Biology subjects

Fukuda, K.

Publications and source records attributed to Fukuda, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Parasitophorous vacuole membranes of Toxoplasma gondii and Plasmodium falciparum lack the lipid asymmetry characteristic of host cell plasma membranes

Apicomplexan parasites, including Toxoplasma gondii and Plasmodium falciparum, reside within a specialized compartment known as the parasitophorous vacuole (PV) during their intracellular life cycle. The PV membrane (PVM), which derives from the host plasma membrane upon invasion, serves as a selective barrier that permits nutrient acquisition while shielding the parasite from host defense mechanisms. Although the protein composition of the PVM has been studied extensively, its lipid organization remains poorly understood. Using the quick-freeze, freeze-fracture replica labeling (QF-FRL) method, we quantitatively analyzed the transbilayer distribution of phosphatidylserine (PtdSer), phosphatidylethanolamine (PtdEtn), and GM3 ganglioside in the PVM of T. gondii and P. falciparum. Unlike host cell plasma membranes, where these lipids exhibit strict asymmetry--PtdSer and PtdEtn confined to the cytoplasmic leaflet and GM3 to the exoplasmic leaflet--we found that all three lipids were symmetrically distributed across both leaflets of the PVM. This striking loss of lipid asymmetry suggests that the PVM undergoes profound remodeling during infection. The presence of PtdSer and PtdEtn in the luminal leaflet may facilitate the binding of perforin-like proteins (PLP1s) during egress. These findings reveal a unique feature of the PVM that redefines our understanding of host-parasite membrane biology.

cell biology↗

bioRxiv2026

Relationship between gonadosomatic index and spawning-capable status based on gonadal histology in the moonfish Mene maculata

The moonfish Mene maculata (Bloch and Schneider, 1801), the sole extant species of the family Menidae, is widely distributed in the Indo-West Pacific. Although its spawning season has previously been inferred from seasonal variation in the gonadosomatic index (GSI), the histological basis for interpreting GSI as an indicator of spawning-capable status remains limited. Here we describe the gonadal structure of male and female M. maculata and evaluate how GSI and standard length relate to spawning-capable status based on germ cell development. The testis was lobular and exhibited an unrestricted spermatogonial distribution, a structure widely observed among neoteleosts, indicating that the phylogenetic distinctiveness of M. maculata was not associated with a distinctive testicular structure. In the spawning-capable female, oocytes at multiple developmental stages, from primary growth to oocyte maturation, co-occurred within the ovary, indicating asynchronous ovarian development. This finding suggests that M. maculata may be a batch spawner rather than a total spawner as previously inferred. The spawning-capable female had a GSI consistent with previously inferred spawning season estimates. By contrast, histologically examined males were spawning capable at GSI values lower than those previously associated with the inferred spawning season, suggesting that male spawning-capable status may persist beyond the period inferred from elevated GSI alone. This study provides the first histological description of reproductive biology in the phylogenetically distinctive M. maculata and establishes a histological basis for interpreting GSI as a reproductive indicator.

ecology↗

bioRxiv2026

Description of the embryonic development in the convict cichlid (Amatitlania nigrofasciata)

We provide a detailed description of embryonic development in the convict cichlid (Amatitlania nigrofasciata) from fertilization to hatching at 26 {degrees}C, together with a practical staging table anchored to established teleost reference frameworks. Fertilized eggs were obtained by both natural spawning and artificial fertilization. Unfertilized eggs were ovoid and adhesive, surrounded by a chorion and a sticky mucous layer. Early development proceeded, in broad outline, through the teleost sequence of meroblastic discoidal cleavage, blastula, gastrula, segmentation, and organogenesis. The first cleavage occurred at 1.75 hours post-fertilization (hpf), with subsequent cleavages at 30 min intervals, reaching the 64-cell stage at 4.25 hpf. Cleavage up to the 64-cell stage progressed on a timescale broadly comparable to that reported for other cichlids, whereas the interval from the 64-cell stage to early epiboly was relatively short in this species. The high, sphere, and dome stages occurred at 8, 9, and 10 hpf, respectively, with epiboly initiating at the dome stage. At the dome stage, a marginal thickening interpreted as the presumptive embryonic shield became apparent. During early epiboly, the blastoderm showed pronounced spatial heterogeneity: it was consistently thicker and advanced more rapidly on the prospective embryonic axis side, yielding a readily detectable asymmetry. A morphologically distinct embryonic axis became visible at 40-50% epiboly, and epiboly was completed at 28.5 hpf. Notably, somitogenesis began before epiboly completion (first somites at 85-90% epiboly), indicating temporal overlap between late gastrulation and early segmentation. Major organ primordia became apparent during the overlapping segmentation/organogenesis interval, and hatching occurred around 70 hpf. Newly hatched larvae possessed three pairs of adhesive glands. This staging reference enables reproducible developmental sampling and should facilitate future comparative, mechanistic, and experimental work using the convict cichlid.

