• Journal of Life Science
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• v.28 no.4
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• pp.408-414
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• 2018

Actein is the well-known active ingredient of Cimicifugae rhizoma (Black cohosh). In this study, we investigated and compared the binding affinity of tubocurarine, actein, and actein derivatives on the B&C domain of the acetylcholine binding protein through in silico computational docking studies. The three-dimensional crystallographic structure of the acetylcholine binding protein B&C domain was obtained from the PDB database (PDB ID: 2XYT). An in silico computational autodocking analysis was performed using PyRx, Autodock Vina, Discovery Studio Version 4.5, and NX-QuickPharm based on scoring functions. The actein showed an optimum binding affinity (docking energy), with the acetylcholine binding protein at -10.50 kcal/mol as compared to the tubocurarine (-9.80 kcal/mol). The interacting amino acids tryptophan 84 and tryptophan 147, in the B domain of the acetylcholine binding protein active site, significantly interacted with the actein and 27-deoxyactein, and (26R)-actein. The centroid XYZ grid position of the tubocurarine was X=38.300689, Y=112.053467, and Z=51.991022, but the actein and its derivatives showed values around X=26.4, Y=127.3, Z=43.7. These results clearly indicated that actein and its derivatives could be a more potent antagonist to the acetylcholine binding protein than tubocurarine. Therefore, the extract of Cimicifugae rhizoma or actein containing biomaterials can substitute for the botulinum toxin-mediated acetylcholine receptor regulation, and be applied to the anti-wrinkle cosmetics industry.

• Research in Plant Disease
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• v.15 no.3
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• pp.217-221
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• 2009

Fludioxonil is derived from the antifungal compound pyrrolnitrin produced by Pseudomonas pyrrocinia and classified as a reduced-risk fungicide by the US EPA. The efficacy of fludioxonil for the control of lettuce gray mold caused by Botrytis cinerea was evaluated under several conditions such as growth stages of host, inoculum concentrations, and amounts of potato dextrose broth (PDB) included in spore suspension of B. cinerea. At 4-leaf stage of lettuce plants, fludioxonil applied at 2 ${\mu}g$/ml was more effective for the control of gray mold than at 5- and 6-leaf stages. However, fludioxonil at more than 10 ${\mu}g$/ml provided similar control activity in all growth stages of lettuce tested. The fungicide (10 and 50 ${\mu}g$/ml) also gave excellent control of gray mold on lettuce seedlings inoculated with spore suspensions of B. cinerea ($2.5{\times}10^5$ to $2{\times}10^6$ spores/ml). But, control efficacy of fludioxonil (2 ${\mu}g$/ml) was negatively correlated with inoculum concentration. Addition of PDB in spore suspension of B. cinerea resulted in higher disease severity than non-treated control. By inoculating spore suspension including 0.5% PDB, the fungicide gave the most control activity on the disease, followed by 1% and 2% PDB. The results suggest that fludioxonil has potential to control gray mold of lettuce, but the fungicide at a concentration having moderate activity may represent low control efficacy on the disease under some conditions.

• Journal of KIISE:Computing Practices and Letters
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• v.11 no.2
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• pp.133-148
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• 2005

Since understanding of similarities and differences among protein structures is very important for the study of the relationship between structure and function, many protein structure comparison systems have been developed. Hut, unfortunately, these systems introduce their own protein data derived from the PDB(Protein Data Bank), which are needed in their algorithms for comparing protein structures. In addition, according to the rapid increase in the size of PDB, these systems require much more computation to search for common substructures in their databases. In this paper, we introduce a protein structure comparison system named WS4E(A Web-Based Searching Substructures of Secondary Structure Elements) based on a PSAML database which stores PSAML documents using the eXist open XML DBMS. PSAML(Protein Structure Abstraction Markup Language) is an XML representation of protein data, describing a protein structure as the secondary structures of the protein and their relationships. Using the PSAML database, the WS4E provides web services searching for common substructures among proteins represented in PSAML. In addition, to reduce the number of candidate protein structures to be compared in the PSAML database, we used topology strings which contain the spatial information of secondary structures in a protein.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.1081-1085
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• 2004

Genome research has become very popular in most nations. In order to enhance the efficiency of collaboration among genome research groups, ways to store and share data, communicate with each other, be guided through right research strategies, and to easily use well-established databases. In addition, since techniques and softwares for genome research groups are well established, a similar research road map could commonly be applied. In this study, we developed a web-based work place for effective genome research, named 'BioPlace.' From the beginning of writing a proposal, research members can work on the same environment with convenient aid to share files or data. BioPlace provides various ways of collaboration methods among genome researchers. The BioPlace system supports two types of workplaces, namely 'Personal Workspace' and 'Team Workspace.' For each BioPlace user, a Persona] Workspace is provided, while a Team Workspace is provided for each group with the same purpose. In addition, BioPlace provides a 'General Research Road Map' for genome research, and several Korean user interfaces for BLAST, PDB, and Primer3. We expect that BioPlace may facilitate collaboration of genome research among the experienced scientists and help beginners in many different ways as well.

