyses further showed that shared and domain-specific prediction patterns were reflected in distinct weight profiles across cortical regions. Connectivity analyses showed task-dependent functional coupling between cross-domain regions and language- or math-related networks. Together, these findings suggest that language and mathematics involve partially shared neural representations alongside domain-specific cortical organization, helping reconcile previous contrasting views on their neural basis.

neuroscience↗

bioRxiv2026

Mind the gap: quantifying population-individual gap in depressive symptom dynamics through energy landscapes

People do not always feel as they appear. Someone who seems stable may struggle internally, whereas someone who appears distressed may experience it differently. This gap matters in psychiatry, where assessment relies on symptom scales and external evaluation. Here we developed mindGAP (Measuring INDividual-population GAPs in psychiatric energy landscapes), a hierarchical variational Bayesian framework that uses longitudinal questionnaire data to estimate population-level and individual-level pairwise maximum entropy models (pMEMs). We applied mindGAP to time-series PHQ-9 data from 248 participants. The population landscape contained three major states, whereas individual-level landscapes often diverged from this shared structure. We quantified this gap as individual-population landscape divergence, which was associated not only with depressive severity but also with modern-type depression-related traits (TACS-22) and interpersonal sensitivity-self traits (IPS-22). Thus, mindGAP opens a route to quantifying a previously unquantified gap between population-level and individual-level symptom organization.

bioinformatics↗

bioRxiv2026

Tubulin Monoglutamylation is Sufficient to Rescue the Ciliary Motility Defects in a Chlamydomonas Polyglutamylation Deficient Mutant

The axonemes of eukaryotic cilia and flagella display high tubulin glutamylation heterogeneity, yet the functional significance of this variation remains elusive. We previously showed that long-chain polyglutamylation is crucial for ciliary motility in Chlamydomonas. However, the respective contributions of long-chain polyglutamylation versus short-chain species to motility remain unclear, as existing mutants did not allow for a clear functional dissection of these two modification states. Here, we generated mutants deficient in deglutamylases, cytosolic carboxypeptidases (CCPs) 1, 2, and 5. Importantly, CCP5 is known to remove the branch-point glutamate residue, the final step in deglutamylation. While axonemal polyglutamylation levels remained largely unaffected in these mutants, abundance of short-chain glutamylation was significantly increased in both the axonemal and cytoplasmic microtubules of ccp5-1, consistent with CCP5s role as a branch-point deglutamylase. Although each single mutant exhibited slightly reduced swimming velocity, the loss of CCP5 in the tpg1 background lacking long polyglutamate side chains resulted in a significant restoration of motility. These findings indicate that the abundance of short-chain species, regulated by CCP5, plays a distinct role in modulating ciliary motility, particularly in the absence of long polyglutamate side chains. This suggests that even minimal glutamylation can functionally support dynein-driven microtubule sliding.

cell biology↗

bioRxiv2025

Tubulin Acetylation Deficiency Promotes Axonemal Turnover and Increases Cytoplasmic Microtubules

Tubulin post-translational modifications regulate microtubule dynamics; among these, -tubulin acetylation has been linked to microtubule stability. We generated a Chlamydomonas mutant lacking the acetyltransferase TAT1, which completely abolished -tubulin K40 acetylation. Surprisingly, the lengths of normally acetylated structures, axonemes and rootlets, were largely unaffected. TAT1 localized to the flagellar tip, suggesting that it is the primary site of acetylation. Loss of acetylation caused an increase in axonemal tubulin turnover, as revealed by dikaryon-fusion assays. Unexpectedly, the tat1 mutant displayed an increased number of dynamic cytoplasmic microtubules and could regenerate long flagella after amputation, even when protein synthesis was inhibited. Despite these cytoskeletal changes, steady-state flagellar length, cell growth, and cell division remained essentially normal. These findings suggest that acetylation modulates microtubule behavior by regulating axonemal tubulin turnover and cytoplasmic microtubule dynamics, while cellular morphology is buffered against variations in microtubule content.

cell biology↗

bioRxiv2025

mKast knockout honey bees show defects in brain functions underlying homing ability

