Biology subjects

Jeong, S.

Publications and source records attributed to Jeong, S..

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

Nanoparticle Albumin-Bound Paclitaxel Targets Pulmonary Neutrophils

Nanoparticle albumin-bound paclitaxel (Abraxane) was among the first clinically approved nanomedicines and is a first-line chemotherapeutic. It enhances therapeutic efficacy and reduces side effects of paclitaxel. Despite its extensive clinical use, mechanisms of Abraxane's therapeutic effects are the subject of ongoing study. This work posits a new mechanism for Abraxane's effects in lung cancers and metastasis. Tracing the albumin component of Abraxane with radioisotopes or fluorophores, we find that Abraxane homes to the lungs. Abraxane's lung tropism is elevated by inflammation and is eliminated in complement protein C3 knockout mice, showing that complement pathway drives the uptake. Flow cytometry and histology show that neutrophils are the dominant cell type taking up Abraxane in the lungs. We demonstrate Abraxane's tropism to pulmonary neutrophils in mice and in human donor lungs. We note previously undocumented side effects associated with Abraxane's lung tropism, including pro-thrombotic and pro-inflammatory responses in acute lung inflammation. We show that Abraxane's efficacy against lung metastases is affected when lung uptake is eliminated by C3 knockout. Our results provide insight into why Abraxane is effective in lung cancer and metastases. These findings may be used to improve outcomes in patients receiving Abraxane and help design next-generation cancer nanomedicines.

bioengineering↗

bioRxiv2026

Mycoplasmal endosymbionts of Trichomonas vaginalis are associated with reduced risk for Chlamydia trachomatis endometrial infection in asymptomatic, coinfected, women.

Trichomonas vaginalis is a protozoan parasite that causes trichomoniasis, the most common curable non-viral sexually transmitted infection, and Chlamydia trachomatis is a bacterial pathogen that can ascend to the upper genital tract and cause pelvic inflammatory disease, infertility, and ectopic pregnancy. T. vaginalis harbors bacterial endosymbionts, including Candidatus Malacoplasma girerdii, an obligate symbiont, and Metamycoplasma hominis, which can live freely or symbiotically. In a 16S rRNA sequencing study of the cervicovaginal microbiome of women at high risk for chlamydial infection, Ca. M. girerdii abundance was one of 13 features predicting lack of chlamydial spread to the endometrium, despite no direct association between T. vaginalis infection and reduced chlamydial ascension. Investigating the relationship between these microorganisms further, we found that T. vaginalis vaginal abundance correlated positively with chlamydial burden in women whose infection was confined to the cervix, while a nonsignificant inverse relationship was seen in women with endometrial spread. Among participants with high chlamydial burden, Ca. M. girerdii was detected exclusively in women without endometrial infection. Both endosymbionts trended toward more frequent detection, and higher abundance, in coinfected women without endometrial spread, while M. hominis abundance correlated strongly with T. vaginalis burden in this group. These findings suggest that mycoplasmal endosymbionts of T. vaginalis, rather than T. vaginalis itself, are microbial factors limiting chlamydial ascension, and point to a three-way interaction between parasite, endosymbiont, and bacterial pathogen that shapes upper genital tract C. trachomatis infection risk.

microbiology↗

bioRxiv2026

Microcystis-triggered shifts in the symbiotic microbiome of Myriophyllum spicatum rapidly suppress Microcystis aeruginosa

