Biology subjects

Yamada, A.

Publications and source records attributed to Yamada, A..

16 recordsLinked to original sources

bioRxiv2026

Collagen Rope Trick: Cell-Laden Fibre Assembly at 1 Liquid Interfaces

Summary ParagraphTissues and organs in living organisms represent centimeter-scale hierarchical architectures comprising nano-to microscale, uniaxially aligned extracellular matrix (ECM) fibres with high mechanical strength, integrated with cellular components, as exemplified in tendon, skin, cartilage, bone, and blood vessels1. Here, we present a liquid-liquid interfacial spinning method to produce highly uniaxially aligned, centimeter-scale collagen fibres. The dried fibres exhibit exceptional mechanical properties, with fracture strength of 280 MPa, Youngs modulus of 6 GPa, and toughness of 17 MJ m-3, comparable to spider silk and tendon collagen, and exceeding supramolecular and double-network hydrogels1. Incorporating living cells into the collagen solution yielded centimeter-scale, cell-laden aligned fibres, with densely adherent, uniaxially aligned cells and over 80% viability. Myoblast-laden fibres recapitulate biological features of fibrotic muscle tissues, as observed in type II diabetes2. Interfacial collagen assembly further enables fabrication of dimension-controlled constructs, like 2D sheets, 0D capsules, and 1D tubes, thus providing modular building blocks for centimeter-scale 3D tissues and organ-like structures. This approach offers a versatile platform to engineer mechanically robust, cell-laden tissues with controlled hierarchical architecture.

bioengineering↗

bioRxiv2026

Soluble TREM2 reduces DAP12 surface expression by dissociating the TREM2-DAP12 complex

Triggering receptor expressed on myeloid cells 2 (TREM2) plays a crucial role in regulating various microglial functions, including phagocytosis, inflammation, chemotaxis, and proliferation. Recent studies have demonstrated that TREM2 cooperates with DAP12 to mediate intracellular signaling essential for these processes. Despite the importance of the TREM2-DAP12 complex in microglial physiology, the mechanisms controlling its expression and activity remain poorly understood. In this study, we report that the soluble ectodomain of TREM2 (sTREM2) regulates microglial phagocytic activity by attenuating the surface expression of DAP12. We found that stimulation of the microglial cell line BV2 with recombinant sTREM2 reduces the membrane expression of DAP12, but not that of TREM2. In addition, sTREM2 binds to full-length TREM2, leading to the uncoupling of TREM2 from DAP12. Furthermore, pre-treatment of BV2 cells with sTREM2 significantly inhibited amyloid-{beta} incorporation. These findings suggest that sTREM2 negatively regulates TREM2 signaling through the destabilization of the TREM2-DAP12 complex, and act as a novel bioactive molecule that modulates TREM2 signaling under physiological and pathological conditions.

molecular biology↗

bioRxiv2026

ABCG transporter knockouts alter integument and eye pigmentation with gene-specific effects on viability in butterflies and moths

Insects possess remarkable diversity in pigmentation across life stages, generated from a limited number of pigment precursors. ABCG transporters play central roles in pigmentation by mediating the intracellular transport of these precursors, yet their functions outside a few model systems remain poorly characterized. Here, we investigate the roles of the ABCG transporter genes white (w), scarlet (st), and oily kinshiryu (ok) across five lepidopteran species representing both butterflies and moths. CRISPR-Cas9 knockouts reveal conserved, tissue-specific functions of ABCG transporters throughout development, affecting larval and pupal integuments as well as adult eyes, but not scale coloration. Notably, our data indicate that both ommochrome and uric acid deposition underlie the coloration and opacity of Lepidoptera larvae and pupae, with the relative contributions of these pathways differing across species and stages. We also reveal that the vivid orange coloration of Gulf fritillary caterpillars arises from the interplay of ommochromes and urate granules, providing a clear example of how these pathways combine to produce diverse integument pigmentation. Loss of white was deleterious in four species examined, whereas scarlet knockouts produced viable individuals with easily detectable pigmentation phenotypes, identifying scarlet mutant backgrounds as a practical genetic marker for functional studies. Together, these findings show that conserved ABCG transporter complexes are differentially deployed across tissues and life stages, providing a mechanistic basis for the evolutionary diversification of pigmentation in Lepidoptera and enabling expanded functional genomics and transgenesis in emerging model species. Research HighlightsCRISPR-Cas9 disruption of ABCG transporters across Lepidoptera reveals conserved, tissue-specific roles in pigmentation. Interactions between ommochrome and uric acid deposition generate stage-specific coloration in larval and pupal integument.

genetics↗

bioRxiv2025

IGF2BP3 is essential for the growth heterogeneity of colorectal adenoma cells by regulating MYC

