Biology subjects

Nakagawa, K.

Publications and source records attributed to Nakagawa, K..

16 recordsLinked to original sources

bioRxiv2026

Light Guiding in Scattering Media Using Focused Laser-Induced Acoustic Waves with an Open Elliptical Reflector

Light scattering in biological tissue limits deep optical imaging. Acoustic waves can modulate optical properties and enhance photon delivery, but source-positioning requirements can complicate integration with other imaging modalities. Here, we present an open elliptical reflector that focuses laser-induced acoustic waves at a spatially separated target while maintaining open optical access. We characterized the spatiotemporal optical modulation induced by the localized acoustic focus. The system increased the local transmitted-light intensity by a factor of 2.57-fold through a 2-mm-thick 1% intralipid hydrogel and enhanced fluorescence signal under two-photon excitation through a 1.5-mm-thick scattering sample. These results demonstrate spatially separated, reflector-based acoustically assisted light guiding for enhanced light delivery and fluorescence excitation through scattering media.

bioengineering↗

bioRxiv2026

Greater gray matter volume in somatosensory and parietal regions in elite skiers compared with other athletes

Elite athletes exhibit sport-specific neural adaptations, yet it remains unclear whether such changes reflect general effects of training or the unique demands of individual sports. Skiing requires postural control and whole-body coordination under dynamically unstable environments, placing high demands on somatosensory processing and sensorimotor integration. The present study aimed to identify structural brain characteristics specific to elite skiers by comparing them with athletes from other sports disciplines and non-athletes. T1-weighted MRI data were analyzed using voxel-based morphometry in 13 skiers, 23 non-ski control athletes and 25 non-athletes. Whole-brain analysis comparing skiers with non-ski athletes revealed a significant cluster showing greater gray matter volume in skiers compared with non-ski athletes in the left postcentral gyrus, extending into the superior parietal lobule. The identified cluster primarily encompassed cytoarchitectonic Areas 2 and 5L. These regions are involved in higher-order somatosensory processing and multisensory integration. Importantly, region-of-interest analysis demonstrated that gray matter volume within this cluster was greater in skiers compared with non-ski athletes and non-athletes, with no difference between non-ski athletes and non-athletes. These findings highlight the relative prominence of structural adaptations within somatosensory-parietal networks, reflecting the unique integration of proprioceptive and other sensory information required for elite skiing. Overall, these findings provide evidence for sport-specific structural brain differences in elite athletes and highlight the importance of somatosensory and parietal regions in sensorimotor integration relevant to skiing. These findings may have implications for understanding neural markers of expertise and may inform future approaches to training and performance evaluation in skiing.

neuroscience↗

bioRxiv2025

Plant-specific tau class glutathione transferases safeguard against lipid oxidation stress through dual detoxification of lipid peroxides and reactive carbonyl species

O_LIOxidation of membrane lipids results in the formation of lipid peroxides (LOOHs) and reactive carbonyl species (RCS), that induce lipid oxidation stress in plants. The plant-specific tau class of glutathione transferases (GSTUs) possess both LOOH peroxidase and RCS-conjugating activities, but their overall contribution to stress tolerance remains unclear. C_LIO_LIWe systematically examined 16 GSTU isozymes of Arabidopsis thaliana and found that all catalysed glutathione-dependent reduction of LOOHs. GSTU17, showing the highest activity, recognized five different isomers of linoleic acid-derived hydroperoxides within comparable catalytic efficiencies. C_LIO_LIT-DNA mutants lacking GSTU3, GSTU17, GSTU18, GSTU19 or GSTU25--isoforms with strong conjugation activities toward acrolein, 4-hydroxynonenal or crotonal--displayed enhanced sensitivity to photooxidative stress, indicating that detoxification of RCS is crucial for oxidative protection. C_LIO_LITranscriptome analyses revealed that exposure to RCS (crotonal, 2-pentenal or 2-hexenal) strongly induced 12 GSTU genes, while other GST classes showed little response. Collectively, these results demonstrate that GSTUs function as a major enzymatic system mitigating lipid oxidation stress in A. thaliana through the combined detoxification of lipid peroxides and their reactive carbonyl products. C_LI

plant biology↗

bioRxiv2025

Transcutaneous auricular vagus nerve stimulation during short-term motor practice drives cortical plasticity without behavioral improvement