While the suppression of toxic cyanobacteria by aquatic plants has long been recognized, few studies have clearly differentiated between the allelopathic effects of the plant itself and the inhibitory influence of its associated microbiome. This study aimed to clarify the primary inhibitory agent by pre-culturing Myriophyllum spicatum (Eurasian watermilfoil) under three conditions: (1) BG11 medium, (2) live Microcystis aeruginosa KW culture, and (3) a Microcystis-symbiotic microbiome (excluding Microcystis cells). After a 7-day pre-culture, Myriophyllum shoots were transferred to fresh Microcystis culture. The Myriophyllum pre-cultured in Microcystis culture exhibited rapid inhibition against Microcystis (84% within day 1), whereas the Myriophyllum pre-cultured in BG11 medium showed delayed responses (89% by day 7). In contrast, inhibition remained below 50% in the Myriophyllum pre-cultured with the Microcystis-symbiotic microbiome. Notably, plant-derived soluble compounds exhibited weak inhibitory effects, whereas the microbiome showed stronger inhibitory activity, indicating that the plant-associated microbiome plays a more dominant role than the plant itself. Exposure to Microcystis triggered significant shifts in plant-symbiotic microbial community composition, leading to rapid enhancement of inhibitory activity in the Myriophyllum microbiome. Microbial community analysis identified 28 bacterial taxa closely associated with the inhibitory response, including strains involved in organic matter degradation, adhesion, biofilm formation, and predatory behavior. Meta-transcriptomic analysis further confirmed increased expression of genes related to bacterial adhesion, biofilm formation, and carbohydrate metabolism following Microcystis exposure, highlighting functional adaptations linked to cyanobacterial suppression. These findings underline the role of microbiome-mediated cyanobactericidal mechanisms, providing new insights into a nature-based solution for mitigating Microcystis-dominated harmful algal blooms.

ecology↗

bioRxiv2026

Fetal MRI Reveals Altered Subplate Development in Congenital Heart Disease

Background: The subplate is a transient fetal brain compartment that provides an early foundation for downstream cerebral development. Congenital heart disease (CHD) alters fetal circulation and cerebral substrate delivery, but its impact on subplate development and whether resulting alterations relate to later neurodevelopmental outcomes remain unclear. Methods: In this retrospective observational cohort study, We used fetal MRI to quantify whole-brain, lobar, and regional (17 bilateral cortical regions) subplate volume and thickness to evaluate group differences between 76 fetuses with CHD and 62 typically developing (TD) fetuses scanned between 21-32 weeks of gestation, and estimated individualized deviations from TD developmental trajectories. Associations with fetal hemodynamic indices (substrate delivery score, cerebroplacental ratio [CPR]) and two-year neurodevelopmental outcomes (Bayley Scales of Infant and Toddler Development, N=46 CHD, N=37 TD) were explored. Results: Whole-brain subplate volume was lower in CHD, corresponding to a 5.7% reduction relative to age- and sex-expected values (p=0.003), but this difference was substantially attenuated after accounting for global brain volume (p=0.090). In contrast, regional analyses identified persistent spatially structured deviations beyond global scaling, most consistently involving posterior parietal, occipital and temporal regions, with a left-hemisphere bias in subplate thickness. Normative modelling demonstrated bidirectional regional deviations and increased inter-individual variability in CHD, with extreme subplate volume deviations enriched across 73% of cortical regions (p=0.009). Higher CPR was associated with lower SP thickness deviations, with the association strengthening after accounting for cerebral substrate delivery (p=0.010), although these analyses were exploratory. In CHD fetuses with postnatal follow-up, prenatal subplate deviations showed modest associations with neurodevelopmental outcomes, with right precuneus subplate thickness associated with receptive ({beta}=-11.87, q=0.017) and expressive ({beta}=-14.50, q=0.039) communication on the Bayley, after correction for multiple comparisons. Conclusions: Fetal subplate alterations in CHD are dominated by global reductions in brain growth but also include spatially heterogeneous and individually variable regional deviations beyond global scaling. Exploratory associations with fetal hemodynamics and postnatal neurodevelopment provide hypotheses for future studies investigating the developmental significance of these prenatal alterations.

