• Journal of Aquaculture
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• v.20 no.4
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• pp.248-254
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• 2007

Representative cDNA libraries were constructed from various tissue sources of Hemibarbus mylodon, an endangered freshwater fish species in Korea, for the mining of expressed sequence tags (ESTs). Randomized and non-normalized EST analysis was performed with 7 unidirectional cDNA libraries generated from brain, intestine, kidney, liver, muscle, ovary or testis. Of 3,383 ESTs in total, the number of singleton was 2,029, and 333 contigs containing 1,354 ESTs were assembled (percent of unigene = 70.0%). Abundantly expressed gene transcripts and broad clustering of putative gene function were tissue-specific in general, and the redundancy was also variable among those libraries. Over half of H. mylodon ESTs were matched with orthologues from other teleosts among which zebrafish gene sequences were the most frequent in those matches. This initial setting of EST libraries achieved in the present study would be a fundamental basis for the banking of gene resources from this endangered fish species.

• Journal of Aquaculture
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• v.13 no.1
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• pp.79-85
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• 2000

The effects of estrogen and androgens on Vg gene expression were examined in primary hepatocyte culture and livers of the immature male trout. Specific primers of Vg cDNA were designed with already reported Vg gene nucleotide sequences. PCR product was sequenced and verified with Vg cDNA of rainbow trout. Total RNA was extracted from the cultured hepatocytes and livers of steroid-treated rainbow trout and then it was analyzed by reverse transcriptase- polymerase chain reaction (RT-PCR) analysis. The Vg mRNA and Vg protein synthesis were increased in rainbow trout in vivo and in vitro with E$_2$ and methyltestosterone (MT) There were dose and time-related effects of E$_2$ and MT on vitellogesis. Androgens such as progesterone androsterone and testosterone also stimulated Vg mRNA expression in vitro. The results show that androgens as well as E$_2$ can induce expression of Vg mRNA in trout in vivo and in vitro.

• Korean Journal of Agricultural Science
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• v.36 no.2
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• pp.167-177
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• 2009

This study was conducted to characterize the DGAT1 gene in Korean Holstein dairy cattle population and examine the relationship of DGAT1 polymorphisms with milk yield and milk fat yield for the genetic improvement of Korean Holstein dairy cattle. Results indicated that the 411 bp PCR products were successfully amplified by DGAT1 specific primers. Sequence analysis indicated that the DGTA1 Q allele had AUG (Lysine, K) nucleotide sequences in 216-218 bp and q allele had GCG (Alanine, A) sequences in the same position. Nucleotide sequence homology between the DGAT1 sequences generated in this study showed 100% homology with bovine DGAT1 sequences in the NCBI database. The genotype frequencies of DGAT1 QQ, Qq, and qq were 16.43, 36.43, and 47.14%, respectively, in Korean Holstein dairy cattle population. The observed Q and q allele frequencies were 0.35 and 0.65, respectively. Statistically significant (P<0.05) results were identified for milk yield and milk fat yield for the DGAT1 genotypes. The Qq genotype Holsteins have significantly higher milk yield and milk fat yield than those of the QQ and qq genotype Holsteins(P<0.05).

• Microbiology and Biotechnology Letters
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• v.25 no.6
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• pp.560-565
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• 1997

DNA fragment assembly is a major concem in shot-gun DNA sequencing project. It is to reconstruct a consensus DNA sequence from a collection of random oritented fragments. We developed a computer program that is useful for DNA fragment assembly. Inputs to the program are DNA fragment sequences including IUB-IUPAC bases. The program produces the most probable reconstruction ot the original DNA sequence as a text format or a PostScript format. The program consists of four phases: the first phase quickly eliminates fragment pairs that can not possibly overlap. In the second phase, the quality of overlap between each pair is calculated to a score. In the third phase, overlap pairs are sorted by their scores and consistency of the overlaps is checked. The last phase determines consensus sequences and displays them. The performance of fragment assembly program was tested on a set of DNA fragment sequences which were generated from long DNA sequences of GenBank by a fragmentation program.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.107-112
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• 2013

With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.

• Journal of Mushroom
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• v.10 no.3
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• pp.120-128
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• 2012

Recently sawdust cultivation of Shiitake mushroom (Lentinula edodes) is increasing. It is important to make mycelia to be brown on the substrate surface. This browned surface in sawdust cultivation plays an important role like as artificial bark of the oak log, which protects the other pests and suppresses water evaporation in the substrate. In order to isolate genes which related to brown color formation, differential display method was used. Two cDNA fragments obtained by DD-PCR were 1.2 and 1.6kb and these were expressed in white colored mycelia from L. edodes, but not brown colored mycelia. Partial sequencing of these cDNA fragments showed that the 1.6kb cDNA had 100% identity with the microsatellites gene from Dugenia polichroa. However, the other 1.2kb cDNA fragment had poly T tail on 3' region of partial open reading frame on 5' region. The new primer designed based on the sequence of 1.2kb cDNA was constructed. RT-PCR analysis using the newly designed 0.12kb cDNA specific primer showed that the gene was only expressed in white color mycelia, but not in brown color mycelia. Sequence analysis of 5' region of this 1.2kb cDNA revealed that this gene contained partial open reading frame consisted of 110 amino acid. Homology search using DNASIS database showed that this gene had high sequence homology of 66.7% in DNA level and 69.2 % in amino acid level with dTDP-glucose 4,6-dehydratases gene from Arabidopsis thaliata. The dTDP-glucose 4,6-dehydratases gene was known to be function to have tolerance with oxidation stress. These results strongly suggest that this gene isolated from white mycelia of L. edodes might have a function of repressor against mycelia browning. Therefore I designated this gene as BCR (Brown Color Repressor) gene.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2000.11a
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• pp.59-75
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• 2000

