Biology subjects

Kobayashi, H.

Publications and source records attributed to Kobayashi, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Complementary cytotoxicity of GD2-targeted photoimmunotherapy and 5-aminolevulinic acid photodynamic therapy in neuroblastoma and osteosarcoma

Phototherapy, a light-activated anticancer treatment, enables localized tumor-cell killing with distinct mechanisms of action. Photoimmunotherapy (PIT) produces immunogenic tumor cell death upon near-infrared light activation of a photoabsorber through antigen-specific targeting. Photodynamic therapy (PDT) produces reactive oxygen species through red-light activation of intracellular protoporphyrin IX generated from 5-aminolevulinic acid uptake and metabolism. PIT may have limited activity in antigen-low cells, whereas PDT has less precise tumor selectivity. We combined these modalities to define their interaction, broaden cytotoxicity, and determine whether dual treatment could reduce light-dose requirements. We conjugated dinutuximab, which targets the GD2 antigen, to IRDye 700DX and characterized plasma-membrane localization by confocal and widefield microscopy. PIT and PDT monotherapies were evaluated across agent and light doses in neuroblastoma (NB) and osteosarcoma (OS) cell lines. Combination matrices were tested using interaction, highest-single-agent, and Bliss analyses. Both monotherapies demonstrated significant light-dose-dependent effects in NB and OS. PIT produced no measurable cytotoxicity in antigen-blunted control cells, whereas PDT remained effective, confirming antigen-dependence of PIT and antigen-independence of PDT. The combination interaction was significant in SK-N-BE(2) but not LM7. At selected combinations, however, dual treatment produced greater killing than the more effective matched monotherapy in both SK-N-BE(2) and LM7 (Padj<0.022). Notably, lowest combination of PIT 10 J/cm2 plus PDT 10 J/cm2 achieved 90.3% killing in SK-N-BE(2), exceeding higher light-dose PIT or PDT monotherapy, suggesting a light-dose sparing effect. These findings establish potent and complementary PIT-PDT activity, supporting dual phototherapy to broaden cytotoxicity and reduce light-dose requirements in GD2-expressing tumor phototherapy.

cancer biology↗

bioRxiv2026

Topological Closure Drives Structural Stabilization and Fast Cooperative Dynamics in Crowded Circular Polysomes

In linear polysomes, excluded-volume interactions among ribosomes can induce dimensional reduction of mRNA. Yet linear architectures allow steric stress to relax at open ends-- limiting how strongly crowding can remodel the mRNA's structure and dynamics. Using coarse-grained molecular-dynamics simulations, we compare circular and linear polysomes over a range of ribosome densities. Circular closure selects a predominantly quasi-planar global conformational ensemble, as indicated by a shape dimensionality dshape {approx} 2 over a range of ribosome densities. Crucially, circular topology and ribosome crowding act cooperatively to suppress structural fluctuations. While closure alone or linear crowding reduces relative global size fluctuations ({Delta}Rg/Rg) only to {approx} 0.16, their combined effect drives this fluctuation down to {approx} 0.07. Within this stabilized architecture, increasing ribosome density drives a distinct in-plane reorganization: the ring becomes more isotropic, global size fluctuations are strongly suppressed, and the scaling exponent increases toward {nu} [~=] 0.74 - 0.77, consistent with two-dimensional self-avoiding walk-like value over the accessible finite-size window, 1000 [≤] N [≤] 4969. Closure shortens the radius-of-gyration decorrelation time of circular polysomes by 40-fold relative to matched linear systems, reflecting the topological elimination of free ends. Within this closureselected ensemble, ribosome crowding further reduces the decorrelation time by up to 20% at the highest density. A fluctuation-informed crossover model links the density dependence of the global scaling exponent to inter-ribosomal subchain statistics. These results distinguish the geometric role of circular closure from the density-dependent steric response that it enables, revealing a confined yet dynamically responsive conformational regime for circular polysomes.

