Biology subjects

Yoon, G.

Publications and source records attributed to Yoon, G..

13 recordsLinked to original sources

bioRxiv2026

Water oxidation-driven histidine dioxidation enables probe-free proximity labeling

Photocatalytic proximity labeling (photo-PL) has emerged as a powerful tool for spatial proteomics in subcellular compartments. However, many photo-PL toolboxes rely on singlet oxygen (1O2) to generate highly unstable endoperoxide intermediates that must be trapped immediately by high concentrations of exogenous probes. This constraint can bias spatial proteome coverage, particularly in dynamic and heterogeneous compartments such as endosomes and exosomes, where probe accessibility is intrinsically nonuniform. Here, we develop IDM, an organic photocatalyst that generates hydroxyl (*OH) and superoxide (O *-) radicals via water oxidation instead of 1O , enabling a synergistic dual-radical mechanism for probe-free proximal protein mapping in live cells (PF-Map). The resulting radicals dioxidize proximal histidine residues into a persistent dioxidized state (His-2O) that is thermodynamically stabilized as lactam tautomers, which remain electrophilic and chemically addressable after cell lysis. By decoupling histidine oxidation from live{square}cell probe capture, PF{square}Map can minimize spatial bias arising from heterogeneous probe distribution. Applying PF{square}Map to intracellular vesicle trafficking, we find that both PF{square}Map and a probe{square}dependent workflow (PD{square}Map) robustly identify exosome markers, whereas PF{square}Map additionally reveals a hidden vesicle trafficking-related subproteome that PD-Map underestimated. Together, we establish a minimally biased photocatalytic strategy for spatial protein mapping in complex biological systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/731337v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@13da43dorg.highwire.dtl.DTLVardef@1e9cb7corg.highwire.dtl.DTLVardef@2e7557org.highwire.dtl.DTLVardef@19e16c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit

Real-time assessment of human pluripotent stem cell (hPSC) quality is critical for reproducibility and safety in regenerative medicine, yet current methods are invasive, labor-intensive, or highly operator-dependent. We present DeepHOPE (Deep-learning-guided Holotomography for Pluripotency Evaluation), a non-invasive, automatizable, and statistics-driven platform that integrates three-dimensional (3D) refractive index imaging with deep learning to assess pluripotency. DeepHOPE performs robustly across diverse contexts, including germ-layer differentiation, retinoic acid-induced differentiation, and mid-reprogramming cultures, enabling streamlined cell production workflows and improving the efficiency of midbrain dopaminergic neuron differentiation through informed colony selection. Mechanistically, DeepHOPE detects minute colony-scale topological changes that precede molecular loss of pluripotency. These early changes are associated with rapid F-actin remodeling, including apical-to-basal redistribution during early differentiation. Consistent with a functional role for cytoskeletal regulation in state transitions, sustained reduction of actomyosin tension decreases pluripotency, identifying cytoskeletal dynamics as an upstream determinant of early pluripotency exit. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/720508v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1d73508org.highwire.dtl.DTLVardef@1dab29aorg.highwire.dtl.DTLVardef@1039f76org.highwire.dtl.DTLVardef@da29a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

FAM84B facilitates tau propagation via RYR3-mediated exocytosis in response to neuroinflammation

The increasing prevalence of dementia underscores the pressing need for effective therapeutic interventions. Despite extensive research into A{beta}, the limited efficacy of existing treatment modalities necessitates a paradigm shift toward tau pathology including tau propagation to slow dementia progression. Here, we identified a novel protein, FAM84B (also known as LRATD2), involved in tau propagation. Elevated FAM84B levels were detected in the postmortem cortex, cerebrospinal fluid, and induced pluripotent stem cell-derived cortical neurons of patients with tauopathy. FAM84B facilitates tau secretion through exosome assembly and RYR3-mediated exocytosis, followed by exosomal uptake into neighboring cells via clathrin-mediated endocytosis, thereby driving tau propagation. We confirmed that neuroinflammation induced by heightened STAT3 activity and cytokine treatment upregulated FAM84B expression, stimulating tau propagation, as evidenced by reduced propagation upon RYR3 inhibition. These findings provide invaluable insights into potential avenues for targeting tau propagation to ameliorate disease progression in tauopathies.

