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Nakamura, T.

Publications and source records attributed to Nakamura, T..

At least 37 records · Page 2Linked to original sources

Digital twins of upright stance reveal mechanistic bifurcations underlying Parkinsonian sway phenotypes

How the central nervous system maintains upright stance--and why this capability collapses in Parkinsons disease (PD)--remains a fundamental open question in computational neuroscience. A primary barrier is a severe topological degeneracy between observable sway kinematics (z-space) and latent neural control policies (-space), causing radically distinct control strategies to mask as identical sway patterns. Here, we establish a dynamical digital twin framework bridging empirical sway time series with mechanistic physical models. Assimilating a large cohort (N = 1, 038) into an intermittent control model via Bayesian inference, we construct a bidirectional mapping (z {leftrightarrow} ) that unmasks these hidden dynamics. We prove that healthy stance is universally governed by flexible intermittent control near an optimal intermittency ratio ({rho} {approx} 0.5), whereas PD progression reflects a structural regression toward rigid continuous control ({rho} [->] 1). Crucially, parameter topology in -space reveals that neural control policies reside on a folded low-dimensional manifold separated by a distinct parameter gap; attractor bifurcation analysis demonstrates that a catastrophic tipping point is embedded within this void, proving that parkinsonian postural breakdown is driven by a discontinuous dynamical phase transition rather than continuous control decay. By unmasking hidden disease severity beneath degenerate sway phenotypes, our framework reframes parkinsonian motor failure as an attractor bifurcation on a neural control manifold, providing a modern computational realization of the classical "dynamical disease" paradigm. SignificancePostural collapse in Parkinsons disease presents a profound neurobiological paradox: cellular degeneration progresses continuously over decades, yet clinical motor failure strikes as a sudden, catastrophic collapse. We resolve this paradox by demonstrating that motor breakdown is not a passive decay of control resources, but a discontinuous dynamical phase transition (attractor bifurcation) triggered when underlying neural control policies cross a latent parameter gap. By unmasking "phenotypic degeneracy"--where radically different neural control strategies produce identical body sway--our digital twin framework redefines neurodegenerative motor failure as a qualitative regime shift in complex control dynamics, offering a universal paradigm for predicting catastrophic transitions in neurological disorders.

neuroscience↗

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta

Cryogenic electron microscopy (cryo-EM) has become a widely used technique for determining the three-dimensional structures of biological macromolecules. Despite its advantages, building accurate structural models from cryo-EM data remains challenging, particularly at non-atomic resolutions. Here, we present CryoZeta, a de novo structure modeling program that leverages a diffusion-based generative deep neural network to integrate cryo-EM map density features with a biomolecular structure prediction pipeline similar to Alphafold3. By jointly leveraging sequence information and density-based features, CryoZeta generates highly accurate structural models that are consistent with the experimental map density. Evaluated on benchmark datasets covering protein complexes, protein-nucleic acid assemblies, and nucleic acid-only systems at resolutions up to 10 [A], CryoZeta consistently outperforms existing cryo-EM modeling methods in atomic accuracy. These results highlight the benefits of directly incorporating cryo-EM density into modern structure prediction pipelines and establish the method as a robust tool for automated, high-fidelity modeling from cryo-EM maps.

bioinformatics↗

MEIS1 is Required for Establishing Bergmann Glia-Specific Properties in the Developing Cerebellum

