Biology subjects

Abe, H.

Publications and source records attributed to Abe, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Intranuclear Quantum Sensing with Fluorescent Nanodiamond Enabled by Electron-Irradiation and Surface-Chemical Optimization for Microinjection

Fluorescent nanodiamonds (FNDs) containing nitrogen-vacancy (NV) centers are promising quantum sensors for intracellular measurements, yet nuclear applications remained out of reach because optically detected magnetic resonance (ODMR) signals are weak and capillary delivery is inefficient. This study addresses both constraints by optimizing the electron irradiation dose to balance NV creation and charge-state stability, and by grafting hyperbranched polyglycerol with terminal carboxyl groups (HPGCOOH) to suppress aggregation and prevent needle clogging. The optimized dose yields strong ODMR contrast while preserving fluorescence suitable for microscopy. HPGCOOH surfaces enable smooth and reproducible microinjection through fine capillaries. Using this strategy, the microinjection of ODMR-active FNDs into the nuclei of living COS7 cells is achieved, and clear intranuclear spectra comparable to cytoplasmic readouts are obtained. Furthermore, field-of-view temperature sensing across multiple cell nuclei is demonstrated, enabling quantitative and spatially resolved thermal mapping within the genomic environment. This methodology provides a practical route to nuclear quantum sensing and opens opportunities for nanoscale physicochemical measurements within the genomic environment.

biophysics↗

bioRxiv2026

Multiplex PCR based Detection Methods of Common Plant Transgenes

Accurate verification of transgenic plant materials is essential for maintaining scientific integrity and ensuring experimental reproducibility. As the number and diversity of transgenic constructs continue to expand, there is a growing need for practical and scalable methods that enable routine confirmation of transgene presence and identity. Reliable detection systems are particularly important for laboratories handling large numbers of genetically modified lines or distributing materials across research groups. To address this need, we developed two complementary methods for efficient detection of commonly used transgenes. The first method, fDET, is a higher-throughput system capable of simultaneously detecting 15 transgenes and three endogenous genes in a single multiplex PCR reaction followed by capillary electrophoresis. This approach provides rapid, high-resolution detection suitable for high-volume or time-sensitive applications. The second method, DET, offers a more accessible workflow that detects 10 transgenes and one endogenous gene using four multiplex PCR reactions followed by agarose gel electrophoresis. Because DET requires only standard molecular biology equipment, it can be readily implemented in a wide range of laboratory environments without specialized instrumentation. Together, these methods provide flexible and practical solutions for verifying the genetic status of both transgenic and non-transgenic plant materials. By enabling efficient and comprehensive transgene detection, they support reproducible experimentation, facilitate quality control in plant research, and streamline the management and exchange of genetically modified lines. These approaches contribute to more reliable and transparent use of transgenic resources across the plant science community.

plant biology↗

bioRxiv2026

Degradation of net ecosystem carbon balance in cool-temperate forests by sika deer-induced stand structure alterations and subsequent soil erosion

Although natural forests sequester carbon, this function may decline under chronic herbivory by abundant ungulates (hereafter overbrowsing). Specifically, overbrowsing alters stand structure, potentially impair carbon exchanges related to the vegetation. Further, overbrowsing may also accelerate soil erosion, especially in heavy-rainfall regions like Monsoon Asia. We quantified these impacts by estimating net ecosystem carbon balance (NECB; g C m-2 yr-1) by subtracting heterotrophic respiration (Rh) and lateral carbon export via erosion (Se) from net primary production (Pn) in southern Kyushu, Japan. Here, about 40-years of overbrowsing by sika deer (Cervus nippon) altered mixed broadleaf-conifer stands with presence of understory (PU) into stands with no understory (NU), then further altered into stands dominated by unpalatable shrublands (SR) or stands with canopy gaps (CG). The PU maintained a positive NECB (plot mean = 307.0 g C m-2 yr-1) because high Pn (721.9) exceeded the sum of Rh (175.4) and Se (239.5). Alteration from PU into NU converted NECB to negative (-98.2 g C m-2 yr-1). This was because the suppressed Pn (400.2 g C m-2 yr-1) could not offset the sum of Rh (170.6) and Se (327.7). Further degradation into CG caused a profound negative NECB (-894.4 g C m-2 yr-1), where Pn (71.9) offset only 7% of the sum of surging Rh (464.8) and Se (501.5). Alteration into SR showed a partially recovered NECB (97.3 g C m-2 yr-1), driven by shrub growth (Pn; 554.5, Rh; 175.4, Se; 239.5). However, this recovery is still limited given that lowered shrub biomass and prior topsoil loss via erosion. Our results validate previous findings that stand alteration from PU to SR or CG through NU leads to up to a 49% loss of ecosystem carbon stocks. Preventing stand alteration and soil erosion are key countermeasures against chronic overbrowsing and subsequent erosion. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/719128v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@167aef0org.highwire.dtl.DTLVardef@e45a6org.highwire.dtl.DTLVardef@fec89borg.highwire.dtl.DTLVardef@1246bea_HPS_FORMAT_FIGEXP M_FIG C_FIG We reported that over 40 years of sika deer overbrowsing and subsequent soil erosion severely degraded the net ecosystem carbon balance (NECB) of mountain forests in Japan. The loss of understory vegetation drove the transition of intact stands into degraded states (no-understory, shrub-dominated, or canopy gaps). Based on field measurements, we quantified that this structural alteration suppressed net primary production (Pn) while increased both heterotrophic respiration (Rh) and lateral carbon loss via soil erosion (Se). Consequently, the forest shifted from a net carbon sink (+307 g C m-{superscript 2} yr-{superscript 1}) to a source (up to -894 g C m-{superscript 2} yr-{superscript 1}). These findings provide compelling empirical evidence that increasing ungulate populations, compounded by the rising frequency of heavy rainfall, may severely undermine the carbon sequestration functions traditionally expected of natural forests.

