Biology subjects

Cho, S. H.

Publications and source records attributed to Cho, S. H..

14 recordsLinked to original sources

bioRxiv2026

Comparative Multi-omics Reveals Conserved Membrane Architecture and Selective Metabolic Cargo Enrichment Across Yeast-Derived Extracellular Vesicles

Extracellular vesicles (EVs) are fundamental mediators of intercellular communication across all kingdoms of life, yet our understanding of EV biology has been derived predominantly from mammalian systems. In contrast, yeast-derived extracellular vesicles (YDEVs) remain poorly characterized despite their potential as scalable, non-pathogenic platforms for biotechnology and metabolic engineering. Here, we combined a high-yield isolation workflow with comparative multi-omics to define the metabolically active cargo and membrane composition of EVs derived from three yeast species and four strains: the conventional model yeast Saccharomyces cerevisiae (SC), the non-model oleaginous yeast Rhodotorula toruloides (RT-88), and two Yarrowia lipolytica strains, wild-type W29 and its engineered derivative Po1f. Using tangential flow filtration coupled with ultracentrifugation, we reproducibly isolated intact, bilayer-enclosed vesicles with conserved nanoscale morphology across all strains despite marked differences in EV yield. Comparative metabolomics revealed selective enrichment of distinct metabolically active cargo, including nucleotide metabolites in SC, fatty acids and acyl-carnitines in RT-88, and strain-specific metabolites within the Yarrowia isolates. Notably, nicotinamide adenine dinucleotide (NAD) was enriched in SC and RT-88 EVs but was nearly absent from Yarrowia-derived vesicles, raising the possibility that EV encapsulation may facilitate protected transport of this otherwise membrane-impermeable cofactor. In contrast to these differences in cargo composition, comparative lipidomics demonstrated a broadly conserved membrane architecture across all strains, with only quantitative remodeling of specific lipid classes and membrane unsaturation profiles. Together, these findings support an organizational principle in which yeast-derived extracellular vesicles preserve a conserved membrane architecture while selectively enriching metabolically active cargo, establishing a comparative framework for understanding EV biology across evolutionarily diverse yeast species.

biochemistry↗

bioRxiv2026

WebCalEM: a browser-based tool for routine and accurate pixel size calibration in cryo-EM

Accurate determination of the image pixel size is critical for quantitative cryo-electron microscopy analyses, yet existing calibration methods remain under-utilized because installation barriers and workflow complexity discourage routine adoption. To fill in this gap, a web-based application, WebCalEM, was developed to transform specialized calibration procedures into an accessible routine practice. Micrographs of any specimen with a known crystalline lattice, such as gold or graphene-oxide, are uploaded through a standard browser, processed entirely client-side, and analyzed with real-time visualization and downloadable statistical outputs. The application is delivered as a single self-contained HTML file that runs in any modern web browser without server-side computation, a configuration well suited to isolated core-facility microscope workstations. Cross-standard consistency between gold and graphene-oxide measurements across two microscopes and ten magnification settings yields a Bland-Altman bias of -0.005% of nominal with 95% limits of agreement of [-0.30%, +0.29%]. By delivering this workflow with no local installation, WebCalEM lowers the practical barrier to documented per-dataset magnification calibration in routine cryo-EM operation. SynopsisWebCalEM is a browser-based, install-free application that performs routine cryo-EM pixel-size calibration directly from gold or graphene-oxide reflections in standard sample-support grids using sub-pixel Fourier-space peak localization; it reproduces the precision of established command-line calibration tools while removing the installation barrier and supporting retrospective per-region calibration on archived datasets.