developmental biology↗

bioRxiv2026

Capturing self-renewing multipotent neural crest stem cells from human pluripotent stem cells

During embryonic development, neural crest cells (NCCs) represent a multipotent population characterized by an inherently transient nature, rapidly differentiating into various lineages. This instability has presented a fundamental challenge, as it is exceedingly difficult to maintain these cells in a stable, multipotent state in vitro. In this study, we report a robust culture system dependent on Wnt and FGF signaling that enables the long-term (>6 months) expansion of human iPSC-derived neural crest stem cells (NCSCs). These NCSCs retain their self-renewal and differentiation capacity, validated at the single-cell clonal level. ATAC-seq analysis indicated that posterior NCSCs maintain a more permissive chromatin structure at neuronal gene loci. Furthermore, ChIP-seq analysis revealed that the key transcription factor SOX10 binds to the regulatory regions of genes involved in both maintenance and differentiation. This system provides a stable source of human NCSCs, offering a valuable platform for developmental biology, disease modeling, and regenerative medicine.

developmental biology↗

bioRxiv2026

Task goals dynamically reconfigure neural working memory representations

A hallmark of human intelligence is the ability to flexibly shift between tasks and modify our behaviour according to current goals and context. Working memory (WM) is thought to be critical for this cognitive flexibility. A key unanswered question is how neural representations of WM are configured to support different task goals. Thirty-four participants performed a shape WM task with different task rules in interleaved blocks: delayed match-to-sample (DMS) and delayed match-to-category (DMC), while electroencephalography (EEG) was collected. Our results show that stimuli from a circular shape space can be decoded from EEG across the memory delay. Neural stimulus patterns initially generalised across tasks but reconfigured to integrate task and category information and became task-dependent in the later delay. In the DMC task, neural patterns for shapes within a category became more similar than across categories, controlling for their physical distance. This category-dependent shift was associated with greater task-dependency in the neural stimulus representation. Together, our results reveal a dynamic reconfiguration of neural WM representations over the course of the delay period to support distinct task demands. Significance statementAs humans, we regularly move between tasks and change our behaviour according to the situation. This cognitive flexibility critically depends on our working memory, the ability to keep information in mind in the short term. It remains poorly understood how working memory configures mental representations to support different tasks. In this study, participants performed two tasks that probed working memory for visual details or object category respectively. Neural representations were initially similar irrespective of task but became more task-dependent over time in memory. The task-dependence in the neural representation was explained by a neural category bias that emerged during the memory delay. Our results demonstrate how neural representations integrate prior knowledge with stimulus representations in a task-dependent manner, supporting flexible cognition.

neuroscience↗

bioRxiv2025

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin

Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. Here, we established Resf1-deficient mice, which exhibited developmental delay, partial embryonic lethality, and placental defects. Notably, retroelements were also upregulated in the Resf1-deficient placenta, correlating with increased expression of nearby genes. To further assess whether Resf1 functions within the trophoblast lineage, we generated Resf1-deficient trophoblast stem cell (TSC) lines. Both undifferentiated TSCs and differentiated TSCs (D-TSCs) display increased retroelement expression along with elevated levels of genes associated with placental development. Moreover, Resf1-deficient TSCs exhibit compromised maintenance of H3K9me3 domains in a manner independent of SETDB1. Collectively, our findings reveal that Resf1 plays multifaceted roles beyond retroelement silencing, underscoring its importance in development and its critical function in trophoblast lineage regulation.

developmental biology↗

bioRxiv2025

Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1

Histone H3 lysine 9 (H3K9) methylation and heterochromatin protein 1 (HP1) are well conserved heterochromatin epigenome and its reader molecule. However, the details of how importance of them in heterochromatin formation still remain unclear. One of the reasons is the redundancy aspects, as there are multiple H3K9 methylation reader molecules, including HP1, and HP1 itself functions as a hub recruiting various effector molecules. To overcome those issues, we took a synthetic biology approach and introduced H3K9 methylation and HP1 into budding yeast Saccharomyces cerevisiae, which does not have this system, and examined its impact on transcription and chromatin compaction. We observed that the mammalian H3K9 methyltransferase can induce genome-wide H3K9 di- and tri-methylation (H3K9me2,3) in the budding yeast which mainly in the gene body region, and HP1 accumulates over the H3K9 methylated regions. The forced expression of H3K9 methyltransferase and HP1 had little impact on transcription. Furthermore, Micro-C-seq analysis revealed no significant effects on the chromatin 3D structure. These results suggest that although H3K9 methylation and recruitment of HP1 play essential roles in the epigenetic regulation of heterochromatin, they alone are not sufficient to alter the higher-order chromatin structure, at least in the gene body regions in budding yeast.