biophysics↗

bioRxiv2026

A universal plug-and-display vaccine platform for mucosal and systemic immunity using Bacillus subtilis membrane vesicles

Many bacterial species naturally secrete membrane vesicles (MVs) that mediate the intercellular transport of biomolecules, including nucleic acids, proteins, and metabolites. Beyond their native physiological roles, MVs hold considerable potential for biomedical applications. Here, we demonstrate that MVs from several Bacillus species exhibit potent intrinsic adjuvant activity, efficaciously eliciting immune responses and facilitating antigen-specific antibody production in mice. Exploiting this adjuvanticity, we engineered a highly adaptable universal vaccine platform that uses B. subtilis MVs as self-adjuvanting carriers. This system employs a modular "plug-and-display" architecture that covalently anchors recombinant antigens to the MV surface through a multi-step bioconjugation cascade. After validation of this methodology using a model antigen, we adapted the platform to target Yersinia pestis, the causative agent of plague. We formulated a Y. pestis vaccine by labeling the MV surface with a modified capsule antigen fraction 1 (mCaf1). Intranasal administration of the mCaf1-MV vaccine effectively elicited both systemic and mucosal immunity. Crucially, this vaccine conferred highly efficacious protection against a lethal Y. pestis infection in a murine model. These findings demonstrate the exceptional protective efficacy of the B. subtilis MV platform and highlight its broad potential for the rapid development of mucosal vaccines against diverse emerging pathogens.

bioengineering↗

bioRxiv2026

Sensory neurons encode long-term inflammatory memory that promotes gastric regeneration and tumorigenesis

Inflammatory memory has emerged as a fundamental principle by which prior injury shapes future tissue responses, yet whether sensory neurons participate in long-term tissue memory remains unknown. Here, we show that vagal sensory neurons acquire a durable, experience-dependent state following gastric injury or Helicobacter pylori infection, leading to enhanced regeneration, metaplasia, and tumor progression upon re-injury. This neuronal program is stable, functionally transferable, and sufficient to drive epithelial responses in vivo. Mechanistically, injury-activated ILC2s establish sensory neuronal memory through IL-13-dependent epigenetic remodeling, inducing SMYD4-mediated H3K4 trimethylation and promoting CGRP-dependent activation of gastric epithelial cells. Together, our findings support a model in which tissue memory is not restricted to epithelial or immune compartments but emerges through coordinated long-term adaptations across multiple cellular systems. Within this framework, sensory neurons provide a persistent substrate for recall responses, linking prior inflammatory experience to sustained epithelial plasticity and cancer susceptibility. HIGHLIGHTSO_LISensory neurons function as a durable compartment of tissue memory. C_LIO_LICGRP-RAMP1 signaling couples neuronal memory to gastric stem cells. C_LIO_LIILC2-derived IL-13 establishes sensory neuronal memory programs. C_LIO_LISMYD4-mediated H3K4me3 stabilizes long-term neuronal memory. C_LIO_LINeuronal memory promotes gastric regeneration and tumor susceptibility. C_LI

cancer biology↗

bioRxiv2026

Quantitative determination of longitudinal CNS cholesterol loss during myelin damage and repair