Adenoma is a major precancerous lesion in colorectal cancer (CRC), and the adenoma-carcinoma sequence is a well-known multistep progression to CRC caused by the accumulation of genetic mutations. On the other hand, the non-genetic mechanisms in the adenoma-carcinoma sequence remain largely unknown. In this study, organoids were established from 31 colorectal adenomas from 19 patients. Some adenomas showed heterogeneity in the proliferative potential of single cells, and this heterogeneity was regulated by non-genetic mechanisms. IGF2BP3 was identified as a differentially expressed gene between organoids with different growth patterns. IGF2BP3 positively regulated MYC expression at the transcriptional level and negatively regulated it at the translational level. This promoted high proliferative potential with high levels of oxidative phosphorylation, while allowing cells to avoid MYC-induced cell death. IGF2BP3 affected the tumorigenicity of mouse adenomas in vivo. Intra-tumor heterogeneity in growth potential is acquired at the precancerous stage in the adenoma-carcinoma sequence of colorectal carcinogenesis, and IGF2BP3 plays an important role in regulating MYC levels. These findings provide new insights into the non-genetic regulation of adenomas during CRC development.

cancer biology↗

bioRxiv2025

Cultivated Beef Meat Has the Potential to Maintain Original Characteristics of Beef Meat with Customizable Features

Cultivated meat (CM) is currently attracting much attention because of its promise to become a solution to issues of environmental sustainability, animal welfare, and decarbonization. While the fabrication process and materials are still the main focus, it is not yet clear what the characteristics of the constructed CMs are and how they take on the original characteristics of beef meat. In this study, the biological, physicochemical and sensory characteristics of three types of beef (Wagyu, Crossbreed and Holstein) meat were systematically analyzed and compared to muscle and fat fibers constructed by three-dimensional printing using satellite and adipose-derived stem cells isolated from these beef meats. The different characteristics of each beef meat were largely taken on by the CM fibers composed of bSC and bADSC of each meat. In addition, some differing properties from those of the respective beef meat were observed in CM fibers such as one of the omega-3 fatty acids, docosahexaenoic acid (DHA; Wagyu fat fibers showed the highest amount). Furthermore, we also found the important possibility to increase the composition of oleic acid to over 80% in monounsaturated fatty acid (Wagyu has around 50% oleic acid). This study revealed the importance of using cells isolated from each beef meat to provide CM that closely resemble the original texture and taste of each meat, and further the possibility of more carefully arranging their properties.

bioengineering↗

bioRxiv2025

Machine Learning-based Identification and Characterization of High-risk Carriers of HTLV-1-Associated Myelopathy (HAM)

HTLV-1-associated myelopathy (HAM) develops in a part of HTLV-1-infected individuals while most of the individuals remain asymptomatic. This complicates the identification of HTLV-1 carriers at elevated risk. In this study, we integrated HTLV-1 proviral load and antibody titers against Tax, Env, Gag p15, p19, and p24 proteins in a machine learning (ML) framework to identify and characterize high-risk individuals likely to develop HAM. We stratified asymptomatic carrier samples employing an anomaly detection model. We further developed and validated classifier models capable of distinguishing three clinical subgroups, carrier, ATL, and HAM for assessing the anomaly carrier samples as unseen test data. With most anomaly carrier samples ([~]76.47%) predicted as HAM, further statistical and interpretative analysis revealed the HAM-like characteristics of the anomaly carrier samples indicating elevated risk. Additionally, significant heterogeneity in immune response was observed among other asymptomatic carriers. Our machine learning-based approach offers a novel and insightful tool for identifying and evaluating high-risk characteristics for HAM, providing a holistic view of the complex immune dynamics of asymptomatic carriers of HTLV- 1.

systems biology↗

bioRxiv2024

Development of a noninvasive olfactory stimulation fMRI system in marmosets

Olfactory dysfunction is associated with aging and the earliest stages of neurodegenerative diseases, such as Alzheimers and Parkinsons diseases; it is thought to be an early biomarker of cognitive decline. In marmosets, a small non-human primate model used in brain research, olfactory pathway activity during olfactory stimulation has not been well studied because of the difficulty in clearly switching olfactory stimuli inside a narrow MRI. Here, we developed an olfactory-stimulated fMRI system using a small-aperture MRI machine. The olfactory presentation system consisted of two tubes, one for supply and one for suction of olfactory stimulants and a balloon valve. A balloon valve installed in the air supply tube controlled the presentation of the olfactory stimulant, which enabled sharp olfactory stimulation within MRI, such as 30 seconds of stimulation repeated five times at five-minute intervals. The olfactory stimulation system was validated in vivo and in a simulated system. fMRI analysis showed a rapid increase in signal values within 30 s of olfactory stimulation in eight regions related to the sense of smell. As these regions include those associated with Alzheimers and Parkinsons diseases, olfactory stimulation fMRI may be useful in clarifying the relationship between olfactory dysfunction and dementia in non-human primates.

