Biology subjects

Oka, T.

Publications and source records attributed to Oka, T..

16 recordsLinked to original sources

bioRxiv2026

Genome-wide conservation and locus-specific coding variation in Teratoramularia rumicicola, a candidate microbial herbicide for Rumex weeds

The Rumex pathogen Teratoramularia rumicicola is a candidate microbial herbicide, but its functional genomic repertoire and variation among isolates remain poorly characterised. We generated a PacBio HiFi reference and evidence-supported gene annotation for TR4 and a short-read assembly for GR1, then compared the isolates using assembly- and read-based analyses. The TR4 and GR1 nuclear assemblies comprised 22.34 Mb (13 contigs; N50, 2.90 Mb) and 21.23 Mb (486 contigs; N50, 0.350 Mb), respectively. The TR4 annotation predicted 8,898 protein-coding genes, and the representative protein set was 96.7% complete in the Benchmarking Universal Single-Copy Orthologues assessment. Functional annotation identified 593 putatively secreted proteins, 258 candidate effectors, 355 carbohydrate-active enzyme (CAZyme) candidates and 20 predicted secondary-metabolite biosynthetic regions. Seven secreted CAZymes were prioritised as potential host-barrier-associated factors based on predicted activities and homology to virulence-related entries in the Pathogen-Host Interactions database. Despite 99.81% average nucleotide identity across aligned regions, read-based comparison identified 28,040 high-confidence isolate-fixed differences. Of 158 reconstructed candidate GR1 alleles, 147 showed strong assembly support. Notable differences included predicted truncations of two Zn(II)2Cys6 transcription factors, one adjacent to an intact nonribosomal peptide synthetase-like core gene, and a separate gene showing a localised repeat-induced point mutation (RIP)-like substitution pattern and predicted premature termination. Together, these resources and candidate loci provide a foundation for investigating pathogenicity and strain variation relevant to microbial herbicide development.

genomics↗

bioRxiv2026

MSLipidMapper: a pathway-centered lipidome analysis environment linking lipid class, acyl-chain subsets, and multi-omics data

Lipids exhibit extensive structural diversity arising from variation in lipid classes, subclasses, and acyl-chain compositions, making systematic interpretation of lipidomics data challenging. Although untargeted lipidomics enables the quantification of hundreds to thousands of lipid molecular species, downstream analyses often treat pathway-level summaries, molecular-species visualization, structural subsetting, and multi-omics interpretation as separate steps. Here, we present MSLipidMapper, an R/Shiny-based lipidomics data exploration environment for pathway-centered and structure-aware analysis of annotated lipidomics datasets. MSLipidMapper reconstructs annotated lipid peak tables as Bioconductor SummarizedExperiment objects, thereby organizing quantitative lipid abundance values, sample metadata, lipid subclass annotations, and parsed acyl-chain features within a unified data structure. Lipid molecular species are summarized on static, curated lipid metabolic pathway maps at the subclass level while retaining direct links to the underlying molecular species and acyl-chain annotations. This design enables users to inspect molecular-species patterns underlying each pathway node, define lipid subsets based on structural features such as specific acyl chains, and re-project these subsets onto the same pathway context. Gene or protein expression data can also be overlaid on pathway-associated reactions to support multi-layer interpretation of lipid metabolism. The program is showcased using publicly available aging lipidome datasets of mice, illustrating how subclass-level pathway summaries can be connected to molecular-species heatmaps, acyl-chain-defined subsets, and transcriptome or proteome information.

bioinformatics↗

bioRxiv2026

Structural basis of lenacapavir-induced HIV-1 capsid disruption during virion maturation

