Biology subjects

Sasaki, H.

Publications and source records attributed to Sasaki, H..

At least 19 recordsLinked to original sources

bioRxiv2026

The "glue-gun ant" Lordomyrma azumai uses an adhesive thread secretion to immobilize opponents

In stinging Hymenoptera, the poison gland and its vesicle have been understood largely as sources of toxic, irritating, or antimicrobial compounds, which the sting injects into a target. However, external uses of poison gland secretions have also been reported: Pseudoneoponera (formerly Pachycondyla) froth a proteinaceous poison gland secretion into foam threads that entangle attacking ants, and Crematogaster smear opponents with a contact toxin generated on a spatulate sting from poison and Dufour gland products4. Here we report that workers of the myrmicine ant Lordomyrma azumai produce, in the poison vesicle, a secretion, likely proteinaceous, that solidifies upon extrusion into an adhesive thread. The sting is retained as the conduit, but the secretion it delivers is applied externally rather than injected, and acts as a structural material: workers wipe the thread onto opponents and tether them to the substrate. To our knowledge, no hymenopteran venom secretion functions as a solid thread; in the closest case, Pseudoneoponera3, the secretion entangles attackers as a foam rather than as a continuous solid filament.

animal behavior and cognition↗

bioRxiv2026

High-plex protein imaging across thick tissue by synchronized amplification

High-plex protein imaging is essential for decoding complex tissue organization, yet it remains largely confined to thin sections. Current approaches in millimeter-thick samples suffer from poor signal penetration and depth-dependent, uneven signal amplification. Even with specialized instrumentation to facilitate probe diffusion, iterative millimeter-thick tissue workflows can take more than four days per staining round, and reported eleven-marker experiments extend beyond a month. We introduce Amplification by Cyclic Extension (ACE), a DNA-barcoded, synchronized in situ amplification strategy that uses thermally controlled cyclic extension to coordinate DNA concatemer growth across tissue depths. By synchronously activating and coordinating reaction progression throughout the sample, ACE enables controlled, uniform signal amplification across tissue depths. Using ACE, we demonstrate 63-plex protein and RNA imaging in thin sections, 22-plex protein imaging in 200 m mouse brain sections, and 16-plex protein imaging in 1 mm-thick brain tissue encompassing over three million cells. For millimeter-thick tissues, ACE reduces per-round target-switching time from multiple days to less than eight hours, shifting volumetric high-plex protein imaging from months to days. Together, these results establish ACE as a synchronized amplification strategy that enables scalable high-plex protein imaging in thick tissues.

bioengineering↗

bioRxiv2026

Identification of novel kolmioviruses in diverse invertebrates.

Kolmioviruses (KoVs; family Kolmioviridae) are circular, single-stranded RNA viruses that have recently been discovered in a wide range of animal species. However, invertebrate-associated KoVs have so far been identified only in termites and their diversity and evolution remain largely unexplored. Here, we comprehensively analyzed publicly available animal RNA-seq datasets and identified six novel KoVs associated with one fish and five invertebrate species: coho salmon (Oncorhynchus kisutch [Walbaum, 1792]), spotted babylon (Babylonia areolata [Link, 1807]), Atlantic pearl oyster (Pinctada imbricata [Roding, 1798]), small emerald moth (Hemistola chrysoprasaria [Esper, 1795]), codling moth (Cydia pomonella [Linnaeus, 1758]), and cocoa pod borer (Conopomorpha cramerella [Snellen, 1904]).

microbiology↗

bioRxiv2026

SOX2 terminates trophectoderm competence in inner cell mass by closing trophectoderm enhancers

