Biology subjects

Hasegawa, T.

Publications and source records attributed to Hasegawa, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Adeno-Associated Virus (AAV) Synthetic Inverted Terminal Repeats Enhance Tissue-Specific Transduction and Alter the Vector Induced Stress Response

While adeno-associated virus (AAV) vectors have shown therapeutic benefit in clinical applications, noted challenges include low transduction efficiencies, poor cellular targeting, and vector related adverse events. Recently, it was demonstrated that a rationally designed synthetic inverted terminal repeat (SynITR) altered the AAV vector-induced DNA damage response and abrogated apoptosis in human embryonic stem cells. To explore the utility of AAV-SynITR for diverse gene therapy applications, vector production, transduction, and the cellular response were evaluated in various contexts. Regarding production, SynITR preparations exhibited comparable titers to wtITR in a serotype/transgene-independent manner. Despite slightly decreased transduction efficiency in various cell lines, intravenous administration of AAV8 vectors showed SynITR enhanced transduction in a tissue-specific manner in liver (>7-fold) and kidney and pancreas (>2-fold) at equivalent vector copy numbers; however, no differences were observed in muscle/heart/spleen tissues. Interestingly, persistent {gamma}H2AX, a marker of aging/chronic inflammation, was abundant in the liver and spleen following wtITR (but not SynITR) transduction. In human corneas, SynITR enhanced transduction up to 16-fold over wtITRs. These data demonstrate that SynITRs elicit tissue-specific transduction enhancement and alter the cellular stress response. Importantly, the SynITRs offer an alternative context to elucidate wtITR biology for targeted, enhanced, and potentially safer human gene therapy.

molecular biology↗

bioRxiv2026

Impaired Motor Awareness of Balance Control is Associated with Postural Instability in Parkinson's Disease

BackgroundBalance instability is a major contributor to disability and falls in people with Parkinsons disease (PwP) and is often insufficiently explained by motor impairment alone. Altered awareness of motor control has been suggested to contribute to sensorimotor dysfunction in PwP, but its relationship with balance performance is poorly understood. ObjectiveTo determine whether awareness of balance control, assessed using a control detection task (CDT), differs between healthy controls (HC) and PwP, and whether CDT performance is associated with balance-related measures. MethodsHealthy older adults (n=20) and PwP (n=22) performed a standing version of the CDT based on center-of-pressure (COP) control, using a force plate. CDT accuracy was used as the primary outcome measure. Static balance during quiet standing was assessed using the COP trajectory length and rectangular area. Dynamic standing balance was assessed using the Index of Postural Stability (IPS). Group differences were examined by independent-samples t-tests. Correlations between CDT accuracy and balance measures were analyzed. ResultsThe PwP group showed significantly lower CDT accuracy. Higher CDT accuracy was associated with better static balance in the HC group and the combined sample, and with higher IPS primarily in the PwP group. ConclusionsMotor awareness during postural tasks is altered in PwP and is associated with balance control. These findings suggest that balance instability in Parkinsons disease may involve altered balance-related action-outcome monitoring in addition to motor dysfunction.

neuroscience↗

bioRxiv2026

Neuroscience-Inspired Deep Learning Brain-Machine Interface Decoder

Brain-machine interfaces (BMIs) aim to decode motor intentions from neural activity to enable direct control of external devices. However, most existing decoders rely on monolithic architectures that fail to capture the distinct neural representations of different joint movement directions, limiting their generalizability. In this work, we propose a Single-Direction CNN-LSTM decoder inspired by motor cortex encoding mechanisms, which separately models extension and flexion dynamics through parallel CNN-LSTM branches. Each branch extracts spatial-temporal features from neural spike data and predicts directional joint variables, which are then combined by subtraction to yield the net angular velocity and torque of upper-limb joints. Using invasive recordings from a macaque during a 2D center-out reaching task, we demonstrate that our decoder achieves comparable performance to a conventional CNN-LSTM when trained on all tasks, while significantly outperforming both CNN-LSTM and linear regression baselines in cross-target generalization scenarios. Moreover, the model can capture physiologically meaningful co-contraction patterns, providing richer insights into motor control. These results suggest that incorporating neuroscience-inspired modular decoding into deep neural architectures enhances robustness and adaptability across tasks, offering a promising pathway for BMI applications in prosthetics and rehabilitation.