1.Cholesterol in the central nervous system (CNS) is largely unesterified (>99%) and is predominantly present in the myelin sheath ([~]70% of total CNS cholesterol). Damage to the myelin sheath can result in the conversion of cholesterol to cholesterol esters, which occurs in many neurological diseases, including multiple sclerosis. In this study, we measured longitudinal CNS free cholesterol and cholesterol ester levels in a genetic mouse model during postnatal myelination, demyelination, and remyelination using gas chromatography-mass spectrometry with single ion monitoring technique (GC-MS-SIM) and liquid chromatography mass spectrometry (LC-MS). Cholesterol levels in healthy mouse brains increased up to 38 weeks. In contrast, cholesterol in the healthy spinal cord increased during postnatal timepoints, but then remained steady out to 38 weeks. Interestingly, cholesterol esters in the spinal cord were highest at P1 and drastically reduced by P42, while the brain had similar levels during all postnatal time points. During demyelination, both brain and spinal cord cholesterol levels were significantly reduced as compared to healthy mice and failed to return to normal cholesterol levels even during remyelination. Absolute quantification of cholesterol esters during peak demyelination revealed that cholesterol esters comprise 19% of the total cholesterol pool in the brain and 65% in the spinal cord. The lack of recovery in CNS cholesterol levels after demyelination suggests that healthy de novo cholesterol synthesis pathways are disrupted in this model. Absolute quantification of CNS cholesterol is critical for revealing mechanisms of cholesterol regulation during disease and identifying targets for restoring cholesterol to promote myelin repair.

neuroscience↗

bioRxiv2026

Minimally invasive measurement of maternal transcripts enables predicting the developmental potential of mammalian zygotes

Maternal transcripts are stored in the oocyte cytoplasm during oogenesis and play a pivotal role in early embryonic development after fertilization. However, specific maternal transcripts that reflect the developmental potential of embryos have not been systematically identified, and the use of maternal transcript levels as an indicator of successful development has not been explored. Here, we link the maternal transcriptome to the zygotes developmental potential by examining transcripts in a single polar body. The transcriptome of a zygote or an oocyte was highly similar to that of its accompanying polar body in mouse, cow, and human. We have identified a set of maternal transcripts whose expression levels fluctuate between poor- and good-quality zygotes. Specifically, Sipa1and Zmym6 were identified as marker transcripts that accurately reflect the developmental potential of zygotes. Using these marker genes, combined with machine learning, the development of zygotes to the blastocyst stage was successfully predicted with more than 80% specificity as early as 12 hours after fertilization. Furthermore, our prediction platform significantly improved implantation rates and live births to term. Thus, we have demonstrated a minimally invasive method for identifying maternal transcripts associated with zygote developmental potential. Our developed prediction system provides a generalizable conceptual framework for human infertility treatment to reduce the risk of implantation failure by excluding embryos with low developmental potential, especially when early embryos are transferred, and for livestock propagation to assess selected expressed maternal trait-associated variants before embryo transfer.

developmental biology↗

bioRxiv2026

Genetic polymorphisms in a mate choice locus are maintained by balancing selection in a wild medaka population

Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii. Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

evolutionary biology↗

bioRxiv2026

Deep Microbial Colonization in 2-Billion-Year-Old Ultramafic Rock from the Bushveld Complex

Archean cratons may provide stable microbial habitats in the deep subsurface, as evidenced by the discovery of billion-year-old crustal fluids1,2. However, the long-term habitability of these cratonic environments is uncertain, as polymetamorphic evolution in most cratons typically destroys microbial habitats through mineral reactions and porosity loss3,4. Preservation of deep microbial habitats is more likely where mantle-derived magma intruded the craton after metamorphic overprinting4. Here we report the discovery of dense microbial colonization at 814 m depth within the 2.05-billion-year-old, unmetamorphosed Bushveld Igneous Complex intrusion, South Africa5. Using advanced contamination-control protocols6,7 and synchrotron-based X-ray spectroscopy, we identified indigenous microbial cells localized at the rims of phlogopite, a hydrous phyllosilicate mineral. Our study reveals that microbial colonization is associated with Fe(III) derived from the structure of phlogopite, where the dehydrogenation likely oxidizes Fe(II) to Fe(III) coupled to H2 generation8. Despite the absence of fracture-driven fluid ingress in the unfractured rock matrix, aqueous alteration evidenced at the rims by potassium removal indicates a self-sustaining habitat driven by an internal redox gradient9. These findings demonstrate that aqueous alteration of ultramafic rocks can sustain isolated microbial life over geological timescales, significantly expanding the potential for long-term habitability on both Earth and Mars4,10.