This study was carried out to develop a DNA marker for identifying between Korean cattle (Hanwoo) and other breeds. First experiment was performed to isolate Hanwoo specific DNA marker at sequence characterized amplified regions (SCARs). Five breeds of cattle including Hanwoo, Holstein, Hereford, Angus and Charolais were represented with the from 8 to 20 individuals. Fourteen primers of 300 arbitrary primers of 10 nucleotides showed reproducible polymorphism across the breeds. An amplified band of 0.9 kb in the primer MG-3 showed the specificity to Holstein breed. And MG-6 and MG-12 detected the Hereford and Hanwoo specific markers at the size of 2.0 kb and 1.0 kb, respectively. A 1.0 kb band of MG-12 was cloned and sequenced. A SCAR primer was designed based on the obtained sequences. It was possible to identify the Hanwoo from Holstein breed. Second experiment was carried out to observe the genotype frequencies of MC1R in 1,044 samples of imported beef and eight different cattle breeds including Hanwoo, Holstein, Angus, Brown-Swiss, Charolais, Limousin, Simmental and Hereford. The primers for the amplification of bovine MC1R gene were designed based on a bovine MC1R gene sequence (GenBank accession no.Y19103). A size of 350 bp was amplified by polymerase chain reaction(PCR), digested with two different restriction enzyme, BsrFI and MspA II, and electrophoresed in 2.5% Metaphore agarose gel for determination of genotypes. Genotype frequencies of Hanwoo were 0.10 in E+e and 0.90 in ee. Allele ED was shown in all of Holstein and Angus breeds tested which have black coat color phenotypes. We suggested that SCAR marker and the bovine MC1R gene could be used as a DNA marker for distinguishing beef between Hanwoo and Holstein.

• Microbiology and Biotechnology Letters
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• v.30 no.4
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• pp.312-319
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• 2002

The Sporosarcina psychrophilia pyrB gene, which encodes aspartate transcarbamylase (ATcase), was cloned on Sau3AI restriction endonuclease fragment inserted into pUC19 plasmid vector, S. psychrophilia pyrB gene was expressed in Escherichia coli pyrB mutant for the complementation test. The sequence of 2,606 nucleotides including putative pyrB gene was determined. The region contained one full open reading frame (ORf) and two partial ORFs. The deduced amino acid sequence of the second ORF showed 59% identity with that of Bacillus caldolyticus ATCase. The first and third partial ORFs were closely related to the uracil permease (pyrP) and dihydroorotase (pyrC), respectively. Besides, potential terminator, antiterminator, and anti-antiterminator structures were found in the intergenic region between pyrP and pyrB. These results suggested that S. psychrophilia pyrimidine nucleotide biosynthesis genes are clustered as well as other Bacillus sp. Over-expressed product of pyrB encoding ATCase was purified and analyzed by the SDS-PAGE. The purified PyrB protein turned out to be molecular mass of 27 kDa and showed ATCase activity.

• Korean Journal of Microbiology
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• v.41 no.2
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• pp.140-145
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• 2005

Streptomyces natalensis ATCC27448 produces natamycin, a commercially important macrolide antifungal antibiotic. For molecular genetic study of S. natalensis, we have developed a system for introducing DNA into S. natalensis via conjugal transfer from Escherichia coli. An effective transformation procedure for S. natalensis was established based on transconjugation from E, coli ET12567/pUZ8002 using a ${\Phi}C31$-derived integration vector, pSET152, containing oriT and attP fragments. The high frequency was obtained on MS medium containing 10 mM $MgCl_2$ using $6.25\times10^8$ of E.coli donor cells without heat treatment of spores. In addition, southern blot analysis of exconjugants and the sequence of plasmids containing DNA flanking the insertion sites from the chromosome revealed that S. natalensis contains a single ${\Phi}C31$ attB site and at least a secondary or pseudo attB site. Similar to the case of various Streptomyces species, a single ${\Phi}C31$ attB site of S. natalensis is present within an ORF encoding a pirin-homolog, but a pseudo-attB site is present within a distinct site (GenBank accession no. $YP\_117731$) and also its sequence deviates from the consensus sequences of attB sequence.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.749-754
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• 2000

PCR primers were designed based on consensus sequences of dTDP-D-glucose 4,6-dehydratase, one of the enzymes involved in the biosynthesis of deoxysugar. The PCR product (360 bp) was obtained from Thermus caldophilus GK24. Colony hybridization was carried out to the cosmid library constructed from T. caldophilus GK24 genomic DNA by the PCR product DNA fragment. We isolated a cosmid clone (pSMTC-1) that was subcloned to call pKCB series plasmid (BamHI fragments), partially sequenced and analyzed. pKCB80 (4.2 kb-BamHI DNA fragment) of them showed ORFs that was orfA, orfB, orfC and orfD. The orfABCD gene cluster is the deosysugar biosynthetic gene ; orfA (glucose-1-phosphate thymidylytransferase), orfB (dTDP-D-glucose 4,6-dehydratase), orfC (dTDP-4-keto-L-rhamnose reductase) and orfD (dTDP-4-keto-6-deoxy-D-glucose 3,5-epimerase). The gene cluster that was related in biosynthesis of dTDP-L-rhamnose was also identified by computer analysis, and we proposed that the biosynthetic pathway of deoxysugar analyzed from DNA sequencing of pKCB80 is from D-glucose-1-phosphate, dTDP-D-glucose, dTDP-4-keto-6-deoxy-D-glucose via dTDP-4-keto-L-rhamnose to dTDP-L-rhamnose.