Biology subjects

Cho, Y. K.

Publications and source records attributed to Cho, Y. K..

10 recordsLinked to original sources

bioRxiv2026

Becoming Biomedical Faculty: A Longitudinal Analysis of Successful Academic Career Aspirants Career Perspectives, Motivations, and Intentions

Seismic shifts within academia over the last several decades have seen the growth of biomedical PhD recipients alongside the relative stagnation of tenure-track research-intensive faculty careers (RIFCs). This hypercompetitive academic job market has prompted interest in the paths of those who attain RIFCs. Understanding what drives recent biomedical PhDs to make their career decisions and persist toward them requires a clear picture of how career perceptions, motivations, and intentions develop and crystallize over time. Using annual in-depth interviews across nearly two decades, this report explores the evolution of career thinking and differentiation among 40 who attained a RIFC from diverse starting points to their attainment of a RIFC. Participants strategies for navigating early scientific experiences were patterned by their varied educational and socioeconomic backgrounds. Nearly half of participants did not start with or maintain stable interest in RIFCs, exhibiting changes in both PhD and postdoctoral phases. Participants highlighted six drivers toward RIFCs including desire for independence/autonomy and contributing to knowledge/health. Our results are instructive for trainees and mentors guiding career exploration and differentiation.

scientific communication and education↗

bioRxiv2026

Circulating miR-10b-5p drives Kawasaki vasculitis through endothelial reprogramming and nominates CXCL8 as an early diagnostic biomarker

BackgroundKawasaki disease (KD) is an acute systemic vasculitis of unknown etiology and the leading cause of acquired heart disease in children. Coronary artery aneurysm formation represents its most serious complication, yet no specific biomarker exists for early diagnosis at emergency department (ED) presentation. We sought to define the molecular mechanisms driving KD vasculitis and to identify a clinically actionable early diagnostic marker. MethodsWhole microRNA sequencing was performed on buffy coat specimens from KD patients and febrile controls presenting to the ED. Disease-associated miRNA candidates were validated in two independent murine KD-like vasculitis models: Lactobacillus casei cell wall extract (LCWE; n=12-20) and Candida albicans water-soluble fraction (CAWS; n=12). The functional role of miR-10b-5p was assessed by antagomir-mediated inhibition in the LCWE model. Transcriptomic and chromatin-level reprogramming were characterized by single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, and assay for transposase-accessible chromatin with sequencing (ATAC-seq) in human coronary artery endothelial cells (HCAECs). Transcription factor binding was validated by in vitro binding assays and chromatin immunoprecipitation. Serum chemokine (C-X-C motif) ligand 8 (CXCL8) was quantified by enzyme-linked immunosorbent assay. ResultsForty miRNAs were upregulated in KD patients and fourteen miRNAs were prioritized for further analysis. miR-10b-5p was consistently elevated across both vasculitis models, and its antagomir-mediated inhibition attenuated aortic root inflammation in vivo. In HCAECs, miR-10b-5p suppressed its direct targets marker of proliferation Ki-67 (MKI67)/Chromobox5 (CBX5), driving a cell-state transition from proliferative/metabolic programs toward a pro-inflammatory phenotype. Consistently, analyses of bulk RNA-seq supported cell-cycle arrest and altered chromatin remodeling. ATAC-seq revealed increased chromatin accessibility at the CXCL8 and Matrix metalloproteinases 10 (MMP10) promoters, and motif analysis identified CCAAT/enhancer-binding protein alpha (CEBPA) as the key transcriptional activator; CEBPA knockdown abrogated miR-10b-5p-induced CXCL8 and MMP10 upregulation. Serum CXCL8 was markedly elevated in KD patients relative to febrile controls at first ED presentation, prior to definitive diagnosis, and declined significantly at 8-week follow-up. ConclusionsWe define a miR-10b-5p-MKI67/CBX5-CEBPA-CXCL8 axis as a mechanistic driver of endothelial reprogramming and neutrophil-recruiting inflammation in KD. Serum CXCL8 emerges as a candidate early diagnostic biomarker that may facilitate timely KD recognition at ED presentation.

molecular biology↗

bioRxiv2024

Impact of Acetate and Optimized Nitrate Levels on Mixotrophic Growth and Protein Dynamics in Chlorella Sorokiniana

