Biology subjects

Kim, Y. J.

Publications and source records attributed to Kim, Y. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Modelling prodromal Parkinson's disease- gastrointestinal pathology and early motor deficits in mice after transient rotenone exposure

Early gastrointestinal (GI) dysfunction is a hallmark feature of Parkinson's disease (PD), yet models capturing prodromal gut and brain pathology in PD remain limited. Motivated by the increased PD risk associated with pesticide exposure, we monitored motor behavior, brain pathology, and GI structure and function over 9 months following 5 daily doses of rotenone in mice. Transient rotenone exposure induced significant nigrostriatal pathology, including {approx}48% loss of dopaminergic neurons and increased -synuclein aggregation in the substantia nigra, without significant changes in gross motor function. Notably, we identified pronounced GI dysfunction including reduced colonic transit velocity, altered motility dynamics, and delayed whole-gut transit. These functional changes were accompanied by enteric dopaminergic neurodegeneration, increased colonic -synuclein accumulation, increased colonic crypt depth, goblet cell hyperplasia with elevated mucin content per goblet cell. The findings are consistent with prodromal PD, suggesting the utility of this model for investigating early disease mechanisms and intervention strategies.

neuroscience↗

bioRxiv2026

Sex-dependent DNA methylation in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) shows well-established sex differences in incidence, age at onset and progression, but their biological basis is unclear. We hypothesised that the DNA methylation changes associated with ALS differ between the sexes, which would point to sex-specific disease processes. To test this, we performed a blood-based epigenome-wide association meta-analysis of ALS cases and controls from Project MinE, an international ALS genomics consortium, and an independent Australian cohort, comprising 8,946 individuals after quality control (5,129 males and 3,817 females; 8,942 with complete covariates in the primary models). We analysed 781,648 autosomal CpGs using complementary sex-stratified case-control models and an ALS-by-sex interaction model that directly tested whether ALS-associated methylation effects differed by sex. Sex-stratified analyses identified no genome-wide significant differences between male and female ALS effects. In contrast, interaction testing identified seven robust sex-dependent ALS-associated differentially methylated positions (P < 9 x 10-8), mapping to KCNQ1, ADPRH, HLA-F, GHRLOS, IRF5, RAD51B and one intergenic region. The strongest signal was at KCNQ1 (P = 3.1 x 10-9). Six of the seven remained genome-wide significant in a four-stratum sensitivity analysis, and none was detected in previous conventional ALS or population sex-associated methylation analyses. Together, these findings suggest a distinct sex-conditional component of the ALS blood methylome, implicating immune, metabolic and ion-channel loci and providing new candidates for investigating biological heterogeneity between males and females with ALS.

genomics↗

bioRxiv2026

A Framework for Quantifying DNA Methylation Heterogeneity and Detecting Co-methylated loci from Native Nanopore Sequencing

DNA methylation is an important epigenetic mechanism involved in gene regulation. Most methods focus on analysing DNA methylation averaged from multiple reads, yet these average methylation profiles obscure heterogeneity between individual DNA molecules and coordinated methylation states across loci. Native Oxford Nanopore Technology (ONT) sequencing directly captures long, native DNA molecules together with their base modifications, allowing methylation to be studied at single-molecule resolution. Here, we present a scalable framework for genome-wide methylation analysis using ONT sequencing at single-molecule resolution, focused on two features that site-level summaries cannot recover. First, it quantifies molecule-to-molecule heterogeneity in DNA methylation by detecting Variable Methylated Domains (VMDs) and Variable Methylated Regions (VMRs). Second, it identifies coordinated methylation, as co-methylated positions (CMPs) and regions (CMRs), from the states observed on the same individual DNA molecules. Using data from human LCL cells, we demonstrate that substantial molecule-level methylation heterogeneity is masked by site-level summaries. Co-methylation analysis reveals coordinated patterns between CpG sites and genomic regions, including shared and sex-specific patterns, uncovering methylation organisation not apparent from average methylation levels. We also show that CMPs can be used to detect TF-pairs that are predicted to have coordinated binding. This framework is integrated within the DMRcaller R/Bioconductor package.