Transcutaneous auricular vagus nerve stimulation (taVNS) is emerging as a promising non-invasive neuromodulation technique to augment neurorehabilitation, yet its mechanisms in humans remain poorly understood. Animal studies suggest that VNS delivered during motor skill practice drives task-specific plasticity in the primary motor cortex (M1), but direct evidence in humans has been lacking. Here, we provide the first demonstration that taVNS paired with motor skill practice selectively enhances cortical plasticity without boosting motor performance beyond practice alone during short-term training. Thirty-one healthy right-handed adults practiced a novel implicit motor task, rotating two balls with the non-dominant hand for 15 minutes. Participants were randomized to receive taVNS to the left tragus or sham stimulation during practice. Motor performance, M1 hand representation (TMS mapping), and spinal excitability (F-wave) were assessed pre- and post-practice, while pupil diameter was continuously monitored as an index of noradrenergic activity. Motor performance improved similarly in both groups, whereas cortical map expansion was significantly greater in the taVNS group than in the sham group. F-wave amplitude increased only in the sham group, suggesting that taVNS-driven plasticity was restricted to cortical circuits. Moreover, taVNS uniquely elicited pupil dilation during practice, consistent with noradrenergic system engagement. These findings reveal that taVNS can promote task-specific cortical reorganization in humans independent of immediate behavioral improvement. By linking taVNS-induced plasticity to noradrenergic modulation and dissociating cortical from spinal effects, this study provides novel mechanistic insight into how taVNS may lay the neural groundwork for enhanced motor recovery, with critical implications for neurorehabilitation. Significance StatementMotor recovery after stroke depends on the brains ability to reorganize motor circuits. Vagus nerve stimulation (VNS) has been proposed as a powerful approach to enhance such plasticity, but the underlying mechanisms in humans remain unclear. Here we show that non-invasive transcutaneous auricular VNS (taVNS), when paired with motor practice, selectively enhances reorganization of the primary motor cortex without additional behavioral improvement. Importantly, these effects were observed after only 15 minutes of practice, demonstrating that taVNS can induce rapid plastic changes. This provides the first evidence in humans that taVNS promotes task-specific cortical plasticity, underscoring its promise as a neuromodulatory tool for neurorehabilitation.

neuroscience↗

bioRxiv2025

Nanopore sequencing-based measurement of paramyxovirus RNA editing reveals virus-specific differences in editing efficiency of mRNA, antigenome and genome

Paramyxovirus polymerase recognizes an RNA editing signal on the viral genome and transcribes mRNA in which guanine nucleotides are inserted in a template-independent manner. This enables the synthesis of multiple proteins from a single gene, which is important for viral growth. We developed a method to quantify RNA editing efficiency using Oxford Nanopore Technologies MinION platform. We performed sequence analysis of reverse transcription (RT)-PCR amplicons with the RNA editing sites in cells infected with Sendai virus (SeV) and canine distemper virus (CDV). By modifying RT primers, we simultaneously assessed RNA editing efficiency in mRNA, antigenome and genome. We observed distinct differences in mRNA editing efficiency between SeV and CDV. Notably, while RNA editing in SeV is confined to mRNA, in CDV it is also observed in antigenome/genome. (Anti)genomes harboring extra nucleotides may deviate from a multiple-of-six sequence, suggesting that RNAs not following the "Rule of Six" are produced in CDV-infected cells. HighlightsO_LIA method was established to quantify RNA editing efficiency in RNAs from paramyxovirus-infected cells using the MinION platform. C_LIO_LIRNA editing efficiency in mRNA differs between Sendai virus and canine distemper virus. C_LIO_LIAlthough RNA editing is confined to mRNA during Sendai virus infection, it is also observed in the antigenome and genome during canine distemper virus infection. C_LI

microbiology↗

bioRxiv2025

FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis

Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.

cell biology↗

bioRxiv2024

Spatial Clustering Analysis with Spectral Imaging-based Single-Step Multiplex Immunofluorescence (SISS-mIF)

