• Korean Journal Plant Pathology
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• v.12 no.1
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• pp.41-46
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• 1996

본 실험은 이병 딸기의 조직에서 분리 동정된 시들음병균(Fusarium oxysporum f. sp. fragariae) 균주들의 유？거 변이를 random amplified polymorphic DNA(RAPD) marker들을 이용하여 조사하였다. 총 24개의 딸기 시들음병 균주들의 DNA를 주형으로 하여 16개의 random 10-mer primer들을 사용하여 증폭시킨 결과 총 231개의 marker들을 이용하여 유전적 변이를 조사해 본 결과 크게 RAPD I과 RAPD II의 2개 그룹으로 나눌 수 있었다. RAPD I그룹에 속하는 균주는 VCG A에 속하는 Y1, K1, K2, K3, K4, N2, N3, N4-1, N6-1, N6-2, N8, N9, N10, M1-2-1 균주, VCG B에 속하는 M4-1 균주 그리고 VCG C에 속하는 N1, Y2 균주들이었고, RAPD II그룹에는 VCG B에 속하는 M1-1, M2-2-1, M2-4-2, M3-2, M3-3-2 균주와 VCG D에 속하는 N1 1 균주가 속하였다. 이들 2그룹 간에는 31%의 유사성이 있었다.

• Proceedings of the Korean Information Science Society Conference
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• 2012.06b
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• pp.357-359
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• 2012

초 고성능 바이오 서열 분석 장비 기술의 발달로 대량의 바이오 정보가 쏟아져 나오고 있으며, 바이오산업의 발달로 개인별 유전체 정보에 의한 맞춤의학의 시대가 도래되고 있다. 수많은 서열에 대한 분석에는 많은 저장장치 및 주기억장치가 필요하므로 슈퍼컴퓨터 급의 서버와 대량의 데이터를 빠르게 처리할 수 있는 프로그램이 필요하다. 이러한 분석에는 염기서열 일치 검색과 이를 기반으로 하는 Alignment와 Assembly 분석이 있으며, 이를 수행하는 기존의 알고리즘 및 대부분의 프로그램들은 염기서열을 문자열로 취급하고, 해쉬 인덱스 테이블, Brujin 그래프의 사용, 버러우즈 휠러 변환(BWT) 등의 기법을 활용하여 효율적인 분석을 도모하였다. 본 논문에서는 염기서열을 문자열이 아닌 k-mer 묶음의 정수형 하나로 변환하여 검색함으로써 저장 공간의 크기를 약 28% 이상으로 줄이고 형 변환 상태에서의 검색을 수행할 수 있는 알고리즘을 제안한다. Assembly 분석 프로그램인 CalcGen 프로그램을 개발하여 본 알고리즘의 효용성 및 효율성을 실험을 통해 검증하였다. 이 연구의 결과는 향후 대량의 유전체 염기서열의 효율적 분석과 저장 및 처리에 또 하나의 새로운 접근 방법을 제안하는데에 그 의미를 둘 수 있다.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.156-158
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• 2012

A synthetic coprisin analog peptide, 9-mer dimer CopA3 (CopA3) was designed based on a defensin-like peptide, Coprisin, isolated from the bacteria-immunized dung beetle Copris tripartitus. Here, CopA3 was investigated for its antimicrobial activity and cancer cell growth inhibition. CopA3 showed antimicrobial activities against various pathogenic bacteria and yeast fungus with MIC values in 2~32 ${\mu}M$ ranges, and inhibited the cell viabilities of pancreatic and hepatocellular cancer cells, except MIA-Paca2, Hep3B, and HepG2 cells, in a dose-dependent manner. The average $IC_{50}$ values of CopA3 against pancreatic and hepatocellular cancer cells were 61.7 ${\mu}M$ and 67.8 ${\mu}M$, respectively. The results indicate that CopA3 has potential in the treatments of pancreatic and hepatocellular cancers as well as microorganism infection disease.

