• Journal of Life Science
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• v.13 no.1
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• pp.128-135
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• 2003

102 ESTs (Expressed Sequence Tags) were obtained by sequencing clones from a library of rainbow trout kidney cDNAs. Of the sequences generated, 55.8% of the ESTs were represented by 37 known genes. The 45 clones of unknown gene products potentially represent 40 novel genes. The genes involved in structural function (14.5%) and transcription/translation (11.6%) account for the major gene expression activities in the kidney Microarray experiment was conducted to compare gene expression of the unique ESTs in young and adult rainbow trout kidneys. While mitochondrion, cytochrome b, rho G, spastin protein, and three unknown genes were down-regulated in the mature fish kidney, calponin 1, calcium binding protein, histone deacetylase 1, and an unknown gene were up-regulated in the mature fish kidney. This research demonstrates the feasibility and power of functional genomics in rainbow trout.

• 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.

• Journal of Life Science
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• v.20 no.9
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• pp.1306-1313
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• 2010

The gene encoding esterase enzyme was cloned from a metagenomic library of cow rumen bacteria. The esterase gene (est1R) was 2,465 bp in length, encoding a protein of 366 amino acid residues, and the molecular weight of the enzyme was 61,166 Da. Est1R of rumen cosmid library shared 5.9% amino acid identity with Est1R (P37967) of PNB carboxylesterase, 6.1% with Est1R (1EEAA) of acetylcholinesterase and 6.1% with Est1R (1H23A) of chain A. BlastP in NCBI database analysis of Est1R revealed that it was not homologous to previous known lipases and esterases. Est1R showed optimum activity at pH 7.0 and $40^{\circ}C$. On the other hand, the enzyme was found to be most active without organic solvent, followed by 95% activity with methanol, and the enzyme activity was highly affected by hexane (lost 51% activity). Therefore, the novel esterase gene est1R is likely obtainable from cow rumen metagenome and may be utilized for industrial purposes.

• 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.

• 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.22 no.8
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• pp.1024-1033
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• 2012

A gene encoding a novel geranylgeranyl pyrophosphate (GGPP) synthase from Kocuria gwangalliensis has been cloned and expressed in Escherichia coli. The deduced amino acid sequence showed 59.6% identity with a putative GGPP synthase (CrtE) from K. rhizophila. An expression plasmid containing the crtE gene was constructed, and E. coli cells containing this plasmid produced a recombinant protein with a theoretical molecular mass of 41 kDa, corresponding to the molecular weight of GGPP synthase. Due to the lack of crtE, crtB, and crtI in E. coli, the biosynthesis of lycopene was only obtained when the plasmid pCcrtE was co-transformed into E. coli expressing the pRScrtBI-carrying carotenoid biosynthesis crtB and crtI genes, which were sub-cloned from Paracoccus haeundaensis. The biochemical studies on the expressed proteins were performed via HPLC. The results obtained from this study will provide a wider base of knowledge regarding the primary structure of CrtE cloned from K. gwangalliensis at the molecular level.

• Research in Plant Disease
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• v.21 no.3
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• pp.235-242
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• 2015

A 2014 nationwide survey in radish fields investigated the distribution of common viruses and possible emerging viruses. Radish leaves with virus-like symptoms were collected and 108 samples assayed by RT-PCR using specific primers for Radish mosaic virus (RaMV), Cucumber mosaic virus (CMV), and Turnip mosaic virus (TuMV); 47 samples were TuMV positive, and RaMV and CMV were detected in 3 and 2 samples, respectively. No samples showed double infection of TuMV/RaMV, or RaMV/CMV, but two double infections of TuMV/CMV were detected. TuMV isolates were sorted by symptom severity, and three isolates (R007-mild; R041 and R065-severe) selected for BLAST and phylogenetic analysis, which indicated that the coat protein (CP) of these isolates (R007, R041, and R065) have approx. 98-99% homology to a previously reported TuMV isolate. RaMV CP showed approx. 99% homology to a previously reported isolate, and the CMV CP is identical to a previously reported Korean isolate (GenBank : GU327368). Three isolates of TuMV showing different pathogenicity (degree of symptom severity) will be valuable to study determinants of pathogenicity.