Precision medicine, based on spatial biology, is crucial for accurately diagnosing cancer and predicting drug responses. Here, we introduce the Spectral Imaging-based Single-Step Multiplex Immunofluorescence (SISS-mIF) technique, utilizing hyperspectral imaging to capture fluorescence spectra simultaneously. This approach optimizes tissue autofluorescence spectra for each image automatically, allowing the use of fluorescent direct-labeled antibodies for multicolor staining in a single step. Unlike conventional methods, the images are generated as standardized intensity independent of capture conditions, enabling consistent comparisons under different imaging conditions. This technique allows the detection of CD3, CD5, and CD7 in T-cell lymphoma on a single slide. The use of fluorescent direct-labeled antibodies enables triple staining of CD3, CD5, and CD7 without cross-reactivity, maintaining the same intensity as single stains. Furthermore, we developed a joint Non-Negative Matrix Factorization-based Spatial Clustering Analysis (jNMF-SCA) with a modified spectral unmixing system, highlighting its potential as a supportive diagnostic tool for T-cell lymphoma.

pathology↗

bioRxiv2024

PRDX6 dictates ferroptosis sensitivity by directing cellular selenium mobilization

Selenium-dependent glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis and prevents unrestrained (phospho)lipid peroxidation by directly reducing phospholipid hydroperoxides (PLOOH) to their corresponding alcohols. However, it remains unclear whether other phospholipid peroxidases can also contribute to ferroptosis prevention, albeit to a varying degree. Here we show that cells lacking GPX4 still exhibit substantial PLOOH reduction capacity, arguing for the presence of alternative PLOOH peroxidases. By scrutinizing potential candidates, we showed that while overexpression of peroxiredoxin 6 (PRDX6), a thiol-specific antioxidant enzyme with reported PLOOH-reducing activity, failed to prevent ferroptosis, its genetic loss markedly sensitizes cancer cells to ferroptosis. Mechanistically, we uncover that PRDX6 facilitates intracellular selenium handling, which is crucial for selenium incorporation into selenoproteins, including GPX4. Consequently, PRDX6 modulates GPX4 expression, thereby dictating the sensitivity of cells to undergo ferroptosis. Our study highlights PRDX6 as a critical factor in ferroptosis prevention by directing cellular selenium mobilization.

cell biology↗

bioRxiv2023

Impact of High Fat Diet and Sex in a Rabbit Model of Carpal Tunnel Syndrome

Carpal tunnel syndrome (CTS) is a common musculoskeletal disorder, characterized by thickening and fibrosis of the subsynovial connective tissue (SSCT). Risk factors for CTS includes sex, metabolic dysfunction and age. In this study we hypothesized that a high-fat diet (HFD), a common driver of metabolic dysfunction, would promote SSCT thickening in CTS and that this response would be sex dependent. To test this, we examined the effects of HFD and sex on SSCT thickening and markers of fibrosis using our established CTS rabbit model of SSCT thickening. Forty-eight (24 male, 24 female) adult rabbits were split into four groups including HFD or standard diet with and without CTS induction. SSCT was collected for histological and gene expression analysis. HFD promoted SSCT thickening and upregulated profibrotic genes, including TGF-{beta}. Fibrotic genes were differentially expressed in males and females. Interestingly while the overall prevalence of CTS is greater in women than in men, under conditions of metabolic dysfunction men have a higher incidence. This suggests a focus on metabolic and sex specific therapeutic strategies for the treatment of patients with CTS.

physiology↗

bioRxiv2023

Label-free ghost cytometry for manufacturing of cell therapy products

Automation and quality control (QC) are critical in manufacturing safe and effective cell and gene therapy products. However, current QC methods, reliant on molecular staining, pose difficulty in in-line testing and can increase manufacturing costs. Here we demonstrate the potential of using label-free ghost cytometry (LF-GC), a machine learning-driven, multidimensional, high-content, and high-throughput flow cytometry approach, in various stages of the cell therapy manufacturing processes. LF-GC accurately quantified cell count and viability of human peripheral blood mononuclear cells (PBMCs) and identified non-apoptotic live cells and early apoptotic/dead cells in PBMCs, T cells and non-T cells in white blood cells (WBCs), activated T cells and quiescent T cells in PBMCs, and particulate impurities in PBMCs. The data support that LF-GC is a non-destructive label-free cell analytical method that can be used to monitor cell numbers, assess viability, identify specific cell subsets or phenotypic states, and remove impurities during cell therapy manufacturing. Thus, LF-GC holds the potential to enable full automation in the manufacturing of cell therapy products with reduced cost and increased efficiency.