synthetic biology↗

bioRxiv2025

Constraints on paternal care capacity favor a monogamous mating system in the group-living gobiid fish Trimma marinae

We examined why Trimma marinae is monogamous despite high potential for polygyny. Previous work suggested males can care for up to three clutches, but four may exceed their capacity. We therefore tested whether a single female can saturate a males care capacity. In established pairs, 49 spawning intervals had a median interval of 2 days. Because eggs hatch on day 3, 75.5% of intervals produced clutch overlap. Under these conditions, mating with an additional female would require care of four clutches, likely exceeding male capacity. These findings support female mate guarding as a strategy to monopolize limited paternal care.

ecology↗

bioRxiv2025

Development of a vehicle for non-invasive oral administration to facilitate behavioral experiments in fish

Pharmacological approaches are increasingly used in diverse fields of fish biology. However, injection-based administration can induce stress or injury, potentially interfering with the natural physiological and behavioral states of the fish. Here, we present a non-invasive vehicle for oral administration of peptide-based compounds. To demonstrate its utility, the oxytocin receptor antagonist atosiban was administered orally using this vehicle. Atosiban was then qualitatively detected in serum by high-performance liquid chromatography. This study provides a proof of concept for an easy-to-use and minimally disruptive tool for various fish experiments.

animal behavior and cognition↗

bioRxiv2025

High-Speed AFM Reveals IDR-Mediated Structural Plasticity of EML4-ALK Modulated by ALK Inhibitors

EML4-ALK is a key oncogenic driver in lung cancer, but variant-specific chemoresistance limits the efficacy of current ALK inhibitors. Because the N-terminus contains an intrinsically disordered region (IDR), how ALK inhibitors affect the structure and dynamics of full-length EML4-ALK remains unclear. Here, using high-speed atomic force microscopy (HS-AFM), we visualize the overall structures of three full-length EML4-ALK variants (v1, v3, and v5) at the single-molecule level. We identified a transient globular subdomain (residues 191-217) within the v3 IDR that contributes to distinct oligomerization patterns. Notably, ALK inhibitors compact the IDR subdomain and reduce oligomerization, whereas this effect is abolished by the resistance mutation ALKG1202R, suggesting that ALK inhibitors not only affect kinase activity but also modulate IDR dynamics. Our findings shed new light on the structural regulation of EML4-ALK and provide a foundation for developing next-generation targeted therapies that account for IDR-driven molecular behavior. TeaserHigh-speed AFM revealed the full-length EML4-ALK structures and their IDR-mediated plasticity caused by ALK kinase inhibitors

cancer biology↗

bioRxiv2025

Regulation of macroautophagy and microautophagic lipophagy by phosphatidylserine synthase Cho1 and external ethanolamine

Phospholipids play crucial roles in autophagy; however, the underlying mechanisms remain elusive. We previously found that the phosphatidylserine (PtdSer) transporter Osh5 is critical for autophagosome formation. Therefore, in this study, we aimed to investigate the impact of the knockout of cho1, which encodes PtdSer synthase, on autophagy. Green fluorescent protein-autophagy-related gene 8 (GFP-Atg8) processing assay revealed a significant defect in the macroautophagic activity of the cho1{Delta} mutant, regardless of the presence or absence of ethanolamine (Etn). Notably, autophagosomes were absent in the cytosol, and macroautophagic bodies were not observed in the vacuoles of the starved cho1{Delta} mutant, underscoring the essential role of PtdSer synthesized using Cho1 in autophagosome biogenesis. In contrast, numerous microautophagic vesicles containing lipid droplets were observed in the vacuoles of cho1{Delta} mutants starved in the presence of Etn, suggesting the crucial role of phosphatidylethanolamine (PtdEtn) synthesized via the Kennedy pathway in microautophagic lipophagy when PtdSer synthesis using Cho1 is disrupted. Given recent evidence pointing to the involvement of the ubiquitination system in various autophagy-related processes, we also examined the role of ubiquitin-conjugating enzyme E2 gene ubc4. Moreover, microautophagic lipophagy was significantly diminished in starved cho1{Delta} yeast with ubc4 knockout. These findings suggest the critical role of Ubc4-mediated ubiquitination in facilitating microautophagic lipophagy of the vacuole in yeast cells.