Compared to normal multipolar astrocytes, Bergmann glial cells (BGs), specifically differentiated astrocytes in the cerebellum, possess unique unipolar morphology and additional cellular functions. However, the molecular mechanisms that confer BG-specific properties onto normal multipolar astrocytes remain unknown. Here, we show that the transcription factor, MEIS1, is involved in BGs acquiring their unique characteristics. Targeted disruption of Meis1 in the whole cerebellum or astroglial lineage cells resulted in a marked reduction of BGs accompanied by an increase in multipolar astrocytes in mice. Postnatal deletion of Meis1 in Bergmann glia-like progenitors (BGLPs), which produce both BGs and multipolar astrocytes, suppressed their differentiation into BGs while promoting into multipolar astrocytes. Single-cell RNA sequencing, immunohistochemistry, and ChIP-Atlas analyses indicated that MEIS1 directly upregulates expression of BG-specific genes, including Vimentin and Zeb2, which are known to contribute to the correct localization and the unipolar process formation of BGs. These findings suggest that MEIS1 promotes the endowment of BG-specific properties to astrocytes by controlling the expression of BG-specific genes, thereby ensuring proper differentiation of BGLPs into BGs.

developmental biology↗

Structure of bacteriophage P1 head provides insight into capsid polymorphism

The highly regulated assembly of different proteins forming mature P1 myophage capsid show a unique polymorphism where the virion population is primarily divided in brackets of two different capsid sizes. The contrasting capsids, sized 95nm (capsid_L), triangulation number (T)=13 and 68nm (capsid_S) with T=7, both in Dextro format and have the same protein forming the phage head with similar intra and inter capsomeric interactions. Comparative study of the electron density maps of the capsids reveals the presence of protein appendages DarA and Hdf below the 5-fold symmetric region inside capsid_L that anchor the phage dsDNA to the capsid-shell. Such densities are also noticed in large capsids depleted off their dsDNA but not observed in capsid_S. Deficiency of these appendages in capsid_S results in a smaller sized dsDNA packed inside capsid_S. Despite missing out on nearly 60% of the phage dsDNA virions with capsid_S has all the essential genes responsible for the formation of a fully mature thermodynamically stable virion particle with structurally identical tail and baseplate as of capsid_L. Co-existence of both stable conformation in a single lysate is a unique phenomenon in the phage community and suggest that DarA and Hdf play an important role in phage capsid morphogenesis.

biophysics↗

Working Memory Selectively Modulates Subjective Perception: A Pilot Study

The present study demonstrates a blindsight-like dissociation between subjective perception and general perceptual capacity in nonclinical observers. Participants performed either a two-interval forced-choice (2-IFC) or a Yes/No face detection task during working memory delay. To match general perceptual processing capacity across conditions, we titrated stimulus luminance contrast in the 2-IFC task and applied the same contrast in the Yes/No task. In Experiment 1, categorically incongruent (i.e., scene) information held in working memory impaired the sensitivity of the Yes/No detection of stimulus presence (face) vs. absence (blank background). In contrast, this effect was absent in Experiment 2, in which the Yes/No task required a discrimination of a face (target) vs. a scrambled face (non-target). These findings indicate that stimulus incongruency in working memory selectively influences subjective perception, dissociating it from general perceptual capacity.

neuroscience↗

Dual resistance to cold and ethanol in Penicillium species persistently contaminating donated cadavers

Modern cadaver preservation techniques, such as low-concentration formaldehyde methods, are increasingly adopted to mitigate health risks and improve tissue fidelity for medical education and surgical training. However, these environments potentially foster fungal contamination. This study aimed to identify contaminating species from cadaveric surfaces stored under specific preservation conditions and establish effective countermeasures. Genetic identification revealed Penicillium paneum as the predominant species, while Penicillium corylophilum was also detected. These species exhibited distinctive traits, including vigorous growth at 4{degrees}C and marked ethanol tolerance, that explain their persistence in this preservation environment. Antifungal susceptibility testing demonstrated that these isolates were highly susceptible to commonly used disinfectants such as benzalkonium chloride, chlorhexidine gluconate, and phenol. Our findings indicate that these Penicillium species are uniquely adapted to low-temperature and ethanol-rich preservation environments. The incorporation of the identified disinfectants into preservation solutions offers a practical and effective strategy for controlling persistent fungal contamination in cadaveric facilities.