cell biology↗

bioRxiv2022

DHCR7 as a novel regulator of ferroptosis in hepatocytes

Recent evidence indicates that ferroptosis is implicated in the pathophysiology of various liver diseases; however, the mechanism of ferroptosis regulation in the liver is poorly understood. Here, using the whole-genome screening approach, we identified 7-dehydrocholesterol reductase (DHCR7), the terminal enzyme of cholesterol biosynthesis, as a novel regulator of ferroptosis in hepatocytes. Genetic and pharmacological inhibition (with AY9944) of DHCR7 suppressed lipid peroxidation and ferroptosis in human hepatocellular carcinoma Huh-7 cells. DHCR7 inhibition increased its substrate, 7-dehydrocholesterol (7-DHC), and extrinsic 7-DHC supplementation in turn suppressed ferroptosis. On the other hand, cholesterol deprivation had no effect on ferroptosis. A 7-DHC-derived oxysterol metabolite, 3{beta},5-dihydroxycholest-7-en-6-one (DHCEO), was increased by a ferroptosis inducer RSL-3 in DHCR7-deficient cells, suggesting that the ferroptosis-suppressive effect of DHCR7 inhibition was driven by intracellular 7-DHC as a radical scavenger. While extrinsic 7-DHC supplementation suppressed ferroptosis in various cancer cells, pharmacological DHCR7 inhibition by AY9944 showed cell-type specific effects, which could be explained by high DHCR7 expression in Huh-7 cells. We further showed that AY9944 suppressed ferroptosis in murine primary hepatocytes in vitro and systemic administration of AY9944 inhibited hepatic ischemia-reperfusion injury in vivo. These findings provide new insights into the regulatory mechanism of liver ferroptosis and suggest that DHCR7 inhibition is a potential therapeutic option for ferroptosis-related liver diseases.

molecular biology↗

bioRxiv2022

A comprehensive list of the replication promoters of Bunyavirales reveals a unique promoter structure in Nairoviridae differing from other virus families

Bunyaviruses belong to the order Bunyavirales, the largest group of RNA viruses. They infect a wide variety of host species around the world, including plants, animals and humans, and pose a major threat to public health. Major families in the order Bunyavirales have tri-segmented negative-sense RNA genomes, the 5 and 3 ends of which form complementary strands that serve as a replication promoter. Elucidation of the mechanisms by which viral RNA-dependent RNA polymerase recognizes the promoter to initiates RNA synthesis is important for understanding viral replication and pathogenesis, and for developing antivirals. A list of replication promoter configuration patterns may provide details on the differences in the replication mechanisms among bunyaviruses. Here, by using public sequence data of all known bunyavirus species, we constructed a comprehensive list of the replication promoters comprising 40 nucleotides in both the 5 and 3 ends of the genome that form a specific complementary strand. We showed that among tri-segmented bunyaviruses, viruses belonging to the family Nairoviridae, including the highly pathogenic Crimean-Congo hemorrhagic fever virus, have evolved a GC-rich promoter structure that differs from that of other bunyaviruses. The unique promoter structure might be related to the large genome size of the family Nairoviridae among bunyaviruses. It is possible that the large genome architecture confers a pathogenic advantage. The promoter list provided in this report is expected to be useful for predicting virus family-specific replication mechanisms of segmented negative-sense RNA viruses.

microbiology↗

bioRxiv2022

Frequency of a nucleotide overhang at the 5' end of hemorrhagic fever mammarenavirus genomes in public sequence data

Mammarenaviruses, such as Lassa virus and South American hemorrhagic fever (SAHF) virus, cause severe hemorrhagic fevers in humans, and pose major threats to public health. Mammarenaviruses consist of a bi-segmented negative-sense RNA genome in which the 5 and 3 ends form complementary strands that serve as a replication promoter. Some mammarenaviruses have a nucleotide overhang at the 5 genome end. By examining the complementarity of 5 and 3 genome ends using public mammarenavirus genome sequences, we found that the 5 guanine overhang (5-G overhang) was present more frequently in Lassa and SAHF viruses than in other viruses. The 5-G overhang in the Lassa and SAHF virus sequences was found to be restricted to the L and S segments, respectively. If the genome end sequence data in the public database are accurate, the 5-G overhang may be related to the high pathogenicity of mammarenaviruses in humans.

