• Korean Journal of Ichthyology
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• v.18 no.1
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• pp.12-19
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• 2006

To examine the relationship of geological distribution and phylogenetic tree of O. latipes in the Far East, we analyzed cytochrome b (cyt b) gene in the mitochondrial genome. In this study we employed the entire sequence of cyt b of 53 samples collected from nine Korean locations and 117 cyt b data retrieved from the GenBank. From 170 Oryzias latipes cyt b sequence data, 142 different haplotypes were identified and phylogenetic relationship was reconstructed based on the dataset. According to the phylogeny, haplotypes were divided into three major haplogroups A, B and C, and their relationships were well correlated to their distributional patterns. Haplogroup A which is widely distribute in the southern part of Korea is separated in the geographical distribution from the haplogroup B which is found from China to the western part of Korea. Haplogroup C is only found in Japan.

• The KIPS Transactions:PartD
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• v.11D no.3
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• pp.519-532
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• 2004

With the explosion of bioinformatics data such proteins and genes, biologists need a integrated system to analyze and organize large datasets that interact with heterogeneous types of biological data. In this paper, we propose a integration system based on a mediated data warehouse architecture using a XML model in order to combine protein related data at biology laboratories. A fact constellation model in this system is used at a common model for integration and an integrated schema it translated to a XML schema. In addition, to track source changes and provenance of data in an integrated database employ incremental update and management of sequence version. This paper shows modeling of integration for protein structures, sequences and classification of structures using the proposed system.

• The KIPS Transactions:PartD
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• v.11D no.4
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• pp.845-854
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• 2004

Motif databases are used in the function and structure prediction of proteins. The frequency of use about these databases increases continuously because of protein sequence data growth. Recently, many researches about motif resource integration are proceeding. However, existing motif databases were developed independently, thus these databases have a heterogeneous search result problem. Database intnegration for this problem resolution has a periodic update problem, a complex query process problem, a duplicate database entry handling problem and BML support problem. Therefore, in this paper, we suppose a database resource integration method for these problem resolution, describe periodically integrated database update method and XML transformation. finally, we estimate the implementation of our prototype and a case database.

• Journal of KIISE:Computer Systems and Theory
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• v.31 no.3_4
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• pp.145-151
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• 2004

We present an efficient data structure to obtain the range minima in an away in constant time. Recently, suffix ways are extensively used to search DNA sequences fast in bioinformatics. In constructing suffix arrays, solving the range minima problem is necessary When we construct suffix arrays, we should solve the range minima problem not only in a time-efficient way but also in a space-efficient way. The reason is that DNA sequences consist of millions or billions of bases. Until now, the most efficient data structure to find the range minima in an way in constant time is based on the method that converts the range minima problem in an array into the LCA (Lowest Common Ancestor) problem in a Cartesian tree and then converts the LCA problem into the range minima problem in a specific array. This data structure occupies O( n) space and is constructed in O(n) time. However since this data structure includes intermediate data structures required to convert the range minima problem in an array into other problems, it requires large space (=13n) and much time. Our data structure is based on the method that directly solves the range minima problem. Thus, our data structure requires small space (=5n) and less time in practice. As a matter of course, our data structure requires O(n) time and space theoretically.

• Korean Journal of Microbiology
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• v.40 no.2
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• pp.172-177
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• 2004

Photosynthetic bacteria, Rhodospirillum rubrum, have been reported to change their metabolic patterns depend-ing on the light condition. The genetic approach for such a metabolic change is one of main subject in pho-tosynthetic bacteria. It has been reported that the extrachromosomal plasmid might be related to this metabolic regulation. In this study, we have determined the partial sequences of R. rubrum plasmid pKYl with HindIII fragments and the predicted pKYl ORFs and physical map. We found the 8 putative proteins related to the genetic recombination of bacterium, which is reported to the alternative gene expression. Our results suggest that the genes located in pKYl are possibly involved in the metabolic switch according to the photocondition.

• Journal of Life Science
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• v.13 no.2
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• pp.191-196
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• 2003

The ars gene of the Neurospora crassa encodes arylsulfatase and is expressed under sulfur limitation. An ars-1 promoter(Pars) translationally-fused to a lacZ gene was transformed into the N. crassa RLM 35-35, a his-3 inl strain and integrated into the his-S locus by a single crossover homologous recombination. $\beta$-galactosidase specific activity was measured from mycelia grown in sulfur-limited Vogel's medium. Enzyme activity reached its maximum at 14 hour after the shift to derepressing condition. When activity from homokaryon generated by microconidiation was measured, it was 17% a higher than that from heterokaryon.

