Biology subjects

Kikuchi, T.

Publications and source records attributed to Kikuchi, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A chromosome-level genome assembly of the classical model nematode Panagrellus redivivus for comparative studies of parasitism evolution

Panagrellus redivivus is a free-living nematode that served as an early model system for nematode biology prior to Caenorhabditis elegans. As a member of Clade IV, a clade harboring major plant-parasitic (e.g., Bursaphelenchus xylophilus) and animal-parasitic (e.g., Strongyloides spp.) species, P. redivivus represents a crucial, phylogenetically proximate non-parasitic reference for investigating the evolution of parasitism. Here, we present a chromosome-level genome assembly of P. redivivus constructed using Oxford Nanopore long reads, Illumina short reads, and Hi-C scaffolding. The assembly is resolved into five chromosome-scale scaffolds, with completeness validated by Hi-C contact maps and the identification of a non-canonical telomeric repeat motif. The assembly demonstrates high gene-space completeness (97.1% BUSCO) and contains 17,839 predicted protein-coding genes. Comparative orthology analysis revealed extensive orthogroup sharing between P. redivivus and Clade IV parasites, enabling comparative evolutionary studies with reduced confounding effects from deep lineage divergence. This high-quality genome provides a key resource for investigating the genetic basis of distinctive biological traits, including ovoviviparity, as well as gene family dynamics and parasite evolution.

genomics↗

bioRxiv2026

Multidimensional semantic representations emerge from multi-frequency representational similarity learning

Current theories of semantic representation are agnostic about how fine-grained neurophysiological activity corresponds to representation of multidimensional semantic information. By applying an innovative multivariate technique (representational similarity learning; RSL), we adjudicated three hypotheses: (1) that multidimensional semantic structure is represented within a single frequency range (e.g., gamma/high gamma); (2) that each semantic dimension is independently represented within a different frequency range; and (3) that multidimensional semantic information is "transfrequency" (at least some information emerges only when multiple frequencies are considered together). RSL was applied to time-frequency power and phase data extracted from electrocorticography (ECoG) grid electrodes on the surface of human ventral anterior temporal lobe (vATL). We found significant decoding of graded, multidimensional semantic information from a wide range of frequencies (4 - 200 Hz), but not from individual frequency bands, providing clear evidence that multidimensional semantic information is coded in a transfrequency fashion.

neuroscience↗

bioRxiv2026

Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome

BackgroundTransposable elements (TEs) serve as powerful drivers of genome innovation but also threaten genome integrity. The PIF/Harbinger superfamily is distinctive among DNA transposons because mobilisation typically requires proteins, a DDE transposase and a MADF DNA-binding protein. Caenorhabditis inopinata, the closest known relative of C. elegans, has a TE-rich genome and lacks multiple components of the ERGO-1-class endogenous small-RNA pathway, making it a useful system for examining TE dynamics in a distinct host context. We identified a spontaneous dumpy mutant of C. inopinata caused by insertion of a PIF/Harbinger-family element into the coding region of Cin-dpy-11. The inserted element, designated Harbinger-1M_cIno, belongs to the Turmoil2 lineage originally defined in C. elegans and retains a MADF domain but lacks a recognisable DDE transposase ORF. Genome-wide curation recovered 258 related copies, revealing a strongly asymmetric family structure. Short noncoding derivatives were predominant, MADF-bearing derivatives were expanded and only one DDE-bearing locus retained an apparently intact transposase gene, suggesting that DDE and MADF functions are partitioned across distinct elements and may be supplied in trans during mobilisation. We also identified a second PIF/Harbinger-derived family, Harbinger-2M_cIno, associated with the Turmoil1 lineage. This family comprises 1,376 copies and therefore records substantial past amplification, but it lacks a detectable DDE source, shows greater sequence divergence and more degraded terminal structures than Harbinger-1M_cIno. Together, these data indicate that the two PIF/Harbinger lineages in C. inopinata differ not in whether amplification occurred, but in when it occurred and whether present-day mobilisation competence has been retained.