During embryonic development, cellular competence to respond to differentiation signals changes dynamically. Although the mechanisms underlying competence acquisition have been extensively studied, those underlying competence loss remain unclear. In preimplantation mouse embryos, Hippo signaling shifts from regulating trophectoderm (TE) fate specification to promoting epiblast maturation. During the blastocyst stage, inner cell mass (ICM) cells lose TE competence in response to the Hippo signaling effector TEAD-YAP. Here, we show that the pioneer factor SOX2 terminates TE competence in the ICM. SOX2 binding to the TEAD-YAP-dependent TE enhancer (TEE) of the TE regulator Gata3 induces chromatin closure, suppressing TEE responsiveness to TEAD-YAP activity. This function of SOX2 requires its interaction with the corepressor TLE4 and histone deacetylase. Similar SOX2-dependent chromatin closure also occurs around other TE genes, including the TE enhancer of another TE regulator, Cdx2. Thus, SOX2 terminates TE competence in ICM cells by closing Hippo signaling-responsive enhancers.

developmental biology↗

bioRxiv2026

HIV-1 can undergo Env-independent retrotransposon-like activity

Retrovirus replication requires coordinated interplay between viral proteins and host cellular machinery, including reverse transcription of the viral RNA genome into DNA and its subsequent integration into the host genomes. SOX2-dependent retrotransposon dynamics have been reported for endogenous retrovirus HERV-K; however, whether a similar intracellular pathway exists for exogenous retroviruses remains unclear. To address whether infection-independent intracellular reverse transcription and partial integration can occur, that is, whether retrovirus can exhibit retrotransposon-like activity, we utilized HeLa and 293T cells, which express no HIV-1 entry receptors. We engineered an Env-deficient HIV-1 NL4-3-based reporter encoding a reverse-oriented, intron-disrupted nanoluciferase cassette that becomes expressible only after splicing followed by reverse transcription. We found that reporter activation depends on reverse transcriptase and protease activities. While integrase is dispensable for early expression, it is essential for long-term maintenance of the nanoluciferase signal. Integration site mapping using next-generation sequencing further confirmed that stable reporter activity requires integrase-dependent proviral insertion. Functional analysis of Gag revealed that membrane binding, multimerization, and budding are prerequisite steps for reporter activation. Concentrated virus preparations from culture supernatants failed to activate the reporter in 293T cells, ruling out a role for reinfection. Electron and confocal microscopy suggested that Gag or viral particles traffic through endosomal compartments. Furthermore, inhibition of dynamin- and clathrin-dependent endocytic pathways reduced reporter activity, indicating that these pathways contribute to efficient reporter activity. Collectively, these finding support the conclusion that HIV-1 can undergo intracellular reverse transcription and partial integration in an infection-independent manner, prompting a reconsideration of the boundary between exogenous retroviruses and endogenous retroelements. Author summaryEnv-independent, infection-independent intracellular reverse transcription and integration in HIV-1 may contribute to integration-site diversity within the same cell. More broadly, this phenomenon suggests continuity between the retroviral life cycle and retrotransposition dynamics, therefore informing our understanding of host-virus coevolution, mechanisms of long-term persistence, and the redesign of therapeutic strategies targeting pre-integration steps.

microbiology↗

bioRxiv2026

Metatranscriptome data support the existence of two distinct morphotypes in a single parmalean species in natural environments

Parmales (Bolidophyceae), the closest relatives of diatoms, includes isolates exhibiting one of two distinct morphotypes: a silicified non-flagellated form (S-type) and a naked flagellated form (F-type). Although alternation of these two forms for a single isolate has not been formally established, previous studies hypothesized that these morphotypes represent alternating stages of a single parmalean. In this study, we investigated the global expression patterns of S- and F-type marker genes by integrating parmalean Metagenome-Assembled Genomes (MAGs) and the metatranscriptomic dataset from Tara Oceans. We detected the expression of both S- and F-type marker genes from individual environmental MAGs. This finding provides the first metatranscriptomic evidence that natural parmalean genomes possess the potential to manifest both morphotypes. Furthermore, our analysis revealed different geographical expression patterns between the two forms. The expression of F-type markers showed a broad distribution, whereas that of S-type markers was more restricted, suggesting distinct niches for the two morpho-phases. Moreover, S-type gene expression appears to require specific environmental triggers that lead to a higher population density, whereas F-type expression is rather constitutively maintained. Overall, our results support the hypothesis of a life cycle involving morphological switching and reconcile the long-standing discrepancy between the ubiquity of parmaleans in molecular surveys and the limited geographical range for the observation of silicified cells. Based on these patterns, we propose a threshold-based model in which F-type-dominated populations persist under conditions unfavorable for growth and a morphological switch to the S-type is triggered once environmental conditions exceed a critical threshold for growth.

