Biology subjects

Song, K.

Publications and source records attributed to Song, K..

At least 19 recordsLinked to original sources

bioRxiv2026

TDP-43 amyloid conversion in cells tracks the net charge of a polyampholyte motif, not condensate solidification

Liquid-liquid phase separation of TDP-43 is implicated in ALS and FTLD, yet how its condensates convert into pathological amyloid in living cells remains poorly defined. Here we identify a polyampholyte motif (PAM) in the linker between RRM2 and the amyloid-forming low-complexity domain as a charge-tunable determinant of fibrillization that operates independently of condensate solidification. In budding yeast expressing GFP-TDP-43{Delta}NLS, charge reversal of three arginines (R268E/R272E/R275E; 3R-E) converted liquid puncta into ProteoStat-positive fibrils. Unexpectedly, fluorescence recovery after photobleaching showed 3R-E condensates to be more mobile than those of wild type, whereas the least mobile condensates, in yeast and in human U2OS cells, remained ProteoStat-negative. Across 24 PAM charge variants, the proportion of fibril-bearing cells scaled linearly with net charge regardless of residue identity, with charge neutralization delaying rather than abolishing conversion. Phosphomimetic substitution of the PAM serines alone induced fibrils, implicating phosphorylation as a potential physiological modulator of PAM charge.

biochemistry↗

bioRxiv2026

Grow2Fold: mapping heterogeneous developmental growth to human brain folding

Cortical folding emerges through complex developmental processes, yet what organizes these processes into the characteristic folding patterns of the human brain remains unclear. Here, we developed an imaging-informed whole-brain modeling framework, Grow2Fold, that integrates developmental cortical regionalization, quantitative growth characterization, and mechanics-guided simulation to investigate how cortical growth shapes brain folding patterns. Using 836 fetal and neonatal MRI sessions from 747 participants spanning 21-45 postmenstrual weeks, we identified a reproducible and hierarchical spatiotemporal organization of cortical expansion characterized by coordinated regional growth trajectories. Rapid expansion occurs earlier around peri-central territories and progressively shifts toward frontal, parietal, and temporal association cortices. We encoded these imaging-derived trajectories into region- and age-specific growth laws and incorporated them into anatomically realistic whole-brain mechanical models. The resulting simulations recapitulate major sulcal landmarks and characteristic folding development across global and regional morphological measures. Comparing regional and uniform growth, we find that differential growth drives cortical instability, while heterogeneous developmental growth organizes this instability into anatomically recognizable folding patterns. Combined with subject-specific anatomy, these population-informed growth laws reproduce individualized longitudinal folding trajectories. Together, our results identify spatiotemporally patterned developmental growth as a key spatial constraint on cortical morphogenesis and establish a quantitative bridge from developmental imaging, through mechanical instability, to anatomically organized folding.

biophysics↗

bioRxiv2026

LoGoPPI enables fast and accurate protein protein interaction mapping at scale

Graph-based protein function analysis is powerful, but protein-protein interaction (PPI) networks exist for only a small fraction of animal and plant genomes. We present LoGoPPI, which infers PPIs from sequence by combining bi-encoder global protein representation with local residue-level late interaction. LoGoPPI matches or exceeds state-of-the-art PLM-based cross-encoders while achieving orders-of-magnitude faster inference, up to ~1,500-fold, and its local branch provides residue-level signals associated with interaction interfaces and structurally flexible regions. This efficiency enables practical proteome-wide PPI reconstruction at scales prohibitive for cross-encoder models, potentially extending interactome mapping to tens of thousands of animal and plant species. LoGoPPI thus provides a scalable framework for comparative and functional analysis of protein networks across diverse taxa.

bioinformatics↗

bioRxiv2026

Toward a global chemogeography of dissolved organic matter: a molecular trait dataset across Earth systems

Dissolved organic matter (DOM) is a central component of biogeochemical cycling, but molecular observations generated by ultrahigh-resolution mass spectrometry remain fragmented across studies, limiting quantitative comparisons among ecosystems. Here, we compile and harmonize a global dataset of DOM molecular traits comprising 3,999 samples from 337 studies published between 2005 and 2026. The dataset includes eight intensity-weighted molecular traits: hydrogen-to-carbon (H/C), oxygen-to-carbon (O/C), nitrogen-to-carbon (N/C), and sulfur-to-carbon (S/C) ratios; molecular mass; double-bond equivalents (DBE); modified aromaticity index (AImod); and nominal oxidation state of carbon (NOSC). Samples span aquatic, terrestrial, atmospheric, plant-associated, petroleum-related, and other environments, and are linked, where available, to geographic, physicochemical, nutrient, and climatic metadata. Molecular data were harmonized using common definitions and restricted to negative-mode electrospray-ionization FT-ICR MS to improve cross-study comparability. This resource enables cross-system comparisons of DOM molecular traits and supports analyses of environmental gradients, geographic coverage, and global DOM chemogeography.