cell biology↗

bioRxiv2025

Resin canal leakage underlying xylem dysfunction in pine wilt disease

During the course of pine wilt disease (PWD), xylem dysfunction is induced (in the absence of water stress) by invasion of pinewood nematodes (PWN) into resin canals, and the infected pine trees wilt. When PWNs are inoculated to Japanese black pine seedlings, massive embolisms develop at the inoculation site. The developmental process of massive embolization to form an embolized zone is not well understood. We studied the development of xylem dysfunction around the inoculation site of one-year-old stems of PWN-infected seedlings using a combination of compact MRI and cryo-SEM. We visualized pathological changes in tracheids and resin canals in the xylem, and found that embolisms occurred in PWN-inoculated seedlings at a negative hydraulic pressure of -0.5 MPa. Resin canals in healthy trees were filled with resin. In PWN-infected seedlings, abnormal embolisms and resin were observed around resin canal near the inoculation wound. Empty tracheids were observed more extensively than resin-filled tracheids. We suggest that abnormal embolisms and resin leakage occur from damages of resin canals. Resin may seep into the tracheids when cell wall of the axial and radial resin canals is crushed. These embolisms under high water potential are unavoidable under natural conditions.

plant biology↗

bioRxiv2025

Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A

In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organization remain incompletely understood. We previously demonstrated that simultaneous depletion of H3K9 methylation, H3K27me3, and H2A monoubiquitination in immortalized mouse embryonic fibroblasts (iMEFs) leads to heterochromatin weakening and alterations in nuclear compartments. However, the overall pattern of A/B compartments remains largely preserved even under these conditions, suggesting the involvement of unknown factors. Since histone deacetylation is a key factor in transcriptional repression, we investigated the impact of histone deacetylase (HDAC) inhibition on nuclear compartments by treating cells depleted of H3K9 methylation, H3K27me3, and H2A K119 monoubiquitylation (H2AK119ub/uH2A) with the HDAC inhibitor Trichostatin A (TSA). We performed Hi-C analysis to assess the nuclear compartment changes. Our results showed that, although TSA treatment globally increased H3K27ac levels, the difference in H3K27ac enrichment between A/B compartments remained evident, and nuclear compartments were minimally affected. These findings suggest that factors other than HDACs maintain nuclear compartmentalization when repressive chromatin modifications are depleted.

molecular biology↗

bioRxiv2025

H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity

The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging. However, the mechanisms controlling CTCF binding remain unclear. Here, we investigated the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We found that H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes were associated with alterations in 3D genome architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing aberrant CTCF binding. Additionally, while CTCF binding sites repressed by H3K9 methylation were bound by CTCF in early mouse embryos, those repressed by both H3K9 and H3K27 methylation remained inaccessible, with early embryonic-specific H3K27 methylation forming at these sites. These findings implicate that H3K27 methylation prevents abnormal CTCF binding in early embryos, ensuring proper genome organization during development.

molecular biology↗

bioRxiv2025

Evolutionary and structural basis of SLAM utilization in morbilliviruses - Its implications for host range and cross-species transmission

