Biology subjects

Hirata, A.

Publications and source records attributed to Hirata, A..

14 recordsLinked to original sources

bioRxiv2026

Dual-site specificity of the archaeal tRNA m2G methyltransferase Trm14

N2-methylguanosine (m2G) is widely found at multiple positions in tRNAs across the three domains of life. Tryptophan tRNA from Thermococcus kodakarensis contains m2G at position 67. We previously proposed that the tRNA m2G methyltransferase Trm14 is responsible for m2G67 formation in tRNATrp from T. kodakarensis, although Trm14 was originally identified as the enzyme catalyzing m2G6 formation in tRNACys in Methanocaldococcus jannaschii. Thus, it remained unclear whether Trm14 could also methylate G67. Here, we characterized archaeal Trm14. Biochemical analyses using recombinant T. kodakarensis Trm14 revealed that the enzyme catalyzes m2G formation at positions 6 and 67 in T. kodakarensis tRNACys and tRNATrp transcripts, respectively. Mass spectrometric analyses demonstrated the loss of m2G6 and m2G67 in native tRNACys and tRNATrp, respectively, from a T. kodakarensis trm14 gene disruptant strain, providing direct evidence for the dual-site specificity of T. kodakarensis Trm14. The growth phenotype of the trm14 gene disruptant strain was comparable to that of the wild-type strain. In contrast, a trm14/trm11 double disruptant, in which trm11 encodes the tRNA m2G10/m22G10 methyltransferase, exhibited severe growth retardation at 95 {degrees}C. This suggests that m2G6/m2G67 and m2G10/m22G10 cooperatively contribute to cellular fitness at high temperatures. Biochemical analyses revealed that Trm14 methylates all 46 T. kodakarensis tRNA transcripts. Furthermore, we found that recombinant M. jannaschii Trm14 methylated both positions. In contrast, the bacterial ortholog TrmN modified only position 6 in tRNA. Overall, this study expands our understanding of archaeal Trm14 by demonstrating its broader substrate specificity and the physiological significance of these modifications under hyperthermophilic conditions.

molecular biology↗

bioRxiv2026

Simulation-informed low-current anodal tDCS accelerates early motor recovery after photochemically induced cortical stroke in rats

Animal transcranial direct current stimulation (tDCS) studies typically use intensities exceeding clinical levels, and the off-line behavioral effects of weak electric fields in rodents remain unclear. We examined whether repeated anodal tDCS, calibrated by electric-field simulation to approximate human-equivalent weak fields, facilitates motor recovery after focal photothrombotic ischemic stroke (PIT) in rats. Simulation estimated that 50 A produced a maximum field of [~]1.96 V/m in the targeted motor cortex, matching clinically relevant intensities. Under isoflurane anesthesia, rats received anodal tDCS at 50 A, 250 A, or 1 mA (5 min/day, 5 days/week, 2 weeks), or sham; motor recovery was assessed weekly by beam-walking for 4 weeks. A linear mixed-effects model revealed significant time, group, and time x group effects. The 50 A group outperformed the PIT group at 1 week, and the 1 mA group at 2 weeks, with no differences thereafter. Low-current tDCS accelerates early post-stroke motor recovery, supporting weak-field neuromodulation.

neuroscience↗

bioRxiv2026

Evaluation of Neuronal Activation Thresholds for Low-Frequency Electromagnetic Exposure Using Morphologically Realistic Neuron Models

International guidelines for low-frequency electromagnetic field exposure (LF EMF) are primarily intended to prevent substantiated adverse effects. In the frameworks, limits on internal electric fields are linked to external exposure levels through computational dosimetry. However, the relationship between internal electric fields and these adverse effects remains incompletely understood. In particular, current approaches often overlook the morphological complexity and diversity of cortical neurons, which may limit the realism of neuronal activation estimates used to support these assessments. This study evaluates LF EMF-induced neural activation using 25 morphologically realistic neuron models spanning all cortical layers, embedded within 11 detailed human head models. The internal electric fields were simulated for uniform magnetic field exposures (100 Hz-100 kHz) along the three anatomical directions, and excitation thresholds were computed using a multi-scale framework combining voxel-based dosimetry with biophysical neuron simulations. A real-world exposure scenario involving a child near an acousto-magnetic article-surveillance deactivator was also analyzed. Thresholds varied across cell type, morphology, cortical location, subject anatomy, frequency, and exposure direction, with L2/3 pyramidal, L4 basket, and L5 thick-tufted pyramidal cells showing the lowest thresholds. Despite this variability, all simulated thresholds were conservative with respect to the basic restrictions and dosimetric reference limits set by IEEE ICES and ICNIRP. The smallest margin occurred at 100 kHz, where the threshold remained a factor of 2.8 above the corresponding limit. These findings indicate that current LF EMF exposure limits remain conservative when evaluated using highly detailed, morphology-based CNS activation models.

