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Park, S.

Publications and source records attributed to Park, S..

At least 73 records · Page 4Linked to original sources

Mitochondrial Double-Stranded RNA Triggers Ferroptosis via PKR-ISR Signaling in Renal Ischemia-Reperfusion Injury

Renal ischemia-reperfusion (IR) injury remains a leading cause of acute kidney injury, although the precise molecular pathways responsible for tissue injury are not fully understood. In this study, we demonstrate that IR initiates ferroptosis through activation of the PKR-dependent integrated stress response (ISR), which is driven by the accumulation of mitochondrial double-stranded RNA (dsRNA). Our mechanistic investigations reveal that IR perturbs mitochondrial homeostasis, leading to the accumulation of mitochondrial dsRNA and its subsequent release into the cytosol, thereby activating the dsRNA-dependent kinase PKR. Activation of PKR results in eIF2 phosphorylation and maladaptive ISR signaling, which facilitates ferroptosis and impairs renal function. Notably, genetic ablation of PKR or pharmacological intervention to inhibit ISR significantly reduced ferroptosis and preserved renal function. Collectively, these results identify the mitochondrial dsRNA-PKR-ISR axis as a critical mediator of ferroptotic renal injury and highlight its potential as a therapeutic target in ischemic acute kidney injury.

cell biology↗

Dual Oxygen-Partitioned Co-Culture Uncovers Microbe-Specific Epithelial Stress and Homeostatic Programs

Direct epithelial-microbial interactions occur across a steep aerobic-anaerobic interface in the intestine, yet mechanistic analysis has been limited by the difficulty of sustaining oxygen-dependent epithelial cells together with strictly anaerobic microbes in vitro. Here, we establish a dual oxygen-partitioned co-culture system that reproducibly maintains aerobic intestinal epithelial cells and obligate anaerobic gut bacteria, enabling controlled analysis of epithelial responses under physiologically relevant oxygen architecture. Using Mediterraneibacter gnavus and Lacticaseibacillus casei as contrasting microbial partners, we identify distinct epithelial programs. M. gnavus induces epithelial stress characterized by tight-junction disruption, suppression of mitochondrial respiration, and activation of chromatin-associated and innate immune regulatory pathways, whereas L. casei preserves barrier integrity and supports mitochondrial capacity with restrained immune modulation. Integrated transcriptomic and proteomic analyses reveal a shared epithelial energy-conserving response to microbial proximity, upon which microbe-specific stress or homeostatic programs are imposed. In vivo analysis using a dextran sodium sulfate-induced colitis model demonstrates that these epithelial programs become physiologically relevant under inflammatory conditions, with L. casei promoting epithelial repair and immune rebalancing. Together, these findings define oxygen-partitioned epithelial-microbial interactions as a determinant of microbe-specific epithelial states.

microbiology↗

Sleep-Wake Transitions Are Impaired in the AppNL-G-FMouse Model of Early Onset Alzheimers Disease

Poor sleep quality and reduced sleep duration are associated with Alzheimers disease (AD)-related {beta}-amyloid (A{beta}) pathologies. We conducted two studies of sleep/wake, activity and body temperature in AppNL-G-F mice, a strain that exhibits three mutations in the human App gene associated with elevated risk for early onset AD. First, AppNL-G-F mice were compared to wildtype (WT) littermates at 14-18 and 18-22 months of age and, at both ages, were found to exhibit more Wake and less NREM and REM sleep than WT littermates. This long wake/short sleep phenotype was evident during the dark phase at 14-18 months but occurred in both the light and dark phases at 18-22 months. AppNL-G-F mice had fewer short (<60 sec) and more long (>260 sec) Wake bouts and were hyperactive at 18-22 months, which undoubtedly contributed to the increased Wake/reduced sleep. Despite this reduced sleep phenotype, AppNL-G-F mice were no sleepier than WT mice and the sleep homeostat was functional in both strains. In the second study, sex differences in these parameters were assessed at 18-24 months. Reduced sleep was evident in both sexes of AppNL-G-F mice but was clearly more evident in females. Wake and REM sleep bout durations were longer in both sexes of AppNL-G-F mice than in WT littermates. EEG spectral power during NREM sleep was reduced in female AppNL-G-F mice between 4.88-10.50 Hz compared to WT mice whereas, during REM sleep, both male and female AppNL-G-F mice exhibited reduced spectral power in the theta range. These results suggest that A{beta} deposition may impair state transition mechanism(s) in AppNL-G-F mice and demonstrate that, as in human AD patients, the long wake/short sleep phenotype was more evident in female AppNL-G-F mice, thus supporting the use of this strain as a model to investigate interventions that mitigate AD burden during early disease stages.

