• Journal of KIISE:Software and Applications
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• v.31 no.4
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• pp.387-393
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• 2004

DNA computing is technology that applies immense parallel castle of living body molecules into information processing technology, and has used to solve NP-complete problems. However, there are problems which do not look for solutions and take much time when only DNA computing technology solves NP-complete problems. In this paper we proposed an algorithm called ACO(Algorithm for Code Optimization) that can efficiently express DNA sequence and create good codes through composition and separation processes as many as the numbers of reaction by DNA coding method. Also, we applied ACO to Hamiltonian path problem of NP-complete problems. As a result, ACO could express DNA codes of variable lengths more efficiently than Adleman's DNA computing algorithm could. In addition, compared to Adleman's DNA computing algorithm, ACO could reduce search time and biological error rate by 50% and could search for accurate paths in a short time.

• Korean journal of applied entomology
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• v.30 no.2
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• pp.138-143
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• 1991

This study was carried out to acquire some basic biochemical informations on the granulosis virus (GV) DNA of Pieris rapae and Pieris brassicae. The thermal denaturation temperature (Tm) and G+C content of the DNA of the viruses were $83.7^{\circ}C$ and 35.5% for P. rapae GV, $84.0^{\circ}C$ and 35.9% for P. brassicae GV, respectively. There were some differences in the DNA fragmentation patterns of the two GV's produced by digestion with restriction endonucleases such as EcoR I , BamH I and Hind m . The homololgy between the two DNAs was caculated to be 97.0%. The size of the genome was estimated to be 103 kbp for P. rapae GV and 108 kbp for P. brassicae GV.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.551-556
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• 2004

According to revealing the DNA sequence of human and living things, it increases that a demand on a new computational processing method which utilizes DNA sequence information. In this paper we propose a classification algorithm based on negative selection of the immune system to classify DNA patterns. Negative selection is the process to determine an antigenic receptor that recognize antigens, nonself cells. The immune cells use this antigen receptor to judge whether a self or not. If one composes n group of antigenic receptor for n different patterns, they can classify into n patterns. In this paper we propose a pattern classification algorithm based on negative selection in nucleotide base level and amino acid level.

• Journal of Radiation Protection and Research
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• v.20 no.2
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• pp.71-78
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• 1995

To develop methods to reduce radiation risk and apply such knowledge to improvement of radiation protection, the effects of cobaltous chloride known as bioantimutagen on the function of E. coli RecA protein involved in the repair of DNA damage were examined. The results demonstrated two distinct effects of cobaltous chloride on the RecA protein function necessary for the strand exchange reaction. Cobaltous chloride enhanced the ability of RecA protein to displace SSB protein from single-stranded DNA and the duplex DNA-dependent ATPase activity. RecA protein was preferentially bound with UV-irradiated supercoiled DNA as compared with nonirradiated DNA The binding of RecA protein to UV-irradiated supercoiled DNA was enhanced in a dose-dependent manner. It is likely that studies on the factors affecting repair efficiency and the DNA repair proteins may provide information on the repair of ionizing radiation-induced DNA damage and the mechanism for DNA radioprotection.

• The Korean Journal of Pesticide Science
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• v.8 no.4
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• pp.288-298
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• 2004

Benzimidazole pesticide carbendazim that is effective against a wide range of fungal plant pathogens is a protective, eradicant, and systemic fungicide. For genetic toxicity evaluation of carbendazim on DNA, genes and chromosome, were investigated with chromosome aberration, bacterial reverse mutation, micronucleus test in mouse born marrow and DNA damage assay by single cell microgel electrophoresis. Substitution and frameshift mutation were not induce at variable concentration of carbendazim on Ames test with or without rat liver microsomal activation. For the result of chromosome aberration test, numerical changes of chromosome were detected at the concentrations higher than $4.0{\mu}g/m{\ell}$, but structural aberration was not induced. Positive control, Mitomycin-C and captafol made a structural aberration, but numerical change of chromosome did not appear. In the micronucleus test for mouse born marrow, carbendazim was negative, but was weak positive in DNA damage assay by single cell microgel electrophoresis because of increased DNA moving length of 20% to control.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.8
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• pp.624-632
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• 2008

In this research, we developed new PDMS-glass based microbiochip consisted of the micromixer and microreactor for DNA ligation. The micromixer was composed of a straight channel integrated with nozzles and pillars, and the microreactor was composed of a serpentine channel. We coated the PDMS chip surface with the 0.25wt.% PVP solution to prevent the bubble generation which was caused by the hydrophobicity of the PDMS. The new micomixer was passive type and the mixing was enhanced by a convective diffusion using the nozzle and pillar. The 10.33mm long micromixer showed the good mixing efficiency of 87.7% at 500 l/min flow rate. We could perform the DNA ligation successfully in the microbiochip, and the ligation time was shortened from 4 hours in conventional laboratory method to 5 min in the microbiochip.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.254-256
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• 2004

