Biology subjects

Ogawa, Y.

Publications and source records attributed to Ogawa, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression

Tandem repeats (TRs) and transposable elements (TEs) occupy substantial fractions of eukaryotic genomes, yet how repeat detection programs affect downstream expression analyses remains poorly explored. Here, we present an improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri. The assembly matches experimentally estimated genome size and chromosome number. It resolves highly expanded TRs that occupy up to 28.0% of the whole genome. Using this assembly and other complete vertebrate genome assemblies, we compared TR and TE-derived regions across combinations of TR detection programs and TE consensus library construction workflows under a standardized TE classification scheme. Choices in TR detection reshaped the apparent TE landscape. TE workflows shared a broad core of TE-derived regions but recovered complementary sets of age- and sex-associated TE loci, evaluated with a sex-balanced killifish multi-tissue aging cohort. Together, the combinatorial use of adaptable programs supports robust, locus-aware detection of complex repeats across genome assemblies.

genomics↗

bioRxiv2026

Paralemmin 2 is a shared, alternatively-spliced regulator of axon initial segments and paranodal junctions in oligodendrocytes

Nervous system function depends on highly specialized axonal membrane domains. For example, axon initial segments (AIS), nodes of Ranvier, and paranodal junctions are essential for action potential initia-tion and saltatory conduction. These domains use shared molecular machinery converging on the master scaffolding protein AnkyrinG (AnkG). Using endogenous AnkG-TurboID proximity proteomics, we identify Paralemmin 2 (Palm2), a previously uncharacterized CNS protein, as a shared component of the AIS and nodes of Ranvier in neurons, and paranodes in oligodendrocytes. Palm2 localizes transiently to the AIS and nodes during development, but is found at paranodes throughout life, reflecting cell type-specific splicing of a lipid-modified domain both necessary and sufficient for AnkG interaction. Mice lacking oli-godendroglial Palm2 assemble normal paranodes during development, but aged mice lose paranode in-tegrity due to loss of paranodal AnkG and Neurofascin-155. Our findings identify Palm2 as a lipid raft-associated regulator of axonal and oligodendroglial membrane domains and reveal cell type-specific pro-tein variants as a recurring principle for specializing axonal and glial membrane architectures.

neuroscience↗

bioRxiv2026

Production of cellobiose from ionic liquid-treated cellulose using the highly thermostable cellobiohydrolase HmCel6A-3SNP at 80°C and analysis of enzymatic accessibility to the substrate

Cellobiose is an important disaccharide used in food, health, and biorefinery applications, but its efficient enzymatic production from crystalline cellulose remains challenging. In this study, crystalline cellulose was dissolved in ionic liquids and regenerated by dilution, and subsequently hydrolyzed at 80{degrees}C using a highly thermostable cellobiohydrolase, HmCel6A-3SNP. The enzyme retained activity in the presence of low concentrations of ionic liquids. Among the pretreatment conditions tested, cellulose treated with 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) showed the highest enzymatic digestibility. After washing to remove residual ionic liquid, the reaction produced reducing sugars at levels 1.5-fold higher than those obtained in the presence of 10% [Bmim]Cl, with cellobiose accounting for approximately 96% of the products. Under the optimized conditions, the hydrolysis yield reached [~]36% after 48 hr. Structural analyses using birefringence imaging, electron microscopy, and Fourier transform infrared spectroscopy indicated that higher-order structural changes in regenerated cellulose strongly influence enzymatic accessibility. These results demonstrate the potential of combining ionic-liquid pretreatment with thermostable enzymes for selective cellobiose production from cellulose.