ecology↗

bioRxiv2026

VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance

Bacterial pathogens spread in clinical and environmental settings, and mobile genetic elements (MGEs), such as plasmids and phages, mediate the transfer of virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) among bacterial communities. Metagenomic analysis of environmental and wastewater samples using highly accurate long-read sequencing technologies, such as PacBio HiFi sequencing, provides valuable insights into monitoring the regional spread of VFGs and ARGs, including dissemination mediated by MGEs. No visualization tool is currently available for the comprehensive display of numerous resulting circular metagenome-assembled genomes (cMAGs) with functional gene annotations. Here, we developed VicMAG, a visualization tool for highly complex cMAGs derived from long-read metagenome assemblies annotated using updated databases of VFGs, ARGs, and MGEs. Using 353 cMAGs from PacBio HiFi sequencing of a wastewater sample, we demonstrated the utility of VicMAG for metagenome visualization. VicMAG provides comprehensive, size-aware visualization of cMAGs representing bacterial chromosomes and plasmids, annotated with VFGs, ARGs, and phages. By simultaneously visualizing all cMAGs in a framework, VicMAG facilitates a holistic understanding of the distribution and genomic context of VFGs and ARGs across complex microbial communities. This tool supports integrated surveillance of bacteria associated with virulence and antimicrobial resistance across clinical, environmental, and One Health contexts.

bioinformatics↗

bioRxiv2026

Tracing the emergence of the novel fluoroquinolone resistance gene qrtA in enterococci through environmental reservoirs and pELF-type linear plasmids

As animal hosts adapted to land, Enterococcus species diverged from a common ancestor shared with Vagococcus species by acquiring genes essential for survival and transmission in the exposed arid environment. In addition to their intrinsic ruggedness, human-associated enterococci now frequently exhibit multidrug resistance, largely driven by the accumulation of antimicrobial resistance genes (ARGs) on mobile genetic elements (MGEs). However, the source of these resistance elements, their diversity in natural reservoirs, and the risk that they pose remain unclear. To investigate the movement of novel ARGs from the environmental reservoir and the elements that convey them into clinically important enterococcal lineages, we examined environmental vancomycin-resistant enterococci (VRE) circulating in a polluted urban river in Hanoi, Vietnam. Whole-genome sequencing of VRE isolates revealed multidrug-resistance pELF-type linear plasmids harboring a novel fluoroquinolone resistance gene (qrtA) encoding a major facilitator superfamily transporter. The qrtA gene appears to have originated on Vagococcus chromosomes and to have been mobilized by IS1216E-associated MGEs. Vagococcus genomes show strong associations between ARGs, IS1216E, and plasmids related to those in enterococci, and conjugation experiments demonstrated that pELF-type linear plasmids can transfer between Enterococcus and Vagococcus without major fitness costs, positioning them as plausible vehicles for importing environmental ARGs into enterococci. Reconstruction of pELF-type linear plasmid evolution in the environment, together with database mining of rare qrtA-positive clinical isolates from Asia and Europe, suggests that qrtA-bearing pELF-type linear plasmids are in an early phase of global dissemination. These findings highlight the need for coordinated international One Health surveillance of ARG and MGE dynamics, including emerging determinants such as qrtA, together with proactive interventions to limit their spread.

