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Do, Y. J.

Publications and source records attributed to Do, Y. J..

3 recordsLinked to original sources

Nano-Sieve Enabled On Chip Concentration and Multiplexed Detection of Raman-Dye Labeled Nanocubes

To address persistent challenges in molecular detection--particularly signal variability, low analyte abundance, and poor spectral reproducibility--a portable bead-stacked nano-sieve platform was engineered to enable robust on-chip Raman signal amplification using silver nanocubes (AgNCs) functionalized with Raman-active thiolated ligands. The microdevice integrates deformable elastomeric channels with magnetic bead stacking to immobilize and concentrate AgNCs within confined nanoscopic junctions, thereby generating densely packed plasmonic hot-spot architectures that markedly enhance Surface-Enhanced Raman Scattering (SERS) efficiency. Time-resolved measurements revealed substantial increases in Raman intensity for both 4-mercaptobenzoic acid (4-MBA) and 4-aminothiophenol (4-ATP), outperforming corresponding off-chip assays and maintaining stable enhancement factors over a four-hour operational window. Furthermore, the platform successfully demonstrated multiplexed sensing capability: mixed-analyte experiments containing 4-MBA, 4-ATP, and cysteamine produced clearly distinguishable spectral fingerprints, even under serial dilution and dynamically pulsed sample delivery. Collectively, these results establish the bead-stacked nano-sieve as a versatile, label-free, and scalable diagnostic architecture capable of achieving high sensitivity and spectral fidelity under continuous-flow conditions. Our technology holds significant promise for real-time, non-invasive molecular surveillance, point-of-care diagnostics, and early disease monitoring in resource-limited or field-deployable settings.

bioengineering↗

Whole genome hybrid assembly and protein-coding gene annotation of the entirely black native Korean chicken breed Yeonsan Ogye

Yeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 551 structural variations including the Fibromelanosis (FM) locus duplication, compared to galGal4 and 5. The completeness (97.6%) of the draft genome (Ogye_1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were expressed in the tissue-specific manner, closely related with the DNA methylation pattern in the promoter regions.

genomics↗

Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

The Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

bioinformatics↗