biochemistry↗

bioRxiv2026

Hoverfly responses to looming stimuli depend on elevation and speed

An object on immediate collision course generates a rapidly expanding visual stimulus on the retina, which will typically trigger a fast reaction, such as an evasive behavior. In hoverflies, for example, visual looming stimuli may be generated if the insect is about to collide with a stationary object in the surround, by an approaching predator, or by conspecifics during territorial interactions. Supporting these behavioral responses is a diverse range of looming sensitive descending neurons that project information from the optic lobes and central brain to the motor control centers in the thoracic ganglia. We here show that the looming sensitive descending neurons are predominantly sensitive to looming stimuli located in the ventral visual field. To investigate if this is matched by behavior, we recorded how tethered hoverflies responded to looming stimuli presented dorsally or ventrally on a visual monitor, at four different speeds (l/|v| of 10 - 667 ms), covering a naturalistic range. We found that ventral stimuli, especially at intermediate speeds (l/|v| = 50 or 200 ms), triggered much stronger behavioral responses than dorsally displayed stimuli. The behavioral data thus not only match the receptive fields of the neurons likely to support the behavior, but also highlight that behavioral output is not entirely reflexive but is strongly modulated by stimulus speed and elevation. Significance StatementIf someone throws a ball at you, this generates a rapidly expanding object across your visual field, which will make you react before you have even had time to think. You may for example duck, dip or dive to avoid the ball, or bring your hands up to grab it. Similarly, many insects respond to rapidly approaching objects. We here show that hoverfly reactions to such looming stimuli depend on stimulus speed and elevation, with the strongest response to stimuli approaching from below. We further demonstrate that the neurons likely supporting these behaviors show highest sensitivity in the ventral visual field, suggesting a close match between neural tuning and behavioral output.

animal behavior and cognition↗

bioRxiv2026

Intracellular photonic crystals in photosynthetic sea slugs form via a kidney-mediated biomineralisation pathway

Sea slugs in the Sacoglossa superorder are some of the few animals capable of photosynthesising by isolating and maintaining functional chloroplasts within their body1,2. While this ability allows some species in this superorder, such as Elysia viridis, to appear green, camouflaging themselves within their surroundings3,4, this species is marked by extremely bright, coloured regions. Here, we show that these animals produce a yet undiscovered class of photonic structure consisting of intracellular mixed amorphous CaCO3 and calcite spherical nanoparticles organised in non-closed-packed face-centred cubic (FCC) lattices and photonic glasses5. By mapping the distribution of the cells containing such architectures, we suggest that their colour is linked both to their function and to their biological formation via the animals renal system. Using a combination of different optical methods and cryo-electron microscopy, we reveal that the biomineralisation pathway proceeds through stages of calcium ion concentration in the kidney, transport via internal vessels, and precipitation from a dense liquid-like precursor, culminating in the formation of monodisperse nanoparticles, which are the building blocks of these photonic structures.

biophysics↗

bioRxiv2026

Biophysical properties of material-colonizing fungal biofilms: multiscale structural and mechanical characterization

Black extremotolerant fungi form persistent biofilms on a wide range of natural and engineered substrates. Able to weather minerals, affect stone monument surfaces, and colonize solar panels, they demonstrate a strong capacity to interact with and modify material surfaces, even under most extreme conditions. In this study, we establish a methodological workflow for the structural and mechanical characterization of melanized biofilms formed by the black fungus Knufia petricola. This species represents a broader group of resilient surface colonizers and provides a model for in-depth investigation. When grown on solid agar/air interface, this species predominantly forms a compact biofilm, composed of spherical cells, while retaining the capacity for filamentous growth, providing a suitable framework to explore morphology-dependent biomechanical responses. The proposed toolbox combines complementary analytical techniques spanning multiple spatial scales, including shear-rheology to quantify bulk viscoelastic behavior, micro-indentation to resolve local stiffness of the biofilm surface, micro-computed tomography for non-destructive three-dimensional visualization of biofilm architecture, and cryogenic preparation methods and electron microscopy for high-resolution ultrastructural analysis. As a case study, we applied this workflow to compare biofilms grown on two nitrogen sources (NO3- vs. NH4+). Our results reveal that the nitrogen source plays a key role in biofilm morphology across multiple hierarchical levels - ranging from cell division patterns and distribution of extracellular polymeric substances (EPS) to overall mechanical properties, where NO3- leads to budding-dominated growth and increased stiffness, whereas NH4+ promotes meristematic growth and softer biofilms. The successful transfer and integration of methods originally developed for bacterial biofilm research highlights the feasibility of quantitative mechanical analyses in fungal systems. This multiscale toolbox provides a foundation for advancing the mechanistic understanding of fungal biofilms and biofilm-material interactions, with implications for geomicrobiology, material biodeterioration, and the design of bio-inspired functional materials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/720134v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7fd08borg.highwire.dtl.DTLVardef@15476c2org.highwire.dtl.DTLVardef@40be50org.highwire.dtl.DTLVardef@8e9410_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Sexual dimorphism in sensorimotor transformation of optic flow

