• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.196-204
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• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• Proceedings of the Korean Society of Crop Science Conference
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• 1999.05a
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• pp.162-163
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• 1999

The goal of this research was (1) to describe the conditions and parameters required for the cell cycle synchronization and the accumulation of large number of metaphase cells in maize and other cereal root tips, (2) to isolate intact metaphase chromosomes from root tips suitable for characterization by flow cytometry, and (3) to construct chromosome-specific libraries from maize. Plant metaphase chromosomes have been successfully synchronized and isolated from many cereal root-tips. DNA synthesis inhibitor (hydroxyurea) was used to synchronize cell cycle, follwed by treatement with trifluralin to accumulate metaphase chromosomes. Maize flow karyotypes show substantial variation among inbred lines. thish variation should be sueful in isolating individual chromosome types. In addition, flow cytometry is a useful method to measure DNA content of individual chromosomes in a genotyps, and to detect chromosomal variations. Individual chromosome peaks have been sorted from the maize hybrid B73/Mol7. Libraries were generated form the DOP-PCR amplification product from each peak. To date, we have analyzed clones from a library constructed from the maize chromosome 1 peak. Hybridization of labeled genomic DNA to clone inserts indicated that $24\%,\;18\%,\;and\;58\%$ of the clones were highly repetitive, medium repetitive, and low copy, respectively. Fifty percent of putative low cpoy clones showed single bands on inbred screening, blots, and the remaining $50\%$ were low copy repeats. Single copy clones showing polymorphism will be mapped using recombinant inbred mapping populations. Repetitive clones are being characterized by Southern blot analysis, and will be screened by in situ hybridization for their potential utility as chromosome specific markers.

• Genomics & Informatics
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• v.17 no.3
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• pp.26.1-26.12
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• 2019

Identification of fusion gene is of prominent importance in cancer research field because of their potential as carcinogenic drivers. RNA sequencing (RNA-Seq) data have been the most useful source for identification of fusion transcripts. Although a number of algorithms have been developed thus far, most programs produce too many false-positives, thus making experimental confirmation almost impossible. We still lack a reliable program that achieves high precision with reasonable recall rate. Here, we present FusionScan, a highly optimized tool for predicting fusion transcripts from RNA-Seq data. We specifically search for split reads composed of intact exons at the fusion boundaries. Using 269 known fusion cases as the reference, we have implemented various mapping and filtering strategies to remove false-positives without discarding genuine fusions. In the performance test using three cell line datasets with validated fusion cases (NCI-H660, K562, and MCF-7), FusionScan outperformed other existing programs by a considerable margin, achieving the precision and recall rates of 60% and 79%, respectively. Simulation test also demonstrated that FusionScan recovered most of true positives without producing an overwhelming number of false-positives regardless of sequencing depth and read length. The computation time was comparable to other leading tools. We also provide several curative means to help users investigate the details of fusion candidates easily. We believe that FusionScan would be a reliable, efficient and convenient program for detecting fusion transcripts that meet the requirements in the clinical and experimental community. FusionScan is freely available at http://fusionscan.ewha.ac.kr/.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.6
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• pp.510-515
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• 2006

The putative EPA synthesis gene cluster was mined from the entire genome sequence of Shewanella oneidensis MR-1. The gene cluster encodes a PKS-like pathway that consists of six open reading frames (ORFs): ORFSO1602 (multi-domain beta-ketoacyl synthase, KS-MAT-4ACPs-KR), ORFSO1600 (acyl transferase, AT), ORFSO1599 (multi-domain beta-ketoacyl synthase, KS-CLF-DH-DH), ORFSO1597 (enoyl reductase, ER), ORFSO1604 (phosphopentetheine transferase, PPT), and ORFSO1603 (transcriptional regulator). In order to prove involvement of the PKS-like machinery in EPA synthesis, a 20.195-kb DNA fragment containing the genes was amplified from S. oneidensis MR-1 by the long-PCR method. Its identity was confirmed by the methods of restriction enzyme site mapping and nested PCR of internal genes orfSO1597 and orfSO1604. The DNA fragment was cloned into Escherichia coli using cosmid vector SuperCos1 to form pCosEPA. Synthesis of EPA was observed in four E. coli clones harboring pCosEPA, of which the maximum yield was 0.689% of the total fatty acids in a clone designated 9704-23. The production yield of EPA in the E. coli clone was affected by cultivation temperature, showing maximum yield at $20^{\circ}C$ and no production at $30^{\circ}C$ or higher. In addition, production yield was inversely proportional to glucose concentration of the cultivation medium. From the above results, it was concluded that the PKS-like modules catalyze the synthesis of EPA. The synthetic process appears to be subject to regulatory mechanisms triggered by various environmental factors. This most likely occurs via the control of gene expression, protein stability, or enzyme activity.

