Biology subjects

Ryu, K.

Publications and source records attributed to Ryu, K..

9 recordsLinked to original sources

bioRxiv2026

Defining Operational UV-C Dose Requirements for Autonomous Disinfection of Clinically Relevant Pathogens Across Healthcare and High-Touch Surfaces

Background: Autonomous ultraviolet-C (UV-C) disinfection systems are increasingly used to supplement manual environmental cleaning, yet evidence-based guidance defining pathogen-specific UV-C dose requirements across representative surfaces remains limited. Aim: To characterize operational UV-C dose requirements for clinically relevant pathogens across diverse high-touch and healthcare surfaces and determine how experimentally derived microbial inactivation can inform operational exposure parameters. Methods: SARS-CoV-2, adenovirus, Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Enterococcus faecalis, Candida auris, and Clostridioides difficile spores were exposed to defined UV-C doses on representative high-touch materials or stainless steel under standardized conditions, including a 10% fetal bovine serum organic soil challenge. Microbial inactivation was quantified by viable recovery. Dose-response analysis and operational modelling were used where supported by the experimental data. Findings: UV-C exposure significantly reduced viable recovery of all pathogens, with substantial differences in the exposure conditions associated with microbial inactivation. SARS-CoV-2 exhibited substantial inactivation at doses as low as 2.6 mJ/cm2, whereas the highest evaluated doses were 1,800 mJ/cm2 for C. difficile spores and 3600 mJ/cm2 for C. auris. For C. auris, multi-dose data estimated that approximately 1,410 mJ/cm2 was associated with a 2-log10 reference reduction, enabling distance-dependent exposure-time predictions. Conclusion: Experimentally quantified UV-C exposures produced substantial microbial inactivation across diverse pathogen classes and surfaces. Integrating delivered dose with microbial reduction provides a quantitative framework for translating laboratory efficacy into operational parameters for autonomous UV-C disinfection.

microbiology↗

bioRxiv2026

Stress granule fusion is a mitochondria-coordinated process for stress adaptation

Stress granules are cytoplasmic membraneless organelles assembled during stress to maintain cellular homeostasis. Although fusion is a hallmark of liquid-like behavior of these condensates, whether this process carries functional significance beyond its physical coalescence remains unclear. Here, we show that stress granule fusion is facilitated by mitochondrial dynamics and membrane potential. Intact mitochondria actively associate with stress granules, facilitating fusion and maturation. In contrast, loss of mitochondrial membrane potential, along with disrupted mitochondrial structure or motility, weakens these interactions and reduces fusion frequency. We find that impaired fusion leads to the accumulation of immature granules that retain fewer sequestered components, which correlates with premature cell death. Remarkably, restoring mitochondrial membrane potential rescues granule fusion and enlargement, and is accompanied by increased cell viability and a corresponding increase in granule-associated apoptotic factors. These results demonstrate that stress granule fusion is actively coordinated by mitochondria rather than driven solely by passive coalescence, reshaping how condensate dynamics are understood to integrate with organelle function during cellular stress response.

cell biology↗

bioRxiv2026

The anatomical compartment defines distinct immune remodeling within human visceral adipose tissue during aging

Age-associated inflammation varies across tissues, but whether distinct visceral adipose tissue (VAT) depots undergo inflammatory remodeling in a depot-specific manner remains unclear. Here we profiled human peri-organ VAT, comparing kidney-associated fat (KF, from kidney transplantation donors) and gallbladder-associated fat (GBF, from asymptomatic cholecystectomy patients with incidental polyps), using single-cell RNA sequencing, flow cytometry, intracellular protein profiling and in situ analysis. GBF showed broad tissue-residency and granzyme K-associated remodeling across conventional, regulatory and innate-like lymphocyte compartments, whereas KF showed stronger B cell remodeling, greater myeloid representation and more compartmentalized changes within resident effector-like CD8+ T cell states. We further identified age-associated CD20+ T cells with features consistent with local B-T cell interaction and an antigen-experienced, granzyme K-associated inflammatory memory phenotype. In situ analysis revealed age-associated myeloid accumulation and crown-like structure remodeling, accompanied by distinct myeloid inflammatory programs in KF and GBF. Finally, depot-specific immune signatures associated with clinical indices of adjacent kidney and liver function. These findings indicate that age-associated distinct immune programs within peri-organ VAT depots track with local tissue context and the state of the adjacent organ.

immunology↗

bioRxiv2026

Characterization of an early-diverging KCNE potassium-channel auxiliary subunit in the jawless vertebrate lamprey

The KCNE (KCNE1-6) proteins are single-pass transmembrane auxiliary subunits of the voltage-gated K+ channel KCNQ1. KCNQ1-KCNE complexes have been well studied in jawed vertebrates ranging from zebrafish to humans, but KCNE subunits from earlier-diverging vertebrates remain poorly characterized. Here, we functionally characterize a single KCNE-like gene in lamprey, a jawless vertebrate, and designate it kcne0 as an early-diverging member of the KCNE family. KCNE0 shows moderate amino acid sequence similarity to KCNE1-6 but is not particularly similar to any single isoform. Both kcnq1 and kcne0 transcripts were detected in multiple lamprey organs. When co-expressed with lamprey KCNQ1, KCNE0 produced a constitutively active current, similar to KCNE3. By contrast, KCNE0 modulated KCNQ1 from other species less effectively, suggesting species-specific tuning of KCNQ1-KCNE compatibility. Introducing into KCNE0 an intracellular tetra-leucine motif analogous to that in KCNE4 markedly reduced KCNQ1 current amplitude, conferring a KCNE4-like inhibitory effect. Overall, this work provides a functional reference for comparing KCNE-dependent modulation of KCNQ1 across vertebrates and suggests an underlying compatibility mechanism.

