Biology subjects

Ando, K.

Publications and source records attributed to Ando, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Optimization of breeding conditions in Danionella cerebrum to advance its use as a vertebrate model

We systematically evaluated tank configuration and spawning-tube parameters to improve egg production and collection efficiency in Danionella cerebrum. A shallow breeding tank with a black bottom significantly increased egg production while facilitating egg collection. Further optimization of spawning-tube parameters revealed a strong effect of tube diameter on reproductive performance, with narrower tubes improving fertilization efficiency and a 4-mm inner diameter yielding the highest egg production. Longer tubes also tended to increase egg production, although the difference between 5- and 10-cm tubes was not significant. While 5-cm tubes facilitated routine egg collection, the trend toward higher egg production and greater water volume of 10-cm tubes enabled short-term in-tube embryo culture, providing an alternative workflow when frequent egg collection is unnecessary. Notably, increasing the number of available spawning tubes did not further enhance egg production; instead, analysis of tube usage revealed a preference for previously used spawning sites. Together, these findings establish practical breeding parameters that improve reproductive output and streamline egg collection and embryo handling in D. cerebrum.

developmental biology↗

bioRxiv2026

The 329HHK331 motif is essential for Alzheimer's disease tau filament fold

Cryo-electron microscopy (cryo-EM) has revealed disease-specific tau filament folds, yet the local sequence elements that determine them remain poorly understood. Here we focused on the 329HHK331 motif near an inter-protofilament interface in Alzheimers disease (AD)-type tau filaments, and analyzed recombinant dGAE filaments of wild-type (WT) and mutants in this motif. All mutants formed amyloid-like filaments in vitro, but their morphologies differed. In cultured cells, WT filaments efficiently seeded WT tau aggregation. Filaments with three-residue changes (deletion or Ala substitution) showed almost no seeding activity, whereas two-residue deletions retained partial activity. Cryo-EM showed that WT dGAE filaments form a quadruple helical filament of two protofilament dimers. Each dimer comprises two C-shaped protofilaments, centered on a 333GGG335-mediated inter-protofilament interaction and supported by flanking 329HHK331-336QVE338 contacts. Three-residue alterations abolished interactions with the QVE motif at the protofilament interface, thereby displacing 333GGG335 and forming non-C-shaped protofilament structures that are intrinsically poor templates for tau seeding. By contrast, two-residue deletions maintained the C-shaped protofilament structure because the remaining residue formed alternative inter-protofilament interactions. These findings suggest that the 329HHK331 region is a key determinant of the AD-like C-shaped protofilament fold and link this motif to tau seeding, providing insight into disease-specific tau filament formation.

neuroscience↗

bioRxiv2026

Mural cell contractility regulates vessel diameter by controlling cell morphology and vessel coverage

Mural cells are key regulators of vascular architecture, yet how their contractility and morphology jointly influence vessel diameter in vivo remains poorly understood. Here, using high-resolution live imaging and single-cell morphometric analysis in zebrafish, we show that vascular smooth muscle cells (vSMCs) and pericytes undergo a developmental reduction in cell size through the progressive retraction of actin-rich primary and secondary processes during vascular remodelling. By specifically manipulating RhoA activity to alter mural cell contractility and shape, we uncover vessel-specific roles for mural cells in diameter regulation. We find that vSMC contractility is dispensable for the initial constriction of the dorsal aorta but is required to stabilise its diameter following vasoconstriction and to maintain vascular tone. In contrast, pericyte contractility is dispensable for both the constriction and stabilisation of intersegmental vessels. In the brain vasculature, vessel diameter is governed by the balance between contractile force and the extent of vessel coverage by vSMCs. Together, our findings redefine the role of mural cell contractility in the control of vessel constraint, demonstrating that morphology and vessel coverage, rather than contractility alone, are key determinants of vascular diameter in vivo.

cell biology↗

bioRxiv2026

Temporal regulation of G2 phase avoids therapy-induced senescence caused by DNA replication stress-inducing drugs and provides synergistic cytotoxicity