microbiology↗

bioRxiv2025

Identification of a novel nidovirus in the common chameleon (Chamaeleo chamaeleon recticrista )

Nidoviruses (the order Nidovirales) are positive strand RNA viruses, and the order currently contains 14 families, 48 genera, and 130 species. Novel nidoviruses have been identified in a variety of animal hosts, but many phylogenetic gaps remain, suggesting the presence of yet-to-be-identified viruses. In this study, we identified a novel nidovirus from publicly available RNA-seq data obtained from the blood of the common chameleon (Chamaeleo chamaeleon recticrista [Boettger, 1880]), and tentatively named it common chameleon nidovirus 1 (CCNV-1). Phylogenetic analysis showed that CCNV-1 is clustered with a member of the family Nanhypoviridae and some unclassified viruses designated as arteriviruses. Further, CCNV-1 genetically distinct from known viruses, exhibiting 50.9% amino acid identity in the RdRp sequence to its closest relative, Jingmen rodent arterivirus 1. Thus, this study provides novel insights into the diversity of nidoviruses.

microbiology↗

bioRxiv2025

Lenacapavir binding to immature Gag triggers the emergence of giant HIV-1 virions

Lenacapavir (LEN), a potent capsid inhibitor, suppresses reverse transcription and nuclear import by disrupting capsid core formation in human immunodeficiency virus type 1 (HIV-1). However, its effect on the late-stage viral assembly remains unclear. Although p24 ELISA suggested that LEN inhibited HIV-1, both RT-dPCR and Vpr-HiBiT assays indicated no reduction in the viral output. This discrepancy was attributed to LEN-induced epitope masking of p24, which was reversed by altered sample processing. Furthermore, LEN induced numerous abnormal, discrete clusters of Gag at the plasma membrane. Mass photometry and transmission electron microscopy revealed heterogeneous viral-like particles (LENiVLPs; diameter >200 nm), containing both Gag and Env proteins. Although LENiVLPs retained membrane fusion capability, they were non-infectious owing to post-entry defects. Thus, LEN binds to the precursor Gag and promotes aberrant particle formation, offering novel insights that could guide the development of next-generation LEN-based therapeutics targeting the late stages of the viral life cycle.

microbiology↗

bioRxiv2024

A deletion at the X-linked ARHGAP36 gene locus is associated with the orange coloration of tortoiseshell and calico cats

The X-linked orange (O) locus in domestic cats controls an unknown molecular mechanism that causes the suppression of black-brownish pigmentation in favor of orange coloration. The alternating black-brownish and orange patches seen in tortoiseshell and calico cats are considered as classic examples of the phenotypic expression of random X-chromosome inactivation (XCI) occurring in female mammals. However, the O gene in the cat genome has not been identified, and the genetic variation responsible for the orange coloration remains unknown. We report here that a 5.1-kilobase (kb) deletion within an intron of the X-linked ARHGAP36 gene, encoding a Rho GTPase activating protein, is closely and exclusively associated with orange coloration. The deleted region contains a highly conserved putative regulatory element, whose removal presumably cause altered ARHGAP36 expression. Notably, ARHGAP36 expression in cat skin tissues is linked to the suppression of many melanogenesis genes, potentially shifting pigment synthesis from eumelanin to pheomelanin. Furthermore, we find evidence that the gene undergoes XCI in female human and mouse cells, and XCI-dependent CpG island methylation consistent with random XCI in female domestic cats. The 5.1-kb deletion seems widespread in domestic cats with orange coat coloration, suggesting a single origin of this coat color phenotype.

genetics↗

bioRxiv2024

Cholesterol sulfate prevents maternal-fetal conflict by locally modulating immune reactivity

