Biology subjects

Jung, K.-H.

Publications and source records attributed to Jung, K.-H..

5 recordsLinked to original sources

bioRxiv2025

RE3DB: A multi-omics phylogenomics platform for rice E3 ubiquitin ligases identifies novel regulators of pollen germination

The ubiquitin proteasome system (UPS) shapes rice development and stress responses through E3 ubiquitin ligases, yet roles of E3 ligases in male gametophyte function remain undiscovered and plant-focused functional informatics resource is absent. We developed the Rice E3 Ubiquitin Ligase Database (RE3DB; https://re3db.khu.ac.kr/) and used it to nominate F-box ligases involved in rice (Oryza sativa) pollen germination. RE3DB combines 15 published datasets comprising 1,602 rice E3-ligase genes; RNA-seq across 25 tissues and stress conditions; protein-to-transcript ratios from 14 tissues; six high-confidence protein-protein interaction resources; and family level phylogenies. Integrated modules provide (i) classification/annotation, (ii) E3-substrate prediction from interaction evidence, co-expression and coordinated proteolytic turnover, and (iii) functional-redundancy assessment using phylogenetic heatmaps. Applying RE3DB, we found extensive reproductive enrichment: 284 F-box genes are preferentially expressed in mature anthers. Comparative transcriptomics across nine male-sterile rice mutants identified 111 F-box genes significantly downregulated in at least one mutant (log2 fold change < -1), resolving distinct co-regulation clusters. Integration with a literature-curated regulatory network positions previously uncharacterized F-box genes within modules governing pollen-tube initiation and elongation, consistent with regulation by the RUPO receptor-like kinase and the OsMADS62/63/68 transcription-factor complex. RE3DB is the first comprehensive multi-omics web platform dedicated to functional characterization of rice E3 ligases. By unifying classification, interaction and expression-based inference, and redundancy analysis, it accelerates hypothesis-driven discovery and guides targeted mutagenesis in molecular plant science. The prioritized F-box cohort provides testable candidates for UPS-mediated control of pollen germination and tube growth, and the framework is readily extensible to other crops, holding significant potential for agricultural biotechnology.

plant biology↗

bioRxiv2025

Discovery of Light-Powered Organic Ion Transport by a Natural Protein

Membrane transport proteins play vital roles in living cells by selectively transporting ions and molecules across biological membranes. Among these, microbial rhodopsins are unique in their unparalleled capacity to harness light to drive ion translocation. This distinctive feature has led to their widespread use as optogenetic tools in neuroscience, physiology, and biomed-ical applications. While not all microbial rhodopsins function as ion transporters, many ion-translocating variants have been discov-ered since the identification of the first member--a light-driven H+ pump--in the 1970s. These proteins share a compact structure composed of only seven transmembrane helices and have long been thought to specialize exclusively in transporting small inorganic ions such as H+, Cl-, and Na+. Here, we show that several anion-pumping microbial rhodopsins can also transport organic anions. In particular, a rhodopsin from cyanobacteria is capable of transporting bulky organic anions, including those containing benzene rings, with molecular volumes up to [~]120 [A]3--five times that of Cl-. These organic ions bind to the dark state and are translocated upon photoactivation, following a mechanism similar to that of inorganic anion transport. Mutational analysis indicates that both classes of substrates share a common binding site. Only anions with pKa values below 2 were transported, suggesting that a retained negative charge is essential for binding to the dark state--a prerequisite for transport. This study expands the known sub-strate repertoire of microbial rhodopsins and introduces new possibilities for optogenetic strategies based on light-driven delivery of bioactive organic molecules.

biophysics↗

bioRxiv2020

Aggregation of Cohorts for Histopathological Diagnosis with Deep Morphological Analysis

There have been substantial efforts in using deep learning (DL) to diagnose cancer from digital images of pathology slides. Existing algorithms typically operate by training deep neural networks (DNNs) either specialized in specific cohorts or an aggregate of all cohorts when there are only a few images available for the target cohort. A trade-off between decreasing the number of models and their cancer detection performance was evident in our experiments with The Cancer Genomic Atlas (TCGA) dataset, with the former approach achieving higher performance at the cost of having to acquire large datasets from the cohort of interest. Constructing annotated datasets for individual cohorts is extremely time-consuming, with the acquisition cost of such datasets growing linearly with the number of cohorts. Another issue associated with developing cohort-specific models is the difficulty of maintenance: all cohort-specific models may need to be adjusted when a new DL algorithm is to be used, where training even a single model may require a non-negligible amount of computation, or when more data is added to some cohorts. In resolving the sub-optimal behavior of a universal cancer detection model trained on an aggregate of cohorts, we investigated how cohorts can be grouped to augment a dataset without increasing the number of models linearly with the number of cohorts. This study introduces several metrics which measure the morphological similarities between cohort pairs and demonstrates how the metrics can be used to control the trade-off between performance and the number of models.

pathology↗

bioRxiv2020

AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic

AT-527, an orally administered double prodrug of a guanosine nucleotide analog, has been shown previously to be highly efficacious and well tolerated in HCV-infected subjects. Herein we report the potent in vitro activity of AT-511, the free base form of AT-527, against several coronaviruses, including SARS-CoV-2, the causative agent of COVID-19. In normal human airway epithelial (HAE) cell preparations, the average concentration of AT-511 required to inhibit replication of SARS-CoV-2 by 90% (EC90) was 0.5 {micro}M, very similar to the EC90 for AT-511 against HCoV-229E, HCoV-OC43 and SARS-CoV in Huh-7 cells. No cytotoxicity was observed for AT-511 in any of the antiviral assays up to the highest concentration tested (100 {micro}M). Surprisingly, AT-511 was 30-fold less active against MERS-CoV. This differential activity may provide a clue to the apparent unique mechanism of action of the guanosine triphosphate analog formed from AT-527.

pharmacology and toxicology↗

bioRxiv2017

Discovery-oriented teaching: The use of chimeric proteorhodopsins for the development of a lab curriculum in marine microbiology and for the discovery of natural red-shifted proteorhodopsins

Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4-5 days, that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions - green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.

microbiology↗