The cellular response to DNA replication stress (DRS) provoked by anticancer drugs involves activation of the G2/M checkpoint (which promotes transient cell cycle arrest at G2 phase) and DNA repair, followed by induction of apoptosis or senescence. Here, we activated the p53-p21 pathway and ATR using DRS-inducing drugs, and found that that the transition to senescence depends on the duration of the G2 phase. Shortening of G2 duration by G2/M checkpoint inhibitors led not only to a switch in cell fate from senescence to mitotic entry, but also to effective cell death through carry-over of chromosomal aberrations (generated by DRS-inducing drugs) into mitosis and subsequent mitotic progression. Such enhanced cell death was also observed in p53 deficient cells, which do not normally undergo senescence. Thus, we propose that temporal regulation of G2 phase is an approach to enhancing the effects of DRS-inducing drugs in a manner that is independent of p53 status.

cell biology↗

bioRxiv2026

Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes

Skeletal muscle plays important locomotive and metabolic functions, yet its formation and maintenance are processes remaining largely unclear mechanistically in any animal. Teleost fishes display extraordinary muscle growth due to their ability to undergo both hyperplasia and hypertrophy throughout life. These phenomena vary greatly even between closely related species, providing opportunities to elucidate growth dynamics and underlying mechanisms through cross-species comparisons. Using histological and genetic approaches, we compared muscle growth dynamics in three closely related danionin species with distinct growth capacities: the giant danio (Devario malabaricus), the zebrafish (Danio rerio), and Danionella cerebrum, as well as the more distantly related African turquoise killifish (Nothobranchius furzeri). Our study reveals alterations in spatial patterning of muscle hyperplasia and developmental timing to be major contributors to observed differences in muscle growth between examined species. Single-cell RNA profiling, in situ hybridization chain reaction and cell type-specific mutagenesis revealed muscle stem cell-specific expression of extracellular matrix genes that mediate stem cell activity, which in turn may drive growth differences between species. Taken together, our findings highlight autonomous regulation of muscle stem cells as a conserved but adaptable mechanism governing muscle patterning and diversification.

evolutionary biology↗

bioRxiv2025

Live visualization of extracellular matrix dynamics during development and regeneration in zebrafish

Extracellular matrix (ECM) plays fundamental roles in animal development, regeneration, and disease. The difficulty of tagging endogenous matrix proteins in vertebrates has limited the understanding of ECM composition and dynamics in complex tissues. To visualize vertebrate ECM components, we tagged zebrafish Laminin, gamma 1 (Lamc1), Collagen, type I, alpha 2 (Col1a2), and Transforming growth factor, beta-induced (Tgfbi) using C-terminus in-fusion genome editing. Analysis of these knock-in lines revealed distinct expression of each protein in various tissues during development and regeneration. Fluorescent recover after photobleaching (FRAP) analysis further indicated that Lamc1 is stable in fin fold matrix but more dynamic in myoseptal matrix of developing zebrafish, while Col1a2 and Tgfbi are stable matrix components in myosepta. Strikingly, we found that Col1a2-mScarlet protein accumulates at the amputation plane during tailfin regeneration, where it remains concentrated for several days and distant from the regeneration blastema. This "foundation" region also displayed a distinct transcriptome suggesting active and dedicated events at the base of the regenerating appendage. Our resource enables live capture of ECM dynamics that can identify new events in developing and regenerating zebrafish. Summary statementExtracellular matrix resources for zebrafish development and tissue regeneration.

developmental biology↗

bioRxiv2025

Buffering of genetic defects in animal development by regeneration programs

Regeneration programs enable animals to restore damaged or lost tissues, and the range of stimuli for these programs is incompletely understood. Here, we used zebrafish, a vertebrate species with exceptional regenerative capacity, to identify chemically induced mutations that alter regeneration-associated gene activation. Transgenic zebrafish with a permissive promoter and EGFP cassette inserted in the vicinity of the pro-regenerative factor gene fgf20a were mutagenized, and larvae homozygous for ENU-induced mutations were assessed for disruptions in fgf20a-directed reporter gene expression following fin fold amputation. One line was identified with heritable, elevated fgf20a:EGFP presence in the absence of experimental injury, localized to regions of fin fold tissue undergoing degeneration. Whole-genome sequencing (WGS) identified a mutation within exon 72 of the fraser syndrome 1 (fras1) gene, mutated in patients with inherited skin disease. fras1 mutant larvae spontaneously displayed elevated expression of other known injury/regeneration-responsive reporter lines in fin fold, and zebrafish crispants for homologs of other genes mutated in human developmental diseases also displayed regeneration-associated gene expression in regions of dysmorphology. Tempering Fgf signaling by transgenic expression of a dominant-negative Fgf receptor in fras1 mutants exacerbated the disease phenotype. Our findings provide evidence that regeneration programs are harnessed in response to developmental defects caused by genetic mutations, potentially buffering deleterious phenotypes.