ecology↗

bioRxiv2026

FFPERescuer: deep unsupervised domain adaptation for the reconstruction of gene expression profiles derived from formalin-fixed paraffin-embedded samples

Formalin-fixed paraffin-embedded (FFPE) tumor tissues often suffer from RNA degradation, posing a long-standing challenge for reliable transcriptomic profiling. Here, we propose FFPERescuer, a deep learning framework employing unsupervised domain adaptation, to rectify distorted gene expression data. FFPERescuer comprises a partial encoder that maps a small subset of genes to high-level representations and a decoder to reconstruct full gene expression profiles. On simulated data with varying noise levels, FFPERescuer faithfully recovered gene expression profiles, achieving high Pearson correlation coefficients (PCCs > 0.85) with the ground truth. In FF-FFPE-matched cohorts, FFPERescuer significantly enhanced expression profile concordance, with average PCCs increased by 23% (P < 0.05). Applying to cancer subtyping, FFPERescuer improved classification accuracy from 67% to 92%, recapitulated subtype-specific biological properties lost in the FFPE-derived data, and enhanced survival associations. Our studies provide a powerful framework for reliable transcriptomic profiling from FFPE-archived tumor samples that are widely available in the clinic.

bioinformatics↗

bioRxiv2026

Heart rate dynamics embed a shared representation of individual brain organization and cognitive function

Idiosyncratic brain functional organization shapes intricate cardiac dynamics through central-peripheral autonomic interactions, yet a comprehensive mapping between multi-scale heart rate dynamics and whole-brain functional architecture remains lacking. Here, combining highly comparative time-series analysis with multi-modal neuroimaging and intracranial electrophysiology, we establish heart rate dynamics as a physiological fingerprint that maps onto whole-brain functional architecture. Partial least squares analysis revealed a generalizable latent axis linking reduced heart rate temporal complexity and elevated micro-scale predictability to heightened resting-state functional connectivity across default mode, salience, and sensorimotor networks. This covariance aligns spatially with serotonergic, noradrenergic, and cholinergic neuromodulatory gradients, persists across physiological confound controls and cross-session validations, derives support from human intracranial electrophysiological recordings, and extends to active cognitive states. Furthermore, brain-covarying heart rate signatures underpin the predictive capacity of heart rate dynamics for individual fluid and crystallized intelligence, demonstrating a shared representational substrate. Our findings demonstrate a robust neurovisceral coupling architecture, establishing well-characterized heart rate dynamics as a scalable, neurobiologically anchored window into human brain functional organization and cognitive traits.

neuroscience↗

bioRxiv2026

Visualization of the architecture of flexible chromatin and the binding of chromatin regulators

Chromatin organization plays a central role in regulating genome accessibility and gene expression in eukaryotic cells. However, the inherent flexibility and structural heterogeneity of chromatin pose significant challenges for its structure determination. Here, we use a Nuc-back strategy with cryo-electron tomography (cryo-ET) and subtomogram averaging methods to visualize chromatin at the nucleosome level by averaging nucleosome at moderate-to-high resolution, classifying the fundamental unit of chromatin, i.e., nucleosome, into distinct classes, and linking different nucleosome structures to chromatin architecture. We reveal that nucleosome heterogeneity is a key factor in chromatin flexibility which disrupts interactions between nucleosomes. In addition, this strategy allows for the localization and visualization of chromatin regulators and their structure on chromatin. These results provide a foundation for future research in 3D genome and epigenetic process visualization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/730377v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b003c8org.highwire.dtl.DTLVardef@c86543org.highwire.dtl.DTLVardef@7033f5org.highwire.dtl.DTLVardef@635485_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Sex-specific hormone-sensitive regulatory architecture in adolescence as a scaffold for depression vulnerability