neuroscience↗

TMPO promotes cellular dissemination and metastasis in circulating tumor cells

Metastasis--the process by which cancer cells spread beyond the primary tumor to distant organs--accounts for the vast majority of cancer-related deaths. To elucidate mechanisms underlying dissemination and metastasis in prostate cancer, we have investigated circulating tumor cells (CTCs) obtained from genetically engineered mouse models (GEMMs). The phenotypic and molecular properties of the CTCs, and organoids derived from these CTCs, closely model the tumor and metastatic phenotypes of their parental GEMMs. Moreover, organoids derived from individual CTCs exhibit molecular and morphological heterogeneity that is associated with distinct metabolic states as well as differences in human prostate cancer outcome. Using computational systems analyses, we have identified TMPO, encoding the nuclear membrane protein lamina-associated polypeptide 2 (Lap2), as a key driver of this heterogeneity. TMPO activity is upregulated in advanced human prostate tumors, metastases, and CTCs, and is associated with adverse clinical outcome. Our findings indicate that TMPO promotes dissemination and metastasis in vivo by enhancing survival in conditions of metabolic stress, and reveal a novel mechanistic link between CTC heterogeneity, stress adaptation, and metastatic potential.

cell biology↗

Genome-Level Hierarchical Attention Transformer with Multi-Head Attention Weighted Sum for Broad-Spectrum Antimicrobial Resistance Prediction and Discovery of Resistance-Related Genomic Contexts

Antimicrobial resistance is a growing global health concern, requiring reliable tools for predicting resistance across a wide range of bacteria and antibiotics. In this study, we introduce a genome-level hierarchical attention transformer (GL-HAT) that integrates a pretrained genomic foundation model with hierarchical attention mechanisms to analyze the full protein sequence context of bacterial genomes. GL-HAT is designed to deliver both accurate resistance predictions and interpretable insights into the genomic features associated with resistance using specialized modules. Trained and validated on a comprehensive dataset of bacterial genomes and antimicrobial susceptibility profiles, the model outperformed traditional machine learning method, with an F1-score of 0.845 and AUROC of 0.953. Moreover, GL-HAT could demonstrate the resistance-related contexts in the genome, such as vanA operon and nearby resolvase genes in vancomycin-resistant Enterococcus and tet(M) gene adjacent to conjugation proteins in tetracycline-resistant Streptococcus pneumoniae. By combining high accuracy with interpretability, GL-HAT offers a practical approach for advancing AMR diagnostics and research, supporting more informed clinical and public health decisions.

bioinformatics↗

A Retinoic Acid Autoregulatory Loop Governing Prefrontal-Motor Arealization

The frontal lobe comprises the prefrontal association cortex (PFC), which supports complex cognition and goal-directed behavior, and the motor cortex (MC), which executes movement. A hallmark of primate brain evolution is PFC expansion accompanied by a posterior displacement of the MC. Retinoic acid (RA) signaling has emerged as a key regulator of PFC specification and expansion. However, the mechanisms that spatially confine RA signaling within the developing PFC, and the downstream RA-responsive gene networks, remain poorly understood. Here we defined an RA-associated gene regulatory network (RA-GRN) in the developing human PFC and identified MEIS2, which encodes a transcription factor linked to intellectual disability and autism spectrum disorder (ASD), as its key hub of this network. Conditional deletion of Meis2 in postmitotic cortical excitatory neurons in mice results in a partial respecification of prospective prefrontal association territories toward motor-like molecular and connectional features, highlighting a critical role of postmitotic neurons in establishing and maintaining cortical areal identities. Concomitant with Meis2 loss, the population of excitatory neurons expressing the RA-synthesizing enzyme ALDH1A3, and consequently RA signaling itself, is markedly reduced in the developing medial prefrontal cortex (mPFC). These findings revealed a conserved autoregulatory loop: RA [->] MEIS2 [->] ALDH1A3 [->] RA that reinforces a PFC-enriched RA gradient and organizes the MC-PFC axis. Together, our findings reveal a postmitotic mechanism by which specific features of neuronal identity reinforce RA signaling to define key features of prefrontal and motor cortical territories, linking a classic morphogen to transcriptional identity, neural circuit formation and function, and potentially to psychiatric disorders.

