Biology subjects

Murata, K.

Publications and source records attributed to Murata, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Non-linear growth models combined with survival rates identify the optimal rearing temperature and harvest timing in edible crickets, Gryllus bimaculatus and Teleogryllus occipitalis

Crickets are gaining attention as sustainable protein sources because of their high nutritional value and low environmental impact. Growth models are essential tools for optimising production by predicting growth characteristics. However, previous studies have not compared multiple non-linear growth models for crickets or explicitly considered environmental factors. We analysed the growth patterns of the two-spotted cricket (Gryllus bimaculatus) and the Asian cricket (Teleogryllus occipitalis) at multiple temperatures (25.0, 27.5, 30.0, 32.5 and 35.0 {degrees}C) using three non-linear models (Gompertz model, logistic model, and von Bertalanffy model) and combined the predicted body mass with observed survival rates to predict the optimal harvest time and temperature. All three models fitted the data well (R2 [≥] 0.97 in both species). The asymptotic body mass was highest at 30.0 {degrees}C, and the growth rate constant increased with temperature, reaching its maximum at 35.0 {degrees}C except for the logistic model in G. bimaculatus (32.5 {degrees}C). In addition, the predicted value of harvest, calculated by combining predicted body mass and observed survival probability, was highest at 30.0 {degrees}C in both species, reaching 13.82 kg/m3 at 38 days in G. bimaculatus and 7.12 kg/m3 at 62 days in T. occipitalis. These results suggest that 30.0 {degrees}C is the most suitable constant-temperature condition for maximising predicted productivity, although the optimal harvest timing differs between species.

physiology↗

bioRxiv2026

MC-Bayes: A Python-based wrapper for MotionCor3 processing of EER files compatible with Bayesian polishing

Here, we present MC-Bayes, a Python-based script for processing cryo-electron microscopy EER movies on one or more GPUs using MotionCor3 in a user-friendly manner. Further, it generates the .star files necessary for RELION to perform Bayesian polishing (a.k.a.: reference-based motion correction) with EER movies. Until now, Bayesian polishing of EER data was only possible if the CPU-based "RELIONCor" implementation of MotionCor2 was used, which is sub-optimal on GPU-heavy cryo-EM processing systems. This wrapper was created for those facilities and/or users who may have (many) powerful GPUs, but for whatever reason have few CPU cores or less system RAM. Leveraging MotionCor3, MC-Bayes allows motion correction of EER data 2 or more times faster (depending on system) than the RELION CPU implementation, except in circumstances where dozens or hundreds of CPU cores with high quantities of system RAM can be utilised.

biophysics↗

bioRxiv2026

Conformational plasticity of the human norovirus GII.3 capsid reveals alternative P domain interaction networks

Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide, yet no effective antiviral therapeutics are currently available. Although environmentally induced capsid conformational changes associated with infectivity have been reported in murine noroviruses (MNVs), comparable conformational switching has not been demonstrated in HuNoVs. In this study, we generated HuNoV GII.3 virus-like particles (VLPs) using a baculovirus expression system and identified two distinct T = 3 particle populations coexisting within VLP preparations derived from a single strain through cryo-electron microscopy single-particle analysis. Comparative structural analysis revealed that these two T = 3 capsid conformations correspond to the resting and rising states of the protruding (P) domain. Rearrangement of the P domain alters intermolecular interactions between adjacent capsid subunits, resulting in distinct capsid surface architectures. In the resting state, intermolecular contacts were mediated predominantly by the P2 subdomain, with limited contribution from the P1 subdomain. In contrast, the rising state exhibited a shift toward an alternative interaction interface primarily involving the P1 subdomain. These findings demonstrate previously unrecognized structural polymorphism in the HuNoV capsid and provide evidence that conformational switching may occur in HuNoVs. Our results offer new insights into norovirus capsid dynamics and may inform future structure-based vaccine and antiviral drug development.

microbiology↗

bioRxiv2026

Near-atomic structures of human astrovirus capsids reveal a subunit-specific maturation mechanism