Adolescence is a critical developmental period during which sex differences in depression risk emerge, yet the underlying molecular mechanisms remain unclear. Here, we integrated longitudinal transcriptomic, epigenomic, and gene regulatory network analyses to characterize sex-specific regulatory dynamics of the brain across adolescence under normative conditions and elucidate how baseline molecular differences may shape later vulnerability. We observed that immediate early genes exhibited the strongest sex-biased signals, with males and females showing opposing developmental trajectories, suggesting a role in sex-specific stress-responsive programs. Across analyses, a consistent pattern emerged: males showed stronger activity-dependent neuronal signatures, whereas females showed stronger stress- and immune-related signatures. Extending these findings to a disease context using single-nucleus chromatin accessibility data, we identified hormone-responsive regulatory elements enriched in depression-associated regions, with sex- and cell type-specific links to genetic risk. Grounded in established models of sex-specific stress responses, these findings offer a developmental regulatory framework for understanding the differential presentation of, and vulnerability to, depression.

genomics↗

bioRxiv2026

Automated Multimodal Correlative Registration for Organelle-Specific Molecular Imaging

Mapping subcellular drug distribution is essential for understanding trafficking and off-target effects. NanoSIMS enables chemical imaging of labeled therapeutics, but signal interpretation requires ultrastructural correlation with electron microscopy, a manual and laborious process. We present an automated AI-driven pipeline for correlating chemical and ultrastructural images, enabling multiscale, organelle-precise imaging of molecules in cells and tissues. The method integrates bidirectional optical flow, confidence-guided affine transformation, and automated template matching for cross-scale EM alignment. Morphology-rich ion channels (e.g., 32S) estimate transformations that propagate to sparse therapeutic signals (e.g., 79Br, 15N), overcoming low signal-to-noise challenges. We validate this framework across diverse cell and tissue types, tracking oligonucleotide and antibody therapeutics in vitro and in vivo to reveal cell-type- and organelle-specific distribution patterns. This work establishes a generalizable platform for automated multimodal registration and organelle-resolved subcellular pharmacology.

bioinformatics↗

bioRxiv2026

BLAST: A blue light-assisted secretion toolkit tunable by reversible protein-protein interactions

Precise control over protein secretion is essential for programming intercellular communication and coordinating complex physiological responses. However, conventional methods relying on transcriptional regulation or chemical induction often lack the spatiotemporal precision and reversibility required to mimic endogenous signaling dynamics. Here, we present the Blue Light-Assisted Secretion Toolkit (BLAST), a genetically encoded system that orchestrates protein release from the endoplasmic reticulum via light-tunable protein-protein interactions. BLAST comprises two complementary modules utilizing both light-induced iLID/SspB association (a-BLAST) and LOV2/Zdk1 dissociation (d-BLAST). Both modules harness the highly conserved RXR motif to enforce strict ER confinement in the dark state. Most importantly, by utilizing non-destructive steric masking rather than enzymatic cleavage, BLAST achieves unprecedented temporal resolution with strict reversibility. We demonstrate that both systems can be repeatedly toggled ON and OFF, instantaneously arresting cargo release upon light withdrawal to generate highly controlled, pulsatile secretion profiles. Leveraging this dynamic control, we successfully achieved the rapid, robust, and light-triggered secretion of complex therapeutic proteins, including insulin and interleukin-12. By bypassing transcriptional delays and irreversible activation steps, BLAST provides a generalized, plug-and-play platform for the on-demand delivery of therapeutic proteins, significantly expanding the optogenetic toolbox for synthetic biology and cell-based therapies.

synthetic biology↗

bioRxiv2026

Microfluidic Mechanical Reactivation of Aged Stem Cells

Stem cell aging significantly impairs therapeutic efficacy, requiring innovative strategies to restore potency. We present a microfluidic cell-compressing platform for reactivation (-CPR) designed to apply controlled hydrodynamic deformation to late-passage stem cells. This mechanical stimulation facilitates functional reactivation without external chemical cues. Within a defined window, -CPR effectively reduces oxidative stress, SA-{beta}-Gal activity, and {gamma}H2AX foci, while simultaneously restoring proliferation and canonical stemness markers (OCT4, SOX2, and KLF4). Mechanical stimulation via -CPR induces coordinated structural remodeling: nuclei become more compact, actin cortex organization is restored, -actinin redistributes to focal adhesions, and microtubule networks are restructured, suggesting a rebalanced intracellular tension. Transcriptomic and proteomic analyses reveal that this process reprograms extracellular matrix remodeling and DNA repair pathways while attenuating pro-fibrotic and senescence-associated secretory phenotype (SASP)-associated pathways. Crucially, this reactivation occurs without compromising fundamental MSC hallmarks, preserving intrinsic immunophenotypes and multilineage differentiation potential. Functionally, -CPR-processed stem cells demonstrate restored in vitro wound closure and enhanced tissue repair in vivo, with efficacy appearing dependent on mechanical dosage. This platform establishes a non-genetic, mechanobiological approach to restoring stem cell function, offering a scalable strategy for functional reactivation and potentially paving the way toward comprehensive cellular rejuvenation.