neuroscience↗

Time-resolved ligand dynamics revealed in a β-lactamase using room-temperature serial crystallography

{beta}-Lactamases catalyze {beta}-lactam antibiotic hydrolysis and are important contributors to bacterial antimicrobial resistance; {beta}-lactamase inhibitors are widely used to overcome {beta}-lactamase-mediated antibiotic resistance. Nucleophilic serine {beta}-lactamases (SBLs) react with their substrates and clinically available inhibitors via a covalent reaction to give complexes which can undergo further reaction. Using room temperature drop on fixed target serial crystallography, where ligands are rapidly mixed with microcrystals, and classical single-crystal crystallography at cryogenic temperatures, we investigate the reversible covalent reaction of the SBL CTX-M-15 with the diazobicyclooctane inhibitor avibactam. We observe avibactam covalently reacted (ring-opened) with the nucleophilic Ser70, at timepoints from 80 ms to minutes (room temperature) and hours (100 K). These crystallographic data reveal time-dependent movement of the avibactam carbamoyl complex, from 1.3 s onwards, that has implications for the 5-exo-trig recyclization mechanism that determines inhibitor reformation. Combined with molecular dynamics simulations and quantum mechanics calculations at the density functional theory level, the results show that in the first seconds of the reaction the avibactam N-sulfate nitrogen is poorly positioned for recyclization. This subsequently equilibrates after 10 s to a stable endpoint that is in a conformation potentially primed to initiate recyclization through attack of the N-sulfate nitrogen on the carbamoyl carbon. These results further demonstrate the capacity of room-temperature serial crystallography to capture time-resolved changes in ligand conformation at an enzyme active site, complementing discrete classical cryo-crystallography. These data inform on ligand dynamics and the stereoelectronics of diazobicyclooctane inhibition, aiding drug discovery efforts to develop inhibitors of nucleophilic enzymes.

biochemistry↗

Drop on fixed target reaction initiation approach for serial and time resolved crystallography

We describe the design and implementation of a drop on fixed target method for time-resolved serial crystallography at both synchrotron and XFEL facilities. A piezoelectric droplet dispensing pipette is employed for addition of picolitre volume (40 - 90 pL) aqueous droplets, containing (co-)substrate(s) or ligand(s), onto enzyme microcrystals immobilised on a solid support. The system was tested with various enzyme systems, including lysozyme and two -lactamases, CTX-M-15 and AmpCEC. Mitigation strategies for cross-well contamination, including the implementation of interleaved controls, are described; the overall performance of the system at synchrotron and X-ray free electron laser facilities was evaluated. This drop on fixed target method is a reliable framework for time-resolved crystallography and will improve the consistency of measurements across facilities.

biophysics↗

From minutes to bounds: A probabilistic UV-C control and a shape-only morphological fingerprint for postharvest Colletotrichum