bioinformatics↗

bioRxiv2026

Tumor control of lysosomal acidification promotes lipoprotein assimilationand ferroptosis resistance

Lysosomes are acidic organelles that fuel cancer progression by facilitating nutrient acquisition and metabolic adaptation, yet the determinants through which cancer cells sustain specialized lysosomal functions are not fully delineated. Notably, assimilation of dietary antioxidants within lipoproteins, a lysosome-dependent process, protects tumors from ferroptosis, an oxidative form of cell death, raising the possibility that tumors evolve mechanisms to enhance this process. Here, we applied genetic screens to identify regulators of lysosome-dependent lipoprotein assimilation and ferroptosis resistance and identified ZNF217, a frequently amplified transcriptional regulator in human cancers, as a driver of tumor lysosomal function and ferroptosis resistance. ZNF217 promoted lipoprotein assimilation through transcriptional maintenance of RAB11FIP4, an endolysosomal protein. Loss of either ZNF217 or RAB11FIP4 impaired lysosomal acidification across multiple cancer types, leading to defective lipoprotein assimilation, increased lipid peroxidation, ferroptosis sensitivity, and impaired tumor growth. Mechanistically, RAB11FIP4 boosts lysosomal acidity through maintenance of RAB7A activity. Finally, disruption of ZNF217 in breast cancer cell lines and patient-derived organoids, a tumor context linked to ZNF217 expression, reduced lysosomal acidity and impaired cancer growth through increased ferroptosis sensitivity. Together, we identify transcriptional regulation of lysosomal acidification as a key metabolic adaptation that enables extracellular antioxidant acquisition and tumor progression.

cancer biology↗

bioRxiv2026

Long-read sequencing reveals novel mitochondrial genome variants undetected by short-read sequencing in Korean population

While long-read sequencing technologies (e.g., PacBio Revio, ONT) have revolutionized high-quality genome assembly for the human pangenome, mitochondrial genome (mtDNA) analysis still largely relies on short-read and Sanger sequencing. However, short-read sequencing often lacks the resolution required to resolve complex variations due to the unique features of mtDNA, such as high mutation rates and repetitive homopolymeric regions, which frequently lead to alignment artifacts and mapping ambiguities. To address this, we evaluated whether applying long-read sequencing to mtDNA improves analytical quality in empirical data. Through comprehensive bioinformatics analyses, we compared the performance of long-read sequencing against short-read sequencing and microarrays. Our results revealed that long-read sequencing detected the highest number of variants (n = 533), significantly outperforming both short-read sequencing (n = 525) and microarrays (n = 49). Notably, both sequencing methods provided significantly higher resolution in haplogroup assignment compared to microarrays in terms of phylogenetic depth (p < 0.05). Long-read sequencing demonstrated superior detection power, particularly for InDels. We identified two novel non-synonymous variants, including a unique InDel detected exclusively by long-read sequencing. Protein modeling and stability analysis validated that this InDel causes structural instability (RMSD > 2.0 [A],{Delta}{Delta} G = -45.21 kcal/mol). Furthermore, we confirmed that this novel InDel is shared among haplogroup A samples in both the 1000 Genomes Project ONT dataset and the Korean population, highlighting the practical implications of long-read sequencing for molecular biology and population genetics.

genomics↗

bioRxiv2026

DanioDecima: A DNA sequence-to-function model of zebrafish embryogenesis

Deep learning DNA sequence-to-function models offer the promise of gaining mechanistic insights into genome regulation, however their performance is often limited by data scarcity in the species of interest. We present DanioDecima, a zebrafish-specific model leveraging transfer learning from human and mouse-trained models to predict tissue- and cell-type-specific gene expression during zebrafish embryogenesis. Initializing DanioDecima with pretrained human and mouse Borzoi and Decima weights raises the median pseudobulk Pearson r sub-stantially across cell-types and improves gene-level correlations of test set genes. An in silico directed-evolution loop guided by DanioDecima scoring generated synthetic promoters whose motif architectures cluster by the expected target lineage. These findings exemplify a cross-species transfer learning methodology for sequence-to-function models, and position DanioDecima as a practical resource for zebrafish regulatory engineering.