• The Korean Journal of Food And Nutrition
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• v.17 no.1
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• pp.47-52
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• 2004

In this study, I attempted to develope the expression and purification system of human mammaglobin proteins in Escherichia coli and to produce anti-human mammaglobin rabbit antibody for the detection of human mammaglobin protein in the peripheral blood of breast cancer patients. Human mammaglobin gene was cloned and sequenced from m-RNAs purified from donated breast cancer tissues using RT-PCR. The cloned gene was inserted into pET30, pET22, and pET32 plasmid. The cloned gene in pET30 yields insoluble proteins which was difficult to purify from the cells extracts. The mammaglobin gene in pET32 was strongly expressed soluble proteins which were isolated using Ni-NTA affinity chromagraphy and DEAE-ion exchange chromatography, followed by enterokinase digestion of the purified proteins. The isolated proteins had enough purity to use as a antigen for the production of anti-mammaglobin antibody in rabbits. The polyclonal antibody produced against the isolated mammaglobin showed a specificity to mammaglobin after Westernblot immuno assay. In conclusion, the isolated mammaglobin protein and the anti-mammaglobin rabbit antibody may be used for diagnosis of breast cancer as well as development of anti-breast cancer drug.

• Parasites, Hosts and Diseases
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• v.34 no.1
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• pp.15-20
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• 1996

Cysts of Entamoebn histoIMtica are still found from humans in Korea, but notall of the cysts are known as pathogenic. The non-pathogenic strain is regarded as a differenL species, E. nispnr. In this study, Korean isolates of conventional E. histolvticn were subjected for the differentiation by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Human stools were screened by routine microscopic examination, and cyst or trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoites were prepared for DNA extraction, and the DNAs were used for PCR with common primers of Pl gene. The PCR products were divested with 3 restriction enzymes and RFLP was observed. Also anti-sense primers containing the cleavage site of each restriction eWe were designed for differentiation only by PCR. The PCR products of Korean isolates 59,512, YS-6, and YS-27 were spliced by Taq I and Xmnl but not byAccl, and the isolates S1, S3, S11, S15, S16, S17, S20, YS- l7, and YS-44 were spliced by Acc I but not by Taq I and Xmn I. These RFLP pattern correlated well with PCR products by the species specific primers. The findings confirm that the Korean isolates 59,512, YS-6, and YS-27 are E. histolwtico and others are E. dispar. In Korea, most of the asymptomatic cyst carriers are infected by E. dispar, not by E. histolytica. Key words: Entcmoebc histolytica, Entcmoebn dispar Korean isolates, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

• Korean Journal of Ichthyology
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• v.29 no.2
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• pp.139-145
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• 2017

The spontaneous color mutant, albino individuals of genus Misgurnus, are rarely discovered in Korea and there are difficult to identify morphological species due to lack melanin pigmentation. In this study, we developed a genetic identification method for the species of albino Misgurnus individuals based on phylogenetic analysis by using recombination activating gene 1 (rag1) and cytochrome b (cytb) region of mitochondrial DNA. As a result of molecular phylogenetic analysis, three clades were identified as Misgurnus mizolepis, M. anguillicaudatus and M. mohoity. The homology of the cytb sequences of M. mohoity was best match to that of M. mohoity sequences in GenBank database. As a result of species identification of 25 albino Misgurnus individuals based on the phylogenetic tree, the red-eye type was identified as 16 M. anguillicaudatus and one M. mizolepis. The remaining three individuals were identified as one M. mizolepis ♀${\times}$M. anguillicaudatus ♂, and two M. mohoity ♀${\times}$M. anguillicaudatus ♂, respectively. In addition, the five black-eye type individuals were identified as one M. anguillicaudatus, three M. mizolepis and one M. mohoity. Therefore, this genetic identification method will be an useful techniques for species or hybrid identification in genus Misgurnus.