microbiology↗

bioRxiv2025

Deep-brain thermo-endomicroscopy

Subtle deviations in biophysical parameters, particularly temperature, within deep-brain regions exert substantial effects on whole-body homeostasis and metabolism. However, the underlying mechanisms remain poorly understood because cellular-resolution measurements of these parameters in the deep brain have been technically inaccessible. Here, we present a lensless fiber-optic quantum-sensing endomicroscopy that enables cellular-resolution temperature mapping in the mouse deep brain. A microwire-coupled, lensless fiber bundle permits simultaneous temperature readout from optically detected magnetic resonance spectra of >50 fluorescent nanodiamonds, achieving cellular resolution (4.88 m) with a precision of 0.49 (minimum precision, 0.18 ) within a 0.28 mm2 field of view. We demonstrated temperature mapping of multiple brain depths in head-fixed and vigorously behaving mice subjected to nociceptive stimulation, detecting lower temperatures during anesthesia compared to the awake state in ventromedial hypothalamic nucleus (VMH) at a 5 mm depth. These mappings reveal that spatio-temporal temperature distribution and its anesthesia-dependent reduction are heterogeneous rather than uniform in VMH. This endomicroscopy provides a promising platform to dissect how deviations in biophysical parameters modulate deep-brain function.

biophysics↗

bioRxiv2025

The Brain/MINDS 3D Digital Marmoset Brain Atlas Version 2.0: Population-based Cortical Region Parcellations with Multi-Modal Standard Templates

We present our new Brain/MINDS 3D digital marmoset brain atlas version 2.0 (BMA2.0), a population-based 3D digital brain atlas of the common marmoset (Callithrix jacchus), designed to overcome the limitations of previous single subject atlases that are prone to structural biases arising from individual variation. Here, manually delineated cortical regions from 10 myelin-stained brains were used to create a generalized cortical parcellation. Newly refined subcortical regions from a previous atlas and a completely new cerebellum parcellation were also incorporated, resulting in a comprehensive whole brain parcellation for both hemispheres. To facilitate multimodal data analysis, the atlas package includes co-registered average templates for myelin and Nissl staining from the same individuals, ex vivo MRI T2 (91 individuals), and in vivo MRI T2 (446 individuals). Cortical flat maps and pial, cortical mid-thickness, and white matter surfaces are also provided. BMA2.0 provides a central brain space for multimodal data integration, spatial analysis, and comparative neuroscience. Standard formats and transformations are provided for easy integration into existing workflows and interoperability with existing atlases.

neuroscience↗

bioRxiv2025

Actin monomers influence the interaction between Xenopus cyclase-associated protein 1 and actin filaments

Cyclase-associated protein (CAP) binds to both actin monomers and filaments and regulates multiple aspects of the actin dynamics including polymerization and depolymerization. CAP has been isolated from multiple species as a stable equimolar complex with actin monomer. However, functional significance of the CAP-actin complex is unknown. We previously demonstrated that native Xenopus cyclase-associated protein 1 (XCAP1) forms a 4:4 complex with actin. Here, we characterized how actin-free XCAP1 and the XCAP1-actin complex interact with actin filaments using high-speed atomic force microscopy and found that XCAP1-bound actin monomers influence dwell time and positional preference of XCAP1 on actin filaments. Actin-free XCAP1 bound to actin filaments transiently with a dwell time of [~]0.2 seconds. The XCAP1-actin complex also bound to actin filaments transiently but with a 3-to 5-fold longer dwell time than actin-free XCAP1. Actin-free XCAP1 bound to both side and ends of actin filaments with moderate preference to ends. However, the XCAP1-actin complex bound preferentially to the side of actin filaments. These results indicate that binding of actin monomers to XCAP1 affects its binding modes to actin filaments, suggesting that this might be a novel mechanism to regulate the effects of CAP on actin filaments.

biochemistry↗

bioRxiv2025

Mitorubin, berberrubine-based compounds that improve mitochondrial function, exhibit cardioprotective effects against age-related cardiac dysfunction

