Biology subjects

Kim, J.

Publications and source records attributed to Kim, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Network-targeted TMS modulates task-related striatal activity during motor skill learning

The striatum, a critical hub for motor skill learning, is located deep within the subcortical region, making noninvasive stimulation particularly challenging. Nevertheless, recent studies suggest that transcranial magnetic stimulation (TMS) can modulate subcortical activity indirectly by targeting functionally connected cortical areas. In this study, we applied TMS to the dorsolateral prefrontal cortex (DLPFC) immediately before the fMRI session measuring task-related activity in the striatum during motor learning. We examined whether continuous theta-burst stimulation (cTBS) and high-frequency stimulation (20 Hz) could modulate motor learning and associated striatal responses with opposing effects. There was no significant effect of either stimulation condition on the overall motor learning performance. However, cTBS significantly reduced performance-related striatal activity, while 20 Hz stimulation did not show any modulatory effect. These findings demonstrate that cTBS targeting the corticostriatal network can suppress striatal activity and suggest its potential use in clinical trials for treating disorders such as addiction associated with hyperactive striatal responses.

neuroscience↗

bioRxiv2026

MosaicTR: tandem repeat somatic instability quantification from long-read sequencing

SummarySomatic instability of tandem repeats modifies disease onset and progression in repeat expansion disorders and serves as a biomarker for mismatch repair deficiency in cancer. MosaicTR quantifies per-locus somatic instability from haplotype-tagged long-read sequencing data without the read-length and PCR stutter limitations of short-read approaches. A motif-unit-weighted metric reduces platform-specific sequencing noise on both PacBio HiFi and Oxford Nanopore data, and pairwise comparison modes support detection of tissue-specific or longitudinal instability changes. AvailabilityMosaicTR is freely available at https://github.com/junsoopablo/mosaictr under the MIT license. Contactjunsoopablo@snu.ac.kr

bioinformatics↗

bioRxiv2026

A microfluidic platform for multi-marker profiling of extracellular vesicles from single-cell-derived clones

Extracellular vesicles (EVs) carry molecular cargo that can reflect the real-time state of parental cells, yet most in vitro EV analyses rely on bulk approaches and therefore average over pronounced heterogeneity in both cell and EV populations. Here, we present a semi-open microfluidic platform that enables multi-marker profiling of EVs released from single-cell-derived clones, allowing EV signatures to be linked to clonal progeny originating from a single parental cell. The platform integrates aligned cell and EV arrays containing 17,305 wells, assembled with a 3D-printed housing to capture released EVs in one-to-one matched wells. Captured EVs are immunolabeled for canonical tetraspanin markers (CD9, CD63, CD81) and EpCAM, imaged by high-resolution fluorescence microscopy, and quantified using an automated image-analysis pipeline. Applying the platform to single-cell-derived PC3 clones revealed substantial heterogeneity in EV marker co-expression, with hierarchical clustering identifying four distinct tetraspanin co-expression profiles. The fraction of EpCAM-positive EVs increased with PC3 cell proliferation, as assessed by endpoint cell number, whereas free (non-EV-associated) EpCAM showed no correlation. This platform enables near single-EV-level, multi-marker profiling from single-cell lineages and provides a practical approach to simultaneously dissect both cellular and EV heterogeneity.

bioengineering↗

bioRxiv2026

Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers

Accurate taxonomic classification of metagenomic sequencing data is essential for identifying the diverse organisms present in environmental and clinical samples. To address this, we previously developed Metabuli, an alignment-free classifier that bridges the gap between nucleotide-level resolution and protein-level sensitivity. Central to this approach is the metamer, a novel joint DNA and amino acid k-mer concept introduced by Metabuli to classify taxa across varying levels of database representation. In this study, we significantly optimized its core metamer search by incorporating advanced techniques. By introducing spaced metamers and reduced amino acid alphabets to boost sensitivity, we improved both precision and recall by 4.7 and 2.8 percentage points in a species exclusion test. Furthermore, integrating syncmers with spaced metamers halved the reference database size and doubled the classification speed; despite a slight decrease in recall, this configuration continued to outperform state-of-the-art alignment-free tools. Contactjbeom@snu.ac.kr and martin.steinegger@snu.ac.kr

bioinformatics↗

bioRxiv2026

Synergistic Electroceutical-Glucocorticoid Intervention Mitigates Dexamethasone-Induced Muscle Atrophy in Aging Skeletal Muscle