genomics↗

bioRxiv2026

Nuclear basket localized proteasomes maintain circadian period through nuclear TOC1 proteolysis

Post-translational control of circadian period can involve changes in protein intracellular localization to affect clock function. Many clock proteins rely on a nuclear presence for their activity. As the primary gateway regulating the movement of molecules between the cytosol and the nucleus, the nuclear pore may assist in circadian system maintenance. We describe roles for the nuclear basket proteins, NUA and NUP136, in the maintenance of Arabidopsis circadian period, through effects on the stability of the core clock protein, TOC1. The circadian period of nua and nup136 mutants is significantly longer than that of wildtype plants. We show that NUP136 interacts with NUA, proteasome components and TOC1 in vivo, recruiting them to the inner nuclear rim. TOC1 interaction with the NUP136-NUA complex leads to a proteasome-dependent degradation of TOC1. Loss of NUP136 or NUA disrupts this regulatory environment, leading to aberrant nuclear TOC1 accumulation and consequent lengthening of circadian period. Our work thus identifies nuclear basket-localized proteasomes as key to the maintenance of circadian period.

plant biology↗

bioRxiv2026

Decoy diversification underpins the regulation of an NLR-mediated autoimmunity

Appropriate activation of innate immune receptors is vital for the plant immune system. Immune activation must be strong and robust upon invasion by rapidly evolving pathogen species, while staying inactive in the absence of a pathogen to avoid constitutive defense responses that inhibit plant growth. Nucleotide-binding leucine-rich repeat receptors (NLRs) are intracellular proteins that surveil for pathogen invasion, often by direct or indirect perception of pathogen effector proteins. Indirect recognition of pathogen effector proteins, through monitoring the integrity of guardee or decoy proteins, can allow for a single NLR to detect a wide range of pathogen effectors. In this work, we investigated how the Solanaceae NLR NbPtr1 can recognize six different effector proteins from the bacterial pathogens Pseudomonas syringae, Xanthomonas perforans, and Ralstonia pseudosolanacearum. We identified several NOI-domain containing proteins that are guarded by NbPtr1. These NOI proteins share homology with, but are distinct from, RPM1 INTERACTING PROTEIN 4 (RIN4), a well-known guardee in Arabidopsis. Virus-induced gene silencing and CRISPR/Cas9-assisted deletion of NbNOI genes resulted in stunted growth dependent on NbPtr1 activity. Negative regulation of NbPtr1 requires the interaction between NbPtr1 and the suppressor NbNOIs. A conserved threonine residue of the NOI proteins is required for this interaction and fits into a putative binding pocket of NbPtr1 based on protein modeling. This threonine residue is modified by some of the recognized effector proteins. Our study uncovers the regulatory mechanism of an autoactive NLR and highlights the importance of decoy diversification in establishing compatibility with NLRs.

plant biology↗

bioRxiv2026

Benchmarking Short-Read ITS2 and Full-Length ITS Sequencing Reveals Pipeline-Dependent Biases in Indoor Fungal Community Profiling

