Biology subjects

Kubota, S.

Publications and source records attributed to Kubota, S..

13 recordsLinked to original sources

bioRxiv2026

Crop-associated differences in soil chemical properties and root-associated bacterial communities between Welsh onion and sweet potato

Crop species may shape soil chemical properties and root-associated microbiota, but direct comparisons between contrasting crops remain limited. We compared soils and root-associated bacterial communities of Welsh onion (Allium fistulosum) and sweet potato (Ipomoea batatas) under the same field context. Sweet potato soil showed significantly lower electrical conductivity, inorganic nitrogen, and Mg saturation than control soil. Root-associated communities differed between crops, whereas alpha diversity did not. Proteobacteria-related taxa were more represented in Welsh onion roots, whereas Actinomycetia-related taxa were more represented in sweet potato roots, providing a basis for future studies on crop-specific soil microbial management.

microbiology↗

bioRxiv2026

Hierarchical neuronal processing in primary somatosensory cortex during action observation

Voluntary movement requires the central nervous system to transform and integrate visual and somatosensory information into coordinated motor outputs. Although mirror-like neuronal activity during both action execution and observation has been extensively described in premotor, motor, and parietal cortices, it remains unknown whether the primary somatosensory cortex (S1) also participates in the action observation network. Here, we recorded single-unit activity from cytoarchitectonically defined areas 3a, 3b, 1, and 2 in macaque S1 while monkeys either executed or observed grasping movements. Approximately one-third of neurons across S1 modulated their firing during action observation, with the proportion of responsive neurons increasing from area 3 to areas 1 and 2, consistent with the hierarchical organization of somatosensory processing. Most action observation neurons showed congruent activity during action execution and observation, suggesting that these responses may reflect top-down motor-related or integrated visuomotor signals and are unlikely to be explained by visual input alone. The higher prevalence of action observation neurons in areas 1 and 2 suggests that action observation-related signals preferentially influence later stages of somatosensory processing, potentially via cortico-cortical interactions with motor and parietal regions.

neuroscience↗

bioRxiv2026

Interleukin-11 promotes the colonic epithelial organoid regeneration from mechanical disruption

The intestinal epithelium relies on rapid repair to maintain homeostasis after injury, and dysregulation of this process contributes to the pathogenesis of inflammatory bowel disease and colorectal cancer. Interleukin-11 (IL-11), a fibroblast-derived cytokine elevated in these diseases, has well-documented effects on stromal cells, but its direct action on intestinal epithelial cells remains poorly characterized. Here, we used mouse colon organoids as an isolated epithelial system to directly examine the effects of IL-11 on epithelial cells. IL-11 stimulation activated the canonical JAK/STAT3 pathway, as evidenced by increased STAT3 phosphorylation and Socs3 induction in a concentration-dependent manner. In a pipetting-based mechanical disruption model, IL-11 significantly increased the number of organoids recovered. Although mechanical disruption dominated the overall transcriptional landscape, RNA-seq analysis identified coordinated upregulation of STAT3 target genes and proliferation-related pathways specifically in response to IL-11. Pharmacological inhibition of STAT3 attenuated the IL-11-induced promotion of organoid recovery, indicating that STAT3 signaling mediates the epithelial response to IL-11 and maintains organoid size under basal conditions. Together, these findings demonstrate that IL-11 directly promotes intestinal epithelial repair after mechanical disruption through STAT3-dependent signaling, providing a mechanistic basis for its protective role in acute colonic injury.

cell biology↗

bioRxiv2025

Protocol for intra-nerve AAV injection and dorsal root potential recording for optogenetic modulation of the peripheral sensory nerve activity

Optogenetic modulation of peripheral sensory nerve activity holds great potential for the treatment of sensory disorders. Here, we present a protocol for applying optogenetic techniques to peripheral sensory nerves using an adeno-associated virus (AAV) vector. We describe the procedure for gene transduction into dorsal root ganglion neurons via retrograde transport following intra-nerve AAV injection. We then outline a terminal, acute electrophysiological experiment to evaluate optogenetic effects at the level of the dorsal root. For complete details on the use and execution of this protocol, please refer to Kosugi et al1. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693516v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@5a2de4org.highwire.dtl.DTLVardef@7ad4f0org.highwire.dtl.DTLVardef@32113aorg.highwire.dtl.DTLVardef@10918c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Stomatal, mesophyll, and biochemical limitation to photosynthesis of soybeans under waterlogging and reoxygenation