Dexamethasone (DEX), a synthetic glucocorticoid widely prescribed for allergic and inflammatory diseases, is known to induce adverse effects, particularly skeletal muscle atrophy. DEX-induced atrophy exacerbates sarcopenia and has a more pronounced impact on aged skeletal muscle than on young skeletal muscle. To address this unmet clinical need, we introduce an electroceutical approach that counteracts DEX-induced muscle atrophy and enhances functional recovery in aging muscle. When applied to both young and aged human-derived skeletal muscle cells (skMCs) exhibiting DEX-induced atrophy, electroceutical treatment promoted recovery of myotube diameter and upregulated hypertrophy-related gene expression. Furthermore, in a preclinical study, young and aged mice treated with DEX to induce muscle atrophy exhibited significant muscle recovery following electroceutical treatment. This effect was evident from the restored cross-sectional area (CSA) of type IIA muscle fibers and the upregulation of hypertrophy-related genes. This study highlights electroceuticals as a pioneering non-pharmacological strategy complementary to glucocorticoid therapies, potentially transforming clinical outcomes and quality of life, particularly for older populations vulnerable to muscle wasting.

bioengineering↗

bioRxiv2026

Application of the Nicking Loop™ targeted library preparation method to DNBSEQ™ sequencing

Nicking Loop is a PCR-free targeted library preparation method that combines conversion of linear target DNA into circular single-stranded DNA (CssDNA) library with early sample indexing in a single step. The resulting CssDNA libraries can be either directly sequenced or optionally amplified, offering maximum flexibility across sequencing applications. This study demonstrates the compatibility of Nicking Loop circular libraries with a MGIs DNBSEQ platform. Compatibility was evaluated against established linear Nicking Loop libraries sequenced on Illumina MiSeq platform. Using synthetic reference samples with defined variant allele frequencies, Nicking Loop method demonstrated matching performance across both library formats and sequencing platforms. Key quality metrics, including unique molecular identifier (UMI) distributions, error profiles and VAF detection, were all highly consistent. Both library types generated over 97% singleton UMIs, indicating uniform template sampling, and VAF measurements were strongly concordant across platforms (Spearmans {rho} = 0.939). Collectively, these findings demonstrate that Nicking Loop method is directly applicable to circular NGS platforms, such as DNBSEQ, strongly supporting its use as a platform-agnostic library preparation strategy for targeted sequencing applications.

molecular biology↗

bioRxiv2026

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Balanced Robertsonian translocation (ROB) is the most common chromosomal rearrangement in humans, with an estimated occurrence of 1 in 800 in newborn studies. Carriers are at increased risk of cancer and often diagnosed at fertility clinics after facing recurrent miscarriages, infertility, or aneuploid offspring. Genotyping carriers with DNA sequencing has been challenging because of gaps and misrepresentation of the translocation fusion site in the human reference genome. Only recently, telomere-to-telomere (T2T) human genomes successfully revealed sequences of the acrocentric short arms, including the most common ROB fusion site. A ROB results in loss of two ribosomal DNA (rDNA) arrays and its adjacent distal sequences, including the highly conserved distal junction (DJ). Here, we present a novel method to type ROB carriers directly from short sequencing reads by estimating DJ copy number. We demonstrate that our method successfully genotypes ROBs using a reference-free approach or alignments to either T2T-CHM13v2 or GRCh38. Applying the method to a cohort of healthy newborns and family members (n=4,172) as well as the UK Biobank (n=490,416), we find candidate ROBs at a frequency consistent with the previously reported 1 in 800 incidence (0.11-0.12%). In addition to ROB carriers, we report the frequency of one DJ loss (9, 2.8-3.4%) or gain (11+, 8.4-9.3%) from the two cohorts and the 1000 Genomes Project (n=3,202), and characterize the underlying structural variation in near-T2T genome assemblies from the Human Pangenome Reference Consortium. Importantly, our method provides the first sequencing-based diagnostic for Robertsonian chromosomes and can be applied to low-coverage sequencing data, enhancing its clinical applicability and enabling new studies of structural variation on the acrocentric chromosomes.

