Biology subjects

Nakamura, J.

Publications and source records attributed to Nakamura, J..

9 recordsLinked to original sources

bioRxiv2026

A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Rapidly converting viral genome information into deployable molecular tests remains a major challenge in outbreak preparedness. We developed CONAN-SWIFT (Simple Workflow for Isothermal Field Testing), a sequence-to-test platform that integrates computational assay design, reverse-transcription loop-mediated isothermal amplification, CRISPR-Cas3 detection, reagent lyophilization and lateral-flow readout. Sequence-guided assays for Andes virus and Bundibugyo virus were established within approximately three weeks and extended to four additional filoviruses. A web-based designer supported crRNA selection, and systematic RT-LAMP primer optimization improved amplification performance. Recombinant Escherichia coli-expressed Cascade enabled standardized preparation of lyophilized Cas3-detection reagents, which were combined with a battery-operated isothermal device. The portable system detected as few as 10 input RNA copies per reaction within approximately 40 min. It also detected viral RNA and biologically contained, replication-incompetent Ebola virus in spiked human blood and concentrated wastewater. These findings establish the analytical feasibility of a rapidly adaptable CRISPR-Cas3 engineering framework for decentralized detection of emerging RNA viruses.

bioengineering↗

bioRxiv2025

Systemic aldehyde storm induced by allyl alcohol exposure results in extensive hepatic ferroptosis in Aldh2*2 knock-in mice

Aldehyde dehydrogenase 2 (ALDH2) is a mitochondrial enzyme that detoxifies multiple aldehyde species in the body. The ALDH2*2 allele (E487K) is one of the most common gene polymorphisms in humans, resulting in dysfunction of its enzyme activity. This study investigated in vivo mechanism of acute liver injury caused by exposure to allyl alcohol (AA) using Aldh2*2 knock-in (KI) mice with the same amino acid replacement as human ALDH2*2. A rapid burst of plasma acrolein as an active metabolite of AA, as well as plasma endogenous reactive aldehydes malondialdehyde (MDA) and formaldehyde, was observed at 10 min after exposure to 75 mg/kg of AA in the Aldh2*2 KI homozygous mice, which was not evident in the wild-type mice. Hepatocellular necrosis was more extensive in the Aldh2*2 KI homozygous mice than in the wild-type mice, which was preceded by hepatic glutathione depletion and was coincident with an accumulation of acrolein, MDA, and 4-hydroxy-2-nonenal adducts and iron deposition, suggesting an involvement of ferroptosis in the exacerbation of hepatic necrosis. Recovery from hepatic glutathione depletion was delayed in the homozygous mice compared with the wild-type mice, with a decreasing tendency of hepatic expression of cystine transporter xCT. These results suggest that increased hepatic glutathione consumption, due to decreased aldehyde detoxification capacity, can sensitize the Aldh2*2 KI homozygous mice to hepatic ferroptosis after the rapid "aldehyde storm". Our study revealed a crosstalk between aldehyde metabolism and ferroptosis pathways and potential health impacts of endogenous reactive aldehydes on ALDH2*2 carriers.

pathology↗

bioRxiv2025

The rice ethylene receptor OsERS1 negatively regulates the shoot growth and salt tolerance in rice seedlings

Ethylene is a gaseous plant hormone that regulates various aspects of growth and development. It promotes shoot growth in etiolated rice seedlings, which is crucial for seedling establishment and has significant agricultural implications. Of the five ethylene receptors in rice, OsERS1 is the most abundantly expressed in seedlings. Therefore, we investigated the localization and role of OsERS1 in shoot growth. When expressed in rice protoplasts, OsERS1 was localized in the endoplasmic reticulum. Knockout mutants of OsERS1 exhibited enhanced shoot growth in etiolated seedlings under normal and ethylene-treated conditions. Additionally, the induction of ethylene-responsive genes was increased in the mutants, indicating an elevated ethylene response due to OsERS1 knockout. The mutants also showed increased salt tolerance. In conclusion, our findings suggest that OsERS1 negatively regulates shoot growth and salt tolerance in etiolated rice seedlings.

plant biology↗

bioRxiv2023

RBM3 deficiency impairs body temperature control in response to cold stimulation

Mammals are thermostatic animals capable of regulating their body temperature within a precise range, irrespective of ambient temperature conditions. However, the precise mechanisms by which a body temperature is controlled dependent on ambient temperature are still unclear. Here, we report that RNA binding motif protein 3 (RBM3), one of the cold-responsive proteins, regulates body temperature via expressing thermogenic genes during the late-postnatal period. The body temperature in Rbm3 knockout (KO) juvenile mice was unstable and increased vulnerability to cold exposure. In addition, Rbm3 KO mice exhibited increased lipid droplets in brown adipose tissue (BAT) and abnormal histology. The single-cell RNA-seq (scRNA-seq) analysis revealed that RBM3 is highly expressed in proliferating and differentiating cells in BAT. Moreover, RBM3 was necessary for upregulating thermogenic genes after cold shock. Notably, RBM3 interacted with UCP1 mRNA in vivo, thereby stabilizing its mRNA levels. Lastly, RBM3 regulated neuronal activity in the dorsomedial hypothalamic nucleus (DMH) under a cold environment. These data suggest that RBM3 regulates thermogenesis in juvenile mice through both upregulating thermogenic genes in BAT and activating DMH neurons after cold exposure.

physiology↗

bioRxiv2022

Mouse behaviour on the trial-unique non-matching-to-location (TUNL) touchscreen task reflects a mixture of distinct working memory codes and response biases