microbiology↗

bioRxiv2026

PANDA: Read-Level Phased Analysis of DNA Amplicons for Methylation Studies

Targeted bisulfite amplicon sequencing is widely used to examine methylation at defined genomic loci, but site-wise methylation estimates can obscure phased patterns among individual reads. We developed PANDA (Phased Analysis for DNA Amplicons), an open-source platform for read-level analysis of targeted bisulfite amplicons generated by Sanger sequencing or amplicon NGS, with graphical and command-line interfaces built on a shared computational core (https://github.com/kubo-azu/PANDA). PANDA integrates reference-coordinate methylation calling and visualization, motif-based haplotype filtering, coordinate linkage of unmerged paired reads, and group comparison. It also implements three complementary heterogeneity metrics: Amplicon PDR (proportion of discordant reads), Window Epipolymorphism, and Amplicon qFDRP (quantitative fraction of discordant read pairs). These metrics use retained read-count weighting and explicit eligibility criteria. Synthetic demonstration datasets illustrated global methylation estimation, sequence-defined haplotype selection, and CpG-level group comparison. The heterogeneity metrics illustrated different aspects of the predefined methylation states. Re-analysis of public chimpanzee and rhesus macaque placental datasets was consistent with the previously reported species-associated methylation contrast and demonstrated coordinate-linked analysis of unmerged paired reads without imputing the unsequenced interval. PANDA provides a reproducible framework for examining phased methylation patterns and within-sample heterogeneity alongside site-wise methylation estimates in amplicon sequencing.

bioinformatics↗

bioRxiv2026

Unconventional Interplay Between GPCRs and RTKs Signaling Pathways Through SH2 Domain-Containing Proteins

Crosstalk across two major receptor families involved in signal transduction, namely receptor tyrosine kinases (RTKs) and G protein-coupled receptors (GPCRs), have been observed at different levels of their signaling cascades. Using newly developed enhanced bystander bioluminescence resonance energy transfer (ebBRET)-based biosensors that monitor the recruitment of SH2 domains to activated RTKs, we assessed the ability of GPCRs to modulate cellular localization of SH2 domains. Receptor-mediated activation of either Gq/11 or G12/13 but not Gs or Gi/o (e.g., thromboxane A2 receptor, TP, and type-2 protease activated receptor, PAR2) resulted in the plasma membrane (PM) dissociation of SH2 domains derived from RTKs effectors such as GRB2, STAT5 and PLC{gamma}1. The role of Gq/11, G12/13, Rho and downstream kinases in the subcellular SH2 domain redistribution was further confirmed using both pharmacological and genetic approaches. BRET imaging and spectrometric analyses showed that the dissociation of SH2 domains from the PM was accompanied by their accumulation in the nucleus and a reduction in RTK signaling activity, as determined using a STAT5 transcriptional assay. The effect of Gq/11 and G12/13 activation on STAT5 transcriptional activity was observed both in engineered systems and in HeLa cells endogenously expressing all the components of the regulatory mechanism. The Gq/11 / G12/13-mediated redistribution of SH2 domain-containing proteins represents an undescribed mechanism through which GPCRs regulate RTKs activity. Significance StatementThis study reveals a novel crosstalk mechanism between G protein coupled receptors and receptor tyrosine kinases showing that Gq/11 and G12/13 activation triggers Rho-dependent translocation of SH2-containing effector proteins, such as GRB2, PLC{gamma}1 and STAT5. This process causes compartmentalization inside the nucleus and thus reduces their availability at the plasma membrane, leading to attenuated RTK responses.

cell biology↗

bioRxiv2026

Amorphous-to-Rodlet Structural Transition Governs the Interfacial Functions of Aspergillus oryzae Hydrophobin RolA