neuroscience↗

bioRxiv2024

Neural Adaptation to the Eye's Optics Through Phase Compensation

How does the brain achieve a seemingly veridical and in-focus perception of the world, knowing how severely corrupted visual information is by the eyes optics? Optical blur degrades retinal image quality by reducing the contrast and disrupting the phase of transmitted signals. Neural adaptation can attenuate the impact of blur on image contrast, yet vision rather relies on perceptually-relevant information contained within the phase structure of natural images. Here we show that neural adaptation can compensate for the impact of optical aberrations on phase congruency. We used adaptive optics to fully control optical factors and test the impact of specific optical aberrations on the perceived phase of compound gratings. We assessed blur-induced changes in perceived phase over three distinct exposure spans. Under brief blur exposure, perceived phase shifts matched optical theory predictions. During short-term ([~]1h) exposure, we found a reduction in blur-induced phase shifts over time, followed by after-effects in the opposite direction-a hallmark of adaptation. Finally, patients with chronic exposure to poor optical quality showed altered phase perception when tested under fully-corrected optical quality, suggesting long-term neural compensatory adjustments to phase spectra. These findings reveal that neural adaptation to optical aberrations compensates for alterations in phase congruency, helping restore perceptual quality over time.

neuroscience↗

bioRxiv2024

Autophagy-mediated CTR1 turnover orchestrates the reciprocal interaction between autophagy and ethylene signaling

The phytohormone ethylene and autophagy are crucial for plant adaptation to various environmental stresses, yet the integration of these signaling networks into stress responses is not fully understood. Here, we report that ethylene signaling and autophagy reciprocally regulate each other through Constitutive Triple Response 1 (CTR1), a negative regulator of ethylene signaling. Autophagy facilitates the turnover of the CTR1 protein, which interacts with the key autophagy-related protein ATG8 as autophagic cargo. Impaired autophagy attenuates ethylene responses. Conversely, ethylene-insensitive mutants exhibit enhanced autophagic flux, while a constitutive ethylene response mutant is hypersensitive to carbon starvation stress, which induces autophagy. This suggests that ethylene suppresses autophagy during carbon limitation. We further elucidated that ethylene receptors with a receiver domain play a primary role in modulating autophagy, while receptor kinase activity is not essential. Our findings uncover that the autophagic control of CTR1 degradation allows reciprocal cross-regulation between autophagy and ethylene transduction cascades, optimizing stress responses and resilience.

plant biology↗

bioRxiv2024

Hidden route of protein damage through confined oxygen gas

Oxidative modifications can severely impair protein structure, fold, and function, closely linked to human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), followed by chemical attacks on the protein surface. Here, we report a hidden route of protein oxidative damage, which we refer to as O2-confinement oxidation pathway. This pathway starts with the initial trapping of dissolved molecular oxygen (O2) within protein cavity spaces, followed by interaction with photosensitizing tryptophan residues. The trapped O2 is then converted to singlet oxygen (1O2), a powerful ROS, through spin-flip electron transfer mechanism under blue light. The generated 1O2 within the protein ultimately attacks the protein core residues through constrained diffusion, accelerating the oxidative damage. This alternative photooxidation pathway through the initial O2 trapping would bypass the antioxidant defense systems which target freely-diffusing ROS, constituting an additional layer of protein oxidative damage in cells and tissues.

biochemistry↗

bioRxiv2023

Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology

Nondestructive pathology based on three-dimensional (3D) optical microscopy holds promise as a complement to traditional destructive hematoxylin and eosin (H&E) stained slide-based pathology by providing cellular information in high throughput manner. However, conventional techniques provided superficial information only due to shallow imaging depths. Herein, we developed open-top two-photon light sheet microscopy (OT-TP-LSM) for intraoperative 3D pathology. An extended depth of field two-photon excitation light sheet was generated by scanning a nondiffractive Bessel beam, and selective planar imaging was conducted with cameras at 400 frames/s max during the lateral translation of tissue specimens. Intrinsic second harmonic generation was collected for additional extracellular matrix (ECM) visualization. OT-TP-LSM was tested in various human cancer specimens including skin, pancreas, and prostate. High imaging depths were achieved owing to long excitation wavelengths and long wavelength fluorophores. 3D visualization of both cells and ECM enhanced the ability of cancer detection. Furthermore, an unsupervised deep learning network was employed for the style transfer of OT-TP-LSM images to virtual H&E images. The virtual H&E images exhibited comparable histological characteristics to real ones. OT-TP-LSM may have the potential for histopathological examination in surgical and biopsy applications by rapidly providing 3D information.

pathology↗

bioRxiv2023

Enhanced Omicron subvariant cross-neutralization efficacy of a monovalent SARS-CoV-2 BA.4/5 mRNA vaccine encoding a noncleaved, nonfusogenic spike antigen