Honey bees visit food sources up to several kilometers away from their hives, which is underpinned by their sophisticated learning and memory, and cognitive abilities. However, the molecular and neural bases for these advanced brain functions remain obscure. Here, we focused on mKast, a gene preferentially expressed in the optic lobes, a visual center, and a specific Kenyon cell subtype in the mushroom bodies, a higher-order center, in the honey bee brain. We successfully produced homozygous mutant honey bee workers by crossing individuals mutated with CRISPR/Cas9 targeting mKast. Through behavioral analyses of mKast mutants using a new conditioning paradigm and a visual response assay, we found that mKast functions in bimodal learning and memory based on olfactory and visual information, and direction-specific motion sensing. We also found that mKast homozygous mutants have defects in survival outside the colony. These findings suggest that mKast modulate brain functions underlying homing ability that is essential for nidificating hymenopteran species.

animal behavior and cognition↗

bioRxiv2025

Blaming Luck, Claiming Skill: Self-Attribution Bias in Error Assignment

Mistakes are valuable learning opportunities, yet in uncertain environments, whether a lack of reward is due to poor performance or bad luck can be hard to tell. To investigate how humans address this issue, we developed a visuomotor task where rewards depended on either skill or chance. Participants consistently displayed a self-attribution bias, crediting successes to their own ability while blaming failures on randomness, an effect that influenced their subsequent decisions. Computational modelling revealed two underlying mechanisms--a distorted perception of ability and a positivity bias in the skill condition. Notably, while distorted self-perception shaped behaviour, it did not affect confidence; instead, self-attribution bias led to overconfidence in external blame. These findings suggest a more complex picture in which self-attribution biases arise from both perceptual distortions and post-decision evaluations, highlighting the need for an interplay between experimental design and computational modelling to understand behavioural biases.

animal behavior and cognition↗

bioRxiv2025

Analysis of molecular and cellular bases of honey bee mushroom body development

Honey bee mushroom bodies (MBs) comprise three class I Kenyon cell (KC) subtypes (lKC, mKC, and sKC) with distinct somata sizes and locations and gene expression profiles. While these KC subtypes have been suggested to function in different behavioral regulations, the molecular and cellular basis of their development remains obscure. Here, we showed that lKCs, mKCs, and sKCs are produced in that order at different pupal stages by labeling proliferating MB cells with 5-ethynil-2-deoxyuridine at various pupal stages. RNA-sequencing analysis of FACS-sorted pupal MB cells identified genes that were upregulated in proliferating and non-proliferating MB cells, respectively. Furthermore, in situ hybridization of some of these genes labeled the proliferating cells or young KCs in the pupal MBs. Our findings reveal the basic scheme of the molecular and cellular processes of honey bee MB development and suggest that they are at least partially different from those of Drosophila MB development.

developmental biology↗

bioRxiv2024

Raman flow cytometry using time delay integration

Raman flow cytometry offers chemically sensitive, label-free measurement of cells and particles; however, the technique suffers from low cell throughput due to the weak Raman signal. Here, we demonstrate the use of time-delay integration to achieve Raman flow cytometry combined with dual-sided line illumination. The use of line illumination from both sides of the cell flow capillary kept the cell stream in the detection area by balancing optical force from the illumination lines. The time-delay integration allowed accumulation of Raman signals from flowing cells without sacrificing the spectrum readout rate. With the developed system, we achieved Raman flow cytometry at throughputs of 32 and 75 events per second for cell and particle detection, respectively. We applied the technique for analyzing lipid uptake in HepG2 cells and degranulation in bone marrow-derived murine mast cells.

biophysics↗

bioRxiv2024

High-Recovery Desalting Tip Columns for a Wide Variety of Peptides in Mass Spectrometry-based Proteomics

In mass spectrometry-based proteomics, loss-minimized peptide purification techniques play a key role in improving sensitivity and coverage. We have developed a desalting tip column packed with thermoplastic polymer-coated chromatographic particles, named ChocoTip, to achieve high recoveries in peptide purification by pipette-tip-based LC with centrifugation (tipLC). ChocoTip identified more than twice as many peptides from 20 ng of tryptic peptides from Hela cell lysate compared to a typical StageTip packed with chromatographic particles entangled in a Teflon mesh in tipLC. The high recovery of ChocoTip in tipLC was maintained for peptides with a wide variety of physical properties over the entire retention time range of the LC/MS/MS analysis, and was especially noteworthy for peptides with long retention times. These excellent properties are attributable to the unique morphology of ChocoTip, in which the thermoplastic polymer covers the pores, thereby inhibiting irreversible adsorption of peptides into mesopores of the chromatographic particles. ChocoTip is expected to find applications, especially in clinical proteomics and single-cell proteomics, where sample amounts are limited.

