Biology subjects

Nakashima, Y.

Publications and source records attributed to Nakashima, Y..

11 recordsLinked to original sources

bioRxiv2026

Extensive membrane lipid remodeling at the host-parasite interface of Toxoplasma gondii

Phosphoinositides regulate diverse membrane trafficking and signaling events in eukaryotic cells, yet their transbilayer distribution remains largely unexplored, particularly at host-parasite membrane interfaces. Here, we determined the membrane leaflet localization of phosphatidylinositol 4-phosphate (PtdIns(4)P) and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) in Toxoplasma gondii using quick-freezing freeze-fracture replica labeling combined with phosphoinositide-specific probes. Both phosphoinositides were predominantly localized to the cytoplasmic leaflet of the parasite plasma membrane, whereas only weak labeling was detected in the inner membrane complex. PtdIns(4)P, but not PtdIns(4,5)P2, was additionally detected on intracellular vesicles, while mature micronemes lacked detectable labeling for either phosphoinositide. Surprisingly, both phosphoinositides exhibited nearly symmetric distributions between the two leaflets of the parasitophorous vacuole membrane (PVM), in striking contrast to their asymmetric localization in the parasite plasma membrane. Together with our previous demonstration that phosphatidylserine and phosphatidylethanolamine also lose their transbilayer asymmetry in the PVM, these findings indicate that the PVM undergoes global membrane lipid remodeling that extends from major phospholipids to phosphoinositides. We propose that this extensive lipid reorganization represents a defining structural feature of the apicomplexan PVM and provides a new framework for understanding membrane identity at the host-parasite interface.

cell biology↗

bioRxiv2026

Reward evokes value-independent arousal and value-dependent reinforcement processing as dissociable physiological consequences

Reward is traditionally thought to drive value-dependent reinforcement processing, whereas recent work suggests reward may instead raise arousal that mimics reinforcement. Because reinforcement and arousal depend on partly distinct neuromodulatory systems yet are co-triggered by reward, they have been widely treated as closely linked, though rarely tested directly, leaving reward's physiological consequences difficult to interpret. We manipulated the value of a primary reward by varying thirst while independently inducing arousal with sound, and measured pupil diameter and electroencephalographic activity. High- and low-value rewards produced comparable pupil dilation, indicating value-independent arousal. In contrast, only high-value reward increased alpha-band power, progressing from anterior to posterior regions, whereas low-value reward and sound produced similar alpha suppression without regional progression. Thus, reward evokes two dissociable consequences: value-independent arousal and value-dependent reinforcement. Rather than a single coupled process, these arise through separable mechanisms, providing a physiological framework for distinguishing each mechanism's contribution to reward processing.

neuroscience↗

bioRxiv2026

Parasitophorous vacuole membranes of Toxoplasma gondii and Plasmodium falciparum lack the lipid asymmetry characteristic of host cell plasma membranes

Apicomplexan parasites, including Toxoplasma gondii and Plasmodium falciparum, reside within a specialized compartment known as the parasitophorous vacuole (PV) during their intracellular life cycle. The PV membrane (PVM), which derives from the host plasma membrane upon invasion, serves as a selective barrier that permits nutrient acquisition while shielding the parasite from host defense mechanisms. Although the protein composition of the PVM has been studied extensively, its lipid organization remains poorly understood. Using the quick-freeze, freeze-fracture replica labeling (QF-FRL) method, we quantitatively analyzed the transbilayer distribution of phosphatidylserine (PtdSer), phosphatidylethanolamine (PtdEtn), and GM3 ganglioside in the PVM of T. gondii and P. falciparum. Unlike host cell plasma membranes, where these lipids exhibit strict asymmetry--PtdSer and PtdEtn confined to the cytoplasmic leaflet and GM3 to the exoplasmic leaflet--we found that all three lipids were symmetrically distributed across both leaflets of the PVM. This striking loss of lipid asymmetry suggests that the PVM undergoes profound remodeling during infection. The presence of PtdSer and PtdEtn in the luminal leaflet may facilitate the binding of perforin-like proteins (PLP1s) during egress. These findings reveal a unique feature of the PVM that redefines our understanding of host-parasite membrane biology.