neuroscience↗

bioRxiv2026

Incorporation of native HCV E1E2 into a nanoparticle vaccine platform

Development of an effective HCV vaccine requires the induction of both broadly neutralizing antibodies (bnAbs) and a robust cellular response. One issue that has arisen is that HCV subunit vaccines have limited immunogenicity, thus requiring multivalent formats in order to elicit a robust anti-HCV immune response. Toward that end, nanoparticle vaccines possess the ability to facilitate a controlled multivalent presentation and trafficking to lymph nodes, where they can interact with both arms of the immune system. Here, we used a soluble, secreted form of E1E2 (sE1E2) to assemble native E1E2 into a nanoparticle platform using a post-purification coupling assembly system. Nanoparticles were assembled by purifying sE1E2 containing a C-terminal SpyTag and an mi3-SpyCatcher fusion separately and covalently coupling the components via incubation. Free sE1E2-SpyTag was removed from nanoparticle preparations via gel filtration. The sE1E2-mi3 nanoparticles are fully competent to bind conformation-dependent bnAbs, indicating retention of a native assembly in the nanoparticle format. Electron microscopy analysis showed a clear incorporation of sE1E2 on the surface of the nanoparticle. Immunogenicity of sE1E2-mi3 nanoparticles was examined relative to sE1E2 alone and membrane-bound E1E2 (mbE1E2) following inoculation of groups of CD1 mice. Assessment of the immunogenicity of the sE1E2-mi3 nanoparticles showed that the nanoparticle assembly has a similar immunogenicity profile to that of mbE1E2 after only a prime and one boost, and overall superior to sE1E2. This proof-of-principle study sets the stage for further exploration of nanoparticles and other multivalent platforms for the development of E1E2-based vaccines. ImportanceHepatitis C virus infects approximately 50 million people, and at present no effective HCV vaccine exists. Due to the high sequence variability of HCV and the resulting difficulty in developing a vaccine that elicits a broadly neutralizing response, multiple efforts are underway to enhance the immunogenicity of HCV vaccine candidates. In this study, we incorporated native soluble, secreted E1E2 (sE1E2) into a 60-mer nanoparticle via the SpyTag-SpyCatcher system and covalent isopeptide bond attachment using the purified components. These nanoparticles are antigenically intact and elicit a neutralizing antibody response at an earlier time point in the immunization regimen than the corresponding subunit vaccine. These studies show that a well-characterized sE1E2 platform compatible with multiple genotypes can be coupled to nanoparticles for use as a vaccine candidate.

microbiology↗

bioRxiv2026

ProteinSketch translates spatial intuition into protein design with bimanual interaction in VR

Generative AI-based protein design can create diverse structures for desired functions but offers human designers limited control over three-dimensional architectures. We developed ProteinSketch, a bimanual virtual reality platform in which immersive backbone sketches and volumetric envelopes are directly created and translated into constraints for diffusion-based protein generation. RFdiffusion-based real-time refinement enabled interactive exploration and construction of user-specified protein topologies. Volumetric conditioning of sketched envelopes enabled high-fidelity control of anisometric geometries, confirmed by cryo-electron microscopy. These user-defined volumetric constraints enabled functional-binder design and extension of pre-existing minibinders to surfaces otherwise difficult to access within complex molecular environments using conventional design approaches. This collaborative human-AI framework integrates human spatial reasoning with generative AI for spatially directed, shape-controlled design of protein structure and function. One-sentence summaryImmersive ProteinSketch embeds human spatial reasoning in AI-guided design of protein topology, shape, and function.

bioengineering↗

bioRxiv2026

Aberrant 3'UTR splicing drives FUS-dependent mRNA condensates and prevents β-catenin from adherens junctions to promote cancer aggressiveness

The protein-coding sequence has long been considered the primary determinant of protein function. Alternative splicing within 3'UTRs (AS-3'UTRs) generates multiple transcript isoforms from a single gene, yet their roles in protein function and disease relevance remain largely unexplored. Through systematic transcriptome-wide identification of cancer-associated AS-3'UTRs, we uncover that AS-3'UTRs of {beta}-catenin mRNA direct distinct subcellular localization of {beta}-catenin mRNA isoforms. Specifically, an aberrantly spliced 3'UTR isoform promotes cytoplasmic mRNA condensate formation through FUS binding to a cancer-associated alternative exon (Exon 16A). Because {beta}-catenin function is exquisitely dependent on its subcellular distribution between adherens junctions and the nucleus, this aberrant 3'UTR isoform reprograms {beta}-catenin localization. By sequestering {beta}-catenin in the cytoplasm, the aberrant 3'UTR isoform prevents its incorporation into E-cadherin-based adherens junctions, thereby inducing epithelial-mesenchymal transition (EMT)-associated transcriptional programs. Notably, the expression signature of the aberrant 3'UTR isoform robustly correlates with poor clinical outcomes in colorectal cancer patients. Together, our findings reveal that AS-3'UTRs operate as a previously unrecognized post-transcriptional regulatory mechanism through which the untranslated region of mRNA, without altering a single amino acid, reprograms protein subcellular fate to drive oncogenic phenotypes.