bioengineering↗

bioRxiv2026

Single-Cell RNA Sequencing Reveals Commensal Microbes Amplify Sex-Specific Immune Programming in the Murine Lung

Sex-based differences in respiratory disease outcomes are well recognized. However, the underlying immunological mechanisms driving this dimorphism remain incompletely understood. While sex hormones influence immune cell development and function, the role of commensal microbes in shaping sex-specific lung immunity has not been explored. Here, we used single-cell RNA sequencing (scRNAseq) and flow cytometry to profile lung immune cells in male and female mice housed under specific pathogen-free (SPF) or germ-free (GF) conditions. Under SPF conditions, males exhibited a striking myeloid bias, with increased monocytes and macrophages, along with broad upregulation of inflammatory mediators, including S100a8, S100a9, and Il1b, across multiple cell types, and enrichment of TNF and interferon (IFN) signaling pathways. In contrast, females displayed lymphocyte-skewed profiles, with higher frequencies of T cells and natural killer (NK) cells. Interestingly, these sex-based differences in immune composition and inflammatory programs were largely absent in GF mice, indicating that microbial exposure amplifies baseline immunological dimorphism between males and females. Notably, select sex-associated features, including female-biased NK cell enrichment, persisted irrespective of microbial status, suggesting intrinsic, microbiota-independent programming. Together, these findings indicate that commensal microbes modulate sex-specific lung immunity by amplifying pre-existing intrinsic differences, highlighting the intersection of extrinsic (microbial) and intrinsic (sex-linked) factors in shaping baseline mucosal immunity.

immunology↗

bioRxiv2025

An integrated workflow for structural virology with a 100 keV electron microscope

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

biochemistry↗

bioRxiv2025

Unveiling the Human Nasopharyngeal Microbiome Compendium: Systematic Characterization of Community Architecture and Function Through a Comprehensive Meta-Analysis

The nasopharyngeal microbiome is critical for respiratory health, yet its compositional architecture remains largely uncharacterized, underlying conflicting reports of increased, decreased, or unchanged diversity during infection. Here, we demonstrate that these contradictions arise from a fundamentally overlooked factor: the nasopharynx is organized into six reproducible nasopharyngeal community state types (NPCSTs) that are associated with intrinsic diversity baselines independent of disease status. By uniformly reprocessing 7,790 16S rRNA gene sequencing samples from 28 studies, we show that NPCSTs explain 52% of community variance, four-fold more than study effects, and that disease-diversity associations are attenuated by over 92% after NPCST adjustment. To identify genuine disease markers, we applied NPCST-aware differential abundance testing to SARS-CoV-2 as a case study. Leave-one-study-out (LOSO) cross-validation across 10 cohorts confirmed 13 reproducible taxa with opposing shifts: obligate anaerobes typically studied in other body compartments were enriched, while resident hub genera were depleted with high directional consistency across LOSO iterations. Co-occurrence network analysis independently validated this pattern, identifying the depleted taxa as structural backbone hubs across all NPCSTs. To bridge microbiome ecology and clinical application, we developed the Nasopharyngeal Microbiome Health Index (NMHI), a continuous community-level wellness score achieving AUC of 0.90 and 0.92 in internal and external validations, respectively, with robust performance across all six NPCSTs (AUC: 0.848-0.953). An independent clinical cohort of 147 specimens confirmed that these NPCST and NMHI characteristics are reproducible. Unlike binary classifiers, NMHI quantifies nasopharyngeal health along a spectrum, establishing NPCST-aware analysis as a foundation for precision respiratory microbiome research.

bioinformatics↗

bioRxiv2025

Polyelectrolyte domains in intrinsically disordered regions differentially regulate intracellular biomolecular condensation