cell biology↗

bioRxiv2025

ADGRG1 blockade drives astrocyte positioning into the extracellular matrix to reduce scar size

After the central nervous system (CNS) injury, inflammatory cells enter the lesion core and a fibrotic extracellular matrix accumulates. Astrocytes subsequently cluster around this matrix, forming a glial scar, but the role of the extracellular matrix in scar formation remains poorly understood. Here, we identify type III collagen, a major fibrotic extracellular matrix component after spinal cord injury, as a key regulator of astrocyte behavior. Using single-nucleus transcriptomics, spatial transcriptomics, and time-lapse cell imaging, we show that type III collagen positions astrocytes at the boundary of the fibrotic matrix by activating the adhesion G protein-coupled receptor G1 (ADGRG1) and its downstream effector RhoA. Blocking ADGRG1 genetically or pharmacologically allows astrocytes to enter the fibrotic matrix, resulting in a smaller scar, improved neuronal regeneration, and better motor recovery. The migration of human-induced pluripotent stem cell-derived astrocytes was inhibited by type III collagen via the ADGRG1-RhoA pathway, supporting their therapeutic potential. Our findings reveal the importance of controlling glial scar positioning via the type III collagen-ADGRG1 axis, providing a novel therapeutic target for CNS injury.

neuroscience↗

bioRxiv2025

Regulation of macroautophagy and microautophagic lipophagy by phosphatidylserine synthase Cho1 and external ethanolamine

Phospholipids play crucial roles in autophagy; however, the underlying mechanisms remain elusive. We previously found that the phosphatidylserine (PtdSer) transporter Osh5 is critical for autophagosome formation. Therefore, in this study, we aimed to investigate the impact of the knockout of cho1, which encodes PtdSer synthase, on autophagy. Green fluorescent protein-autophagy-related gene 8 (GFP-Atg8) processing assay revealed a significant defect in the macroautophagic activity of the cho1{Delta} mutant, regardless of the presence or absence of ethanolamine (Etn). Notably, autophagosomes were absent in the cytosol, and macroautophagic bodies were not observed in the vacuoles of the starved cho1{Delta} mutant, underscoring the essential role of PtdSer synthesized using Cho1 in autophagosome biogenesis. In contrast, numerous microautophagic vesicles containing lipid droplets were observed in the vacuoles of cho1{Delta} mutants starved in the presence of Etn, suggesting the crucial role of phosphatidylethanolamine (PtdEtn) synthesized via the Kennedy pathway in microautophagic lipophagy when PtdSer synthesis using Cho1 is disrupted. Given recent evidence pointing to the involvement of the ubiquitination system in various autophagy-related processes, we also examined the role of ubiquitin-conjugating enzyme E2 gene ubc4. Moreover, microautophagic lipophagy was significantly diminished in starved cho1{Delta} yeast with ubc4 knockout. These findings suggest the critical role of Ubc4-mediated ubiquitination in facilitating microautophagic lipophagy of the vacuole in yeast cells.

cell biology↗

bioRxiv2025

Distribution of myogenic stem cell activator, hepatocyte growth factor, in skeletal muscle extracellular matrix and effect of short-term disuse and reloading