Long-acting lenacapavir (LEN) has emerged as a highly effective, potentially game-changing therapy for HIV treatment and prevention1-5. Although its mechanism of action in the early phase of HIV-1 replication, when the capsid directs key post-entry steps such as reverse transcription, nuclear import, and integration, has been well characterized1,2,6-8, its effects during the late phase of replication, when the capsid assembles and matures within budding virions, remain poorly understood. Here, we determine the cryo-electron microscopy structure of the mature HIV-1 capsid lattice assembled within virus-like particles in the presence of LEN. Our structural analyses revealed that LEN alters interhexamer interactions, perturbs capsid lattice curvature, and thereby prevents the formation of a functional cone-shaped capsid. Biochemical analyses further demonstrated that LEN-containing cores lose reverse transcriptase due to a compromised capsid integrity, whereas integrase and viral RNA remain associated. Functionally, viruses produced in the presence of LEN exhibited markedly reduced infectivity, low reverse transcription activity, and poor integration. Together, these findings provide mechanistic insight into the late-phase action of LEN and provide key directions for the design of future inhibitors.

microbiology↗

bioRxiv2025

Regulatory mechanism of heme-regulated inhibitor through autophosphorylation-driven activation and heme-induced deactivation

Heme-regulated inhibitor (HRI) is a key modulator of hemoglobin synthesis, exerting such effects by sensing intracellular heme levels. Under heme-deficient conditions, HRI dissociates from heme, becomes activated, and phosphorylates the translation initiation factor eIF2. However, the precise regulatory mechanisms governing HRI activation remain incompletely understood. In this study, we delineate part of the regulatory mechanism involving autophosphorylation-dependent activation and heme-mediated deactivation of HRI. HRI formed a dimer in solution through its N-terminal domain, irrespective of its phosphorylation state. However, a mutant with deletion of the N-terminal domain retained autophosphorylation activity, indicating that N-terminal domain-mediated dimerization is not essential for activation. Phosphorylated HRI formed a stable complex with eIF2, whereas the dephosphorylated form failed to bind, indicating that autophosphorylation is required for eIF2 recognition. Biochemical analyses, together with modeling based on the predicted structure, revealed that the phosphate groups of Thr488 and Thr493 interact with adjacent basic residues. These interactions enhance eIF2 recognition and phosphorylation. Additionally, heme-induced deactivation selectively targeted the dephosphorylated kinase domain and suppressed autophosphorylation. These findings provide multiple mechanistic insights into regulation of the activity of HRI, highlighting distinct roles for autophosphorylation, structural elements, and heme responsiveness in controlling its function.

biochemistry↗

bioRxiv2025

Retrospective metabolomics via dual-dimensional deconvolution using ZT Scan DIA 2.0

We present a scanning data-independent acquisition (DIA) strategy, ZT Scan DIA, combined with dual-dimensional tandem mass spectrometry spectral filtering and deconvolution along both the quadrupole and retention time axes to reconstruct compound-specific MS2 spectra from complex mixtures. This approach is particularly effective for hydrophilic metabolomics data, where spectral similarity-based annotation is widely used, increasing annotation rates by 119-193% compared with conventional data-dependent acquisition (DDA) and window-based DIA methods. In lipidomics, deconvolution improved annotation precision by removing contaminant product ions and enabled separate quantification of co-eluting isomers using MS2 chromatograms, although common diagnostic ions could also be erroneously removed. Nevertheless, optimization of analysis parameters minimized this negative effect. Furthermore, we developed a practical data processing pipeline in which raw ZT Scan DIA-MS2 chromatograms are directly used for isomer separation and MS2-based quantification, covering 1,393 and 3,020 molecules for human plasma and mouse liver tissues, respectively. All data processing steps, including direct import of vendor raw data, are supported in MS-DIAL.

bioengineering↗

bioRxiv2024

Dynamic cognitive differences between internal and external attention are associated with depressive and anxiety disorders

The internal/external attention framework characterises attention focused on internal representations, such as emotions, versus external representations, such as perceptual stimuli. The inability to focus ones attention is considered a critical factor in psychiatric disorders. While these different attentional foci are likely generated by the dynamic interplay of multiple cognitive processes, previous studies have generally examined single cognitive dimensions. We developed a new method, cognitive dynamic similarity analysis (C-DSA), to clarify how cognitive processes differ between experimental conditions. In an MR scanner, participants performed a word-processing task in which they focused on either their own emotions or the number of letters associated with a stimulus. To extract cognitive dynamics at the single-trial level, we applied cognitive dynamics estimation, a recently developed method that generates whole-brain activation maps for four cognitive dimensions (emotion processing, selective attention, self-referential thought, and working memory) using a meta-analytic platform. We then performed C-DSA to calculate the difference between internal and external attention for each cognitive dimension. C-DSA revealed significant differences between internal/external attention in all cognitive dimensions, but especially in emotion processing. Moreover, the difference between attention conditions of selective attention was negatively associated with the severity of depression and state-anxiety, but positively associated with trait-anxiety. Our findings suggest that C-DSA applies to both naturalistic and controlled dynamic processes and may be valuable in clinical settings by linking dynamic cognitive mechanisms with issues like ageing and psychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/615274v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1a1bbb4org.highwire.dtl.DTLVardef@12a587forg.highwire.dtl.DTLVardef@1181b45org.highwire.dtl.DTLVardef@1a6716c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data

Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence is still guaranteed by manual curation by analytical chemists, although various software tools have been developed for automatic spectral processing based on rule-based fragment annotations. In this study, we provide a novel machine learning model, MS2Lipid, for the prediction of lipid subclasses from MS/MS queries to provide an orthogonal decision of lipidomics software programs to determine the lipid subclass of ion features, in which a new descriptor, MCH (mode of carbon and hydrogen), was designed to increase the specificity of lipid subclasses in nominal mass resolution MS data. The model trained with 5,224 and 5,408 manually curated MS/MS spectra for the positive- and negative-ion modes mapped the query into one or several categories of 97 lipid subclasses, with an accuracy of 95.5% queries in the test set. Our program outperformed the CANOPUS ontology prediction program, providing correct annotations for 38.7% of the same test set. The program was further validated using various datasets from different machines and curators, and the average accuracy exceeded 87.4 %. Furthermore, the function of MS2Lipid was showcased by the annotation of novel esterified bile acids, whose abundance was significantly increased in obese patients in a human cohort study, suggesting that the machine learning model provides an independent criterion for lipid subclass classification, in addition to an environment for annotating lipid metabolites that have been previously unknown.

bioinformatics↗

bioRxiv2024

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

bioRxiv2024

Large ungulates will be present in most of Japan by 2050 owing to natural expansion and human population shrinkage

The aims of this study were to elucidate factors contributing to the expansion of the distributions of sika deer and wild boar in Japan and to predict the expansion of their distributions by 2025, 2050, and 2100. A site occupancy model was constructed using information on species distribution collected by the Ministry of the Environment in 1978, 2003, 2014, and 2018, days of snow cover, forested and road areas, elevation, human population, and distance from occupied grid cells as covariates to calculate the probability of distribution change. Factors contributing to distribution expansion were elucidated and distribution expansion was predicted. Distance from occupied grid cells had the strongest influence on distribution expansion, followed by the inherent ability of each species to expand its distribution. For sika deer, human population had a strong negative effect and elevation and number of days of snow cover were important. For wild boar, forest area and elevation had high importance. Predictions of future distribution showed that both species will be distributed over 90% of Japan by 2050 and over 100% by 2100.

ecology↗

bioRxiv2023

Discovery of N-Glycan Outer Chain like α-(1->6)-linked Mannan Structures in Aspergillus fumigatus Mycelium