• Journal of Microbiology and Biotechnology
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• v.17 no.6
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• pp.952-959
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• 2007

His-His-Leu (HHL), a tripeptide derived from a Korean soybean paste, is an angiotensin-I-converting enzyme (ACE) inhibitor. We report here a method of producing this tripeptide efficiently by expressing tandem multimers of the codons encoding the peptide in E. coli and purifying the HHL after hydrolysis of the peptide multimers. The HHL gene, tandemly multimerized to a 40-mer, was ligated with ubiquitin as a fusion gene (UH40). UH40 was inserted into vector pET29b; the UH40 fusion protein was then produced in E. coli BL21. The recombinant UH40 protein was purified by cation-exchange chromatography with a yield of 17.3mg/l and analyzed by matrixassisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry and protein N-terminal sequencing. Leucine aminopeptidase was used to cleave a 405-Da HHL monomer from the UH40 fusion protein and the peptide was purified using reverse-phase high-performance liquid chromatography (HPLC) on a C18 HPLC column, with a final yield of 6.2mg/l. The resulting peptide was confirmed to be HHL with the aid of MALDI-TOF mass spectrometry, glutamine-TOF mass spectrometry, N-terminal sequencing, and measurement of ACE inhibiting activity. These results suggest that our production method is useful for obtaining a large quantity of recombinant HHL for functional antihypertensive peptide studies.

• Archives of Pharmacal Research
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• v.24 no.5
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• pp.455-465
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• 2001

The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-ones insoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., $5^1$-T$AT_2$A*-$3^1$), while Bizelesin prefers purely AT-rich sequences (i.e., $5^1$-T$AT_4$A*-$3^1$, where /(equation omitted) represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field $^1$H-NMR and rMD studies are conducted on the 1 1-mer DNA duplex adduct of the Pyrrole where the 5′(equation omitted)TAGTTA*-3′sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central C/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.52 no.1
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• pp.51-54
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• 2007

Soybean has a morphological type with a broadened and flattened stem. Fasciation has been suggested as a new gene for soybean research. SSR marker linked to the $\Large f$ locus that controls fasciation phenotype has not identified within 10 cM. A mapping population consisting of 94 $F_2$ progenies was derived from a cross between wild type Clark (FF) and fasciation mutant C32 (${\Large f}{\Large f}$). The phenotype of $F_2$ individual plants was recorded at R2 and R3 growth stage from field. One-thousand 10-mer oligonucleotide RAPD primers and 29 SSR primers selected from the D1b+W of the soybean molecular linkage map were used. A genetic map was constructed from the segregating 35 RAPD, four SSR markers and one phenotypic(wild type/fasciation) marker. The segregation ratios of 3 : 1 observed in the $F_2$ population and the Chi-square values strongly suggest that the fasciation trait is controlled by a single recessive gene. Satt537 marker was linked to $\Large f$ locus at a distance of 9.6 cM. Assignment of the $\Large f$ locus to linkage group D1b+W and identification of markers can be used as an initial step for fine mapping of the $\Large f$ gene.

• BMB Reports
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• v.35 no.2
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• pp.206-212
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• 2002

The NS2B-NS3(pro) polyprotein segment from the dengue virus serotype 2 strain 16681 was purified from overexpressing E. coli by metal chelate affinity chromatography and gel filtration. Enzymatic activity of the refolded NS2B-NS3(pro) protease complex was determined in vitro with dansyl-labeled peptide substrates, based upon native dengue virus type 2 cleavage sites. The 12mer substrate peptides and the cleavage products could be separated by reversed-phase HPLC, and were identified by UV and fluorescence detection. All of the peptide substrates (representing the DEN polyprotein junction sequences at the NS2A/NS2B, NS2B/NS3, NS3/NS4A and NS4B/NS5 sites) were cleaved by the recombinant protease NS2B-NS3(pro). No cleavage was observed with an enzymatically inactive S135A mutant of the NS3 protein, or with a modified substrate peptide of the NS3/NS4A polyprotein site that contained a K2093A substitution. Enzymatic activity was dependent on the salt concentration. A 50% decrease of activity was observed in the presence of 0.1M sodium chloride. Our results show that the NS3 protease activity of the refolded NS2B-NS3(pro) protein can be assayed in vitro with high specificity by using cleavage-junction derived peptide substrates.

