• Journal of Digital Convergence
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• v.14 no.4
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• pp.349-353
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• 2016

The studies on the human environment and ecosystem analysis is being actively researched. In recent years, The service of genome analysis has been offering the customized service to prevent the disease as reading an individual's genome information. The genome information by analyzing technology is being required accurate and fast analyses of ecosystem-dielectrics due to the spread of the disease, the use of genetically modified organism and the influx of exotic. In this paper the algorithm of K-Mean clustering for a new classification system was utilized. It will provide new dielectrics information as quickly and accurately for many biologists.

• Genomics & Informatics
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• v.10 no.3
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• pp.206-211
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• 2012

DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.

• Genomics & Informatics
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• v.17 no.3
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• pp.28.1-28.9
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• 2019

Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up-and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 ㎛, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 ㎛, 48K) could represent ~10,000 up-/ down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.

• Journal of Ginseng Research
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• v.42 no.4
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• pp.436-446
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• 2018

Background: The potential therapeutic values of Korean Red Ginseng extract (KRGE) in autoimmune disorders of nervous system have not been fully investigated. Methods: We used an acute experimental autoimmune encephalomyelitis animal model of multiple sclerosis and determined the effects and mechanism of KRGE on spinal myelination. Results: Pretreatment with KRGE (100 mg/kg, orally) for 10 days before immunization with myelin basic protein $(MBP)_{68-82}$ peptide exerted a protective effect against demyelination in the spinal cord, with inhibited recruitment and activation of immune cells including microglia, decreased mRNA expression of detrimental inflammatory mediators (interleukin-6, interferon-${\gamma}$, and cyclooxygenase-2), but increased mRNA expression of protective inflammatory mediators (insulin-like growth factor ${\beta}1$, transforming growth factor ${\beta}$, and vascular endothelial growth factor-1). These results were associated with significant downregulation of p38 mitogen-activated protein kinase and nuclear factor-${\kappa}B$ signaling pathways in microglia/macrophages, T cells, and astrocytes. Conclusion: Our findings suggest that KRGE alleviates spinal demyelination in acute experimental autoimmune encephalomyelitis through inhibiting the activation of the p38 mitogen-activated protein kinase/nuclear factor-${\kappa}B$ signaling pathway. Therefore, KRGE might be used as a new therapeutic for autoimmune disorders such as multiple sclerosis, although further investigation is needed.

• Genomics & Informatics
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• v.2 no.4
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• pp.191-194
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• 2004

Exponentially increasing biopathway data in recent years provide us with means to elucidate the large-scale modular organization of the cell. Given the existing information on metabolic and regulatory networks, inferring biopathway information through scientific reasoning or data mining of large scale array data or proteomics data get great attention. Naturally, there is a need for a user-friendly system allowing the user to combine large and diverse pathway data sets from different resources. We built a data warehouse - BIOWAY - for analyzing and visualizing biological pathways, by integrating and customizing resources. We have collected many different types of data in regards to pathway information, including metabolic pathway data from KEGG/LIGAND, signaling pathway data from BIND, and protein information data from SWISS-PROT. In addition to providing general data retrieval mechanism, a successful user interface should provide convenient visualization mechanism since biological pathway data is difficult to conceptualize without graphical representations. Still, the visual interface in the previous systems, at best, uses static images only for the specific categorized pathways. Thus, it is difficult to cope with more complex pathways. In the BIOWAY system, all the pathway data can be displayed in computer generated graphical networks, rather than manually drawn image data. Furthermore, it is designed in such a way that all the pathway maps can be expanded or shrinked, by introducing the concept of super node. A subtle graphic layout algorithm has been applied to best display the pathway data.

• Genomics & Informatics
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• v.14 no.3
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• pp.78-84
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• 2016

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

• Journal of Ginseng Research
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• v.42 no.3
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• pp.379-388
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• 2018

Background: Ginsenosides are the main ingredients of Korean Red Ginseng. They have extensively been studied for their beneficial value in neurodegenerative diseases such as Parkinson's disease (PD). However, the multitarget effects of Korean Red Ginseng extract (KRGE) with various components are unclear. Methods: We investigated the multitarget activities of KRGE on neurological dysfunction and neurotoxicity in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD. KRGE (37.5 mg/ kg/day, 75 mg/kg/day, or 150 mg/kg/day, per os (p.o.)) was given daily before or after MPTP intoxication. Results: Pretreatment with 150 mg/kg/day KRGE produced the greatest positive effect on motor dysfunction as assessed using rotarod, pole, and nesting tests, and on the survival rate. KRGE displayed a wide therapeutic time window. These effects were related to reductions in the loss of tyrosine hydroxylase-immunoreactive dopaminergic neurons, apoptosis, microglial activation, and activation of inflammatory factors in the substantia nigra pars compacta and/or striatum after MPTP intoxication. In addition, pretreatment with KRGE activated the nuclear factor erythroid 2-related factor 2 pathways and inhibited phosphorylation of the mitogen-activated protein kinases and nuclear factor-kappa B signaling pathways, as well as blocked the alteration of blood-brain barrier integrity. Conclusion: These results suggest that KRGE may effectively reduce MPTP-induced neurotoxicity with a wide therapeutic time window through multitarget effects including antiapoptosis, antiinflammation, antioxidant, and maintenance of blood-brain barrier integrity. KRGE has potential as a multitarget drug or functional food for safe preventive and therapeutic strategies for PD.

• Genomics & Informatics
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• v.3 no.3
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

• Journal of the Korean Society for Marine Environment & Energy
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• v.17 no.1
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• pp.46-51
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• 2014

Increasing of waste FRP (fiber reinforced plastics) has caused environmental problems. Recently, the technology of making fibers from waste FRP, which can be used to reinforce the concrete, was developed and the reinforced concretes were tested to study the structural performance. The purpose of this study is to investigate the effect of the powder, obtained together with F-fiber from the waste FRP, on the compressive strength and the fire resistance performance as in the high strength concrete. Strength tests show that the use of recycled FRP powder does not reduce the compressive strength of high strength concrete if the volume fraction of FRP powder is less than 0.7%. Electric furnace test results also show that the use of recycled FRP powder may increase the fire resistance performance of high strength concrete significantly.

• Journal of agriculture & life science
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• v.45 no.3
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• pp.19-23
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• 2011

In this study three types of domatia; Tuft (T), Pocket-Tuft (PT) and Pocket (P) were observed on some species of the genus Cornus. Cornus officinalis Sieb & Zuee and C. florida Linnaeus possess T type, C. controversa Hemsl and C. walteri Wangerin possess PT type while C. alba Linnaeus possess P type. A total of 120 leaves were investigated for foliar mite's population. T type domatia was the habitat of 329 mites (48.89%), followed by PT type where 198 mites (29.41%) were found, and the least favored was the P type domatia that accommodated 146 mites (21.70%) out of 673 mites in total. The mean number of mites per domatia was $8({\pm}0.22)$, $4({\pm}0.95)$ and $3({\pm}0.70)$ for T, PT and P type, respectively. The alternative hypothesis that foliar mites prefer T type domatia as a habitat than PT and P type domatia was accepted based on these findings at a probability of P<0.05. Thus, it was concluded that foliar mites prefer T type domatia than the other two types. This could be due to the nature and efficiency of T type domatia in ensuring mites protection from predators and unfriendly environmental conditions. Therefore, the presence of denser tufts lowers the risks of predation and unfriendly environmental conditions and results in a higher number of mites.