The rapid emergence of diverse SARS-CoV-2 variants, notably the Omicron variant, poses challenges to vaccine development. Here, we present a noncleaved, nonfusogenic spike (S) protein eliciting robust B- and T-cell immune responses against Omicron BA.5. The antigen incorporates the R685S and R815A mutations, effectively preventing the shedding of the S1 subunit and eliminating fusogenic activity of the resulting S antigen, termed S(SA). Through reverse genetic analysis, we found that the noncleaved form S protein with the R685S mutation enhances ACE2-dependent viral entry in vitro compared to the wild-type S protein, without increasing the virulence of the mutant virus in mice. The mRNA vaccine encoding the Omicron BA.4/5 S(SA) antigen conferred protective immunity in mice following two doses of 1 g {Psi}-UTP- or UTP-incorporated mRNA vaccines. Despite a roughly 6-fold reduction in neutralizing potency, both mRNA vaccines exhibited broad neutralizing efficacy against Omicron subvariants, including the XBB lineage variants XBB.1.5 and XBB.1.16.

immunology↗

bioRxiv2021

Seeing the World Like Never Before: Human stereovision through perfect optics

Stereovision is the ability to perceive fine depth variations from small differences in the two eyes images. Using adaptive optics, we show that even minute optical aberrations that are not clinically correctable, and go unnoticed in everyday vision, can affect stereo acuity. Hence, the human binocular system is capable of using unnaturally fine details that are not encountered in everyday vision. More importantly, stereoacuity was still considerably variable even with perfect optics. This variability can be attributed to neural adaptation. Our visual system tries to compensate for these aberrations through neural adaptation that optimizes stereovision when viewing stimuli through ones habitual optics. However, the same adaptation becomes ineffective when the optics are changed, even if improved. Beyond optical imperfections, we show that stereovision is limited by neural adaptation to ones own optics. Significance statementHumans, and animals with front-facing eyes, view the world from slightly different vantage points. This creates small differences in the left and right images that can be utilized for fine depth perception (stereovision). Retinal images are also subject to imperfections that are often different in the optics of the two eyes. Using advanced optical correction techniques, we show that even the smallest imperfections that escape clinical detection affect stereovision. We also find that neural processes become adapted to a persons own optics. Hence, stereovision is directly impacted by the optics of the eyes, and indirectly via neural adaptation. Since the optics change over the lifespan, our results imply that the adult binocular system is adaptable with possibilities for binocular rehabilitation.

neuroscience↗

bioRxiv2020

Ethylene-triggered subcellular trafficking of CTR1 suppresses the response to ethylene gas

Ethylene gas controls plant growth and stress responses. Ethylene-exposed dark-grown seedlings exhibit dramatic growth reduction, yet the seedlings rapidly return to the basal growth rate when ethylene gas is removed. However, the underlying mechanism governing this reversible acclimation of dark-grown seedlings to ethylene remains enigmatic. Here, we report that ethylene triggers the translocation of the Raf-like protein kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1), a negative regulator of ethylene signaling, from the endoplasmic reticulum to the nucleus. Nuclear-localized CTR1 stabilizes the ETHYLENE-INSENSITIVE3 (EIN3) transcription factor via interaction with the EIN3-BINDING F-box (EBF) proteins, thus enhancing the ethylene response and delaying growth recovery. These findings uncover a mechanism of the ethylene signaling pathway that links the spatiotemporal dynamics of cellular signaling components to organismal responses.

plant biology↗

bioRxiv2020

Functional reorganization of visual processing following long-term adaptation to optical defects

How we see is fundamentally limited by the eyes optics, which determine retinal image quality and constrain neural processing. Elucidating how long-term exposure to optical defects alters visual processing is vital for understanding the human brains capacity for and limits of sensory plasticity. Using adaptive optics to bypass the eyes optical aberrations, we assessed changes in visual processing in neurotypically-developed adults with keratoconus (KC)--a corneal disease causing severe optical aberrations during adulthood that cannot be fully corrected using conventional methods. As a result, KC patients are chronically exposed to degraded retinal images in their everyday life, making them an ideal model to understand how prolonged exposure to poor optical quality alters visual processing. Here, we show that when tested under similar fully-corrected optical conditions as neurotypical observers, KC patients exhibited altered contrast sensitivity, with impaired sensitivity for fine spatial details and better sensitivity for coarse spatial details. Both gains and losses in contrast sensitivity were more pronounced in patients with poorer habitual optical quality. Moreover, using an equivalent noise paradigm and a computational model of visual processing, we show that these alterations in visual processing are mediated by changes in signal enhancement of spatial frequency selective mechanisms. The present findings uncover fundamental properties of neural compensation mechanisms in response to long-term exposure to optical defects, which alter sensory processing and limit the benefits of improved optics. The outcome is a large-scale functional reorganization favoring the processing of sensory information less affected by the eyes optics. Significance statementThe eyes optics represent an intrinsic limit to human visual perception, determining the quality of retinal images. Neural adaptation optimizes the brains limited sensory processing capacity to the structure of the degraded retinal inputs, providing an exceptional quality of vision given these optical limitations. Here, we show that prolonged exposure to poor optical quality results in a functional reorganization of visual processing that favors sensory information less affected by the eyes optics. The present study helps elucidate how optical factors shape the way the brain processes visual information. Notably, the resulting adaptive neural plasticity limits the immediate perceptual benefits of optical interventions, a factor that must be taken into consideration when treating the increasing human population affected by optical defects.