neuroscience↗

bioRxiv2025

The viable but non-culturable (VBNC) state of Campylobacter jejuni lacks propagation ability in the mouse intestinal tract

Campylobacter jejuni is a foodborne pathogen found worldwide. It can exist in a viable but non-culturable (VBNC) state under environmental stresses and cannot be cultured in this state. Whether C. jejuni retains its pathogenicity or causes food poisoning by resuscitation from the VBNC state remains unclear. This research aimed to evaluate whether C. jejuni in the VBNC state should be accounted for in prevention strategies against Campylobacter food poisoning. The VBNC state of C. jejuni strain NCTC11168 was induced at 4{degrees}C under aerobic conditions. A mouse model (C57BL/6, 3-week-old male) was prepared by administering a defined zinc-deficient diet and antibiotics in drinking water. Each mouse was administered C. jejuni with approximately 107 colony-forming units of culturable cells, cells in the VBNC state, or Muller-Hinton broth as a control. In culturable cell-infected mice, an increase in the number of C. jejuni in stool was observed using colony counting and quantitative polymerase chain reaction. No culturable cells were present in VBNC cell-infected mice. Clinical signs, weight loss, or significant increase in lipocalin-2 and myeloperoxidase levels, as inflammatory biomarkers, were not observed in culturable cell- or VBNC cell-infected mice. Thus, culturable cells colonized the mouse intestinal tract, whereas cells in the VBNC state could not. In the VBNC state, C. jejuni may not pose a risk of food poisoning. Further investigations on the colonization and pathogenicity of C. jejuni in the VBNC state in the human intestinal tract are required.

microbiology↗

bioRxiv2025

A facile method for fluorescent visualization of newly synthesized fibrous collagen by capturing the allysine aldehyde groups serving as cross-link precursors

The fibrous structures of collagen provide physical strength and stability to tissues and organs. Abnormalities in their orientation, growth, and remodeling cause morphogenetic defects and diseases including fibrosis, highlighting the importance of understanding how collagen fibers are organized within tissues. However, this process remains difficult to study, as methods for fluorescently labeling collagen fibers with simple protocols and visualizing their three-dimensional structure are still limited. Here we describe a convenient method for fluorescent labeling of collagen fibers in vertebrate tissues. Using DAF-FM, a probe originally developed for nitric oxide detection, premature collagen fibers can be visualized through covalent binding to allysine residues, which serve as precursors of collagen cross-linking. We further show that combining two probes with different emission spectra, DAF-FM and DAR-4M, enables pulse-chase labeling of newly synthesized collagen fibers. This approach provides a practical tool for investigating collagen dynamics during tissue development and remodeling.

developmental biology↗

bioRxiv2025

A transfer RNA methyltransferase with an unusual domain composition catalyzes 2'-O-methylation at position 6 in tRNA.

Thermococcus kodakarensis tRNATrp contains 2'-O-methylcytidine at position 6 (Cm6). However, the tRNA methyltransferase responsible for the modification has not been identified. Using comparative genomics we predicted TK1257 as a candidate for the modification. Biochemical and mass spectrometry studies of purified recombinant TK1257 gene product show it to possess a tRNA methyltransferase activity for Cm6 formation. This protein has a highly unusual composition of domains, containing N-terminal ferredoxin-like, SPOUT catalytic and THUMP domains. Previous to this study, all known THUMP-related tRNA methyltransferases were shown to contain a Rossmann fold catalytic domain and the nucleosides they produced were N2-methylguanosine and/or N2, N2-dimethylguanosine. Therefore, our findings extend the knowledge of architecture of tRNA methyltransferases. We named the TK1257 gene product TrmTS and showed it can synthesize Am6 and Um6 as well as Cm6. A trmTS gene deletion strain showed slight growth retardation at high temperatures. Site-directed mutagenesis studies based on structural model revealed catalytically and structurally important amino acid residues in TrmTS and identified a TrmTS-specific linker is structurally essential. We showed that TrmTS recognizes the 3'-CCA terminal region and a stretch loop connected with at least two stems in RNA. Finally, we constructed a model of the binding between TrmTS and tRNA.

biochemistry↗

bioRxiv2025

Cerebellum involvement in visuo-vestibular interaction for the perception of gravitational direction: a repetitive transcranial magnetic stimulation study