genomics↗

bioRxiv2026

Systemic delivery of drug-free polymeric nanoparticles reprograms innate immunity in a sex-dependent manner after spinal cord injury

Sex differences influence distinct inflammatory responses after spinal cord injury (SCI), yet their impact on immune-modulating nanotherapeutics remains unclear. Here, we investigated the sex-dependent effects of drug-free poly(lactic-co-glycolic acid) (PLGA)-based nanoparticles (NPs) following SCI. Systemic NP administration enhanced locomotor recovery in both sexes and eliminated the functional gap observed in controls. Mechanistically, NPs engaged distinct immune pathways between sexes. Females accumulated more NPs in the spleen, leading to reduced monocyte-derived macrophage infiltration, whereas males showed greater NP accumulation at the lesion and attenuated microglial activation. Transcriptomic analysis showed preferential modulation of eicosanoid-related pathways in females and NF-{kappa}B-linked signaling in males. These sex-specific, yet convergent NPs-induced immunomodulatory effects reduced fibrotic scarring and enhanced remyelination, with females showing greater Schwann cell-mediated repair and males exhibiting marked suppression of microglial activation. Collectively, these findings demonstrate that NPs promote comparable functional recovery in both sexes through distinct, sex-influenced immune mechanisms and establish a translational framework for sex-informed immune targeting and nanotherapeutic design in SCI and other inflammation-mediated diseases. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/709912v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@5af2ecorg.highwire.dtl.DTLVardef@1027071org.highwire.dtl.DTLVardef@12449ceorg.highwire.dtl.DTLVardef@169a327_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

The complete genome of the KOLF2.1J reference iPSC line

While induced pluripotent stem cells (iPSCs) have gained popularity in studying neurodegenerative diseases, the heterogeneity of stem cells used across studies impacts cross-study comparison. The iPSC Neurodegenerative Disease Initiative (iNDI) selected the KOLF2.1J cell line and prioritized its use as a reference standard for studying the effects of pathogenic variants on cell biology due to its stability and neutral neurodegenerative disease genetic risk. This cell line, and its derivatives expressing over 100 variants related to Alzheimers disease, Parkinsons disease, and other neurological diseases, are available for academic and industry access. Current genomic data analyses are limited by the use of a human reference genome that does not capture the complete genetic background of a given iPSC line. While in the future this issue may be partially mitigated by the creation of a comprehensive human pangenome, previous work has shown that generating custom genomes is of value both to characterize the variation present and to serve as a more appropriate genomic reference. Here, we generated and characterized a custom complete genome assembly from KOLF2.1J. Mapping of sequencing reads to a personalized diploid assembly results in more comprehensive mapping compared to traditional linear references (i.e GRCh38). In addition, we provide a comprehensive custom gene annotation along with isoform expression and differential methylation analyses across multiple cell types. The assembly and all additional data is browsable and publicly available. This resource will enable more accurate investigation of the KOLF2.1J cell line and any genomics data generated compared to using traditional generalized references, while also serving as a foundational approach for establishing custom reference assemblies for other high-value iPSC lines.

genomics↗

bioRxiv2026

Lung endothelial niche signaling governs self-renewal and fate transitions of human alveolar stem cells