bioengineering↗

bioRxiv2026

Single-cell RNA sequencing reveals collagen interactions between detached osteoclasts and activated fibroblasts in granulation tissue surrounding sequestra in medication-related osteonecrosis of the jaw

ObjectivesMedication-related osteonecrosis of the jaw (MRONJ) is a rare but serious complication of anti-resorptive agents used for osteoporosis and bone metastasis. As the global population ages, the number of patients with MRONJ continues to rise. Resorptive osteoclasts firmly attached to bone surfaces cannot be detected using single-cell RNA-Seq (scRNA-Seq); however, we hypothesized that multinucleated giant and detached osteoclasts (DetOCs) can be detected by this method. This study aimed to characterize DetOCs with scRNA-seq. Materials and MethodsscRNA-Seq and immunohistochemistry staining was performed on granulation tissues surrounding sequestra from four patients with MRONJ and radicular cysts, a common odontogenic infectious disease with normal bone metabolism. ResultsscRNA-Seq and immunohistochemistry staining revealed that DetOCs were detected exclusively in the granulation tissues of MRONJ. These DetOCs expressed well-known osteoclast markers as well as COL27A1. Subcluster analysis revealed that SPP1+ TREM2+ macrophages differentiated into DetOCs and expressed several types of collagens. Immunostaining confirmed the expression of COL27A1 not only in DetOCs in MRONJ but also in osteoclasts in mandibular cancer. CellChat analysis revealed interactions mediated by collagen signaling pathways between DetOCs, myeloid cells, and activated fibroblasts. ConclusionsWe successfully characterized DetOCs and identified a distinctive microenvironment involving DetOCs and activated fibroblasts in the granulation tissues surrounding sequestra in MRONJ. Clinical RelevanceIdentification of DetOCs and their unique interaction with activated fibroblasts in MRONJ lesions provides novel insight into the pathophysiology of sequestrum formation, suggesting potential therapeutic targets to ameliorate MRONJ.

immunology↗

bioRxiv2024

Development of a new genotype-phenotype linked antibody screening system

Antibodies are powerful tools for the therapy and diagnosis of various diseases. In addition to conventional hybridoma-based screening, recombinant antibody-based screening has become a common choice; however, its application is hampered by two factors: 1) screening starts after Ig gene cloning and recombinant antibody production only, and 2) the antibody is composed of paired chains, heavy and light, commonly expressed by two independent expression vectors. Here, we introduce a method for the rapid screening of recombinant monoclonal antibodies by establishing a Golden Gate-based dual-expression vector and in-vivo expression of membrane-bound antibodies. Using this system, we demonstrate the rapid isolation of influenza cross-reactive antibodies with high affinity from immunized mice within 7 days. This system is particularly useful for isolating therapeutic or diagnostic antibodies, e.g., during foreseen pandemics. Impact StatementA Golden Gate-based dual-expression vector enables rapid screening, which facilitates efficient isolation of high-affinity cross-reactive antibodies for therapeutic or diagnostic use and provides a crucial advance for pandemic preparedness.

bioengineering↗

bioRxiv2023

Revealing the spatial characteristics of rice heat exposure in Japan through panicle temperature analysis