Although placental mammals are at high risk of maternal-fetal immune conflict, it is unclear how the semi-allogeneic fetus avoids rejection. Cholesterol sulfate (CS) is a bioactive metabolite that inhibits leukocyte migration and activation. This study investigated the roles and cells associated with CS in pregnant mice and humans. CS was sequentially produced by maternal-derived endometrial cells and fetal-derived placental trophoblasts before and after placentation. When mated with allogeneic males, CS-deficient mice showed increased fetal resorption rates under induced placental inflammation. This phenotype disappeared when the activity of the CS-producing enzyme was restored in the placenta. Placental CS levels were reduced in patients with "villitis of unknown etiology." Thus, we uncovered the spatiotemporal control of CS production and its relevance to local immunosuppression during pregnancy.

immunology↗

bioRxiv2024

Blastocoel expansion and AMOT degradation cooperatively promote YAP nuclear localization during epiblast formation

The epiblast is a pluripotent cell population formed in the late blastocyst stage of preimplantation embryos. During the process of epiblast formation from the inner cell mass (ICM) of the early blastocyst, activation of the Hippo pathway transcription factor TEAD by the nuclear translocation of the coactivator protein YAP is required for the robust expression of pluripotency factors. However, the mechanisms that alter YAP localization during epiblast formation remain unknown. Here, we reveal two such mechanisms. Expansion of the blastocoel promotes nuclear YAP localization by increasing cytoplasmic F-actin and reducing YAP phosphorylation. Additionally, cell differentiation regulates YAP. Expression of the junctional Hippo component, AMOT, gradually decreases during epiblast formation through a tankyrase-mediated degradation. SOX2 expression in the ICM is necessary for the reduction of AMOT and YAP phosphorylation. These two mechanisms function in parallel. Thus, the blastocoel-F-actin and SOX2-AMOT axes cooperatively suppress YAP phosphorylation and promote YAP nuclear localization during epiblast formation. The cooperation of these two distinct mechanisms likely contributes to the robustness of epiblast cell differentiation.

developmental biology↗

bioRxiv2024

Fate specification triggers a positive feedback loop of TEAD-YAP and NANOG to promote epiblast formation in preimplantation embryos

In preimplantation embryos, epiblast (EPI) fate specification from the inner cell mass is controlled by the segregation of NANOG and GATA6 expression. TEAD-YAP interaction is activated during EPI formation, and is required for pluripotency factor expression. These events occur asynchronously with similar timing during EPI formation, and their relationship remains elusive. Here, we examined the relationship between NANOG-GATA6 and TEAD-YAP. The nuclear accumulation of YAP takes place only in EPI-specified cells, and a positive feedback loop operates between NANOG and TEAD-YAP. The effects of TEAD-YAP on SOX2 upregulation in EPI-specified cells are likely indirect. EPI fate specification also alters the response of Nanog, Sox2 and Cdx2 to TEAD-YAP. These results suggest that EPI-fate specification alters the transcriptional network from the morula-like to the EPI-specified state and activates TEAD-YAP to trigger a positive feedback loop with NANOG, which stabilizes the EPI fate. The coordinated occurrence of these processes in individual cells likely supports proper EPI formation under the condition of asynchronous EPI-fate specification. Summary statementEpiblast fate specification by segregation of NANOG from GATA6 alters the transcriptional network and activates TEAD-YAP, triggering a positive feedback loop with NANOG to promote epiblast formation.

developmental biology↗

bioRxiv2024

CENP-C-Mis12 complex establishes a regulatory loop through Aurora B for chromosome segregation

