Biology subjects

Oh, S.-H.

Publications and source records attributed to Oh, S.-H..

11 recordsLinked to original sources

bioRxiv2026

Ultrasensitive Detection of Alpha-Synuclein Oligomers in Human Plasma Using Optimized Nano-QuIC

Early diagnosis of Parkinsons disease (PD) is critical, as clinical symptoms typically emerge only after substantial neuronal loss. While -synuclein (-Syn) oligomers in blood are promising biomarkers for early detection, their clinical utility is limited by their low abundance and the presence of inhibitory components in the plasma matrix. To address these limitations, we tailored the Nanoparticle-enhanced Quaking-Induced Conversion (Nano-QuIC) platform specifically for the ultrasensitive detection of -Syn oligomers in human plasma. We identified critical reaction determinants by investigating buffer pH, ionic strength, detergent types, and shaking conditions. Furthermore, the integration of silica nanoparticles (siNPs) proved essential in mitigating plasma matrix interference, ensuring robust and reproducible protein aggregation. Under these optimized conditions, the assay achieved a detection limit of 100 pg/mL for -Syn oligomers spiked into human plasma. These results demonstrate that our adapted Nano-QuIC platform provides a highly sensitive and minimally invasive method for detecting pathological -Syn species, offering a significant advancement toward the development of early-stage PD diagnostics.

bioengineering↗

bioRxiv2025

Surface Transmon Resonance (STR): a handheld nanogap biosensor for real-time, label-free molecular binding kinetics

Despite the exponential growth of microelectronics driven by Moores law over half a century, biosensing has remained largely dominated by optical methods such as fluorescence assays and surface plasmon resonance (SPR). Electronic biosensors, particularly field-effect transistor (FET)-based platforms, have historically faced challenges related to Debye screening and the lack of compact, high-frequency instrumentation necessary for label-free, high-sensitivity measurements in conductive solutions. Here, we present a Surface Transmon Resonance (STR) biosensor; a nanogap-enabled electronic platform that exploits a handheld vector network analyzer (nanoVNA) for real-time, phase-resolved detection of protein-protein interactions. Operating at radio frequencies in the hundreds of MHz range, STR decreases Debye screening limitations and provides an SPR-like readout with significantly reduced cost and footprint compared to benchtop optical systems. By characterizing specific bovine serum albumin (BSA) and anti-BSA binding kinetics, we demonstrate that STR biosensors can quantitatively assess molecular affinity and interaction dynamics, capabilities traditionally reserved for optical gold-standard techniques like SPR. This work positions STR as a compact, scalable, and cost-effective electronic alternative to conventional optical biosensors.

bioengineering↗

bioRxiv2024

AI-QuIC: Machine Learning for Automated Detection of Misfolded Proteins in Seed Amplification Assays

Advancements in AI, particularly deep learning, have revolutionized protein folding modeling, offering insights into biological processes and accelerating drug discovery for protein misfolding diseases. However, detecting misfolded proteins associated with neurodegenerative disorders, such as Alzheimers, Parkinsons, ALS, and prion diseases, relies on Seed Amplification Assays (SAAs) analyzed through manual, time-consuming, and potentially inconsistent methods. We introduce AI-QuIC, an AI-driven platform that automates the analysis of Real-Time Quaking- Induced Conversion (RT-QuIC) assay data, a type of SAA crucial for detecting misfolded proteins. Utilizing a well-labeled RT-QuIC dataset of over 8,000 wells--the largest curated dataset for chronic wasting disease prion detection--we applied various AI models to classify true positive, false positive, and negative reactions. Notably, our deep-learning-based model achieved over 98% sensitivity and 97% specificity. By learning directly from raw fluorescence data, deep learning simplifies the SAA-analysis workflow. Automating and standardizing SAA data interpretation with AI-QuIC provides robust, scalable, and consistent diagnostic solutions.

bioinformatics↗

bioRxiv2024

QuICSeedR: An R package for analyzing fluorophore-assisted seed amplification assay data

SummaryFluorophore-assisted seed amplification assays (F-SAAs), such as real-time quaking-induced conversion (RT-QuIC) and fluorophore-assisted protein misfolding cyclic amplification (F-PMCA), have become indispensable tools for studying protein misfolding in neurodegenerative diseases. However, analyzing data generated by these techniques often requires complex and time-consuming manual processes. Additionally, the lack of standardization in F-SAA data analysis presents a significant challenge to the interpretation and reproducibility of F-SAA results across different laboratories and studies. Here, we present QuICSeedR (pronounced as "quick seeder"), an R package that addresses these challenges by providing a comprehensive toolkit for the automated processing, analysis, and visualization of F-SAA data. Importantly, QuICSeedR also sets up the foundation for building an F-SAA data management and analysis framework, enabling more consistent and comparable results across different research groups. Availability and implementationQuICSeedR source code is freely available at: https://github.com/mancili/QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials. Supplementary informationSupplementary Materials are available with the manuscript.