Elevated temperatures during the flowing stage contribute to heat-induced spikelet sterility in rice, posing a major threat to production considering climate change projections. Developing effective strategies for stable rice production through breeding and crop management is critical; however, our understanding of regional, seasonal, and long-term trends in rice heat exposure remains limited. Previous studies on spikelet sterility revealed that panicle temperature, estimated using a micrometeorological model and common meteorological factors, serves as a reliable indicator of rice heat exposure. In this study, we employed this model to identify the differences between panicle and air temperatures (DPAT) and their causes over the past 45 years in Japan. A gridded daily meteorological dataset covering Japan was interpolated at an hourly time step and used as input data of the micrometeorology model for estimating panicle temperatures during flowering. Statistical analysis of the resulting data revealed an increasing trend in the frequency of rice panicle heat exposure over time across many locations in Japan. During heat-receptive periods, panicle temperature generally exceeded air temperature, indicating the inadequacy of relying solely on air temperature to gauge rice heat stress. DPAT values showed substantial inter-regional variations in both mean values (from -0.5 to 3.0) and seasonality. Through machine learning and statistical methods, the relationship between DPAT and meteorological factors was characterized, delineating the effects of the meteorological factors on regional and seasonal DPAT variations. Focusing on major high-risk regions, we show that mitigation strategies should be adapted to consider regional characteristics and avoid high DPAT conditions during rice heading periods.

plant biology↗

bioRxiv2023

Mapping adipocyte interactome networks by HaloTag enrichment mass-spectrometry

Mapping protein interaction complexes in their natural state in vivo represents the holy grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused this, yet this may be solved by artificial intelligence and proteomics. Here, we describe the development of HaloMS, a high-throughput HaloTag-based affinity purification-mass spectrometry assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assay. As a proof-of-principle, we used HaloMS to evaluate protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and artificial intelligence-based prediction tools. The application of HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor-protein complexes, revealing proteome-wide human adipocyte transcription factor networks, and shedding light on how different pathways are integrated.

biochemistry↗

bioRxiv2023

Distinct adrenal gland macrophages regulate corticosteroid production

The adrenal glands are hormone secreting glands that sit on top of the kidneys. Adrenal glands produce glucocorticoids, mineralocorticoids, and catecholamines, and are therefore critical regulators of the stress response, the immune response, metabolism, and blood pressure. Despite being identified for more that 30 years, our understanding of adrenal macrophages remains incomplete. In numerous other tissues, macrophages carry out a plethora of physiological and homeostatic roles in addition to their classical immune functions. The aim of this study was to characterise the macrophage compartment of the adrenal gland and assess its contribution to adrenal function. Using an in vivo approach, we herein describe two morphologically and spatially distinct subsets of adrenal macrophages - dendritic-like macrophages that are present throughout the gland in young and old mice, and "foamy" lipid-laden macrophages that accumulate in the murine adrenal cortex in an age and diet-dependent manner. Furthermore, we present data showing that these foamy-like macrophages accumulate cholesterol and thereby regulate adrenal hormonal output, at steady state and in the context of obesity. We hereby provide novel insights into the physiological roles of macrophages in the adrenal gland and the mechanisms by which adrenal hormone production is regulated.

immunology↗

bioRxiv2023

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were found across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.

microbiology↗

bioRxiv2023

Time-, tissue- and treatment-associated heterogeneity in tumour-residing migratory DCs

Tumour dendritic cells (DCs) internalise antigen and upregulate CCR7, which directs their migration to tumour-draining lymph nodes (dLN). CCR7 expression is coupled to a maturation programme enriched in regulatory molecule expression, including PD-L1, termed mRegDC. However, the spatio- temporal dynamics and role of mRegDCs in anti-tumour immune responses remain unclear. Using photoconvertible mice to precisely track DC migration, we found that mRegDCs were the dominant DC population arriving in the dLN, but a subset remained tumour-resident despite CCR7 expression. These tumour-retained mRegDCs were phenotypically and transcriptionally distinct from their dLN counterparts and were heterogeneous. Specifically, they demonstrated a progressive reduction in the expression of antigen presentation and pro-inflammatory transcripts with more prolonged tumour dwell-time. Tumour mRegDCs spatially co-localised with PD-1+CD8+ T cells in human and murine solid tumours. Following anti-PD-L1 treatment, tumour-residing mRegDCs adopted a state enriched in lymphocyte stimulatory molecules, including OX40L, which was capable of augmenting anti- tumour cytolytic activity. Altogether, these data uncover previously unappreciated heterogeneity in mRegDCs that may underpin a variable capacity to support intratumoural cytotoxic T cells, and provide insights into their role in cancer immunotherapy.