developmental biology↗

bioRxiv2025

Single-cell-level digital twins for preterm birth prevention strategies

Digital twin models can accelerate therapeutic development by enabling low-risk testing of candidate interventions. In preterm labor (PTL), a major pregnancy complication where clinical trials face unique ethical and financial barriers, digital twins are especially valuable for evaluating new therapies targeting immune dysfunctions driving PTL. Yet, current models lack single-cell resolution, limiting detection of cell-type-specific mechanisms, off-target effects, and the design of personalized interventions. We present Simulated Immunome Modeling of Clinical Outcomes (SIMCO), a single-cell-level digital twin framework that models immunomodulatory treatment effects on the timing of labor using immunome-wide, single-cell simulations. SIMCOs digital twins are trained and validated on a newly generated mass cytometry atlas of the pregnant immunome exposed to nine candidate drugs preselected for PTL prevention. Applying SIMCO to an independent cohort of pregnant individuals, we simulate treatment effects on gestational length, screening for candidate drugs that delay labor timing and providing system-level mechanistic insight for each drug candidate. Tetrahydrofolate, maprotiline, and the combination of aspirin and lansoprazole emerged as top candidates for PTL prevention, delaying labor onset primarily through enhanced mTOR signaling in innate immune cells and attenuated JAK/STAT signaling in naive CD4 T cells. The codebase is available at https://github.com/ofondeur/SIMCO/.

immunology↗

bioRxiv2025

MARK2 in glial cells suppresses inflammatory responses and mitigates tau toxicity

Neuroinflammation is a pathological hallmark of Alzheimers disease and related neurodegenerative diseases. However, signaling molecules that regulate glial activation status are not fully understood. Microtubule affinity-regulating kinase 2 (MARK2) has been implicated in both immune responses and AD pathology. Here, we report that MARK2 negatively regulates glial immune responses, which protects against neurodegeneration. We found that MARK2 knockdown in the BV2 murine microglial cell line enhanced IL-6 expression in response to LPS. MARK2 knockdown enhanced IL-6 expression induced by TLR7 agonist but not stimulation of RLR pathways and cGAS-STING. In the brains of PS19 tauopathy mice, MARK2 was elevated in homeostatic microglia but reduced in activated microglia. In Drosophila expressing human tau in the retina, expression of AMP downstream of the Toll pathway in the pigment glia enhances degeneration of photoreceptor neurons. Glial knockdown of Par-1, the Drosophila ortholog of MARK2, enhanced Toll-mediated AMP expression and neurodegeneration, whereas overexpression of Par-1 in the pigment glia suppressed them. These results suggest that MARK2/Par-1 in glia negatively regulates Toll pathway-driven inflammation and protects against tau-induced neurodegeneration. These findings provide insight into the molecular underpinnings of glial inflammation in neurodegenerative conditions and highlight MARK2 as a potential therapeutic target for modulating neuroinflammatory responses.

neuroscience↗

bioRxiv2025

MARK4 enhances stress granule formation and increases tau accumulation

Stress granules (SGs) are membrane-less organelles that are formed in response to cellular stress. SG formation protects cells against stress; however, their dysregulation and longer persistence may disrupt proteostasis. Abnormal activity of Microtubule-affinity regulating kinase 4 (MARK4) has been linked to cancer and Alzheimers disease. Here, we report that MARK4 is a component of SGs and enhances SG formation. MARK4 is found in SGs in mammalian cultured cells and primary neurons with T-cell intracellular antigen 1 (TIA1). MARK4 expression enhances SG formation induced by hydrogen peroxide. The spacer domain of MARK4 mediates its localization to SGs, and its kinase activity is required for the enhancement of SG formation. MARK4 suppresses TIA1 dimerization induced by hydrogen peroxide. Furthermore, we found that MARK4 and TIA1 synergistically promoted tau accumulation in cultured cells, and knockdown of a fly TIA1 homolog suppressed tau toxicity in a Drosophila model. These results indicate that MARK4 regulates TIA1 and SG formation and suggest that MARK4 and TIA1 synergistically contribute to tau toxicity.