Postharvest losses in high-value horticultural crops such as cacao and coffee are often driven by Colletotrichum spp. and other latent fruit pathogens. Ultraviolet-C (UV-C) is increasingly deployed as a chemical-free postharvest technology, yet prescriptions remain framed in minutes rather than in probabilistic guarantees of disease control and safety. We present a dual framework that (1) establishes conservative confidence bounds on survival and (2) validates a "shape-only" morphological fingerprint. This approach addresses the biological complexity of host-pathogen interactions by quantifying isolate-specific heterogeneity, rather than averaging it away. We utilized a large Colletotrichum dataset (n = 5,363) from cacao and coffee, spanning diverse treatments including UV-C, UV-B, and sonication. First, focusing on the Coffee UV-C cohort ([~]10 min), we quantified this heterogeneity; the most conservative Clopper-Pearson upper 95% bound on survival reached 1.000, highlighting partial survival events (e.g., isolate P24-88) under otherwise high-efficacy conditions. This probabilistic framework captures the "tail-risk" of biological resilience instead of assuming complete kill. Second, we trained machine learning models on the full dataset using only geometric features (e.g., aspect ratio, asymmetry), explicitly excluding all primary size metrics. Serving as a rapid physiological indicator of UV-induced stress, these "shape-only" models successfully predicted pathogen host-origin (Accuracy {approx} 0.93) and post-treatment survival (R{superscript 2} {approx} 0.74). The signals ability to generalize across UV-B and sonication confirms that geometry, not just growth reduction, carries a robust and transferable physiological stress signature. This work provides a device-agnostic, probabilistic control platform, replacing time-based heuristics with quantitative guarantees and a generalizable, shape-based diagnostic. HighlightsO_LIA conservative upper 95 % confidence bound (on survival = 1.000) was observed for the Coffee UV-C ([~]10 min) cohort, revealing strong isolate-specific heterogeneity rather than a universal kill guarantee C_LIO_LIIsolate-specific heterogeneity (e.g., localized P24-88 survival) was quantified rather than averaged away. C_LIO_LIA size-free morphological fingerprint predicted host-origin (Accuracy {approx} 0.93) and survival (R{superscript 2} {approx} 0.74). C_LIO_LIThe shape-only signal generalized across diverse stressors, including UV-C, UV-B, and sonication. C_LIO_LIA probabilistic, device-agnostic control framework replaces traditional time-based heuristics. C_LI

microbiology↗

Precision at Every Scale: Efficiency in AI-Driven De Novo Antibody Design

The precise de novo design of antibodies remains a therapeutic challenge. The AI platform, GaluxDesign, was evaluated in a high-efficiency Precision-Scale Workflow by synthesizing and testing only 50 full-length IgG candidates per epitope across eight distinct epitopes from six therapeutic targets. This campaign yielded a 10.5% binder rate (estimated EC50 < 100 nM), identifying target-specific binders for seven of eight epitopes, with multiple candidates exhibiting sub-nanomolar to single-digit nanomolar dissociation constants (Kd). We further assessed the same workflow on nine shared benchmark targets selected for external comparison, where GaluxDesign identified target-specific binders for eight of nine targets, demonstrating strong target-level performance relative to previously reported de novo antibody design approaches. Together, these results establish a high-efficiency, precision-scale workflow for generating novel, high-affinity therapeutic antibodies.

bioengineering↗

Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome

We present KOREF1-G-TTAGGA, the first Telomere-to-Telomere Accurate and Gapless Genome Assembly, standing as the Korean standard reference genome. The paternal and maternal haplotypes spanned 2.91 and 3.03 Gb. Genome-wide, at least 99.15% of assembled sequences were reliably haplotype-resolved, and over 95% remained accurate even in the most error-prone loci, including centromeric satellite arrays and segmental duplications. Rare-k-mer copy-number concordance within satellite arrays held up 98.9% and 98.8% per haplotype. Bionano optical maps fully spanned all canonical rDNA arrays on the five acrocentric chromosomes. The assembly quality index (AQI) of 99.77 and 99.69 exceeded the reference-quality threshold of 90, and more than 99.99% of gene and cCRE sequence was free of structural error. Both haplotypes further showed high base-level accuracy, with consensus quality value (QV) of 81.19 and 79.03, corresponding to one error per 131 and 80 Mb. KOREF1-G-TTAGGA is among the highest-quality East Asian telomere-to-telomere assemblies. It moreover anchors a decade-spanning multi-ome reference dataset for defining individual molecular states. Together, these resources define the personal referenceome as a foundation for individual biology and precision medicine, with the assemblies, annotations, and all multi-omic data openly available at https://koreanreference.org.