The cellular surface of the pathogenic filamentous fungus Aspergillus fumigatus is enveloped in a mannose layer, featuring well-established fungal-type galactomannan and O-mannose type galactomannan. This study reports the discovery of cell wall component in the mycelium that resemble N-glycan outer chains found in yeast. The glycosyltransferases involved in their biosynthesis in A. fumigatus were identified, with a focus on two key -(1[->]2)-mannosyltransferases, Mnn2 and Mnn5, and two crucial -(1[->]6)-mannosyltransferases, Mnn9 and Van1. In vitro examination revealed the roles of Mnn2 and Mnn5 in transferring -(1[->]2)-mannosyl residues. 1H-NMR analysis of cell wall extracts from the {Delta}mnn2{Delta}mnn5 strain indicated the existence of an -(1[->]6)-linked mannan backbone in the mycelium, with Mnn2 and Mnn5 adding -(1[->]2)-mannosyl residues to this backbone. The -(1[->]6)-linked mannan-derived chemical shift was absent in strains where mnn9 or van1 was disrupted in the parental {Delta}mnn2{Delta}mnn5 strain. Co-expressed Mnn9 and Van1 functioned as -(1[->]6)-linked mannan polymerases in heterodimers, suggesting their crucial role in biosynthesizing the -(1[->]6)-linked mannan backbone. Disruptions in these mannosyltransferases did not affect fungal-type galactomannan biosynthesis. The study provides insights into the complexity of fungal cell wall architecture and a comprehensive understanding of mannan biosynthesis in A. fumigatus, including the presence of outer chain like mannan structures and their potential role in cell wall integrity. ImportanceThis study unravels the complexities of mannan biosynthesis in A. fumigatus, a key area for antifungal drug discovery. It reveals the presence of outer chain like mannan structures, offering fresh insights into the fungal cell walls design. Key enzymes Mnn2, Mnn5, Mnn9, and Van1 are instrumental in this process, with Mnn2 and Mnn5 adding specific mannose residues and Mnn9 and Van1 assembling the outer chain like structures. While fungal-type galactomannanspresence in the cell wall is known, the existence of outer chain like mannan adds a new dimension to our understanding. This intricate web of mannan biosynthesis opens avenues for further exploration and enhances our understanding of fungal cell wall dynamics, paving the way for targeted drug development.

microbiology↗

bioRxiv2023

Study on Vibrational Behavior of Cytoskeletons Modeled by Cylindrical Tensegrity Structure

The dynamic mechanism of a cellular cytoskeleton is essential for the role of the cell, and its accurate characterization has been a long-standing problem for cell scientists. A cytoskeletons vibrations are highly influenced by interactions of filamentous proteins mediated by axial vibration of the stiff microtubules (compressive member) and lateral vibration of F-actin (tensile member). Among various structures in a cell, the cytoplasmic contractile bundles, lamellipodia, and filipodia cells can be modeled by a symmetrical cylinder-shaped self-equilibrium tensegrity structure with different radii at the top and bottom of the cylinder. The truncated conelike cylinder model is made to be small in height compared to both radii. This study investigates the tensegrity self-vibrational behavior of the cellular cytoskeleton to calculate its natural frequencies, composed of the individual vibration of microtubules and F-actins from measured data. The spectral element method is adopted based on the Wittrick-Williams procedure to solve the vibrational behaviors of the cellular cytoskeleton. Various n-polygon cylindrical truncated cone-shaped tensegrity structures to mimic the cellular cytoskeletons are presented to demonstrate the robustness of the present study.

cell 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↗

bioRxiv2021

The 3' end of the human norovirus antigenomic sequence is required for its genomic RNA synthesis by RNA-dependent RNA polymerase

Norovirus genome is a single-stranded positive-strand RNA. To reveal the mechanism underlying the initiation of the norovirus genomic RNA synthesis by its RNA-dependent RNA polymerase (RdRp), we used an in vitro assay to detect the complementary RNA synthesis activity. Results showed that the purified recombinant RdRp synthesized the complementary positive-sense RNA from the 100 nt template corresponding to the 3' end region of the viral antisense genome sequence, but that RdRp did not synthesize the antisense genomic RNA from the 100 nt template, corresponding to the 5' end region of the positive-sense genome sequence. The 31 nt region at the 3' end of the RNA antisense template was then predicted to form the stem-loop structure. Its deletion resulted in the loss of complementary RNA synthesis by RdRp. The connection of the 31 nt to the 3' end of the positive-sense RNA template allowed to be recognized by the RdRp. Similarly, an electrophoretic mobility shift assay further revealed that RdRp bound to the antisense RNA specifically, but the 31 nt deletion at the 3' end lost the binding to RdRp. Therefore, combining this observation with further deletion and mutation analysis, we concluded that the predicted stem-loop structure in the 31 nt and region close to the antisense viral genomic stem sequences are important for initiating the positive-sense human norovirus genomic RNA synthesis by its RdRp.