cell biology↗

bioRxiv2025

IAP antagonists potentiate TNFα-triggered apoptosis but selectively eliminate senescent tumor cells independently of TNFα

Therapy-induced senescence (TIS) is a state of cell division arrest induced by chemotherapy that blocks tumor growth. TIS tumor cells affect the tumor microenvironment through their senescence-associated secretory phenotype and independently acquire stemness, which makes them more aggressive and causes relapse once they regrow. To eradicate tumors by chemotherapy, long-lived TIS tumor cells must be efficiently eliminated. Here, we show that AZD5582 and AT406, which are potent antagonists of inhibitor of apoptosis proteins (IAP antagonists) that suppress the activities of cellular inhibitor of apoptosis protein 1 (cIAP1), cellular inhibitor of apoptosis protein 2 (cIAP2), and X-linked inhibitor of apoptosis protein (XIAP), selectively induced apoptosis mediated by caspase 8 and effector caspases in TIS tumor cells, which produced and secreted tumor necrosis factor (TNF). However, these IAP antagonists were still selectively cytotoxic to TIS tumor cells even when TNF was absent (TNF-knockout cells) or neutralized (by a neutralizing antibody), indicating they have TNF-independent senolytic activity. Consistently, these IAP antagonists also sensitized tumor cells that had been induced to become senescent by nutlin-3a, which activates p53 but does not trigger TNF production. Furthermore, TNF sensitized tumor cells treated with these IAP antagonists irrespective of their senescence status. Collectively, these data indicate that IAP antagonists that inhibit cIAPs and XIAP not only potentiate TNF-triggered apoptosis but also have TNF-independent senolytic activity. We propose that IAP antagonists are good concomitant drugs of chemotherapy that induces TIS, not only as senolytic drugs but also as sensitizers of adjacent non-senescent tumor cells mediated by paracrine TNF.

cancer biology↗

bioRxiv2025

Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration

Regeneration of an amputated salamander limb or fish fin restores pre-injury size and structure, illustrating the phenomenon of positional memory. Although appreciated for centuries, the identity of position-dependent cues and how they control tissue growth are not resolved. Here, we quantify Erk signaling events in whole populations of osteoblasts during zebrafish fin regeneration. We find that osteoblast Erk activity is dependent on Fgf receptor signaling and organized into millimeter-long gradients that extend from the distal tip to the amputation site. Erk activity scales with the amount of tissue amputated, predicts the likelihood of osteoblast cycling, and predicts the size of regenerated skeletal structures. Mathematical modeling suggests gradients are established by the transient deposition of long-lived ligands that are transported by tissue growth. This concept is supported by the observed scaling of expression of the essential epidermal ligand fgf20a with extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signaling and cycling to control skeletal size in regenerating appendages.

developmental biology↗

bioRxiv2024

Glucose uptake in pigment glia suppresses tau-induced inflammation and photoreceptor degeneration in Drosophila

Brain inflammation contributes to the pathogenesis of neurodegenerative diseases such as Alzheimers disease (AD). Glucose hypometabolism and glial activation are pathological features seen in AD brains; however, the connection between the two is not fully understood. Using a Drosophila model of AD, we identified that glucose metabolism in glia plays a critical role in neuroinflammation under disease conditions. Expression of human Tau in the retinal cells, including photoreceptor neurons and pigment glia, causes photoreceptor degeneration accompanied by inclusion formation and swelling of the lamina cortex. We found that inclusions are formed by glial phagocytosis, and swelling of the laminal cortex correlates with the expression of antimicrobial peptides. Co-expression of human glucose transporter 3 (GLUT3) with Tau in the retina does not affect tau levels but suppresses these inflammatory responses and photoreceptor degeneration. We also found that expression of GLUT3, specifically in the pigment glia, is sufficient to suppress inflammatory phenotypes and mitigate photoreceptor degeneration in the tau-expressing retina. Our results suggest that glial glucose metabolism contributes to inflammatory responses and neurodegeneration in tauopathy. Summary StatementGlucose uptake into pigment glia suppresses inflammatory responses and photoreceptor degeneration in the fly model of tauopathy.