Establishing the correct kinetochore-microtubule attachment is crucial for faithful chromosome segregation. The kinetochore has various regulatory mechanisms for establishing correct bipolar attachment. However, how the regulations are coupled is not fully understood. Here, we demonstrate a regulatory loop between the kinetochore protein CENP-C and Aurora B kinase, which is critical for the error correction of kinetochore-microtubule attachment. This regulatory loop is mediated through the binding of CENP-C to the outer kinetochore Mis12 complex (Mis12C). Although the Mis12C binding region of CENP-C is dispensable for mouse development and proliferation in human RPE-1 cells, those cells lacking this region display increased mitotic defects. The CENP-C-Mis12C interaction facilitates the centromeric recruitment of Aurora B and the mitotic error correction in human cells. Given that Aurora B reinforces the CENP-C-Mis12C interaction, our findings reveal a positive regulatory loop between Aurora B recruitment and the CENP-C-Mis12C interaction, which ensures chromosome bi-orientation for accurate chromosome segregation.

cell biology↗

bioRxiv2024

Cellulose Rich Food Leads Anxiety through Gut-Brain Axis-mediated Amygdalar Dopamine Upregulation.

It is widely said that healthy intestinal environment takes essential role for better mental condition. One of the known dietary nutrients which maintains intestinal environment is the dietary fiber. Recent study showed that maintaining intestinal environment by dietary fiber succeeded to alleviate the psychiatric disorder symptoms in animals. However, such effects have only been reported with soluble fiber, which is highly fermentable and promotes short-chain fatty acid (SCFA) production, and not with insoluble fiber. Therefore, we aimed to verify whether insoluble fiber, such as cellulose, can alter emotion via changes in the gut. We divided mice into two groups and fed either standard diet (SD, contains both insoluble and soluble dietary fibers) or cellulose rich diet (CRD, contains cellulose alone as the dietary fibers). The CRD-fed mice displayed 1) the increased the anxiety-like behavior accompanied with 2) the modified amygdalar dopamine signaling. We further found the decreased intestinal SCFA levels along with intestinal permeability, dysmotility and hypersensitivity in CRD-fed mice. These behavioral and physiological effect of CRD has been completely abolished in vagotomized mice, indicating the direct link between intestinal environment exacerbation to the emotion through gut-brain axis. Additionally, the opioid antagonist abolished the CRD-induced anxiety, suggesting the involvement of opioidergic system to the anxiety which may evoked by increased amygdalar dopamine levels. Altogether, our findings suggest that consumption of cellulose alone as the dietary fiber may evoke intestinal abnormalities which fires the vagus nerve then opiodergic system and amygdalar dopamine upregulation, resulting in the enhancement of anxiety. Graphical Abstract: Possible mechanism of CRD-induced anxiety unveiled by current studyOur study clarified that long-consumption of cellulose-rich food (CRD) will lead decrease of SCFAs which may cause the intestinal disability, including decreased motility and increased intestinal permeability as well as upregulation of TRPA1 and SGLT1. These physiological modifications resulted as the intestinal hypersensitivity, which possibly overstimulate the vagal transmission which may activate endogenous opioidergic systems such as enkephalin (Enk) at the nucleus tractus solitarii (NTS). The activation of opioidergic system may suppress the GABAergic neuron in ventral tegmental area (VTA), resulting in the excess release of dopamine and further receptor modification in amygdala (Amyg), which might in the end cause the characteristic anxiety. The figure was created with BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/593082v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1a0c4aborg.highwire.dtl.DTLVardef@1cfefceorg.highwire.dtl.DTLVardef@88cfc0org.highwire.dtl.DTLVardef@1ff5b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Immunogenicity and safety of a live-attenuated SARS-CoV-2 vaccine candidate based on multiple attenuation mechanisms