Hydrophobins are low-molecular-weight biosurfactant proteins that coat the cell surface of filamentous fungi, making it hydrophobic and supporting morphogenesis. On conidia, hydrophobins self-assemble to form rod-shaped multimeric structures known as rodlets. Previously, we reported that hydrophobin RolA from the industrial fungus Aspergillus oryzae first forms an amorphous film at the air-water interface and then undergoes structural rearrangement to form a densely packed rodlet film. This raised the question of whether the amorphous or the rodlet film is more important for the biological functions of RolA. In this study, to compare the properties of amorphous films with those of rodlet films, we used RolA mutants that had lost the ability to form rodlets and therefore remained in the amorphous state. We found that the rodlet film was more rigid than the amorphous film and had stronger surface activity and a greater capacity to change surface wettability. RolA altered the properties of A. oryzae conidia only when it was in the rodlet state. These findings highlight the functional versatility of RolA and show that their dynamic structural transitions directly modulate their function.

microbiology↗

bioRxiv2026

Self-induced Dimensional Reduction and Scaling Transition of mRNA in Polysomes: A Multiscale Simulation Study

The spatial architecture and mechanical rigidity of polysomes are crucial determinants of translational efficiency and mRNA stability. In this study, we investigate the conformational statistics of an mRNA backbone decorated with high-density ribosomes at varying densities using large-scale, extensive molecular dynamics simulations based on the Kremer-Grest bead-spring model. To address the extreme spatial asymmetry between mRNA monomers and ribosomes, we used an efficient tree-based neighbour list algorithm, enabling the analysis of mRNA chains up to N = 4, 969. Our results demonstrate that the excluded volume of massive ribosomes induces a significant and robust expansion of the scaling exponent v from 0.59 to approximately 0.7. In the conformation of mRNA, this shift translates to a self-induced dimensional reduction from a three-dimensional random coil toward a stretched, a quasi-two-dimensional architecture at biologically relevant scales. Such a transition is further evidenced by a periodic "regain" of the bond-bond correlation function C(n) at ribosome attachment sites, indicating a geometric alignment absent in standard homopolymers. These findings reveal that the geometric crowding of ribosomes itself provides a robust physical prerequisite for the formation of higher-order polysome architectures, bridging the gap between polymer physics and structural properties of mRNA during translation.

biophysics↗

bioRxiv2025

Oligomeric coiled-coil adhesins that drive chain-like adhesion diversify surface colonization strategies in Shiga toxin-producing Escherichia coli

Bacteria frequently colonize host and environmental surfaces under fluid flow. Chain-like adherence pattern (CLAP) is an EibG-mediated surface colonization phenotype of certain Shiga toxin-producing Escherichia coli (STEC) that lack the locus of enterocyte effacement (LEE). EibG, an immunoglobulin-binding oligomeric coiled-coil adhesin, drives CLAP, but the temporal dynamics and genetic diversity underlying chain formation remain unclear. Here, we use live-cell time-lapse imaging to show that chains arise from single cells that elongate and divide without separation. Under flow, chains resist detachment and undergo shear-dependent fragmentation at cell-cell junctions, releasing viable clonal units that disperse downstream. Comparative genomics reveals substantial diversity among EibG-related adhesins and identifies distinct lineages, including chain-like adhesins (cla) that mediate CLAP while lacking IgG binding. Screening of 1,354 LEE-negative STEC genomes from England shows that claB is present in 95.6% of strains from major LEE-negative STEC serotypes, highlighting its epidemiological prevalence. Targeted mutagenesis demonstrates that chain formation and IgG binding are mediated by distinct structural domains, revealing the modular functional architecture of these adhesins. In a mouse infection model, deletion of eibG reduced lethality, indicating that EibG contributes to virulence. Collectively, these findings establish CLAP as a dynamic, surface-associated strategy of LEE-negative STEC and reveal previously unrecognized diversification among adhesins that drive this behavior.

microbiology↗

bioRxiv2025

Holding a Steady Look at the Human Eye: Rebuttal to Critiques of the Gaze-Signalling and Cooperative Eye Hypotheses