neuroscience↗

bioRxiv2019

VPS41 recessive mutation causes ataxia and dystonia with retinal dystrophy and mental retardation by inhibiting HOPS function and mTORC1 signaling

The vacuolar protein sorting protein 41 (VPS41) is a neuroprotective protein in models of Parkinsons disease (PD). As part of the HOPS (Homotypic fusion and Protein Sorting) complex, VPS41 regulates fusion of lysosomes with late endosomes and autophagosomes. Independent of HOPS, VPS41 regulates transport of newly synthesized lysosomal membrane proteins and secretory proteins. Here we report two brothers with compound heterozygous mutations in VPS41 (VPS41R662* and VPS41S285P), born to healthy and non-consanguineous parents. Both patients displayed transient retinal dystrophy, ataxia and dystonia, with brain MRI findings of cerebellar atrophy and a thin saber-shape corpus callosum. Patient-derived fibroblasts contained enzymatically active lysosomes that were poorly reached by endocytic cargo and failed to attract the mTORC1 complex. Consequently, transcription factor TFE3, a driver of autophagy and lysosomal genes, showed continuous nuclear localization which resulted in elevated LC3-II levels and an impaired response to nutrient starvation. CRISPR/CAS VPS41 HeLa knockout cells showed a similar phenotype that could be rescued by wildtype VPS41 but not by VPS41S285P or VPS41R662*. mTORC1 inhibition was also seen after knockout of HOPS subunits VPS11 or VPS18. Regulated neuropeptide secretion in PC12 VPS41 knockout cells was rescued by VPS41S285P expression, indicating that this HOPS-independent function was preserved. Co-expression of the VPS41S285P and VPS41R662* variants in a C. elegans model of PD abolished the protective effect of VPS41 against -synuclein-induced neurodegeneration. We conclude that both disease-associated VPS41 variants specifically abrogate HOPS function, which leads to a delay in endocytic cargo delivery to lysosomes, mTORC1 inhibition and irresponsiveness to autophagic clues. Our studies signify a link between HOPS function and mTORC1 signaling and imply that HOPS function is required for the neuroprotective effect of VPS41 in PD.

cell biology↗

bioRxiv2019

Microbial networks in SPRING - Semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data

High-throughput microbial sequencing techniques, such as targeted amplicon-based and metagenomic profiling, provide low-cost genomic survey data of microbial communities in their natural environment, ranging from marine ecosystems to host-associated habitats. While standard microbiome profiling data can provide sparse relative abundances of operational taxonomic units or genes, recent advances in experimental protocols give a more quantitative picture of microbial communities by pairing sequencing-based techniques with orthogonal measurements of microbial cell counts from the same sample. These tandem measurements provide absolute microbial count data albeit with a large excess of zeros due to limited sequencing depth. In this contribution we consider the fundamental statistical problem of estimating correlations and partial correlations from such quantitative microbiome data. To this end, we propose a semi-parametric rank-based approach to correlation estimation that can naturally deal with the excess zeros in the data. Combining this estimator with sparse graphical modeling techniques leads to the Semi-Parametric Rank-based approach for INference in Graphical model (SPRING). SPRING enables inference of statistical microbial association networks from quantitative microbiome data which can serve as high-level statistical summary of the underlying microbial ecosystem and can provide testable hypotheses for functional species-species interactions. Due to the absence of verified microbial associations we also introduce a novel quantitative microbiome data generation mechanism which mimics empirical marginal distributions of measured count data while simultaneously allowing user-specified dependencies among the variables. SPRING shows superior network recovery performance on a wide range of realistic benchmark problems with varying network topologies and is robust to misspecifications of the total cell count estimate. To highlight SPRINGs broad applicability we infer taxon-taxon associations from the American Gut Project data and genus-genus associations from a recent quantitative gut microbiome dataset. We believe that, as quantitative microbiome profiling data will become increasingly available, the semi-parametric estimators for correlation and partial correlation estimation introduced here provide an important tool for reliable statistical analysis of quantitative microbiome data.

bioinformatics↗