molecular biology↗

bioRxiv2026

Structural Basis for C8 methylation of 23S ribosomal RNA by Cfr

Cfr methylates C8 of adenosine 2503 (A2503) in 23S ribosomal RNA (rRNA) and will also methylate C2 of A2503 after methylating C8. C8 methylation confers resistance to more than five classes of clinically used antibiotics, highlighting it as a worrisome mechanism of antibiotic resistance. Here, we report the structure of Cfr, determined by cryogenic electron microscopy (Cryo-EM). Despite its small size ([~]36 kDa), we exploit a transient protein-RNA crosslink that forms during catalysis, which requires Cys105 to resolve. Using a Cfr Cys105Ala variant and an 87-nucleotide strand of rRNA, we isolate the crosslinked species and determine its structure to 3.0 [A] resolution. Notably, the 87-mer rRNA adopts an L-shaped conformation characteristic of tRNAs, rather than the conformation it assumes in the ribosome. One Sentence SummaryCryo-EM structure of Cfr, a radical S-adenosylmethionine methylase that confers antibiotic resistance

biochemistry↗

bioRxiv2025

Synthetic auxotrophy reveals metabolic regulation of plasma cell generation, affinity maturation, and cytokine receptor signaling

The efficiencies with which activated B lymphocytes proliferate and develop into antibody (Ab)-secreting plasma cells are critical determinants of adaptive humoral immunity and sustain certain autoimmune diseases. Specific pathways in intermediary metabolism, or their substrate supply, influence lymphocyte differentiation and function. We now show that although stringent restriction of glutamine supply decreases proliferation and differentiation of B cells into plasma cells, glutaminolysis - a major means of metabolism of this amino acid - was only conditionally crucial in B cells and the Ab responses derived from them. Strikingly, Gls, the gene encoding the main glutaminase of lymphocytes, promoted anti-NP Ab responses at the primary and recall phases if either glucose uptake into B cells or pyruvate into their mitochondria was also impaired but otherwise was dispensable. This synthetic auxotrophy, i.e., conditional requirement of glutaminase for processes in addition to survival and proliferation, involved support to a progressive expansion of mitochondrial respiration followed by plasma cell differentiation. Surprisingly, impairment of glutaminase and the mitochondrial pyruvate channel decreased IL-21 stimulation of STAT3 phosphorylation as well as interferon stimulation of STAT1 activation. Together, our findings establish not only a powerful collaboration of metabolic pathways in programming increased respiration and the development of Ab-secreting cells, but also reveal modulation of cytokine receptor signaling by metabolism.

immunology↗

bioRxiv2024

B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size

The qualities of antibody (Ab) responses provided by B lymphocytes and their plasma cell (PC) descendants are crucial facets of responses to vaccines and microbes. Metabolic processes and products regulate aspects of B cell proliferation and differentiation into germinal center (GC) and PC states as well as Ab diversification. However, there is little information about lymphoid cell-intrinsic functions of enzymes that mediate ether lipid biosynthesis, including a major class of membrane phospholipids. Imaging mass spectrometry (IMS) results had indicated that concentrations of a number of these phospholipids were substantially enhanced in GC compared to the background average in spleens. However, it was not clear if biosynthesis in B cells was a basis for this finding, or whether such cell-intrinsic biosynthesis contributes to B cell physiology or Ab responses. Ether lipid biosynthesis can involve the enzyme PexRAP, the product of the Dhrs7b gene. Using combinations of IMS and immunization experiments in mouse models with inducible Dhrs7b loss-of-function, we now show that B lineage-intrinsic expression of PexRAP promotes the magnitude and affinity maturation of a serological response. Moreover, the data revealed a Dhrs7b-dependent increase in ether phospholipids in primary follicles with a more prominent increase in GC. Mechanistically, PexRAP impacted B cell proliferation via enhanced survival associated with controlling levels of ROS and membrane peroxidation. These findings reveal a vital role of this peroxisomal enzyme in B cell homeostasis and the physiology of humoral immunity.

immunology↗

bioRxiv2024

Development and Utilization of 3D Anatomy Education Content using Metaverse and XR for Remote Telemedicine Education