Chronic lung diseases such as pulmonary fibrosis are characterized by the irreversible loss of alveolar type 1 (AT1) cells, yet the mechanisms governing human alveolar stem cell self-renewal and differentiation remain poorly defined. Here, we identify a lung endothelial niche that sustains the self-renewal of human alveolar type 2 (AT2) stem cells through MAPK signaling, enabling robust long-term expansion while preserving stem cell fate. Although YAP activation initiates AT1 transcriptional programs, it is insufficient to complete lineage maturation. We show that MAPK inhibition together with LATS inhibition promotes nuclear translocation of YAP, enhancing AT1 differentiation. Expanded human AT2 stem cells engraft in fibrotic lungs and contribute to alveolar regeneration while undergoing directed differentiation within diseased human lung tissue. Together, our findings define a niche-controlled signaling mechanism governing human alveolar stem cell fate and advance our understanding of alveolar regeneration.

cell biology↗

bioRxiv2026

Rapid Orthographic and Delayed Phonological Processing: ERP and Oscillatory Evidence from Masked Priming in Korean

A central question in visual word recognition concerns whether orthographic and phonological codes are coordinated sequentially or in parallel during lexical access. Korean Hangul, an alpha-syllabic writing system with morphophonemic spelling principles, allows independent manipulation of orthographic and phonological syllable overlap. In a masked priming lexical decision task with EEG (N = 30), we contrasted orthographically identical primes (e.g., -), phonologically overlapping primes (e.g., -), and unrelated primes. Event-related potentials and time-frequency representations (theta: 4-8 Hz, lower beta: 13-20 Hz, upper beta: 20-30 Hz) were analyzed to capture both evoked and oscillatory neural dynamics. Orthographic priming produced a cascade of facilitative effects: early fronto-central P200 enhancement (150-250 ms) with upper beta synchronization (30-290 ms), followed by centro-parietal N400 reduction (350-550 ms) with frontal theta suppression (400-730 ms), and behavioral facilitation. Phonological priming, by contrast, elicited an inhibitory behavioral effect and sustained lower beta activity over central regions (310-590 ms) but produced no early electrophysiological modulation, consistent with lexical competition. This spatiotemporal dissociation suggests that orthographic syllable processing can emerge at early stages and cascades into later lexical-level processing, whereas phonological syllable effects are confined to later processing stages. These findings provide support for a sequential or cascaded account of orthographic-phonological coordination, as predicted by dual-route models, while challenging strong forms of parallel activation, and suggest that the alpha-syllabic structure of Korean may enable a processing strategy in which orthographic parsing serves as an efficient entry route to the lexicon.

neuroscience↗

bioRxiv2026

Maternal age modulates progeny social behavior via a small RNA-neuropeptide axis

Parental age influences offspring traits across species, yet the molecular pathways by which maternal state modulates progeny neural function remain poorly defined. Here we demonstrate that maternal age in C. elegans regulates progeny avoidance of the social pheromone by modulating the activity of a defined sensory circuit. Progeny of young mothers exhibit stronger activity of the pheromone-sensing ADL neurons and enhanced pheromone avoidance, whereas progeny of old mothers display reduced neuronal responses and weaker repulsion. We identify an ERI-1-microRNA-neuropeptide signaling axis operating in peptidergic AVH interneurons that modulates ADL circuit responsiveness. ERI-1 promotes expression of the neuropeptide gene flp-26 by repressing mir-8207, and signaling from AVH to ADL establishes pheromone sensitivity. Maternal aging is associated with reduced ERI-1 expression in progeny AVH neurons and dampening this signaling pathway. Consequently, progeny of young mothers, though developmentally less robust, disperse more readily from crowded, pheromone-rich environments, offsetting their early-life disadvantages. Our findings reveal a molecular and circuit-level mechanism by which maternal physiology adaptively configures offspring neural computation and behavioral strategy across generations.

neuroscience↗

bioRxiv2026

Beyond the skin barrier: optical clearing enables non-invasive cortex-wide optical coherence angiography in mice in-vivo