The trial-unique non-matching to location (TUNL) touchscreen task shows promise as a translational assay of working memory deficits in disorders including autism, ADHD, and schizophrenia. Although it is commonly assumed that the TUNL task predominantly measures spatial working memory in rodents, this proposition has not previously been tested. In this project, we used computational modelling of behaviour from mice performing the TUNL task (total N = 163 mice across three datasets; 158,843 total trials). Contrary to common assumptions, behaviour on the TUNL task did not exclusively reflect spatial working memory. Instead, choice behaviour was explained as a mixture of both retrospective (spatial) working memory and prospective working memory for an intended behavioural response, as well as animal-specific response biases. We suggest that these findings can be understood within a resource-rational cognitive framework, and propose several task-design principles that we predict will maximise spatial working memory and minimise alternative behavioural strategies.

animal behavior and cognition↗

bioRxiv2022

Semaphorin 3G exacerbates joint inflammation through the accumulation and proliferation of macrophages in the synovium

ObjectiveMethotrexate (MTX) is an anchor drug for rheumatoid arthritis (RA) treatment; however, the exact mechanisms by which MTX improves RA activity are still debatable. This study aimed to understand the roles of molecules whose expression is affected by MTX in RA patients and find novel therapeutic targets. MethodsCD4+ T cells from 28 treatment naive RA patients before and 3 months after the initiation of MTX treatment were subjected to DNA microarray analyses. The expression of Semaphorin 3G (Sema3G), as one of the differentially-expressed genes, and its receptor, Neuropilin-2 (Nrp2), was evaluated in RA synovium and collagen-induced arthritis (CIA) synovium. CIA and collagen antibody-induced arthritis (CAIA) were induced in Sema3G-deficient (Sema3G-/-) mice and control mice, and the clinical score, histological score, and serum cytokines were assessed. The migration and proliferation of Sema3G-stimulated bone marrow-derived macrophages (BMMs) were analyzed in vitro. The effect of local Sema3G administration during CAIA on the clinical score and the quantity of infiltrating macrophages was evaluated. ResultsThe expression of Sema3G in CD4+ T cells was downregulated by MTX treatment in RA patients. Sema3G was expressed in RA but not osteoarthritis synovium, and its receptor Nrp2 was mainly expressed on activated macrophages. Sema3G deficiency ameliorated CIA and CAIA. Sema3G stimulation enhanced the migration and proliferation of BMMs. The local administration of Sema3G deteriorated CAIA and increased infiltrating macrophages. ConclusionsUpregulation of Sema3G in RA synovium is a novel mechanism to deteriorate joint inflammation through the accumulation of macrophages. Key messagesSemaphorin 3G is expressed in the inflamed synovium in human and mice. The receptor of Semaphorin 3G is mainly expressed on M1 macrophages. Semaphorin 3G deteriorates inflammatory arthritis through macrophage proliferation and migration.

pathology↗

bioRxiv2021

In vivo CRISPRi screen reveals the differential requirement for mitochondrial respiratory chain function between in vivo and in vitro tumor growth

The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and significant processes such as tumor dissemination and metastases remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells downregulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial metabolism impact in vivo tumor growth in a context-specific manner and provides systems-level evidence that respiratory function modulates tumor growth in vivo, suggesting that ATP limits growth and metastatic potential.

cancer biology↗

bioRxiv2021

Liquid-liquid phase separation of florigen activation complex induces flowering

Floral transition, regulated by the systemic action of the mobile florigen protein FLOWERING LOCUS T (FT), is essential for successful plant reproduction1. How FT controls downstream gene expression remains incompletely understood, although it relies on the florigen activation complex (FAC), a core component of FT function2-4. The FAC is a nucleus-localized transcriptional activator of genes encoding MADS-box transcription factors critical to reproductive development and consists of florigen FT; a scaffold 14-3-3 protein that is a key component for complex assembly; and FD, a basic leucine-zipper protein that recruits the FAC to DNA. Here we report that the FAC exhibits phase separation. In rice shoot apical meristem cells, rice florigen Heading date 3a (Hd3a) fused to the green fluorescent protein formed speckles in the nucleus. The FAC speckle is formed in a FAC-dependent manner in tobacco cells. Recombinant Hd3a, but not OsFD1, phase-separated in vitro, and this effect was enhanced in the presence of 14-3-3 protein. Furthermore, mutations affecting functionally important residues in the pocket region or C-terminal disordered region of Hd3a affected FAC phase separation, providing a biochemical framework for the proteins effect on flowering. The ability to form condensates via phase transition represents a previously unknown mechanism for gene activation by the FAC.

plant biology↗

bioRxiv2018

Cytokine profile in human olfactory cleft mucus and associated changes in olfactory function

Multiple factors, including physical changes of the nasal mucosa and epithelium and exposure to air-borne environmental agents, appear to contribute to age-related olfactory loss. However, the molecular aspects of aging-associated olfactory loss in humans are not well understood. Although inflammation can be a significant underlying cause for olfactory impairment, whether aging increases the levels of inflammatory cytokines in the human olfactory mucosa and whether any inflammatory markers are associated with age-related olfactory loss remain unclear. Using a noninvasive method for collecting human olfactory mucus, we characterized and compared inflammatory cytokines, chemokines, and some growth factors, in the mucus collected from the olfactory cleft or the anterior nasal cavity from 12 healthy, young (18-40 years old) and 12 elderly (60-85 years old) individuals. We also hoped to identify candidate molecular biomarkers associated with age-associated olfactory loss in humans. Olfactory thresholds were obtained for two odorants and individual mucus samples were analyzed using multiplex assays for the levels of 30 cytokines. Results indicated elevated levels of certain inflammatory cytokines (IL-12, MCP-1) in olfactory mucus of the elderly, and high levels of some inflammatory factors (MCP-1, IL-8, IL-13 and VEGF) were associated with reduced olfactory sensitivity, suggesting that inflammation may play a role in olfactory decline associated with aging.

neuroscience↗