genomics↗

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↗

Exclusive ipsilateral representation of sequential tactile differences challenges contralateral dominance

Tactile perception has long been thought to be processed primarily in the contralateral somatosensory (S1), yet the functional role of ipsilateral S1 in human tactile discrimination remains unclear. We designed an fMRI experiment to investigate the neural representation of sequential vibrotactile discrimination as participants judged which of two successive stimuli delivered to the fingertip was higher in frequency. Contralateral S1 showed robust activation during unilateral stimulation, whereas ipsilateral S1 exhibited overall suppression. Interestingly, we found reliable frequency-dependent modulation in ipsilateral S1, which was absent in a control condition requiring no comparison between stimuli. Multivariate representational analyses further demonstrated that the difference in the neural representations between successive stimuli was strengthened under memory demands, particularly within ipsilateral S1 and parietal cortices. The ipsilateral representation was observed for stimulation of either hand, suggesting a bilateral and symmetric encoding mechanism rather than a hand-specific effect. Together, these findings demonstrate that the ipsilateral S1 contributes to tactile discrimination despite its overall suppression during unilateral stimulation, challenging classic contralateral models of somatosensory processing. Our results highlight interhemispheric coordination as a key mechanism underlying perceptual decisions.

neuroscience↗

Human Norovirus NS7 Protein Activates Canonical Inflammasome Pathways via NLRP6 in Intestinal Epithelial Cells

Human norovirus (HNoV) is a leading cause of acute gastroenteritis, yet the mechanisms by which it interfaces with host innate immunity remain elusive. Here, we demonstrate that the HNoV NS7 protein, an RNA-dependent RNA polymerase, acts as a direct activator of canonical inflammasomes. Using reconstituted cell systems and human intestinal enteroids (HIEs), we found that NS7 interacts with both NLRP3 and NLRP6, promoting ASC speck formation, caspase-1 cleavage, and secretion of IL-1{beta} and IL-18. HNoV infection of HIEs recapitulated these events, including gasdermin D processing and robust IL-18 release. Importantly, CRISPR/Cas9-mediated NLRP6 deficiency abrogated inflammasome activation and markedly enhanced viral replication, underscoring the essential role of NLRP6 in epithelial antiviral defense. These findings identify NS7 as a novel inflammasome activator and establish NLRP6 as a key determinant of innate immune control of HNoV. Our study highlights inflammasome signaling as a potential therapeutic target for norovirus infection. Author summaryIn this study, we used human intestinal organoid models to explore how norovirus infection triggers a specific immune response known as inflammasome, which helps protect the gut from viral invaders. We focused on a viral protein called NS7 and discovered that it directly activates two types of inflammasome sensors, NLRP3 and NLRP6. We found that NLRP6, which is abundant in the gut lining, is especially important for detecting norovirus and launching an immune response. When we removed NLRP6 from intestinal cells, the virus was able to replicate more easily, and normal immune activation was lost. Our results reveal that norovirus uses its NS7 protein to interact with the bodys immune machinery in the intestine, and that NLRP6 plays a key role in controlling infection. This work highlights a new way in which the gut senses and responds to norovirus and may help guide future efforts to develop treatments that target these immune pathways.

immunology↗

Genomic Prediction and SNP Importance Analysis for Agronomic Traits in Two Coffea canephora Populations

This study reveals that distinct breeding populations of Coffea canephora can achieve agronomic success through fundamentally different biological strategies. To uncover this, we performed a comparative genomic analysis of two populations ( Premature and Intermediate), integrating single-SNP association, machine learning (Bootstrap Forest), and Gene Ontology (GO) pathway analysis. The genetic architecture of the Premature population was linked to specialized metabolic pathways, including lipid modification and processes within the organelle lumen, a finding supported by the identification of a putative caffeine synthase 3 gene. In contrast, traits in the Intermediate population were governed by variation in core cellular machinery, with significant enrichment for pathways related to actin cytoskeleton regulation and salicylic acid signaling. This discovery provides a new biological context for important candidate genes involved in disease resistance (e.g., RPP13-like, NB-ARC, CERK1). These findings demonstrate that population-specific biological routes underpin agronomic performance, providing a powerful foundation for designing more targeted breeding programs in coffee. We release population-specific, ranked SNP lists and GO gene sets as a reusable resource to enable meta-analyses and benchmarking in coffee and perennial crops.