Non-invasive, high-resolution visualization of mouse brain vasculature remains challenging due to significant light scattering and absorption by mammalian tissues, hence many optical imaging protocols require scalp and/or skull excision. Here we present a fully reversible tartrazine-based optical clearing strategy that enables cortex-wide optical coherence tomography angiography (OCTA) through intact scalp and skull. We characterized tartrazine properties in the near infrared (NIR)-II band of the 1.3 {micro}m swept-source OCTA system, confirming minimal absorption across 1.25-1.35 {micro}m wavelength range and an effectively constant refractive index, suggesting negligible OCTA distortions. Spatially selective agent application showed that intracranial vessels emerge selectively within the treated region of interest (ROI), whereas untreated regions retain strong interference by the scalp vascular features. Depth-encoded projections and cross-sectional OCTA demonstrated an increased signal recovery at depth and an extended vessel-detection range after clearing. Vessel-map changes were quantified using intersection-over-union and Dice coefficients, yielding high similarity outside the ROI and reduced similarity within the ROI, consistent with a transition from scalp to brain vasculature. Reproducibility was confirmed in three independent 11-week-old mice and validated against scalp-removed reference OCTA. Screening tartrazine in the 0.3-0.8 Molar concentration range (7-min application) identified 0.6 M as optimal for whole-cortex scanning, balancing clearing efficacy and solution handling. Finally, the protocol generalized across mice aged 5-18 weeks. This approach provides a practical route to non-invasive structural cerebrovascular mapping with OCTA.

bioengineering↗

bioRxiv2026

A Novel Pilus System in Candidate Phyla Radiation Bacteria

The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15-50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primarily identified through metagenomic approaches. Candidatus Mycosynbacter amalyticus is a parasitic CPR bacterium that specifically targets Gordonia amarae, an actinobacterium with a hydrophobic, mycolic acid-rich cell envelope. Previous cryo-electron tomography indicated that Ca. M. amalyticus assembles thin extracellular filaments that are important for host interaction, yet their molecular identity remains unknown. Here, we applied single-particle cryo-electron microscopy to determine high-resolution structures of these filaments (2.8 and 3.6 [A]), enabling the unambiguous identification of two previously uncharacterized pilins from the experimental density maps. These pilins, designated PamA and PamB, assemble into unique helical filaments distinct from all previously characterized filaments in both domain architecture and assembly mechanism. Despite low sequence identity, both PamA and PamB share conserved structural principles, including Ig-like folds and donor-strand exchange-mediated assembly. Phylogenetic analysis indicates that Pam pilins are exclusive to CPR bacteria, with homologues distributed predominantly across the classes Saccharimonadia and Microgenomatia. Analysis of the conserved pam operon identifies putative chaperones (PamC and PamD) and assembly factors structurally homologous to chaperone-usher pili components, suggesting an analogous but distinct assembly pathway. These findings expand the known diversity of bacterial pilus systems and demonstrate the power of structural approaches for characterizing uncharacterized proteins encoded within CPR genomes.

microbiology↗

bioRxiv2026

Bioactivity-driven discovery of repurposable antivirals as OSCAR inhibitors that promote cartilage protection via transcriptomic reprogramming

Osteoarthritis (OA) is a progressive degenerative joint disorder characterized by cartilage degradation, chronic pain, and impaired joint function. The avascular nature of cartilage isolates chondrocytes from systemic circulation, presenting significant challenges for therapeutic intervention. Despite extensive efforts, no clinically effective disease-modifying osteoarthritis drugs (DMOADs) are currently available. Targeting chondrocyte-specific receptors has therefore emerged as a promising strategy. The osteoclast-associated receptor (OSCAR), expressed on chondrocytes, has been implicated in the regulation of cartilage homeostasis and OA pathogenesis. Here, we applied sBEAR (Structurally similar Bioactive compound Enrichment by Assay Repositioning), a bioactivity-driven virtual screening framework independent of target structural information, to identify small-molecule inhibitors of the OSCAR-collagen interaction. By mining large-scale bioactivity profiles, we identified adefovir (ADV) and brivudine (BRV), as candidate OSCAR inhibitors. Molecular docking analyses indicated that both compounds occupy the collagen-recognition pocket within the OSCAR D2 domain. Intra-articular administration of these compounds in a post-traumatic OA mouse model significantly attenuated OA progression and enhanced chondrocyte regeneration. Both compounds increased Sox9 expression, and transcriptomic analyses revealed that BRV reverses inflammatory and extracellular matrix-degrading transcriptional programs. Together, these findings establish OSCAR as a therapeutically actionable target in OA and highlight ADV and BRV as potential DMOAD candidates.

