Biology subjects

Tamura, K.

Publications and source records attributed to Tamura, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Individual leadership in cattle persists when collective movement is induced by robotic herding

In social species, some individuals consistently lead collective movements while others follow, but whether these roles persist when movement is externally induced remains unknown. Robotic herding offers a way to address this: animals are displaced by an approaching device, yet retain the option to stay, to move or to follow a conspecific that has moved. We recorded spontaneous group departures in a herd of 18 Japanese Black cows on three days, then recorded which individuals initiated movement away from a quadruped robot, which followed and which remained, across an eight-day herding trial. Cows that frequently initiated spontaneous departures and attracted followers also initiated movement away from the robot more often and drew more followers, whereas habitual followers tended to be less effective initiators. Follower frequency during herding was unrelated to any characteristic measured. Individual leadership therefore persists when movement is induced by a robot. Behavioural roles may thus be expressed under moderate external constraint, provided animals retain some freedom of choice. Identifying leaders from spontaneous departures offers a practical route to more efficient robotic herding.

animal behavior and cognition↗

bioRxiv2026

Gut microbiome signatures precede chronic kidney disease diagnosis in a large canine cohort

Chronic kidney disease (CKD)-associated dysbiosis is well described after diagnosis, but whether microbial changes precede clinical recognition is unclear. We integrated insurance claims, fecal and oral 16S rRNA profiles, and clinical laboratory data from companion dogs. Among 140,025 dogs, lower gut microbial diversity was associated with incident CKD after adjustment for age, sex and body size. Prediagnostic samples showed reduced evenness-related diversity, modest community shifts and seven differentially abundant genera. A five-genus score was elevated more than two years before diagnosis, although it was derived and evaluated in the same cohort and was not intended as a predictive model. In a laboratory subset, microbial changes preceded the largest increases in blood urea nitrogen and creatinine. Paired oral-gut samples showed limited exploratory associations between periodontal-associated taxa and the gut score. These findings identify microbial features associated with future claims-defined canine CKD and support independent validation and mechanistic investigation.

microbiology↗

bioRxiv2026

Animal-robot interaction in the field: stronger responses and slower habituation of grazing cattle to a quadruped robot than to a drone

Robotic herding offers a promising off-animal approach to controlling the spatial distribution of grazing livestock. Nevertheless, the habituation of cattle to herding stimuli remains a critical obstacle to its practical use. This study presents the first field investigation of behavioral responses of grazing cattle to herding by a quadruped robot. We compared the herding efficacy of a drone and a quadruped robot, and tracked daily changes in responsiveness during continuous herding. Trials were conducted in a 1.1-ha pasture with Japanese Black breeding cows from June to October 2023. The quadruped robot elicited stronger avoidance responses with shorter latencies than the drone, and herding was more successful with the robot. During consecutive daily herding with the robot, behavioral responsiveness declined progressively over the initial 5 days, at a markedly slower rate than previously reported for drone herding. Following a 24-day interruption, responsiveness partially increased, but declined rapidly again over the subsequent two days. These results indicate that the quadruped robot constitutes a more persistent aversive stimulus than a drone for grazing cattle, although habituation management strategies (such as diversifying stimuli or combining sensory modalities) will be necessary for sustained control of grazing distribution.

animal behavior and cognition↗

bioRxiv2026

Tiny Subsamples and Upsampling Tame Big Data Evolutionary Analysis in Phylogenomics

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework, in which small subsamples of sites from a concatenated alignment are expanded by upsampling before inference, and the resulting analyses are then aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-data analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures, while reducing runtime and memory requirements by orders of magnitude. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical across diverse datasets. We suggest that PSU is a general strategy for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

evolutionary biology↗

bioRxiv2026

Gluconeogenesis and glycogen metabolism in the epidermis and endoderm of Xenopus tropicalis embryos and larvae.

