Biology subjects

Tanaka, F.

Publications and source records attributed to Tanaka, F..

7 recordsLinked to original sources

bioRxiv2026

Rice brown spot resistance gene bsr1 also confers resistance to bacterial blight by suppressing sucrose efflux

Brown spot (BS), caused by the fungal pathogen Bipolaris oryzae, is a major disease threatening global rice production. However, the genetic basis of host BS resistance remains unclear. Here, we identified brown spot resistance 1 (bsr1), a quantitative trait locus conferring BS resistance, by map-based cloning. We show that bsr1 encodes a sucrose transporter and that a near-isogenic line carrying bsr1 (bsr1-NIL) in the susceptible Koshihikari genetic background exhibited resistance to BS by suppressing sucrose efflux into the apoplast after pathogen attack. Furthermore, bsr1-NIL also showed strain-specific resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae through the same mechanism. These findings demonstrate that bsr1 confers dual resistance to fungal and bacterial diseases by regulating sucrose efflux. Our study identifies a previously unrecognized mechanism underlying resistance to both BS and bacterial blight and highlights bsr1 as a promising target for breeding disease-resistance rice cultivars. Rice (Oryza sativa L.) is a staple food for more than half of the worlds population1. Brown spot (BS), caused by the fungus Bipolaris oryzae, is one of the most prevalent fungal diseases of rice, and its incidence has increased under global warming2. BS infects coleoptiles, leaves, leaf sheaths, panicle branches, glumes, and spikelets, and severe infection can substantially reduce grain yield.

plant biology↗

bioRxiv2026

From wag to affect: Tail kinematic signatures of canine emotional states in computer-controlled environments

From facial expressions to gestures, animals use multiple signal modalities to express emotions and communicate. In dogs, tail movements are conspicuous behaviours associated with emotional states, but this link remains debated. We investigated canine emotional states underlying tail wagging by systematically analysing differences in tail movements in a computer-controlled task encompassing two non-social Conditions - Rewarded (positive) and Unrewarded (negative), and two Epochs (pre-response and outcome anticipation). Using pose-tracking we found that 11 out of 23 dogs did not wag their tails in at least 75% of trials, suggesting that some dogs may inherently wag less or that tail wagging is primarily a social signal. Our results showed that dogs were more likely to wag during positive anticipation; whereas in the negative condition, despite tail amplitude being more prominent, increased speeds reflected arousal rather than valence. Further work should assess tail kinematics in social contexts to test and extend these findings.

animal behavior and cognition↗

bioRxiv2023

The ENCODE Uniform Analysis Pipelines

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses. Database URL: https://www.encodeproject.org/

bioinformatics↗

bioRxiv2020

Interleukin-19 alleviates experimental autoimmune encephalomyelitis by attenuating antigen-presenting cell activation

Interleukin-19 (IL-19) acts as an anti-inflammatory cytokine in various inflammatory diseases. Multiple sclerosis (MS) is a major neuroinflammatory disease in the central nervous system, but it remains uncertain how IL-19 contributes to MS pathogenesis. Here, we demonstrate that IL-19 deficiency aggravates experimental autoimmune encephalomyelitis (EAE), a mouse model of MS, by promoting IL-17-producing helper T cell (Th17 cell) infiltration into the central nervous system. In addition, IL-19-deficient splenic macrophages expressed elevated levels of major histocompatibility complex class II, co-stimulatory molecules, and Th17 cell differentiation-associated cytokines such as IL-1{beta}, IL-6, IL-23, TGF-{beta}1, and TNF-. These observations indicated that IL-19 plays a critical role in suppression of MS pathogenesis by inhibiting macrophage antigen presentation, Th17 cell expansion, and subsequent inflammatory responses. Furthermore, treatment with IL-19 significantly abrogated EAE. Our data suggest that IL-19 could provide significant therapeutic benefits in patients with MS.

