• Genomics & Informatics
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• v.12 no.1
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• pp.21-34
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• 2014

A visual analysis approach and the developed supporting technology provide a comprehensive solution for analyzing large and complex integrated genomic and biomedical data. This paper presents a methodology that is implemented as an interactive visual analysis technology for extracting knowledge from complex genetic and clinical data and then visualizing it in a meaningful and interpretable way. By synergizing the domain knowledge into development and analysis processes, we have developed a comprehensive tool that supports a seamless patient-to-patient analysis, from an overview of the patient population in the similarity space to the detailed views of genes. The system consists of multiple components enabling the complete analysis process, including data mining, interactive visualization, analytical views, and gene comparison. We demonstrate our approach with medical scientists on a case study of childhood cancer patients on how they use the tool to confirm existing hypotheses and to discover new scientific insights.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.72-77
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• 2005

Orthologs are genes having the same function across different species that specialize from a single gene in the last common ancestor of these species. Orthologous groups are useful in the genome annotation, studies on gene evolution, and comparative genomics. However, the construction of an orthologous group is difficult to automate and it takes so much time. It is also hard to guarantee the accuracy of the constructed orthologous groups. We propose a system to construct orthologous groups on many genomes automatically and rapidly. We utilize the grid computing to reduce the sequence alignment time, and we use clustering algorithm in the application of database to automate whole processes. We have generated orthologous groups for 20 complete prokaryotes genomes just in a day because of the grid computing. Furthermore, new genomes can be accommodated easily by the clustering algorithm and grid computing. We compared the generated orthologous groups with COGs (Clusters of orthologous Group of proteins) and KO (KEGG Ortholog). The comparison shows about 85 percent similarity compared with previous well-known orthologous databases.

• BMB Reports
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• v.29 no.2
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• pp.137-141
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• 1996

A partial cDNA encoding a Korean radish isoperoxidase was obtained from a cDNA library prepared from 9 day old radish root. In order to obtain Korean radish isoperoxidase cDNA, 5' RACE (rapid amplification cDNA end) PCR was performed and a cDNA (prxK1) encoding a complete structural protein was obtained by RT (reverse transcription)-PCR. Sequence analysis revealed that the length of the cDNA was 945 base pairs, and that of the mRNA transcript was ca. 1.6 kb. The deduced amino acid of the protein were composed of 315 amino acid residues and the protein was 92% homologous to turnip peroxidase, and 46% to 50% homologous to other known peroxidases. The 945 bp cDNA encoding Korean radish isoperoxidase was overexpressed in Escherichia coli up to approximately 9% of total cellular protein. The recombinant fusion protein exhibited 43 kDa on SDS-PAGE analysis and the activity level of the recombinant nonglycosylated protein was two fold higher in IPTG induced cell extracts than that of uninduced ones.

• Animal Systematics, Evolution and Diversity
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• v.28 no.1
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• pp.36-41
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• 2012

The larvae of Chaoborus are widely distributed in lakes, ponds, and reservoirs. These omnivorous Chaoborus larvae are crucial predators and play a role in structuring zooplankton communities, especially for small-sized prey. Larvae of Chaoborus are commonly known to produce predator-induced polyphenism in Daphnia sp. Nevertheless, their taxonomy and molecular phylogeny are very poorly understood. As a fundamental study for understanding the role of Chaoborus in predator-prey interactions in a freshwater ecosystem, the molecular identification and phylogenetic relationship of Chaoborus were analyzed in this study. A molecular comparison based on partial mitochondrial cytochrome oxidase I (COI) between species in Chaoborus was carried out for the identification of Chaoborus larvae collected from 2 localities in Korea. According to the results, the Chaoborus species examined here was identified as C. flavicans, which is a lake-dwelling species. Furthermore, partial mitochondrial genome including COI, COII, ATP6, ATP8, COIII, and ND3 were also newly sequenced from the species and concatenated 5 gene sequences excluding ATP8 with another 9 dipteran species were compared to examine phylogenetic relationships of C. flavicans. The results suggested that Chaoborus was more related to the Ceratopogonidae than to the Culicidae. Further analysis based on complete mitochondrial DNA sequences and nuclear gene sequences will provide a more robust validation of the phylogenetic relationships of Chaoborus within dipteran lineages.

• Journal of Microbiology and Biotechnology
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• v.16 no.7
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• pp.1017-1025
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• 2006

Hantaviruses possess three RNA segments of negative sense. Co-infection of closely related hantaviruses may result in generation of a progeny virus with genomic polyploidy, containing a partial or complete set of genome originated from more than one parental virus. To characterize the formation of viral genomic polyploidy, cultured Vero-E6 cells were co-infected with two closely related hantaviruses, Hantaan and Maaji, and the progeny viruses examined. The genotype of plaque-purified viruses was analyzed by a virus-specific RT-PCR. Seventy percent (67/96) of the progeny virus was categorized as Hantaan and 3.3% (2/96) was classified as Maaji, whereas 20% (21/96) was considered polyploidy as they contained both types of the S RNA segment. Most of the polyploidy progeny viruses were unstable and gave rise to either one of the parental viruses or a reassortant after several rounds of plaque purification. No recombination between the heterologous pair of S RNA was observed for those polyploid viruses during three consecutive plaque-to-plaque passages. These data suggest that the viral polyploidy formation constitutes a primary mechanism underlying the generation of a newly emerged hantavirus.