Human astrovirus (HAstV) is a major cause of acute gastroenteritis, yet the structural basis of capsid maturation and infectivity remains poorly understood. Here, we report near-atomic cryo-electron microscopy structures of HAstV serotype 4 in immature and mature states at 1.79 [A] and 1.73 [A] resolution, respectively. These structures reveal a subunit-specific maturation mechanism in which differential protease accessibility drives selective removal of spike (P2) domains. Structural comparisons show that only A-B dimers form a broad cavity beneath the P2 domains that is permissive for trypsin entry, whereas the corresponding region in C-C dimers is sterically restricted. Proteolytic maturation induces pronounced conformational rearrangements, particularly in subunit B, linking capsid geometry to asymmetric protease susceptibility. Despite these changes, the inner capsid architecture and presumptive RNA-associated densities remain conserved, indicating that genome release occurs at a later stage of infection. Together, our findings establish a mechanistic framework in which capsid geometry governs proteolysis-driven activation.

microbiology↗

bioRxiv2026

A single PLAT domain protein couples reproductive arrest and carotenoid pigmentation during diapause in the two-spotted spider mite, Tetranychus urticae Koch

Adult females of the two-spotted spider mite, Tetranychus urticae Koch, enter a photoperiodically induced diapause to overwinter. Diapause in T. urticae is accompanied by reproductive arrest and the orange body coloration that arises from the accumulation of astaxanthin esters. How these two traits are coordinated at the molecular level remains poorly understood. Here, we compared the proteomes of adult females reared under diapause-inducing (long-night) and non-diapause-inducing (short-night) photoperiods using liquid chromatography-tandem mass spectrometry, followed by RNA interference (RNAi) of candidate genes. The carotenoid biosynthesis enzymes phytoene desaturase (TuPDS) and lycopene cyclase/phytoene synthase (TuLCPS), both encoded by genes horizontally transferred from fungi, were more abundant in diapausing females than in non-diapausing females. RNAi of the genes encoding TuPDS and TuLCPS markedly reduced orange pigmentation as well as {beta}-carotene and astaxanthin contents, demonstrating that these enzymes are required for diapause-associated pigmentation. Our proteomic analysis further identified a single PLAT (Polycystin-1, Lipoxygenase, Alpha-toxin) domain protein, TuPLAT10, as one of the most strongly upregulated proteins in diapausing females. The PLAT domain is a lipid-binding module, suggesting a role for TuPLAT10 in lipid metabolism. In addition to the suppression of orange pigmentation, RNAi of the TuPLAT10 gene restored reproduction even under diapause-inducing conditions and selectively reduced TuPDS and TuLCPS protein levels, despite the absence of sequence similarity to their genes. We propose that TuPLAT10 acts as a lipid-allocation switch that, in response to photoperiodic information, partitions fatty acids between astaxanthin esterification and yolk lipid supply, thereby coupling reproductive arrest and carotenoid pigmentation during diapause in T. urticae.

physiology↗

bioRxiv2026

Structural basis for Ca2+-dependent, RyR2-selective stabilization by Ryanozole in CPVT

The cardiac ryanodine receptor (RyR2) is a Ca{superscript 2} release channel essential for excitation-contraction coupling. RyR2 mutations cause severe arrhythmogenic disorders, including catecholaminergic polymorphic ventricular tachycardia (CPVT), through gain-of-function (GOF) effects leading to aberrant Ca{superscript 2} release. We have recently developed Ryanozole, a potential therapeutic compound for CPVT, which selectively stabilizes RyR2 in a Ca2+-dependent manner. Here, we define the mechanism of action of Ryanozole by combining high-resolution cryo-electron microscopy, targeted mutagenesis and functional assays. Ryanozole binds to the interface between the Ca{superscript 2}-binding site and the pore-forming S6 helix, interfering with conformational changes required for Ca{superscript 2}-induced channel opening at low Ca2+. We identified key residues for the binding and isoform-specific modulation of Ryanozole. Notably, Ryanozole-bound RyR2 retains its ability to open at high Ca2+ via unique conformational changes. These findings provide a structural basis for CPVT-targeted therapy and redefine the paradigm of small molecule-based regulation of large ion channels.

