• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• Transactions of the Korean Society of Automotive Engineers
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• v.18 no.6
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• pp.31-37
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• 2010

In proportion to increasing interest in vehicle safety, many country have regulated vehicle safety and performed NCAP(New Car Assessment Program). However vehicles which had good results in these compliance and NCAP frontal crash test have caused problems such as the fork effect and over-riding in real car-to-car accidents. To complement these issues, new frontal crash test modes using new barrier like FWDB and PDB have been developed by EEVC WG15. In this paper, FWDB frontal crash test was performed and the result was compared with the full frontal crash test using the rigid wall in order to comprehend the characteristic of FWDB. The results of FWDB test were compared with one of USNCAP and KNCAP. Using USNCAP data, vehicle performance like deformation and wall force were studied. A comparative study of dummy injuries was made by using KNCAP result. The results showed that vehicle performance of FWDB test like displacement and effective acceleration was similar in spite of absorbing energy of FWDB due to the greater vehicle deformation of rigid wall test. In FWDB test, driver dummy head bottomed out but most of injuries were superior to the injury of rigid wall test.

• Journal of Integrative Natural Science
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• v.9 no.4
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• pp.268-274
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• 2016

Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi (wBm) offers an unprecedented opportunity to identify new wolbachia drug targets. Hence the enzyme carbonic anhydrase from wolbachia endosymbiont of Brugia malayi (wBm) which is responsible for the reversible interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa) is chosen as the drug target for filariasis. This enzyme is thought to play critical functions in bacteria by involving in various steps of their life cycle which are important for survival, The 3D structure of wBm carbonic anhydrase is predicted by selecting a suitable template using the similarity search tool, BLAST. The BLAST results shows a hexapeptide transferase family protein from Anaplasma phagocytophilum (PDB ID: 3IXC) having 77% similarity and 54% identity with wBm carbonic anhydrase. Hence the above enzyme is chosen as the template and the 3D structure of carbonic anhydrase is predicted by the tool Modeller9v7. Since the three dimensional structure of carbonic anhydrase from wolbachia endosymbiont of Brugia malayi has not yet solved, attempts were made to predict this protein. The predicted structure is validated and also molecular docking studies are carried out with the suitable inhibitors that have been solved experimentally.

• Journal of Integrative Natural Science
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• v.7 no.4
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• pp.241-252
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• 2014

A series of N-benzoylated ligands incorporating three different benzoyl groups 2,2'-(benzoyliminodiethylene)-4-substituted phenols ($L^{1,4,7}$), 2,2'-(4-nitrobenzoyliminodiethylene)-4-substituted phenols ($L^{2,5,8}$) and 2,2'-(3,5-dinitrobenzoyliminodiethylene)-4-substituted phenols ($L^{3,6,9}$) were synthesized and characterized by IR, $^1H$ NMR, $^{13}C$ NMR and mass spectroscopy. The In vitro antibacterial activity of investigated ligands were tested against human pathogenic bacteria such as four Gram (-) Enterococcus faecalis, Pseudomonas aeruginosa, Staphylococcus aureus, Vibrio cholera, Vibrio harveyi and two Gram (+) Staphylococcus aureus, Streptococcus mutans. Furthermore, docking studies were undertaken to gain insight into the possible binding mode of these compounds with the binding site of the topoisomerase II (PDB: 4FM9) enzyme which is involved in DNA superhelicity and chromosome seggregation. The N-benzoylated derivatives $L^{5,7,8}$ have significant anticancer activity as Topoisomerase inhibitors. The ligands $L^5$ and $L^8$ were tested for their anticancer activity against human liver adenocarcinoma (HepG2) cell line with the MTT assay.

• The Korean Journal of Pharmacology
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• v.32 no.2
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• pp.211-219
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• 1996

The inhibitory effect of cyclosporin A (CsA) on nitric oxide production is not related to the immunosuppressive action of the drug, but to the renal toxicity and arterial hyper-tension. In this study the experimental interventions to reverse the inhibition of nitric oxide production by cyclosporin A in rat aortic smooth muscle cells were examined. CsA inhibited the accumulation of nitrite, the stable end product of nitric oxide, in culture media in a concentration $(0.1{\sim}100{\mu}g/ml)-dependent$ manner. The inhibitory effect of CsA on nitrite accumulation were not antagonized by arginine (10 mM), a substrate of nitric oxide synthase, nor by calcium ionophore A23187 $(7{\mu}M)$. Forskolin, an activator of adenylate cyclase, which enhanced iNOS induction at transcriptional level, completely reversed the inhibitory action of CsA on nitrite accumulation. However, PMA (2 nM) and PDB (50 nM), PKC activators, increased the inhibitory action of CsA on nitrite accumulalion. From these results, it is suggested that cyclic AMP-elevating agents may be candidates of therapeutic agents in prevention and treatment of renal toxicity and arterial hypertension induced by CsA. Among conventional antihypertensive drugs, calcium channel blockers and ${\alpha}-blockers$ are preferred to ${\beta}-blockers$.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.946-951
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• 2006