• Proceedings of the Korean Information Science Society Conference
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• 2001.04b
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• pp.556-558
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• 2001

전체 영상을 이용하지 않고 영상 안에 포함된 특정 객체 혹은 영역만을 이용하는 "영역에 의한 질의(query-by-region)" 방법은 내용기반 영상 검색 중 상위개념의 방법 이지만, 영상 분할의 한계, 여러개로 분할된 영역을 모두 검색하기 위한 인덱싱 문제, 유사성 측정 시 선형적으로 분리되지 않는 특징 값들에 대한 무리한 선형 조합으로 인한 검색 오류와 같은 많은 문제점을 안고 있다. 따라서 본 논문에서는 영역 기반 영상 검색 시스템인 FRIP에 대하여 영상 분할의 한계를 극복하고, 사용자의 주관성을 영상 검색에 적용하기 위해 확률적 연관성 학습 모델(MPFRL)을 유사성 측정 단계에서 적용 하였고, 아울러 검색 모델로는 기존에 일반적으로 사용되어 오던, 선형 모델을 사용하지 않고 선형 모델보다 유연한 검색 결과를 보여주는 확률적 이접 부울 모델(PDB)을 사용하였다. 또한, 검색 시간을 단축 시키기 위해, 선형 검색 방법에 부울 AND 연산자를 적용 시킴으로써, 검색 시간을 상당부분 단축 할 수 있었다. 실험 결과, 본 논문에서 제안하는 방법(MPFRL+PDB)을 사용할 경우 검색 결과가 선형 조합 보다 향상되는 것을 알 수 있었다. 아울러 사용자 피드백을 통해 사용자가 특징 가중치를 일일이 조절하지 않더라도 단순한 몇 번의 클릭만으로 사용자의 주관성을 반영하고 보다 정확한 검색 결과를 보여 줄 수 있는 시스템을 설계 할 수 있었다.

• Genomics & Informatics
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• v.11 no.4
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• pp.289-291
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• 2013

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

• Journal of Life Science
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• v.12 no.6
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• pp.708-714
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• 2002

A new leaf blight was found on the perilla leaves at the major perilla-cultivating areas such as Kangdong in Busan and Miryang in Kyungnam province. Symptoms of the disease initially appeared on the edge of perilla leaves showing black necrosis and drying, and the infected leaves were finally fell down. The SD1 isolate showing strong pathogenicity and forming abundant conidial spores on the diseased lesions was isolated. Among the tested media, mycelial growth was abundant on PDA (Potato Dextrose Agar) medium at $25^{\circ}C$ under dark condition, but conidial formation was greater on V8A (V-8 juice A8ar) medium than that on PDA medium. Optimal temperatures for mycelial growth and conidial formation on PDA medium were respectively $25^{\circ}C$ and 3$0^{\circ}C$. The rate of conidial germination and the elongation of germ tube were more effective in 10% tomato juice than those in PDB (Potato Dextrose Broth) and sterile water. In 10% tomato juice, the rate of conidial germination and the length of germ tube were 100% after incubation for 24k and 535.2${\mu}{\textrm}{m}$ after incubation for 36hr, respectively. According to the result of pathogenicity, it revealed that conidial suspention with 10% tomato juice was the most effective for pathogenicity test showing as 100% of disease incidence, and the symptoms caused by artificial inoculum were same as those of naturally infected perilla. In this study, the SD1 isolate according to the results of morphological characteristics, the incubation characteristics and pathogenicity was firstly identified A. alternata, and named as leaf blight of perilla.

• Journal of Mushroom
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• v.15 no.1
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• pp.38-44
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• 2017

Sparassis latifolia (formerly S. crispa) is used in food and nutraceuticals or dietary supplements, as rich in flavor compounds and ${\beta}-glucan$. Some previous studies have reported the effects of mushroom on brain function, including its neuroprotective effect. Thus, for this mushroom to be used as an effective nutraceutical for brain function, it would be desirable for it to contain other compounds such as ${\gamma}-aminobutyric$ acid (GABA) in addition to ${\beta}-glucan$. In this study, the enhancement of growth and GABA production in the mycelium of medicinal and edible mushroom S. latifolia was investigated. Amino acids were added externally as the main source of nutrition, and the effects of amino acids were investigated using liquid medium, specifically amino acid-free potato dextrose broth (PDB). The amino acids added were L-glutamic acid (named PDBG medium) and L-ornithine (named PDBO medium). The growth of mycelia was determined to be $0.9{\pm}0.00g/L$, $2.2{\pm}0.16g/L$, and $1.93{\pm}0.34g/L$ PDBG respectively. The GABA content was $21.3{\pm}0.9mg/100g$ in PDB medium, and it in PDBG 1.4% medium, at $115.4{\pm}30.2mg/100g$. However, the PDBO medium was not effective in increasing the GABA content of mycelia. Amino acids had little effect on the ${\beta}-glucan$ content of mycelia. The ${\beta}-glucan$ content was $39.7{\pm}1.4mg/100mg$, $34.4{\pm}0.2mg/100mg$, and $35.2{\pm}9.2mg/100mg$ in PDB, PDBG 1.8% and PDBO 1.4% media, respectively. Addition of glutamic acid and ornithine positively affected the growth of S. latifolia mycelia, and glutamic acid positively affected GABA production; no degradation of GABA was observed with addition of glutamic acid.