Intracellular condensation is a hallmark of many proteins containing intrinsically disordered regions (IDRs). Decoding the regulatory mechanisms of condensation encoded within the amino acid sequences of condensate-forming proteins is essential for understanding both how intracellular condensates assemble and how they contribute to various disease pathologies. Here, we investigated the budding yeast P-body proteins Nst1 and Edc3, which exhibit pronounced intracellular self-condensation, and identified charged amino acid clusters in the low complexity regions (LCRs) that modulate their phase behavior. Guided by the stickers-and-spacers framework, we hypothesized that clusters of charged residues within IDRs function in promoting intracellular condensation process. Using a sliding-window approach, we designated and dissected the polyelectrolyte (PE) domains of Nst1 and Edc3 and established their essential contributions to condensate coalescence. In Nst1, the polyanionic (PA) subdomain enhances intermolecular attraction and promotes coalescence, whereas the polyampholyte (PAM) subdomain imparts rigidity to the condensate as a distinct modulatory element and functions as a platform in condensation process of other P-body components. PA of Edc3 also regulates coalescence. Extending these findings to the neurodegenerative disease-associated protein TDP-43, we show that its PA regions are critical for coalescence, consistent with the presence of negatively charged amino acid clusters as potent molecular stickers functioning in condensate coalescence in cells. These results highlight charged-residue clusters as important sequence determinants of protein phase behavior and suggest that they represent promising novel regulatory targets for modulating TDP-43 condensation in cells.

cell biology↗

bioRxiv2025

The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia

Cilia are complex, microtubule-based organelles that protrude from many eukaryotic cells and have important roles in sensing, signaling, and motility. Recent studies have revealed the atomic structures of many multi-component ciliary complexes, providing new insights into their mechanisms of action that are vital for cilias biological functions. However, little is known about the structure, proteome, and function of full-length radial spoke 3 (RS3), which is distinct from the structurally well-characterized RS1 and RS2. Radial spokes are conserved megadalton complexes that transmit mechanochemical signals from the central pair of microtubules to the dynein motors, thereby coordinating ciliary motility. Here, we combined cryo-electron microscopic single-particle reconstruction, cryo-electron tomography (cryo-ET), proteomic analysis, and computational modeling to determine the 3D structure and atomic model of RS3 from mouse respiratory cilia. Our structure reveals all protein components of RS3, including regulatory and metabolic enzymes, such as a protein kinase A subunit, adenylate kinases and malate dehydrogenases. We have confirmed the important role of adenylate kinase 7 in RS3 by cryo-ET analyses of respiratory cilia in AK7-deficient mice, which display primary ciliary dyskinesia. Our findings suggest that RS3 is an important regulatory hub and cluster of metabolic proteins that helps to maintain ATP at the levels required for sustained dynein motor activity and ciliary beating. This work advances our understanding of the structure and function of RS3 in ciliary motility and provides insights into the etiology of ciliopathies.

biophysics↗

bioRxiv2025

The structure of a thermostable phage's Portal Vertex and Neck Complex illuminates its maturation process

Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged into its capsid shell through the portal complex. The portal complex then closes to retain DNA and connects to the tail, which is required for host recognition and infection. The trigger to stop pumping DNA and assemble the mature virus has been a longstanding conundrum in the field. We determined the structure of the portal, the proteins that connect it to the tail, and portal vertex in the hyperthermophilic phage Oshimavirus using cryo-Electron Microscopy (cryo-EM). We find highly intertwined loop structures, like in a wicker basket, stabilizing the portal vertex against high temperatures. Moreover, we observe that the portal protrudes from the capsid in mature virions. We propose that portal is repositioned by packaged DNA, forming a pressure-sensitive switch that terminates genome packaging and triggers tail attachment in headful phages.

microbiology↗

bioRxiv2025

Cryo-ET Analysis Unveils the Minimum Structural Unit and Hierarchical Ultrastructure of Silk Fibers in Silkworm and Spider

Silkworm silk and spider silk are renowned for their exceptional mechanical properties, with the toughness of spider dragline silk exceeding that of silkworm silk and even outperforming high-performance synthetic fibers such as Kevlar and nylon. The mechanical properties of silk fibers are determined by their ultrastructure, including the size, morphology, and arrangement of their fundamental structural units. In this study, we employed the state-of-the-art cryo-electron tomography to investigate the in situ ultrastructure of silkworm silk, spider silk, and artificial silk. Our findings reveal that the fundamental structural unit of silkworm silk is a nanofibril approximately 3.6 nm in diameter, connected by numerous bridges, representing the smallest structural unit currently observable. These nanofibrils are aligned parallel to the fiber axis and organized into a herringbone pattern oriented in a specific direction. Multiple layers of this herringbone pattern stack together to form the final micron-scale fiber. In spider silk, a dense structure featuring nanofibrils is clearly visible, with their long axes tightly aligned parallel to the flow direction, leaving no discernible gaps. By contrast, silkworm silk exhibits larger, regionally varying gaps between nanofibrils, while artificial silk lacks the highly ordered arrangement characteristic of natural silks. Our study provides new insights into silk formation and offers valuable principles for designing ultrastrong silk.

biophysics↗