The objective of this study is to explore innovative integration within the field of anatomy education by leveraging HoloLens 2 Augmented Reality Head-Mounted Display (AR HMD) technology and real-time cloud rendering. Initial 3D datasets, comprising extensive anatomical information for each bone, were obtained through the 3D scanning of a full-body cadaver of Korean male origin. Subsequently, these datasets underwent refinement processes aimed at enhancing visual fidelity and optimizing polygon counts, utilizing Blender software. Unity was employed for the development of the Metaverse platform, incorporating tailored 3D User Experience (UX) and User Interface (UI) components to facilitate interactive anatomy education via imported cadaver models. Integration with real-time remote rendering cloud servers, such as Azure, was implemented to augment the performance and rendering capabilities of the HoloLens 2 AR HMD. The extended reality (XR) content uses the Photon Cloud network for real-time data synchronization and HoloLens 2 voice functionality. The metaverse platform supports user interaction through room creation and joining, with various tools for bone manipulation, color differentiation, and surface output. Collaboration features enable sharing and synchronization of model states. The study highlights the importance of technological innovation in anatomy education for future medical professionals. The proposed content aims to address limitations of traditional methods and enhance learning experiences. Continued efforts in developing and improving such technologies are crucial to equip learners with essential skills for adaptation in the evolving healthcare landscape. keyword: Metaverse, Anatomy, Cadaver, Extended Reality(XR), Virtual Reality(VR)

scientific communication and education↗

bioRxiv2023

Plasma cell differentiation, antibody quality, and initial germinal center B cell population depend on glucose influx rate

Antibody secretion into sera, selection for higher affinity BCR, and the generation of higher Ab affinities are important elements of immune response optimization, and a core function of germinal center reactions. B cell proliferation requires nutrients to support the anabolism inherent in clonal expansion. Glucose usage by GC B cells has been reported to contribute little to their energy needs, with questions raised as to whether or not glucose uptake or glycolysis increases in GC B cells compared to their naive precursors. Indeed, metabolism can be highly flexible, such that supply shortage along one pathway may be compensated by increased flux on others. We now show that elimination of the glucose transporter GLUT1 after establishment of a pre-immune B cell repertoire, even after initiation of the GC B cell gene expression program, decreased initial GC B cell population numbers, affinity maturation, and PC outputs. Glucose oxidation was heightened in GC B cells, but this hexose flowed more into the pentose phosphate pathway (PPP), whose activity was important in controlling reactive oxygen (ROS) and ASC production. In modeling how glucose usage by B cells promotes the Ab response, the control of ROS appeared insufficient. Surprisingly, the combination of galactose, which mitigated ROS, with provision of mannose - an efficient precursor to glycosylation - supported robust production of and normal Ab secretion by ASC under glucose-free conditions. Collectively, the findings indicate that GC depend on normal glucose influx, especially in PC production, but reveal an unexpected metabolic flexibility in hexose requirements. KEY POINTSO_LIGlucose influx is critical for GC homeostasis, affinity maturation and the generation of Ab-secreting cells. C_LIO_LIPlasma cell development uses the Pentose Phosphate Pathway, and hexose sugars maintain redox homeostasis. C_LIO_LIPCs can develop and achieve robust Ab secretion in the absence of glucose using a combination of hexose alternatives. C_LI

immunology↗

bioRxiv2022

Ion exchange biomaterials to capture daptomycin and prevent resistance evolution in off-target bacterial populations

