Biology subjects

Ose, T.

Publications and source records attributed to Ose, T..

10 recordsLinked to original sources

bioRxiv2026

Rabies virus antagonizes interferon signaling by targeting phosphorylated STAT1 tetramers

AO_SCPLOWBSTRACTC_SCPLOWRabies virus phosphoprotein (P protein) antagonizes interferon signalling by selectively targeting activated STAT1 protein, but the structural basis for the selective recognition of activated STAT1 has remained unclear. Here we report cryo-EM structures of tyrosine-phosphorylated STAT1 (pY-STAT1) in complex with the C-terminal domain of P protein (P-CTD). P-CTD engages the pY-STAT1 tetramer through three discrete interfaces, contacting two DNA-binding domains within a pY-mediated STAT1 dimer and the N-terminal domain of a third STAT1 protomer. This binding mode explains how P-CTD selectively recognizes activated STAT1, occludes surfaces required for importin 5 and DNA binding, and stabilizes the compact tetrameric state, thereby restricting the conformational transition required for cooperative DNA binding. Cell-based assays further indicate that distinct P-CTD surfaces differentially contribute to antagonism of type I and type II interferon signalling. Further, by acting as an anchoring molecule, P-CTD also enabled structural elucidation of the complete STAT1 structures in the tetramer. Together, these data reveal critical mechanisms in viral immune evasion and pathogenesis, and fundamental innate immune signaling.

molecular biology↗

bioRxiv2025

Predicting protein complexes in biosynthetic gene clusters

Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse proteins responsible for natural product biosynthesis. These proteins collectively produce various secondary metabolites with complex chemical structure, including antibiotics and mycotoxins, yet the complete biosynthetic pathways have been experimentally resolved for only a limited number of compounds. Protein-protein interactions within BGCs have recently been recognized as key determinants of intermediate transfer, enzymatic regulation, and structural stability. However, many BGCs still contain proteins of unknown function that cannot be predicted by conventional sequence-based bioinformatics tools, hindering a comprehensive understanding of their biosynthetic pathways. To address this challenge, we built a high-throughput complex prediction pipeline by replacing AlphaFold3s multiple sequence alignment generation with a faster MMSeqs2. We systematically screened 487,828 protein pairs derived from 2,437 BGCs registered in the Minimum Information about a Biosynthetic Gene cluster (MIBiG) database and predicted 15,438 heteromeric interactions with an ipTM [≥] 0.6. Among them, 1,390 protein pairs exhibited structural homology with an RMSD [≤] 2.0 [A]. These predictions highlight interesting molecular mechanisms involving proteins previously annotated as "uncharacterized" or "potentially dysfunctional". Our analysis further showed that the ipSAE metric can distinguish correct heterocomplex pairs when multiple functionally homologous proteins are present within a BGC. Overall, our computational analysis revealed molecular interaction networks among proteins encoded by each BGC and identified enzyme complexes that are likely functional only when assembled. These predicted complexes may represent previously unrecognized links in their biosynthetic pathways. The complete results are available in a reusable format at https://doi.org/10.5281/zenodo.17451667 to support future experimental validation.

bioinformatics↗

bioRxiv2025

Development of a 24-Channel 3T Phased-Array Coil for fMRI in Awake Monkeys - Mitigating Spatiotemporal Artifacts in Ferumoxytol-Weighted Functional Connectivity Estimation

Functional magnetic resonance imaging (fMRI) of awake macaque monkeys holds promise for advancing our understanding of primate brain organization, including humans. However, estimating functional connectivity in awake animals is challenging due to the limited duration of imaging sessions and the relatively low sensitivity to neural activity. To overcome these challenges, we developed a 24-channel 3T receive radiofrequency (RF) coil optimized for parallel imaging of awake macaques. This enabled the acquisition of multiband and GRAPPA-accelerated ferumoxytol-weighted resting-state fMRI. The Human Connectome Project-style data processing pipelines were adapted to address the unique preprocessing demands of cerebral blood volume-weighted (CBVw) imaging, including motion correction, functional-to-structural image co-registration, and training a multi-run independent component analysis-based X-noiseifier (ICA-FIX) classifier for removal of structured artifacts. Our CBVw fMRI approach resulted in an elevated contrast-to-noise ratio compared to blood oxygenation level dependent (BOLD) imaging in anesthetized macaques. However, structured imaging artifacts still contributed more variance to the functional timeseries than neural activity. By applying the ICA-FIX classifier, we achieved highly reproducible parcellated functional connectivity at the single-subject level. At the group-level, we identified dense functional networks with spatial features homologous to those observed in humans. The developed RF receive coil, image acquisition protocols, and data analysis pipelines are publicly available, providing the broader scientific community with tools to leverage these advances for further research.