biochemistry↗

bioRxiv2024

Downregulation of Semaphorin 4A in keratinocytes reflects the features of non-lesional psoriasis

AbstractPsoriasis is a multifactorial disorder mediated by IL-17-producing T cells, involving immune cells and skin-constituting cells. Semaphorin 4A (Sema4A), an immune semaphorin, is known to take part in T helper type 1/17 differentiation and activation. However, Sema4A is also crucial for maintaining peripheral tissue homeostasis and its involvement in skin remains unknown. Here, we revealed that while Sema4A expression was pronounced in psoriatic blood lymphocytes and monocytes, it was downregulated in the keratinocytes of both psoriatic lesions and non-lesions compared to controls. Imiquimod application induced more severe dermatitis in Sema4A knockout (KO) mice compared to wild-type (WT) mice. The naive skin of Sema4AKO mice showed increased T cell infiltration and IL-17A expression along with thicker epidermis and distinct cytokeratin expression compared to WT mice, which are hallmarks of psoriatic non-lesions. Analysis of bone marrow chimeric mice suggested that Sema4A expression in keratinocytes plays a regulatory role in imiquimod-induced dermatitis. The epidermis of psoriatic non-lesion and Sema4AKO mice demonstrated mTOR complex 1 upregulation, and the application of mTOR inhibitors reversed the skewed expression of cytokeratins in Sema4AKO mice. Conclusively, Sema4A- mediated signaling cascades can be triggers for psoriasis and targets in the treatment and prevention of psoriasis.

immunology↗

bioRxiv2023

Modification of clinical dental impression methods to obtain dental traits from living and whole non-mammalian vertebrates

Dental impressions, developed for accurate capture of oral characteristics in human clinical settings, are seldom used in research on non-livestock, non-primate, and especially non-mammalian, vertebrates due to a lack of appropriate tools. Studies of dentitions in most vertebrate species usually require euthanasia and specimen dissection, microCT and other scans with size and resolution tradeoffs, and/or ad-hoc individual impressions or removal of single teeth. These approaches prevent in-vivo studies that factor in growth and other chronological changes and separates teeth from the context of the whole mouth. Here, we describe a non-destructive method for obtaining high resolution dentition-related traits that can be used on both living animals and museum specimens for almost all vertebrates, involving a customizable and printable dental impression tray. This method has repeatedly and accurately capture whole-mouth morphology and detailed features at high resolution in the living non-teleost actinopterygian fish, Polypterus senegalus, in a laboratory setting. It can be used for comparative morphology and to observe temporal changes such as the presence of microwear, tooth replacement rates, and occlusal and morphological changes through ontogeny. Summary statementThis study presents a cheap and customizable method using a printable tray to measure oral morphological traits in vertebrates humanely and accurately.

evolutionary biology↗

bioRxiv2023

Time-deterministic cryo-optical microscopy

We developed a technique to rapidly freeze biological systems during observation under an optical microscope, which allows for detailed optical observation at a precise time in the biological dynamics at high spatial resolution and quantifiability under low-temperature conditions. Our study further found that ion distributions and molecular conformations can be fixed in space and time, demonstrated by visualization of calcium waves rapid-frozen at an instant using fluorescent ion indicators. These results show that time-deterministic cryo-optical microscopy can suspend cellular dynamics while maintaining molecular and ionic states, allowing us to view cellular dynamics in a way that has not been possible before. One-Sentence SummaryRapid freezing of dynamic biological systems during optical observation presents time information to the fixed samples

biophysics↗

bioRxiv2023

Selective plane activation structured illumination microscopy

Resolution enhancement in structured illumination microscopy is hindered when volumetric samples are observed owing to background signals from out-of-focus planes. In this study, we utilized selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. We demonstrated high-resolution fluorescence imaging of volumetric samples, including dense fluorescent objects in a cell spheroid.

biophysics↗

bioRxiv2023

Analysis of antennal responses to motion stimuli in the honey bee by automated tracking using DeepLabCut