To study the effect of iron on Saccharomyces cerevisiae, whole-cell proteins of Saccharomyces cerevisiae were extracted and subjected to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and differentially expressed proteins were identified. The proteins separated were further identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and were compared with a protein database. Of more than 300 spots separated by molecular weight and isoelectric points, 27 differentially expressed spots were identified. Ten proteins were found to be differentially expressed at high iron concentration. Triosephosphate isomerase (TPI), YDR533C hypothetical protein, superoxide dismutase (SOD), 60 kDa heat-shock protein (HSP60), pyruvate dehydrogenase beta subunit 1 (PDB1), and old yellow enzyme 2 (OYE2) were upregulated, whereas thiol-specific antioxidant (TSA), regulatory particle non-ATPase subunit 8 (RPN8), thiol-specific peroxiredoxin 1 (AHP1), and fructose-1, 6-bisphosphate adolase (FBA) were downregulated by iron. Based on the result, we propose that SOD upregulated by iron would protect the yeast from oxidative stress by iron, and that TSA downregulated by iron would render cells hypersensitive to oxidative stress.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.103.1-103
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• 2003

An antagonistic bacteria, Stenotrophomonas maitophilia BW-13 strain which was effectively inhibited mycerial growth of Bottom rot pathogen, Rhizoctonia solani PY-1 strain was isolated from the rhizosphere of the lettuce in Uiryeong-Gun, Gyeongsangnam-Do from 2002 to 2003. For the biological control, the most suitable inoculum and its density of pathogen, PY-1 strain ware tested prior biological control test, For the pathogenicity test, A inoculum (wheat bran)sawdust+rice bran+PDB) showing disease incidence of 100％ was selected as the most suitable inoculum, which showed more effective than B inoculum (sawdust＋rice bran＋DW) and mycelial disc. also, In selection of the amount of inoculum (40g, 50g, 60g, 70g, 80g), most suitable amount of inoculum of pathogen determined as 40g showing disease incidence of 80％. For the selection of effective microorganism to control bottom rot on lettuce, about 200 isolates were isolated from the diseased soil and lettuce leaves, and examined their antifungal activity to the pathogen on PDA. As the pots assay, BW-13 strain showed the highest control value as 90％, and followed by R-13 and R-26 strain as 80％ and 60％, respectively. Selected BW-13 isolates identified as 5. maltophilia (GeneBank accession no. AJ293473.1, 99％) by 16S rRNA sequencing. This is the first report on the biological control using by S. maltophilia to the bottom rot pathogen, Rhizoctonia solani PY-1 strain.

• Journal of Mushroom
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• v.3 no.1
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• pp.24-30
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• 2005

To study the cultural characteristics and wood rotting ability of the secondary mycellia of Armillaria mellea, it was cultivated on the various media. The optimal mycelial growth condition was 20~27 and pH 5.0~6.5 on PDB. A. mellea grew well on MEA, PDA and GP. Lactose and mannitol as carbon sources and glutamic acid as nitrogen sources were found to be effective as additives. A. mellea employed in this study have the characteristics of white rot types. Pine and oak wood were selected as candidates for sawdust substrate.

• Journal of Forest and Environmental Science
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• v.34 no.5
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• pp.395-404
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• 2018

Since the mass mortality of Quercus mongolica has been first reported in Gyeonggi province at 2004, the disease spread rapidly over Korean peninsula annually. Ambrosia beetle (Platypus koryoensis) was known as the insect vector of oak wilt fungus, Raffaelea quercus-mongolicae, and control methods of the disease had mainly been focused on eradication of insect vector. However, for the efficient management of the disease, combined control methods for both of the pathogenic fungus and insect vector are strongly required. As one of the efforts to suppress the pathogenic fungus, antifungal activities of Streptomyces isolated from oak forest soil were assayed in this study. Optimum culture condition for the selected isolates was also studied, As a result, Streptomyces blastmyceticus cultured in PDB (Potato Dextrose Broth) at $25^{\circ}C$ for 1 week showed the strongest antifungal activity against oak wilt fungus. Mycelial growth inhibition rates (MGIRs) of Streptomyces isolates were compared on culture media supplemented with heated and unheated culture filtrates of S. blastmyceticus. MGIRs on culture media with unheated culture filtrates were generally higher than those on culture media with heated culture filtrates. Antagonistic mechanism to get involved in the inhibition of hyphal growth and spore formation of the pathogen is due to the antifungal metabolites produced by Streptomyces. This study will provide the fundamental information in developing biocontrol agents for the environment-friendly management of oak wilt disease.

• The Korean Journal of Mycology
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• v.26 no.1 s.84
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• pp.20-24
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• 1998

The effects of liquid spawn to sawdust substrate on the growth of Flammulina velutipes were conducted for two years. The duration of optimal incubation for preculture and main culture of liquid spawn was 4 days and 6 days, respectively. When using liquid spawn, the application time for the first pinhead formation was similar with sawdust spawn, and incubation time of sawdust substrate was variable with liquid spawn and inoculum quantity. But, the overall yield of mushroom fruitbody was increased by using liquid spawn, excepting sesame hull extract medium.