Daptomycin (DAP), a cyclic anionic lipopeptide antibiotic, is among the last resorts to treat multidrug resistant (vancomycin resistant Enterococcus faecium or methicillin resistant Staphylococcus aureus) Gram-positive bacterial infections. DAP is administered intravenously and biliary excretion results in the introduction of DAP ([~]5-10 % of the intravenous DAP dose) arriving in the gastrointestinal (GI) tract where it drives resistance evolution in off-target populations of Enterococcus faecium bacteria. Previously, we have shown that the oral administration of cholestyramine, an ion exchange biomaterial (IXB) sorbent, prevents DAP treatment from enriching DAP-resistance in populations of E. faecium shed from mice. Here, we engineer the biomaterial-DAP interfacial interactions to uncover the antibiotic removal mechanisms. The IXB-mediated DAP capture from aqueous media was measured in both controlled pH/electrolyte solutions and in simulated intestinal fluid (SIF) to uncover the molecular and colloidal mechanisms of DAP removal from the GI tract. Our findings show that the IXB electrostatically adsorbs the anionic antibiotic via a time-dependent diffusion-controlled process. Unsteady-state diffusion-adsorption mass balance describes the dynamics of adsorption well, and the maximum removal capacity is beyond the electric charge stoichiometric ratio because of DAP self-assembly. This study may open new opportunities for optimizing cholestyramine adjuvant therapy to prevent DAP resistance, as well as designing novel biomaterials to remove off-target antibiotics from the GI tract. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/495716v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@ec034eorg.highwire.dtl.DTLVardef@cd1106org.highwire.dtl.DTLVardef@118dbcborg.highwire.dtl.DTLVardef@106287c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

Selective pharmaceutical inhibition of PARP14 mitigates allergen-induced IgE and mucus overproduction in a mouse model of pulmonary allergic response

The type 2 cytokines IL-4 and IL-13, which share use of an IL-4 receptor alpha chain and its nuclear induction of the transcription factor STAT6, are crucial in elicitation and maintenance of allergic conditions that include asthma. Prior work has shown a physical and functional association of STAT6 with PARP14, an ADP-ribosyl monotransferase. Moreover, elimination of all PARP14 expression by gene targeting led to altered recall antibody responses and attenuation of ovalbumin-specific allergic lung inflammation with no apparent health issues for mice lacking this protein. However, an unanswered question is whether or not inhibition of the catalytic function has any biological consequence since PARP14 has multiple functional domains apart from the portion that catalyzes ADP-ribosylation. As reported separately, iterative structural analyses and medicinal chemistry fostered the generation of a compound, RBN2759, that is highly selective in its inhibition of PARP14 with negligible impact on other members of the PARP gene family. We show here that administration of this compound to mice previously sensitized to the allergen Alternaria alternata achieved biochemically active levels and altered physiological responses to the antigen. These results show for the first time that in vivo administration of a specific inhibitor of the ADP-ribosyltransferase activity encoded by PARP14 is sufficient to alter biological responses. Specifically, the orally absorbable pharmaceutical compound decreased allergen-induced mucus, blunted the induced increases in circulating IgE, and prevented suppression of IgG2a. We conclude that the catalytic activity can contribute to pathogenesis in allergic processes and propose that other biological endpoints that depend on ADP-ribosylation by PARP14 can be targeted using selective inhibition.

immunology↗

bioRxiv2021

Novel Paju Apodemus Paramyxovirus 1 and 2, Harbored by Apodemus agrarius in The Republic of Korea