genetics↗

bioRxiv2026

Deletion of TNFR1 in astrocytes restores memory in aged Alzheimer's disease mice

Astrocytes participate in local inflammation and cognitive decline in Alzheimers disease (AD). Aberrant cytokine TNF signaling via astrocyte type-1 receptor (aTNFR1) could causally link the two AD pathology aspects. To verify this hypothesis, we crossed transgenic AD mice with mice enabling astrocyte-specific conditional TNFR1 deletion (aTNFR1KO). Induction of aTNFR1KO at early AD stages, preserved memory and reduced {beta}-amyloid load and astrogliosis in the aged mice. Induction of aTNFR1KO at late AD stages, in mice already memory-impaired, surprisingly produced rapid memory rescue, without affecting {beta}-amyloid load and astrogliosis. Single nucleus-RNA-seq analysis of all hippocampal cell populations revealed that late-stage aTNFR1KO rapidly modifies gene expression mainly in neurons, primarily targeting synaptic pathways, causing combined glutamatergic downregulation and GABAergic up-regulation. Consistently, hippocampal EEGs showed a pro-inhibitory effect of aTNFR1KO, which thus restores memory by "rebalancing" hippocampal circuitry excitability. This pro-memory effect identifies a new mechanism and astrocyte target against cognitive decline in AD.

neuroscience↗

bioRxiv2026

In vivo xenogenic reconstitution of human alveolar epithelial architecture and function

An urgent need exists for lung models that accurately replicate human physiological profiles. We developed a chimeric mouse model enabling targeted ablation of alveolar type 2 (AT2) cells and lung macrophages, creating niches for endoscopically transplanted human induced pluripotent stem cell (hiPSC)-derived lung progenitors (hLPs). These engrafted cells were retained for 24 weeks, demonstrating self-renewal and differentiation potential, surfactant protein secretion, and maintaining alveolar phosphate homeostasis, suggesting their maturation into AT2 cells. Furthermore, transplantation of hLPs derived from disease-specific hiPSCs recapitulated the phenotype of pulmonary alveolar microlithiasis. The architecture, function, and metabolism of human alveolar epithelium were accurately replicated in vivo. This model has the potential to link experimental models and first-in-human studies, facilitating the development of novel therapies for intractable lung diseases.

developmental biology↗

bioRxiv2025

Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes

In most organisms, all cells inherit the same genome, and many mechanisms exist to preserve its integrity across cell divisions. Programmed DNA elimination (PDE), the targeted removal of specific genomic regions from somatic cell lineages during early embryogenesis, is a striking exception. Since its discovery in parasitic nematodes over a century ago, PDE has been observed in diverse eukaryotes, including ciliates, arthropods, and vertebrates. However, the mechanisms, functions, and evolutionary origins of PDE remain poorly understood. Here, we describe the discovery of PDE in three species of the free-living nematode genus Caenorhabditis. Multiple genomic regions are precisely eliminated from somatic cells during early embryogenesis, resulting in chromosome fragmentation and the loss of key germline genes. The sites of elimination are strongly associated with conserved sequence motifs that likely direct DNA breakage. Comparative analyses indicate that PDE was present in the last common ancestor of Caenorhabditis and subsequently lost early during the evolution of many species, including C. elegans. The presence of PDE in the ancestors of one of biologys most important model organisms, together with recent discoveries in other eukaryotic lineages, reveals PDE to be a far more widespread and significant feature of evolution and development than previously recognised.

evolutionary biology↗

bioRxiv2025

A chromosome-level genome resource for the lethal tapeworm Sparganum proliferum, with candidate genomic safe harbours for functional genetics