biochemistry↗

bioRxiv2026

A Heart-on-a-Chip Microdevice with Aligned Fibers for Cardiotoxicity Assessment

Background and ObjectivesCardiovascular cells differentiated from human induced pluripotent stem cells (iPSCs), including cardiomyocytes, are valuable for evaluating human cardiac pharmacology and toxicity. Early assessment of cardiotoxicity, especially for novel drugs like anticancer agents, is essential for improving drug development efficiency and reducing costs. This study aimed to develop a highly sensitive bioassay system capable of evaluating the physiological function of human cardiac tissue in vitro. MethodsHuman iPSCs were differentiated into cardiovascular cell types (cardiomyocytes, vascular endothelial cells, and vascular mural cells) and assembled into a cardiac tissue model on aligned fiber device. This tissue was cultured dynamically to induce the formation of vascular network-like structure. By combining the fiber device with our previously developed heart-on-a-chip microdevice (HMD), we created a new model of HMD (Aligned Fiber-based HMD; AF-HMD) with improved throughput and stability. Pulsatile force changes induced by drug exposure were quantified by tracking the displacement of fluorescent microbeads within the microchannels. ResultsAF-HMD demonstrated functional responses to known cardiac agonists and toxicants, such as doxorubicin. The device also replicated clinically relevant cardiotoxic events, including the synergistic effects of trastuzumab and doxorubicin, showing marked reductions in contractile force and beat rate, mirroring clinical observations. ConclusionsThe AF-HMD system provides a sensitive and reproducible platform for evaluating cardiotoxicity in drug development. It offers a promising tool for preclinical screening, with potential applications in personalized medicine and predicting cardiotoxic risk in cancer therapy.

bioengineering↗

bioRxiv2026

Self-Organized Vascularized Cardiac Microtissues Derived from Human iPS Cells Promote Myocardial Repair through Functional Host-Graft Vascular Integration

ObjectivesCardiac regenerative therapy using human induced pluripotent stem cell (hiPSC)-derived tissues and organoids holds great promise for treating heart diseases. Successful clinical translation requires biomimetic cardiac tissues that not only recapitulate native myocardial architecture but also actively integrate with host vasculature. We aimed to engineer self-organized, vascularized cardiac microtissues (VCMs) and evaluate their therapeutic and regenerative potential in a rat model of myocardial infarction (MI). MethodsVCMs composed of hiPSC-derived cardiomyocytes, vascular endothelial cells, and vascular mural cells were cultured under dynamic conditions to promote self-organization and prevascular network formation. One week after MI induction by coronary artery ligation in athymic immunodeficient rats, VCMs were transplanted onto the infarcted myocardium. Cardiac function was assessed by echocardiography and magnetic resonance imaging. Three-dimensional host-graft vascular architecture was visualized by light-sheet fluorescence microscopy following tissue clearing, and functional perfusion was evaluated by intravenous DyLight 488-conjugated lectin injection via host systemic circulation prior to tissue harvest. ResultsVCM transplantation significantly improved cardiac function and reduced infarct size compared with controls. Histological analyses demonstrated enhanced graft survival and neovascularization. Three-dimensional imaging revealed human-derived self-organized vascular networks within engrafted VCMs. Lectin perfusion confirmed functionally perfused, reciprocal host-graft vascular integration, including extension of graft-derived vessels into host myocardium, accompanied by myocardial regeneration. Early graft engraftment was significantly higher in the VCM group than in non-prevascularized controls. ConclusionsSelf-organized prevascularization of hiPSC-derived cardiac microtissues enable active host-graft vascular integration through functional vascular networks, thereby enhancing myocardial regeneration and therapeutic efficacy. This strategy represents an advanced approach for cardiac regenerative medicine. SummaryThis study aimed to develop self-organized, vascularized cardiac microtissues (VCMs) derived from human induced pluripotent stem cells (hiPSCs) and to evaluate their myocardial regenerative potential in a rat model of myocardial infarction (MI). VCMs were engineered from hiPSC-derived cardiomyocytes, endothelial cells, and vascular mural cells and cultured under dynamic conditions to enable self-organization and prevascular network formation. One week after MI induction, VCMs were transplanted onto the infarcted myocardium. Cardiac function was evaluated using echocardiography and magnetic resonance imaging. Light-sheet fluorescence microscopy combined with tissue clearing was used to visualize three-dimensional vascular architecture and host-graft integration, while lectin perfusion analysis assessed functional blood flow. VCM transplantation significantly improved cardiac function, increased early graft engraftment, and enhanced neovascularization. Importantly, self-organized human-derived vascular networks within the VCMs actively integrated with the host vasculature, forming functional, perfused host-graft vascular connections. These findings indicate that prevascularized VCMs do not merely survive after transplantation but actively promote vascular integration and myocardial regeneration through functional vascular networks. Together, these results demonstrate that self-organized vascularization markedly enhances graft integration, survival, and therapeutic efficacy, underscoring the clinical potential of VCM-based strategies for cardiac regenerative therapy.