While waterlogging stress slows photosynthetic rate (Asat), the underlying processes remain poorly understood. Here, we aimed to characterize the limitations to photosynthesis imposed by stomatal conductance (gs), mesophyll conductance (gm), and biochemical processes under waterlogging and subsequent reoxygenation. Two soybean cultivars (Glycine max L. cv. Fukuyutaka and Iyodaizu) were subjected to 6 days of waterlogging, after which excess water was drained. The responses of Asat, gs, gm, and the maximum carboxylation rate (Vcmax) were investigated. In both cultivars, A declined significantly within 4 days of waterlogging and did not recover completely by two weeks of reoxygenation. During waterlogging, CO2 concentration at carboxylation site decreased in parallel with gs and gm, indicating that photosynthesis was mainly limited by diffusional factors (combination of gs and gm). After drainage, diffusional limitation persisted during early reoxygenation, whereas biochemical limitation due to reduced Vcmax became dominant after 7 days of reoxygenation. Therefore, maintaining high diffusional conductances and Vcmax during waterlogging and reoxygenation, respectively, is important for enhancing photosynthetic tolerance to waterlogging stress. Overall, our results demonstrate that Asat under waterlogging and reoxygenation is dynamically constrained by multiple factors, emphasizing the need for comprehensive assessment of gas diffusion and carbon assimilation processes.

plant biology↗

bioRxiv2025

Dynamic and context-dependent modulation of proprioceptive input in primate primary motor cortex

During voluntary movement, somatosensory input is attenuated--sensory gating--which may prevent the CNS from being overwhelmed by predictable afferent feedback not essential for motor control. In the cerebral cortex, sensory gating has been demonstrated in primary (S1) and higher-order sensory areas. The primary motor cortex (M1) is the major cortical output relay to the spinal cord and muscles, and proprioceptive feedback is crucial for shaping motor output, much as in S1. However, whether proprioceptive signals to M1 are attenuated during movement, and if so, why, remains unclear. We recorded somatosensory-evoked potentials (SEPs) in M1 of two monkeys performing a wrist task while electrically stimulating muscle and cutaneous afferents innervating forearm extensors and adjacent skin. Both local field potentials and single-neuron recordings revealed significant suppression of muscle-evoked SEPs during Active movement and Static hold phases, providing direct evidence that proprioceptive input to M1 is generally gated during motor execution, as previously reported for cutaneous input. Yet, amidst this suppression, SEPs in a subset of M1 neurons were preserved during Static hold, especially those evoked by antagonist muscle afferents. Because monkeys had to maintain precise joint angles for stable posture, these results suggest that proprioceptive signals from antagonist muscles--likely reflecting spindle activity in lengthening muscles--escape attenuation to provide information essential for joint angle control. Overall, our findings demonstrate that while proprioceptive input to M1 is broadly suppressed during motor output, specific afferent signals from antagonist muscles are selectively maintained in a context-dependent manner to support posture control.

neuroscience↗

bioRxiv2025

Impact of Low-Dose Narrowband UV Radiation on Skin Tissue and Mast Cells in a Canine Model

Narrowband ultraviolet radiation (NB-UVR) therapy is widely utilized in dermatology worldwide. While the immunosuppressive effects of ultraviolet radiation are well-documented, its non-inflammatory effects remain poorly understood. This study evaluated the effects of sub-minimal erythema dose (MED) narrowband ultraviolet radiation using a canine model. The effects of narrowband-ultraviolet B (310 nm) and A2 wavelengths (320 and 330 nm) were compared. Initially, we demonstrated the therapeutic potential of NB-UVR in dogs with spontaneous atopic dermatitis (n = 6, p < 0.05). Following 300 mJ/cm{superscript 2} sub-MED ultraviolet radiation exposure, intradermal skin testing, skin mast cell counts, and RNA sequencing analysis were conducted. Additionally, cell viability (WST assay) and apoptosis (DAPI staining) were assessed in vitro using a canine mast cell line. Ultraviolet radiation exposure significantly reduced intradermal skin test scores across all wavelengths and decreased skin mast cell counts at 310 nm (n = 3, p < 0.05). In vitro, cell viability was significantly reduced at 310 and 320 nm (p < 0.05), and 310 nm irradiation specifically increased apoptotic cell numbers (p < 0.05). RNA sequencing identified 71 differentially expressed genes at 320 nm, with enrichment analysis highlighting muscle cell components and functions, potentially associated with arrector pili muscle activity. These findings suggest that 310 nm irradiation induces apoptosis, while 320 nm elicits non-inflammatory modulatory effects, highlighting distinct wavelength-specific therapeutic mechanisms of narrowband ultraviolet radiation.