Sparganum proliferum is an enigmatic and highly proliferative cestode known for its ability to form invasive larval infections in mammalian hosts. Here, we present the first chromosome-level genome assembly for a member of the order Diphyllobothriidea, generated using a hybrid sequencing approach that integrates Oxford Nanopore/PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C scaffolding. The final genome assembly spanned approximately 681 megabases (Mb) across nine chromosomes. BUSCO analysis revealed 81.9% completeness, whereas repeat annotation identified 55.8% of the genome as repetitive elements. Gene annotation uncovered approximately 29,000 protein-coding genes including [~]6200 transposon associated genes, highlighting the complex genomic landscape underlying parasitic lifestyles. Synteny analysis with other cestode linages including Echinococcus and Hymenolepis provided insights into the structural organisation and evolutionary trajectory of S. proliferum. In addition, we identified candidate genomic safe harbour (GSH) loci and promoters from housekeeping genes, offering potential for stable transgene integration. This high-quality genome serves as a critical resource for studying parasite evolution, host adaptation mechanisms, and the molecular basis of invasive proliferation in cestodes.

genomics↗

bioRxiv2025

All spectral frequencies of neural activity reveal semantic representation in the human anterior ventral temporal cortex

Intracranial electrophysiology offers a unique insight into the nature of information representation in the brain - it can be used to disentangle information encoded in local neuronal activity (gamma and high gamma frequencies) from information encoded via long-range interactions (lower frequencies). We used regularised logistic regression to decode animacy from time-frequency power and phase extracted from electrocorticography (ECoG) grid electrode data recorded on the surface of human vATL. Power in gamma (30 - 60 Hz) and high gamma (60 - 200 Hz) produced reliable decoding, indicating that semantic information is indeed expressed by local populations in vATL. However, power from a wide range of frequencies (4 - 200 Hz) produced significantly higher decoding accuracy and also exhibited the same rapidly-changing dynamic code previously observed when decoding voltage. These findings support the theory that semantic information is encoded by a local vATL "hub" that interacts with distributed cortical "spokes".

neuroscience↗

bioRxiv2025

Polysialylated NCAM distinguishes differentiated myoblasts from proliferating myoblasts prior to fusion

The differentiation of skeletal muscle myoblasts is a crucial step in muscle regeneration and hypertrophy. However, the phenotypic changes that occur in myoblasts just before myotube formation have remained poorly understood. In this study, we established a novel flow cytometric method to examine these changes. We identified two distinct populations in human desmin-positive myoblasts based on immunological NCAM (neural cell adhesion molecule) staining intensity after paraformaldehyde fixation. Our results indicate that these populations correspond to differentiated and proliferating myoblast phenotypes. Further analyses revealed that antigenicity for a polysialylated-NCAM (PSA-NCAM) antibody is strongly correlated with this fixation-resistant antigenicity of NCAM, suggesting that polysialylation is associated with myogenic differentiation. Using magnetic-activated cell sorting (MACS), we separated PSA-NCAM positive and negative myoblast fractions and demonstrated that PSA-NCAM positive cells show higher differentiation marker expression and faster myotube formation. These findings suggest that PSA-NCAM can serve as a valuable surface marker to distinguish between proliferating and differentiated myoblasts. Our method provides new insights into the phenotypic heterogeneity of myoblasts and offers an approach to studying the early stages of muscle cell differentiation before myotube formation.

cell biology↗

bioRxiv2025

Induction and long-term maintenance of hindbrain-like neural stem cells in xeno- and basic fibroblast growth factor-free conditions

Neurons exhibit region-specific identities corresponding to functional distinctions across different brain areas. Region-restricted neural stem cells (NSCs) have previously been generated from pluripotent stem cells; however, maintaining their regional identity over extended passages remains challenging. Here, we report the generation of hindbrain-like induced NSCs (Hb-LiNSCs) with upregulated hindbrain-specific markers and downregulated forebrain, midbrain, and spinal cord markers under xeno- and basic fibroblast growth factor-free conditions using three chemicals--CHIR99021 (at a high concentration), a potent activator of the Wnt pathway, A-83-01, a potent inhibitor of the TGF-{beta}/Activin/Nodal pathway, and LDN193189, a potent inhibitor of the bone morphogenetic protein pathway. Hb-LiNSCs maintained their chromosomal integrity, multipotency, and differentiation capacity even after long-term culture for more than 60 weeks. This innovative approach enhances our understanding of neurodevelopmental and neurodegenerative processes in the hindbrain region and paves the way for developing targeted cell-based therapy as well as disease modeling for drug discovery.