physiology↗

bioRxiv2023

Distinct Local and Global Functions of Aβ Low-Threshold Mechanoreceptors in Mechanical Pain Transmission

The roles of A{beta} low-threshold mechanoreceptors (LTMRs) in transmitting mechanical hyperalgesia and in alleviating chronic pain have been of great interest but remain contentious. Here we utilized intersectional genetic tools, optogenetics, and high-speed imaging to specifically examine functions of SplitCre labeled A{beta}-LTMRs in this regard. Genetic ablation of SplitCre-A{beta}-LTMRs increased mechanical pain but not thermosensation in both acute and chronic inflammatory pain conditions, indicating their modality-specific role in gating mechanical pain transmission. Local optogenetic activation of SplitCre-A{beta}-LTMRs triggered nociception after tissue inflammation, whereas their broad activation at the dorsal column still alleviated mechanical hypersensitivity of chronic inflammation. Taking all data into consideration, we propose a new model, in which A{beta}-LTMRs play distinctive local and global roles in transmitting and alleviating mechanical hyperalgesia of chronic pain, respectively. Our model suggests a new strategy of global activation plus local inhibition of A{beta}-LTMRs for treating mechanical hyperalgesia.

neuroscience↗

bioRxiv2023

Complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes

Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average GC content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and T. matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least three groups in Tricholoma. Specifically, all T. bakamatsutake strains belonged to the "bakamatsutake" clade, which is most proximal to the "caligatum" clade consisting of T. caligatum and T. fulvocastaneum. The constructed highly contiguous telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.

genomics↗

bioRxiv2022

Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization of NEAT1 in Naked Mole-rat

Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2, that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.

molecular biology↗

bioRxiv2022

Topology of connective tissues: a key parameter in cellular heterogeneity, beyond composition and stiffness

Cellular plasticity is essential in physiological contexts, including pathological ones. It is the basis of morphogenesis and organogenesis, as well as tumorigenesis and metastasis. The extracellular matrix (ECM) is a key player in the generation of cellular heterogeneity. Advances in our understanding of cell plasticity rely on our ability to provide relevant in vitro models. This requires to catch the characteristics of the tissues that are essential for controlling cell fate. To do this, we must consider the diversity of tissues, the diversity of physiological contexts, and the constant remodeling of ECM along these processes. To this aim, we have fabricated a library of ECM models for reproducing the scaffold of connective tissues and basement membrane with different biofabrication routes based on the electrospining and drop casting of biopolymers. Using a combination of multiphoton imaging and nanoindentation, we show that we can vary independently protein composition, topology of connective tissues and stiffness of ECM models. Reproducing the features of a tissue and physiological context in turns allows to generate the complexity of the phenotypic landscape associated with the epithelial-to-mesenchymal transition (EMT) in human ovarian cancer. We show that EMT shift cannot be directly correlated with a unique ECM feature, which reflects the multidimensionality of living environments. Very importantly, our combinatorial approach allows us to provide in vitro models, where the impact of the topological cues on cellular phenotypes can be revealed, beyond protein composition and stiffness of the ECM matrix. On this line, this work is a further step towards the development of ECM models recapitulating the constantly remodeled scaffolding environment that cells face and provides new insights for the development of cell-free matrices.

bioengineering↗

bioRxiv2021

High-throughput tuning of ovarian cancer spheroids for on-chip invasion assays

We developed an invasion assay by using microfabricated culture devices. First, ovarian tumor spheroids were generated with a culture patch device consisting of an agarose membrane formed with a honeycomb microframe - the patch - and gelatin nanofiber backbone. By changing the dimensions of the honeycomb compartments we were able to control the number of cells and size of the spheroids. When the spheroids were placed on a patch coated with a thin membrane of fibrillary type I collagen, spheroid disruption was observed due to substrate induced cell migration. This process is straightforward and should be applicable to other cancer types, as well as assays under microfluidic conditions, thereby holding the potential for use in tumor modeling and anti-cancer drug development.