Short-read amplicon sequencing is widely used for fungal surveys but can limit taxonomic resolution. Long-read sequencing enables recovery of the full internal transcribed spacer (ITS) region and may improve ecological and taxonomic inference. Here, we conducted a paired comparison of Illumina ITS2 and PacBio HiFi full-length ITS sequencing using identical DNA extracts from built-environmental air and surface samples (n = 68) collected across homes, a dormitory, and laboratories. Both datasets were taxonomically assigned using the same algorithm and reference database. We performed paired statistics, in-silico ITS2 trimming of long-read sequences, and cross-platform mapping at multiple identity thresholds. Full-length ITS provided higher taxonomic resolution, assigning a greater fraction of ASVs at the family (98% vs. 88%) and species (42% vs. 32%) ranks than ITS2 (paired Wilcoxon q = 0.002). Alpha-diversity comparisons showed similar Shannon diversity across pipelines, whereas richness metrics were consistently higher for full-length ITS. Beta-diversity analyses indicated broadly comparable community-level patterns, although full-length ITS revealed stronger sample-type- and location-associated structure (PERMANOVA R{superscript 2} [≥] 0.06, p = 0.0001). In-silico ITS2 trimming reduced these differences, indicating that amplicon length is a major contributor to enhanced taxonomic resolution and ecological inference. Cross-platform mapping further showed extensive one-to-many relationships between ITS2 and full-length ITS ASVs, consistent with increased sequence resolution in long-read data. Together, these results show that ITS2 sequencing provides robust community-level profiling, while full-length ITS enables improved richness estimates and finer ecological and taxonomic resolution. This paired, bias-aware framework provides a practical template for selecting fungal amplicon sequencing strategies in built-environment mycobiome studies. ImportanceFungal communities in built environments influence indoor air quality and human exposure, yet their characterization depends strongly on sequencing strategy. This study provides a controlled, paired comparison of short-read ITS2 and long-read full-length ITS sequencing, showing that differences in amplicon length substantially contribute to variation in taxonomic resolution and ecological inference. While both approaches yield comparable community-level patterns, full-length ITS improves richness estimates, species-level assignment, and environmental discrimination by resolving sequence variation collapsed in ITS2 surveys. By integrating paired diversity analyses, in-silico ITS2 trimming, and cross-platform ASV mapping, this work offers a bias-aware framework for evaluating fungal amplicon pipelines. Importantly, improved species-level resolution enables functional interpretation of indoor fungi, for example the identification of taxa associated with pathogenic traits, allergen production, or toxin synthesis, supporting the development of more informative exposure metrics and targeted assays relevant to human health in built environments.

microbiology↗

bioRxiv2026

Mitochondrial respiration modulates Hsf1 activation and the heat shock response.

Cells employ a bevy of transcriptional and post-translational stress responses to tolerate the burden of misfolded proteins induced by stress. In particular, the heat shock response facilitates the upregulation of molecular chaperones and protein remodeling factors that mediate proteostasis in response to accumulated misfolded proteins in the nucleus and cytosol. However, in response to stress neurons struggle to induce a canonical heat shock response, highlighting our poor understanding of how neurons maintain proteostasis. Specifically, the ability of post-mitotic respiring cells to regulate the heat shock response in comparison to their rapidly dividing, predominantly glycolytic counterparts has been under-studied. In this study, we employ yeast models that are easily manipulated to generate energy via glycolysis or mitochondrial respiration by changing the carbon source in the media. Using this model, we demonstrate that Hsf1 activity, the heat shock response and proteostasis are impaired in respiring cells. Interestingly, our data show that reduced Hsf1 activity regulates viability of respiring cells, with respiring cells poorly tolerating constitutively activated Hsf1. Finally, we describe alternative post-translational programming of the molecular chaperones Hsp70 and Hsp104 that plausibly enables respiring cells to mediate proteostasis despite a dampened heat shock response. Our findings offer new insights into possible proteostatic strategies employed by cells in different metabolic conditions.

molecular biology↗

bioRxiv2026

Wireless Magnetomechanical Stimulation of Targeted Vagal Gut-Brain Circuits

Causal manipulation of gut-brain neural circuits empowers studies of metabolism and interoception. However, the anatomy and cytoarchitecture of peripheral ganglia relaying gut-brain circuits pose challenges to deployment of optical or electrical stimulation probes. To enable implant-free, cell-type specific, and temporally precise control of defined gut-brain pathways, we develop a neuromodulation platform based on magnetic nanodiscs (MNDs) targeted to peripheral neurons via genetically delivered anchoring moieties. The anchored MNDs selectively transduce externally applied weak magnetic fields to mechanical torque, thereby activating endogenous mechanosensitive pathways in specified cell types with sub-second latency. When targeted to nodose ganglia neurons expressing oxytocin or glucagon-like peptide 1 receptors, MND-mediated stimulation enables robust and reversible activation of gut-brain signaling, which engages hindbrain satiety circuits and regulates feeding behavior. These findings establish MND-mediated stimulation as a genetically targetable, implant-free strategy for modulating gut-brain neural circuits and highlight its potential in studies of brain-body physiology and bioelectronic medicines.

bioengineering↗

bioRxiv2026

Retrotransposons Promote Clonal Hematopoiesis Through Aging-Related Stromal Inflammation