mRNA vaccines against SARS-CoV-2 were rapidly developed and effective during the pandemic. However, some limitations remain to be resolved, such as the short-lived induced immune response and certain adverse effects. Therefore, there is an urgent need to develop new vaccines that address these issues. While live-attenuated vaccines are a highly effective modality, they pose a risk of adverse effects, including virulence reversion. In the current study, we constructed a live-attenuated vaccine candidate, BK2102, combining naturally occurring virulence-attenuating mutations in the NSP14, NSP1, spike and ORF7-8 coding regions. Intranasal inoculation with BK2102 induced humoral and cellular immune responses in Syrian hamsters without apparent tissue damage in the lungs, leading to protection against a SARS-CoV-2 D614G and an Omicron BA.5 strains. The neutralizing antibodies induced by BK2102 persisted for up to 364 days, which indicated that they confer long-term protection against infection. Furthermore, we confirmed the safety of BK2102 using transgenic (Tg) mice expressing human ACE2 (hACE2), that are highly susceptible to SARS-CoV-2. BK2102 did not kill the Tg mice, even when virus was administered at a dose of 106 plaque-forming units (PFU), while 102 PFU of the D614G strain or an attenuated strain lacking the furin cleavage site (FCS) of the spike was sufficient to kill mice. These results suggest that BK2102 is a promising live-vaccine candidate strain that confers long-term protection without significant virulence.

microbiology↗

bioRxiv2024

Nobiletin, a Polymethoxyflavonoid, Activates the Desuccinylase Activity of SIRT5 and Prevents the Development of Heart Failure

Nobiletin is a natural compound useful for the prevention and treatment of several diseases. However, the precise role of nobiletin in heart failure is unclear. Nobiletin treatment prevents pressure overload- and myocardial infarction-induced heart failure. Using affinity purification of biotinylated nobiletin from rat heart cell lysates, we identified sirtuin 5 (SIRT5) as a novel nobiletin-binding protein. Nobiletin enhanced the desuccinylase activity of SIRT5 in vitro. Compared to wild-type mice, SIRT5-overexpressing transgenic mice resisted pressure overload-induced systolic dysfunction. Conversely, SIRT5 knockout disrupted the nobiletin-mediated therapeutic effects on heart failure in mice. SIRT5 desuccinylated p300 at lysine 1568 and reduced the histone acetyltransferase (HAT) activity of p300. The desuccinylated p300 mutant suppressed the phenylephrine-induced cardiomyocyte hypertrophic responses. These findings suggest that nobiletin prevents heart failure development through SIRT5-dependent inhibition of p300-HAT activity. Nobiletin, a nontoxic dietary compound, is a potential therapeutic agent for heart failure in humans.

molecular biology↗

bioRxiv2023

Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells

DNA methyltransferase 3A (DNMT3A) and its catalytically inactive cofactor DNA methyltransferase 3-Like (DNMT3L) proteins form functional heterotetramers to deposit DNA methylation in mammalian germ cells. While both proteins have an ATRX-DNMT3-DNMT3L (ADD) domain that recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0), the combined and differential roles of the domains in the two proteins have not been fully defined in vivo. Here we investigate DNA methylation landscapes in female and male germ cells derived from mice with loss-of-function amino acid substitutions in the ADD domains of DNMT3A and/or DNMT3L. Mutations in either the DNMT3A-ADD or the DNMT3L-ADD domain moderately decreases global CG methylation levels, but to different degrees, in both germ cells. Furthermore, when the ADD domains of both DNMT3A and DNMT3L lose their functions, the CG methylation levels are much more reduced, especially in oocytes, comparable to the impact of the Dnmt3a/3L knockout. In contrast, aberrant accumulation of non-CG methylation occurs at thousands of genomic regions in the double mutant oocytes and spermatozoa. These results highlight the critical role of the ADD-H3K4me0 binding in proper CG and non-CG methylation in germ cells and the various impacts of the ADD domains of the two proteins.

cell biology↗

bioRxiv2022

Three-dimensional structured illumination microscopy with enhanced axial resolution

We present two distinct, complementary methods for improving axial resolution in three-dimensional structured illumination microscopy (3D SIM) with minimal or no modification to the optical system. First, we show that placing a mirror directly opposite the sample enables 4-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with [~]120 nm lateral and 160 nm axial resolution. Second, we develop an improved deep learning method that can be directly applied to 3D SIM data, obviating the need for additional hardware. This procedure results in [~]120 nm isotropic resolution and can be combined with denoising to facilitate volumetric imaging spanning dozens of time points. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers, and visualizing rich cytoskeletal dynamics within T-cells in the early stages of immune synapse formation.

cell biology↗