cell biology↗

bioRxiv2026

PETase Kubu enables near-complete enzymatic depolymerization of commercial PLA/PBAT blend mulch film

Agricultural mulch films improve crop productivity, but post-use recovery and recycling remain difficult because the films are thin, fragmented, dispersed across fields, and contaminated. Commercial PLA/PBAT blends are increasingly used as biodegradable mulch film materials, yet these films exhibit slow or incomplete degradation under environmental conditions. Here, we show that Kubu, a thermostable PETase from Kutzneria buriramensis, rapidly depolymerizes commercial PLA/PBAT mulch film without pretreatment at 60 {degrees}C, achieving 95% mass loss within 96 h and releasing terephthalate, adipate, and lactate, detected by LC-MS/MS and HPLC, as the major monomeric products of both PBAT and PLA components. GPC and SEM revealed extensive degradation at the polymer-water interface. DiffDock docking against Kubu, IsPETase, and TfCut indicates that the canonical W/F(Y) cleft of the PETase/Cutinase fold accommodates aliphatic and aromatic ester bonds with comparable geometry, suggesting that substrate promiscuity is an inherent property of the cleft architecture. Kubus distinctive contribution combines this permissive cleft with catalytic activity sufficient for near-complete blend depolymerization within 24 h. Integration with a socioeconomic analysis shows that complete enzymatic depolymerization could avoid social costs up to $4,087 per ton of mulch film. These findings establish a single-enzyme approach to end-of-life management of heterogeneous polyester blends.

bioengineering↗

bioRxiv2026

Fetal MRI reveals altered prenatal cortical surface area in fetuses later diagnosed with autism spectrum disorder

Autism spectrum disorder (ASD) is increasingly conceptualized as a condition rooted in altered prenatal neurodevelopment, yet in vivo evidence from fetal brain imaging remains limited. Using retrospective fetal MRI and surface-based morphometry, we investigated cortical development in 15 fetuses later diagnosed with ASD (77%; mean gestational age [GA] = 26.7 weeks) without major structural brain abnormalities and compared them with 60 typically developing controls (57% male; mean GA = 28.4 weeks). Fetuses later diagnosed with ASD showed significantly reduced whole-brain inner cortical plate surface area compared with controls ({beta} = -0.08 {+/-} 0.02 SE, p = 0.002, partial {superscript 2} = 0.13), corresponding to an estimated [~]7.7% reduction (predicted at GA = 28.1 weeks). Lobar mixed-effects analyses demonstrated broadly distributed reductions across all cortical lobes (FDR-corrected p = <0.001-0.024; Cohens d = -0.06 to -0.10), with modest regional heterogeneity indicating relatively greater frontal and insular involvement (groupxlobe: F = 19.31, p = 0.002, {superscript 2} = 0.08). Surface area findings remained directionally stable across sensitivity analyses, including restriction to neurodevelopmentally confirmed controls and models accounting for image quality variability, although effect sizes were attenuated after quality adjustment. Normative modeling further demonstrated subtle negative deviations from typical prenatal cortical surface area trajectories in ASD (mean Z = -0.27, p = 0.018). These findings suggest that aspects of cortical morphogenesis may diverge prenatally in individuals later diagnosed with ASD and suggest the feasibility of fetal MRI-based surface morphometry for studying early neurodevelopmental variation associated with ASD risk.