Microalgae are well-known for their role as sustainable bio-factories, offering a promising solution to the global food and nutrition crisis. To clarify the potential of Chlorella sorokiniana UTEX 1230 for food applications, particularly as an alternative protein source, the study employed a mixotrophic cultivation mode with sodium acetate (NaAc) as a cost-effective organic carbon (NaAc-C) source. Varying levels of NaAc-C and nitrate-sourced nitrogen were investigated, optimizing the effect of metabolic characteristics of the microalgal growth. The designed heterotrophic cultivation confirmed the ability of C. sorokiniana UTEX 1230 to grow on NaAc-C, and then the mixotrophic cultures, when supported by both NaAc-C and CO2, exhibited superior growth performance, achieving double the biomass concentration compared to the autotrophic control. The addition of nitrogen (750 mg/L NaNO) facilitated the thorough metabolism of NaAc-C and enhanced photosynthetic activity indicated by a 196% increase in pigment levels, which resulted in a maximum biomass concentration of 2.82 g/L in the 150 mM NaAc-C group. A detailed analysis of nitrogen and protein concentrations over time revealed that higher nitrogen availability led to greater protein accumulation which was then degraded to support essential life activities under nitrogen starvation. Therefore, it is suggested that supplementing nitrate on the 3rd day and harvesting on the 4th day could be strategically implemented to increase protein yield from 0.17 g/L/d to 0.34 g/L/d. These findings offer theoretical guidance for further refining this microalgal strain for use as an alternative protein.

bioengineering↗

bioRxiv2023

E-cadherin biointerfaces reprogram collective cell migration and cell cycling by forcing homeostatic conditions

Cells attach to the world around them in two ways--cell:extracellular-matrix adhesion and cell:cell adhesion--and conventional biomaterials are made to resemble the matrix to encourage integrin-based cell adhesion. However, interest is growing for cell-mimetic interfaces that mimic cell-cell interactions using cadherin proteins, as this offers a new way to program cell behavior and design synthetic implants and objects that can integrate directly into living tissues. Here, we explore how these cadherin-based materials affect collective cell behaviors, focusing specifically on collective migration and cell cycle regulation in cm-scale epithelia. We built culture substrates where half of the culture area was functionalized with matrix proteins and the contiguous half was functionalized with E-cadherin proteins, and we grew large epithelia across this Janus interface. Parts of the tissues in contact with the matrix side of the Janus interface exhibited normal collective dynamics, but an abrupt shift in behaviors happened immediately across the Janus boundary onto the E-cadherin side, where cells formed hybrid E-cadherin junctions with the substrate, migration effectively froze in place, and cell-cycling significantly decreased. E-cadherin materials suppressed long-range mechanical correlations in the tissue and mechanical information reflected off the substrate interface. These effects could not be explained by conventional density, shape index, or contact inhibition explanations. E-cadherin surfaces nearly doubled the length of the G0/G1 phase of the cell cycle, which we ultimately connected to the exclusion of matrix focal adhesions induced by the E-cadherin culture surface.

bioengineering↗

bioRxiv2022

Targeted degradation of microtubule-associated protein tau using an engineered nanobody-E3 ubiquitin ligase adapter fusion

Reducing the level of microtubule-associated protein tau has recently emerged as a promising therapeutic approach for a range of neurodegenerative diseases. Among the various approaches, targeted protein degradation provides a reversible means to rapidly reduce and specifically target disease-relevant forms of tau. However, in aging cells, the protein turnover activity is generally weakened, reducing the efficacy of protein degradation. A potential solution to this is to harness the nuclear proteasomal activity. The nucleus has a high proteasomal content and the degradation activity remains relatively unaffected even in aged cells. Here we show that an E3 ligase F-box domain from the nuclear protein human speckle type BTB/POZ protein (SPOP) is effective in degrading the microtubule-associated protein tau in primary mouse hippocampal neurons. Using EGFP-tagged tau and a GFP-binding nanobody fused to SPOP, we found that the native nuclear localization signal in SPOP causes nuclear sequestration of the target protein. However, degradation of the sequestered target proteins is incomplete, resulting in nuclear accumulation. Replacing the native SPOP nuclear localization signal (NLS) with variants having altered nuclear localization efficiency dramatically affects in the degree of nuclear accumulation of the target protein. Interestingly, nanobody-SPOP with no NLS was more efficient than that with a NLS in reducing overall tau level, causing an approximately 50% reduction in ectopically expressed human tau in mouse neurons. These results show the potential for harnessing the nuclear proteasomal activity for targeted tau degradation in cells and demonstrate a new modality of regulating intracellular protein degradation.

bioengineering↗

bioRxiv2022

Yeast biopanning for detecting antibody binding to site-specific phosphorylations in tau

The detection of phosphorylated tau (p-tau) levels in clinical samples is of extreme importance for the detection of Alzheimers Disease (AD) as well as other neurodegenerative diseases. Recent reports show that detecting low levels of p-tau in plasma can be used as a reliable biomarker for detecting AD prior to the onset of memory loss. The ability to detect such low levels of p-tau is dependent on antibodies specific to the post translationally modified protein. However, the need for reliable phospho-site specific antibodies persists due to a lack of approaches for identifying monoclonal antibodies and characterizing non-specific binding. Here, we report a novel approach using the principles of yeast biopanning to create a robust platform that uses synthetic peptides as target antigens. Using peptides as antigens enables screening antibodies against defined post-translational modification sites, particularly for targeting intrinsically disordered proteins such as the human tau protein. To readily assess yeast binding and distinguish non-specific binding, we developed bi-directional expression vectors that allow antibody fragment surface display and intracellular fluorescent protein expression. We show that our platform can specifically and robustly detect a specific site within the p-tau target peptide when compared against non-phosphorylated controls. By improving biopanning parameters, we enabled phospho-specific capture of yeast cells displaying single-chain variable region fragments (scFvs) against p-tau with a wide range of affinities (KD = 0.2 to 60 nM). These results demonstrate that yeast biopanning can robustly capture yeast cells based on phospho-site specific antibody binding, opening doors for facile identification of high-quality monoclonal antibodies.