• Korean Journal of Environmental Agriculture
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• v.20 no.1
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• pp.1-7
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• 2001

We investigated the capability of the phosphate-solubilizing fungus, Penicillium sp. GL-101, to solubilize in vitro some insoluble rock phosphate via possible mechanisms: acidification of the medium, production of chelating metabolites, redox activity, and so on. GL-101 was able to solubilize rock phosphate (mostly calcium phosphate) in a liquid potato dextrose broth(PDB) medium, as determined by spectrophotometric analyses. Acidification was the major mechanism of solubilization since the pH of cultures fell below 4.0 and in cultures containing 1.0%(w/v) loess the pH dropped from 7.0 to 3.2. More than 10 mg/mL concentrations of citric acids were detected by high-performance liquid chromatography(HPLC) in the culture supernatants. Also this fungus showed the phosphatase activity (over 1.3 unit) to contribute partially releasing phosphate from rock phosphate, when supplemented with 1.0% loess in culture broth. The chelating activity of GL-101 in culture supernatants was not present because 2-ketogluconic acid, a chelating agent for the phosphate, was produced only a basal level. Therefore, the solubilization mechanism of rock phosphate by Penicillium sp. GL-101 involves both acidification due to citric acid production and phosphatase activity.

• The Korean Journal of Physiology and Pharmacology
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• v.2 no.4
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• pp.435-441
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• 1998

We examined effects of interleukin $1{\alpha}$ ($IL1{\alpha}$) and phorbol 12, 13 dibutyrate (PDB), an activator of protein kinase C, on mRNA for Prostaglandin H synthase (PGHS) and prostanoid production in cultured ovine meningeal fibroblasts. Immuno- and morphologically-identified fibroblasts were derived from cerebral cortex and white matter from fetal lambs (approximately 120 days gestation) and grown to confluence on glass coverslips in 12 well plates. Levels of prostaglandin $F_{2{\alpha}}$ and the stable hydrolysis product of prostacyclin (i.e., $6-keto-PGF_{1{\alpha}}$) were determined using enzyme immunoassay. Relative amounts of mRNA were determined by in situ hybridization using ovine cDNA for PGHS1. $IL1{\alpha}$ (10 ng/ml) increased mRNA levels over baseline by $62{\pm}19%$ (p＜0.05) at 60 min., $37{\pm}12%$ (NS) at 120 min., and $36{\pm}18%$ (NS) at 240 min (n=12). Levels of $6-keto-PGF_{1{\alpha}}$ were $148{\pm}18%$ pg/ml during baseline, $246{\pm}41%$ pg/ml at 60 min., $248{\pm}40%$ pg/ml at 120 min., and $259{\pm}62%$ pg/ml at 240 min (all p＜0.05) (n=12). $PGF_{2{\alpha}}$ was increased although it wasn't statistically significant. However, $IL1{\alpha}$ decreased $PGE_2$ level significantly (all p＜0.05). PDB $(10^{-6}M)$ increased mRNA levels over baseline by $25{\pm}6%$ after 30 min., $40{\pm}6%$ after 60 min., and $20{\pm}8%$ after 90 min. (n=9) (all p＜0.05). Levels of $6-keto-PGF_{1{\alpha}}$ were $200{\pm}43%$ pg/ml during baseline, $202{\pm}43%$ pg/ml after 30 min. (NS), $268{\pm}58%$ pg/ml after 60 min. (p＜0.05), and $296{\pm}60%$ pg/ml after 90 min. (p＜0.05) (n=9). Levels of $PGF_{2{\alpha}}$ were $178{\pm}26%$ pg/ml during baseline, $300{\pm}30%$ pg/ml after 30 min., $299{\pm}35%$ pg/ml after 60 min., and $355{\pm}32%$ pg/ml after 90 min (all p＜0.05) (n=6). Actinomycin-D (1 mg/ml) prevented increases in mRNA, $6-keto-PGF_{1{\alpha}}$, and $PGF_{2{\alpha}}$ at 60 min. for both $IL1{\alpha}$ and PDB. We conclude that cerebral fibroblasts are avid producers of prostanoids, and that enhanced production of PGHS is responsible for augmented $PGF_{2{\alpha}}$ and prostacyclin production in the presence of an activator of protein kinase C and for decreased $PGE_2$ and increased prostacyclin production in the presence of $IL1{\alpha}$.