Motion vision underpins a wide range of adaptive behaviours essential for individual and species survival. In hoverflies, some visual behaviours are sexually dimorphic, including for example male high-speed pursuit of conspecifics, matched by improved optics, and faster photoreceptors. Other visual behaviours are sexually monomorphic, with for example similar foraging flight speeds in male and female hoverflies. However, whether the descending neurons responsible for sensorimotor transformation of optic flow are sexually dimorphic is unknown. To address this, we combined morphological analysis with electrophysiology of optic flow sensitive descending neurons and compared neural responses to the behavioural output in tethered hoverflies. We found that while optomotor flight behaviour is largely sexually monomorphic, the underlying neural responses are sexually dimorphic, especially at higher optic flow velocities. Additionally, behavioural responses were noticeably slower than neural responses. Together, our findings uncover a nuanced, sex- and stimulus- dependant sensorimotor transformation, shaped by both neural architecture and behavioural demands.

neuroscience↗

bioRxiv2025

Localization of Fascin to Dendritic Protrusions Regulates Postsynaptic Plasticity

The Fascin family of actin-bundling proteins is best known for organizing actin filaments (F-actin) into tightly packed bundles that drive dynamic membrane protrusions such as filopodia. In neurons, fascin has been thought to primarily function in axons, as previous studies reported its absence from dendritic filopodia and spines. Here, we demonstrate that fascin is both present and functionally important in dendritic compartments. Using optimized immunocytochemistry and CRISPR-based endogenous tagging of fascin1 in cultured hippocampal neurons, we show that fascin is concentrated in developing dendritic filopodia and enriched in mature dendritic spines. Super- resolution imaging further reveals that fascin is organized into discrete nanoscale foci within spine heads, but not the spine neck. Finally, we show that CRISPR-mediated knockout of fascin1 in mature hippocampal neurons impairs synaptic potentiation, without affecting baseline excitatory synaptic transmission. Together, our findings uncover a previously overlooked aspect of actin organization in dendritic spines and establish fascin as a critical regulator of postsynaptic plasticity. Summary StatementThe actin bundling protein fascin localizes to dendritic filopodia and spines, where it regulates activity-dependent synaptic plasticity.

neuroscience↗

bioRxiv2025

Cryo-EM structure of Chlamydomonas Photosystem I complexedwith the alternative electron donor cytochrome c6

Photosynthetic electron transfer relies on small soluble carriers that shuttle electrons between the cytochrome bf complex and Photosystem I (PSI). While copper-containing plastocyanin (Pc) serves this role in plants, algae and cyanobacteria employ the heme protein cytochrome c (Cyt c) as well. Here we present a cryo-electron microscopy structure of a Cyt c:PSI complex from Chlamydomonas reinhardtii. The Cyt c heme is positioned [~]11 [A] from P700, stabilized by extensive contacts involving the N-terminal domain of PSAF. Importantly, R66 in Cyt c, a key residue in ancestral donors, forms a putative electrostatic contact with PsaB-D623 and participates in a tri-planar {pi}-stacking interaction with nearby aromatic residues. Our findings provide a structural framework for ancestral PSI interactions and illuminate the evolutionary diversification of electron transfer pathways.

biochemistry↗

bioRxiv2025

Pulsed-laser lensing for phase modulation in electron microscopy

Phase contrast electron microscopy is fundamental for visualizing unstained biological specimens. Advances in electron detection have not yet overcome the low contrast caused by weak scattering. Here, we demonstrate that an orthogonal pulsed laser-electron beam interaction produces a pronounced peak phase shift of 430 radians through ponderomotive defocusing, leading to a maximum angular deflection of 45 {micro}rad. Experiments encompassing a variety of probe pulse energies and pump positions verified the properties of the electron pulses in a range of pulse durations from 5.8 {+/-} 1.9 ps to 13.4 {+/-} 0.9 ps and a width of 15.0 {+/-} 2.6 {micro}m at the interaction region. The stability of the beam was also tested across 10 hours of cumulative acquisition time, with only small variations in laboratory conditions resulting in a gradually shifting baseline measurement. Pulsed laser lensing of the electron beam offers the potential for refinement in phase shift and electron beam shaping with careful consideration to the overlap between laser and electron pulses. Calculations of phase shifts across a wide experimental envelope show that poorly chosen laser parameters can generate large incoherent distributions at both 30 keV and 300 keV. Thus, a delicate balance between laser and electron widths and pulse durations must be struck to adequately achieve uniform phase shifts, particularly when singling out specific beamlets in the back-focal-plane.

biophysics↗

bioRxiv2025

Inducible degradation of endogenous proteins by AlissAID system and development of a photoactivatable inducer.

Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target protein remains a common challenge. Here, we demonstrated the efficiency of the affinity-linker-based super-sensitive AID system for condition-knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with small-molecule antibodies, enabling the control of GFP and mCherry fusion proteins. Additionally, this system can be used to degrade endogenous targets, such as Ras proteins. We also developed a novel inducer, caged 5-adamantyl-IAA, that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.

cell biology↗

bioRxiv2024

Differentiation of Mesenchymal Stem/ Stromal Cells into CD45+ Macrophage-like Cells: Expanding Insights into MSC Plasticity

Mesenchymal stem/stromal cells (MSCs) are notable for their differentiation potential and immunomodulatory properties. They share several features with macrophages that are also similar to those of fibrocytes. This study aimed to investigate the relationship between MSCs, fibrocytes, and macrophages, focusing on the hypothesis of a possible direct lineage. This study focuses on a freshly isolated murine MSC population known as PSmMSCs (CD45- TER119- Sca-1+ PDGFR+). Transplanting PSmMSCs from transgenic GFP mice into irradiated recipients produced GFP+ cells expressing the macrophage markers CD45, CD68, and CD115, indicating a macrophage-like phenotype. Further analysis showed that PSmMSCs cultured in macrophage differentiation media acquired characteristics of M2 macrophages (CD45, CD68, and CD206). These results were confirmed in two different mouse strains as well as in human MSCs (hMSCs). Single-cell RNA sequencing revealed macrophage-like and fibrocyte-like populations among the PSmMSCs. These findings demonstrate the phenotypic plasticity of freshly isolated MSCs to transition into macrophage-like and/or fibrocyte-like states, which has not been reported, particularly in long-term cultured MSCs. This study provides new insights into MSC plasticity and its potential roles in immune regulation and tissue repair.

cell biology↗

bioRxiv2024

Visual physiology of Australian stingless bees

Stingless bees engage in a range of visually guided behaviours that require relatively high spatial resolution and contrast sensitivity. Although the eyes of honeybees, bumblebees, carpenter bees, and sweat bees have been studied extensively, there is limited knowledge of stingless bees. Here, we studied two sympatric Australian species, Tetragonula carbonaria and Austroplebeia australis, which are important crop pollinators. The bigger A. australis had more and larger ommatidial facets compared to T. carbonaria. Using pattern electrophysiology, we showed that A. australis had higher contrast sensitivity (13.07) compared to T. carbonaria (5.99), but their spatial resolving power did not differ (0.53 cycles deg-1). We discuss these differences in visual physiology in the context of the distinct foraging behaviours of the two species.

evolutionary biology↗

bioRxiv2024

Conservation of cis-regulatory codes over half a billion years of evolution

The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. Here, we show that the retinas highly conserved cellular architecture is mirrored by deep conservation of the underlying cis-regulatory codes that control gene expression. We use comparative single-cell chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas-- representing over half a billion years of evolutionary divergence--to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. This conservation persists despite extensive turnover of cis-regulatory regions between distant species. Conservation manifests as the clustering of multiple distinct high-affinity transcription factor (TF) binding sites toward the center of cell-class-specific open chromatin regions with little cross-species preservation of higher-order syntax. Hierarchical clustering of machine-learning models of retinal cis-regulatory codes from diverse species recovers six clusters corresponding to the six retinal cell classes. Thus, the retinas cellular Bauplan is controlled by cis-regulatory codes which predate the divergence of extant vertebrates and persist despite nearly complete enhancer turnover.

evolutionary biology↗

bioRxiv2024

Two types of regeneration mechanism in acute liver injury

The liver has a strong regenerative capacity, but the mechanisms of liver regeneration are not well understood. Furthermore, many previous studies on liver regeneration have been conducted in partial hepatectomy models, which may differ from acute liver injury with inflammation and necrosis, as observed in many clinical cases. In this study, we conducted a single-cell RNA-seq analysis (scRNA-seq) of liver regeneration in mice treated with acetaminophen (APAP) using publicly available data. We discovered that two cell proliferation populations appeared simultaneously during a single regenerative process. The two populations differed significantly in terms of differentiation, localization, proliferation rate, and signal response. Furthermore, one of the populations was induced by contact with necrotic tissue and exhibited a higher proliferative capacity with a dedifferentiated feature. These findings can shed new light on liver regeneration and aid in the development of therapeutic strategies for liver failure.

pathology↗

bioRxiv2024

TRIM46 is not required for axon specification or axon initial segment formation in vivo