Hepatocyte growth factor (HGF) is a key myogenic stem cells (satellite cells) activator, that resides in the extracellular matrix (ECM). However, HGF distribution in the ECM varies depending on the muscle fiber type. Furthermore, aging impedes the binding of HGF to its receptors due to nitration by peroxynitrite (ONOO-). Though oxidative stress increases rapidly during muscle disuse atrophy, satellite cells are rapidly activated upon reloading. In this study, we investigated the distribution of HGF in the ECM in various muscle fiber types, and examined nitration of HGF in disuse and reloading models. Immunofluorescence staining was performed on the soleus (Sol), plantaris (Pla), and gastrocnemius (Gas) muscles of 10-week-old mice. Three mice were used to assess HGF distribution, while 12 mice, divided into control, disuse, and reloading groups were used for qualitative evaluation of nitrated HGF (nitroHGF). In Sol muscle, type IIa and IIx muscle fibers exhibited higher HGF distribution in the ECM (70.7{+/-}1.9% and 63.9{+/-}2.6%, respectively) than type I fibers (28.0{+/-}1.7%; p<0.001). In Pla and Gas muscle, type IIa (65.4{+/-}2.3% and 70.3{+/-}2.2%, respectively) and type IIx fibers (55.3{+/-}1.8% and 61.4{+/-}3.2%, respectively) had significantly higher HGF distribution in the ECM than type IIb fibers (13.1{+/-}1.8% and 5.9{+/-}1.6%; p<0.001, respectively). The amount of nitroHGF increased in the disuse group compared to that in the control group but decreased in the reloading group compared to that in the disuse group. This preferential HGF distribution around type IIa and IIx muscle fibers indicates a distinct mechanism for satellite cell activation, differing from the satellite cell-rich environment associated with type I fibers and the lower HGF association with type IIb fibers. Disuse-induced HGF nitration may inhibit satellite cell activation. Reloading likely triggers mechanisms that counteract nitration, enabling satellite cell reactivation in young muscle.

biochemistry↗

bioRxiv2024

A novel VCP modulator, KUS121, attenuates atherosclerosis progression by maintaining intracellular ATP and mitigating ER stress in endothelial cells

BackgroundEndoplasmic reticulum (ER) stress signaling pathways have pivotal roles in atherosclerosis progression. Recently, we have developed Kyoto University Substance (KUS) 121, which selectively inhibits ATPase activities of valosin-containing protein (VCP) and consequently saves intracellular ATP consumption and mitigates ER stress. Methods and ResultsWe assessed the efficacy of KUS121 against atherosclerosis by its daily injection into Apoe-/- mice fed with Western Diet (WD) for 8 weeks. Consequently, KUS121 treatment reduced atherosclerosis progression by approximately 40% in atherosclerotic plaques. Interestingly, we found that C/EBP homologous protein (CHOP), an established ER stress marker, was mainly expressed in plaque endothelium. Therefore, we assessed the action of KUS121 in endothelial cells using the human endothelial cell line (EA.hy926 cells). As a result, KUS121 prevented ER stress-induced apoptosis and downregulated the IRE1 (Inositol-requiring enzyme) -associated inflammatory pathways. Consistent with these in vitro findings, KUS121 treatment also significantly reduced endothelial apoptosis assessed by TUNEL staining and inflammation examined by immunostaining of Nuclear factor kappa B (NF-{kappa}B) and Intercellular adhesion molecule (ICAM) 1 at plaque endothelium. We also demonstrated that KUS121 maintained ATP levels in EA.hy926 cells and atherosclerotic plaque lesions using the single-wavelength or the FRET-based fluorescent ATP sensor. Supplementation of intracellular ATP by Methyl pyruvate (MePyr) attenuated ER stress-induced apoptotic and inflammatory pathways in endothelial cells, which could be the main mechanism how KUS121 reduces ER stress. ConclusionsKUS121 can be a new therapeutic option for atherosclerotic diseases by maintaining intracellular ATP levels and attenuating ER stress-induced apoptosis and inflammation in plaque endothelium.

pathology↗

bioRxiv2021

A practical guide for estimating animal density using camera traps: Focus on the REST model

