• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.83.2-83
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• 2003

A full length cDNA, OsLEUZIP, encoding leucine zipper containing protein from rice EST of rice (0ryza sativa L. cv. Dongjin) treated Xanthomonas oryzae pv. oryzae 10331. OsLEUZIP contains 1,227 bp nucleotides and encodes a protein of 408 amino acid residues with predicted molecular weight of 47,229 Da. The deduced amino acid sequence of OsLEUZIP has consensus sequence of leucine zipper from PROSITE (PDOC00029), L-X(6)-L-X(6)-L-X(6) -L. OsLEUZIP gene were preferentially induced in rice during incompatible interaction with Xanthomonas oryzae pv. oryzae 10331 and Pyracuraria grisea KJ-301. Expression of OsLEUZIP gene was also induced by treatment of abiotics such as ethephon and ABA. Our data represented in this study suggesting that OsLEUZIP gene may play an important role in the rice defense-related. Further studies of this gene, overexpression in rice, yeast-two hybrid assay, electrophoretic mobility shift assay and northern blot analyses of transgenic plant, would be useful to elucidate the role of the OsLEUZIP gene in defense responses of rice.

• Proceedings of the IEEK Conference
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• 2000.06b
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• pp.103-106
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• 2000

The electronic properties of carbon nanotube are currently the focus of considerable interest. In this paper, the electronic properties of finite length effect in carbon nanotube for cabon nanoscale device is presented. To calculate the electronic properties of carbon nanotube, Empirical potential method (Brenner' hydrocarbon potential) for carbon and Tight binding molecular dynamic (TBMD) simulation are used. As a result of study, we have known that the value of the band gap decreases with increasing the length of the tube. The energy band gap of (6, 6) armchair carbon nanotube have the ranges between 0.3 eV and 2.5 eV. Also, our results were compared with the results of the other computational techniques. As that result, our results are very well united.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3790-3794
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• 2013

Molecular dynamics simulations were performed to study the structure and stability of a nanoscale self-assembled monolayer (SAM) of alkanethiol on a gold (111) surface. The tilt angle and orientational order of the alkyl chains in the SAM island were examined by systematically varying the size of the island. The chain length dependence of the SAM island was examined by considering alkanethiols containing 12, 16, 20, and 24 carbon atoms. The minimum diameter of SAM islands made from 1-tetracosanethiol, 1-ecosanethiol, 1-hexadecanethiol and 1-dodecanethiol were 2.29, 1.9, 4.7 and 4.76 nm, respectively. These set the ultimate resolution that can be patterned by soft nanolithography. As the length of alkanethiol increases, the SAM islands became more ordered in both orientation and conformation of the alkyl chains.

• BMB Reports
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• v.46 no.9
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• pp.471-476
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• 2013

The PIDDosome, which is an oligomeric signaling complex composed of PIDD, RAIDD and caspase-2, can induce proximity-based dimerization and activation of caspase-2. In the PIDDosome assembly, the adaptor protein RAIDD interacts with PIDD and caspase-2 via CARD:CARD and DD:DD, respectively. To analyze the PIDDosome assembly, we purified all of the DD superfamily members and performed biochemical analyses. The results revealed that caspase-2 CARD is an insoluble protein that can be solubilized by its binding partner, RAIDD CARD, but not by full-length RAIDD; this indicates that full-length RAIDD in closed states cannot interact with caspase-2 CARD. Moreover, we found that caspase-2 CARD can be solubilized and interact with full-length RAIDD in the presence of PIDD DD, indicating that PIDD DD initially binds to RAIDD, after which caspase-2 can be recruited to RAIDD via a CARD:CARD interaction. Our study will be useful in determining the order of assembly of the PIDDosome.