• The Plant Pathology Journal
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• v.36 no.4
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• pp.364-377
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• 2020

Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.7
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• pp.953-957
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• 2006

The eukaryotic elongation factor 1 A (EEF1A) participates in protein synthesis by forming the eEF1A GTP tRNA complex to deliver aminoacyl-tRNA to the A site of ribosomes. This study described cDNA sequences and partial genomic structure of porcine EEF1A1. The porcine EEF1A1 gene encoded a protein with 462 amino acids, which shared complete homology with human, chimpanzee and dog. The temporal expression pattern showed the diversity of EEF1A1 level in mRNA was relatively minor in prenatal embryo skeletal muscle, however, the expression decreased during aging after birth in skeletal muscle of the Chinese Tongcheng pig. The spatial expression patterns indicated that the gene expressed in skeletal muscle, heart, lung, liver, kidney, fat and spleen. In addition, we assigned the gene to porcine chromosome 1 using a radiation hybrid panel.

• Research in Plant Disease
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• v.21 no.3
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• pp.180-185
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• 2015

In the present work, a pair of primers specific to Tomato yellow leaf curl virus (TYLCV) was designed to allow specific amplification of DNA fragments from any TYLCV isolates using an extensive alignment of the complete genome sequences of TYLCV isolates deposited in the GenBank database. A pair of primers which allows the specific amplification of tomato ${\beta}$-tubulin gene was also analyzed as an internal PCR control. A duplex PCR method with the developed primer sets showed that TYLCV could be directly detected from the leaf crude sap of infected tomato plants. In addition, our developed duplex PCR method could determine PCR errors for TYLCV diagnosis, suggesting that this duplex PCR method with the primer sets is a good tool for specific and sensitive TYLCV diagnosis. The developed duplex PCR method was further verified from tomato samples collected from some farms in Korea, suggesting that this developed PCR method is a simple and reliable tool for rapid and large-scale TYLCV detections in tomato plants.

• Journal of Microbiology
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• v.44 no.2
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• pp.217-225
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• 2006

Kaposi's sarcoma-associated herpesvirus (KSHV) RTA transcription factor is recruited to its responsive elements through interaction with RBP-Jk that is a downstream transcription factor of the Notch signaling pathway that is important in development and cell fate determination. This suggests that KSHV RTA mimics cellular Notch signal transduction to activate viral lytic gene expression. Here, I demonstrated that unlike other B lymphoma cells, KSHV -infected primary effusion lymphoma BCBL1 cells displayed the constitutive activation of ligand-mediated Notch signal transduction, evidenced by the Jagged ligand expression and the complete proteolytic process of Notch receptor I. In order to investigate the effect of Notch signal transduction on KSHV gene expression, human Notch intracellular (hNIC) domain that constitutively activates RBP-Jk transcription factor activity was expressed in BCBL1 cells, TRExBCBL1-hNIC, in a tetracycline inducible manner. Gene expression profiling showed that like RTA, hNIC robustly induced expression of a number of viral genes including KS immune modulatory gene resulting in downregulation of MHC I and CD54 surface expression. Finally, the genetic analysis of KSHV genome demonstrated that the hNIC-mediated expression of KS during viral latency consequently conferred the downregulation of MHC I and CD54 surface expression. These results indicate that cellular. Notch signal transduction provides a novel expression profiling of KSHV immune deregulatory gene that consequently confers the escape of host immune surveillance during viral latency.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.71-76
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• 2006

Comparative genomic hybridization (CGH) is a technique for studying chromosomal changes in cancer. As cancerous cells multiply, they can undergo dramatic chromosomal changes, including chromosome loss, duplication, and the translocation of DNA from one chromosome to another. Chromosome aberrations have previously been detected using optical imaging of whole chromosomes, a technique with limited sensitivity, resolution, quantification, and throughput. Efforts in recent years to use microarrays to overcome these limitations have been hampered by inadequate sensitivity, specificity and flexibility of the microarray systems. The oligonucleotide CGH microarray system overcomes several scientific hurdles that have impeded comparative genomic studies of cancer. This new system can reliably detect single copy deletions in chromosomes. The system includes a whole human genome microarray, reagents for sample preparation, an optimized microarray processing protocol, and software for data analysis and visualization. In this study, we determined the sensitivity, accuracy and reproducibility of the new system. Using this assay, we find that the performance of the complete system was maintained over a range of input genomic DNA from 5 ug down to 0.15 ug.