cell biology↗

bioRxiv2025

Defective pollen meiosis in Arabidopsis due to combined arabinan and galactan insufficiency

The development of pollen is critical or seed plants, and depends on precise cellular and molecular mechanisms. It is known that the cell wall plays a key role in the progression of pollen maturation. An earlier phase in pollen development is the meiosis of pollen mother cells (PMCs), the fundamental process for producing viable pollen grains. However, the significance of the cell wall during pre-meiosis processes has remained unclear. Pectin, a major component of the cell wall, is known to accumulate abundantly in pollen. To investigate the significance of the cell wall during pollen meiosis, we generated an arad1 gals2 gals3 triple mutant of Arabidopsis thaliana, lacking the genes responsible for normal synthesis of arabinan and galactan, which constitute the side chains of pectin. Although vegetative growth and cell wall properties were comparable in wild-type (WT) and arad1 gals2 gals3, the pollen development in the mutant failed during meiosis. Immunohistochemical analysis showed that pectic arabinan and galactan accumulated in WT PMCs before meiosis, but this was not observed in mutant PMCs. We believe that this study is the first to demonstrate the critical role of cell wall components, specifically pectic arabinan and galactan, in the pre-meiosis processes of pollen development. HighlightPectic arabinan and galactan accumulate on the surface of pollen mother cells and this accumulation is essential for pollen meiosis.

plant biology↗

bioRxiv2024

The heterogeneity of dermal mesenchymal cells reproduced in skin equivalents regulate barrier function and elasticity.

The heterogeneity of dermal mesenchymal cells, including perivascular mesenchymal cells and papillary and reticular fibroblasts, plays critical roles in skin homeostasis. Herein, we present human skin equivalents (HSEs), in which pericytes, papillary fibroblasts, and reticular fibroblasts are spatially organized through autonomous three-cell interactions among epidermal keratinocytes, dermal fibroblasts, and vascular endothelial cells. The replication of dermal mesenchymal cell heterogeneity enhances skin functions, including epithelialization, epidermal barrier formation, and dermal elasticity, enabling in vitro evaluation of drug efficacy using methodologies that are identical to those used in human clinical studies. Furthermore, ascorbic acid-induced epidermal turnover and synthesis of well-aligned extracellular matrix via perivascular niche cells play crucial roles in improving skin barrier function and elasticity. Therefore, HSEs with heterogeneous dermal mesenchymal cells may improve our understanding of the mechanisms underlying skin homeostasis through cell-to-cell communication and serve as a model to animal experiments for developing precision medicine.

bioengineering↗

bioRxiv2024

Odor sensory tests vs. In-silico prediction for the high-definition quantification of olfaction dynamics