The Cooperative Eye Hypothesis (CEH) and the Gaze-Signalling Hypothesis (GSH) propose that the human eye--distinguished by pronounced scleral exposure and a uniformly white sclera-- evolved as a unique trait among primates to enhance eye-gaze visibility and facilitate cooperative communication. A recent review by Perea-Garcia and colleagues (2025) questioned four central premises of these hypotheses: (1) that human eye morphology is unique among primates, (2) that it is expressed consistently across individuals and populations, (3) that it improves gaze-following, and (4) that it is linked to the evolution of social cognition. Here, we revisit each claim through reevaluation of evidence and reanalysis of published data. First, we show that although some primates exhibit scleral depigmentation, humans uniquely combine this with high scleral exposure, resulting in markedly greater gaze visibility. Second, despite variation in scleral brightness, cross-species comparisons of sclera-iris-skin contrast confirm that human eyes remain distinct from those of other closely related apes. Third, experimental studies demonstrate that the white sclera confers a clear communicative advantage under ecologically relevant conditions, and that only humans consistently exploit these cues. Finally, developmental, cross-cultural, and neurocognitive evidence indicates that humans possess dedicated perceptual mechanisms for eye-gaze, consistent with its evolutionary embedding in social cognition. We conclude that while claims of human uniqueness should be moderated, the CEH and GSH remain the most plausible explanations for the evolution of human eye morphology. We also highlight key directions for future behavioral, anatomical, and genetic research.

evolutionary biology↗

bioRxiv2025

Microbiome composition modulates the lethal outcome of Drosophila A virus infection

Host-associated microbiomes can strongly influence viral infection outcomes, yet how minor variations in commensal bacterial composition modulate viral pathogenesis remain poorly understood. Here, we used Drosophila melanogaster to investigate how bacterial microbiome composition affects pathogenesis of enteric RNA viruses. Lactiplantibacillus plantarum supplementation increased bacterial microbiome diversity without altering total bacterial load, while Acetobacter pomorum supplementation had minimal impact on the bacterial microbiome. L. plantarum-enriched flies exhibited an additional [~]15% reduction in lifespan from Drosophila A virus (DAV) infection despite showing reduced viral protein accumulation and similar viral RNA levels. The reduction in tolerance to viral infection required live bacteria and was observed only for DAV, as no change in mortality was observed with Nora virus or Drosophila C virus infections. Mechanistic investigations revealed that tolerance reduction occurs independently of transcriptional immune responses, as DAV-infected flies showed similar transcriptional profiles regardless of bacterial microbiome composition. Intestinal barrier function assays demonstrated that L. plantarum-supplemented flies died before developing signs of gut barrier disruption, suggesting that extra-intestinal mechanisms contribute to mortality; this interpretation is further supported by similar levels of intestinal damage markers observed in virus-infected flies under both microbiome conditions. Viral genomic sequencing ruled out microbiome-driven selection of more pathogenic viral variants, as no adaptive mutations were observed between microbiome conditions that could account for the differential pathogenesis. These findings describe how subtle shifts in microbiome composition modulate viral infection outcomes through pathways that operate independently of canonical immune responses, viral evolution, and intestinal damage.

microbiology↗

bioRxiv2025

Submedius Thalamus Modulates Orbitofrontal Cortex Representations During Maternal Behavior in Mice