bioinformatics↗

bioRxiv2024

Detection and decontamination of chronic wasting disease prions during venison processing

Prion diseases, including chronic wasting disease (CWD), are caused by prions, which are misfolded aggregates of normal cellular prion protein. Prions possess many characteristics that distinguish them from conventional pathogens, in particular, an extraordinary recalcitrance to inactivation and a propensity to avidly bind to surfaces. In mid to late stages of CWD, prions begin accumulating in cervid muscle tissues. These features collectively create scenarios where occupational hazards arise for workers processing venison and pose risks to consumers through direct prion exposure via ingestion and cross-contamination of food products. In this work, we show that steel and plastic surfaces used in venison processing can be directly contaminated with CWD prions and that cross-contamination of CWD-negative venison can occur from equipment that had previously been used with CWD-positive venison. We also show that several decontaminant solutions (commercial bleach and potassium peroxymonosulfate) are efficacious for prion inactivation on these same surfaces.

microbiology↗

bioRxiv2023

Blood-based Nano-QuIC: Accelerated and Inhibitor-resistant Detection of Misfolded Alpha-synuclein

A hallmark of -synucleinopathies (e.g. Parkinsons disease) is the misfolding and aggregation of -synuclein in tissues and biological fluids. Protein amplification assays like real-time quaking-induced conversion (RT-QuIC) are sensitive yet currently limited to semi-invasive sample types such as cerebrospinal fluid because more accessible samples, such as blood, contain inhibitors. Here, we show that Nanoparticle-enhanced Quaking-induced Conversion (Nano-QuIC) can double the speed of reactions spiked with misfolded -synuclein while increasing sensitivity 100-fold in human plasma. Nano-QuIC detected spike concentrations down to 90 pg/ml in lysed whole blood, while reactions without nanoparticles (RT-QuIC) failed to have any detection due to the presence of strong inhibitors. Moreover, Nano-QuIC showed increased seeding activity in plasma samples from Parkinsons patients (n=4) versus healthy controls (n=4). This sets the groundwork for the noninvasive diagnostic use of Nano-QuIC, potentially enabling early disease detection and management through blood-based testing. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/552630v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1141573org.highwire.dtl.DTLVardef@18c63d6org.highwire.dtl.DTLVardef@1ee9524org.highwire.dtl.DTLVardef@81af13_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Microfluidic Quaking-Induced Conversion (Micro-QuIC) for Rapid On-Site Amplification and Detection of Misfolded Proteins

Protein misfolding diseases, such as prion diseases, Alzheimers, and Parkinsons, share a common molecular mechanism involving the misfolding and aggregation of specific proteins. There is an urgent need for point-of-care (POC) diagnostic technologies that can accurately detect these misfolded proteins, facilitating early diagnosis and intervention. Here, we introduce the Microfluidic Quaking Induced Conversion (Micro-QuIC), a novel acoustofluidic platform for the rapid and sensitive detection of protein misfolding diseases. We demonstrate the utility of our technology using chronic wasting disease (CWD) as a model system, as samples from wild white-tailed deer are readily accessible, and CWD shares similarities with human protein misfolding diseases. Acoustofluidic mixing enables homogeneous mixing of reagents in a high-Reynolds-number regime, significantly accelerating the turnaround time for CWD diagnosis. Our Micro-QuIC assay amplifies prions by an order of magnitude faster than the current gold standard, real-time quaking-induced conversion (RT-QuIC). Furthermore, we integrated Micro-QuIC with a gold nanoparticle-based, naked-eye detection method, which enables visual discrimination between CWD positive and negative samples without the need for a bulky fluorescence detection module. This integration creates a rapid, POC testing platform capable of detecting misfolded proteins associated with a variety of protein misfolding diseases. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/549283v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@885eeaorg.highwire.dtl.DTLVardef@10f820eorg.highwire.dtl.DTLVardef@12396eaorg.highwire.dtl.DTLVardef@188fe0f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