In many oviparous animals, egg yolk is the sole source of nutrition until feeding begins, and carbohydrates are present in only small amounts in the yolk. Glucose plays an important role in the developmental processes of various animals. In addition, gluconeogenesis has been reported to occur in the yolk syncytial layer (YSL) of cartilaginous fish and teleosts. In contrast, the role of gluconeogenesis in tetrapods remains unclear. In this study, we used Xenopus tropicalis, an anuran amphibian, which lacks YSL, and therefore provide an opportunity to examine the evolutionary conservation of gluconeogenic mechanisms among vertebrates. In X. tropicalis, liquid chromatography/mass spectrometry revealed that glucose levels increased before liver formation. Subsequent tracer experiments using 13C-labeled metabolic substrates detected gluconeogenesis activity from glycerol and lactate. Expression analyses showed that gluconeogenic genes are expressed in the epidermis and endoderm. Consistently, generation 0 (G0) knockout of fbp1, a key gluconeogenic gene, resulted in a significant reduction in glucose levels, affecting brain development. These findings first demonstrate that gluconeogenesis supports development of X. tropicalis. To the best of our knowledge, gluconeogenesis in developing epidermis has not been reported, highlighting previously unrecognized diversity in tissue-specific metabolism during vertebrate development. Comparative analyses across species will provide further insights into the evolution and functional significance of embryonic gluconeogenesis and nutrient metabolism.

developmental biology↗

bioRxiv2026

A cyanobacterial adenine prenyltransferase enables longer-chain N6 prenylation

Adenine, a ubiquitous nucleobase found in biomolecules such as nucleic acids, cofactors, and signaling molecules, mediates diverse molecular interactions. Here, we identify TvAPT, an adenine prenyltransferase from the cyanobacterium Trichormus variabilis NIES-23. TvAPT efficiently catalyzes the unprecedented N6-prenylation of adenine-containing substrates using extended C10 and C15 prenyl donors, whereas canonical adenine prenyltransferases are generally limited to C5-dimethylallylation. X-ray structural analyses and protein engineering revealed that an enlarged prenyl-binding pocket enables the accommodation of extended prenyl donors, providing a structural basis for rationally tuning prenyl-donor preference. Together, these findings establish TvAPT as an adenine prenyltransferase that accepts a range of adenine-containing substrates, with a preference for nucleoside 5-monophosphates. Beyond expanding the known catalytic scope of adenine prenyltransferases, TvAPT provides access to nucleotide derivatives with enhanced membrane permeability and analogues of plant signaling molecules.

biochemistry↗

bioRxiv2026

A collagen orientation switch reshapes fin architecture

The orientation and distribution of fibrillar collagen are critical determinants of the shape and mechanical properties of bones and organs.1-3 However, how they are spatially organized within tissues is still poorly understood,4-7 as visualizing these collagen architectures remains challenging. Actinotrichia (AT), the spear-shaped fibrillar collagen structures located at the distal tips of fish fins, are easily observable due to their large size and distinctive morphology8-14 and have recently emerged as a model system for studying collagen fiber organization.15-19 In this study, we generated knockout lines for the fish-specific extracellular matrix (ECM) genes actinodin1 and actinodin2 (and1/2), which are lost in tetrapods.12 Loss of these genes dramatically altered the orientation of collagen fibers, thereby inducing changes in fin morphology. In the wild-type fins, AT are orderly arranged beneath the epidermis, forming layers parallel to the fin surface, and their individual fibers radiate distally toward the fin tip. In contrast, double knockout (dKO) of and1/2 results in overall fin reduction accompanied by increased thickness. Examination of the collagen structure distribution revealed the presence of aberrant collagen fibers oriented perpendicular to the fin epidermis. Moreover, the vertically oriented fibers contributed to thickening of the mesenchymal region in which they were distributed. The number of abnormal fibers increased with the severity of and1/2 deficiency, suggesting that collagen fibers in fins inherently tend to align perpendicular to the epidermis when these genes are absent. Furthermore, in tetrapods lacking the and gene family--specifically amphibians, the tetrapod group most closely related to fish20--examination of the developing limb, the organ homologous to paired fins in fish,21 revealed collagen fibers oriented perpendicular to the epidermis. The distribution pattern also resembled that observed in the fin buds of and1/2 dKO fish. Together, these findings highlight collagen patterning alterations as a previously unrecognized factor contributing to the evolutionary divergence between thinned fins and thickened limbs. Moreover, the identification of mutants that dramatically alter collagen fiber orientation is unprecedented, suggesting that analysis of Actinodin (And) function unveil the mechanisms underlying collagen matrix formation.22-28

developmental biology↗

bioRxiv2025

Genome editing of the flavanone 3-hydroxylase gene produces a green Perilla line with elevated luteolin accumulation

