• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.94-94
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• 2003

Rotavirus는 유아나 어린아이들에게 가장 일반적으로 나타나는 심한 위장염의 원인자이며 설사로 인한 심한 탈수 증세를 일으켜 급속히 성장하는 유아의 균형적인 영양 공급을 방해함으로써 유아들의 발육과 성장 그리고 심하면 생명에 커다란 영향을 미치게 된다. 한편 모유로 키운 유아들은 설사병의 낮은 발병율과 연관이 있었다. 특히 모유의 뮤신 복합체는 rotavirus에 특이적으로 결합하여 항 바이러스활동을 보여주는 것으로 나타났다. 이러한 배경에서 본 연구는 human breast tissue로부터 lactadherin의 cloning 및 sequence 분석을 통하여 유전자의 다양성을 조사하기로 하였다. 한국 여성 9명의 유두 근처 조직에서 lactadherin을 cloning하여 그 sequence를 보고 된 서양여성의 염기서열과 비교 분석결과 여러 곳에서 single nucleotide variation이 발견되었고 본 연구에서 클론한 lactadherin(31bp-1518bp)의 염기서열과 보고된 서양여성 lactadherin gene의 SNP와 비교하였을 때 8개의 SNP중 3부분만이 일치한다는 것을 확인하였다. 또한 같은 조직중 정상 조직과 암 조직 부분에서 각각 lactadherin을 클론하여 염기서열을 비교 분석하였는데 정상 조직에서 2곳의 silent mutation있었고 암조직에서 2곳의 mutation과 1곳의 silent mutation을 발견하였으며 전체 적으로 정상조직과 암 조직 부분에서 lactadherin을 clone하여 염기서열을 분석해본 결과 암조직일수록 유전자의 변이 비율이 높다는 것을 알 수 있었다. 그리고 동일한 염기서열 상에서 많은 변이가 일어났는데 286dp(A->C), 1418dp(G->C)은 mutation이었고 327dp (A->G), 454(C->T)은 silent mutation이었다. 그 외 DNA상에서 여러 부근에 변이가 존재하였는데 이 결과로 보아 coding region에 위치한 cSNP 중 amino acid 변화를 일으켜 protein structure 또는 function에 영향을 줄 수 있는 non-synonymous cSNP 일 것으로 예상되어지며 natural selection의 영향을 받고 있음을 암시하고 있다. 본 연구에서 관찰되어진 각각의 염기 서열의 변이는 한국 사람이 가지는 lactadherin gene의 cSNP의 일부라고 판단하였다.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.709-710
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• 2000

Genosensor technology utilizes a patterned array of DNA molecules immobilized on solid supports for biomedical analysis. The detection capability of the sensor depended mainly on the way the capture probes are attached to the support as well as the sequence. We compared two different. coupling methods currently used to covalently graft DNA molecules onto a glass surface.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.264-270
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• 1994

A gene coding for a novel putative $\sigma$ factor of RNA polymerase has been identified from Streptomyces coelicolor A3(2) using Escherichia coli rpoS gene fragment as a probe. The 486 bp rpoS gene fragment was amplified from E. coli genomic DNA by PCR with two synthetic oligonucleotides, the sequences of which were deduced from the amino acid sequences in the regions 2.3 and 4.2 conserved among various bacterial factors. When E. coli genomic DNA fragments were hybridized with cloned rpoS probe, only one band corresponding to rpoS gene (3.2 kb PvuII fragment or 2.3 kb KpnI fragment) was detected. In S. coelicolor, however, two bands were detected both in PvuII digested DNA and SalI digested DNA. 3.5 kb PvuII fragment which binds the rpoS gene probe was cloned (pMS1) from the sublibrary, and the nucleotide sequences of 1.0 kb BamH'/HincII subclone (pBH2) was partially determined. The nucleotide sequences revealed extensive similarity to other $\sigma$ factor genes of S. coelicolor (hrdA, hrdB, hrdC, hrdD), S. aureofaciens (hrdA, hrdB, hrdC, hrdD), Synechococcus species, Pseudomonas aeruginosa, Stigmatella aurantiaca, and Anabaena species. The nucleotide sequences in regions 1.2 and 4 were compared with the corresponding regions of 5 known ${\sigma}$ factor genes of S. coelicolor by multiple alignment. It turned out that the cloned gene is most closely related to hrdA showing 88% amino acid similarity in region 1.2 and 75% in region 4.