microbiology↗

bioRxiv2021

Acoustic light-sheet microscopy

Light-sheet imaging of 3D objects with high spatial resolution remains an open challenge because of the trade-off between field-of-view (FOV) and axial resolution originating from the diffraction of light. We developed acoustic light-sheet microscopy (acoustic LSM), which actively manipulates the light propagation inside a large sample to obtain wide-field microscopic images deep inside a target. By accurately coupling a light-sheet illumination pulse into a planar acoustic pulse, the light-sheet can be continuously guided over large distances. We imaged a fluorescence-labeled transparent mouse brain for the FOVs of 19.3 x 12.4 mm2 and 9.7 x 5.9 mm2 with resolved microstructures and single cells deep inside the brain. Acoustic LSM creates new opportunities for the application of light-sheet in the field of industry to basic science. One Sentence SummaryAn acoustic-optical method overcomes a trade-off between field-of-view and axial resolution in light-sheet microscopy.

bioengineering↗

bioRxiv2021

Age-related Cellular and Microstructural Changes in the Rotator Cuff Enthesis

Rotator cuff injuries increase with age. The enthesis is the most frequent site of rotator cuff injury and degeneration. Understanding age-related changes of the enthesis are essential to determine the mechanism of rotator cuff injuries, degeneration, and to guide mechanistically driven therapies. In this study, we explored age-related cellular changes of the rotator cuff enthesis in young, mature, and aged rats. Here we found that the aged enthesis is typified by an increased mineralized zone and decreased non-mineralized zone. Proliferation, migration, and colony forming potential of rotator cuff derived cells (RCECs) was attenuated with aging. The tenogenic and chondrogenic potential were significantly reduced, while the osteogenic potential increased in aged RCECs. The adipogenic potential increased in RCECs with age. This study explores the cellular differences found between young, mature, and aged rotator cuff enthesis cells and provides a basis for further delineation of mechanisms and potential therapeutics for rotator cuff injuries.

cell biology↗

bioRxiv2018

Eldecalcitol is more effective for promoting osteogenesis than alfacalcidol in Cyp27b1-knockout Mice

Calcium (Ca) absorption from the intestinal tract is promoted by active vitamin D (1,25D3). Vitamin D not only promotes Ca homeostasis, but it also inhibits bone resorption and promotes osteogenesis, thus playing a role in the maintenance of normal bone metabolism. Because 1,25D3 plays an important role in osteogenesis, vitamin D formulations, such as alfacalcidol (ALF) and eldecalcitol (ELD), are used for treating osteoporosis. While it is known that, in contrast to ALF, ELD is an active ligand that directly acts on bone, the reason for its superior osteogenesis effects is unknown. Cyp27b1-knockout mice (Cyp27b1-/- mice) are congenitally deficient in 1,25D3 and exhibit marked hypocalcemia and high parathyroid hormone levels, resulting in osteodystrophy involving bone hypocalcification and growth plate cartilage hypertrophy. However, because the vitamin D receptor is expressed normally in Cyp27b1-/- mice, they respond normally to 1,25D3. Accordingly, in Cyp27b1-/- mice, the pharmacological effects of exogenously administered active vitamin D derivatives can be analyzed without being affected by 1,25D3. We used Cyp27b1-/- mice to characterize and clarify the superior osteogenic effects of ELD on the bone in comparison with ALF. The results indicated that compared to ALF, ELD strongly induces ECaC2, calbindin-D9k, and CYP24A1 in the duodenum, promoting Ca absorption and decreasing the plasma concentration of 1,25D3, resulting in improved osteogenesis. Because bone morphological measurements demonstrated that ELD has stronger effects on bone calcification, trabecular formation, and cancellous bone density than ALF, ELD appears to be a more effective therapeutic agent for treating postmenopausal osteoporosis, in which cancellous bone density decreases markedly. By using Cyp27b1-/- mice, this study was the first to succeed in clarifying the osteogenic effect of ELD without any influence of endogenous 1,25D3. Furthermore, ELD more strongly enhanced bone mineralization, trabecular proliferation, and cancellous bone density than did ALF. Thus, ELD is expected to show an effect on postmenopausal osteoporosis, in which cancellous bone mineral density decreases markedly.

biochemistry↗