• Journal of Society of Preventive Korean Medicine
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• v.27 no.2
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• pp.35-48
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• 2023

Objective : We studied prognostic biomarkers discovery for lung cancer based on the pattern identification for the personalized Korean medicine. Methods : Using 30 tissue samples, we performed a whole exome sequencing to examine the genetic differences among three groups. Results : The exome sequencing identified among 23,490 SNPs germline variants, 12 variants showed significant frequency differences between Xu and Stasis groups (P<0.0005). As similar, 18 and 10 variants were identified in analysis for Xu vs. Gentleness group and Stasis vs. Gentleness group, respectively (P<0.001). Our exome sequencing also found 8,792 lung cancer specific variants and among the groups identified 6, 34, and 12 variants which showed significant allele frequency differences in the comparison groups; Xu vs. Stasis, Xu vs. Gentleness group, and Stasis vs. Gentleness group. As a result of PCA analysis, in germline data set, Xu group was divided from other groups. Analysis using somatic variants also showed similar result. And in gene ontology analysis using pattern identification variants, we found genes like as FUT3, MYCBPAP, and ST5 were related to tumorigenicity, and tumor metastasis in comparison between Xu and Stasis. Other significant SNPs for two were responsible for eye morphogenesis and olfactory receptor activity. Classification of somatic pattern identification variants showed close relationship in multicellular organism reproduction, anion-anion antiporter activity, and GTPase regulator activity. Conclusions : Taken together, our study identified 40 variants in 29 genes in association with germline difference of pattern identification groups and 52 variants in 47 genes in somatic cancer tissues.

• Genomics & Informatics
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• v.5 no.4
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• pp.143-151
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• 2007

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.427-433
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• 2005

With the completely discovery of the Drosophila genome sequence, the next great challenge is to extract its biological information by systematic expression and to perform functional analysis of the gene. Here we reported a proteome analysis of D. melanogaster with two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS). The cell extracts of D. melanogaster, $200{\mu}g$ were resolved to more than 400 silver-stained spots by 2-DE. The most abundant protein spots were ranged from 4.0-7.5 of pI and from 15-90 kDa of molecular weight. The excised spots were destained and in-gel digested by trypsin. The masses of the resulting peptide mixtures were measured by MALDI-TOF-MS. Identified proteins were compared with measured peptide mass and a dynamic peptide searching database which is accessible via the internet. The results revealed that identified proteins were produced by 59 genes derived from 65 protein spots.

• Journal of Ginseng Research
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• v.47 no.2
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• pp.291-301
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• 2023

Introduction: Non-small cell lung cancer (NSCLC) patients are particularly vulnerable to the Coronavirus Disease-2019 (COVID-19). Currently, no anti-NSCLC/COVID-19 treatment options are available. As ginsenoside Rg3 is beneficial to NSCLC patients and has been identified as an entry inhibitor of the virus, this study aims to explore underlying pharmacological mechanisms of ginsenoside Rg3 for the treatment of NSCLC patients with COVID-19. Methods: Based on a large-scale data mining and systemic biological analysis, this study investigated target genes, biological processes, pharmacological mechanisms, and underlying immune implications of ginsenoside Rg3 for NSCLC patients with COVID-19. Results: An important gene set containing 26 target genes was built. Target genes with significant prognostic value were identified, including baculoviral IAP repeat containing 5 (BIRC5), carbonic anhydrase 9 (CA9), endothelin receptor type B (EDNRB), glucagon receptor (GCGR), interleukin 2 (IL2), peptidyl arginine deiminase 4 (PADI4), and solute carrier organic anion transporter family member 1B1 (SLCO1B1). The expression of target genes was significantly correlated with the infiltration level of macrophages, eosinophils, natural killer cells, and T lymphocytes. Ginsenoside Rg3 may benefit NSCLC patients with COVID-19 by regulating signaling pathways primarily involved in anti-inflammation, immunomodulation, cell cycle, cell fate, carcinogenesis, and hemodynamics. Conclusions: This study provided a comprehensive strategy for drug discovery in NSCLC and COVID-19 based on systemic biology approaches. Ginsenoside Rg3 may be a prospective drug for NSCLC patients with COVID-19. Future studies are needed to determine the value of ginsenoside Rg3 for NSCLC patients with COVID-19.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.354-362
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• 2018

Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.666-675
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• 2019

Background: Korean Red Ginseng (KRG) has been widely used as an herbal medicine to normalize and strengthen body functions. Although many researchers have focused on the biological effects of KRG, more studies on the action mechanism of red ginseng are still needed. Previously, we investigated the proteomic changes of the rat spleen while searching for molecular signatures and the action mechanism of KRG. The proteomic analysis revealed that differentially expressed proteins (DEPs) were involved in the increased immune response and phagocytosis. The aim of this study was to evaluate the biological activities of KRG, especially the immune-enhancing response of KRG. Methods: Rats were divided into 4 groups: 0 (control group), 500, 1000, and 2000 mg/kg administration of KRG powder for 6 weeks, respectively. Isobaric tags for relative and absolute quantitation was performed with Q-Exactive LC-MS/MS to compare associated proteins between the groups. The putative DEPs were identified by a current UniProt rat protein database search and by the Gene Ontology annotations. Results: The DEPs appear to increase the innate and acquired immunity as well as immune cell movement. These results suggest that KRG can stimulate immune responses. This analysis refined our targets of interest to include the potential functions of KRG. Furthermore, we validated the potential molecular targets of the functions, representatively LCN2, CRAMP, and HLA-DQB1, by Western blotting. Conclusion: These results may provide molecular signature candidates to elucidate the mechanisms of the immune response by KRG. Here, we demonstrate a strategy of tissue proteomics for the discovery of the molecular function of KRG.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.107-107
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• 2017