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a potential threat to public health. Currently, 78 species and 17 genera of paramyxoviruses are classified and harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Jeilongvirus has been proposed as a novel paramyxovirus genus containing J-, Beilong, and Tailam viruses, found in wild rodents. Using RT-PCR, 824 Apodemus agrarius individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was detected in 108 (13.1%) rodents captured at 14 trapping sites in Korea. We first present two genetically distinct novel paramyxoviruses (genus Jeilongvirus), Paju Apodemus paramyxoviruses 1 (PAPV-1) and 2 (PAPV-2), from A. agrarius. Six PAPV strains were completely sequenced using next-generation and Sanger sequencing. PAPV-1 genome comprised 19,716 nucleotides, with eight genes (3'-N-P/V/C-M-F-SH-TM-G-L-5'), whereas PAPV-2 genome contained 17,475 nucleotides, with seven genes (3'-N-P/V/C-M-F-TM-G-L-5'). The disparity between PAPV-1 and -2 revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogenies of PAPV-1 and -2 belong to distinct genetic lineages of Jeilongvirus despite being from the same natural host. PAPV-1 clustered with Beilong and Tailam viruses, while PAPV-2 formed a genetic lineage with Mount Mabu Lophuromys virus-1. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. Therefore, this study provides profound insights into the molecular epidemiology, virus-host interactions, and zoonotic potential of novel rodent-borne paramyxoviruses. ImportanceParamyxoviruses are a critical public health and socio-economic burden to humans. Rodents play a crucial role in transmitting pathogens to humans. In the last decade, novel paramyxoviruses have been discovered in different rodents. Here, we found that Apodemus agrarius harbored two distinct genotypes of the novel paramyxoviruses, Paju Apodemus paramyxovirues 1 (PAPV-1) and 2 (PAPV-2), possessing unique genome structures that are responsible for encoding TM and G proteins of different sizes. In addition, PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III IFNs, ISGs, and proinflammatory cytokines. Thus, this study provides significant insights into molecular prevalence, virus-host interactions of paramyxoviruses. These observations raise the awareness of physicians and scientists about the emergence of new rodent-borne paramyxoviruses.

microbiology↗

bioRxiv2021

Generalizing about GC (hypoxia): Dys- & Dat-InformaticaComment on Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis

Steadily accumulating evidence supports the concept that the outputs of immune responses are influenced by local nutrient and metabolite conditions or concentrations, as well as by the molecular programming of intermediary metabolism within immune cells. Humoral immunity and germinal center reactions are one setting in which these factors are under active investigation. Hypoxia has been highlighted as one example of how a particular nutrient is distributed in primary and secondary follicles during an antibody response, and how its sensors could impact the qualities of antibody output after immunization. Based on a bio-informatic analysis of mRNA levels in germinal center and other B cells, recently published work challenges the concept that there is any hypoxia or that it has any influence. In this perspective, we perform new analyses of published genomics data to explore potential sources of disparity and elucidate aspects of what on the surface might seem to be conflicting conclusions. In particular, the replicability and variance among data sets derived from different naive as well as germinal center B cells are considered. The results of the investigation highlight several broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. From one finding of this re-analysis, it is proposed that a standard should be expected in which the relationship of new data sets compared to prior "fingerprints" of cell types should be reported transparently to referees and readers. In light of the strong evidence for diversity in the constituencies within germinal centers elicited by protein immunization, it also is proposed that a core practice should be to avoid overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features.

immunology↗

bioRxiv2020

Antibody Escape by Polyomavirus Capsid Mutation Facilitates Neurovirulence

JCPyV polyomavirus, a member of the human virome, causes Progressive Multifocal Leukoencephalopathy (PML), an oft-fatal demyelinating brain disease in individuals receiving immunomodulatory therapies. Mutations in the major viral capsid protein, VP1, are common in JCPyV from PML patients (JCPyV-PML) but whether they confer neurovirulence or escape from virus-neutralizing antibody (nAb) in vivo is unknown. A mouse polyomavirus (MuPyV) with a sequence-equivalent JCPyV-PML VP1 mutation replicated poorly in the kidney, a major reservoir for JCPyV persistence, but retained the CNS infectivity, cell tropism, and neuropathology of the parental virus. This mutation rendered MuPyV resistant to a monoclonal Ab (mAb), whose specificity overlapped the endogenous anti-VP1 response. Using cryo EM and a custom subvolume refinement approach, we resolved an MuPyV:Fab complex map to 3.1 [A] resolution. The structure revealed the mechanism of mAb evasion. Our findings demonstrate convergence between nAb evasion and CNS neurovirulence in vivo by a frequent JCPyV-PML VP1 mutation.

