• Proceedings of the Korean Nutrition Society Conference
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• 1995.11a
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• pp.1129-1169
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• 1995

• Proceedings of the Korean Nutrition Society Conference
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• 1995.11b
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• pp.9-9
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• 1995

• Journal of Institute of Control, Robotics and Systems
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• v.10 no.12
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• pp.1189-1195
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• 2004

This paper investigates construction of gene (interaction) networks from gene expression time-series data based on evolutionary computation. To illustrate the proposed approach in a comprehensive way, we first assume an artificial gene network and then compare it with the reconstructed network from the gene expression time-series data generated by the artificial network. Next, we employ real gene expression time-series data (Spellman's yeast data) to construct a gene network by applying the proposed approach. From these experiments, we find that the proposed approach can be used as a useful tool for discovering the structure of a gene network as well as the corresponding relations among genes. The constructed gene network can further provide biologists with information to generate/test new hypotheses and ultimately to unravel the gene functions.

• Animal cells and systems
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• v.7 no.1
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• pp.63-68
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• 2003

Until recently, interest in human complement receptor type I (CR1) has focused on immune complex processing, which contributed to our understanding of regulatory mechanism of complement activation. However, the promoter structure and transcriptional regulation of human CR1 gene has not been clear. To study the unique regulation of human CR1 gene expression, we assessed promoter activity of the $5^1$-flanking region of human CR1 gene using transient transfection and gel mobility shift assays. In this study we demonstrated that NF-Y binds to the inverted CCAAT element and that the functional interaction with protein(s) which bind to the GC-rich motif may be necessary for optimal transcription of human CR1 gene. We also show that sequence elements which located at-95/58 and +45/+50 are important for optimal transcription of CR1 gene.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.207-215
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• 2003

Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is the most important process in annotating genes and greatly affects gene analysis and genome annotation. As eukaryotic genes have more complicated stuructures in DNA sequences than those of prokaryotic genes, analysis programs for eukaryotic gene structure prediction have more diverse and more complicated computational models. We have developed EGSP, a eukaryotic gene structure program, using duration hidden markov model. The program consists of two major processes, one of which is a training process to produce parameter values from training data sets and the other of which is to predict protein coding regions based on the parameter values. The program predicts multiple genes rather than a single gene from a DNA sequence. A few computational models were implemented to detect signal pattern and their scanning efficiency was tested. Prediction performance was calculated and was compared with those of a few commonly used programs, GenScan, GeneID and Morgan based on a few criteria. The results show that the program can be practically used as a stand-alone program and a module in a system. For gene prediction of eukaryotic microbial genomes, training and prediction analysis was done with Saccharomyces chromosomes and the result shows the program is currently practically applicable to real eukaryotic microbial genomes.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.656-659
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• 2005

Small peptides synthesized by nonribosomal peptide synthetases (NRPSs) genes are found in bacteria and fungi. While some microbial taxa have few, others make a large number and variety. However, biochemical characterization of the products synthesized by NPRS demands a great deal of efforts. Since the completion of genome projects of numerous microorganisms, the numbers of available NRPSs genes are being expanded. Prediction of the peptides encoded by NRPS could save time and efforts. We chose the NRPS gene from Bradyrhizobium japonicum as a model to predict the peptide structure encoded by NRPS genes. Using computational analyses, the domain structure of this gene was defined, and the structure of a peptide synthesized by this NRPS was deduced. It was found that it encoded a tripeptide consisting of proline-serine-phenylalanine. This method would be helpful to predict the structure of small peptides with various NPRS genes from the genome sequence.

• Journal of Ecology and Environment
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• v.43 no.4
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• pp.454-461
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• 2019

Background: Ikonnikov's whiskered bat (Myotis ikonnikovi) is found throughout the Korean Peninsula, as well as in Kazakhstan, Russia, Mongolia, China, and Japan. It is small-sized and primarily inhabits old-growth forests. The decrease and fragmentation of habitats due to increased human activity may influence the genetic structure of bat populations. This study was designed to elucidate the population genetic structure of M. ikonnikovi using mitochondrial genes (cytochrome oxidase I and cytochrome b). Results: The results showed that M. ikonnikovi populations from Korea have high genetic diversity. Although genetic differentiation was not detected for the COI gene, strong genetic differentiation of the Cytb gene between Mt. Jeombong and Mt. Jiri populations was observed. Moreover, the results indicated that the gene flow of the maternal lineage may be limited. Conclusions: This study is the first to identify the genetic population structure of M. ikonnikovi. We suggest that conservation of local populations is important for sustaining the genetic diversity of the bat, and comprehensive studies on factors causing habitat fragmentation are required.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.182-190
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• 2003

A new phaC gene cluster encoding polyhydroxyalkanoate (PHA) synthase I PHA depolymerase, and PHA synthase II was cloned using the touchdown PCR method, from medium-chain length (mcl-) PHA-producing strain Pseudomonas putida KT2440. The molecular structure of the cloned phaCl gene was analyzed, and the phylogenic relationship was compared with other phaCl genes cloned from Pseudomonas species. The cloned phaCl gene was expressed in a recombinant E. coli to the similar level of PHA synthase in the parent strain P. putida KT2440, but no significant amount of mcl-PHA was accumulated. The isolated phaCl gene was re-introduced into the parent strain P. putida KT2440 to amplify the PHA synthase I activity, and the recombinant P. purida accumulated mcl-PHA more effectively, increasing from 26.6 to $43.5\%$. The monomer compositions of 3-hydroxylalkanoates in mcl-PHA were also modified significantly in the recombinant P. putida enforcing the cloned phaCl gene.

• Mycobiology
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• v.44 no.2
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• pp.105-111
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• 2016

Paclitaxel (taxol) has long been used as a potent anticancer agent for the treatment of many cancers. Ever since the fungal species Taxomyces andreanae was first shown to produce taxol in 1993, many endophytic fungal species have been recognized as taxol accumulators. In this study, we analyzed the taxol-producing capacity of different Colletotrichum spp. to determine the distribution of a taxol biosynthetic gene within this genus. Distribution of the taxadiene synthase (TS) gene, which cyclizes geranylgeranyl diphosphate to produce taxadiene, was analyzed in 12 Colletotrichum spp., of which 8 were found to contain the unique skeletal core structure of paclitaxel. However, distribution of the gene was not limited to closely related species. The production of taxol by Colletotrichum dematium, which causes pepper anthracnose, depended on the method in which the fungus was stored, with the highest production being in samples stored under mineral oil. Based on its distribution among Colletotrichum spp., the TS gene was either integrated into or deleted from the bacterial genome in a species-specific manner. In addition to their taxol-producing capacity, the simple genome structure and easy gene manipulation of these endophytic fungal species make them valuable resources for identifying genes in the taxol biosynthetic pathway.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.616-628
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• 2022

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.