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

NetCrafter: Ontology-derived gene network modeling and interpretation

Understanding the complex nature of multi-functional interactions among genes is crucial for interpreting omics data. We developed NetCrafter, an ontology-driven platform for constructing de novo gene networks that are specific to each input gene list and quantitatively defined by ontology-weighted similarity. By incorporating the probabilistic association of ontology or curated gene sets into a weighted Tanimoto similarity metric, NetCrafter transforms enrichment results into quantitative semantic similarity scores between genes, enabling the creation of context-specific statistical networks. These networks can be further decomposed into optimal sub-networks, facilitating multi-functional interpretation and the identification of gene interaction hotspots. NetCrafter also supports the integration of heterogeneous omics-derived gene lists through consensus ontology scoring. Importantly, this list-specific, quantitative framework reveals functional hotspots and target-biomarker relationships - even in cases where ontology terms alone are not predictive of node-level attributes such as CRISPR efficacy. NetCrafter provides an interactive platform for constructing and interpreting dynamic, context-specific gene networks, leveraging ontology-based functional associations to uncover underlying mechanisms and identify key nodes. It is freely available at https://netcrafter.sookmyung.ac.kr and integrated into Q-omics platform (https://qomics.ai) to enhance the utility of cancer omics data.

bioinformatics↗

bioRxiv2025

Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells

Chronic alcohol use can cause pancytopenia and diminished immune responses against pathogens. However, its underlying molecular mechanisms remain unclear. Furthermore, whether chronic alcohol consumption directly induces inflammation in human hematopoietic stem progenitor cells (HSPCs) or whether it affects aging hematopoiesis differently is unknown. To examine how chronic alcohol use influences HSPCs, we performed single-cell RNA-seq in murine and human HSPCs and single-cell ATAC-seq in aged murine HSPCs following alcohol exposure. In the native murine bone marrow, chronic alcohol exposure primed HSPCs to differentiate into myeloid cells and to exhibit heightened inflammation, DNA damage, and epigenetic reactivation of transposable elements (TEs) in an age-dependent manner. Alcohol-exposed aged long-term hematopoietic stem cells (LT-HSCs) displayed increased chromatin accessibility at TE-containing loci correlated with aberrant TE transcription. This transposon derepression was associated with the accumulation of dsRNAs in aged bone marrow cells, and activation of innate immune pathways, perpetuating HSC inflammaging. Furthermore, we identified two epigenetically distinct LT-HSC clusters, LT-HSC1 and LT-HSC2, with the LT-HSC2 cluster expanding in response to chronic alcohol consumption, resembling activated HSCs. In xenotransplanted human HSPCs, chronic alcohol feeding resulted in a significant myeloid bias, heightened inflammation, upregulation of double-stranded RNA (dsRNA) sensors, activation of type I interferon responses, and increased expression of endogenous retroviruses. Despite these molecular alterations, we did not observe a decrease in long-term repopulation capacity in either human or murine HSCs. This suggests that HSC function may recover following alcohol cessation. However, previous chronic alcohol exposures imprint murine HSPCs to exhibit long-term myeloid bias and reduced cell cycle entry upon bacterial LPS challenge. Our data illuminate potential interactions between alcohol and aging that can reinforce inflammaging and epigenetic dysregulation in HSPCs. KeypointsO_LIAging perpetuates alcohol-induced myeloid bias, inflammation, DNA damage, and TE upregulation in murine HSPCs C_LIO_LIPrior chronic alcohol consumption does not affect long-term repopulation but causes persistent myeloid bias and inefficient stress responses after LPS challenge C_LIO_LIChronic alcohol consumption alters chromatin accessibility in TE-overlapping regions C_LIO_LIChronic alcohol consumption promotes myeloid bias, inflammation, and upregulation of endogenous retroviruses in xenotransplanted human HSPCs. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/696246v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@e0357aorg.highwire.dtl.DTLVardef@1d702fdorg.highwire.dtl.DTLVardef@10553ddorg.highwire.dtl.DTLVardef@c4e62e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Typical development of the human fetal subplate: regional heterogeneity, growth, and asymmetry assessed by in vivo T2-weighted MRI

