Biology subjects

Arima, K.

Publications and source records attributed to Arima, K..

5 recordsLinked to original sources

bioRxiv2026

Revising the genetic and epigenetic architecture of in vitro regeneration capacity in natural Arabidopsis thaliana populations

Plant regeneration is a dynamic developmental process that spans from cell dedifferentiation to organ reconstruction in response to inductive cues, such as wounding stress and hormonal signals. Although this capacity varies widely both between and within species, a comprehensive understanding of the genetic and epigenetic bases of this variation remains incomplete. To address this issue, we revisited published datasets on natural variation in in vitro regeneration capacity in Arabidopsis thaliana. Using quantitative genetic approaches, including meta-analyses of genome-wide association studies (GWAS) and multi-locus models, we dissected the genetic architecture underlying regeneration traits. Our results showed that shoot regeneration capacity is primarily explained by allelic variation in the cis-regulatory region of WUSCHEL (WUS), a key regulator of shoot meristem formation. Notably, these polymorphisms are also associated with epigenetic variants of the DNA transposon ATDNA2T9C, which is located within the regulatory region. Furthermore, allelic variation in ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a positive regulator of cytokinin signaling, is associated with callus formation and greening traits and may promote shoot formation through genetic interactions with WUS alleles. Although in vitro regeneration is controlled by complex, multilayered gene regulatory networks, our results suggest that, in A. thaliana, natural variation in regeneration capacity is largely shaped by a small number of major-effect modifiers together with epigenetic variation and genetic interactions, despite the substantial heterogeneity observed among natural populations.

genetics↗

bioRxiv2025

Wakeful targeted memory reactivation during short rest periods modulates motor learning via the lateral orbitofrontal cortex network

This study investigated whether wakeful targeted memory reactivation (TMR) during short rest intervals improves motor learning. Participants were randomly assigned to the following four groups and performed a sequential key-press task under each condition: (1) TMRno group: no auditory stimuli, (2) TMRregular group: auditory cues played at the same speed as the previous task, (3) TMRfast group: auditory cues played 1.3 times faster, and (4) TMRrandom group: auditory cues randomized in pitch. The TMRregular group suppressed early learning gains compared with the TMRno and TMRfastgroups. Electroencephalogram revealed reduced functional connectivity centered on the lateral orbitofrontal cortex (lOFC) in the TMRregular group. In contrast, the TMRfastgroup preserved early learning and exhibited improved lOFC-centered functional connectivity compared with the TMRregulargroup. Therefore, wakeful TMR might either hinder or support motor learning, depending on cue timing and structure, emphasizing the need to optimize sensory parameters for effective learning improvement.

neuroscience↗

bioRxiv2025

3D multimodal histological atlas and coordinate framework for the mouse brain and head

Brain reference atlases are essential for neuroscience experiments and data integration. However, histological atlases of the mouse brain, crucial in biomedical research, have not kept pace. Autofluorescence-based volumetric brain atlases are increasingly used but lack microscopic histological contrast, cytoarchitectonic information, corresponding MRI datasets, and often have truncated brainstems. Here, we present a multimodal, multiscale atlas of the laboratory mouse brain and head. The new reference brains include the whole head with consecutive Nissl and myelin serial section histology in three planes of section with 0.46 {micro}m in-plane resolution, including intact brainstem, cranial nerves, and associated sensors and musculature. We provide reassembled histological volumes with 20mu isotropic resolution in stereotactic coordinates, determined using co-registered in vivo MRI and CT. In addition to conventional MRI contrasts, we provide diffusion MRI-based in vivo and ex vivo microstructural information, adding a valuable co-registered contrast modality that bridges MRI with cell-resolution histological data. We shift emphasis from compartmental annotations to stereotactic coordinates in the reference brains, offering a basis for evolving annotations over time and resolving conflicting neuroanatomical judgments by different experts. This new reference atlas facilitates integration of molecular cell type data and regional connectivity, serves as a model for similar atlases in other species, and sets a precedent for preserving extra-cranial nervous system structures.

neuroscience↗

bioRxiv2025

Simultaneous knockout of VITAMIN C DEFECTIVE 2 and 3 exacerbates ascorbate deficiency and light stress sensitivity

Light-dependent activation of ascorbate biosynthesis is essential for accumulating ascorbate to mitigate photooxidative stress. The VTC2 and VTC3 genes play key roles in this process: VTC2 encodes GDP-L-galactose phosphorylase (GGP), the rate-limiting enzyme in ascorbate biosynthesis, and VTC3 encodes a putative protein kinase/phosphatase with an unknown function. Here, we investigated their functional and genetic relationship. In vtc3 mutants, VTC2 transcription and GGP activity were slightly enhanced, suggesting that VTC3 is not required for VTC2 expression. Additionally, the vtc3 mutation had negligible effects on the transcriptome and the activity of enzymes involved in ascorbate redox cycle regulation, narrowing down the possible roles of VTC3 in ascorbate biosynthesis. Under low-light conditions, ascorbate levels were lower in vtc2 than in vtc3 mutants, but vtc2 retained the ability to increase ascorbate levels under high-light stress, unlike vtc3. The simultaneous knockout of VTC2 and VTC3 further reduced ascorbate levels compared to single mutants and severely impaired light stress-induced ascorbate accumulation, resulting in impaired non-photochemical quenching and enhanced photooxidative damage. These findings highlight the additive effects of VTC2 and VTC3 on ascorbate biosynthesis and stress tolerance. The vtc2 vtc3 double mutants provide a valuable model for further elucidating the physiological roles of ascorbate in plants.

plant biology↗

bioRxiv2020

Tumor-Immune Partitioning and Clustering (TIPC) algorithm reveals distinct signatures of tumor-immune cell interactions within the tumor microenvironment

Growing evidence supports the importance of understanding tumor-immune spatial relationship in the tumor microenvironment in order to achieve precision cancer therapy. However, existing methods, based on oversimplistic cell-to-cell proximity, are largely confounded by immune cell density and are ineffective in capturing tumor-immune spatial patterns. Here we developed a novel computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), to offer an effective solution for spatially informed tumor subtyping. Our method could measure the extent of immune cell partitioning between tumor epithelial and stromal areas as well as the degree of immune cell clustering. Using a U.S. nation-wide colorectal cancer database, we showed that TIPC could determine tumor subtypes with unique tumor-immune spatial patterns that were significantly associated with patient survival and key tumor molecular features. We also demonstrated that TIPC was robust to parameter settings and readily applicable to different immune cell types. The capability of TIPC in delineating clinically relevant patient subtypes that encapsulate tumor-immune spatial relationship, immune density, and tumor morphology is expected to shed light on underlying immune mechanisms. Hence, TIPC can be a useful bioinformatics tool for effective characterization of the spatial composition of the tumor-immune microenvironment to inform precision immunotherapy.

cancer biology↗