Perilla frutescens var. crispa is widely cultivated in East Asia and produces a diverse range of secondary metabolites with nutritional and medicinal value. Based on anthocyanin content, perilla is classified into red and green chemotypes. The anthocyanin biosynthetic pathway is highly conserved among plants, and the flavanone 3-hydroxylase gene (F3H) in red perilla is considered essential for this pathway. Here, we used CRISPR-Cas9 genome editing to generate novel Perilla lines with altered metabolite profiles. In four edited T plants, multiple biallelic indels, including a -3 bp in-frame deletion, were introduced at the target site. In the T generation, these mutations and the transgene segregated in a Mendelian manner, resulting in recovery of null-segregant plants. Metabolite analysis revealed strong suppression of anthocyanin biosynthesis and a significant increase in luteolin accumulation in edited lines compared with the wild type. Transcriptome analysis further confirmed the loss of F3H function, demonstrating a metabolic shift of the flavonoid pathway toward luteolin production. This study provides the first functional validation of F3H in perilla and highlights its potential application in breeding cultivars with controlled bioactive compound contents. Our findings also demonstrate practical strategies for implementing genome editing in non-model crops and developing high-value functional cultivars. Practitioner PointsO_LIEditing a single flavonoid biosynthetic gene (F3H) effectively alters pigment composition in perilla leaves. C_LIO_LIIncreased accumulation of luteolin-related compounds suggests potential for enhancing functional metabolites without complex pathway engineering. C_LIO_LIGenome editing offers a feasible tool for perilla improvement in breeding and functional food development. C_LI

plant biology↗

bioRxiv2025

Replication-independent eviction of H2B.8 reveals chromatin reprogramming during seed imbibition

The transition from seed to seedling involves major changes in nuclear organization and gene expression, yet the extent to which this developmental transition requires chromatin reprogramming remains largely unexplored. Here, we report that Arabidopsis dry seed embryos accumulate the histone variant H2B.8, which contributes to higher-order chromatin organization by forming spatial clusters that structure the 3D nuclear space. H2B.8 forms heterotypic nucleosomes at euchromatic transposons and lowly expressed genes and, during imbibition, modulates the transcriptional activation of a subset of these genes. Imbibition triggers a decrease in H2B.8 transcripts and the eviction of H2B.8 proteins in a process that operates independently of DNA replication but requires protein translation and de novo transcription. Histone eviction is not limited to H2B.8 as imbibition also induces the turnover of the H3.3 histone variant, thereby initiating a broad, replication-independent chromatin reprogramming process. These findings highlight a fundamental mechanism of epigenetic regulation during early plant development.

molecular biology↗

bioRxiv2025

Citizen science data indicates morphological complexity of galls depends on the originating plant organ

Galls are abnormal plant structures formed through interactions between host plants and insects, providing shelter and nutrients for gall-inducing insects. As distinct insect species can generate unique gall morphologies even on the same host plant, galls are often viewed as an extended phenotype of the insect. However, since galls consist of plant-derived cells, plant factors are also hypothesized to shape their morphology. Previous studies exploring this possibility have been restricted to one or a few plant species, limiting broad evolutionary inference. Here, we used citizen science observations to analyze gall morphological complexity across 26 plant orders. Quantitative comparisons using fractal dimension indices revealed that stem-derived galls display significantly less morphological variation than leaf-derived galls. Generalized linear mixed models indicated that stems possess lower morphological plasticity than leaves. These results held even after accounting for insect and plant phylogeny, suggesting that gall form is influenced by both insect species and the developmental properties of the host organ. Our findings highlight the role of plant organ identity in modulating gall morphology and demonstrate that tissue plasticity constrains insect-induced developmental outcomes. This study provides the large-scale cross-species analysis of gall formation and illustrates the power of citizen science in studying morphological evolution across taxa.

plant biology↗

bioRxiv2025

Identification of stem cell marker-positive subpopulations in the vocal fold of the larynx through transcriptomic analyses

Information on the maintenance of tissue homeostasis is important for the development of effective therapeutic methods, however, reports on the cellular composition and tissue stem cells of the larynx were scarce. Therefore, we analyzed mouse laryngeal mucosa using scRNA-seq, and spatial transcriptomics by photo-isolation chemistry, and performed the generation of laryngeal organoid used as an in vitro model from mouse laryngeal mucosa. As a result, we found a SOX9-positive basal cell subpopulation and a Lgr5-positive fibroblast subpopulation in the mouse vocal fold, and obtained three types of epithelial organoids from laryngeal epithelium. We also confirmed the differences in pseudostratified ciliated columnar epithelium composition between the supraglottis and subglottis of the mouse larynx. These findings provide novel insights and valuable tools for future research in laryngology and stem cell biology.