biophysics↗

bioRxiv2025

An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex

Antibodies that recognize peptide-loaded class I major histocompatibility complex (pMHC I) molecules could enable therapeutic targeting of intracellular oncogenic proteins, yet their discovery has been hampered by the small size of peptide antigens and allele-specificity. We describe an integrated in silico-in vitro workflow for generating high-affinity, selective antibodies to KRAS(G12D)10 presented by HLA-C*08:02, a clinically validated cancer neoantigen. In silico, multiple human antibody-derived variable fragments (Fvs) plausibly docked to the target pMHC were generated, followed by limited complementarity-determining region (CDR) sequence design. In vitro, CDR diversity was introduced at 3-4 positions per Fv to construct yeast surface display library for iterative selections. This workflow yielded antibodies with exclusive binding to KRAS(G12D)10/HLA-C*08:02 without cross-reactivity. Affinity maturation achieved nanomolar dissociation constants, and incorporation into chimeric antigen receptor T cells enabled specific activation against target-positive cells. This study establishes a practical design-to-function pipeline for TCR-like antibody discovery, and demonstrates the feasibility of therapeutic targeting against KRAS(G12D)-driven malignancies.

biochemistry↗

bioRxiv2024

Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria

Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled the precise introduction of base substitutions and the effective removal of genomes carrying harmful mutations. However, the reconstitution of mtDNA deletions responsible for severe mitochondrial myopathies and age-related diseases has not yet been achieved in human cells. Here, we developed a method to engineer specific mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. As a proof-of-concept, we used mito-EJ and mito-ScaI to generate a panel of clonal cell lines harboring a [~]3.5 kb mtDNA deletion with the full spectrum of heteroplasmy. Investigating these isogenic cells revealed a critical threshold of [~]75% deleted genomes, beyond which cells exhibited depletion of OXPHOS proteins, severe metabolic disruption, and impaired growth in galactose-containing media. Single-cell multiomic analysis revealed two distinct patterns of nuclear gene deregulation in response to mtDNA deletion accumulation; one triggered at the deletion threshold and another progressively responding to increasing heteroplasmy. In summary, the co-expression of mito-EJ and programable nucleases provides a powerful tool to model disease-associated mtDNA deletions in different cell types. Establishing a panel of cell lines with a large-scale deletion at varying levels of heteroplasmy is a valuable resource for understanding the impact of mtDNA deletions on diseases and guiding the development of potential therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=143 HEIGHT=200 SRC="FIGDIR/small/618543v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@ab900corg.highwire.dtl.DTLVardef@17e094dorg.highwire.dtl.DTLVardef@194a10corg.highwire.dtl.DTLVardef@d925e5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICombining prokaryotic end-joining with targeted endonucleases generates specific mtDNA deletions in human cells C_LIO_LIEngineering a panel of cell lines with a large-scale deletion that spans the full spectrum of heteroplasmy C_LIO_LI75% heteroplasmy is the threshold that triggers mitochondrial and cellular dysfunction C_LIO_LITwo distinct nuclear transcriptional programs in response to mtDNA deletions: threshold-triggered and heteroplasmy-sensing C_LI

molecular biology↗

bioRxiv2023

Lactate activates the mitochondrial electron transport chain independent of its metabolism

Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.

cell biology↗

bioRxiv2022

Topology of gene regulatory compartments relative to the nuclear matrix

Summary ParagraphInside the nucleus, there are special compartments with characterized functions, some of which are involved in gene expression1. These compartments include transcriptional condensates and nuclear speckles, which contain factors required for transcription and splicing, respectively. While the characteristics of these intranuclear compartments were extensively investigated, spatial relationship between them is yet unclear. Meanwhile, RNA-protein structural network named the nuclear matrix has been observed inside the nucleus and suggested as a framework for the spatial segregation of the intranuclear space2-6. However, concept of the nuclear matrix was not widely accepted due to its lack of in vivo evidence7. Here, we report visualization of the nuclear matrix and intranuclear compartments using super-resolution fluorescence microscopy. We found the nuclear matrix is dynamic in live cells and easily disrupted upon transcription inhibition. Remarkably, we observed an orderly layered distribution of transcriptional condensates and nuclear speckles relative to the nuclear matrix. We also observed a separation of chromosome territories from transcriptional condensates and nuclear speckles by the nuclear matrix. Based on our findings, we propose a topological model for the regulation of transcription across the nuclear matrix.

cell biology↗

bioRxiv2018

Conversion of a soluble protein into a potent chaperone in vivo

Protein-folding assistance and aggregation inhibition by cellular factors are largely understood in the context of molecular chaperones. As an alternative and complementary model, we previously proposed that, in general, soluble cellular macromolecules including chaperones with large excluded volume and surface charges exhibit the intrinsic chaperone activity to prevent aggregation of their connected polypeptides, irrespective of the connection types, and thus to aid productive protein folding. As a proof of concept, we here demonstrated that a model soluble protein with an inactive protease domain robustly exerted chaperone activity toward various proteins harboring a short protease-recognition tag of 7 residues in Escherichia coli. The chaperone activity of this protein was similar or even superior to that of representative E. coli chaperones in vivo. Furthermore, in vitro refolding experiments confirmed the in vivo results. Our findings revealed that a soluble protein exhibits the intrinsic chaperone activity, which is manifested, upon binding to aggregation-prone proteins. This study gives new insights into the ubiquitous chaperoning role of cellular macromolecules in protein-folding assistance and aggregation inhibition underlying the maintenance of protein solubility and proteostasis in vivo.

biochemistry↗