microbiology↗

bioRxiv2021

Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy

Sapovirus is a cause of acute gastroenteritis in humans and animals. Infants and younger children have the greatest disease burden. Although it shares many similarities with norovirus, the lack of detailed structural information has hampered the development of vaccines and therapeutics. Here, we investigated the human sapovirus VLP by single particle cryo-electron microscopy and are the first to report the atomic structure of the capsid at 2.9 [A] resolution. The atomic model revealed the domain interactions of the capsid protein and functionally important amino acid residues. The extended loop from the P1 subdomain was involved in interactions in the P2 domain, forming unique arch-like dimeric protrusions of capsid proteins. All hypervariable regions that are important candidates for immune response or receptor binding, formed a large cluster at the top of the P domain. These results pave the way for developing vaccines, antiviral drugs, and diagnostic systems for this infectious disease.

microbiology↗

bioRxiv2020

Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization

Human ether-a-go-go-related gene potassium channel 1 (hERG) is a voltage-gated potassium channel, the voltage-sensing domain (VSD) of which is targeted by a gating-modifier toxin, APETx1. Although it is known that APETx1 inhibits hERG by stabilizing the resting state, it remains unclear where and how APETx1 interacts with the VSD in the resting state. Here, we prepared a recombinant APETx1, which is structurally and functionally equivalent to the natural product. Electrophysiological analyses using wild type and mutants of APETx1 and hERG revealed that their hydrophobic residues, in addition to a previously reported acidic hERG residue, play key roles in the inhibition of hERG by APETx1. Docking models of the APETx1-VSD complex that satisfy the results of mutational analysis suggest a molecular recognition mode between APETx1 and the resting state of hERG; this would provide a structural basis for designing ligands that control hERG function by binding to the VSD.

molecular biology↗

bioRxiv2019

Biosynthesis of β-(1->5)-Galactofuranosyl Chains of Fungal-Type and O-Mannose-Type Galactomannans within the Invasive Pathogen Aspergillus fumigatus

The pathogenic fungus Aspergillus fumigatus contains galactomannans localized on the surface layer of its cell walls, which are involved in various biological processes. Galactomannans comprise -(1[->]2)-/-(1[->]6)-mannan and {beta}-(1[->]5)-/{beta}-(1[->]6)-galactofuranosyl chains. We previously revealed that GfsA is a {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferase involved in the biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains. Here, we clarified the entire biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains in A. fumigatgus. Two paralogs exist within A. fumigatus: GfsB and GfsC. We show that GfsB and GfsC, in addition to GfsA, are {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferases by biochemical and genetic analyses. GfsA, GfsB, and GfsC can synthesize {beta}-(1[->]5)-galactofuranosyl oligomers up to lengths of 7, 3, and 5 galactofuranoses within an established in vitro highly efficient assay of galactofuranosyltransferase activity. Structural analyses of galactomannans extracted from the strains {Delta}gfsB, {Delta}gfsC, {Delta}gfsAC, and {Delta}gfsABC revealed that GfsA and GfsC synthesized all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans, and GfsB exhibited limited function in A. fumigatus. The loss of {beta}-(1[->]5)-galactofuranosyl residues decreased the hyphal growth rate and conidia formation ability as well as increased the abnormal hyphal branching structure and cell surface hydrophobicity, but this loss is dispensable for sensitivity to antifungal agents and virulence toward immune-compromised mice.\n\nIMPORTANCE{beta}-(1[->]5)-galactofuranosyl residues are widely distributed in the subphylum Pezisomycotina of the phylum Ascomycota. Pezizomycotina includes many plant and animal pathogens. Although the structure of {beta}-(1[->]5)-galactofuranosyl residues of galactomannans in filamentous fungi was discovered long ago, it remains unclear which enzyme is responsible for biosynthesis of this glycan. Fungal cell wall formation processes are complicated, and information concerning glycosyltransferases is essential for their understanding. In this study, we show that GfsA and GfsC are responsible for the biosynthesis of all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans. The data presented here indicates that {beta}-(1[->]5)-galactofuranosyl residues are involved in cell growth, conidiation, polarity, and cell surface hydrophobicity. Our new understanding of {beta}-(1[->]5)-galactofuranosyl residue biosynthesis provides important novel insights into the formation of the complex cell wall structure and the virulence of the subphylum Pezisomycotina.

microbiology↗