bioengineering↗

bioRxiv2020

Compromised nuclear envelope integrity drives tumor cell invasion

While mutations leading to a fragile envelope of the cell nucleus are well known to cause diseases such as muscular dystrophies or accelerated aging, the pathophysiological consequences of the recently discovered mechanically induced nuclear envelope ruptures in cells harboring no mutation are less known. Here we show that repeated loss of nuclear envelope integrity in nuclei experiencing mechanical constraints promotes senescence in nontransformed cells, and induces an invasive phenotype including increased collagen degradation in human breast cancer cells, both in vitro and in a mouse xenograft model of breast cancer progression. We show that these phenotypic changes are due to the presence of chronic DNA damage and activation of the ATM kinase. In addition, we found that depletion of the cytoplasmic exonuclease TREX1 is sufficient to abolish the DNA damage in mechanically challenged nuclei and to suppress the phenotypes associated with the loss of nuclear envelope integrity. Our results also show that TREX1-dependent DNA damage induced by physical confinement of tumor cells inside the mammary duct drives the progression of in situ breast carcinoma to the invasive stage. We propose that DNA damage in mechanically challenged nuclei could affect the pathophysiology of crowded tissues by modulating proliferation and extracellular matrix degradation of normal and transformed cells.

cell biology↗

bioRxiv2019

Correlation between increased atrial expression of genes related to fatty acid metabolism and autophag y in patients with chronic atrial fibrillation

Atrial metabolic disturbance contributes to the onset and development of atrial fibrillation (AF). Autophagy plays a role in maintaining the cellular energy balance. We examined whether the altered atrial expression of genes related to fatty acid metabolism is linked to that related to autophagy in chronic AF. Right atrial tissue was obtained during heart surgery from 51 patients with sinus rhythm (SR, n=38) or chronic AF (n=13). Preoperative fasting serum free-fatty-acid levels were significantly higher in the AF patients. The atrial gene expression of fatty acid binding protein 3 (FABP3), which is involved in the cells fatty acid uptake and intracellular fatty acid transport, was significantly increased in AF patients compared to SR patients; in the SR patients it was positively correlated with the right atrial diameter and intra-atrial EMD, parameters of structural and electrical atrial remodeling that was evaluated by an echocardiography. In contrast, the two groups atrial contents of diacylglycerol (DAG), a toxic fatty acid metabolite, were comparable. Importantly, the atrial gene expression of microtubule-associated protein light chain 3 (LC3) was significantly increased in the AF patients, and autophagy-related genes including LC3 were positively correlated with the atrial expression of FABP3. In conclusion, in chronic AF patients, the atrial expression of FABP3 was upregulated in association with autophagy-related genes without altered atrial DAG content. Our findings may support the hypothesis that dysregulated cardiac fatty acid metabolism contributes to the progression of AF and induction of autophagy has a cardioprotective effect against cardiac lipotoxicity in chronic AF.

molecular biology↗

bioRxiv2018

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

genomics↗

bioRxiv2018

Benefit-cost analysis of the policy of mandatory annual rabies vaccination of domestic dogs in rabies-free Japan

Japan is one of the few rabies-free countries/territories which implement the policy of mandatory vaccination of domestic dogs. In order to assess the economic efficiency of such policy in reducing the economic burden of a future canine rabies outbreak in Japan, a benefit-cost analysis (BCA) was performed using probabilistic decision tree modelling. Input data derived from simulation results of published mathematical model, field investigation conducted by the authors at prefectural governments, literature review, international or Japanese database and empirical data of rabies outbreaks in other countries/territories. The current study revealed that the annual costs of implementing the current vaccination policy would be US$160,472,075 (90% prediction interval [PI]: $149,268,935 - 171,669,974). The economic burden of a potential canine rabies outbreak in Japan were estimated to be US$1,682,707 (90% PI: $1,180,289 - 2,249,283) under the current vaccination policy, while it would be US$5,019,093 (90% PI: $3,986,882 - 6,133,687) under hypothetical abolition of vaccination policy, which is 3-fold higher. Under a damage-avoided approach, the annual benefits of implementing the current vaccination policy in expected value were estimated to be US$85.75 (90% PI: $55.73 - 116.89). The benefit-cost ratio (BCR) was estimated to be 5.35 x 10-7 (90% PI: 3.46 x 10-7 - 7.37 x 10-7), indicating that the implementation of the current policy is very economically inefficient for the purpose of reducing the economic burden of a potential canine rabies outbreak. In worse-case scenario analysis, the BCR would become above 1 (indicating economic efficiency) if the risk of rabies introduction increased to 0.04 corresponding to a level of risk where rabies would enter Japan in 26 years while the economic burden of a rabies outbreak under the abolition of vaccination policy increased to $7.53 billion. Best-case analysis further revealed that the economic efficiency of the current policy could be improved by decreasing the vaccination price charged to dog owners, relaxing the frequency of vaccination to every two to three years and implementing the policy on a smaller scale, e.g. only in targeted prefectures instead of the whole Japan.

epidemiology↗