immunology↗

bioRxiv2024

Population genomics reveals demographic history and climate adaptation in Japanese Arabidopsis halleri

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history, and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge ([~]50 kya). The ecological niche modeling predicted the range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans, and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.

evolutionary biology↗

bioRxiv2023

Bioinformatic and fine-scale chromosomal mapping uncover the essence and evolution of eliminated chromosomes in the Japanese hagfish, Eptatretus burgeri, through repetitive DNA family analysis

In the Japanese hagfish, Eptatretus burgeri, approximately 21% of the genomic DNA in germ cells (2n=52) consists of 16 chromosomes (eliminated [E]-chromosomes) that are eliminated from presumptive somatic cells (2n=36). To uncover the eliminated genome (E-genome), we have identified 16 eliminated repetitive DNA families from eight hagfish species, with 11 of these repeats being selectively amplified in the germline genome of E. burgeri. Furthermore, we have demonstrated that six of these sequences, namely EEEb1-6, are exclusively localized on all 16 E-chromosomes. This has led to the hypothesis that the eight pairs of E-chromosomes are derived from one pair of ancestral chromosomes via multiple duplication events over a prolonged evolutionary period. NGS analysis has recently facilitated the re-assembly of two distinct draft genomes of E. burgeri, derived from the testis and liver. This advancement allows for the prediction of not only nonrepetitive eliminated sequences but also over 100 repetitive and eliminated sequences, accomplished through K-mer-based analysis. In this study, we report four novel eliminated repetitive DNA sequences (designated as EEEb7-10) and confirm the relative chromosomal localization of all eliminated repeats (EEEb1-10) by fluorescence in situ hybridization (FISH). With the exception of EEEb10, all sequences were exclusively detected on EEEb1-positive chromosomes. Surprisingly, EEEb10 was detected as an intense signal on EEEb1-positive chromosomes and as a scattered signal on other chromosomes in germ cells. The study further divided the eight pairs of E-chromosomes into six groups based on the signal distribution of each DNA family, and fiber-FISH experiments showed that the EEEb2-10 family was dispersed in the EEEb1-positive extended chromatin fiber. These findings provide new insights into the mechanisms underlying chromosome elimination and the evolution of E-chromosomes, supporting our previous hypothesis.

molecular biology↗

bioRxiv2023

Modulation of somatosensory signal transmission in the primate cuneate nucleus during voluntary hand movement

Successful extraction of tactile and kinematic information is crucial for appropriate motor actions in daily life. To achieve this objective, sensory signals should be effectively regulated during motor actions. This regulation is understood both empirically and conceptually, but it is not well known where and how it is implemented in the central nervous system. Here, we show that, during voluntary movement, sensory signals are already attenuated in the primate cuneate nucleus, an early processing site in the ascending lemniscus pathway. The degree of suppression was comparable with the one reported in the cortex, suggesting that psychological attenuation of somatosensation could be ascribed to the cuneate. The results also revealed that this sensory attenuation was of descending origin, suggesting that cortical sensory prediction signals could regulate cuneate sensory transmission for extracting meaningful, and attenuate unnecessary, signals for movement regulation. This recurrent sensory modulation mechanism between cortical and subcortical areas may generalize to other sensory modalities and cognitive processes.

neuroscience↗

bioRxiv2020

SARM1 depletion rescues NMNAT1 dependent photoreceptor cell death and retinal degeneration.