Polymerase chain reaction (PCR) is a powerful tool for precisely amplifying selected DNA sequences that have had a broad impact on genomic studies. When examining human $\alpha$- and $\beta$- tryptase genes which have 95% DNA homology, inconsistent PCR amplification of genomic sequences hampered our progress. This study suggests that long PCR technique on the original DNA digested with restriction enzymes improves both efficiency and sensitivity of PCR. These improved results seem to derived from the effective denaturation of the original genomic DNA template or reduction of formation of secondary structures that block either primer annealing or extension in PCR. Elimination of homo- or hetero-duplex products derived from highly homologous genes provides an additional advantage in this study. This communication describes how the use of restriction enzymes improved these efficiencies, and also facilitated studies of highly homologous genes including tryptase genes.

• The Korean Journal of Zoology
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• v.38 no.1
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• pp.87-95
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• 1995

한국산 담수어류의 잉어목, 황어아과(Leuciscinae) 어류 2속 5종의 계통적 유연관계를 구명하기 위하여 mtDNA분석을 실시하였다 6 base를 인지하는 10개의 제한효소를 처리하여 얻어진 강tDNA의 크기는 16.5-17.5 Kb였으며 Bcl I, Bgl I, Bgl II, Hin dIII, Pvu II, Xba I 등은 종간 차이가 뚜렷하였다. 각종의 집단간 mtDNA분화정도는 매우 낮았으나(p=1% 미만) M. oxyephalus의 무주집단과 제주집단은 예리적으로 큰 차이를 보였다(p=5.3%) Moroco속의 종간 분화정도를 비교한 결과 M. oxycephafus와 M. lagowsk서 사이가 평균 f=7.2%로 근면관계가 제일 가까웠고 M. keumkang과 M. semotilus는 타종들과 근연관계가 제일 멀었다. Moroco속과 Phoxinus속간의 평균 유전적 분화정도는 f=13.7%로 현저한 차이를 보였다. Brown 등(1979)의 공식을 이용하여 이들 황어아과 2속 5종의 분화시기를 추정한 결과 이들은 후기 선신세(Pliocene)와 흥적세(Pleistocene) 사이에 분화된 것으로 추정되었으며 이 결과는 동위효소 연구에서 얻어진 결파(Yang and Min, 1989)와 잘 일치한다.

• Journal of KIISE:Databases
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• v.32 no.3
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• pp.263-275
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• 2005

In a large DNA database, indexing techniques are widely used for rapid approximate sequence searching. However, most indexing techniques require a space larger than original databases, and also suffer from difficulties in seamless integration with DBMS. In this paper, we suggest a space-efficient and disk-based indexing and query processing algorithm for approximate DNA sequence searching, specially exact match queries, wildcard match queries, and k-mismatch queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as R*-tree. Especially, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in index space. Our query processing algorithm converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle. The experiments with real biological data sets revealed that the proposed method is at least three times, twice, and several orders of magnitude faster than the suffix-tree-based method in exact match, wildcard match, and k- mismatch, respectively.

• Journal of Life Science
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• v.23 no.8
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• pp.963-969
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• 2013

Although it is popularly believed that vitamin C protects cells from various genotoxicants, the degrees and mechanisms of itsprotective actions are not fully understood. In this study, vitamin C's protective effects against various genotoxicants were quantified, together with subsequent analyses on the mechanisms of these protective effects. Comet assay was employed to measure the degree of DNA damage in Chinese hamster ovary cells (CHO-K1) exposed to five genotoxicants, $H_2O_2$, $HgCl_2$, N-methyl-N-nitro-N-nitrosoguanidine (MNNG), 4-nitroquinoline-1-oxide (4NQO), and UV-irradiation. In cases cells were treated with $H_2O_2$, $HgCl_2$, and 4NQO together with vitamin C, the damage to DNA decreased to the level of the control group. In cases of UV-irradiation, the protective effect of vitamin C appeared, but did not reach the control levels. Interestingly, vitamin C did not have protective effects against the genotoxicity of MNNG. The degrees of DNA damage of cells treated with vitamin C prior to exposure togenotoxicants were 28~49% lower than those of cells treated with vitamin C after being exposed to genotoxicants. In conclusion, vitamin C had strong antioxidanteffects against genotoxicants by being a primary antioxidant blocking genotoxicity reaching the cells, rather than being a secondary antioxidant acting on post-exposure DNA repair processes. However, vitamin C's protective effects appearto be limited, as there are genotoxicants, such as MNNG, whosegenotoxicityis not affected by vitamin C. Therefore, the results of this study warrant furtherstudies on toxic mechanisms of genotoxicants and their interactions with protective mechanisms of vitamin C.