Clonal hematopoiesis (CH) is an age-related phenomenon driven by the expansion of mutant hematopoietic stem cell (HSC) clones, most commonly harboring mutations in DNMT3A. While inflammation is known to promote CH, the upstream triggers of this inflammatory state remain unclear. We show that aging selectively upregulates retrotransposons in the non-hematopoietic cell compartment of the murine bone marrow, particularly in mesenchymal stromal cells. Using in vivo competitive transplant models, we demonstrate that retrotransposon-induced inflammation cell-extrinsically promotes Dnmt3a-mutant HSC expansion. This competitive advantage arises from mutant HSC resistance to inflammation-driven cell cycle perturbations. Mechanistically, we show that retrotransposon activation induces type I interferon signaling via viral mimicry, such that stromal knockdown of either Irf3 or Sting abrogates the competitive advantage of Dnmt3a-mutant HSCs. Our findings establish stromal-selective retrotransposon reactivation as a previously unrecognized, non-cell-autonomous source of inflammation that contributes to age-associated CH. Key PointsO_LIRetrotransposons remodel the aging niche through viral mimicry pathways to promote Dnmt3a-mutant clonal hematopoiesis. C_LIO_LIRetrotransposon-mediated inflammation impairs wild-type HSC fitness, while Dnmt3a-mutant HSCs resist inflammatory changes. C_LI

cancer biology↗

bioRxiv2025

Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins

Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the highest rates of antibiotic resistance, yet no vaccines or alternative therapies are available despite decades of research. Here, we developed a repertoire of potent, high affinity nanobodies (Nbs) targeting key toxins in S. aureus infection, including superantigens (SAgs) SEB, SEC, TSST-1, and Hla. Comprehensive cryo-EM and AlphaFold3 analyses of these Nbs, which were elicited with clinical cocktail vaccines, revealed diverse neutralizing epitopes and mechanisms that provide strategic insights for immunotherapy and vaccine design. Guided by these findings, we engineered highly stable, multivalent, and multifunctional Nb constructs. These constructs included an aerosolizable trimeric Nb with enhanced neuralization activity against Hla and SEC, and an ultrapotent decameric Nb-IgG-Fc fusion construct against a wide range of major toxins in S. aureus sepsis (SEB, SEC, TSST-1, and Hla). These multifunctional Nbs demonstrated promising protective activity in murine models of pneumonia and sepsis, underscoring their potential as versatile immunotherapies that address the complex virulence profiles of S. aureus. Our work lays a foundation for precision immunotherapies beyond current treatment options to combat complex bacterial infections with multiple virulence mechanisms. Significance statementS. aureus is among the most common, antibiotic-resistant, and deadly causes of bacterial infections. We developed nanobodies against clinically significant virulence factors in S. aureus sepsis and pneumonia, including superantigens (SAgs) SEB, SEC, and TSST-1 as well as pore forming toxin Hla. These nanobodies displayed complete and potent neutralization of each toxin, exploiting a wide variety neutralizing mechanisms. Structural investigation of these diverse neutralizing nanobodies, which were elicited in llamas using clinically investigated cocktail vaccines, highlighted the importance of disrupting SAg interaction with TCR or MHCII and potential flaws in targeting poorly neutralizing conserved SAg epitopes using vaccine cocktails. Nb leads against each toxin were combined in different multivalent configurations, including an aerosolizable trimeric Nb and a half-life extended decameric Nb IgG Fc fusion construct. This work highlights multivalent nanobodies as a comprehensive yet therapeutically precise drug platform that addresses the complex virulence profiles of bacterial infectious diseases.

microbiology↗

bioRxiv2025

Proteostasis Remodeling Across Development Defines Fetal, Neonatal, and Adult Hematopoietic Stem Cell States