Accurate perception of the direction of gravity relies on the integration of multisensory information, particularly from the visual and vestibular systems, within the brain. Although a recent study of patients with cerebellar degeneration suggested a cerebellar role in visuo-vestibular interaction in the perception of gravitational direction, direct evidence remains limited. To address this gap, we conducted two experiments with 42 healthy participants to evaluate the impact of repetitive 1-Hz transcranial magnetic stimulation (rTMS) over the posterior cerebellum on visual dependency, quantified by the subjective visual vertical bias induced by rotating optokinetic stimulation (OKS). Electric field simulations in high-resolution head models were used to ensure focal stimulation of the cerebellum at the group level. The results demonstrated that repetitive transcranial magnetic stimulation (rTMS) applied to the cerebellar vermis significantly attenuated the OKS-induced shift in visual vertical (SVV) bias. This effect was not observed when stimulation was applied to the early visual cortex (V1-2) or the cerebellar hemisphere. Also, the vermis rTMS had no effect on the judgement precision in the absence of visual motion cues, suggesting that the rTMS may reduce visual weight in visuo-vestibular processing by increasing visual motion noise rather than affecting vestibular function. These findings suggest a direct involvement of the cerebellar vermis in the visuo-vestibular interaction underlying the perception of gravitational direction, providing new insights into cerebellar contributions in human spatial orientation. Significance StatementThe cerebellum has been implicated in multisensory integration for spatial orientation, but its direct role in visuo-vestibular interactions remains limited. Using 1-Hz rTMS, we demonstrated that stimulation of the cerebellar vermis significantly reduced visual dependency in the perception of gravitational direction, as measured by the subjective visual vertical bias induced by rotating optokinetic stimulation. This effect was absent when adjacent areas, such as early visual cortex and the cerebellar hemisphere, were stimulated. These results suggest that the cerebellar vermis is directly involved in visuo-vestibular interaction, providing new insights into the cerebellar contribution to spatial orientation in humans.

neuroscience↗

bioRxiv2023

HERC3 E3 ligase provides an ERAD branch eliminating select membrane proteins

Aberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, each with distinct substrate specificity, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. In this study, we have discovered a cytosolic Ub ligase called HERC3, which fulfills a distinct role in facilitating the ERAD of select polytopic membrane proteins. Using a series of multiplex knockdown/knockout experiments, we have demonstrated that HERC3 functions independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to facilitate the ubiquitination, retrotranslocation, and ERAD of misfolded CFTR. Furthermore, HERC3 collaborates with RNF5/185 to enhance the association of UBQLN proteins, thereby augmenting the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 specifically promotes the ERAD of CFTR, likely due to its ability to interact with the less hydrophobic membrane-spanning domains of CFTR. HERC3 may detect exposed transmembrane domains on the cytoplasmic surface of the ER, thereby facilitating the recruitment of UBQLN and subsequently accelerating the ERAD of select polytopic membrane proteins.

cell biology↗

bioRxiv2020

Global trends in biodiversity and ecosystem services from 1900 to 2050

Despite the scientific consensus on the extinction crisis and its anthropogenic origin, the quantification of historical trends and of future scenarios of biodiversity and ecosystem services has been limited, due to the lack of inter-model comparisons and harmonized scenarios. Here, we present a multi-model analysis to assess the impacts of land-use and climate change from 1900 to 2050. During the 20th century provisioning services increased, but biodiversity and regulating services decreased. Similar trade-offs are projected for the coming decades, but they may be attenuated in a sustainability scenario. Future biodiversity loss from land-use change is projected to keep up with historical rates or reduce slightly, whereas losses due to climate change are projected to increase greatly. Renewed efforts are needed by governments to meet the 2050 vision of the Convention on Biological Diversity. One Sentence SummaryDevelopment pathways exist that allow for a reduction of the rates of biodiversity loss from land-use change and improvement in regulating services but climate change poses an increasing challenge.

ecology↗

bioRxiv2020

Tongue thickness measured by ultrasonography is associated with tongue pressure in the Japanese elderly