genetics↗

A chromatin-associated pool of Aurora A controls kinetochore-microtubule attachments to ensure chromosome biorientation

Accurate chromosome segregation requires dynamic kinetochore-microtubule attachments that, under the regulation of Aurora family kinases, biorient and align replicated chromosomes. In C. elegans, Aurora A acts with the TPX2-related activator TPXL-1 to regulate these attachments and control spindle length. We show that, in addition to prominent spindle pole localization, TPXL-1-AurA has a chromatin-associated pool positioned between the sister kinetochores. Structural modeling and biochemical analysis support TPXL-1 directly recognizing the nucleosome acidic patch via an arginine anchor. Disrupting this interaction selectively removed chromatin-bound TPXL-1-AurA and caused chromosome missegregation, whereas elevation of the chromatin pool disrupted chromosome alignment. These opposing perturbations inversely affected kinetochore recruitment of the microtubule-binding Ska complex. These results support spatially distinct TPXL-1-AurA populations acting sequentially, with the spindle pole pool controlling spindle length by switching kinetochores out of a depolymerization-coupled state, and the chromatin pool controlling attachment stabilization to ensure biorientation prior to anaphase.

cell biology↗

Sensory Neural Noise as a Limiting Factor in Visual Working Memory Precision in Neurotypicals and Schizophrenia

The neural mechanisms that determine the capacity limits of working memory (WM) are not well understood, with traditional views identifying prefrontal circuitry as the main source of WM limits. Sensory noise, however, remains an underexplored explanation for WM limits despite its unavoidable influence on brain systems that encode and relay sensory information. Here, we show that individual differences in internal sensory noise during visual processing predict visual WM capacity. We further demonstrate that the well-documented WM deficits observed in schizophrenia can be associated with atypically high levels of visual sensory noise, offering a new explanatory framework for these deficits. By experimentally manipulating sensory noise via transcranial direct current stimulation applied to the visual cortex, we also show that changes in sensory noise led to corresponding changes in visual WM precision in individuals with schizophrenia. Finally, a computational model demonstrates that the same sensory noise measured during visual perception can limit WM precision during WM maintenance. These findings show that sensory noise may explain a significant amount of variance in WM function in both neurotypical adults and individuals with schizophrenia.

neuroscience↗

Ethylene-induced host responses enhance resistance against the root-parasitic plant Phelipanche aegyptiaca

AbstractsThe root parasitic plant Phelipanche aegyptiaca and related species pose a grand challenge for agriculture. By directly attaching to host crops to acquire resources, they can severely decrease yields. At the same time, their underground location hides them from sight for much of their life and protects them from typical weed control methods. New strategies for parasitic weed control are needed, with host resistance among the most attractive, but the mechanisms by which hosts respond to parasitic plant attacks are still unclear. In plants, the phytohormone ethylene is a crucial modulator responding to various stresses such as flooding and pathogen attack, and our data suggest that ethylene signaling may be important in host response to P. aegyptiaca. Here, we demonstrated that ethylene plays a role against P. aegyptiaca using two host plants, Arabidopsis and tomato. Arabidopsis plants with the ethylene reporter construct (EBS::GUS) were analyzed and revealed that stress from excess water and P. aegyptiaca parasitism both induced ethylene responses in the host Arabidopsis roots. We also observed that applying an ethylene precursor (ACC) to host roots inhibits the attachment of P. aegyptiaca. Lines of Arabidopsis and tomato with mutations in Ethylene-Resistant 1 (ETR1) and Constitutive Triple-Response 1 (CTR1) have altered tolerance to P. aegyptiaca, suggesting that the ethylene signaling pathway is associated with enhanced resistance to parasitism. These results point to ethylene-mediated responses as a starting point to gain insight into host response to parasitism, with potential to increase host resistance to parasitic plants.

plant biology↗