Morbilliviruses, including measles virus (MV), canine distemper virus (CDV), and cetacean morbillivirus, pose a significant threat to humans and animals. While the host range of morbilliviruses is generally well-defined, severe cross-species transmission events also have been reported. Their entry into immune cells, the primary targets of morbilliviruses, relies on the signaling lymphocytic activation molecule (SLAM), a receptor whose species-specific variations influence viral host range. However, the extent to which SLAM diversity is a barrier to cross-species transmission remains poorly understood. In this study, we systematically investigated SLAM-mediated host specificity. We found that most morbilliviruses efficiently utilize SLAM from multiple host species, except for human SLAM. Among the morbilliviruses tested, only MV efficiently utilized human SLAM. Bats are natural reservoirs for many zoonotic viruses. Recent discoveries of novel morbilliviruses in bats provide new insights into morbillivirus evolution. Bats may have played a significant role in morbillivirus evolution because bat (Myotis) SLAM also functioned as an efficient receptor for multiple morbilliviruses. Unlike other morbilliviruses, MV utilized Myotis bat SLAM inefficiently. We conducted an MV adaptation experiment with Myotis bat SLAM to better understand SLAM recognition by morbilliviruses. MV readily adapted to utilize Myotis bat SLAM by acquiring a single N187Y mutation in its hemagglutinin protein, and computational structural modeling and fragment molecular orbital calculations with molecular dynamics simulations revealed key interaction changes that facilitated MVs adaptation to Myotis bat SLAM. These findings highlight the adaptability of morbilliviruses in utilizing diverse animal SLAMs. Notably, hypothetical ancestral SLAMs reconstructed in this study acted as universal receptors for all morbilliviruses. These results reinforced that morbillivirus receptor usage is primarily supported by evolutionarily conserved structural features of SLAM, highlighting a molecular basis that enables morbilliviruses to rapidly adapt to diverse animal SLAMs. Author SummaryOur study explores how viruses in the genus morbillivirus, such as measles virus, canine distemper virus, and rinderpest virus, which are notorious for deadly outbreaks in humans and animals, can jump between species. The host range of morbilliviruses is significantly influenced by a receptor molecule on cell surfaces known as the signaling lymphocytic activating molecule (SLAM). By examining SLAMs from various animals, including humans, dolphins, dogs, seals, and bats, we observed how these viruses can infect or adapt to infect different hosts. We found that in some cases slight differences in SLAM may act as initial barriers to cross-species transmission. However, these viruses rapidly overcome such barriers, showing a remarkable ability to adapt. Our research highlights the importance of monitoring these viruses to predict and prevent potential cross-species infections, which is crucial for protecting public health and animal welfare over time.

microbiology↗

bioRxiv2025

H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation

Heterochromatin is a key architectural feature of eukaryotic chromosomes, essential for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organization remain incompletely understood. Histone H3 lysine 9 and lysine 27 trimethylation (H3K9me3 and H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Previously, we found that the redistribution of H3K27me3 following the loss of H3K9 methylation contributes to heterochromatin maintenance, while the simultaneous loss of both H3K27me3 and H3K9 methylation induces heterochromatin decondensation in mouse embryonic fibroblasts. However, nearly all B compartments were preserved despite the loss of these repressive chromatin modifications. These findings suggest that other factors are responsible for maintaining B compartments under these conditions. In this study, we explored the role of another repressive chromatin modification, PRC1-mediated H2A K119 monoubiquitylation (H2AK119ub/uH2A), in maintaining heterochromatin structure following the loss of H3K9/K27 methylation. We found that uH2A and H3K27me3 independently accumulate in the B compartments after the loss of H3K9 methylation in iMEFs and cooperatively maintain heterochromatin. Our data indicates that the PRC1-uH2A pathway contributes to maintain heterochromatin organization following the loss of H3K9/K27 methylation in mammalian cells.

molecular biology↗

bioRxiv2024

Executive control can query hidden human memories

When we try to retrieve a representation from visual long-term memory there is a chance that we will fail to recall seeing it even though the memory is stored in our brain. Here we show that although mechanisms of explicit memory retrieval are sometimes unable to retrieve stored memories, that mechanisms of executive control can quickly query memory and determine if a representation is stored therein. Our findings suggest that the representations stored in human memory that cannot be accessed explicitly at that moment are nonetheless directly accessible by the brains higher level control mechanisms.

neuroscience↗

bioRxiv2024

Facial Coloration as a Social Signal in a Neotropical Cichlid: Testing the Facial Expression Hypothesis

The face is a uniquely distinctive stimulus, encapsulating a wealth of information. Among the myriad of social cues conveyed by the face, emotional signals, known as facial expressions, are paramount not only for humans but also for numerous social animals. The evolution of facial expressions in these animals can also manifest in taxa other than mammals, as suggested by various studies highlighting the socio-ecological benefits of facial expressions. In this study, we elucidated the social function of facial coloration, determined by melanophores, in the neotropical social cichlid Symphysodon aequifasciatus. In this species, facial coloration exhibits instantaneous changes in response to varying social contexts. Through behavioral observations and experimental manipulation, we confirmed that facial coloration in S. aequifasciatus serves to attenuate unnecessary aggressive competition among conspecifics. Furthermore, we observed that the facial area subjected to coloration in this species is innervated by the adenosine triphosphate- and noradrenaline-ergic nervous system. These findings indicated that facial expression in S. aequifasciatus depends on the sympathetic nervous system and has evolved independently of mammalian facial expressions. Our study highlights teleost fishes as valuable animal models for exploring the universality of facial expressions and their underlying cognitive mechanisms in vertebrates.

animal behavior and cognition↗