• Journal of fish pathology
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• v.20 no.3
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• pp.307-313
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• 2007

In this study, a QCM biosensor was made to detect Edwardsiella tarda (E. tarda) using a specific antibody. A 9 MHz AT-cut piezoelectric wafer layered with two gold electrodes of 5mm diameter had a reproducibility of 0.1 Hz in frequency response and was used as the transducer of the QCM biosensor. Self assembled layer (SAM) was conformed on a quartz crystal by treating with 3-mer-captopropionic acid (MPA) and activated with N-ethyl-N'-(3-dimethyl-aminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The resulting NHS group was further converted to hydrazide by the reaction with hydrazine. Aldehyde group was introduced into the carbohydrate moiety of anti-E. tarda antibody by the reaction with periodic acid and was used to immobilise the antibody through the reaction with hydrazide group on the electrode surface. A baseline was established in the presence of phosphate-buffered saline (PBS) and a resonant frequency (F1) was measured. Sample was added to the sensor surface and second resonant frequency (F2) was measured after unbound substances were washed out with PBS several times. Finally, the frequency shift (ΔF) representing the mass change was calculated by subtracting F2 from F1. After adding the oxidized anti-E. tarda antibody to the electrode surface containing hydrazide group, frequency shift of 288.811.4 Hz (mean S.E) was observed, thus proving that considerable amount of antibody was immobilized. In the immunoassay test, the frequency shift of 1877.75 Hz, 580.67 Hz, 221.39 Hz, 7.671.83 Hz (mean S.E) were observed at doses of 1000, 500, 100, 50 g of bacterial cells, respectively. It was also demonstrated that the prepared sensor chip was stable enough to withstand repeated surface regeneration with 0.2 M Tris-glycine and 1 % DMSO, pH 2.3 more than ten times.

• Proceedings of the Korea Inteligent Information System Society Conference
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• 2001.01a
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• pp.73-77
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• 2001

In this paper, we propose a virtual action system based on information agents, We call the system the MultiHammer, MultiHammer can be used for studying and analyzing online actions. MuiltiHammer provides functions of implement-ing a meta online action site and an experiment environ-ment. We have been using MultiHammer as an experiment as an experiment environment for BiddinBot. BiddingBot aims at assisting users to bid simultaneously in multiple online auctions. In order to bid simultaneously in multiple online auctions. In order to analyze the behavior of BiddngBot, we need to pur-chase a lot of items. It is hard for us to prepare a lot of fund to show usability and advantage of BiddingBot. MultiHam-mer enables us to effectively analyze the behavior of BiddingBot. MultiHammer consists of three types of agents for information collecting data storing and auctioning. Agents for information wrappers. To make agent work as wrarp-pers, we heed to realize software modules for each online action site. Implementing these modules reguires a lot of time and patience. To address this problem, we designed a support mechanism for developing the modules. Agents for data storing record the data gathered by agents for informa-tion collecting. Agents for auctioning provide online services using data recorded by agents for data storing. By recording the activities in auction sites. MultiHammer can recreate any situation and trace auction for experimentation, Users can participate in virtual using the same information in real online auctions. Users also participate in real auc-tions via wrapper agents for information collecting

• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1707-1716
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• 2019

The development of new antimicrobial agents is essential for the effective treatment of diseases such as sepsis. We previously developed a new short peptide, Pap12-6, using the 12 N-terminal residues of papiliocin, which showed potent and effective antimicrobial activity against multidrug-resistant Gram-negative bacteria. Here, we investigated the antimicrobial mechanism of Pap12-6 and a newly designed peptide, Pap12-7, in which the 12^th Trp residue of Pap12-6 was replaced with Val to develop a potent peptide with high bacterial selectivity and a different antibacterial mechanism. Both peptides showed high antimicrobial activity against Gram-negative bacteria, including multidrug-resistant Gram-negative bacteria. In addition, the two peptides showed similar anti-inflammatory activity against lipopolysaccharide-stimulated RAW 264.7 cells, but Pap12-7 showed very low toxicities against sheep red blood cells and mammalian cells compared to that showed by Pap12-6. A calcein dye leakage assay, membrane depolarization, and confocal microscopy observations revealed that the two peptides with one single amino acid change have different mechanisms of antibacterial action: Pap12-6 directly targets the bacterial cell membrane, whereas Pap12-7 appears to penetrate the bacterial cell membrane and exert its activities in the cell. The therapeutic efficacy of Pap12-7 was further examined in a mouse model of sepsis, which increased the survival rate of septic mice. For the first time, we showed that both peptides showed anti-septic activity by reducing the infiltration of neutrophils and the production of inflammatory factors. Overall, these results indicate Pap12-7 as a novel non-toxic peptide with potent antibacterial and anti-septic activities via penetrating the cell membrane.