bioengineering↗

bioRxiv2026

Human platelet lysate drives clinically compliant generation of vascular mural cells from human pluripotent stem cells

BackgroundVascular mural cells (MC) are essential components of vasculature, playing critical roles in tissue regeneration and cell therapy. The use of animal derived ancillary materials, like fetal bovine serum (FBS), in the induction of MC from human pluripotent stem cells (hPSCs), represents one of the biggest limitations to guarantee preclinical safety standards required to use this products in clinical settings. This study aimed to validate human platelet lysate (hPL) as a serum-free alternative for MC differentiation from hPSCs. MethodsComparison of MC differentiation efficiency from hiPSC using FBS vs hPL supplemented cultures was performed, along with functionality and gene expression assessment through bulk RNA sequencing. ResultsOptimization of hPL concentration identified hPL1% as the most effective condition, yielding PDGFR-{beta}+/CNN1+ MC, with a comparable efficiency to FBS10% and similar interaction with endothelial cells in vascular formation assays. However, distinct transcriptional profiles revealed that FBS10% and hPL1% drive differentiation toward different MC subphenotypes; hPL1% promoted contractile gene expression, while FBS10% enriched extracellular matrix pathways. Higher hPL concentrations further shifted differentiation toward cardiomyocytes. ConclusionIn monolayer in vitro differentiation of MC from hiPSC, the differentiation efficiency using hPL 1% supplementation is equivalent to FBS 10%, while supporting a more contractile phenotype. These findings establish hPL as a xeno-minimized, clinically compliant substitute for FBS for hPSC-derived MC differentiation, an important breakthrough for regenerative medicine.

cell biology↗

bioRxiv2025

N-Ethylmaleimide-Sensitive Factor Deletion in Dopamine D2 Receptor Cells and Associated Neuronal and Behavioural Changes in Mice

N-ethylmaleimide-sensitive factor (NSF) plays a crucial role in neurotransmitter release and membrane molecule trafficking by regulating membrane fusion. Dysfunction of NSF has been linked to neuropsychiatric disorders. Although the interaction of NSF with dopamine receptor 2 (D2R) and the resulting excitotoxicity from its reduction in vitro have been demonstrated, the role of NSF in D2R-expressing cells in vivo remains unclear. This study investigated the effects of NSF loss on the survival of D2R-expressing cells and on mouse behaviour. We generated D2R-specific NSF conditional knockout (Nsff/f;D2R-Cre) mice. Targeted deletion of NSF in D2R-expressing cells led to a significant decrease in D2R-expressing neurons, accompanied by increased apoptosis during postnatal development, reduced striatal volume, and substantially lowered dopamine levels in the striatum. Further evidence of dopaminergic dysfunction was shown by reduced dopamine transporter expression in the striatum and tyrosine hydroxylase expression in the striatum and substantia nigra. The Nsff/f;D2R-Cre mice exhibited attention deficit hyperactivity disorder (ADHD)-like behaviours, including hyperactivity and impulsivity. Notably, combined administration of methylphenidate and a D2R agonist effectively alleviated hyperactivity and impulsivity, indicating a potential synergistic approach for ADHD treatment. These findings highlight the critical role of NSF in the survival of D2R-expressing neurons and suggest that disruption of the NSF-D2R interaction may contribute to ADHD-like phenotypes. This study underscores the translational relevance of the Nsff/f;D2R-Cre model for ADHD and suggests that targeting D2R dysfunction, particularly in treatment-resistant cases, may represent a promising therapeutic strategy for ADHD.

neuroscience↗

bioRxiv2025

Hedonic hotspot in rat olfactory tubercle: map for mu-opioid, orexin, and muscimol enhancement of sucrose 'liking'.