bioinformatics↗

bioRxiv2026

Prefusion-specific glycoprotein B human antibodies protect against neonatal HSV-2 infection

Herpes simplex virus (HSV) causes severe neonatal infections and long-term neurological issues, with antivirals offering limited efficacy and no approved vaccines. Viral entry requires glycoprotein B (gB) for membrane fusion, yet no human antibodies to the prefusion form of gB have been identified, and antibodies targeting vulnerable epitopes are limited. We used prefusion-stabilized HSV-2 gB and LIBRA-seq technology to analyze B cells from seropositive and healthy donors, discovering four prefusion-specific human antibodies binding unique gB epitopes as determined by cryo-EM. Antibodies 5-18 and 3-6 showed strong cross-neutralization against HSV-1 and HSV-2, offering protection in a neonatal mouse model. These findings highlight the molecular and structural determinants of HSV-2 prefusion gB recognition by human antibodies and demonstrate the translational potential of prefusion-specific gB antibodies.

immunology↗

bioRxiv2026

A dual-color miniature endoscope for calcium imaging in behaving mice

Calcium imaging with miniature endoscopes has become an essential tool in neuroscience, but conventional miniscopes typically record signals from only a single calcium indicator. Here, we present a dual-color miniature endoscope (miniscope) that enables simultaneous calcium imaging from two neuronal populations using spectrally distinct genetically encoded indicators. In freely moving mice, we used this system to record activity from striatal neurons of the direct (dSPN) and indirect (iSPN) pathways. We showed that dSPNs were activated earlier than iSPNs during contraversive movements, with dSPNs preferentially active during acceleration and iSPNs during deceleration. During ipsiversive turns, however, this temporal relationship was reversed. These findings indicate that dSPNs and iSPNs are not concurrently active, but instead exhibit complementary, direction-dependent dynamics that govern movement velocity. Our dual-color miniscope provides a compact, cost-effective platform for simultaneous two-population imaging, offering new opportunities to dissect coordinated activity across neural circuits in freely behaving animals.

neuroscience↗

bioRxiv2026

Cellular Chemical Dynamics Governing Signal Transduction and Adaptive Gene Expression: Beyond Classical Kinetics

Cellular adaptation is inherently nonstationary processes with complex stochastic dynamics1-5. Despite remarkable progress in quantitative biology6-11, a quantitative understanding of the cell adaptation dynamics in terms of the underlying cellular network remains elusive. Here, we present the next-generation chemical dynamics model and theory for cellular networks, providing an effective, quantitative description of the adaptive gene expression dynamics in living cells responding to external stimuli. Unlike conventional kinetics, chemical dynamics of cellular network modules are characterized by their reaction-time distributions, rather than by rate coefficients12. For a general model of cell signal transduction and adaptive gene expression, we derive exact analytical expressions for the time-dependent mean and variance of protein numbers produced in response to external stimuli, validated by accurate stochastic simulations. These results provide a unified, quantitative explanation of the stochastic responses of diverse E. coli genes to antibiotic stress and transcriptional induction. Our analysis reveals existence of a general quadratic relationship between the mean and variance of activation times across diverse genes. The gene activation process influences transient dynamics of downstream protein levels, but not their steady-state levels. In contrast, post-translational maturation process affects both transient dynamics and steady-state variability of mature protein levels. This finding indicates that the gene expression variability measured by fluorescent reporter proteins depends on the maturation time of the reporters. This work suggests a new direction for the development of digital twins of living cells.

biophysics↗