The subplate (SP) is a transient fetal brain compartment supporting neuronal migration, axonal ingrowth, and early cortical activity, yet the dynamics of its regional development remain poorly understood in vivo. Using T2-weighted fetal MRI of 68 typically developing fetuses (22-32 weeks gestational age, GA), we developed a semi-automated pipeline to quantify regional SP morphology (thickness, surface area, and volume). SP characteristics scaled strongly with GA and residual brain volume and showed marked regional differences. After correcting for geometric confounds, regional variation of SP thickness persisted, with highest values in parietal and perisylvian regions, suggesting that SP thickness may serve as a sensitive marker of intrinsic developmental differences. Between late 2nd and early 3rd trimester, mean SP thickness increased by 39.2% with large variation across regions ({+/-}11.0 SD), whereas surface area growth was more uniform (64.3% {+/-}0.7 SD). Continuous growth trajectories clustered into distinct spatiotemporal profiles: early-developing regions (e.g., pericentral and medial occipital cortices) contrasted with later-developing regions (prefrontal, temporal, and parietal cortices). These patterns partially recapitulate primary-to-association, medial-to-lateral, and posterior-to-anterior maturational hierarchies, pointing to organized developmental program. SP development also showed region-specific hemispheric asymmetries, including leftward thickness and volume asymmetry in superior temporal and precentral gyri. Some asymmetries amplified, others attenuated or reversed with age, suggesting both transient states and potential precursors of postnatal lateralization. Together, these findings provide a framework for regional SP quantification and position SP morphology, particularly thickness, as a promising early biomarker that might link fetal SP changes to subsequent cortical development and neurodevelopmental outcomes. Significance StatementThe subplate (SP) is a transient fetal brain compartment that provides an early foundation for downstream cerebral development. Using fetal MRI, we show that SP morphology is regionally heterogeneous and that its growth follows distinct regional trajectories. Principal spatiotemporal patterns differentiate early-from later-developing regions and partially recapitulate sensory-to-association hierarchies of cortical maturation. SP also exhibits dynamic hemispheric asymmetries as early as the second trimester, with some amplifying as potential precursors of postnatal lateralization, and others reversing with age, emphasizing the importance of evaluating developmental trajectories rather than single time points. This framework positions SP morphology as an accessible early marker of fetal brain organization with potential relevance for later neurodevelopment.

neuroscience↗

bioRxiv2025

Machine Learning-assisted Raman Spectral Analysis of Serotonin-responsive ssDNA-SWCNT Nanosensor for Improved Selectivity against Dopamine

Serotonin (5-hydroxytryptamine, 5-HT) plays critical roles in neuromodulation, yet current detection methods struggle for real-time sensing of 5HT with high sensitivity and selectivity. We previously developed nIRHT (near-infrared serotonin nanosensor), which consists of ssDNA-wrapped single walled carbon nanotube that sensitively detects 5-HT. However, nIRHTs fluorescence response cannot discriminate between 5HT and dopamine (DA), limiting its practical applications. In this study, Raman spectroscopy combined with machine learning overcomes this selectivity challenge. G-band spectral features revealed distinct signatures for 5HT versus DA binding to nIRHT, with DA causing greater G- band suppression. We employed differential Raman ({Delta}Raman) to isolate analyte-specific spectral changes and trained three machine learning models for classification. The random forest model with {Delta}Raman achieved optimal performance with 95.8% accuracy, significantly outperforming models using raw Raman spectra. This approach showed improved specificity, with negligible responses to acetylcholine, GABA, and glutamate, and achieved a detection limit of 0.1 M suitable for physiological applications. This Raman based approach transforms the non-selective nIRHT fluorescence sensor into a platform capable of robust neurotransmitter discrimination, overcoming selectivity issues in SWCNT-based molecular sensing.

bioengineering↗

bioRxiv2025

Prediction of zoonotic virus-host transmissibility using comparative airway organoids

AbstractThe emergence of new pandemic zoonotic diseases is accelerating. However, current approaches to control after outbreaks often allow the epidemic or pandemic spread of new zoonotic diseases, exemplified by the case of COVID-19. Prediction of zoonotic transmissibility will help minimize the outbreaks and socioeconomic damage. Here, we established highly efficient comparative airway organoids with minimal components from a panel of mammalian species for long-term culture and passaging and validated their utility to predict the transmissibility of zoonotic pathogens. Airway organoids from each species recapitulated the airway histology and contained the major cell types in the airway. They recapitulated the known susceptibility of their host species and tissues to diverse viruses. Transcriptomic analyses revealed that organoids from susceptible species induced genes of anti-viral immune responses only in common upon exposure to the same virus, although each species organoids displayed differential gene expression profiles. Also, organoids of the same species displayed differential transcriptomic responses against different viruses but induced anti-viral immune genes only in common. Our work provides a roadmap for comprehensive species- and tissue-level organoid panels for quick and reproducible uncharacterized pathogen surveillance to predict and prevent the next pandemic.