Camera traps are increasingly popular in wildlife research and have the potential to be reliable and cost-effective for estimating animal density. Although density estimation using this automatic technique has long been restricted to species with individually recognizable markings, several analytical approaches have been proposed to target animals lacking such markings (i.e., unmarked populations). Among these approaches, the random encounter and staying time (REST) model may be an efficient and cost-effective approach, even though the procedures for the implementations have not yet been shared with researchers. This paper presents a working protocol for implementing the REST model our research group has been developing. We also present the R code to perform parameter estimation with a maximum likelihood and Bayesian approach. We suggest that this model has potential for further development. We strongly hope that this paper will encourage many researchers to use the REST for density estimation in a wide variety of species in various habitats and make a significant contribution to advancing wildlife conservation and management.

ecology↗

bioRxiv2021

Double-observer approach with camera traps: Towards an unbiased density estimation of unmarked animal populations

Camera traps are a powerful tool for wildlife surveys. However, camera traps may not always detect animals passing in front. This constraint may create a substantial bias in estimating critical parameters such as the density of unmarked populations. We proposed the double-observer approach with camera traps to counter the constraint, which involves setting up a paired camera trap at a station and correcting imperfect detection with a hierarchal capture-recapture model for stratified populations. We performed simulations to evaluate this approachs reliability and determine how to obtain desirable data for this approach. We then applied it to 12 mammals in Japan and Cameroon. The results showed that the approach could correct imperfect detection as long as paired camera traps detect animals nearly independently (Correlation coefficient < 0.2). Camera traps should be installed to monitor a predefined small focal area from different directions to satisfy this requirement. The field surveys showed that camera trap might miss animals by 3 %-40%, suggesting that current density estimation models relying on perfect detection may underestimate animal density by the same order of magnitude. We hope that our approach will be incorporated into existing density estimation models to improve their accuracy.

ecology↗

bioRxiv2021

Perception of invisible masked objects in early infancy

Recurrent loops in the visual cortex play a critical role in visual perception, which is likely not mediated by purely feedforward pathways. However, the development of recurrent loops is poorly understood. The role of recurrent processing has been studied using visual backward masking, a perceptual phenomenon in which a visual stimulus is rendered invisible by a following mask, possibly because of the disruption of recurrent processing. Anatomical studies have reported that recurrent pathways are immature in early infancy. This raises the possibility that younger infants process visual information mainly in a feedforward manner, and thus, they might be able to perceive visual stimuli that adults cannot see because of backward masking. Here, we show that infants under 7 months of age are immune to visual backward masking and that masked stimuli remain visible to younger infants while older infants cannot perceive them. These results suggest that recurrent processing is immature in infants under 7 months and that they are able to perceive objects even without recurrent processing. Our findings indicate that the algorithm for visual perception drastically changes in the second half of the first year of life.

neuroscience↗

bioRxiv2020

CTDSP1 inhibitor rabeprazole regulates DNA-PKcs dependent topoisomerase I degradation and irinotecan drug resistance in colorectal cancer

Irinotecan specifically targets topoisomerase I (topoI), and is used to treat various solid tumors, but only 13-32% of patients respond to the therapy. Now, it is understood that the rapid rate of topoI degradation in response to irinotecan causes irinotecan resistance. We have published that the deregulated DNA-PKcs kinase cascade ensures rapid degradation of topoI and is at the core of the drug resistance mechanism of topoI inhibitors, including irinotecan. We also identified CTD small phosphatase 1 (CTDSP1) (a nuclear phosphatase) as a primary upstream regulator of DNA-PKcs in response to topoI inhibitors. Previous reports showed that rabeprazole, a proton pump inhibitor (PPI) inhibits CTDSP1 activity. The purpose of this study was to confirm the effects of rabeprazole on CTDSP1 activity and its impact on colon cancer. Using HCT116 and HT29, with high and low CTDSP1 expression respectively and a retrospective analysis of patients receiving irinotecan with or without rabeprazole have indicated the effect of CTDSP1 in irinotecan response. These results indicate that CTDSP1 promotes sensitivity to irinotecan and rabeprazole prevents this effect, resulting in drug resistance. To ensure the best chance at effective treatment, rabeprazole may not be a suitable PPI for cancer patients treated with irinotecan.

cancer biology↗