Pleasure plays a crucial role in positive reinforcement and motivation. Brain regions able to amplify positive hedonic reactions to sweetness, known as hedonic hotspots, are distributed within the mesocorticolimbic reward systems. The olfactory tubercle (OT), a part of the ventral striatum that receives olfactory input, contains distinct functional domains: the anteromedial domain mediates approach motivation toward odors associated with food, whereas the lateral domain mediates avoidance motivation away from odors associated with danger. However, it has remained unclear whether the OT modulates hedonic reactions to pleasant sensations. In this study, we made pharmacological microinjections in OT of in rats to examine whether these OT subregions can modulate hedonic reactions, as assessed by the taste reactivity test. Sweet oral infusions of sucrose solution were delivered into the mouth via an intraoral cannula, and the rats orofacial and somatic hedonic reactions were recorded and analyzed. We compared three pharmacological agents: mu-opioid receptor agonist DAMGO, orexin-A peptide, and GABAA receptor agonist muscimol. Microinjection of any of these drugs into the anteromedial OT subregion enhanced hedonic liking reactions to sucrose. Furthermore, DAMGO injection into the anteromedial OT subregion recruited distant Fos expression in other hedonic hotspots, including in the caudal ventral pallidum and the rostromedial orbitofrontal cortex. By contrast, the same microinjections into the anterolateral OT subregion failed to enhance liking reactions and, DAMGO oppositely increased aversive disgust reactions. These findings suggest that the anteromedial OT contains a hedonic hotspot, whereas the anterolateral OT may contain a suppressive opioid hedonic coldspot. Thus, OT subregions may help causally modulate hedonic reactions to sweetness and flavor perception.

neuroscience↗

bioRxiv2025

A subtype of ultrasonic vocalizations during highly palatable food consumption in rats identified by machine learning-assisted classification

Identifying behavioral and physiological responses to rewarding stimuli is essential for understanding positive emotional states in animals and for investigating their neural basis. Ultrasonic vocalizations (USVs) in rats are modulated by various behavioral contexts and are thought to represent affective-like states. However, their diversity during palatable food consumption remains underexplored. In this study, we investigated acoustic features of USVs in male rats consuming chocolate, a highly palatable food. Using a machine-learning-assisted logistic regression model trained on spectrogram features, we identified a distinct USV subtype--the 40-kHz inverted-U type--that was selectively emitted during chocolate consumption. The emission of this subtype was tightly time-locked to chocolate feeding behavior. Systemic administration of naloxone, an opioid receptor antagonist, significantly reduced the emission of the 40-kHz inverted-U USVs during chocolate intake. These findings suggest that these USVs may reflect internal states associated with palatable feeding and are under modulation by the endogenous opioid system. Moreover, our data demonstrate the utility of machine learning for high-throughput, objective classification of USV subtypes. This framework provides a promising approach for decoding emotion-related vocal expressions in rats and highlights the potential of specific USVs as behavioral readouts for studying the neurobiology of positive emotions. Significance StatementUltrasonic vocalizations (USVs) are high-frequency calls produced by rats known to correlated with emotional and motivational states, yet their diversity and functional relevance remain underexplored. In this study, we identified a novel 40-kHz inverted-U USV subtype associated with chocolate consumption. These calls were closely tied to feeding behavior and were selectively suppressed by an opioid receptor antagonist, suggesting modulation by the brains reward system. Using machine learning-assisted classification, we established a robust method to detect these vocalizations. Our findings highlight the potential of specific USVs as non-invasive, real-time behavioral indicators of internal states, offering new tools for studying affect, reward, and communication in animal models.

neuroscience↗

bioRxiv2025

Integrative structural interactomics reveals protein organization and structure in a giant virus

Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrated cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocated 88 viral proteins to different virion sub-compartments and proposed topologies of 25 inner membrane proteins. We assigned eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.

biochemistry↗

bioRxiv2025

Unilateral damage to the entopeduncular nucleus causes forelimb motor dysfunction in rats