Mitochondria play a central role in cellular energy metabolism and homeostasis, and their dysfunction is closely linked to the progression of age-related diseases. The mitochondrial ubiquitin ligase MITOL (also known as MARCHF5) is a key regulator of mitochondrial dynamics and function, and reduced MITOL expression in the mouse heart has been implicated in mitochondrial dysfunction and cardiac aging. In this study, we identified berberrubine as a compound that promotes MITOL expression and activates mitochondria. We further assembled a group of berberrubine-based compounds, including its quinoid form and a newly developed water-soluble derivative, and collectively named them "Mitorubin" as mitochondria-activating compounds with therapeutic potential. While conventional berberrubine has poor water solubility, the addition of acetic acid significantly improved its solubility, enabling formulation as a solution. Mitorubin enhanced MITOL expression in cultured cells, increased mitochondrial DNA content and expression of mitochondrial proteins, and promoted mitochondrial respiration. In a model of age-related cardiac dysfunction, oral administration of Mitorubin restored mitochondrial function, improved cardiac performance, suppressed myocardial hypertrophy, and alleviated pulmonary congestion. Moreover, Mitorubin did not shorten lifespan in aged mice and significantly extended lifespan in high-fat diet-fed mice, suggesting both safety and efficacy under chronic administration. These findings suggest that Mitorubin is a promising mitochondrial activator and may represent a novel therapeutic strategy for age-related diseases.

biochemistry↗

bioRxiv2025

A bright synthetic near-infrared luciferin enhances the capabilities of deep-tissue bioluminescence imaging using firefly luciferases

Synthetic bioluminescence reactions exhibiting near-infrared (NIR)-shifted spectra have been explored to improve deep-tissue imaging through the design of firefly luciferin analogues. Although the NIR bioluminescence reactions improve the tissue penetration of bioluminescence signals from deep tissues, their photon output is markedly lower compared to the natural reaction with D-luciferin and firefly luciferase (Fluc), often by an order of magnitude or more. Consequently, in most instances, the sensitivity of NIR bioluminescence imaging (NIR-BLI) has not yet substantially surpassed that of BLI with the natural firefly reaction. Here, we present a synthetic firefly luciferin, named AkaSuke, that generates intense NIR bioluminescence ({lambda}max = 680 nm) in reaction with Fluc, greatly improving the detection sensitivity beyond that of the D-luciferin/Fluc reaction for targeting deep tissue. AkaSuke enables sensitive visualizations of ectopic hematogenesis through entire tissues of mice over time following transplantation of bone marrow stem cells labeled with Fluc. We additionally identify a Japanese firefly luciferase, DkumLuc1, that displays higher catalytic activities for bioluminescence emission of AkaSuke compared to typical Fluc, resulting in detection sensitivity comparable to that of AkaLumine/Akaluc reaction, one of the most sensitive bioluminescence systems for deep tissue imaging. We further propose the potential of the AkaSuke/DkumLuc1 reaction as an orthogonal pair with the AkaLumine/Akaluc for sensitive dual-target tracking in mice. Overall results suggest that AkaSuke enhances the capabilities of deep-tissue bioluminescence imaging using Fluc and its variant, and could serve as an emerging benchmark for the molecular design of NIR luciferin analogues.

cancer biology↗

bioRxiv2024

Multi-objective computational optimization of human 5' UTR sequences

The computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5' UTR sequences, key upstream elements of mRNA. However, fully automated design of 5' UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5' UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.

bioinformatics↗

bioRxiv2024

Serial Two-Photon Tomography Imaging of the whole marmoset brain for neuroanatomical analyses

Serial Two photon tomography (STPT) imaging is a technique to image a mass of tissue in its three-dimensional shape by combining two-photon imaging with automatic stage control and microtome slicing. We successfully implemented this technique for tracing the axonal projections in the marmoset brain. Here we describe the detailed experimental procedures that realized reliable volumetric imaging of the whole marmoset brain. We also introduce auxiliary histological techniques including visualization of myelin structure by simple light reflection, and immunological detection of non-fluorescent anterograde and retrograde tracers, which further enhance the utility of STPT data.

neuroscience↗

bioRxiv2024

Ca2+-driven PDIA6 phase separation to ensure proinsulin quality control

The endoplasmic reticulum (ER) plays key roles in protein quality control1,2 and dynamic Ca2+ storage3,4 in eukaryotic cells. However, the protein homeostasis (proteostasis) system that regulates these ER functions is still incompletely characterised. Previous study revealed the importance of oligomerization in the function PDIA1, an ER-resident disulfide isomerase and molecular chaperone, regulates oligomeric states in accordance with client folding5. This result suggests that at least some of the 20 members of other PDI family may undergo regulated self-assembly in order to optimally function. Here, we show that Ca2+ triggers the phase separation of PDIA6 into liquid-like condensates. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the Ca2+-driven condensation of PDIA6 recruits PDIA3 and proinsulin, thus increasing their local concentrations. This process results in the 30-fold enhancement of proinsulin folding and in the inhibition of proinsulin aggregation. Our findings shed light on a condensation-driven Ca2+-mediated proteostasis cascade in the ER by revealing how the efficiency of the protein folding process can be enhanced within quality control granules.