Hematopoietic stem cells (HSCs) must preserve protein homeostasis (proteostasis) despite dramatic changes in proliferative and biosynthetic demands during development, yet how proteostasis is regulated across these transitions is poorly understood. Here, we show that fetal and neonatal HSCs operate through distinct, stage-specific proteostasis programs that differ fundamentally from those in adulthood. Using quantitative in vivo assays spanning embryonic through adult stages, we uncover an unanticipated decoupling between protein synthesis and protein quality control during development, revealing that fetal and neonatal HSCs employ specialized mechanisms to safeguard proteome integrity under developmental stress. Developing HSCs experience a distinctive proteostasis landscape characterized by elevated protein synthesis, increased unfolded protein burden, and selective engagement of stress-buffering and protein degradation pathways that are largely dispensable in young adult HSCs. Disruption of these pathways compromises early life HSC function and long-term fitness, establishing proteostasis control as a key regulator of stem cell maturation. These findings define previously unrecognized mechanisms by which HSCs manage the proteome during early life and reveal fundamental principles governing stem cell proteostasis across ontogeny.

developmental biology↗

bioRxiv2025

10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

We present Korea10K, the largest genomic dataset of the Korean population, comprising 10,239 high-coverage whole genomes (mean depth 30x) with matched multiomic profiles and phenotype data. Korea10K achieves complete and near-complete discovery of very rare and ultra-rare alleles, respectively, at 9,000 Korean genomes. This dataset provides the high-quality population-specific imputation panel, enabling accurate inference of low-frequency variants. Admixture analyses confirm the genetic homogeneity of the Korean population, despite its diverse Y-chromosomal, mitochondrial, and HLA repertoires. This pattern reflects a long and continuous lineage history characterized by persistent internal admixture and genomic homogenization over thousands of years on the Korean peninsula. We also identified 16.8 million genomic variants that directly modify CG sites by creating or abolishing CG dinucleotides, providing the population-scale evidence of coordinated genomic-epigenomic regulatory mechanism in Koreans.

genomics↗

bioRxiv2025

ecDNA-driven oncogene super-expressors shape immunoevasive tumor microenvironment

ecDNA contributes to cancer genetic heterogeneity through random segregation during mitosis. Emerging evidence links ecDNA to immune evasion, but the mechanism remains elusive. Using genetically engineered mouse models of pancreatic ductal adenocarcinoma (PDAC), we show that Kras and Myc oncogenes are amplified either on ecDNAs or as homogeneously staining regions (HSRs) on chromosomes. ecDNA-driven tumors are more aggressive in immunocompetent mice. Single-cell transcriptomic and histological analyses reveal that ecDNA-driven tumors rapidly establish an immunoevasive tumor microenvironment (TME), marked by increased myofibroblastic cancer-associated fibroblasts (myCAFs) and reduced T cell infiltration. Mechanistically, ecDNA heterogeneity generates a subset of cancer cells with extremely high Kras expression, termed super-expressors, which secrete amphiregulin to promote myCAF expansion and suppress T cell infiltration. Clonally organized super-expressors establish an immunoevasive niche in the TME from patients with PDAC. Our findings demonstrate a causal role of ecDNA in TME remodeling, offering insights into cancer heterogeneity and immune evasion.

cancer biology↗

bioRxiv2025

Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane

Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in most cases, unknown. Here we present an expanded view of plasma membrane (PM) phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). PM pools of PI4P are generated by PI 4-kinase Type III (PI4KIII/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA, in the PM. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of PM PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes also lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of PA, a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

cell biology↗

bioRxiv2025

Retrospective attention reveals a decaying theta rhythm in conscious access to a preceeding stimulus

Conscious perception is often presumed to arise immediately upon external stimulation. However, the phenomenon of retroperception-conscious access to a stimulus after it has disappeared-challenges this view by demonstrating that awareness can emerge retrospectively. The fine-grained temporal dynamics governing this process, however, remain unknown. Here, we tested three competing models for the temporal architecture of retroperception: a monotonic decay, a sustained oscillation, and a damped oscillation. We implemented an established retro-cue paradigm and densely sampled behavioral reports. Through spectral analysis and computational modeling, we revealed that both behavioral accuracy and subjective visibility exhibited damped oscillations in the theta-band, superimposed on a time-dependent decay. Furthermore, we demonstrated that these oscillations in accuracy and visibility were temporally aligned, advocating a functional interplay between attention and perception in the post-stimulus period. These results reveal a rhythmically structured and temporally constrained window for conscious reactivation, redefining the limits of when and how the mind can become aware of the past.

neuroscience↗