Vertebrate nervous systems use the axon initial segment (AIS) to initiate action potentials and maintain neuronal polarity. The microtubule-associated protein tripartite motif containing 46 (TRIM46) was reported to regulate axon specification, AIS assembly, and neuronal polarity through the bundling of microtubules in the proximal axon. However, these claims are based on TRIM46 knockdown in cultured neurons. To investigate TRIM46 function in vivo, we examined TRIM46 knockout mice. Contrary to previous reports, we find that TRIM46 is dispensable for AIS formation and maintenance, and axon specification. TRIM46 knockout mice are viable, have normal behavior, and have normal brain structure. Thus, TRIM46 is not required for AIS formation, axon specification, or nervous system function. We also show TRIM46 enrichment in the first [~]100 m of axon occurs independently of ankyrinG (AnkG), although AnkG is required to restrict TRIM46 only to the AIS. Our results suggest an unidentified protein may compensate for loss of TRIM46 in vivo and highlight the need for further investigation of the mechanisms by which the AIS and microtubules interact to shape neuronal structure and function. SIGNIFICANCE STATEMENTA healthy nervous system requires the polarization of neurons into structurally and functionally distinct compartments, which depends on both the axon initial segment (AIS) and the microtubule cytoskeleton. In contrast to previous reports, we show that the microtubule-associated protein TRIM46 is not required for axon specification or AIS formation in mice. Our results emphasize the need for further investigation of the mechanisms by which the AIS and microtubules interact to shape neuronal structure and function.

neuroscience↗

bioRxiv2024

A new leaf sensing organ in a predatory insect group, the praying mantises (Mantodea)

Animals sensory systems enable them to navigate and interact with their environments. Adaptive specializations of these systems can generate novel structures or organs that support highly unique niche adaptations. We report the discovery of a novel sensory organ in a group of praying mantises (Insecta, Mantodea, Nanomantoidea), which have an unusual "leaf-planking" ecomorphic life strategy, laying against the undersides of broadleaf vegetation. Histology, scanning electron microscopy, and x-ray computed tomography all support the novelty of this distinct morphology while electrophysiology reveals that the sensory organ, herein designated the gustifolium organ, detects plant volatiles. The location of the gustifolium organon the ventral thoracic surface of these mantises appears to facilitate the chemical detection of the leaves on which it resides. The gustifolium is a novel plant volatile-detecting sensory structure in an obligate predatory insect, directly linked to a newly-identified, highly-adapted life strategy.

zoology↗

bioRxiv2024

Combining Unity with machine vision to create low latency, flexible, and simple virtual realities

O_LIIn recent years, virtual reality arenas have become increasingly popular for quantifying visual behaviors. By using the actions of a constrained animal to control the visual scenery, the animal is provided the perception of moving through a simulated environment. As the animal is constrained in space, this allows detailed behavioral quantification. Additionally, as the world is generally computer-generated this allows for mechanistic quantification of visual triggers of behavior. C_LIO_LIWe created a novel virtual arena combining machine vision with the gaming engine Unity. For tethered flight, we enhanced an existing multi-modal virtual reality arena, MultiMoVR (Kaushik et al., 2020) but tracked hoverfly wing movements using DeepLabCut-live (DLC-live, Kane et al., 2020). For trackball experiments, we recorded the motion of a ball that a tethered crab was walking on using FicTrac (Moore et al., 2014). In both cases, real-time tracking was interfaced with Unity to control the movement of the tethered animals avatars in the virtual world. We developed a user-friendly Unity Editor interface, CAVE, to simplify experimental design and data storage without the need for coding. C_LIO_LIWe show that both the DLC-live-Unity and the FicTrac-Unity configurations close the feedback loop effectively with small delays, less than 50 ms. Our FicTrac-Unity integration highlighted the importance of closed-loop feedback by reducing behavioral artifacts exhibited by the crabs in open-loop scenarios. We show that Eristalis tenax hoverflies, using the DLC-live-Unity integration, navigate towards flowers. The effectiveness of our CAVE interface is shown by implementing experimental sequencing control based on avatar proximity to virtual structures. C_LIO_LIOur results show that combining Unity with machine vision tools such as DLC-live and FicTrac provides an easy and flexible virtual reality (VR) environment that can be readily adjusted to new experiments and species. This can be implemented programmatically in Unity, or by using our new tool CAVE, which allows users to design and implement new experiments without programming in code. We provide resources for replicating experiments and our interface CAVE via GitHub, together with user manuals and instruction videos, for sharing with the wider scientific community. C_LI

animal behavior and cognition↗