BackgroundThe entopeduncular nucleus (EP), corresponding to the human globus pallidus internal segment, is a basal ganglia output nucleus, and plays a critical role in motor control. However, the impact of EP damage on skilled motor function and the relationship between its damage in stroke, such as internal capsule hemorrhage (ICH), and motor dysfunction remains unclear. This study aimed to clarify whether EP damage causes motor dysfunction in two disease models. MethodsEP-related motor dysfunction was investigated by inducing localized unilateral EP damage in Long-Evans rats using a stereotactic kainic acid (KA) injection. Motor function was assessed using a single-pellet reaching task pre-injection and on postoperative days 2, 7, 14, 21, and 28. Immunohistochemical staining for NeuN, somatostatin (SST), and parvalbumin was conducted to quantify damage and its correlation with motor outcomes. In addition, unilateral ICH was induced via stereotactic injection of collagenase type IV, which dissolves the vascular basement membrane, into the internal capsule (IC) of Long-Evans rats. Injury sites were classified into the IC, dorsomedial region from the IC, ventral lateral region from the IC, and EP, and their volumes were measured. Measured volumes were analyzed for correlations with motor function assessments. ResultsKA-induced EP damage significantly reduced reaching success rates on postoperative day 2 compared to those in the control group (p<0.05). Immunohistochemical analysis showed that reaching success rates on day 28 positively correlated with the numbers of remaining NeuN-positive and SST-positive neurons (p<0.05). In the ICH experiment, all rats significantly reduced the success rate of the reaching task to 0% on day 2, and the success rate on day 28 correlated positively with the remaining EP volume, but not with total lesion volume. ConclusionsEP damage was strongly associated with motor impairments, highlighting its critical role in motor control and recovery.

neuroscience↗

bioRxiv2025

Eukaryotes' closest relatives are internally simple syntrophic archaea

Eukaryotes are theorized to have originated from an archaeal phylum Promethearchaeota (formerly Asgard archaea)1,2. The first cultured representatives revealed valuable insight3,4 but are distantly related to the first eukaryotic common ancestor (FECA), leaving many unknowns regarding this archaeons biology. Here, we report isolation of two strains belonging to the order proposed as FECAs closest relative, Hodarchaeales,5 as members of a pure co- and tri-culture with methanogenic partners. Both are obligately anaerobic, syntrophic, peptide-degrading, and mesophilic archaea that have simple internal cell structure and produce protrusions and vesicles, like Promethearchaeales3,4. All strains demonstrate behavior focused on cell construction rather than division, unlike typical prokaryotes6. Strain HC1 possesses genes associated with aerobic lifestyles but lacks complete pathways for aerobic respiration and co-cultures cannot grow under (micro)aerobic conditions, suggesting the genes support oxygen detoxification rather than respiration. Reflecting this, HC1 can survive and grow under microaerobic conditions only when aerobic organisms are present. Phylogenetic analyses indicate FECA may have possessed these genes and thus some aerotolerance. Physiological, genomic, and phylogenetic observations indicate FECA was a simple-celled anaerobic syntrophic peptide-degrading archaeon with a non-growth-centric lifestyle and potential adaptations towards an oxygenated planet--the archaea-eukaryote transition was steep in both cell structure and aerobiosis.

microbiology↗

bioRxiv2025

Characterization of an enigmatic tubular ultrastructure in the bacterial defensive symbiont of the Asian citrus psyllid

"Candidatus Profftella armatura" (Betaproteobacteria) is a unique organelle-like defensive symbiont harbored intracellularly within the symbiotic organ of a devastating citrus pest, the Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera). Our previous two-dimensional transmission electron microscopy identified an unprecedented ultrastructure that appeared tubular in Profftella, but their detailed architecture, three-dimensional arrangement, and components were unknown. To address these issues, this study conducted serial block-face scanning electron microscopy, high-voltage electron tomography, and fluorescence in situ hybridization. The results revealed that highly elongated (2.8-136 {micro}m observed), string-shaped Profftella cells contain tubes of various numbers (1-43 per cell observed) and length (up to 45 m observed), depending on the cell length. The tubes were evenly distributed throughout the cells, occupying an average of 6.3% of the total cell volume. Each tube consisted of five or six thin fibers twisted into a right-handed helix, maintaining a consistent diameter of approximately 230 nm along its entire length. Even without fixation or embedding, the tubes retained their shape under high vacuum conditions in electron microscopes, demonstrating their remarkable stability and robustness. These findings suggest that the tubes may help provide mechanical stability to the highly elongated and potentially vulnerable Profftella cells. Further analysis showed that the tubes are closely associated with ribosomes, suggesting a role in protein synthesis. Overall, these results offer new insights into the structural and functional evolution of bacteria, with potential implications for developing novel pest control strategies. Significance statementBacteria generally have simple intracellular structures, lacking organelles. Here, we report a highly elongated, elaborate organelle-like structure with a tubular shape in a bacterial symbiont of an important agricultural pest. The tube, which exhibits high durability and robustness, may contribute to the mechanical stability of the notably elongated symbiont cell. They are closely associated with numerous ribosomes, suggesting a potential role in gene expression. These findings not only enhance our understanding of bacterial evolution but may also provide clues for developing novel strategies for pest control.