microbiology↗

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the Tetrahymena ribozyme at 2.2-2.3 [A] resolution, collected through target R1260 in the CASP16 competition. 26 groups participated in this solvation cryo-ensemble prediction challenge, submitting over 350 million atoms in total, offering the first opportunity to compare blind predictions of dynamic solvent shell ensembles to cryo-EM density. Predicted atomic ensembles were converted to density through local alignment and these densities were compared to the cryo-EM densities using Pearson correlation, Spearman correlation, mutual information, and precision-recall curves. These predictions show that an ensemble representation is able to capture information of transient or dynamic water and ions better than traditional atomic models, but there remains a large accuracy gap to the performance ceiling set by experimental uncertainty. Overall, molecular dynamics approaches best matched the cryo-EM density, with blind predictions from bussilab_plain_md, SoutheRNA, bussilab_replex, coogs2, and coogs3 outperforming the baseline molecular dynamics prediction. This study indicates that simulations of water and ions can be quantitatively evaluated with cryo-EM maps. We propose that further community-wide blind challenges can drive and evaluate progress in modeling water, ions and other previously hidden components of biomolecular systems.

biophysics↗

Tegmental atrophy in isolated REM sleep behaviour disorder: Ex vivo-informed in vivo imaging

Isolated rapid eye movement (REM) sleep behaviour disorder (iRBD) is an early-stage synucleinopathy characterized by brainstem pathology. In rodents, the pontine tegmentum contains an REM sleep centre, the sublaterodorsal nucleus (SLD), which expresses corticotropin-releasing hormone binding protein (CRHBP). While the involvement of brainstem pathophysiology is thus implicated in iRBD, its solid evidence remains scarce in humans due to the difficulty in identifying small brainstem nuclei with conventional MRI technology alone. Here, we aimed to detect tegmental atrophy in iRBD with voxel-based morphometry (VBM) analysis combined with a novel human brainstem atlas. Structural MRIs from 98 patients with iRBD and 114 controls were analysed to investigate grey matter volume (GMV) using VBM. Our unique approach involved detailed assessments of the VBM results, guided by a high-resolution MRI-based atlas of the human brainstem. This brainstem atlas was founded on ex vivo MRI of 10 postmortem human specimens. We validated it with CRHBP immunostaining, which aided in identifying putative REM sleep-regulating nuclei in humans. We applied this brainstem atlas to identify atrophy in specific brainstem regions in iRBD and correlate their volumes with clinical measures, including autonomic functions. VBM revealed a focal cluster of grey matter atrophy in the dorsal pontine tegmentum of iRBD patients, including the laterodorsal tegmental nucleus, ventral part (LDTgV) and the pedunculopontine tegmental nucleus (PTg). Our atlas-based analysis confirmed the LDTgV as the site of most conspicuous atrophy, revealing a significant volume reduction in iRBD patients compared to controls with a moderate effect size (Cohens d = 0.46, Bonferroni-corrected p = 0.019). Furthermore, greater atrophy in the LDTgV and the PTg was associated with more severe autonomic dysfunction as measured by Scales for Outcomes in Parkinsons Disease-Autonomic dysfunction (SCOPA-AUT) scores (partial r = -0.237, p = 0.019 and partial r = -0.236, p = 0.019, respectively). Histological analysis confirmed that the LDTgV is selectively enriched with CRHBP-positive neurons, a putative marker for REM sleep-on neurons. We provided novel evidence for the involvement of LDTgV, the putative human homolog of the murine SLD, in iRBD. The present findings advance our understanding of the neuroanatomical basis of iRBD and will contribute to the development of early biomarkers for -synucleinopathies.

neuroscience↗

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Sequence homology reveals evolutionary gene correspondences, but identifying functionally corresponding genes within specific cell types or during cell fate specification remains non-trivial. Here, frameworks that translate insights from model organisms into other species would accelerate wet-lab studies, so we develop Species-OT, a cross-species transcriptome analysis framework using Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validate Species-OT using bulk RNA-seq data for cell fate specification from pluripotent stem cells in mice, monkeys, and humans and scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identifies gene correspondences within cell fate specification, while transcriptomic discrepancies recapitulate expected species relationships.