• Journal of the Korean Geographical Society
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• v.40 no.1 s.106
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• pp.27-46
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• 2005

Land suitability assessment(LSA) is a useful method to assess land characteristics according to its physical, locational, and environmental characteristics, and then to classify it into several categories based on its usability and the necessity for conservation. Therefore, the credibility of this assessment result depends on the rationality of assessment method such as computation of suitability values and the criteria of ranking the land grade. This study focused on identifying problems in current LSA method by critically reviewing it, and aimed to suggest a suitable method for the assessment of land suitability. As a alternative method in this study, linear transformation method was used for scoring factors instead of critical values and the weight for each assessment factor. and all values of those factors were added to produce comprehensive suitability values. Those values were ordered and categorizied with suitability level based on the ratio of square measure. After comparing existing LSA method to the suggested alternative method, it is concluded that the alternative method was more suitable to assess the characteristics of lands than existing LSA method. This method was also suitable to represent the characteristics of various assessment factors. Field survey using satellite image clearly revealed the suitability of the alternative method compared to an existing method of land assessment. Furthermore, the alternative method of grading the land suitability improves the problem of using standardiZiation method and gives more flexibility, which makes this method very rational.

• Korean Journal of Ichthyology
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• v.19 no.4
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• pp.266-273
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• 2007

Heat shock proteins (HSPs) are a family of highly conserved proteins playing an important role in the functioning of unstressed and stressed cells. The HSP70 family, the most widely studied of the hsps, is constitutively expressed (hsc70) in unstressed cells and is also induced in response to stressors (hsp70), especially those affecting the protein machinery. The HSP/HSC70 proteins act as molecular chaperones and are crucial for protein functioning, including folding, intracellular localization, regulation, secretion, and protein degradation. Here, we report the identification and characterization of the putative amino acid sequence deduced from one cDNA clone identified as heat shock protein 70. The alignment showed that the putative sequence is 100% identical to the heat shock protein 70 cognate (HSC 70) of olive flounder. The 5'-flanking region sequence (approximately 1 kb) ahead of the hsc70 gene was cloned by genome walking and a putative core promoter region and transcription elements were identified. We characterized the promoter of the olive flounder hsc70 gene by examining the ability of 5'-upstream fragments to drive expression of green fluorescent protein (GFP) in live embryos.

• Korean journal of applied entomology
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• v.55 no.3
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• pp.245-256
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• 2016

Elytra of Harmonia axyridis exhibit varied color patterns. In the present study, we deciphered the genetic basis for intraspecific diversity of elytra color patterns in H. axyridis, using amplified fragment length polymorphism (AFLP). Twenty-eight AFLP reactions were performed to generate a total of 2,741 bands. Of these, 20 bands were polymorphic for each color pattern. The polymorphic bands showed differences of genetic character among different color patterns of H. axyridis. Among them, ten candidate AFLP markers were color-linked. S1, S2, and S20 markers were detected in Succinea 1 and 2 variants of H. axyridis, whereas S3 and S5 were specifically detected in the Conspicua variant. S15, S18, and S19 were specific to the Succinea 2 variant. Polymerase chain reaction (PCR) products of these ten AFLP markers were sequenced. BLAST analysis of these sequences against the GenBank database revealed their homology to DNA fragments of unknown function. Based on the color-linked AFLP markers, sequence characterized amplified region (SCAR) markers were designed for PCR amplification of genomic DNA. Of the ten AFLP markers, five were successfully converted into SCAR markers, which could discriminate elytra color polymorphism in H. axyridis.

• Development and Reproduction
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• v.10 no.2
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• pp.127-133
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• 2006

[ $17\;{\alpha}-hydroxylase/17,20-lyase(P450_{C17})$ ] is the key enzyme mediating the conversion of progesterone to $17\;{\alpha}-hydroxyprogesterone$, ultimately to androstenedione during steroidogenesis. R. dybowskii's ovarian $P450_{C17}$ cDNA was cloned to understand the regulatory mechanism of ovarian steroidogenic pathway at the molecular level in amphibian. A 2.5kb cDNA clone encoding a single open-reading frame with a 519 deduced amino acid was isolated with the screening of ovarian cDNA library. This sequence contained the three highly conserved domains as seen in $P450_{C17}$ of other species. The comparison of amino acid sequence of Rana $P450_{C17}$ with other animal's $P450_{C17}$ showed relatively high identity with 76% in Xenopus, 63% in chicken, 60% in rainbow trout, and 45% in human. Phylogenic analysis also indicated that Rana $P450_{C17}$ gene was evolutionary well conserved among vertebrate. Northern analysis indicated that the two different sizes of $P450_{C17}$ transcripts with approximately 2.5 and 3.6kb were detected in ovary tissue, but not in other tissues. The expression vector of Rana $P450_{C17}$ clearly showed the $17\;{\alpha}-hydroxylase$ activity converting the exogenous progesterone into $17\;{\alpha}-hydroxyprogesterone$ in the nonsteroidogenic COS-1 cells. Therefore, Rana $P450_{C17}$ cDNA is very useful to investigate the molecular mechanism of the ovarian steroidogenesis in amphibian.