The term "oral frailty" reflects the fact that oral health is associated with physical frailty and mortality. Tongue thickness measurement is one of the evaluations for swallowing function. The aim of this study was to investigate the relationship between tongue thickness and tongue pressure in the Japanese elderly. We evaluated 254 elderly patients; all the participants underwent tongue ultrasonography and tongue pressure measurement. To determine tongue thickness, we measured the vertical distance from the surface of the mylohyoid muscle to the tongue dorsum using ultrasonography. Result analyses revealed that tongue thickness was linearly associated with tongue pressure in both sexes. In male participants, dyslipidemia, lower leg circumference, and tongue pressure were independently significantly associated with tongue thickness. In female participants, body mass index and tongue pressure were independently significantly associated with tongue thickness. Tongue thickness was significantly decreased by age for both men and women. The optimal cutoff for tongue thickness to predict the tongue pressure of < 20 kPa was 41.3 mm in males, and 39.3 mm in females. In the Japanese elderly, tongue thickness using ultrasonography is associated with tongue pressure. Tongue thickness and tongue pressure, which are sensitive markers for oral frailty, decrease in aging. The tongue ultrasonography provides a less invasive technique for determining tongue thickness and related aspiration risks for elderly patients.

neuroscience↗

bioRxiv2020

Quantitative assessment of pain threshold induced by a single-pulse transcranial magnetic stimulation

ObjectiveTranscranial magnetic stimulation (TMS) is commonly used in basic research to evaluate human brain function. Although scalp pain is a side effect, no studies have quantitatively assessed the TMS intensity threshold for inducing pain and whether sensitivity to TMS-induced pain differs between sexes. MethodsWe measured pain thresholds when single-pulse TMS was applied over either Brocas area (BA) or left primary motor cortex (M1). We compared these thresholds with motor threshold for inducing motor evoked potential (MEP) through M1 stimulation. We also compared pain thresholds for BA and M1 between males and females. ResultsPain thresholds for both sites were significantly lower than motor threshold. Further, the pain threshold for BA was much lower than that for M1. No significant difference was observed between sexes. ConclusionThe results suggest that TMS at an intensity equivalent to motor thresholds, which is often used in experimental or clinical studies, causes slight scalp pain. SignificanceExperimental designs using TMS to evaluate functional relationships between brain and behaviors should consider scalp pain and reduce its likelihood as much as possible. HighlightsO_LIWe investigated pain thresholds induced by a single-pulse TMS over the head. C_LIO_LIPain thresholds for TMS over Brocas area (BA) and primary motor cortex (M1) were much lower than motor threshold. C_LIO_LINo significant differences in the pain thresholds were observed between sexes. C_LI

neuroscience↗

bioRxiv2019

Group-Level Analysis of Induced Electric Field in Deep Brain Regions by Different TMS Coils

Deep transcranial magnetic stimulation (dTMS) is a non-invasive technique used in treating depression. In this study, we computationally evaluate group-level dosage during dTMS with the aim of characterizing targeted deep brain regions to overcome the limitation of using individualized head models to characterize coil performance in a population.\n\nWe use an inter-subject registration method adapted to deep brain regions that enable projection of computed electric fields (EFs) from individual realistic head models (n = 18) to the average space of deep brain regions. The computational results showed consistent group-level hotspots of the EF in deep brain region with intensities between 20%-50% of the maximum EF in the cortex. Large co-activation in other brain regions was confirmed while half-value penetration depth from the cortical surface was smaller than 2 cm. The halo figure-8 assembly and halo circular assembly coils induced the highest EFs for caudate, putamen, and hippocampus.\n\nGeneralized induced EF maps of deep regions show target regions despite inter-individual difference. This is the first study that visualizes generalized target regions during dTMS and provides a method for making informed decisions during dTMS interventions in clinical practice.

biophysics↗

bioRxiv2018

Electric field dependent effects of motor cortical TDCS

Transcranial direct current stimulation (TDCS) can modulate motor cortical excitability. However, its after-effects are highly variable between individuals. Individual cranial and brain anatomy may contribute to this variability by producing varying electric fields in each subjects brain. Here we show that these fields are related to excitability changes following anodal TDCS of the primary motor cortex (M1). We found in two experiments (N=28 and N=9) that the after-effects of TDCS were proportional to the individual electric field in M1, calculated using MRI-based models. Individuals with the lowest and highest local electric fields in M1 tended to produce opposite changes in excitability. Furthermore, the effect was field-direction dependent and non-linear with stimulation duration or other experimental parameters. The electric field component pointing into the brain was negatively proportional to the excitability changes following 1 mA 20 min TDCS of right M1 (N=28); the effect was opposite after 1 mA 10 min TDCS of left M1 (N=9). Our results demonstrate that a large part of variability in the after-effects of motor cortical TDCS is due to inter-individual differences in the electric fields. We anticipate that individualized electric field dosimetry could be used to control the neuroplastic effects of TDCS, which is increasingly being explored as a treatment for various neuropsychiatric diseases.

neuroscience↗

bioRxiv2018

A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios

Abstract.To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land use and climate change on biodiversity and ecosystem services (i.e. natures contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenarios selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem service models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modelling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modelling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

ecology↗