bioinformatics↗

Hyperactivity is linked to elevated cortisol levels: comprehensive behavioral analysis in the prenatal valproic acid-induced marmoset model of autism

Hyperactivity is frequently observed in individuals with autism spectrum disorder (ASD) and significantly affects various aspects of life. This underscores the critical need for effective intervention methods tailored to the needs of individuals with ASD. Non-human primate models offer a promising avenue for elucidating the intricate interplay between ASD characteristics and developing individualized therapeutic strategies. This study examined the activity levels and behavioral dynamics in a prenatal valproic acid-induced (VPA) common marmoset model of ASD using ultraminiature data loggers, employing a more detailed approach to behavioral pattern analysis than is traditionally utilized. Although the overall activity levels showed no significant differences, the VPA group exhibited increased activity during specific hours, which is consistent with human ASD studies. Sample Entropy, a statistical measure used to quantify the regularity and unpredictability of time-series data, was higher during daytime in the VPA group, indicating reduced regularity in activity patterns akin to impulsive behavior in ASD. Subtle patterns that were not discernible through simple group comparisons were identified, highlighting the potential of this method as a valuable tool for the behavioral analysis of human ASD. Associations between erratic activity patterns, brief resting intervals, and elevated cortisol levels were observed, all of which correspond to stress phenotypes in individuals with ASD. The findings revealed variations in activity among the adult VPA groups, potentially linked to stress responses. Additionally, VPA juvenile marmosets showed increased locomotor activity in the social interaction test, complementing the adult behavioral findings and suggesting age-dependent manifestations of hyperactivity in this model. This non-human primate model effectively replicates real-world scenarios encountered by individuals with ASD exhibiting hyperactivity, thus holding significant implications for the advancement of personalized therapeutic strategies.

neuroscience↗

Representational Geometries of Perception and Working Memory: A Pilot Study

This study examined the representational geometry of visual working memory using human 7T fMRI. Observers viewed a facescene blended sample, attended to either the face or scene, and judged whether the attended aspect matched a subsequent test image. We found that the coding dimension distinguishing faces and scenes rotated between encoding and maintenance phases, in both visual and association areas. In these regions, exclusive combinations (i.e., encoded face and maintained scene vs. encoded scene and maintained face) were linearly decodable, indicating encoding and maintenance phases represent visual information using distinct subspaces. Such high-dimensional, flexible geometry can, in principle, protect maintained visual information from incoming input. At the same time, robust crossdecoding was observed across phases, reflecting the stability and generalizability of the represented contents. The balance between representational flexibility and stability varied along the cortical hierarchy: early sensory regions emphasized flexibility, whereas transmodal regions showed greater stability.

neuroscience↗

Redox regulation of neuroinflammatory pathways contributes to damage in Alzheimers disease brain

The mechanism(s) whereby redox stress mediates aberrant immune signaling in age-related neurological disorders remains largely unknown. Normally, the innate immune system mounts a robust response to infectious stimuli. However, unintentional activation by host-derived factors, such as aggregated proteins associated with neurodegenerative disorders or by cytoplasmic genomic or mitochondrial DNA, can elicit aberrant immune responses. One such immune response is represented by the cytosolic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. Using redox chemical biology and mass spectrometry approaches, we identified S-nitrosylation of STING cysteine 148 as a novel posttranslational redox modification underlying aberrant type 1 interferon signaling in Alzheimers disease (AD). Critically, we observed S-nitrosylated STING (SNO-STING) in postmortem human AD brains, in hiPSC-derived microglia (hiMG) exposed to amyloid-{beta} (A{beta})/-synuclein (Syn) aggregates, and in 5xFAD transgenic mice. Mechanistically, our findings reveal that STING S-nitrosylation is critical in initiating signaling cascades by promoting the formation of disulfide-bonded STING oligomers. This leads to neuroinflammation early in the course of disease in vivo in 5xFAD mice with consequent synaptic loss. Collectively, our research supports the role of SNO-STING in neuroinflammation associated with AD, and points to a novel druggable cysteine residue in STING to prevent this S-nitrosylation reaction with its inherent inflammatory response. One Sentence SummaryS-Nitrosylation of STING triggers activation of cGAS-STING signaling in Alzheimers disease brain and subserves a novel link between excessive nitrosative stress and dysregulated innate immunity, thus contributing to disease progression.