microbiology↗

bioRxiv2024

Charting Cortical-Layer Specific Area Boundaries Using Gibbs Ringing Attenuated T1w/T2w-FLAIR Myelin MRI

Cortical areas have traditionally been defined by their distinctive layer cyto- and/or myelo- architecture using postmortem histology. Recent studies have delineated many areas by measuring overall cortical myelin content and its spatial gradients using the T1w/T2w ratio MRI in living primates, including humans. While T1w/T2w studies of areal transitions might benefit from using the layer profile of this myelin-related contrast, a significant confound is Gibbs ringing artefact, which produces signal fluctuations resembling cortical layers. Here, we address these issues with a novel approach using cortical layer thickness-adjusted T1w/T2w-FLAIR imaging, which effectively cancels out Gibbs ringing artefacts while enhancing intra-cortical myelin contrast. Whole-brain MRI measures were mapped onto twelve equivolumetric layers, and layer-specific sharp myeloarchitectonic transitions were identified using spatial gradients resulting in a putative 182 area/subarea partition of the macaque cerebral cortex. The myelin maps exhibit notably high homology with those in humans, suggesting cortical myelin shares a similar developmental program across species. Comparison with histological Gallyas myelin stains explains over 80% of the variance in the laminar T1w/T2w-FLAIR profiles, substantiating the validity of the method. Altogether, our approach provides a novel, noninvasive means for precision mapping layer myeloarchitecture in the primate cerebral cortex, advancing the pioneering work of classical neuroanatomists.

neuroscience↗

bioRxiv2024

Nanoscale visualization of Drosophila E-cadherin ectodomain fragments and their interactions using DNA origami nanoblocks

The adhesive function of cell surface proteins can be visually assessed through direct observation; however, the underlying structures that mediate adhesion typically remain invisible at the nanoscale level. This hinders knowledge on the diversity of molecular architectures responsible for cell-cell adhesion. Drosophila E-cadherin (DE-cadherin), a classical cadherin with a unique domain structure, demonstrates adhesive function; however, it lacks a structural model that explains its adhesion mechanism. In this study, we present a novel application of DNA origami technology to create a cell-free, flat environment in which full DE-cadherin ectodomains are anchored using SNAP-tags and biotin-streptavidin interactions. DNA origami was assembled into a 120 nm long block, bearing 5 or 14 biotin:streptavidin sites that were evenly spaced on one lateral face. DE-cadherin ectodomain fragments were attached via biotinylated SNAP-tags. These decorated DNA origami nanoblocks were subjected to transmission electron and high-speed atomic force microscopy, which revealed a hinge-like site that separated the membrane-distal and -proximal portions of the DE-cadherin ectodomain, suggesting a role in mechanical flexibility. We also observed interactions between DE-cadherin ectodomains via their membrane-distal portions on single DNA origami nanoblocks. We reconstituted an adhesion-like process via pairing DNA origami nanoblocks using DE-cadherin ectodomain interactions. Homophilic associations of functional DE-cadherin ectodomains between the paired DNA origami nanoblocks were visualized at the nanoscale, displaying strand-like molecular configurations, likely representing the extracellular cadherin repeats without regular arrays of structural elements. This study introduces a DNA origami-based platform for reconstituting and visualizing cadherin ectodomain interactions, with potential applications for a broader range of adhesion molecules. HighlightsO_LIDNA origami technology was applied to perform a structure-function study of cadherin. C_LIO_LIDNA origami nanoblocks decorated with DE-cadherin ectodomains were observed by TEM/HS-AFM. C_LIO_LIA hinge-like site that separated the membrane-distal and -proximal portions of the DE-cadherin ectodomain was revealed. C_LIO_LIAn adhesion-like process was mimicked via pairing two nanoblocks using DE-cadherin ectodomain interactions. C_LIO_LIHomophilic associations of DE-cadherin ectodomains between the nanoblocks were visualized at the nanoscale level. C_LI

molecular biology↗