The intricate dynamics of volatile organic compounds (VOCs) in the human respiratory system remain poorly understood. In the present study, we integrate odor sensory tests (OSTs) coupled with computational fluid dynamics and a physiologically based pharmacokinetic (CFD-PBPK) model to elucidate various aspects of the olfaction process. Safe yogurt-derived substances were incorporated in OSTs to prevent harmful exposure. Acetaldehyde was identified as a key active component in determining odor intensity, prompting further analysis of acetone and other four constituents of yogurt. Logarithmic correlations were established between the perceived odor intensity from the OSTs and both time-averaged absorption flux and equilibrium concentration within the olfactory mucus layer. These parameters were numerically captured, enabling the logarithmic approximation of odor intensity for different breathing profiles and the development of reliable prediction models for odor sensation based on quantifiable physiological parameters. The CFD-PBPK model captured detailed spatial and temporal variations of these parameters, which offers potential for future integrated/in-silico applications. Minor peaks of odor concentration were observed in the posterior olfactory regions during exhalation, revealing a retro-nasal phenomenon. Location-specific analysis revealed the nostrils and olfactory regions as the most accurate indicators of perceived odor intensity, proving the limitations of rough sensory assessments in the indoor/breathing zone scales. Acetone exhibited distinct absorption and desorption trends during the transitional phase between inhalation and exhalation, owing to the physical properties (diffusion and partition coefficients) that strongly characterize the olfaction dynamics. Author SummaryWe developed an integrated method using odor sensory tests (OSTs) coupled with computational fluid dynamics and physiologically based pharmacokinetic models (CFD-PBPK) to assess the temporal and spatial transport of yogurt odorants to the human olfactory region. Multiple phenomena were observed, including ortho-nasal and retro-nasal olfaction, temporal changes in the perceived odor intensity associated with breathing/sniffing profiles, absorption and desorption curves of acetone in the mucus epithelium, and regional-based olfaction distribution. The perceived odor intensity from OSTs can be predicted logarithmically in correlation with both the time-averaged absorption flux and the equilibrium concentration in the olfactory mucus layer, offering a reliable in-silico prediction model for odor sensation based on numerically quantifiable parameters. This model offers potential implications for multiple computational, biomedical, and industrial applications, such as the electric noses, smart odor sensors, food assessments, and fragrance development, particularly for long-term exposure in the industries that emit odorous compounds. It can open the door for more accurate predictions of the complex micro-fluid dynamics in the microbial ciliated tissues in the olfactory receptors.

bioengineering↗

bioRxiv2023

Cell wall pectic β-1,4-galactan contributes to increased plant freezing tolerance induced by cold acclimation

Subzero temperatures are often lethal to plants. Many temperate plants have a mechanism called cold acclimation that allows them to sense a drop in temperature and prepare for freezing stress through accumulation of soluble sugars and cryoprotective proteins. Plant cells are surrounded by a cell wall and as ice formation primarily occurs in the extracellular matrix (the apoplast), cell wall properties are important for plant freezing tolerance. Although previous studies have shown that the amounts of constituent sugars of the cell wall, in particular those present in pectic polysaccharides, are altered by cold acclimation, the significance of this change during cold acclimation has not been clarified. We found that {beta}-1,4-galactan, which forms neutral side chains of pectin, accumulates in the cell walls of Arabidopsis and various freezing tolerant vegetables during cold acclimation. The gals1 gals2 gals3 triple mutant, which has reduced {beta}-1,4-galactan in the cell wall, exhibited reduced freezing tolerance compared with wild-type Arabidopsis during initial stages of cold acclimation. Expression of genes involved in the galactan biosynthesis pathway such as GALACTAN SYNTHASES and UDP-glucose 4-epimerases were induced during cold acclimation in Arabidopsis explaining galactan accumulation. Cold acclimation resulted in a decrease in extensibility and an increase in rigidity of the cell wall in the wild type, whereas these changes were not observed in the gals1 gals2 gals3 triple mutant. These results indicate that the accumulation of pectic {beta}-1,4-galactan contributes to acquired freezing tolerance by cold acclimation via changes in cell wall mechanical properties.

plant biology↗

bioRxiv2023

Single worm long read sequencing reveals genome diversity in free-living nematodes

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from Dorylaimia, Enoplia, and early-branching species in Chromadoria. These free-living species had larger genome sizes, ranging from 147-792 Mb, compared to those of the parasitic lifestyle. Nine mitogenomes were fully assembled and displaying a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

genomics↗

bioRxiv2023

The stability of NPM1 oligomers regulated by acidic disordered regions controls the quality of liquid droplets