• Applied Biological Chemistry
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• v.47 no.2
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• pp.182-186
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• 2004

Morphological observation of roots and molecular technique were used to investigate the symbiotic relationships between arbuscular mycorrhizal (AM) fungi and ginseng roots. Korean ginseng, Panax ginseng, was collected from 8 sites in Korea. Colonization pattern of AM fungi in ginseng roots was determined as an Arum type under light microscopes. Nested PCR using AM fungal specific primers was employed to amplify a partial region on 18s rDNA of AM fungi from the root extracted mixed DNA. The amplified DNA was cloned and analyzed by random fragment length polymorphism (RFLP) with restriction enzymes, AluI, HinfI and AsuC21. One from each RFLP pattern was selected for sequencing. A total 16 clones were sequenced and identified as 2 species of AM fungi; Paraglomus brasilianum and Glomus spurcum. Paramglomus brasilianum was found from most of the ginseng roots, in this syudy suggesting that this species of AM fungi could have specific relationship with the ginseng root. Possible roles of AM fungal species in ginseng roots are discussed.

• Journal of Aquaculture
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• v.21 no.3
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• pp.139-145
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• 2008

Morphological classification of echinoid species has many difficulties because of their phenotypic variations. In the present study, we analyzed morphotypes and partial mitochondrial 12S rDNA sequences of four sea urchin species classified as Pseudocentrotus depressus, Anthocidaris crassispina, Hemicentrotus pulcherrimus and Strongylocentrotus nudus, and unidentified four species collected from the coasts of the East sea. Their genomic DNAs were extracted from gonads and mitochondrial 12S rDNA sequences were amplified by the polymerase chain reaction (PCR) method. The sequence identities among the known four sea urchin species were 87.4-95.6%. The sequence identities among the unidentified four species were 99.4-99.6% and showed the highest homology to S. intermedius(99.8%). Thus, our phylogenetic tree indicates that the unidentified four species belong to S. intermedius.

• Journal of Marine Bioscience and Biotechnology
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• v.1 no.2
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• pp.119-125
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• 2006

To understand the comprehensive mechanisms of biological function for insulin-like growth factor-I (IGF-I) in vertebrates, we have investigated the cDNA sequence of this gene in the korean rockfish (Sebastes schlegeli). The mature form of korean rockfish IGF-I was found to be comprised of 67 amino acid residues, showing about a 7 kDa molecular weight. In this study, we used the polymerase chain reaction (PCR) to obtain a korean rockfish IGF-I (KR IGF-I) cDNA fragment, and methods of rapid amplification of cDNA ends (RACE) to obtain a full length of the KR IGF-I sequence. The KR IGF-I encoded for a predicted amino acid sequence showed identities of 93.6 %, 90.7 %, and 85.4 % in comparison with flounder, chinook salmon, and human IGF-I, respectively. To obtain recombinant biologically active polypeptides, korean rockfish B-C-A-D domains were amplified using the PCR, then the isolated cDNA was expressed in the E. coli BL21(DE3). The recombinant KR IGF-I protein biological function was measured by stimulation of [$^3H$] thymidine incorporation, suggesting the cDNA codes for the korean rockfish proIGF-I.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.12
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• pp.2329-2334
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• 2006

In this paper, we proposed a method complementing failure of combining DNA fragments, defect of conventional contig assembly programs. In the proposed method, very long DNA sequence data are made into a prototype of fragment of about 700 bases that can be analyzed by automatic sequence analyzer at one time, and then matching ratio is calculated by comparing a standard prototype with 3 fragmented clones of about 700 bases generated by the PCR method. In this process, the time for calculation of matching ratio is reduced by Compute Agreement algorithm. Two candidates of combined fragments of every prototype are extracted by the degree of overlapping of calculated fragment pairs, and then degree of combination is decided using a fuzzy reasoning method that utilizes the matching ratios of each extracted fragment, and A, C, G, T membership degrees of each DNA sequence, and previous frequencies of each A, C, G, T. In this paper. DNA sequence combination is completed by the iteration of the process to combine decided optimal test fragments until no fragment remains. For the experiments, fragments or about 700 bases were generated from each sequence of 10,000 bases and 100,000 bases extracted from 'PCC6803', complete protein genome. From the experiments by applying random notations on these fragments, we could see that the proposed method was faster than FAP program, and combination failure, defect of conventional contig assembly programs, did not occur.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.124-131
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• 1999