neuroscience↗

Targeting FSP1 triggers ferroptosis in lung cancer

Pre-clinical and clinical studies have demonstrated how dietary antioxidants or mutations activating antioxidant metabolism promote cancer, highlighting a central role oxidative stress in tumorigenesis. However, it is unclear if oxidative stress ultimately increases to a point of cell death. Emerging evidence indicates that cancer cells are susceptible to ferroptosis, a form of cell death triggered by uncontrolled lipid peroxidation1-3. Despite broad enthusiasm about harnessing ferroptosis as a novel anti-cancer strategy, whether ferroptosis is a barrier to tumorigenesis and if it can be leveraged therapeutically remains unknown4,5. Using genetically-engineered mouse models (GEMMs) of lung adenocarcinoma (LUAD), we performed tumor specific loss-of-function studies of the two key ferroptosis suppressors, glutathione peroxidase 4 (Gpx4)6,7 and ferroptosis suppressor protein 1 (Fsp1)8,9, and observed increased lipid peroxidation and robust suppression of tumorigenesis, suggesting that lung tumors are highly sensitive to ferroptosis. Furthermore, across multiple pre-clinical models, we found that FSP1 was required for ferroptosis protection in vivo, but not in vitro, underscoring a heightened need to buffer lipid peroxidation under physiological conditions. Lipidomic analyses revealed that Fsp1-knockout (Fsp1KO) tumors had an accumulation of lipid peroxides, and inhibition of ferroptosis with genetic, dietary, or pharmacological approaches effectively restored the growth of Fsp1KO tumors in vivo. Unlike GPX4, FSP1 expression was prognostic for disease progression and poorer survival in LUAD patients, highlighting its potential as a viable therapeutic target. To this end, we demonstrated that pharmacologic inhibition of FSP1 had significant therapeutic benefit in pre-clinical lung cancer models. Our studies highlight the importance of ferroptosis suppression in vivo and pave the way for FSP1 inhibition as a therapeutic strategy in lung cancer patients.

cancer biology↗

Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex

Divergence to the infectivity practice by extracellular contractile injection systems (eCISs) is displayed by myophage P1 in its lytic phase involving its baseplate receding away from the host bacterium during infection. Atomic structure of the proteins forming P1s Tail Baseplate (TB) complex, determined here, using cryo electron microscopy are employed to identify a sequence of viral events explaining this unique phenomenon. The P1 baseplate is found to be devoid of protein appendages that are necessary for anchoring it to the host bacterium. To compensate this deficiency, P1s Long Tail Fibers (LTFs) affix to the hosts exterior, straighten up imparting stability to the virion for pursuing the infection process, thereby eliciting the baseplate hub and the tail sheath to ascend away, resulting in uniform compression of the latter. Upon the maximum unkinking of LTFs, a descending corkscrew motion commences that results in the non-uniform downward compression of the tail sheath, the tail tube and baseplate needle that perforates through the hosts membrane-cytoplasm, leading to a successful phage-bacterium infection.

biophysics↗

A highly efficient knock-in strategy using fast-annealed 3'-extended dsDNA templates for emerging model insects