immunology↗

bioRxiv2023

Effectiveness of heat tolerance rice cultivars in preserving grain appearance quality under high temperatures - A meta-analysis

BackgroundClimate change, particularly rising temperatures, negatively affects rice grain quality, increasing chalky grain percentage (CG) and hampering rice grade and price. Heat-tolerant cultivars have been bred and released since the 2000s, but the effectiveness of heat tolerance in reducing the occurrence of CG has yet to be quantified. ObjectivesThis study aimed to measure the effectiveness of breeding for better heat tolerance in reducing the negative impact of high temperatures on rice quality. MethodsThrough a systematic literature search, we developed a dataset including 1297 field observations covering 48 cultivars from five different heat tolerant ranks (HTRs) at 44 sites across Japan. A linear mixed-effect model (LME) and a random forest model (RF) were fitted to the data to analyze the effect of HTR and climatic factors such as the cumulative mean air temperature above 26 {degrees}C (TaHD), mean solar radiation, and mean relative humidity for 20 days after heading on CG. ResultsThe LME model explained 63 % of the variation with a 14% RMSE. The RF partial dependence plot revealed that the logit-transformed CG response to climate factors was linear, supporting the assumption of LME. The statistical analysis showed that CG increased as a function of TaHD (P < 0.001), with significant differences among HTRs (P < 0.001). The strongest effect of TaHD was obtained for the lowest HTR and was found to decrease with increasing HTR. CG also increased with higher relative humidity (P < 0.001) and solar radiation (P < 0.01). Based on our modeling, we estimated that as TaHD increased from 20 to 80 {degrees}Cd (equivalent to a mean temperature increase from 27 {degrees}C to 30 {degrees}C), CG increased by 66 % points (difference in CG) for cultivars with the lowest HTR, 45 % points for cultivars with an intermediate HTR, and 19 % points for cultivars with the highest HTR. Raising HTR by just one step (from intermediate to moderately tolerant) is projected to increase the proportion of first-grade rice at a grain-filling temperature of 27 {degrees}C, but tolerance levels need to be improved further in case of stronger warming. ConclusionsThe effect of high temperatures on CG was highly dependent on the cultivars HTR. Improvements in HTR effectively reduce the negative impacts of high temperatures on rice grain quality. SignificanceHeat-tolerant cultivars are projected to suppress the prevalence of CG more than threefold compared with heat-sensitive cultivars when grain-filling temperature increases from 27 to 30 {degrees}C.

plant biology↗

bioRxiv2023

Cytotoxic CD4+ T cells eliminate senescent cells by targeting cytomegalovirus antigen

Senescent cell accumulation has been implicated in the pathogenesis of aging-associated diseases including cancer. The mechanism that prevents the accumulation of senescent cells in aging human organs is unclear. Here, we demonstrate that a virus-immune axis controls the senescent fibroblast accumulation in the human skin. Senescent fibroblasts increased in old compared with young skin. However, they did not increase with advancing age in the elderly. Increased CXCL9 and cytotoxic CD4+ T cell (CD4 CTL) recruitment were significantly associated with reduced senescent fibroblasts in the old skin. Senescent fibroblasts expressed human leukocyte antigen class II (HLA-II) and human cytomegalovirus glycoprotein B (HCMV-gB), becoming direct CD4 CTL targets. Skin-resident CD4 CTL eliminated HCMV-gB+ senescent fibroblasts in an HLA-II-dependent manner, and HCMV-gB activated CD4 CTL from the human skin. Collectively, our findings demonstrate HCMV reactivation in senescent cells, which can be directly eliminated by CD4 CTL through the recognition of the HCMV-gB antigen.