biochemistry↗

bioRxiv2023

ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline

H3K9 tri-methylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that, in male meiosis, ATF7IP2 amasses on autosomal and X pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the proteins essential roles in the maintenance of MSCI, suppression of retrotransposons, and global upregulation of autosomal genes. We propose that ATF7IP2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.

developmental biology↗

bioRxiv2023

Atypical heat shock transcription factor HSF5 is critical for male meiotic prophase under non-stress conditions

Meiotic prophase progression is differently regulated in males and females. In males, pachytene transition during meiotic prophase is accompanied by robust alteration in gene expression. However, how gene expression is regulated differently to ensure meiotic prophase completion in males remains elusive. Herein, we identified HSF5 as a male germ cell-specific heat shock transcription factor (HSF) for meiotic prophase progression. Genetic analyses and single-cell RNA-sequencing demonstrated that HSF5 is essential for progression beyond the pachytene stage under non-stress conditions rather than heat stress. Chromatin binding analysis in vivo and DNA-binding assays in vitro suggested that HSF5 binds to promoters in a subset of genes associated with chromatin organization. HSF5 recognizes a DNA motif different from typical heat shock elements recognized by other canonical HSFs. This study suggests that HSF5 is an atypical HSF that enforces the gene expression program for pachytene transition during meiotic prophase in males.

developmental biology↗

bioRxiv2023

The odor of a nontoxic tetrodotoxin analog, 5,6,11-trideoxytetrodotoxin, is detected by specific olfactory sensory neurons of the green spotted puffers but is processed in overlapping olfactory bulbar area with food odors.

Toxic puffers accumulate tetrodotoxin (TTX), a well-known neurotoxin, by feeding on TTX-bearing organisms and using it to defend themselves from predators. Our previous studies have demonstrated that toxic puffers are attracted to 5,6,11-trideoxytetrodotoxin (TDT), a nontoxic TTX analog that is simultaneously accumulated with TTX in toxic puffers and their prey. In addition, activity labeling using immunohistochemistry targeting neuronal activity marker suggests that TDT activates crypt olfactory sensory neurons (OSN) of the green spotted puffer. However, it remains to be determined whether individual crypt OSNs can physiologically respond to TDT. By employing electroporation to express GCaMP6s in OSNs, we successfully identified a distinct group of oval OSNs that exhibited a specific calcium response when exposed to TDT in green spotted puffers. These oval OSNs showed no response to amino acids (AAs), which serve as food odor cues for teleosts. Furthermore, oval morphology and surface positioning of TDT-sensitive OSNs in the olfactory epithelium closely resemble that of crypt OSNs. These findings further substantiate that TDT is specifically detected by crypt OSNs in green spotted puffer. The TDT odor may act as a chemoattractant for finding conspecific toxic puffers and for feeding TTX-bearing organisms for effective toxification.

zoology↗

bioRxiv2022

Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

Magnetic resonance imaging (MRI) is a noninvasive neuroimaging method beneficial for the identification of normal developmental and aging processes and data sharing. Marmosets have a relatively shorter life expectancy (approximately 10 years) than other primates, including, humans because they grow and age faster. Hence, the common marmoset model is effective in aging research. The current study investigated the aging process of the marmoset brain and provided an open MRI database on marmosets with a wide age range. The Brain/MINDS Marmoset Brain MRI Dataset contains brain MRI information on 216 marmosets aged between 1 and 10 years. During its release date, it is the largest public dataset worldwide. Further, it comprises multi contrast MRI images. In addition, 91 of 216 animals have corresponding ex vivo high-resolution MRI datasets. Our MRI database, which is available at the Brain/MINDS Data portal might help understand the effects of different factors, such as age, sex, body size, and fixation, on the brain. Moreover, it can contribute to and accelerate brain science studies worldwide.

neuroscience↗

bioRxiv2022

T cell responses induced by SARS-CoV-2 mRNA vaccination are associated with clonal replacement

mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, its not known whether T cell clonotypes responding to the first vaccination repeatedly expand with booster vaccinations. Here, we temporally tracked the CD8+ T-cell repertoire in individuals who received three shots of the BNT162b2 mRNA vaccine. By analyzing the kinetic profile of CD8+ T-cell clonotypes responding to the first, second, or third shot, we demonstrated that newly expanded clonotypes elicited by the second shot replaced many of those that responded to the first shot. Although these 2nd responder clonotypes expanded after the third shot, their clonal diversity was skewed, and they were partially replaced by newly elicited the 3rd responders. Furthermore, this replacement of vaccine-responding clonotypes occurred within the same Spike epitope. These results suggest that CD8+ T-cell memory induced by repetitive mRNA vaccination is characterized by the emergence of new dominant clones.

immunology↗