bioengineering↗

bioRxiv2021

Timescale of degradation-driven protein level fluctuation in the yeast Saccharomyces cerevisiae

Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 minute-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.

bioengineering↗

bioRxiv2020

A novel PS4 criterion approach based on symptoms of rare diseases and in-house frequency data in a Bayesian framework.

The American College of Medical Genetics (ACMG) and Genomics/Association for Molecular Pathology (AMP) previously reported standardized guidance for the assessment of genetic variants. One of the criteria regarding the prevalence in a case-control study, PS4, is important due to its evidence of pathogenicity. Despite recent studies approaching gene- and disease-specific probands, interpretation of a variant to PS4 still has certain limitations for rare variants. Here, we suggest a generalized method, Bayesian odds ratio (BayesianOR), applicable to PS4 via decomposing a disease to its symptoms and applying a Bayesian framework. Using this approach, we demonstrate reproducibility of the calculation of the original odds ratio from well-studied epilepsy data and verify the applicability to in-house frequencies for various rare diseases. In addition, BayesianOR showed a significant difference in tendency with different ClinVar pathogenicity, using in-house data. Thus, the novel method described here should provide an improved interpretation of sequence variants. Furthermore, we anticipate that it will enhance the diagnosis of patients with rare diseases.

genetics↗

bioRxiv2020

Optogenetics in Sinorhizobium meliloti enables spatial control of exopolysaccharide production and biofilm structure

Microorganisms play a vital role in shaping the soil environment and enhancing plant growth by interacting with plant root systems. Due to the vast diversity of cell types involved, combined with dynamic and spatial heterogeneity, identifying the causal contribution of a defined factor, such as a microbial exopolysaccharide (EPS), remains elusive. Synthetic approaches that enable orthogonal control of microbial pathways are a promising means to dissect such complexity. Here we report the implementation of a synthetic, light-activated, transcriptional control platform in the nitrogen fixing soil bacterium Sinorhizobium meliloti. By fine tuning the system, we successfully achieved optical control of an EPS production pathway without significant basal expression under non-inducing (dark) conditions. Optical control of EPS recapitulated important behaviors such as a mucoid plate phenotype and formation of structured biofilms, enabling spatial control of biofilm structures in S. meliloti. The successful implementation of optically controlled gene expression in S. meliloti enables systematic investigation of how genotype and microenvironmental factors together shape phenotype in situ. SignificanceMicroorganisms are key players in sustaining the soil environment and plant growth. Symbiotic associations of soil microbes and plants provide a major source of nitrogen in agricultural systems, prevent water contamination from synthetic fertilizer application, and support crop growth in marginal soils. However, measuring the impact of microbial gene products on beneficial function remains a major challenge. This work provides a critical step toward addressing this challenge by implementing external gene regulation in a well characterized nitrogen fixing soil bacterium. We show that light exposure enables spatial and temporal control of the extracellular polysaccharide production functionality essential for symbiosis. Remote control of genes enables the benefits of candidate microorganisms to be systematically measured and enhanced within complex natural settings.

synthetic biology↗

bioRxiv2019

Yeast surface display of full-length human microtubule-associated protein tau

Microtubule-associated protein tau is an intrinsically-disordered, highly soluble protein found primarily in neurons. Under normal conditions, tau regulates the stability of axonal microtubules and intracellular vesicle transport. However, in patients of neurodegeneration such as Alzheimers disease (AD), tau forms neurofibrillary deposits, which correlates well with the disease progression. Identifying molecular signatures in tau, such as post-translational modification, truncation, and conformational change has great potential to detect earliest signs of neurodegeneration, and develop therapeutic strategies. Here we show that full-length human tau, including the longest isoform found in the adult brain can be robustly displayed on the surface of yeast Saccharomyces cerevisiae. Yeast-displayed tau binds to anti-tau antibodies that cover epitopes ranging from the N-terminus to the 4R repeat region. Unlike tau expressed in the yeast cytosol, surface-displayed tau was not phosphorylated at sites found in AD patients (probed by antibodies AT8, AT270, AT180, PHF-1). However, yeast-displayed tau showed clear binding to paired helical filament (PHF) tau conformation-specific antibodies Alz-50, MC-1, and Tau-2. Although the tau possessed a conformation found in PHFs, oligomerization or aggregation into larger filaments were undetected. Taken together, yeast-displayed tau enables robust measurement of protein interactions, and is of particular interest for characterizing conformational change.

bioengineering↗