immunology↗

bioRxiv2019

Tuned normalization in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior

Current dominant views hold that perceptual confidence reflects the probability that a decision is correct. Although these views have enjoyed some empirical support, recent behavioral results indicate that confidence and the probability of being correct can be dissociated. An alternative hypothesis suggests that confidence instead reflects the magnitude of evidence in favor of a decision while being relatively insensitive to the evidence opposing the decision. We considered how this alternative hypothesis might be biologically instantiated by developing a simple leaky competing accumulator neural network model incorporating a known property of sensory neurons: tuned normalization. The key idea of the model is that each accumulator neurons normalization tuning dictates its contribution to perceptual decisions versus confidence judgments. We demonstrate that this biologically plausible model can account for several counterintuitive findings reported in the literature, where confidence and decision accuracy were shown to dissociate -- and that the differential contribution a neuron makes to decisions versus confidence judgments based on its normalization tuning is vital to capturing some of these effects. One critical prediction of the model is that systematic variability in normalization tuning exists not only in sensory cortices but also in the decision-making circuitry. We tested and validated this prediction in macaque superior colliculus (SC; a region implicated in decision-making). The confirmation of this novel prediction provides direct support for our model. These findings suggest that the brain has developed and implements this alternative, heuristic theory of perceptual confidence computation by capitalizing on the diversity of neural resources available. SignificanceThe dominant view of perceptual confidence proposes that confidence optimally reflects the probability that a decision is correct. But recent empirical evidence suggests that perceptual confidence exhibits a suboptimal confirmation bias, just as in human decision-making in general. We tested how this bias might be neurally implemented by building a biologically plausible neural network model, and showed that the bias emerges when each neurons degree of divisive normalization dictates how it drives decisions versus confidence judgments. We confirmed the models biological substrate using electrophysiological recordings in monkeys. These results challenge the dominant model, suggesting that the brain instead capitalizes on the diversity of available machinery (i.e., neuronal resources) to implement heuristic -- not optimal -- strategies to compute subjective confidence.

neuroscience↗

bioRxiv2017

Superior Colliculus Neuronal Ensemble Activity Signals Optimal Rather Than Subjective Confidence

Recent studies suggest that neurons in sensorimotor circuits involved in perceptual decision-making also play a role in decision confidence. In these studies, confidence is often considered to be an optimal readout of the probability that a decision is correct. However, the information leading to decision accuracy and the report of confidence often co-varied, leaving open the possibility that there are actually two dissociable signal types in the brain: signals that correlate with decision accuracy (optimal confidence) and signals that correlate with subjects behavioral reports of confidence (subjective confidence). We recorded neuronal activity from a sensorimotor decision area, the superior colliculus (SC) of monkeys, while they performed two different tasks. In our first task, decision accuracy and confidence co-varied, as in previous studies. In our second task, we implemented a novel motion discrimination task with stimuli that were matched for decision accuracy but produced different levels of confidence as reflected by behavioral reports. We used a multivariate decoder to predict monkeys choices from neuronal population activity. As in previous studies on perceptual decision-making mechanisms, we found that neuronal decoding performance increased as decision accuracy increased. However, when decision accuracy was matched, performance of the decoder was similar between high and low subjective confidence conditions. These results show that the SC likely signals optimal decision confidence similar to previously reported cortical mechanisms, but is unlikely to play a critical role in subjective confidence. The results also motivate future investigations to determine where in the brain signals related to subjective confidence reside.\n\nSignificance StatementConfidence is thought to reflect the rational or optimal belief concerning ones choice accuracy. Here, we introduce a novel version of the dot-motion discrimination task with stimulus conditions that produce similar accuracy but different subjective behavioral reports of confidence. We decoded decision performance of this task from neuronal signals in the superior colliculus (SC), a subcortical region involved in decision-making. We found that SC activity signaled a perceptual decision for visual stimuli, with the strength of this activity reflecting decision accuracy, but not the subjective level of confidence as reflected by behavioral reports. These results demonstrate an important role for the SC in perceptual decision-making and challenge current ideas about how to measure subjective confidence in monkeys and humans.

neuroscience↗