A nucleolus is a typical membrane-less nuclear body that is formed by liquid-liquid phase separation (LLPS) of its components. A major component that drives LLPS in the nucleolus is nucleophosmin (NPM1). The oligomer formation and inter-oligomer interactions of NPM1 are suggested to cooperatively contribute to the induction of LLPS. However, the molecular mechanism of how the quality of the liquid droplets formed by NPM1 is regulated is currently not well understood. In this manuscript, we revealed the regulatory mechanism of NPM1 oligomer formation and its relationship with the ability to form liquid droplets. Molecular dynamics simulations and mutant protein analyses suggest that the acidic amino acids in the N-terminal and central disordered regions of NPM1 disturb the key interactions between monomers. We also demonstrate that mutants with attenuated oligomer stability form liquid droplets as do the wild-type; the fluidity of the formed liquid droplets was greater than that of the wild-type. These results suggest that the stability of NPM1 oligomers is a critical determinant of liquid droplet quality. Furthermore, we observed that when the net negative charges in the acidic disordered regions were increased by phosphomimetic mutations at Ser125, the NPM1 oligomer stability decreased, which increased the fluidity of the liquid droplets. Our results provide a novel mechanistic insight into how nucleolar dynamics are regulated during the cell cycle.

biochemistry↗

bioRxiv2022

Efficient Gene Transduction in Pigs and Macaques with the Engineered AAV Vector AAV.GT5 for Hemophilia B Gene Therapy

Gene therapy for hemophilia using adeno-associated virus (AAV) vectors allows long-term coagulation factor expression. We examined the potential of a novel engineered liver-tropic AAV3B-based vector AAV.GT5 for hemophilia B gene therapy. In vitro transduction with AAV.GT5 in human hepatocytes was more than 100 times higher than with AAV-Spark100, while in vivo transduction efficacy into the liver and the increase in coagulation factor IX (FIX) antigen following intravenous injection of these vectors were similar in PXB mice (chimeric mice with a humanized liver) and macaques. The discrepancy was due to the low recovery and short half-life of AAV.GT5 in blood, depending on the positive charge of the heparin-binding site in the original AAV3B. The intra-hepatic vascular administration of AAV.GT5, but not AAV-Spark100, enhanced vector transduction into the liver and reduced vector distribution to the kidney in pigs. In macaques, the intra-hepatic artery injection of AAV.GT5 yielded a comparable increase in FIX antigen with a one-third dosage of peripheral venous administration. Two of four macaques who received AAV.GT5 intravenously did not develop neutralizing antibodies (NAbs) against AAV.GT5, while AAV-Spark100 induced serotype-specific NAbs in all four macaques. The NAb produced after the administration was relatively specific to the serotype and less responsive to the other serotype. As a result, the administration of AAV.GT5 successfully boosted FIX expression in one animal previously given AAV-Spark100. Thus, AAV.GT5 has different biodistribution and immunogenic characteristics compared with AAV-Spark100, and the intra-hepatic vascular administration may lessen the vector dose and avoid vector distribution to other organs. Key PointsO_LIThe AAV.GT5 vector has a strong transduction efficacy in human hepatocytes but has a faster clearance after systemic administration. C_LIO_LIIntra-hepatic vascular administration of the AAV.GT5 vector is an effective liver transduction method for hemophilia gene therapy. C_LI

genetics↗

bioRxiv2022

Representational similarity learning reveals a graded multi-dimensional semantic space in the human anterior temporal cortex

Neurocognitive models of semantic memory have proposed that the ventral anterior temporal lobes (vATLs) encode a graded and multidimensional semantic space--yet neuroimaging studies seeking brain regions that encode semantic structure rarely identify these areas. In simulations we show that this discrepancy may arise from a crucial mismatch between theory and analysis approach. Utilizing an analysis recently formulated to investigate graded multidimensional representations, representational similarity learning (RSL), we decoded semantic structure from ECoG data collected from the vATL cortical surface while participants named line drawings of common items. The results reveal a graded, multidimensional semantic space encoded in neural activity across the vATL, which evolves over time and simultaneously expresses both broad and finer-grained semantic structure amongst animate and inanimate concepts. The work resolves the apparent discrepancy within the semantic cognition literature and, more importantly, suggests a new approach to discovering representational structure in neural data more generally. Conflict of interestThe Department of Epilepsy, Movement Disorders, and Physiology, Kyoto University Graduate School of Medicine conducts Industry-Academia Collaboration Courses, supported by Eisai Co., Ltd, Nihon Kohden Corporation, Otsuka Pharmaceutical Co., and UCB Japan Co., Ltd.

neuroscience↗