immunology↗

bioRxiv2023

Palmitoylation of gasdermin D directs its membrane translocation and pore formation in pyroptosis

Gasdermin D (GSDMD)-mediated macrophage pyroptosis plays a critical role in inflammation and host defense. Plasma membrane perforation elicited by caspase-cleaved GSDMD N-terminal domain (GSDMD-NT) triggers membrane rupture and subsequent pyroptotic cell death, resulting in release of pro-inflammatory IL-1{beta} and IL-18. However, the biological processes leading to its membrane translocation and pore formation are not fully understood. Here, using a proteomics approach, we identified fatty acid synthase (FASN) as a GSDMD-binding partner and demonstrated that post-translational palmitoylation of GSDMD at Cys191/Cys192 (human/mouse) led to membrane translocation of GSDMD-NT but not full-length GSDMD. GSDMD lipidation, mediated by palmitoyl acyltransferases ZDHHC5/9 and facilitated by LPS-induced reactive oxygen species (ROS), was essential for GSDMD pore-forming activity and pyroptosis. Inhibition of GSDMD palmitoylation with palmitate analog 2-bromopalmitate or a cell permeable GSDMD-specific competing peptide suppressed pyroptosis and IL-1{beta} release in macrophages, mitigated organ damage, and extended the survival of septic mice. Collectively, we establish GSDMD-NT palmitoylation as a key regulatory mechanism controlling GSDMD membrane localization and activation, providing a novel target for modulating immune activity in infectious and inflammatory diseases. One Sentence SummaryLPS-induced palmitoylation at Cys191/Cys192 is required for GSDMD membrane translocation and its pore-forming activity in macrophages.

immunology↗

bioRxiv2022

Nitrogen uptake pattern of dry direct-seeding rice and its contribution to yield in a cool temperate climate

Dry direct-seeding rice (DDSR) cultivation is expected to reduce production costs compared with transplanted rice (TPR); however, its low nitrogen (N) use efficiency (NUE) has hindered cost reduction. Additionally, polymer-coated urea application in rice cultivation is reduced for plastic pollution regulation. The split application of urea can be an alternative, but it has not been used in northeastern Japan, hence needs to be investigated. We conducted DDSR and TPR field experiments for three years using two cultivars and three or two N regimes to determine factors limiting yield and NUE using a standard cultivar ( Akitakomachi) and a high-yielding cultivar ( Yumiazusa) grown under different N regimes. The yield, yield components, and N uptake of DDSR were analyzed, and examined the contribution of N uptake until panicle initiation and heading for spikelet number by multiple regression compared to that of TPR. Additionally, we investigated the detailed N uptake pattern on DDSR until PI using the two parameters, which were calculated by exponential regression of N uptake during the vegetative period. DDSR yield was lower than that of TPR by 11% and revealed that both fertilizer recovery rate and crop NUE (yield per unit N uptake) contributed to the lower yield. N uptake until the fifth leaf age significantly influenced the N uptake until panicle initiation. DDSR yield with normal urea in this study proportion was not significantly different compared to coated urea application, indicating the possibility to be an alternative N application method.

plant biology↗

bioRxiv2021

A global dataset for the projected impacts of climate change on four major crops

Reliable estimates of the impacts of climate change on crop production are critical for assessing the sustainability of food systems. Global, regional, and site-specific crop simulation studies have been conducted for nearly four decades, representing valuable sources of information for climate change impact assessments. However, the wealth of data produced by these studies has not been made publicly available. Here, we develop a global dataset by consolidating previously published meta-analyses and data collected through a new literature search covering recent crop simulations. The new global dataset builds on 8314 simulations from 203 studies published between 1984 and 2020. It contains projected yields of four major crops (maize, rice, soybean, and wheat) in 91 countries under major emission scenarios for the 21st century, with and without adaptation measures, along with geographical coordinates, current temperatures, local and global warming levels. This dataset provides a basis for a comprehensive understanding of the impacts of climate change on crop production and will facilitate the rapidly developing data-driven machine learning applications.