immunology↗

bioRxiv2019

Long-read sequencing identifies GGC repeat expansion in human-specific NOTCH2NLC associated with neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells. The wide range of clinical manifestations in NIID makes ante-mortem diagnosis difficult 1-8, but skin biopsy realized its ante-mortem diagnosis 9,10 and many NIID cases have been diagnosed by skin biopsy11,12. Most cases of NIID are sporadic, but several familial cases are known. Using a large NIID family, we conducted linkage mapping, found a 58.1-Mb linked-region at 1p22.1-q21.3 with a maximum logarithm of odds (LOD) score of 4.21, and successfully identified a GGC repeat expansion in the 5 portion of NOTCH2NLC in all affected members by long-read sequencing, but not in unaffected members. We further found the similar expansions in additional 8 unrelated families with NIID as well as 39 sporadic NIID patients. Repeat-primed PCR consistently detected the GGC repeat expansion in all the familial and sporadic patients diagnosed by skin biopsy, but never in unaffected family members nor 200 controls. This shows that pathogenic changes in a human-specific gene evolutionarily generated by segmental duplication indeed causes a human disease.

genetics↗

bioRxiv2018

Changes in clock gene expression in esophagus in rat reflux esophagitis

Background and AimsGastroesophageal reflux disease (GERD) is strongly associated with sleep disturbances. Clock genes harmonize circadian rhythms by their periodic expression and regulate several physiological functions. However, the association between clock genes and GERD is still unknown. We investigated whether reflux esophagitis affects circadian variability of clock genes in the esophagus and other organs using a rat reflux esophagitis model.\n\nMethodsReflux esophagitis was induced in 7-week-old male Wistar rats. Sham-operated rats were used as controls. Rats were sacrificed at 09:00 (light period) and 21:00 (dark period) 3 days (acute phase) and 21 days (chronic phase) after induction of esophagitis. The expression levels of clock gene mRNAs such as Per1, Per2, Per3, Cryl, Cry2, Arntl, and Clock in the esophagus were investigated by qPCR. Arntl expression was examined in stomach, small intestine, colon, and liver tissues. Serum melatonin and IL-6 levels were measured by ELISA.\n\nResultsHistological examination of reflux esophagitis mainly revealed epithelial defects with marked inflammatory cell infiltration in the acute phase, and mucosal thickening with basal cell hyperplasia in the chronic phase. Circadian variability of clock genes, except Cry1, was present in the normal esophagus, and was completely disrupted in reflux esophagitis during the acute phase. The circadian variability of Per2, Per3, and Arntl returned to normal, but disruption of Per1, Cry2, and Clock was present in the chronic phase. Disruption of circadian variability of Arntl was observed in the esophagus, as well as in the stomach, small intestine, and liver tissues in reflux esophagitis during the acute phase. There were no significant differences in serum melatonin and IL-6 levels between control and reflux esophagitis animals in both acute and chronic phases.\n\nConclusionDisruption to circadian variability of clock genes may play a role in the pathogenesis of GERD.

pathology↗

bioRxiv2017

Multiple strategies for heat adaptation in rice endosperms revealed by on-site cell-specific analysis

Plant cells have multiple strategies to adapt to environmental stresses. Rice endosperms form chalkiness in a part of the tissue under heat conditions during the grain-filling stage, although nitrogen supply reduces chalky rice. Air spaces formed in the cells cause an irregular light reflection and create chalkiness, yet what exactly occurs remains unclear at cell level. Through on-site cell-specific analysis, we show that heat-treated cells adjust osmotically and retard protein synthesis to preserve protein storage vacuoles in the cytosol, resulting in air space formation. Application of nitrogen enhances heat tolerance to sustain protein body and amyloplast development during strong osmotic adjustment, which diminishes air spaces to avoid chalkiness. Hence, we conclude that rice endosperm cells could alter organelle compartments spatially during the heat adaptation, depending on the available nitrogen level. Our findings provide new insight into the cellular mechanism of rice chalky formation as a strategy for heat acclimation.

plant biology↗