• Transactions on Electrical and Electronic Materials
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• v.3 no.1
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• pp.23-29
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• 2002

The electronic properties of Carbon Nanotube(CNT) are currently the focus of considerable interest. In this paper, the electronic properties of finite length effect in CNT for the carbon nano-scale device is presented. To Calculate the electronic properties of CNT, Empirical potential method (the extended Brenner potential for C-Si-H) for carbon and Tight Binding molecular dynamic (TBMD) simulation are used. As a result of study, we have known that the value of the band gap decreases with increasing the length of the tube. The energy band gap of (6,6) armchair CNT have the ranges between 0.3 eV and 2.5 eV. Also, our results are in agreements with the result of the other computational techniques.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.295-300
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• 2002

The construction of the T-shaped post-column flow cell has been changed to enhance the practicability as a UV-visible absorbance detector for capillary electrophoresis. In this new design, a rectangular cube-shaped inner structure is employed, which completely fits the outer rectangular tubing. This arrangement has greatly facilitated the fabrication of the T-cells. In addition, the volume for the auxiliary flow has been dramatically reduced down to 300 ${\mu}L$, and its volume flow rate is optimized at 4.2 ${\mu}L$/min. The short optical path length in the sheath flows (500 ${\mu}m$ on each side) minimizes background absorption, and thus enhances its performance in low-UV wavelengths. We have optimized the auxiliary flow rate at 50 ${\mu}m$/s, so that migration times are insensitive to the flow rate. This optimization has improved repeatabilities in migration times and peak heights. A double-beam detection scheme using a pair of photodiodes is employed to increase the signal-to-noise ratio.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.599-606
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• 2004

Gram-positive antagonistic bacilli were isolated from agricultural soils for possible use in biocontrol of plant pathogenic fungi, Fusarium oxysporum, Rhizoctonia solani, and/or Pythium ultimum. Among the 65 antagonistic Gram-positive soil isolates, 22 strains were identified as Bacillus species by 16S rDNA sequence analyses. Four strains, including DF14, especially exhibited multiple antagonistic properties against the three damping-off fungi. Genotypic properties of the Bacillus isolates were characterized by rapid molecular fingerprinting methods using repetitive extragenic palindromic-PCR (REP-PCR), ribosomal intergenic spacer-length polymorphisms (RIS-LP), 16S rDNA PCR-restriction fragment length polymorphisms (PCR-RFLP), and strain-specific PCR assays. The results indicated that the REP-PCR method was more valuable than the RIS-LP and 16S rDNA PCR-RFLP analyses as a rapid and reliable approach for bacilli typing and identification. The use of strain-specific primers designed based on 16S rDNA sequence comparisons enabled it to be possible to selectively detect a strain, DF14, which is being used as a biocontrol agent against damping-off fungi.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.

• Environmental Analysis Health and Toxicology
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• v.24 no.2
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• pp.107-117
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• 2009

Metal pollution of aquatic ecosystems is a problem of economic and health importance. Information regarding molecular responses to metal exposure is sorely needed in order to identify potential biomarkers. To determine the effects of heavy metals on chironomids, the full-length cDNA of alcohol dehydrogenase (ADH3) from Chironomus riparius was determined through molecular cloning and rapid amplification of cDNA ends (RACE). The expression of ADH3 was analyzed under various cadmium and copper concentrations. A comparative and phylogenetic study among different orders of insects and vertebrates was carried out through analysis of sequence databases. The complete cDNA sequence of the ADH3 gene was 1134 bp in length. The sequence of C. riparius ADH3 shows a low degree of amino acid identity (around 70%) with homologous sequences in other insects. After exposure of C. riparius to various concentrations of copper, ADH3 gene expression significantly decreased within 1 hour. The ADH3 gene expression was also suppressed in C. riparius after cadmium exposure for 24 hour. However, the effect of cadmium on ADH3 gene expression was transient in C. riparius. The results show that the suppression of ADH3 gene by copper exposure could be used as a possible biomarker in aquatic environmental monitoring and imply differential toxicity to copper and cadmium in C. riparius larvae.

• Genomics & Informatics
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• v.1 no.1
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• pp.25-31
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• 2003

Local alignment is an important task in molecular biology to see if two sequences contain regions that are similar. The most popular approach to local alignment is the use of dynamic programming due to Smith and Waterman, but the alignment reported by the Smith-Waterman algorithm has some undesirable properties. The recent approach to fix these problems is to use the notion of normalized scores for local alignments by Arslan, Egecioglu and Pevzner. In this paper we consider the problem of finding all local alignments whose normalized scores are above a given threshold, and present a fast heuristic algorithm. Our algorithm is 180-330 times faster than Arslan et al.'s for sequences of length about 120 kbp and about 40-50 times faster for sequences of length about 30 kbp.