Considering recent developments in gene manipulation methods for honey bees, establishing simple, robust, and indoor assay systems which can analyze behavioral components in detail is important for the rise of honey bee behavioral genetics. We focused on the movements of antennae of the honey bee, which are used for not only multimodal sensory perception but also interactions between individuals. We developed an experimental system for analyzing the antennal responses (ARs) of the honey bee using DeepLabCut, a markerless posture-tracking tool using deep learning. The tracking of antennal movements during the presentation of vertical (downward and upward) motion stimuli using DeepLabCut successfully detected the ARs reported in the previous studies, where bees tilted their antennae in the direction opposite to the motion stimuli. In addition, we successfully detected ARs in response to horizontal (forward and backward) motion stimuli. An investigation of the developmental maturation of honey bee ARs showed that ARs to motion stimuli were not detected in bees immediately after emergence but became detectable through post-emergence development in an experience-independent manner. Furthermore, unsupervised clustering analysis using multidimensional data created by processing tracking data using DeepLabCut classified antennal movements into different clusters, suggesting that data-driven behavioral classification can apply to AR paradigms. These results reveal novel AR to visual stimuli and developmental maturation of ARs and suggest the efficacy of data-driven analysis for behavioral classification in behavioral studies of the honey bee. Summary statementAutomated tracking using DeepLabCut was successfully applied to measure the antennal response to motion stimuli and unsupervised classification of antennal movements in honey bees.

animal behavior and cognition↗

bioRxiv2023

Distinct roles of α- and β-tubulin C-terminal tails for ciliary function as revealed by a CRISPR/Cas9 mediated gene editing in Chlamydomonas

- and {beta}-tubulin have an unstructured glutamate-rich region at their C-terminal tails (CTT). The function of this region in cilia/flagella is still unclear, except that glutamates in CTT act as the sites for posttranslational modifications that affect ciliary motility. A unicellular alga Chlamydomonas possesses only two -tubulin genes and two {beta}-tubulin genes, each pair encoding an identical protein. This simple gene organization may enable a complete replacement of the wild-type tubulin with its mutated version. Here, using CRISPR/Cas9, we generated mutants expressing tubulins with modified CTTs. We found that the mutant whose four glutamate residues in the -tubulin CTT have been replaced by alanine almost completely lacked polyglutamylated tubulin and displayed paralyzed cilia. In contrast, the mutant lacking the glutamate-rich region of the {beta}-tubulin CTT assembled short cilia without the central apparatus. This phenotype is similar to the mutants harboring a mutation in a subunit of katanin, whose function has been shown to depend on the {beta}-tubulin CTT. Therefore, our study reveals distinct and important roles of - and {beta}-tubulin CTT in the formation and function of cilia. Summary statementChlamydomonas mutants were produced by CRISPR/Cas9 mediated gene editing to investigate ciliary function of tubulin C-terminal tails (CTTs). We found that - and {beta}-tubulin CTTs are essential for ciliary motility and assembly.

cell biology↗

bioRxiv2022

TRIAC disrupts cerebral thyroid hormone action via a negative feedback loop and heterogenous distribution among organs

3,3,5-triiodothyroacetic acid (TRIAC) is a metabolite of endogenous thyroid hormones (THs) that can bind to and activate TH receptors. As TRIAC was previously detected in sewage effluent, we aimed to investigate exogenous TRIACs potential for endocrine disruption. We administered either TRIAC or 3,3,5-triiodo-L-thyronine (LT3) to both euthyroid mice and 6-propyl-2-thiouracil-induced hypothyroid mice. In hypothyroid mice, TRIAC alleviated growth retardation, suppressed the hypothalamus-pituitary-thyroid (HPT) axis, and upregulated TH-responsive genes in the pituitary gland, liver, and heart. We observed that, unlike LT3, TRIAC does not upregulate the expression of TH-responsive genes in the cerebrum. Measurement of organ-specific TRIAC levels suggested that TRIAC was not efficiently trafficked into the cerebrum. Furthermore, by analyzing euthyroid mice, we found that cerebral TRIAC levels did not increase despite TRIAC administration at higher concentrations, whereas serum and cerebral TH levels were substantially decreased. Hence, TH-responsive genes in the cerebrum appear to be downregulated by TRIAC. In summary, TRIAC administration decreases circulating TH levels by suppressing the HPT axis, while the consequent attenuation of TH actions was compensated by TRIAC in peripheral tissues but not in the cerebrum due to the relative impermeability of the blood-brain barrier towards TRIAC. We verified that exogenous TRIAC disrupts TH actions in the cerebrum. This disruption is apparently due to the additive effects of circulating endogenous THs being depleted via a negative feedback loop involving the HPT axis and heterogenous distribution of TRIAC among different organs. Our findings indicate that environmental TRIAC poses a potential neurodevelopmental risk.

ecology↗