neuroscience↗

bioRxiv2024

Charting Cortical-Layer Specific Area Boundaries Using Gibbs Ringing Attenuated T1w/T2w-FLAIR Myelin MRI

Cortical areas have traditionally been defined by their distinctive layer cyto- and/or myelo- architecture using postmortem histology. Recent studies have delineated many areas by measuring overall cortical myelin content and its spatial gradients using the T1w/T2w ratio MRI in living primates, including humans. While T1w/T2w studies of areal transitions might benefit from using the layer profile of this myelin-related contrast, a significant confound is Gibbs ringing artefact, which produces signal fluctuations resembling cortical layers. Here, we address these issues with a novel approach using cortical layer thickness-adjusted T1w/T2w-FLAIR imaging, which effectively cancels out Gibbs ringing artefacts while enhancing intra-cortical myelin contrast. Whole-brain MRI measures were mapped onto twelve equivolumetric layers, and layer-specific sharp myeloarchitectonic transitions were identified using spatial gradients resulting in a putative 182 area/subarea partition of the macaque cerebral cortex. The myelin maps exhibit notably high homology with those in humans, suggesting cortical myelin shares a similar developmental program across species. Comparison with histological Gallyas myelin stains explains over 80% of the variance in the laminar T1w/T2w-FLAIR profiles, substantiating the validity of the method. Altogether, our approach provides a novel, noninvasive means for precision mapping layer myeloarchitecture in the primate cerebral cortex, advancing the pioneering work of classical neuroanatomists.

neuroscience↗

bioRxiv2024

Structural and functional insights into Cdc45 recruitment by Sld7-Sld3 for CMG complex formation

DNA replication requires recruitment of Cdc45 and GINS into the MCM double hexamer by initiation factors to form an active helicase, the Cdc45-MCM-GINS (CMG) complex, at the replication origins. The initiation factor Sld3 is a central regulator of Cdc45 and GINS recruitment, working with Sld7 together. However, the mechanism through which Sld3 regulates CMG complex formation remains unclear. Here, we present the structure of the Sld3 Cdc45-binding domain in complex with Cdc45 (Sld3CBD-Cdc45), showing detailed interactions and conformational changes required for binding to each other. The mutant analysis indicated that the binding between Sld3CBD and Cdc45 could be broken easily. We also revealed that Sld3CBD, GINS, and MCM bind to different sites on Cdc45 in the Sld3CBD-CMG model, indicating that after recruitment of Cdc45, Sld7-Sld3 could remain in Cdc45-MCM until CMG formation. The consistency between the particle size of Sld7-Sld3-Cdc45 and the distance between Sld3CBDs in the Cdc45-MCM dimer indicated the binding manner of the Cdc45-Sld3-[Sld7]2-Sld3-Cdc45 off/on MCM double hexamer. A DNA-binding assay of Sld3 and its complexes with single-stranded ARS1 fragments revealed a relationship between the dissociation of Sld7-Sld3 from CMG and the unwound single-stranded DNA. These findings help to further our understanding of the molecular basis of the regulation of CMG complex formation by Sld3.

molecular biology↗

bioRxiv2024

Mapping vascular network architecture in primate brain using ferumoxytol-weighted laminar MRI

Mapping the vascular organization of the brain is of great importance across various domains of basic neuroimaging research, diagnostic radiology, and neurology. However, the intricate task of precisely mapping vasculature across brain regions and cortical layers presents formidable challenges, resulting in a limited understanding of neurometabolic factors influencing the brains microvasculature. Addressing this gap, our study investigates whole-brain vascular volume using ferumoxytol-weighted laminar-resolution multi-echo gradient-echo imaging in macaque monkeys. We validate the results with published data for vascular densities and compare them with cytoarchitecture, neuron and synaptic densities. The ferumoxytol-induced change in transverse relaxation rate ({Delta}R2*), an indirect proxy measure of cerebral blood volume (CBV), was mapped onto twelve equivolumetric laminar cortical surfaces. Our findings reveal that CBV varies 3-fold across the brain, with the highest vascular volume observed in the inferior colliculus and lowest in the corpus callosum. In the cerebral cortex, CBV is notably high in early primary sensory areas and low in association areas responsible for higher cognitive functions. Classification of CBV into distinct groups unveils extensive replication of translaminar vascular network motifs, suggesting distinct computational energy supply requirements in areas with varying cytoarchitecture types. Regionally, baseline R2* and CBV exhibit positive correlations with neuron density and negative correlations with receptor densities. Adjusting image resolution based on the critical sampling frequency of penetrating cortical vessels allows us to delineate approximately 30% of the arterial-venous vessels. Collectively, these results mark significant methodological and conceptual advancements, contributing to the refinement of cerebrovascular MRI. Furthermore, our study establishes a linkage between neurometabolic factors and the vascular network architecture in the primate brain. HighlightsCortical layer vascular mapping using ferumoxytol-weighted R2* MRI Vascular volume is high in primary sensory areas and low in association areas Correlation between R2* and vascular volume with neuron and receptor densities Vascularization co-varies with densities of specific interneuron types