This study was carried out to identify the phylogenetic relationship among Phellinus species by comparing the DNA sequences of the 5.8S ribosomal DNA (rDNA) and the internal transcribed spacers (ITSs), ITS1 and ITS2 regions. Two primers from the 3' end of 18S rDNA and the 5' end of 28S rDNA sequences were chosen to amplify the specific ITS regions of Phellinus spp. Phellinus strains used in the study were divided into four clusters by the phylogenetic tree based on the amplified regions of ITS and 5.8S rDNA sequences. The first cluster consist of Phellinus hartigii IMSNU 32041 and Phellinus robustus IMSNU 32068, and the second cluster consists of Phellinus linteus strains and Phellinus weirianus IMSNU 32021. Phellinus laevigatus KCTC 6229, KCTC 6230 and Phellinus igniarius KCTC 6227, KCTC 6228 belong to the third cluster. Finally, Phellinus chrysoloma KCTC 6225 and Phellinus chrysoloma KCTC 6226 are the fourth cluster. In the second cluster the differentiation between Phellinus linteus strains and Phellinus weirianus species were not possible by the comparison of the ITS sequences. These results revealed that Phellinus linteus and Phellinus weirianus cannot be established the concept of species level only by the ITS sequences. Therefore, both physiological and molecular biological methods as well as the sequences of type strains are necessary to classify the strains of these two species accurately. The comparison of the ITS sequences of four Phellinus species indicated that the sequences of the ITS1 generally are more divergent than those of the ITS2. Although the ITS sequences are varied in some species, the conserved regions in both ITS1 and ITS2 are useful tool to differentiate the species. Phellinus linteus and related species have their specific sequences in the ITS1 compared to the other species.

• The KIPS Transactions:PartD
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• v.16D no.5
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• pp.661-672
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• 2009

Recently it was found that various genetic structural variations such as CNV(copy number variation) exist in the human genome, and these variations are closely related with disease susceptibility, reaction to treatment, and genetic characteristics. In this paper we propose a new CNV detection algorithm using millions of short DNA sequences generated by giga-sequencing technology. Our method maps the DNA sequences onto the reference sequence, and obtains the occurrence frequency of each read in the reference sequence. And then it detects the statistically significant regions which are longer than 1Kbp as the candidate CNV regions by analyzing the distribution of the occurrence frequency. To select a proper read alignment method, several methods are employed in our algorithm, and the performances are compared. To verify the superiority of our approach, we performed extensive experiments. The result of simulation experiments (using a reference sequence, build 35 of NCBI) revealed that our approach successfully finds all the CNV regions that have various shapes and arbitrary length (small, intermediate, or large size).

• Korean Journal of Ichthyology
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• v.11 no.2
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• pp.163-171
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• 1999

The complete sequences of mtDNA control regions of six salmonines were determined: 1089 bp in lenok (Brachymystax lenok); 999 bp in cherry salmon (Oncorhynchus masou masou) and Ishikawa's cherry salmon (O. masou ishikauiae); 1002 bp in chum salmon (O. keta), and 1003 bp in rainbow trout (O. mykiss) and an albino mutant of rainbow trout. The estimated interspecific sequence divergences from PCR/direct sequencing data ranged from 5.42% to 16.49%. The organization of this region is similar to that of other vertebrates. A 81 bp tandemly repeated sequence, associated with length variation was observed in the 3' end of the salmonids control region in this study. In addition, The phylogenetic tree based on the control region sequences supported that cherry salmon was closer to chum salmon than to rainbow trout, while lenok was most distantly related species among six salmonines.