Leber congenital amaurosis type 9 is an autosomal recessive retinopathy caused by mutations of the NAD+ synthesis enzyme NMNAT1. Despite the ubiquitous expression of NMNAT1, patients do not manifest pathologies other than retinal degeneration. Here we demonstrate that widespread NMNAT1 depletion in adult mice mirrors the human pathology, with selective loss of photoreceptors highlighting the exquisite vulnerability of these cells to NMNAT1 loss. Conditional deletion demonstrates that NMNAT1 is required within the photoreceptor. Mechanistically, loss of NMNAT1 activates the NADase SARM1, the central executioner of axon degeneration, to trigger photoreceptor death and vision loss. Hence, the essential function of NMNAT1 in photoreceptors is to inhibit SARM1, highlighting an unexpected shared mechanism between axonal degeneration and photoreceptor neurodegeneration. These results define a novel SARM1-dependent photoreceptor cell death pathway and identifies SARM1 as a therapeutic candidate for retinopathies.

neuroscience↗

bioRxiv2019

Correlation between increased atrial expression of genes related to fatty acid metabolism and autophag y in patients with chronic atrial fibrillation

Atrial metabolic disturbance contributes to the onset and development of atrial fibrillation (AF). Autophagy plays a role in maintaining the cellular energy balance. We examined whether the altered atrial expression of genes related to fatty acid metabolism is linked to that related to autophagy in chronic AF. Right atrial tissue was obtained during heart surgery from 51 patients with sinus rhythm (SR, n=38) or chronic AF (n=13). Preoperative fasting serum free-fatty-acid levels were significantly higher in the AF patients. The atrial gene expression of fatty acid binding protein 3 (FABP3), which is involved in the cells fatty acid uptake and intracellular fatty acid transport, was significantly increased in AF patients compared to SR patients; in the SR patients it was positively correlated with the right atrial diameter and intra-atrial EMD, parameters of structural and electrical atrial remodeling that was evaluated by an echocardiography. In contrast, the two groups atrial contents of diacylglycerol (DAG), a toxic fatty acid metabolite, were comparable. Importantly, the atrial gene expression of microtubule-associated protein light chain 3 (LC3) was significantly increased in the AF patients, and autophagy-related genes including LC3 were positively correlated with the atrial expression of FABP3. In conclusion, in chronic AF patients, the atrial expression of FABP3 was upregulated in association with autophagy-related genes without altered atrial DAG content. Our findings may support the hypothesis that dysregulated cardiac fatty acid metabolism contributes to the progression of AF and induction of autophagy has a cardioprotective effect against cardiac lipotoxicity in chronic AF.

molecular biology↗

bioRxiv2019

Pool walking may temporarily improve renal function by suppressing renin-angiotensin-aldosterone system in pregnant women

BackgroundThis study aimed to examine the effect of pool walking on renal function in pregnant women. MethodsFifteen pregnant women (mean gestational age, 37.8 weeks) walked in a pool (depth 1.3 m) for 1 h. A few days later, they walked on a street for 1 h. Within each activity, the starting and ending levels of plasma renin activity (PRA) and serum aldosterone (SA) were compared using paired t-test. Total urine volume, creatinine clearance, and change in PRA levels between each activity were compared by t-test. Regression coefficients for total urine volume and creatinine clearance during pool walking were estimated by linear regression and additionally controlled for the change in PRA levels. Land walking served as the reference group. ResultsWithin each activity, the renin-angiotensin-aldosterone levels were suppressed during pool walking: the mean starting and ending values of PRA and SA were 6.8 vs. 5.5 ng/mL/h (p=0.002) and 654 vs. 473 pg/mL (p=0.02), respectively. Compared to land walking, the decrease in PRA level was more evident in pool walking (-1.27 vs. 0.81 ng/mL/h, p=0.004), resulting in higher total urine volume and creatinine clearance in pool walking (both p<0.05). In regression analysis, after controlling for the change in PRA levels, the significantly elevated regression coefficients for total urine volume and creatinine clearance in pool walking were attenuated. ConclusionsPool walking may temporarily improve renal function in pregnant women, partly through the suppressed renin-angiotensin-aldosterone system. Clinical Trial RegistrationURL: https://upload.umin.ac.jp/cgi-bin/ctr/ctr_view_reg.cgi?recptno=R000010618 Unique Identifier: UMIN000009051

clinical trials↗