neuroscience↗

bioRxiv2024

A single microRNA miR-195 rescues the arrested B cell development induced by EBF1 deficiency

Accumulated studies have reported that hematopoietic differentiation was primarily regulated by transcription factors. Early B cell factor 1 (EBF1) is an essential transcription factor for B lymphopoiesis. Contrary to the canonical notion, we found that a single miRNA, miRNA-195 (miR-195) transduction let EBF1 deficient hematopoietic progenitor cells (HPCs) express CD19, carry out V(D)J recombination and class switch recombination, which implied that B cell matured without EBF1. A part of the mechanism was caused by FOXO1 accumulation via inhibition of FOXO1 phosphorylation pathways in which targets of miR-195 are enriched. These results suggested that some miRNA transductions could function as alternatives to transcription factors.

immunology↗

bioRxiv2024

An immune signature of postoperative cognitive decline in elderly patients

Postoperative cognitive decline (POCD) is the predominant complication affecting elderly patients following major surgery, yet its prediction and prevention remain challenging. Understanding biological processes underlying the pathogenesis of POCD is essential for identifying mechanistic biomarkers to advance diagnostics and therapeutics. This longitudinal study involving 26 elderly patients undergoing orthopedic surgery aimed to characterize the impact of peripheral immune cell responses to surgical trauma on POCD. Trajectory analyses of single-cell mass cytometry data highlighted early JAK/STAT signaling exacerbation and diminished MyD88 signaling post-surgery in patients who developed POCD. Further analyses integrating single-cell and plasma proteomic data collected before surgery with clinical variables yielded a sparse predictive model that accurately identified patients who would develop POCD (AUC = 0.80). The resulting POCD immune signature included one plasma protein and ten immune cell features, offering a concise list of biomarker candidates for developing point-of-care prognostic tests to personalize perioperative management of at-risk patients. The code and the data are documented and available at https://github.com/gregbellan/POCD. TeaserModeling immune cell responses and plasma proteomic data predicts postoperative cognitive decline.

neuroscience↗

bioRxiv2024

Axonal distribution of mitochondria maintains neuronal autophagy during aging via eIF2β

Neuronal aging and neurodegenerative diseases are accompanied by proteostasis collapse, while the cellular factors that trigger it have not been identified. Impaired mitochondrial transport in the axon is another feature of aging and neurodegenerative diseases. Using Drosophila, we found that genetic depletion of axonal mitochondria causes dysregulation of protein degradation. Axons with mitochondrial depletion showed abnormal protein accumulation and autophagic defects. Lowering neuronal ATP levels by blocking glycolysis did not reduce autophagy, suggesting that autophagic defects are associated with mitochondrial distribution. We found that eIF2{beta} was increased by the depletion of axonal mitochondria via proteome analysis. Phosphorylation of eIF2, another subunit of eIF2, was lowered, and global translation was suppressed. Neuronal overexpression of eIF2{beta} phenocopied the autophagic defects and neuronal dysfunctions, and lowering eIF2{beta} expression rescued those perturbations caused by depletion of axonal mitochondria. These results indicate the mitochondria-eIF2{beta} axis maintains proteostasis in the axon, of which disruption may underlie the onset and progression of age-related neurodegenerative diseases. HighlightsO_LILoss of axonal mitochondria impairs autophagy and accumulates proteins in the axon C_LIO_LILoss of axonal mitochondria increases eIF2{beta} and decreases p-eIF2 C_LIO_LINeuronal upregulation of eIF2{beta} induces autophagic defects and locomotor dysfunction C_LIO_LILowering eIF2{beta} rescues autophagic defects caused by loss of axonal mitochondria C_LI

cell biology↗

bioRxiv2023

Molecular Dynamics Simulation Analysis of Structural Dynamic Cross Correlation Induced by Odorant Hydrogen-Bonding in Mouse Eugenol Olfactory Receptor

Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlfaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the -carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 [->] Phe182 [->] (Leu259 or Tyr260) [->] Tyr291 induced by the ligand binding with a time scale of 4-6 ns.

biophysics↗

bioRxiv2023

Precise immunofluorescence canceling for highly multiplexed imaging capturing specific cell state

Cell states are regulated by the response of signaling pathways to receptor ligand-binding and inter-cellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we developed Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.

cell biology↗