cell biology↗

bioRxiv2025

Actinotrichia-independent developmental mechanisms of spiny rays facilitate the morphological diversification of Acanthomorpha fish fins

Skeletal forms in vertebrates have been regarded as good models of morphological diversification. Fish fin forms are greatly diversified, and their bone structure is classified into soft rays and spiny rays. In fish evolution, spiny-ray morphologies are known to be sometimes extremely modified; however, it remains unknown how the developmental mechanisms of spiny-rays have contributed to their morphological diversification. By using the rainbowfish Melanotaenia praecox for examination of the extracellular matrix (ECM) and cell dynamics of spiny-ray development, we demonstrate that spiny-ray developments are independent of the actinotrichia (needle-shaped collagen polymers at the tip of fish fins), which are known as an important ECM in soft-ray morphogenesis. Furthermore, we found that in the thorny spiny-ray of the filefish Stephanolepis cirrhifer, the lateral protrusions equip the BMP positive osteoblast condensation, as in the state of the spiny-ray tips in M. praecox and S. cirrhifer. Taken together, our findings reveal that osteoblast distribution and signaling-molecule intensity would contribute to spiny-ray modification. In comparison to soft rays development, the independence from actinotrichia in spiny-rays would facilitate growth direction change, leading to their morphological diversification. This indicates that the cell distribution and ECM usage would be major factors driving the morphological diversification in animals.

evolutionary biology↗

bioRxiv2025

Continuous and widespread population interactions in the Jomon society via geometric morphometrics on 3D data of human crania

This study examines the morphological variations within and between regional populations via geometric morphometrics of larger samples of three-dimensional data of J[o]mon human crania (N = 363, including 146 females, 215 males and two unknown-sex individuals) from 97 sites to investigate the population interactions in the period, which Japanese anthropologists and archaeologists have extensively discussed. The results show that morphological variations are more pronounced within individual populations especially in the principal component one, relating to the facial width, degree of prognathism, and location of occipital areas, in contrast to the relatively smaller variations observed between different phases and geographical regions. This observation is consistent with the possibility that the population interactions of the J[o]mon people had been widespread and continuous, and which has an important implication for their resilience against severe climate changes at that time: The relative stability of the J[o]mon society might be sustained by their frequent interactions with various populations, as suggested by insights from relevant archaeological, ethnographic, and genetic research.

evolutionary biology↗

bioRxiv2025

Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits

Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present a novel comparative genomics approach to build genetic models that underlie the independent origins of convergent traits using evolutionary sparse learning. We test the hypothesis that common genes and sites are involved in the convergent evolution of two key traits: C4 photosynthesis in grasses and echolocation in mammals. Genetic models were highly predictive of independent cases of convergent evolution of C4 photosynthesis. These results support the involvement of sequence substitutions in many common genetic loci in the evolution of convergent traits studied. Genes contributing to genetic models for echolocation were highly enriched for functional categories related to hearing, sound perception, and deafness (P < 10-6); a pattern that has eluded previous efforts applying standard molecular evolutionary approaches. We conclude that phylogeny-informed machine learning naturally excludes apparent molecular convergences due to shared species history, enhances the signal-to-noise ratio for detecting molecular convergence, and empowers the discovery of common genetic bases of trait convergences.

evolutionary biology↗

bioRxiv2024

Biochemical state in tissue can be detected through ultrasound signal

Three-dimensional (3D) cell cultures, such as spheroids, are indispensable models for investigating cellular behaviors and responses under conditions that closely resemble in vivo environments. Conventional imaging techniques, including optical microscopy, are often limited by penetration depth and phototoxicity, complicating the analysis of structural and biochemical changes within dense 3D systems. This study demonstrates the application of ultrasound imaging for the non-invasive evaluation of internal dynamics in cancer spheroids over a 15-day period. Scattering-based acoustic parameters revealed spatial variations in brightness and density, correlating with cellular proliferation, apoptosis, and necrosis. Brightness values in central regions progressively decreased after Day 3, approaching near-zero by Day 15, reflecting necrotic core formation. Artificial inhibition of myosin contractility significantly influenced these patterns, providing insights into biomechanical contributions to spheroid organization. The findings establish ultrasound imaging as a label-free, high-penetration technique capable of addressing critical challenges in 3D culture analysis, offering new opportunities for studying cellular dynamics and therapeutic responses in spheroids and organoid models.