CRISPR-Cas genome editing toolkits have expanded the scope of genetic studies in various emerging model organisms. However, their applications are limited mainly to knockout experiments due to technical difficulties in establishing knock-in strains, which enable in vivo molecular tagging-based experiments. Here, we investigated knock-in strategies in the harlequin ladybug Harmonia axyridis, a model insect for evolutionary developmental biology, which shows more than 200 color pattern variations within a species. We tested several knock-in strategies using synthetic DNA templates. We found that ssDNA templates generated founder knock-in strains efficiently (2.5-11%), whereas the 5 regions of ssDNA templates were frequently deleted when the insert length exceeded [~]40 bases. To overcome this limitation, we designed several 3 extended DNA templates. Fast-annealed 3-extended double-stranded DNA templates, which were designed for tagging endogenous proteins with epitope tags, showed high founder generation efficiency (9.9-20.9%) and accuracy (30.8-85.7%). This strategy is also applicable to the two-spotted cricket Gryllus bimaculatus, suggesting that the fast-annealed 3-extended dsDNA template is a versatile DNA template for generating knock-in strains in emerging model insects for developmental genetic studies. Summary statementFast-annealed 3-extended dsDNA templates facilitate efficient CRISPR-Cas9-mediated knock-in in emerging model insects.

bioengineering↗

Covalent anti-HIV compound that induces HIV-1 capsid multimerization and degradation decomposes the viral core

Covalent inhibitors form strong, essentially irreversible interactions with their targets, offering enhanced structural selectivity within the target cavity and prolonged target engagement even at low doses. Here, we report that ACAi-001, an HIV-1 capsid (CA)-targeting compound identified through in silico screening of the hydrophobic cavity in the CA N-terminal domain (CA-NTD), inhibits HIV-1 replication in cell-based assays. ACAi-001 covalently binds CA to induce aberrant CA multimerization and degradation in vitro, a pharmacological property distinct from that of existing CA inhibitors such as lenacapavir. This mechanism was confirmed by Western blotting (WB), size exclusion chromatography (SEC), differential scanning fluorimetry (DSF), and liquid chromatography-mass spectrometry (LC-MS). These results suggest that ACAi-001, with two putative covalent interactions in its chemical structure, binds directly to Ser16 in the N-terminal domain targeting cavity in addition to Cys198 or Cys218 in the C-terminal domain of CA. The treatment of viral particles with ACAi-001 results in the loss of intact, conical HIV-1 cores, as directly visualized by transmission electron microscopy (TEM), establishing the HIV-1 core as the direct target of ACAi-001. These findings demonstrated that ACAi-001 may be a promising next-generation anti-HIV-1 CA inhibitor with unique mechanisms of action, offering new insight into HIV-1 core assembly and disassembly.

microbiology↗

Non-uniform temporal scaling of neurogenesis for species-specific dosing of cortical excitatory subtypes

Mammals share a laminar cerebral cortex, with excitatory neuron subtypes organized in distinct layers. Although this framework is conserved, subtype balance varies markedly between species due to unknown mechanisms. This study shows that species-specific neuronal composition arises from non-uniform scaling of the temporal dynamics of neurogenesis. Comparative histology of eight mammalian species revealed a significant, rat-specific expansion of the cortical deeper layer (DL). This species difference results from a specific extension of the early neurogenetic phase for DL neuron production before transitioning to the upper layer (UL) in rats, as confirmed by birthdating and single-cell transcriptomics. The duration of DL neuron production is regulated by a genetic program controlling progenitor aging, including canonical Wnt signaling. Comparative single-cell transcriptomics revealed that cortical progenitors in rats exhibit significantly elevated Wnt ligand expression. Thus, while sequential cortical neurogenesis is conserved, its progression is non-uniformly scaled in each species. Such precise heterochronic fine-tuning allows evolutionary refinement of cellular configuration without drastic remodeling of the conserved corticogenesis program. TeaserDifferential temporal progression of neural progenitor program contributes to species-specific cellular composition of mammalian cerebral cortex

developmental biology↗

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↗