Sweet corns are enjoyed worldwide as processed products and fresh ears. Types of sweet corn are based on the gene(s) involved. The oldest sweet corn type has a gene called "sugary (su)". Sugary-based sweet corn was typically named "sweet corn". With its relatively short shelf life and the discovery of a complementary gene, "sugary enhanced (se)", the sweet corn (su only) was rapidly replaced with another type of sweet corns, sugary enhanced sweet corn, which has recessive homozygous su/su, se/se genotype. With the incorporation of se/se genotype into existing su/su genotype, sugary enhanced sweet corn has better shelf life and increased sweetness while maintaining its creamy texture due to high level of water soluble polysaccharide, phytoglycogen. Super sweet corn as the name implies has higher level of sweetness and better shelf life than sugary enhanced sweet corn due to "shrunken2 (sh2)" gene although there's no creamy texture of su-based sweet corns. Distinction between sh2/sh2 and su/su genotypes in seeds is phenotypically possible. The Involvement of se/se genotype under su/su genotype, however, is visually impossible. The genotype sh2/sh2 is also phenotypically epistatic to su/su genotype when both genotypes are present in an individual, meaning the seed shape for double recessive sh2/sh2 su/su genotype is much the same as sh2/sh2 +/+ genotype. Hence, identifying the double and triple recessive homozygous genotypes from su, se and sh2 genes involves a testcross to single recessive genotype, chemical analysis or DNA-based marker development. For these reasons, sweetcorn breeders were hastened to put them together into one cultivar. This, however, appears to be no longer the case. Sweet corn companies began to sell their sweet corn hybrids with different combinations of abovementioned three genes under a few different trademarks or genetic codes, i.g. Sweet $Breed^{TM}$, Sweet $Gene^{TM}$, Synergistic corn, Augmented Supersweet corn. A total of 49 commercial sweet corn F1 hybrids with B73 as a check were genotyped using DNA-based markers. The genotype of field corn inbred B73 was +/+ +/+ +/+ for su, se and sh2 as expected. All twelve sugary enhanced sweet corn hybrids had the genotype of su/su se/se +/+. Of sixteen synergistic hybrids, thirteen cultivars had su/su se/se sh2/+ genotype while the genotype of two hybrids and the remaining one hybrid was su/su se/+ sh2/+, and su/su +/+ sh2/+, respectively. The synergistic hybrids all were recessive homozygous for su gene and heterozygous for sh2 gene. Among the fifteen augmented supersweet hybrids, only one hybrid was triple recessive homozygous (su/su se/se sh2/sh2). All the other hybrids had su/su se/+ sh2/sh2 for one hybrid, su/su +/+ sh2/sh2 for three hybrids, su/+ se/se sh2/sh2 for three hybrids, su/+ se/+ sh2/sh2 for four hybrids, and su/+ +/+ sh2/sh2 for three hybrids, respectively. What was believed to be a classic super sweet corn hybrids also had various genotypic combination. There were only two hybrids that turned out to be single recessive sh2 homozygous (+/+ +/+ sh2/sh2) while all the other five hybrids could be classified as one of augmented supersweet genotypes. Implication of the results for extension service and sweet corn breeding will be discussed.

• Journal of Life Science
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• v.25 no.8
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• pp.861-869
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• 2015

One of the domesticated species; the dog has been selectively bred for various aims by human. The dog has many breeds, which are artificially selected for specific behaviors and morphologies. Dogs contribute their life to human as working dogs for guide, rescue, detection or etc. Working dogs requires good personality, such as gentleness, robustness and patience for performing their special duty. Many studies have concentrated on finding genetic marker for selecting the high-quality working dog. In this study, we confirmed quantitative expression patterns of eight genes (ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2; BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 and TBR1; T-Box, Brain, 1) among brains tissues from four dog breeds (Beagle, Sapsaree, Shepherd and Jindo), because these genes were expressed and have functions in brain mostly. Specially, BARX2, SEPT9, SLC10A4, TBR1 and WNT1 genes were highly expressed in Beagle and Jindo, and Sapsaree and German Shepherd were vice versa. The biological significance of total genes was estimated by database for annotation, visualization and integrated discovery (DAVID) to determine a different gene ontology (GO) class. In these analyses, we suppose to these eight genes could provide influential information for brain development, and intelligence of organisms. Taken together, these results could provide clues to discover biomarker related to functional traits in brain, and beneficial for selecting superior working dogs.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.283-292
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• 2006

Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the kidney mRNA of olive flounder (Paralichthys olivaceus). In the survey of 390 ESTs chosen from the kidney cDNA library, 250 ESTs showed significant homology to previously described genes while 140 ESTs were unidentified or novel. Comparative analysis of the 250 identified ESTs showed that 14 (5.6%) clones were representing 11 unique genes identified as homologous to the previously reported olive flounder ESTs, 198 (79.2%) clones representing 160 unique genes were identified as orthologs of known genes from other organisms, and orthologs were established for 38 (15.2%) clones representing 37 genes of known sequences with unknown functions. We also identified several kinds of immune associated proteins, indicating EST as a powerful method for identifying immunerelated genes of fish as well as identifying novel genes. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

• Animal Bioscience
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• v.36 no.7
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• pp.991-1002
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• 2023

Objective: This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. Methods: We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. Results: The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. Conclusion: This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.