The orbitofrontal cortex (OFC) is central to cognitive and social functions, yet its presynaptic partners remain incompletely defined. In female mice, the OFC modulates infant-directed maternal caregiving behaviors essential for offspring survival in an experience-dependent manner. Here, we identify the submedius thalamus (SMT) as a major presynaptic partner of the OFC. Trans-synaptic tracing revealed intensive inputs from both the SMT and mediodorsal thalamus (MD) to OFC layer 5 excitatory neurons. A mouse line Tnnt1-Cre enabled selective targeting of these higher-order thalamic nuclei. Axonal tracing demonstrated complementary projection patterns of SMT and MD across prefrontal regions. Microendoscopic Ca2+ imaging demonstrated pup retrieval encoding in SMT and MD, but only SMT exhibited learning-related plasticity, characterized by enhanced anticipatory responses as acquired maternal behaviors. Projection-specific chemogenetic silencing demonstrated that only SMT modulates OFC activity during pup retrieval. These findings demonstrate SMT as a previously uncharacterized thalamic hub shaping cortical representations of maternal behavior. HighlightsO_LIOFCRbp4 neurons receive strong inputs from higher-order thalamic nuclei (SMT, MD). C_LIO_LISMT and MD show complementary axonal projections across prefrontal cortical cortex. C_LIO_LISMT ensembles encode pup retrieval with experience-dependent plasticity. C_LIO_LISMT inputs selectively modulate pup retrieval representation in OFCRbp4 neurons. C_LI

neuroscience↗

bioRxiv2025

Temporal dynamics of CNS cholesterol esters correlate with demyelination and remyelination

Elevated cholesterol ester levels have been observed in the CNS of patients with neurological diseases, yet the source of cholesterol ester accumulation and whether it is directly linked to demyelination remains undefined. This study investigates the temporal dynamics of cholesterol esters using the Plp1-iCKO-Myrf mouse model, which features distinct phases of demyelination and remyelination. Our findings reveal that cholesterol ester levels increased with demyelination in both the brain and the spinal cord. In the brain, cholesterol esters declined to normal levels during remyelination, whereas cholesterol esters remained elevated in the spinal cord, which had limited remyelination. Expression of both acetyl-CoA-acyltransferase 1 (ACAT1) and lecithin-cholesterol acyltransferase (LCAT) were elevated during demyelination, suggesting the potential involvement of both proteins in the formation of cholesterol esters. Co-localization studies revealed that ACAT1 is predominantly expressed by microglia and LCAT is predominantly expressed by astrocytes during demyelination highlighting the active roles of glia cells in cholesterol ester metabolism. In addition, we showed that administering the remyelinating drug, Sob-AM2, effectively reduced the level of cholesterol ester accumulation in the brain during demyelination underscoring the potential that manipulating cholesterol ester regulatory pathways may offer for restoring cholesterol homeostasis and promoting remyelination in demyelinating diseases.

neuroscience↗

bioRxiv2025

DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana

Heterosis, or hybrid vigor, is characterized by superior phenotypic performance in F hybrids compared to their parental lines, and its expression is influenced by both genetic and epigenetic factors. In this study, we investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana accessions Columbia-0 and C24. Loss of DDM1 function in F hybrids resulted in a significant reduction of rosette diameter, confirming that DDM1 is essential for heterosis. Transcriptomic and epigenomic analyses revealed extensive genotype-specific changes in gene expression and DNA methylation patterns in ddm1 mutants. Notably, ddm1-F hybrids exhibited upregulation of genes categorized into xyloglucan:xyloglucosyl transferase activity and downregulation of genes categorized into circadian rhythm, which may contribute to reduced growth vigor. Whole-genome bisulfite sequencing showed widespread hypomethylation in ddm1 mutants, yet the overlap between differentially methylated and expressed genes was limited, suggesting indirect or context-dependent regulatory effects. Additionally, we examined the role of salicylic acid (SA) in heterosis using SA-deficient mutants and found that variations in endogenous SA levels did not correlate with biomass heterosis under normal conditions. Our findings suggest that heterosis in A. thaliana is dependent on the maintenance of parental epigenetic divergence, particularly in DNA methylation patterns mediated by DDM1. Disruption of DDM1 compromises this epigenetic complementarity, leading to transcriptomic imbalances that reduce heterosis. HighlightLoss of DDM1 reduces biomass heterosis in Arabidopsis thaliana hybrids by disrupting DNA methylation and transcriptome stability, revealing a novel salicylic acid-independent epigenetic mechanism.

plant biology↗