• Genomics & Informatics
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• v.2 no.1
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• pp.45-52
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• 2004

The self-splicing group I intron from Tetrahymena thermophila has been demonstrated to perform splicing reaction with its substrate RNA in the trans configuration. In this study, we explored the potential use of the trans-splicing group I ribozymes to replace a specific RNA with a new RNA that exerts any new function we want to introduce. We have chosen thymidine phosphorylase (TP) RNA as a target RNA that is known as a valid cancer prognostic factor. Cancer-specific expression of TP RNA was first evaluated with RT-PCR analysis of RNA from patients with gastric cancer. We determined next which regions of the TP RNA are accessible to ribozymes by employing an RNA mapping strategy, and found that the leader sequences upstream of the AUG start codon appeared to be particularly accessible. A specific ribozyme recognizing the most accessible sequence in the TP RNA with firefly luciferase transcript as a 3' exon was then developed. The specific trans-splicing ribozyme transferred an intended 3' exon tag sequence onto the targeted TP transcripts, resulting in a more than two fold induction of the reporter activity in the presence of TP RNA in mammalian cells, compared to the absence of the target RNA. These results suggest that the Tetrahymena ribozyme can be a potent anti-cancer agent to modify TP RNAs in tumors with a new RNA harboring anti-cancer activity.

• Korean Journal of Breeding Science
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• v.40 no.1
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• pp.1-7
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• 2008

An attempt was made to link rice embryo proteins to DNA sequences and to understand their functions. One hundred of the 700 spots detected on the embryo 2-DE gels were microsequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were unknown in functions as previously reported (Woo et al. 2002). In addition, twenty-four protein spots with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available rice EST databases at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). The chromosomal location of some proteins were also obtained from the rice genetic map provided by Japanese Rice Genome Research Program (http://rgp.dna.affrc.go.jp). The DNA sequence databases including EST have been reported for rice (Oryza sativa L.) now provides whole or partial gene sequence, and recent advances in protein characterization allow the linking proteins to DNA sequences in the functional analysis. This work shows that proteome analysis could be a useful tool strategy to link sequence information and to functional genomics.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.259-259
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• 2022

Soil salinity is a major factor that reduces crop yields. The amount of soil affected by salinity is about 83 million hectares (FAO 2000), which is increasing due to the effects of climate change. In soybean [Glycine max (L.) Merr.], nutritional properties such as protein, starch, and sucrose content together with biomass and yield tends to reduce due to excessive salt. As a result of QTL mapping using the 169 F_2:3 population from the KA-1285 (salt-tolerant) × Daepung (salt-sensitive) in a previous study, two major QTLs (Gm03_39796778 and Gm03_40600088) related to salt tolerance were found on chromosome 3. In this study, the CDS region of the Gmsalt3 gene was analyzed using the ABI 3730x1 DNA Analyzer (Macrogen, Korea). The sequence of Gmsalt3 gene in KA-1285 was compared with Williams 82.a4.vl and PI483463 (Glycine soja). Two transversions were found at exon6 in KA-1285 and PI483463. Currently, whole genome sequencing and variation analysis using the Illumine Novaseq 6000 machine (Illumina, USA) are in progress. The results of this study can provide useful molecular markers for the selection of salt-tolerant soybeans and can be used as basic data for future salt-tolerant gene research.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.336-341
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• 2015