neuroscience↗

bioRxiv2022

Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain

Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses. HighlightsO_LIAchieved sub-millimeter localization accuracy of subject-wise brain region C_LIO_LIPropose a dedicated non-invasive multi-modal subject-specific registration pipeline C_LIO_LIConstruct brain coordinate system in AC-PC and grayordinate spaces C_LIO_LIEstablish multi-modal MRI and CT brain and cortical templates, MarmosetRIKEN20 C_LIO_LIQuantify intersubject variabilities in marmoset brain C_LIO_LISignificant bias and uncertainty exist in marmoset stereotactic positioning C_LI

neuroscience↗

bioRxiv2020

Brain/MINDS Beyond Human Brain MRI Study: Multi-Site Harmonization for Brain Disorders Throughout the Lifespan

Psychiatric and neurological disorders are afflictions of the brain that can affect individuals throughout their lifespan. Many brain magnetic resonance imaging (MRI) studies have been conducted; however, imaging-based biomarkers are not yet well established for diagnostic and therapeutic use. This article describes an outline of the planned study, the Brain/MINDS Beyond human brain MRI project (FY2018 [~] FY2023), which aims to establish clinically-relevant imaging biomarkers with multi-site harmonization by collecting data from healthy traveling subjects (TS) at 13 research sites. Collection of data in psychiatric and neurological disorders across the lifespan is also scheduled at 13 sites, whereas designing measurement procedures, developing and analyzing neuroimaging protocols, and databasing are done at three research sites. The Harmonization protocol (HARP) was established for five high-quality 3T scanners to obtain multimodal brain images including T1 and T2-weighted, resting state and task functional and diffusion-weighted MRI. Data are preprocessed and analyzed using approaches developed by the Human Connectome Project. Preliminary results in 30 TS demonstrated cortical thickness, myelin, functional connectivity measures are comparable across 5 scanners, providing high reproducibility and sensitivity to subject-specific connectome. A total of 75 TS, as well as patients with various psychiatric and neurological disorders, are scheduled to participate in the project, allowing a mixed model statistical harmonization. The HARP protocols are publicly available online, and all the imaging, demographic and clinical information, harmonizing database will also be made available by 2024. To the best of our knowledge, this is the first project to implement a rigorous, prospective harmonization protocol with multi-site TS data. It explores intractable brain disorders across the lifespan and may help to identify the disease-specific pathophysiology and imaging biomarkers for clinical practice.

neuroscience↗

bioRxiv2019

Structure of HIV-2 Nef reveals unique features distinct from HIV-1 involved in immune regulation

The HIV accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2 infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The dileucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2 mediated endocytosis for CD3. The highly-conserved C-terminal region forms a -helix, absent from HIV-1. We further determined the structure of SIV Nef harboring this region, demonstrating similar C-terminal -helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide new insights into the distinct pathogenesis of HIV-2 infection.

biophysics↗

bioRxiv2019

Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing

Macaque monkeys are an important model species for understanding cortical organization of primates, yet tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the relatively thin macaque cortex, high spatial, temporal, and angular resolutions are required while maintaining high signal-to-noise ratio to ensure good image quality. To address these challenges, we developed a macaque 24-channel receive coil for 3-T MRI with parallel imaging capabilities. This coil enabled adaptation of the Human Connectome Project (HCP) image acquisition protocols to the macaque brain. We also adapted HCP preprocessing methods optimized for the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provided high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold acceleration for dMRI and fMRI, respectively. Automated parcellation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. The resulting HCP-style in vivo macaque MRI data show considerable promise for analyzing cortical architecture and functional and structural connectivity using advanced methods that have previously only been available for humans.\n\nHighlights[tpltrtarr] 24-channel 3T MR receive coil designed for the smaller macaque brain.\n[tpltrtarr]In vivo macaque imaging protocols adapted according to guidelines from the HCP.\n[tpltrtarr]Parallel imaging yields five- and four-fold acceleration in fMRI and dMRI sampling.\n[tpltrtarr]HCPs minimal preprocessing and denoising pipelines adapted for macaques.\n[tpltrtarr]The multi-modal MRI data show considerable promise for HCP-style analyses.

neuroscience↗