plant biology↗

bioRxiv2021

Visualization of ecological successions in lakes subdivided by volcanic eruption at Akan Caldera, Hokkaido, Japan

It is not feasible to continuously observe ecological succession in lakes because of the long time-scales generally involved. Thus, the process has been inductively deduced by comparing many lakes with different succession states, or indirectly simulated by tracking studies of smaller water bodies, experiments using microcosms or mesocosms, and reconstruction of lake history by sediment analysis. However, the reality of succession processes in large lakes with slow succession is not well understood, and new approaches are needed. Theoretically, in a group of large and small lakes of similar ages and with similar initial and watershed environments, the rate of nutrient accumulation in each lake depends on the ratio of watershed area to lake size, and the lakes are predicted to evolve to different trophic levels over time. Here, we tested this hypothesis on the 10 lakes of varying sizes in Akan Caldera, Japan, which were formed thousands of years ago by fragmentation due to volcanic eruptions within the caldera. Topographic and water quality studies showed that the ratio of accumulated watershed area to lake size (area and volume), expressed logarithmically, had a positive linear regression with the total phosphorus concentration, an indicator of trophic level. The trophic levels of the lakes were diverse, including oligotrophic, mesotrophic, and eutrophic types in the traditional "lake type" classification based on total phosphorus and chlorophyll-a concentrations. Furthermore, 21 species of aquatic macrophytes were observed by a diving survey, and the plant species composition was classified into five groups corresponding to the trophic status of the lakes, indicating a conventional "hydrarch succession". The diversity of water quality and aquatic vegetation in a group of lakes with similar origins paves the way for new comparative studies of lakes, including large lakes.

ecology↗

bioRxiv2021

Subthalamic nucleus stabilizes movements by reducing neural spike variability in monkey basal ganglia: chemogenetic study

AbstractsThe subthalamic nucleus (STN) projects to the external pallidum (GPe) and internal pallidum (GPi), the relay and output nuclei of the basal ganglia (BG), respectively, and plays an indispensable role in controlling voluntary movements. To elucidate the neural mechanism by which the STN controls GPe/GPi activity and movements, we utilized a chemogenetic method to reversibly suppress the motor subregion of the STN in three macaque monkeys (Macaca fuscata, both sexes) engaged in reaching tasks. Systemic administration of chemogenetic ligands prolonged movement time and increased spike train variability in the GPe/GPi, but only slightly affected firing rate modulations. Across-trial analyses revealed that the irregular discharge activity in the GPe/GPi coincided with prolonged movement time. STN suppression also induced excessive abnormal movements in the contralateral forelimbs, which was preceded by STN and GPe/GPi phasic activity changes. Our results suggest that the STN stabilizes spike trains in the BG and achieves stable movements.

neuroscience↗

bioRxiv2021

Trophic transfer of microplastics enhances tissue accumulation of chemical additives in fish

Organisms ingest microplastics directly from environments and indirectly from food sources. Ingesting microplastics can lead to an organism accumulating plastic-derived chemicals. However, the relative contributions of the two exposure routes (direct ingestion vs. indirect ingestion) to plastic-derived chemical accumulation in an organism are unknown. Using microplastics containing different types of plastic additives, we performed exposure experiments to compare chemical accumulation patterns in fish (Myoxocephalus brandti) between the exposure from the water and prey (Neomysis spp.). We found significantly higher brominated flame retardant concentrations in fish fed microplastic-contaminated prey than fish exposed to microplastics suspended in the water. The results indicate that prey-mediated ingestion of microplastics can be a more significant route for organisms accumulating plastic-derived chemicals, suggesting that organisms at higher trophic levels are more exposed to microplastics and associated chemicals than organisms at lower trophic levels.

pharmacology and toxicology↗