A Field-Deployable Diagnostic Assay for the Visual Detection of Misfolded Prions

Chronic Wasting Disease (CWD), a prion disease of cervids, has been identified across North America, Northern Europe and Korea. Diagnostic tools for the rapid and reliable detection of prion diseases are limited. Here, we combine gold nanoparticles (AuNPs) and quaking induced conversion (QuIC) technologies for the visual detection of amplified misfolded prion proteins from tissues of wild white-tailed deer infected with Chronic Wasting Disease (CWD). Our newly developed diagnostic test, MN-QuIC, enables both naked-eye and light-absorbance measurements for the detection of misfolded prions. The MN-QuIC assay leverages basic laboratory equipment that is cost-effective and portable, thus facilitating real-time prion diagnostics across a variety of settings. To test the portability of our assay, we deployed to a rural field station in southeastern Minnesota and tested for CWD on site. We successfully demonstrated that MN-QuIC is functional in a non-traditional laboratory setting by performing a blinded analysis in the field and correctly identifying all CWD positive and CWD not detected (independently confirmed with ELISA and/or IHC tests) animals at the field site, thus documenting the portability of the assay. Additionally, we show that electrostatic forces and concentration effects help govern the AuNP/prion interactions and contribute to the differentiation of CWD-prion positive and negative samples. We examined 17 CWD-positive and 24 CWD-not-detected white-tailed deer tissues that were independently tested using ELISA, IHC, and RT-QuIC technologies, and results secured with MN-QuIC were 100% consistent with these tests. We conclude that hybrid AuNP and QuIC assays, such as MN-QuIC, have great potential for sensitive, field-deployable diagnostics for a variety of protein misfolding diseases.

molecular biology↗

bioRxiv2020

In-vivo histology of iron and myelin in the brain using magnetic susceptibility source separation in MRI

Obtaining a histological fingerprint from the in-vivo brain has been a long-standing target of magnetic resonance imaging (MRI). In particular, non-invasive imaging of iron and myelin, which are involved in normal brain functions and are histopathological hallmarks in neurodegenerative diseases, has practical utilities in neuroscience and medicine. Here, we propose a biophysical model that describes the individual contribution of paramagnetic (e.g., iron) and diamagnetic (e.g., myelin) susceptibility sources to the frequency shift and transverse relaxation of MRI signals. Using this model, we develop a method,{chi} -separation, that generates the voxel-wise distributions of the two sources. The method is validated using computer simulation and phantom experiments, and applied to ex-vivo and in-vivo brains. The results delineate the well-known histological features of iron and myelin in the specimen, healthy volunteers, and multiple sclerosis patients. This new technology may serve as a practical tool for exploring the microstructural information of the brain.

neuroscience↗

bioRxiv2019

Inhibiting xCT/SLC7A11 induces ferroptosis of myofibroblastic hepatic stellate cells and protects against liver fibrosis

Background and AimsLiver fibrosis develops in the context of excessive oxidative stress, cell death and accumulation of myofibroblasts (MFs) derived from hepatic stellate cells (HSCs). Ferroptosis is a type of regulated cell death that can be caused by inhibiting the cystine/glutamate antiporter xCT. However, while xCT is induced in various liver diseases, its role in HSC activation and liver fibrosis is unknown. We hypothesized that xCT is required for HSCs to antagonize ferroptosis and remain myofibroblastic. MethodsxCT activity was disrupted by siRNA or pharmacological inhibitors in MF-HSC cell lines to determine its effect on redox homeostasis, growth, myofibroblastic activity and viability. xCT expression was then determined by RNA sequencing and RT-PCR during primary HSC activation, and its role in HSC trans-differentiation was assessed. For comparison, xCT expression and function were also determined in primary hepatocytes. Finally, the roles of xCT in HSC accumulation and liver fibrosis were assessed in mice treated acutely with CCl4. ResultsInhibiting xCT in MF-HSCs decreased intracellular glutathione (GSH), suppressed growth and fibrogenesis, and induced cell death. These effects were rescued by antioxidants, an iron chelator, and a canonical ferroptosis inhibitor, but not by inhibitors of apoptosis or necrosis. xCT was dramatically up-regulated during primary HSC activation, and inhibiting xCT suppressed myofibroblastic trans-differentiation and induced ferroptosis. In contrast, healthy hepatocytes were relatively insensitive to ferroptosis induced by xCT inhibition. In vivo, inhibiting xCT systemically reduced MF-HSC accumulation and liver fibrosis after a single dose of CCl4 without exacerbating liver injury or reducing hepatocyte regeneration. ConclusionCompared to healthy hepatocytes, MF-HSCs are exquisitely sensitive to ferroptosis induced by inhibiting xCT. In acutely injured livers, systemic inhibitors of xCT can inhibit fibrosis without worsening liver injury. Further research is needed to determine if this therapeutic window remains sufficiently robust to safely target MF-HSCs and inhibit fibrogenesis in chronically injured liver.

cell biology↗

bioRxiv2017

Prometheus: omics portals for interkingdom comparative genomic analyses

Functional analyses of genes are crucial for unveiling biological responses, for genetic engineering, and for developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history. To this end, we present Prometheus (http://prometheus.kobic.re.kr),web-based omics portal that contains more than 17,215 sequences from prokaryotic and eukaryotic genomes. This portal supports interkingdom comparative analyses via a domain architecture-based gene identification system, Gene Search, and users can easily and rapidly identify single or entire gene sets in specific pathways. Bioinformatics tools for further analyses are provided in Prometheus or through BioExpress, a cloud-based bioinformatics analysis platform. Prometheus suggests a new paradigm for comparative analyses with large amounts of genomic information.

bioinformatics↗