Blueberry (Vaccinium spp.) is a bush that grows well at special cultural environments such as acid soil, high organic matter content, and a good drainage and aeration compared to other general crops. Blueberries are well known to contain high amounts of anthocyanins and phenolic compounds, resulting in high antioxidant activity that provides health benefits, and expanding the cultivation areas and consumer's demand in the worldwide. However, the full genome of blueberry has not been announced until now. Furthermore, the genomic analysis and transcriptome approaches are not so popular compare to major crops such as orange, apple, and grape. The aim of the review about blueberry genomic research is to establish the platform for setting blueberry breeding target, increasing proficiency of blueberry research, and making the practical cultivation techniques in Korea. The main topics in the blueberry genomic research including transcriptome, genetic mapping, and various markers are related with cold hardiness, chilling requirement, hot tolerance, anthocyanin content, and flavonoid synthesis pathway on various tissues like flower bud, leaf bud, shoot, root, and berry fruit. The review of the current status of blueberry genomic research will provide basic information to the breeders and researchers and will contribute to development of blueberry industry with sustainable productions and increase of blueberry consumption as new profitable crops in Korea.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.73-73
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• 2018

Bacterial leaf blight(BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a collection of 192 accessions was used in the genome-wide association study (GWAS) for BLB resistance loci against four Korean races of Xoo that were represented by the prevailing BLB isolates under Xoo differential system. A total of 192 accessions of rice germplasm were selected on the basis of the bioassay using four isolated races of Xoo such as K1, K2, K3 and K3a. The selected accessions was used to prepare 384-plex genotyping by sequencing (GBS) libraries and Illumina HiSeq 2000 paired- end read was used for GBS sequencing. GWAS was conducted using T ASSEL 5.0. The T ASSEL program uses a mixed linear model (MLM). T he results of the bioassay using a selected set of 192 accessions showed that a large number of accessions (93.75%) were resistant to K1 race, while the least number of accessions (34.37%) resisted K3a race. For races K2 and K3, the resistant germplasm proportion remained between 66.67 to 70.83%. T he genotypic data produced SNP matrix for a total of 293,379 SNPs. After imputation the missing data was removed, which exhibited 34,724 SNPs for association analysis. GWAS results showed strong signals of association at a threshold of [-log10(P-value)] more than5 (K1 and K2) and more than4 (K3 and K3a) for nine of the 39 SNPs, which are plausible candidate loci of resistance genes. T hese SNP loci were positioned on rice chromosome 2, 9, and 11 for K1 and K2 races, whereas on chromosome 4, 6, 11, and 12 for K3 and K3a races. The significant loci detected have also been illustrated, NBS-LRR type disease resistance protein, SNARE domain containing protein, Histone deacetylase 19, NADP-dependent oxidoreductase, and other expressed and unknown proteins. Our results provide a better understanding of the distribution of genetic variation of BLB resistance to Korean pathogen races and breeding of resistant rice.

• Research in Plant Disease
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• v.17 no.2
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• pp.211-215
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• 2011

Cucumber mosaic virus (CMV)-like isolate was collected from Raphanus sativus (cv. Choon-hyang), which showed mosaic symptoms. The isolate was confirmed to a strain of CMV by host responses in Vigna unguiculata, Chenopodium amaranticolor and Gomphrena globosa, by viral genome composition with RT-PCR and PCR-RFLP, and by serological analysis. Symptom developed by the strain of CMV was severe in Nicotiana benthamiana, N. glutinosa, N. tabacum (cv. Samsun, cv. Xanthi), Cucumis melo (cv. Early hanover), Cucumis sativus (cv. White wonder), Capsicum annuum (cv. Chung-yang and cv. Geum-top), but mild symptom was developed in Raphanus sativus (cv. Choon-hyang), Brassica rapa ssp. pekinensis (cv. Bul-Am No. 3), and B. juncea (cv. Daenong Jukgot). Newly isolated strain of CMV could infect diverse crops including Solanaceae, Cucurbitaceae and Brassicaceae. We designated the new strain of CMV as Gn-CMV based on the novel infectivity of Brassicaceae. In double-stranded (ds) RNA analysis, Gn-CMV consisted of 3.3, 3.0, and 2.2 kb genomes likewise other strains of CMV. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) showed 28 kDa of the CMV coat protein. By restriction enzyme mapping using Cac8I, ClaI and MspI of RT-PCR products indicated that Gn-CMV belongs to CMV subgroup I.