Biology subjects

Koizumi, M.

Publications and source records attributed to Koizumi, M..

5 recordsLinked to original sources

bioRxiv2026

The role of world knowledge in sentence comprehension under working-memory constraints: An fMRI study

Introduction: Comprehension of thematic roles, i.e., "who did what to whom," relies on limited cognitive resources, and constraints on these resources can alter the use of plausibility information derived from world knowledge. Although sentence-processing studies have described how plausibility information constrains interpretation, it remains unclear how this process is supported by the architecture of working memory. This study examines whether the phonological loop, one of the components of working memory, contributes to thematic-role processing based on world knowledge. Methods: Using articulatory suppression and functional magnetic resonance imaging, we examined whether constraining the function of the phonological loop modulates behavioral and neural responses to sentences in which syntactically assigned thematic roles are plausible or implausible given world knowledge. To constrain the phonological loop, we manipulated the task: a single task and a dual task involving concurrent articulation. Results: We found no significant interaction between task and plausibility, although equivalence analyses did not provide evidence for the absence of a plausibility effect during articulation. In contrast, a robust main effect of thematic-role plausibility was observed: implausible sentences elicited greater activation than plausible sentences in the left inferior frontal gyrus (LIFG) and medial superior frontal gyrus (mSFG) at the whole-brain level, and in both the pars triangularis and pars orbitalis of the LIFG in the ROI analyses. Discussion: These findings provide no conclusive evidence that constraining the phonological loop substantially modulates the use of world knowledge in comprehension of thematic roles, while also leaving open the possibility of a smaller task-dependent effect. At the same time, the robust neural responses to implausibility indicate that the LIFG and mSFG consistently contribute to the processing of plausibility information derived from world knowledge.

neuroscience↗

bioRxiv2026

BCCWJ-Brain: A Multi-Modal fMRI, MEG, and EEG Dataset of Naturalistic Japanese Reading

We present the BCCWJ-Brain dataset, a multi-modal neuroimaging resource comprising functional magnetic resonance imaging (fMRI), magnetoencephalography (MEG), and electroencephalography (EEG) data recorded from native Japanese speakers reading newspaper articles from the Balanced Corpus of Contemporary Written Japanese (BCCWJ). Neural data were collected from 112 participants (36 fMRI, 35 MEG, and 41 EEG) as they read twenty newspaper articles presented in a Rapid Serial Visual Presentation (RSVP) paradigm. By providing three complementary neuroimaging modalities collected under identical naturalistic reading stimuli, this dataset provides a cognitive benchmark for computational models such as large language models. The dataset is publicly available on the OpenNeuro platform, offering a valuable resource for neuroscience, natural language processing, and related research fields.

neuroscience↗

bioRxiv2025

Linear ubiquitination triggers Amph-mediated T-tubule biogenesis

T-tubules are specialized invaginations of the plasma membrane essential for muscle contraction. While their physiological importance is well established, the mechanisms underlying T-tubule formation remain elusive. Here, we identify LUBEL/RNF31, a ubiquitin E3 ligase responsible for linear (M1-linked) ubiquitination, as a key regulator of T-tubule biogenesis through proximity proteomics and RNAi screening in Drosophila. Loss of LUBEL leads to the formation of Amphiphysin (Amph)-positive membrane sheets instead of tubular networks in muscle cells. Mechanistically, the ubiquitin ligase activity of LUBEL, and direct interaction with Amph, a BAR domain protein involved in membrane tubule extension, are crucial for proper T-tubule morphology. LUBEL and M1-linked ubiquitin chains assemble into condensates on membranes, facilitating Amph-mediated membrane tubulation. Notably, the Amph-LUBEL/RNF31 interaction is evolutionarily conserved across a broad range of species, underscoring a fundamental role for linear ubiquitination in membrane remodeling. Our findings uncover a previously unrecognized role for linear ubiquitination in membrane deformation driven by BAR domain proteins.

cell biology↗

bioRxiv2025

Establishment of a second-generation transgenic marmoset model of polyglutamine disease recapitulating neurological symptoms and pathology

Neurodegenerative diseases, including polyglutamine diseases, remain a major clinical challenge, partly because of limited animal models that recapitulate human disease. Here, we describe a second-generation transgenic marmoset model of spinocerebellar ataxia 3 (SCA3), a polyglutamine disease, which stably expresses expanded CAG repeats in ATXN3. All five offspring of the founder marmoset harbored the transgene with reduced transgene integration sites and without repeat instability or genetic mosaicism, offering improved construct validity. Three of the five marmosets developed progressive motor impairments that segregated into two distinct phenotypes: early onset with rapid progression and late onset with mild progression, accompanied by corresponding patterns in body weight gain and grip strength. Pathological analysis revealed cerebellar Purkinje cell loss, spinal cord neurodegeneration, and widespread intranuclear inclusions. The severity of motor phenotypes correlated with transgene expression levels in disease-relevant brain regions, including the cerebellum, spinal cord, and striatum. By overcoming the common translational limitations of rodent systems, our second-generation model offers a powerful platform for investigating disease mechanisms and testing potential therapeutic interventions. Our results advance the utility of transgenic marmosets as clinically relevant models of neurodegenerative diseases. Summary StatementSecond-generation transgenic marmoset models of spinocerebellar ataxia 3 replicated the progressive motor deficits and neuropathology of the founder marmoset, providing a powerful platform for studying disease mechanisms and developing therapies.

neuroscience↗

bioRxiv2024

Transcriptional Dynamics Uncover the Role of BNIP3 in Mitophagy during Muscle Remodeling in Drosophila

Differentiated muscle cells contain myofibrils and well-organized organelles, enabling powerful contractions. Muscle cell reorganization occurs in response to various physiological stimuli; however, the mechanisms behind this remodeling remain enigmatic due to the lack of a genetically trackable system. Previously, we reported that a subset of larval muscle cells is remodeled into adult abdominal muscle through an autophagy-dependent mechanism in Drosophila. To unveil the underlying mechanisms of this remodeling, we performed a comparative time-course RNA-seq analysis of isolated muscle cells with or without autophagy. It revealed both transcriptional dynamics independent of autophagy and highlighted the significance of BNIP3-mediated mitophagy in muscle remodeling. Mechanistically, we found that BNIP3 recruits autophagic machinery to mitochondria through its LC3-interacting (LIR) motif and minimal essential region (MER), which interact with Atg8a and Atg18a, respectively. Loss of BNIP3 leads to a substantial accumulation of larval mitochondria, ultimately impairing muscle remodeling. In summary, this study demonstrates that BNIP3-dependent mitophagy is critical for orchestrating the dynamic process of muscle remodeling. Impact statementA time-course RNA-seq analysis of muscle remodeling reveals transcriptional dynamics independent of autophagy and highlights the significance of BNIP3 in mitochondrial degradation in vivo.

cell biology↗