developmental biology↗

bioRxiv2025

Tropomyosin 1 promotes platelet adhesion and clot contraction separate from its roles in developmental hematopoiesis

Genome-wide associations studies (GWAS) have linked the Tropomyosin 1 (Tpm1) gene locus to quantitative blood trait variation, but related mechanisms are unclear. Tpm1 encodes an actin-binding protein that stabilizes actin filaments and influences cell adhesion, signaling, and actomyosin contractility. Murine Tpm1 deficiency enhances embryonic hemogenic endothelial cell specification, but it was unclear if these effects extended to postnatal hematopoiesis. We used Cdh5Cre or VavCre models to conditionally ablate Tpm1 in endothelium or hematopoietic cells. Both models produced knockout mice in normal Mendelian ratios with complete Tpm1 ablation in postnatal blood. Endothelial Tpm1 deletion increased hemogenic endothelial cell specification, but did not change hematopoietic progenitor cell production nor adult blood counts. This suggested separate roles for Tpm1 in the embryonic and adult blood systems. GWAS suggested genetic architecture specifically linking decreased TPM1 expression to increased platelet count. We examined platelet lifespan and function to explain these findings. Tpm1KO increased platelet lifespan and diminished adhesion to fibronectin and fibrinogen. Decreased platelet clearance could explain increased platelet count in GWAS. Platelet fibrin binding is necessary for blood clot contraction, which reduces vascular occlusion following initial hemostasis. Tpm1KO reduced clot contraction and enhanced clot formation with worsened vascular occlusion in a ferric chloride-induced stroke model. These findings reveal a new role for Tpm1 in platelet function, offering insight into how cytoskeletal regulation impacts human platelet traits and pointing to novel targets to modify stroke risk and thrombotic disease.

cell biology↗

bioRxiv2025

Asymmetrical recognition and processing of double-strand breaks formed during DNA replication

DNA end resection to generate 3' ssDNA overhangs is the first step in homology-directed mechanisms of double-strand break (DSB) repair. While end resection has been extensively studied in the repair of endonuclease-induced DSBs, little is known about how resection proceeds at DSBs generated during DNA replication. We previously established a system to generate replication-dependent double-ended DSBs at the sites of nicks induced by the Cas9D10A nickase in the budding yeast genome. Here, we suggest that these DSBs form in an asymmetric manner, with one break end being blunt or near blunt, and the other bearing a 3' ssDNA overhang of up the size of an Okazaki fragment. We find that Mre11 preferentially binds blunt ends and is required for the removal Ku from these DSB ends. In contrast, the ends predicted to have 3' overhangs have minimal Ku binding, and end resection at these break ends can proceed in a mostly Mre11-independent manner through either the Exo1 or Dna2-Sgs1 long-range resection pathways. These findings indicate that resection proceeds differently at replication-dependent DSBs than at canonical DSBs, and reveals that Ku selectively binds nearly blunt ends, potentially explaining why replication-dependent DSBs are poorly repaired by non-homologous end joining. Significance StatementDNA end resection is a critical early step in the repair of DNA double-strand breaks by homologous recombination. Studies using endonucleases that generate DSBs in all phases of the cell cycle have shown that end resection proceeds by the sequential action of the Mre11 complex and long-range resection nucleases, Exo1 or Dna2-Sgs1. In this study, we restricted DSB generation to S-phase and found that the genetic requirements for end resection at more physiologically relevant DSBs are different to those at endonuclease-induced DSBs. The asymmetrical recognition and processing of replication-dependent DSBs may also explain the bias toward homologous recombination mediated repair over non-homologous end joining.

genetics↗