bioengineering↗

bioRxiv2024

MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing

We introduce the 12th version of the Molecular Evolutionary Genetics Analysis (MEGA) software. This latest version brings many significant improvements by reducing the computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These improvements are achieved by implementing heuristics that minimize likely unnecessary computations. Analyses of empirical and simulated datasets show substantial time savings by using these heuristics without compromising the accuracy of results. MEGA12 also implements an evolutionary sparse learning approach to identify fragile clades and associated sequences in evolutionary trees inferred through phylogenomic analyses. In addition, this version includes fine-grained parallelization for ML analyses, support for high-resolution monitors, and an enhanced Tree Explorer. The MEGA12 beta version can be downloaded from https://www.megasoftware.net/beta_download.

evolutionary biology↗

bioRxiv2024

Image retrieval based on closed-loop visual-semantic neural decoding

Neural decoding via the latent space of deep neural network models can infer perceived and imagined images from neural activities, even when the image is novel for the subject and decoder. Brain-computer interfaces (BCIs) using the latent space enable a subject to retrieve intended image from a large dataset on the basis of their neural activities but have not yet been realized. Here, we used neural decoding in a closed-loop condition to retrieve images of the instructed categories from 2.3 million images on the basis of the latent vector inferred from electrocorticographic signals of visual cortices. Using a latent space of contrastive language-image pretraining (CLIP) model, two subjects retrieved images with significant accuracy exceeding 80% for two instructions. In contrast, the image retrieval failed using the latent space of another model, AlexNet. In another task to imagine an image while viewing a different image, the imagery made the inferred latent vector significantly closer to the vector of the imagined category in the CLIP latent space but significantly further away in the AlexNet latent space, although the same electrocorticographic signals from nine subjects were decoded. Humans can retrieve the intended information via a closed-loop BCI with an appropriate latent space.

neuroscience↗

bioRxiv2024

Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices

The extensive long-range axonal projections of diverse classes of neocortical excitatory neurons are thought to contribute importantly to the highly integrative brain-wide interactions underlying the processing of sensory, cognitive and motor signals. Here, we investigated the long-range axonal output of various classes of genetically-defined projection neurons with cell bodies located in the whisker-related somatosensory cortices of the mouse through brain-wide light-sheet imaging of fluorescently-labeled axons segmented by specifically-trained convolutional networks quantified within the Allen Mouse Brain Atlas Common Coordinate Framework. We injected Cre-dependent virus to express GFP or tdTomato in the posterior primary somatosensory barrel cortex and the posterior supplemental somatosensory cortex, which contain the representations of the large posterior mystacial whiskers. We investigated the six following transgenic mouse lines which preferentially express Cre in different glutamatergic neocortical cell classes: Rasgrf2-dCre for layer 2/3 intratelencephalic projection neurons, Scnn1a-Cre for layer 4 intratelencephalic projection neurons, Tlx3-Cre for layer 5 intratelencephalic projection neurons, Sim1-Cre for layer 5 pyramidal tract projection neurons, Rbp4-Cre for layer 5 projection neurons and Ntsr1-Cre for layer 6 corticothalamic neurons. We found long-range axonal projections in many diverse downstream brain areas with largely similar output from primary and secondary cortices, but with genetically-defined cell classes showing distinct innervation patterns, with Rbp4-Cre mice showing the broadest innervation targets, subsets of which were innervated in the other mouse lines. To test whether the revealed axonal projections might underpin functional circuits, we compared the spatial organization of the axonal innervation with functional connectivity maps obtained from optogenetic stimulation of sensory cortex and wide-field imaging of the activity propagation to frontal cortices. Both methods indicated that neurons located more laterally in somatosensory cortex topographically signaled to more anteriorly located regions in motor cortex. The current methodology therefore appears to quantify brain-wide axonal innervation patterns supporting brain-wide signaling, and, together with further technological advances, this will help provide increasingly detailed connectivity information of the mouse brain, essential for understanding the complex neuronal circuitry underlying even simple goal-directed behaviors.

neuroscience↗